diff options
Diffstat (limited to 'lib/stwcs')
55 files changed, 0 insertions, 10634 deletions
diff --git a/lib/stwcs/__init__.py b/lib/stwcs/__init__.py deleted file mode 100644 index 9f12bce..0000000 --- a/lib/stwcs/__init__.py +++ /dev/null @@ -1,33 +0,0 @@ -""" STWCS - -This package provides support for WCS based distortion models and coordinate -transformation. It relies on PyWCS (based on WCSLIB). It consists of two -subpackages: updatewcs and wcsutil. - -updatewcs performs corrections to the -basic WCS and includes other distortion infomation in the science files as -header keywords or file extensions. - -Wcsutil provides an HSTWCS object which extends pywcs.WCS object and provides -HST instrument specific information as well as methods for coordinate -transformation. wcsutil also provides functions for manipulating alternate WCS -descriptions in the headers. - -""" -from __future__ import absolute_import, print_function # confidence high -import os - -from . import distortion -from stsci.tools import fileutil -from stsci.tools import teal - -__docformat__ = 'restructuredtext' - -from .version import * - -try: - from . import gui - teal.print_tasknames(gui.__name__, os.path.dirname(gui.__file__)) - print('\n') -except: - print('No TEAL-based tasks available for this package!') diff --git a/lib/stwcs/distortion/__init__.py b/lib/stwcs/distortion/__init__.py deleted file mode 100644 index e69de29..0000000 --- a/lib/stwcs/distortion/__init__.py +++ /dev/null diff --git a/lib/stwcs/distortion/coeff_converter.py b/lib/stwcs/distortion/coeff_converter.py deleted file mode 100644 index 415b512..0000000 --- a/lib/stwcs/distortion/coeff_converter.py +++ /dev/null @@ -1,142 +0,0 @@ -from __future__ import division, print_function # confidence high - -import numpy as np -from astropy.io import fits -from astropy import wcs as pywcs - -def sip2idc(wcs): - """ - Converts SIP style coefficients to IDCTAB coefficients. - - Parameters - ---------- - wcs : `astropy.io.fits.Header` or `astropy.wcs.WCS` object - """ - if isinstance(wcs, fits.Header): - ocx10 = wcs.get('OCX10', None) - ocx11 = wcs.get('OCX11', None) - ocy10 = wcs.get('OCY10', None) - ocy11 = wcs.get('OCY11', None) - order = wcs.get('A_ORDER', None) - sipa, sipb = _read_sip_kw(wcs) - if None in [ocx10, ocx11, ocy10, ocy11, sipa, sipb]: - print('Cannot convert SIP to IDC coefficients.\n') - return None, None - elif isinstance(wcs, pywcs.WCS): - try: - ocx10 = wcs.ocx10 - ocx11 = wcs.ocx11 - ocy10 = wcs.ocy10 - ocy11 = wcs.ocy11 - except AttributeError: - print('First order IDCTAB coefficients are not available.\n') - print('Cannot convert SIP to IDC coefficients.\n') - return None, None - try: - sipa = wcs.sip.a - sipb = wcs.sip.b - except AttributeError: - print('SIP coefficients are not available.') - print('Cannot convert SIP to IDC coefficients.\n') - return None, None - try: - order = wcs.sip.a_order - except AttributeError: - print('SIP model order unknown, exiting ...\n') - return None, None - - else: - print('Input to sip2idc must be a PyFITS header or a wcsutil.HSTWCS object\n') - return - - - if None in [ocx10, ocx11, ocy10, ocy11]: - print('First order IDC coefficients not found, exiting ...\n') - return None, None - idc_coeff = np.array([[ocx11, ocx10], [ocy11, ocy10]]) - cx = np.zeros((order+1,order+1), dtype=np.double) - cy = np.zeros((order+1,order+1), dtype=np.double) - for n in range(order+1): - for m in range(order+1): - if n >= m and n>=2: - sipval = np.array([[sipa[m,n-m]],[sipb[m,n-m]]]) - idcval = np.dot(idc_coeff, sipval) - cx[n,m] = idcval[0] - cy[n,m] = idcval[1] - - cx[1,0] = ocx10 - cx[1,1] = ocx11 - cy[1,0] = ocy10 - cy[1,1] = ocy11 - - return cx, cy - -def _read_sip_kw(header): - """ - Reads SIP header keywords and returns an array of coefficients. - - If no SIP header keywords are found, None is returned. - """ - if "A_ORDER" in header: - if "B_ORDER" not in header: - raise ValueError( - "A_ORDER provided without corresponding B_ORDER " - "keyword for SIP distortion") - - m = int(header["A_ORDER"]) - a = np.zeros((m+1, m+1), np.double) - for i in range(m+1): - for j in range(m-i+1): - a[i, j] = header.get("A_%d_%d" % (i, j), 0.0) - - m = int(header["B_ORDER"]) - b = np.zeros((m+1, m+1), np.double) - for i in range(m+1): - for j in range(m-i+1): - b[i, j] = header.get("B_%d_%d" % (i, j), 0.0) - elif "B_ORDER" in header: - raise ValueError( - "B_ORDER provided without corresponding A_ORDER " - "keyword for SIP distortion") - else: - a = None - b = None - - return a , b - - -""" -def idc2sip(wcsobj, idctab = None): - if isinstance(wcs,pywcs.WCS): - try: - cx10 = wcsobj.ocx10 - cx11 = wcsobj.cx11 - cy10 = wcsobj.cy10 - cy11 = wcsobj.cy11 - except AttributeError: - print - try: - order = wcs.sip.a_order - except AttributeError: - print 'SIP model order unknown, exiting ...\n' - return - else: - print 'Input to sip2idc must be a PyFITS header or a wcsutil.HSTWCS object\n' - return - - if None in [ocx10, ocx11, ocy10, ocy11]: - print 'First order IDC coefficients not found, exiting ...\n' - return - idc_coeff = np.array([[wcsobj.cx11, wcsobj.cx10], [wcsobj.cy11, wcsobj.cy10]]) - cx = numpy.zeros((order+1,order+1), dtype=numpy.double) - cy = numpy.zeros((order+1,order+1), dtype=numpy.double) - for n in range(order+1): - for m in range(order+1): - if n >= m and n>=2: - sipval = numpy.array([[wcsobj.sip.a[n,m]],[wcsobj.sip.b[n,m]]]) - idcval = numpy.dot(idc_coeff, sipval) - cx[m,n-m] = idcval[0] - cy[m,n-m] = idcval[1] - - return cx, cy -""" diff --git a/lib/stwcs/distortion/models.py b/lib/stwcs/distortion/models.py deleted file mode 100644 index 231a9f1..0000000 --- a/lib/stwcs/distortion/models.py +++ /dev/null @@ -1,362 +0,0 @@ -from __future__ import absolute_import, division, print_function # confidence high - - -import numpy as np - -# Import PyDrizzle utility modules -from . import mutil -from .mutil import combin - -yes = True -no = False - -################# -# -# -# Geometry/Distortion Classes -# -# -################# - -class GeometryModel: - """ - Base class for Distortion model. - There will be a separate class for each type of - model/filetype used with drizzle, i.e., IDCModel and - DrizzleModel. - - Each class will know how to apply the distortion to a - single point and how to convert coefficients to an input table - suitable for the drizzle task. - - Coefficients will be stored in CX,CY arrays. - """ - # - # - # - # - # - # - # - NORDER = 3 - - def __init__(self): - " This will open the given file and determine its type and norder." - - # Method to read in coefficients from given table and - # populate the n arrays 'cx' and 'cy'. - # This will be different for each type of input file, - # IDCTAB vs. drizzle table. - - # Set these up here for all sub-classes to use... - # But, calculate norder and cx,cy arrays in detector specific classes. - self.cx = None - self.cy = None - self.refpix = None - self.norder = self.NORDER - # Keep track of computed zero-point for distortion coeffs - self.x0 = None - self.y0 = None - - # default values for these attributes - self.direction = 'forward' - - self.pscale = 1.0 - - def shift(self, xs, ys): - """ - Shift reference position of coefficients to new center - where (xs,ys) = old-reference-position - subarray/image center. - This will support creating coeffs files for drizzle which will - be applied relative to the center of the image, rather than relative - to the reference position of the chip. - """ - - _cxs = np.zeros(shape=self.cx.shape,dtype=self.cx.dtype) - _cys = np.zeros(shape=self.cy.shape,dtype=self.cy.dtype) - _k = self.norder + 1 - # loop over each input coefficient - for m in range(_k): - for n in range(_k): - if m >= n: - # For this coefficient, shift by xs/ys. - _ilist = list(range(m, _k)) - # sum from m to k - for i in _ilist: - _jlist = list(range(n, i - (m-n)+1)) - # sum from n to i-(m-n) - for j in _jlist: - _cxs[m,n] += self.cx[i,j]*combin(j,n)*combin((i-j),(m-n))*pow(xs,(j-n))*pow(ys,((i-j)-(m-n))) - _cys[m,n] += self.cy[i,j]*combin(j,n)*combin((i-j),(m-n))*pow(xs,(j-n))*pow(ys,((i-j)-(m-n))) - self.cx = _cxs.copy() - self.cy = _cys.copy() - - def convert(self, tmpname, xref=None,yref=None,delta=yes): - """ - Open up an ASCII file, output coefficients in drizzle - format after converting them as necessary. - First, normalize these coefficients to what drizzle expects - Normalize the coefficients by the MODEL/output plate scale. - - 16-May-2002: - Revised to work with higher order polynomials by John Blakeslee. - 27-June-2002: - Added ability to shift coefficients to new center for support - of subarrays. - """ - cx = self.cx/self.pscale - cy = self.cy/self.pscale - x0 = self.refpix['XDELTA'] + cx[0,0] - y0 = self.refpix['YDELTA'] + cy[0,0] - #xr = self.refpix['XREF'] - #yr = self.refpix['YREF'] - xr = self.refpix['CHIP_XREF'] - yr = self.refpix['CHIP_YREF'] - - - - ''' - if xref != None: - # Shift coefficients for use with drizzle - _xs = xref - self.refpix['XREF'] + 1.0 - _ys = yref - self.refpix['YREF'] + 1.0 - - - if _xs != 0 or _ys != 0: - cxs,cys= self.shift(cx, cy, _xs, _ys) - cx = cxs - cy = cys - - # We only want to apply this shift to coeffs - # for subarray images. - if delta == no: - cxs[0,0] = cxs[0,0] - _xs - cys[0,0] = cys[0,0] - _ys - - # Now, apply only the difference introduced by the distortion.. - # i.e., (undistorted - original) shift. - x0 += cxs[0,0] - y0 += cys[0,0] - ''' - self.x0 = x0 #+ 1.0 - self.y0 = y0 #+ 1.0 - - # Now, write out the coefficients into an ASCII - # file in 'drizzle' format. - lines = [] - - - lines.append('# Polynomial distortion coefficients\n') - lines.append('# Extracted from "%s" \n'%self.name) - lines.append('refpix %f %f \n'%(xr,yr)) - if self.norder==3: - lines.append('cubic\n') - elif self.norder==4: - lines.append('quartic\n') - elif self.norder==5: - lines.append('quintic\n') - else: - raise ValueError("Drizzle cannot handle poly distortions of order %d" % self.norder) - - str = '%16.8f %16.8g %16.8g %16.8g %16.8g \n'% (x0,cx[1,1],cx[1,0],cx[2,2],cx[2,1]) - lines.append(str) - str = '%16.8g %16.8g %16.8g %16.8g %16.8g \n'% (cx[2,0],cx[3,3],cx[3,2],cx[3,1],cx[3,0]) - lines.append(str) - if self.norder>3: - str = '%16.8g %16.8g %16.8g %16.8g %16.8g \n'% (cx[4,4],cx[4,3],cx[4,2],cx[4,1],cx[4,0]) - lines.append(str) - if self.norder>4: - str = '%16.8g %16.8g %16.8g %16.8g %16.8g %16.8g \n'% (cx[5,5],cx[5,4],cx[5,3],cx[5,2],cx[5,1],cx[5,0]) - lines.append(str) - lines.append("\n") - - str = '%16.8f %16.8g %16.8g %16.8g %16.8g \n'% (y0,cy[1,1],cy[1,0],cy[2,2],cy[2,1]) - lines.append(str) - str = '%16.8g %16.8g %16.8g %16.8g %16.8g \n'% (cy[2,0],cy[3,3],cy[3,2],cy[3,1],cy[3,0]) - lines.append(str) - if self.norder>3: - str = '%16.8g %16.8g %16.8g %16.8g %16.8g \n'% (cy[4,4],cy[4,3],cy[4,2],cy[4,1],cy[4,0]) - lines.append(str) - if self.norder>4: - str = '%16.8g %16.8g %16.8g %16.8g %16.8g %16.8g \n'% (cy[5,5],cy[5,4],cy[5,3],cy[5,2],cy[5,1],cy[5,0]) - lines.append(str) - - output = open(tmpname,'w') - output.writelines(lines) - output.close() - - - def apply(self, pixpos,scale=1.0,order=None): - """ - Apply coefficients to a pixel position or a list of positions. - This should be the same for all coefficients tables. - Return the geometrically-adjusted position - in arcseconds from the reference position as a tuple (x,y). - - Compute delta from reference position - """ - - """ - scale actually is a ratio of pscale/self.model.pscale - what is pscale? - """ - if self.cx == None: - return pixpos[:,0],pixpos[:,1] - - if order is None: - order = self.norder - - # Apply in the same way that 'drizzle' would... - _cx = self.cx / (self.pscale * scale) - _cy = self.cy / (self.pscale * scale) - _convert = no - _p = pixpos - - # Do NOT include any zero-point terms in CX,CY here - # as they should not be scaled by plate-scale like rest - # of coeffs... This makes the computations consistent - # with 'drizzle'. WJH 17-Feb-2004 - _cx[0,0] = 0. - _cy[0,0] = 0. - - if isinstance(_p, list) or isinstance(_p, tuple): - _p = np.array(_p,dtype=np.float64) - _convert = yes - - dxy = _p - (self.refpix['XREF'],self.refpix['YREF']) - # Apply coefficients from distortion model here... - c = _p * 0. - for i in range(order+1): - for j in range(i+1): - c[:,0] = c[:,0] + _cx[i][j] * pow(dxy[:,0],j) * pow(dxy[:,1],(i-j)) - c[:,1] = c[:,1] + _cy[i][j] * pow(dxy[:,0],j) * pow(dxy[:,1],(i-j)) - xc = c[:,0] - yc = c[:,1] - - # Convert results back to same form as original input - if _convert: - xc = xc.tolist() - yc = yc.tolist() - # If a single tuple was input, return just a single tuple - if len(xc) == 1: - xc = xc[0] - yc = yc[0] - - return xc,yc - - def setPScaleCoeffs(self,pscale): - self.cx[1,1] = pscale - self.cy[1,0] = pscale - - self.refpix['PSCALE'] = pscale - self.pscale = pscale - - -class IDCModel(GeometryModel): - """ - This class will open the IDCTAB, select proper row based on - chip/direction and populate cx,cy arrays. - We also need to read in SCALE, XCOM,YCOM, XREF,YREF as well. - """ - def __init__(self, idcfile, date=None, chip=1, direction='forward', - filter1='CLEAR1',filter2='CLEAR2',offtab=None, binned=1): - GeometryModel.__init__(self) - # - # Norder must be derived from the coeffs file itself, - # then the arrays can be setup. Thus, it needs to be - # done in the sub-class, not in the base class. - # Read in table. - # Populate cx,cy,scale, and other variables here. - # - self.name = idcfile - self.cx,self.cy,self.refpix,self.norder = mutil.readIDCtab(idcfile, - chip=chip,direction=direction,filter1=filter1,filter2=filter2, - date=date, offtab=offtab) - - if 'empty_model' in self.refpix and self.refpix['empty_model']: - pass - else: - self.refpix['PSCALE'] = self.refpix['PSCALE'] * binned - self.cx = self.cx * binned - self.cy = self.cy * binned - self.refpix['XREF'] = self.refpix['XREF'] / binned - self.refpix['YREF'] = self.refpix['YREF'] / binned - self.refpix['XSIZE'] = self.refpix['XSIZE'] / binned - self.refpix['YSIZE'] = self.refpix['YSIZE'] / binned - - self.pscale = self.refpix['PSCALE'] - - -class WCSModel(GeometryModel): - """ - This class sets up a distortion model based on coefficients - found in the image header. - """ - def __init__(self,header,rootname): - GeometryModel.__init__(self) - - - if 'rootname' in header: - self.name = header['rootname'] - else: - self.name = rootname - # Initialize all necessary distortion arrays with - # default model... - #self.cx,self.cy,self.refpix,self.order = mutil.defaultModel() - - # Read in values from header, and update distortion arrays. - self.cx,self.cy,self.refpix,self.norder = mutil.readWCSCoeffs(header) - - self.pscale = self.refpix['PSCALE'] - - - -class DrizzleModel(GeometryModel): - """ - This class will read in an ASCII Cubic - drizzle coeffs file and populate the cx,cy arrays. - """ - - def __init__(self, idcfile, scale = None): - GeometryModel.__init__(self) - # - # We now need to read in the file, populate cx,cy, and - # other variables as necessary. - # - self.name = idcfile - self.cx,self.cy,self.refpix,self.norder = mutil.readCubicTable(idcfile) - - # scale is the ratio wcs.pscale/model.pscale. - # model.pscale for WFPC2 is passed from REFDATA. - # This is needed for WFPC2 binned data. - - if scale != None: - self.pscale = scale - else: - self.pscale = self.refpix['PSCALE'] - - """ - The above definition looks wrong. - In one case it's a ratio in the other it's pscale. - - """ - -class TraugerModel(GeometryModel): - """ - This class will read in the ASCII Trauger coeffs - file, convert them to SIAF coefficients, then populate - the cx,cy arrays. - """ - NORDER = 3 - - def __init__(self, idcfile,lam): - GeometryModel.__init__(self) - self.name = idcfile - self.cx,self.cy,self.refpix,self.norder = mutil.readTraugerTable(idcfile,lam) - self.pscale = self.refpix['PSCALE'] - # - # Read in file here. - # Populate cx,cy, and other variables. - # - - diff --git a/lib/stwcs/distortion/mutil.py b/lib/stwcs/distortion/mutil.py deleted file mode 100644 index ed6a1ea..0000000 --- a/lib/stwcs/distortion/mutil.py +++ /dev/null @@ -1,703 +0,0 @@ -from __future__ import division, print_function # confidence high - -from stsci.tools import fileutil -import numpy as np -import calendar - -# Set up IRAF-compatible Boolean values -yes = True -no = False - -# This function read the IDC table and generates the two matrices with -# the geometric correction coefficients. -# -# INPUT: FITS object of open IDC table -# OUTPUT: coefficient matrices for Fx and Fy -# -#### If 'tabname' == None: This should return a default, undistorted -#### solution. -# - -def readIDCtab (tabname, chip=1, date=None, direction='forward', - filter1=None,filter2=None, offtab=None): - - """ - Read IDCTAB, and optional OFFTAB if sepcified, and generate - the two matrices with the geometric correction coefficients. - - If tabname == None, then return a default, undistorted solution. - If offtab is specified, dateobs also needs to be given. - - """ - - # Return a default geometry model if no IDCTAB filename - # is given. This model will not distort the data in any way. - if tabname == None: - print('Warning: No IDCTAB specified! No distortion correction will be applied.') - return defaultModel() - - # Implement default values for filters here to avoid the default - # being overwritten by values of None passed by user. - if filter1 == None or filter1.find('CLEAR') == 0 or filter1.strip() == '': - filter1 = 'CLEAR' - if filter2 == None or filter2.find('CLEAR') == 0 or filter2.strip() == '': - filter2 = 'CLEAR' - - # Insure that tabname is full filename with fully expanded - # IRAF variables; i.e. 'jref$mc41442gj_idc.fits' should get - # expanded to '/data/cdbs7/jref/mc41442gj_idc.fits' before - # being used here. - # Open up IDC table now... - try: - ftab = fileutil.openImage(tabname) - except: - err_str = "------------------------------------------------------------------------ \n" - err_str += "WARNING: the IDCTAB geometric distortion file specified in the image \n" - err_str += "header was not found on disk. Please verify that your environment \n" - err_str += "variable ('jref'/'uref'/'oref'/'nref') has been correctly defined. If \n" - err_str += "you do not have the IDCTAB file, you may obtain the latest version \n" - err_str += "of it from the relevant instrument page on the STScI HST website: \n" - err_str += "http://www.stsci.edu/hst/ For WFPC2, STIS and NICMOS data, the \n" - err_str += "present run will continue using the old coefficients provided in \n" - err_str += "the Dither Package (ca. 1995-1998). \n" - err_str += "------------------------------------------------------------------------ \n" - raise IOError(err_str) - - #First thing we need, is to read in the coefficients from the IDC - # table and populate the Fx and Fy matrices. - - if 'DETECTOR' in ftab['PRIMARY'].header: - detector = ftab['PRIMARY'].header['DETECTOR'] - else: - if 'CAMERA' in ftab['PRIMARY'].header: - detector = str(ftab['PRIMARY'].header['CAMERA']) - else: - detector = 1 - # First, read in TDD coeffs if present - phdr = ftab['PRIMARY'].header - instrument = phdr['INSTRUME'] - if instrument == 'ACS' and detector == 'WFC': - skew_coeffs = read_tdd_coeffs(phdr, chip=chip) - else: - skew_coeffs = None - - # Set default filters for SBC - if detector == 'SBC': - if filter1 == 'CLEAR': - filter1 = 'F115LP' - filter2 = 'N/A' - if filter2 == 'CLEAR': - filter2 = 'N/A' - - # Read FITS header to determine order of fit, i.e. k - norder = ftab['PRIMARY'].header['NORDER'] - if norder < 3: - order = 3 - else: - order = norder - - fx = np.zeros(shape=(order+1,order+1),dtype=np.float64) - fy = np.zeros(shape=(order+1,order+1),dtype=np.float64) - - #Determine row from which to get the coefficients. - # How many rows do we have in the table... - fshape = ftab[1].data.shape - colnames = ftab[1].data.names - row = -1 - - # Loop over all the rows looking for the one which corresponds - # to the value of CCDCHIP we are working on... - for i in range(fshape[0]): - - try: - # Match FILTER combo to appropriate row, - #if there is a filter column in the IDCTAB... - if 'FILTER1' in colnames and 'FILTER2' in colnames: - - filt1 = ftab[1].data.field('FILTER1')[i] - if filt1.find('CLEAR') > -1: filt1 = filt1[:5] - - filt2 = ftab[1].data.field('FILTER2')[i] - if filt2.find('CLEAR') > -1: filt2 = filt2[:5] - else: - if 'OPT_ELEM' in colnames: - filt1 = ftab[1].data.field('OPT_ELEM') - if filt1.find('CLEAR') > -1: filt1 = filt1[:5] - else: - filt1 = filter1 - - if 'FILTER' in colnames: - _filt = ftab[1].data.field('FILTER')[i] - if _filt.find('CLEAR') > -1: _filt = _filt[:5] - if 'OPT_ELEM' in colnames: - filt2 = _filt - else: - filt1 = _filt - filt2 = 'CLEAR' - else: - filt2 = filter2 - except: - # Otherwise assume all rows apply and compare to input filters... - filt1 = filter1 - filt2 = filter2 - - if 'DETCHIP' in colnames: - detchip = ftab[1].data.field('DETCHIP')[i] - if not str(detchip).isdigit(): - detchip = 1 - else: - detchip = 1 - - if 'DIRECTION' in colnames: - direct = ftab[1].data.field('DIRECTION')[i].lower().strip() - else: - direct = 'forward' - - if filt1 == filter1.strip() and filt2 == filter2.strip(): - if direct == direction.strip(): - if int(detchip) == int(chip) or int(detchip) == -999: - row = i - break - - joinstr = ',' - if 'CLEAR' in filter1: - f1str = '' - joinstr = '' - else: - f1str = filter1.strip() - if 'CLEAR' in filter2: - f2str = '' - joinstr = '' - else: - f2str = filter2.strip() - filtstr = (joinstr.join([f1str,f2str])).strip() - if row < 0: - err_str = '\nProblem finding row in IDCTAB! Could not find row matching:\n' - err_str += ' CHIP: '+str(detchip)+'\n' - err_str += ' FILTERS: '+filtstr+'\n' - ftab.close() - del ftab - raise LookupError(err_str) - else: - print('- IDCTAB: Distortion model from row',str(row+1),'for chip',detchip,':',filtstr) - - # Read in V2REF and V3REF: this can either come from current table, - # or from an OFFTAB if time-dependent (i.e., for WFPC2) - theta = None - if 'V2REF' in colnames: - v2ref = ftab[1].data.field('V2REF')[row] - v3ref = ftab[1].data.field('V3REF')[row] - else: - # Read V2REF/V3REF from offset table (OFFTAB) - if offtab: - v2ref,v3ref,theta = readOfftab(offtab, date, chip=detchip) - else: - v2ref = 0.0 - v3ref = 0.0 - - if theta == None: - if 'THETA' in colnames: - theta = ftab[1].data.field('THETA')[row] - else: - theta = 0.0 - - refpix = {} - refpix['XREF'] = ftab[1].data.field('XREF')[row] - refpix['YREF'] = ftab[1].data.field('YREF')[row] - refpix['XSIZE'] = ftab[1].data.field('XSIZE')[row] - refpix['YSIZE'] = ftab[1].data.field('YSIZE')[row] - refpix['PSCALE'] = round(ftab[1].data.field('SCALE')[row],8) - refpix['V2REF'] = v2ref - refpix['V3REF'] = v3ref - refpix['THETA'] = theta - refpix['XDELTA'] = 0.0 - refpix['YDELTA'] = 0.0 - refpix['DEFAULT_SCALE'] = yes - refpix['centered'] = no - refpix['skew_coeffs'] = skew_coeffs - # Now that we know which row to look at, read coefficients into the - # numeric arrays we have set up... - # Setup which column name convention the IDCTAB follows - # either: A,B or CX,CY - if 'CX10' in ftab[1].data.names: - cxstr = 'CX' - cystr = 'CY' - else: - cxstr = 'A' - cystr = 'B' - - for i in range(norder+1): - if i > 0: - for j in range(i+1): - xcname = cxstr+str(i)+str(j) - ycname = cystr+str(i)+str(j) - fx[i,j] = ftab[1].data.field(xcname)[row] - fy[i,j] = ftab[1].data.field(ycname)[row] - - ftab.close() - del ftab - - # If CX11 is 1.0 and not equal to the PSCALE, then the - # coeffs need to be scaled - - if fx[1,1] == 1.0 and abs(fx[1,1]) != refpix['PSCALE']: - fx *= refpix['PSCALE'] - fy *= refpix['PSCALE'] - - # Return arrays and polynomial order read in from table. - # NOTE: XREF and YREF are stored in Fx,Fy arrays respectively. - return fx,fy,refpix,order -# -# -# Time-dependent skew correction coefficients (only ACS/WFC) -# -# -def read_tdd_coeffs(phdr, chip=1): - ''' Read in the TDD related keywords from the PRIMARY header of the IDCTAB - ''' - # Insure we have an integer form of chip - ic = int(chip) - - skew_coeffs = {} - skew_coeffs['TDDORDER'] = 0 - skew_coeffs['TDD_DATE'] = "" - skew_coeffs['TDD_A'] = None - skew_coeffs['TDD_B'] = None - skew_coeffs['TDD_CY_BETA'] = None - skew_coeffs['TDD_CY_ALPHA'] = None - skew_coeffs['TDD_CX_BETA'] = None - skew_coeffs['TDD_CX_ALPHA'] = None - - # Skew-based TDD coefficients - skew_terms = ['TDD_CTB','TDD_CTA','TDD_CYA','TDD_CYB','TDD_CXA','TDD_CXB'] - for s in skew_terms: - skew_coeffs[s] = None - - if "TDD_CTB1" in phdr: - # We have the 2015-calibrated TDD correction to apply - # This correction is based on correcting the skew in the linear terms - # not just set polynomial terms - print("Using 2015-calibrated VAFACTOR-corrected TDD correction...") - skew_coeffs['TDD_DATE'] = phdr['TDD_DATE'] - for s in skew_terms: - skew_coeffs[s] = phdr.get('{0}{1}'.format(s,ic),None) - - elif "TDD_CYB1" in phdr: - # We have 2014-calibrated TDD correction to apply, not J.A.-derived values - print("Using 2014-calibrated TDD correction...") - skew_coeffs['TDD_DATE'] = phdr['TDD_DATE'] - # Read coefficients for TDD Y coefficient - cyb_kw = 'TDD_CYB{0}'.format(int(chip)) - skew_coeffs['TDD_CY_BETA'] = phdr.get(cyb_kw,None) - cya_kw = 'TDD_CYA{0}'.format(int(chip)) - tdd_cya = phdr.get(cya_kw,None) - if tdd_cya == 0 or tdd_cya == 'N/A': tdd_cya = None - skew_coeffs['TDD_CY_ALPHA'] = tdd_cya - - # Read coefficients for TDD X coefficient - cxb_kw = 'TDD_CXB{0}'.format(int(chip)) - skew_coeffs['TDD_CX_BETA'] = phdr.get(cxb_kw,None) - cxa_kw = 'TDD_CXA{0}'.format(int(chip)) - tdd_cxa = phdr.get(cxa_kw,None) - if tdd_cxa == 0 or tdd_cxa == 'N/A': tdd_cxa = None - skew_coeffs['TDD_CX_ALPHA'] = tdd_cxa - - else: - if "TDDORDER" in phdr: - n = int(phdr["TDDORDER"]) - else: - print('TDDORDER kw not present, using default TDD correction') - return None - - a = np.zeros((n+1,), np.float64) - b = np.zeros((n+1,), np.float64) - for i in range(n+1): - a[i] = phdr.get(("TDD_A%d" % i), 0.0) - b[i] = phdr.get(("TDD_B%d" % i), 0.0) - if (a==0).all() and (b==0).all(): - print('Warning: TDD_A and TDD_B coeffiecients have values of 0, \n \ - but TDDORDER is %d.' % TDDORDER) - - skew_coeffs['TDDORDER'] = n - skew_coeffs['TDD_DATE'] = phdr['TDD_DATE'] - skew_coeffs['TDD_A'] = a - skew_coeffs['TDD_B'] = b - - return skew_coeffs - -def readOfftab(offtab, date, chip=None): - - -#Read V2REF,V3REF from a specified offset table (OFFTAB). -# Return a default geometry model if no IDCTAB filenam e -# is given. This model will not distort the data in any way. - - if offtab == None: - return 0.,0. - - # Provide a default value for chip - if chip: - detchip = chip - else: - detchip = 1 - - # Open up IDC table now... - try: - ftab = fileutil.openImage(offtab) - except: - raise IOError("Offset table '%s' not valid as specified!" % offtab) - - #Determine row from which to get the coefficients. - # How many rows do we have in the table... - fshape = ftab[1].data.shape - colnames = ftab[1].data.names - row = -1 - - row_start = None - row_end = None - - v2end = None - v3end = None - date_end = None - theta_end = None - - num_date = convertDate(date) - # Loop over all the rows looking for the one which corresponds - # to the value of CCDCHIP we are working on... - for ri in range(fshape[0]): - i = fshape[0] - ri - 1 - if 'DETCHIP' in colnames: - detchip = ftab[1].data.field('DETCHIP')[i] - else: - detchip = 1 - - obsdate = convertDate(ftab[1].data.field('OBSDATE')[i]) - - # If the row is appropriate for the chip... - # Interpolate between dates - if int(detchip) == int(chip) or int(detchip) == -999: - if num_date <= obsdate: - date_end = obsdate - v2end = ftab[1].data.field('V2REF')[i] - v3end = ftab[1].data.field('V3REF')[i] - theta_end = ftab[1].data.field('THETA')[i] - row_end = i - continue - - if row_end == None and (num_date > obsdate): - date_end = obsdate - v2end = ftab[1].data.field('V2REF')[i] - v3end = ftab[1].data.field('V3REF')[i] - theta_end = ftab[1].data.field('THETA')[i] - row_end = i - continue - - if num_date > obsdate: - date_start = obsdate - v2start = ftab[1].data.field('V2REF')[i] - v3start = ftab[1].data.field('V3REF')[i] - theta_start = ftab[1].data.field('THETA')[i] - row_start = i - break - - ftab.close() - del ftab - - if row_start == None and row_end == None: - print('Row corresponding to DETCHIP of ',detchip,' was not found!') - raise LookupError - elif row_start == None: - print('- OFFTAB: Offset defined by row',str(row_end+1)) - else: - print('- OFFTAB: Offset interpolated from rows',str(row_start+1),'and',str(row_end+1)) - - # Now, do the interpolation for v2ref, v3ref, and theta - if row_start == None or row_end == row_start: - # We are processing an observation taken after the last calibration - date_start = date_end - v2start = v2end - v3start = v3end - _fraction = 0. - theta_start = theta_end - else: - _fraction = float((num_date - date_start)) / float((date_end - date_start)) - - v2ref = _fraction * (v2end - v2start) + v2start - v3ref = _fraction * (v3end - v3start) + v3start - theta = _fraction * (theta_end - theta_start) + theta_start - - return v2ref,v3ref,theta - -def readWCSCoeffs(header): - - #Read distortion coeffs from WCS header keywords and - #populate distortion coeffs arrays. - - # Read in order for polynomials - _xorder = header['a_order'] - _yorder = header['b_order'] - order = max(max(_xorder,_yorder),3) - - fx = np.zeros(shape=(order+1,order+1),dtype=np.float64) - fy = np.zeros(shape=(order+1,order+1),dtype=np.float64) - - # Read in CD matrix - _cd11 = header['cd1_1'] - _cd12 = header['cd1_2'] - _cd21 = header['cd2_1'] - _cd22 = header['cd2_2'] - _cdmat = np.array([[_cd11,_cd12],[_cd21,_cd22]]) - _theta = np.arctan2(-_cd12,_cd22) - _rotmat = np.array([[np.cos(_theta),np.sin(_theta)], - [-np.sin(_theta),np.cos(_theta)]]) - _rCD = np.dot(_rotmat,_cdmat) - _skew = np.arcsin(-_rCD[1][0] / _rCD[0][0]) - _scale = _rCD[0][0] * np.cos(_skew) * 3600. - _scale2 = _rCD[1][1] * 3600. - - # Set up refpix - refpix = {} - refpix['XREF'] = header['crpix1'] - refpix['YREF'] = header['crpix2'] - refpix['XSIZE'] = header['naxis1'] - refpix['YSIZE'] = header['naxis2'] - refpix['PSCALE'] = _scale - refpix['V2REF'] = 0. - refpix['V3REF'] = 0. - refpix['THETA'] = np.rad2deg(_theta) - refpix['XDELTA'] = 0.0 - refpix['YDELTA'] = 0.0 - refpix['DEFAULT_SCALE'] = yes - refpix['centered'] = yes - - - # Set up template for coeffs keyword names - cxstr = 'A_' - cystr = 'B_' - # Read coeffs into their own matrix - for i in range(_xorder+1): - for j in range(i+1): - xcname = cxstr+str(j)+'_'+str(i-j) - if xcname in header: - fx[i,j] = header[xcname] - - # Extract Y coeffs separately as a different order may - # have been used to fit it. - for i in range(_yorder+1): - for j in range(i+1): - ycname = cystr+str(j)+'_'+str(i-j) - if ycname in header: - fy[i,j] = header[ycname] - - # Now set the linear terms - fx[0][0] = 1.0 - fy[0][0] = 1.0 - - return fx,fy,refpix,order - - -def readTraugerTable(idcfile,wavelength): - - # Return a default geometry model if no coefficients filename - # is given. This model will not distort the data in any way. - if idcfile == None: - return fileutil.defaultModel() - - # Trauger coefficients only result in a cubic file... - order = 3 - numco = 10 - a_coeffs = [0] * numco - b_coeffs = [0] * numco - indx = _MgF2(wavelength) - - ifile = open(idcfile,'r') - # Search for the first line of the coefficients - _line = fileutil.rAsciiLine(ifile) - while _line[:7].lower() != 'trauger': - _line = fileutil.rAsciiLine(ifile) - # Read in each row of coefficients,split them into their values, - # and convert them into cubic coefficients based on - # index of refraction value for the given wavelength - # Build X coefficients from first 10 rows of Trauger coefficients - j = 0 - while j < 20: - _line = fileutil.rAsciiLine(ifile) - if _line == '': continue - _lc = _line.split() - if j < 10: - a_coeffs[j] = float(_lc[0])+float(_lc[1])*(indx-1.5)+float(_lc[2])*(indx-1.5)**2 - else: - b_coeffs[j-10] = float(_lc[0])+float(_lc[1])*(indx-1.5)+float(_lc[2])*(indx-1.5)**2 - j = j + 1 - - ifile.close() - del ifile - - # Now, convert the coefficients into a Numeric array - # with the right coefficients in the right place. - # Populate output values now... - fx = np.zeros(shape=(order+1,order+1),dtype=np.float64) - fy = np.zeros(shape=(order+1,order+1),dtype=np.float64) - # Assign the coefficients to their array positions - fx[0,0] = 0. - fx[1] = np.array([a_coeffs[2],a_coeffs[1],0.,0.],dtype=np.float64) - fx[2] = np.array([a_coeffs[5],a_coeffs[4],a_coeffs[3],0.],dtype=np.float64) - fx[3] = np.array([a_coeffs[9],a_coeffs[8],a_coeffs[7],a_coeffs[6]],dtype=np.float64) - fy[0,0] = 0. - fy[1] = np.array([b_coeffs[2],b_coeffs[1],0.,0.],dtype=np.float64) - fy[2] = np.array([b_coeffs[5],b_coeffs[4],b_coeffs[3],0.],dtype=np.float64) - fy[3] = np.array([b_coeffs[9],b_coeffs[8],b_coeffs[7],b_coeffs[6]],dtype=np.float64) - - # Used in Pattern.computeOffsets() - refpix = {} - refpix['XREF'] = None - refpix['YREF'] = None - refpix['V2REF'] = None - refpix['V3REF'] = None - refpix['XDELTA'] = 0. - refpix['YDELTA'] = 0. - refpix['PSCALE'] = None - refpix['DEFAULT_SCALE'] = no - refpix['centered'] = yes - - return fx,fy,refpix,order - - -def readCubicTable(idcfile): - # Assumption: this will only be used for cubic file... - order = 3 - # Also, this function does NOT perform any scaling on - # the coefficients, it simply passes along what is found - # in the file as is... - - # Return a default geometry model if no coefficients filename - # is given. This model will not distort the data in any way. - if idcfile == None: - return fileutil.defaultModel() - - ifile = open(idcfile,'r') - # Search for the first line of the coefficients - _line = fileutil.rAsciiLine(ifile) - - _found = no - while _found == no: - if _line[:7] in ['cubic','quartic','quintic'] or _line[:4] == 'poly': - found = yes - break - _line = fileutil.rAsciiLine(ifile) - - # Read in each row of coefficients, without line breaks or newlines - # split them into their values, and create a list for A coefficients - # and another list for the B coefficients - _line = fileutil.rAsciiLine(ifile) - a_coeffs = _line.split() - - x0 = float(a_coeffs[0]) - _line = fileutil.rAsciiLine(ifile) - a_coeffs[len(a_coeffs):] = _line.split() - # Scale coefficients for use within PyDrizzle - for i in range(len(a_coeffs)): - a_coeffs[i] = float(a_coeffs[i]) - - _line = fileutil.rAsciiLine(ifile) - b_coeffs = _line.split() - y0 = float(b_coeffs[0]) - _line = fileutil.rAsciiLine(ifile) - b_coeffs[len(b_coeffs):] = _line.split() - # Scale coefficients for use within PyDrizzle - for i in range(len(b_coeffs)): - b_coeffs[i] = float(b_coeffs[i]) - - ifile.close() - del ifile - # Now, convert the coefficients into a Numeric array - # with the right coefficients in the right place. - # Populate output values now... - fx = np.zeros(shape=(order+1,order+1),dtype=np.float64) - fy = np.zeros(shape=(order+1,order+1),dtype=np.float64) - # Assign the coefficients to their array positions - fx[0,0] = 0. - fx[1] = np.array([a_coeffs[2],a_coeffs[1],0.,0.],dtype=np.float64) - fx[2] = np.array([a_coeffs[5],a_coeffs[4],a_coeffs[3],0.],dtype=np.float64) - fx[3] = np.array([a_coeffs[9],a_coeffs[8],a_coeffs[7],a_coeffs[6]],dtype=np.float64) - fy[0,0] = 0. - fy[1] = np.array([b_coeffs[2],b_coeffs[1],0.,0.],dtype=np.float64) - fy[2] = np.array([b_coeffs[5],b_coeffs[4],b_coeffs[3],0.],dtype=np.float64) - fy[3] = np.array([b_coeffs[9],b_coeffs[8],b_coeffs[7],b_coeffs[6]],dtype=np.float64) - - # Used in Pattern.computeOffsets() - refpix = {} - refpix['XREF'] = None - refpix['YREF'] = None - refpix['V2REF'] = x0 - refpix['V3REF'] = y0 - refpix['XDELTA'] = 0. - refpix['YDELTA'] = 0. - refpix['PSCALE'] = None - refpix['DEFAULT_SCALE'] = no - refpix['centered'] = yes - - return fx,fy,refpix,order - -def factorial(n): - """ Compute a factorial for integer n. """ - m = 1 - for i in range(int(n)): - m = m * (i+1) - return m - -def combin(j,n): - """ Return the combinatorial factor for j in n.""" - return (factorial(j) / (factorial(n) * factorial( (j-n) ) ) ) - - -def defaultModel(): - """ This function returns a default, non-distorting model - that can be used with the data. - """ - order = 3 - - fx = np.zeros(shape=(order+1,order+1),dtype=np.float64) - fy = np.zeros(shape=(order+1,order+1),dtype=np.float64) - - fx[1,1] = 1. - fy[1,0] = 1. - - # Used in Pattern.computeOffsets() - refpix = {} - refpix['empty_model'] = yes - refpix['XREF'] = None - refpix['YREF'] = None - refpix['V2REF'] = 0. - refpix['XSIZE'] = 0. - refpix['YSIZE'] = 0. - refpix['V3REF'] = 0. - refpix['XDELTA'] = 0. - refpix['YDELTA'] = 0. - refpix['PSCALE'] = None - refpix['DEFAULT_SCALE'] = no - refpix['THETA'] = 0. - refpix['centered'] = yes - return fx,fy,refpix,order - -# Function to compute the index of refraction for MgF2 at -# the specified wavelength for use with Trauger coefficients -def _MgF2(lam): - _sig = pow((1.0e7/lam),2) - return np.sqrt(1.0 + 2.590355e10/(5.312993e10-_sig) + - 4.4543708e9/(11.17083e9-_sig) + 4.0838897e5/(1.766361e5-_sig)) - - -def convertDate(date): - """ Converts the DATE-OBS date string into an integer of the - number of seconds since 1970.0 using calendar.timegm(). - - INPUT: DATE-OBS in format of 'YYYY-MM-DD'. - OUTPUT: Date (integer) in seconds. - """ - - _dates = date.split('-') - _val = 0 - _date_tuple = (int(_dates[0]), int(_dates[1]), int(_dates[2]), 0, 0, 0, 0, 0, 0) - - return calendar.timegm(_date_tuple) diff --git a/lib/stwcs/distortion/utils.py b/lib/stwcs/distortion/utils.py deleted file mode 100644 index 4228f62..0000000 --- a/lib/stwcs/distortion/utils.py +++ /dev/null @@ -1,270 +0,0 @@ -from __future__ import division, print_function # confidence high - -import os - -import numpy as np -from numpy import linalg -from astropy import wcs as pywcs - -from stwcs import wcsutil -from stwcs import updatewcs -from numpy import sqrt, arctan2 -from stsci.tools import fileutil - -def output_wcs(list_of_wcsobj, ref_wcs=None, owcs=None, undistort=True): - """ - Create an output WCS. - - Parameters - ---------- - list_of_wcsobj: Python list - a list of HSTWCS objects - ref_wcs: an HSTWCS object - to be used as a reference WCS, in case outwcs is None. - if ref_wcs is None (default), the first member of the list - is used as a reference - outwcs: an HSTWCS object - the tangent plane defined by this object is used as a reference - undistort: boolean (default-True) - a flag whether to create an undistorted output WCS - """ - fra_dec = np.vstack([w.calc_footprint() for w in list_of_wcsobj]) - wcsname = list_of_wcsobj[0].wcs.name - - # This new algorithm may not be strictly necessary, but it may be more - # robust in handling regions near the poles or at 0h RA. - crval1,crval2 = computeFootprintCenter(fra_dec) - - crval = np.array([crval1,crval2], dtype=np.float64) # this value is now zero-based - if owcs is None: - if ref_wcs is None: - ref_wcs = list_of_wcsobj[0].deepcopy() - if undistort: - #outwcs = undistortWCS(ref_wcs) - outwcs = make_orthogonal_cd(ref_wcs) - else: - outwcs = ref_wcs.deepcopy() - outwcs.wcs.crval = crval - outwcs.wcs.set() - outwcs.pscale = sqrt(outwcs.wcs.cd[0,0]**2 + outwcs.wcs.cd[1,0]**2)*3600. - outwcs.orientat = arctan2(outwcs.wcs.cd[0,1],outwcs.wcs.cd[1,1]) * 180./np.pi - else: - outwcs = owcs.deepcopy() - outwcs.pscale = sqrt(outwcs.wcs.cd[0,0]**2 + outwcs.wcs.cd[1,0]**2)*3600. - outwcs.orientat = arctan2(outwcs.wcs.cd[0,1],outwcs.wcs.cd[1,1]) * 180./np.pi - - tanpix = outwcs.wcs.s2p(fra_dec, 0)['pixcrd'] - - outwcs._naxis1 = int(np.ceil(tanpix[:,0].max() - tanpix[:,0].min())) - outwcs._naxis2 = int(np.ceil(tanpix[:,1].max() - tanpix[:,1].min())) - crpix = np.array([outwcs._naxis1/2., outwcs._naxis2/2.], dtype=np.float64) - outwcs.wcs.crpix = crpix - outwcs.wcs.set() - tanpix = outwcs.wcs.s2p(fra_dec, 0)['pixcrd'] - - # shift crpix to take into account (floating-point value of) position of - # corner pixel relative to output frame size: no rounding necessary... - newcrpix = np.array([crpix[0]+tanpix[:,0].min(), crpix[1]+ - tanpix[:,1].min()]) - - newcrval = outwcs.wcs.p2s([newcrpix], 1)['world'][0] - outwcs.wcs.crval = newcrval - outwcs.wcs.set() - outwcs.wcs.name = wcsname # keep track of label for this solution - return outwcs - -def computeFootprintCenter(edges): - """ Geographic midpoint in spherical coords for points defined by footprints. - Algorithm derived from: http://www.geomidpoint.com/calculation.html - - This algorithm should be more robust against discontinuities at the poles. - """ - alpha = np.deg2rad(edges[:,0]) - dec = np.deg2rad(edges[:,1]) - - xmean = np.mean(np.cos(dec)*np.cos(alpha)) - ymean = np.mean(np.cos(dec)*np.sin(alpha)) - zmean = np.mean(np.sin(dec)) - - crval1 = np.rad2deg(np.arctan2(ymean,xmean))%360.0 - crval2 = np.rad2deg(np.arctan2(zmean,np.sqrt(xmean*xmean+ymean*ymean))) - - return crval1,crval2 - -def make_orthogonal_cd(wcs): - """ Create a perfect (square, orthogonal, undistorted) CD matrix from the - input WCS. - """ - # get determinant of the CD matrix: - cd = wcs.celestial.pixel_scale_matrix - - - if hasattr(wcs, 'idcv2ref') and wcs.idcv2ref is not None: - # Convert the PA_V3 orientation to the orientation at the aperture - # This is for the reference chip only - we use this for the - # reference tangent plane definition - # It has the same orientation as the reference chip - pv = updatewcs.makewcs.troll(wcs.pav3,wcs.wcs.crval[1],wcs.idcv2ref,wcs.idcv3ref) - # Add the chip rotation angle - if wcs.idctheta: - pv += wcs.idctheta - cs = np.cos(np.deg2rad(pv)) - sn = np.sin(np.deg2rad(pv)) - pvmat = np.dot(np.array([[cs,sn],[-sn,cs]]),wcs.parity) - rot = np.arctan2(pvmat[0,1],pvmat[1,1]) - scale = wcs.idcscale/3600. - - det = linalg.det(wcs.parity) - - else: - - det = linalg.det(cd) - - # find pixel scale: - if hasattr(wcs, 'idcscale'): - scale = (wcs.idcscale) / 3600. # HST pixel scale provided - else: - scale = np.sqrt(np.abs(det)) # find as sqrt(pixel area) - - # find Y-axis orientation: - if hasattr(wcs, 'orientat') and not ignoreHST: - rot = np.deg2rad(wcs.orientat) # use HST ORIENTAT - else: - rot = np.arctan2(wcs.wcs.cd[0,1], wcs.wcs.cd[1,1]) # angle of the Y-axis - - par = -1 if det < 0.0 else 1 - - # create a perfectly square, orthogonal WCS - sn = np.sin(rot) - cs = np.cos(rot) - orthogonal_cd = scale * np.array([[par*cs, sn], [-par*sn, cs]]) - - lin_wcsobj = pywcs.WCS() - lin_wcsobj.wcs.cd = orthogonal_cd - lin_wcsobj.wcs.set() - lin_wcsobj.orientat = arctan2(lin_wcsobj.wcs.cd[0,1],lin_wcsobj.wcs.cd[1,1]) * 180./np.pi - lin_wcsobj.pscale = sqrt(lin_wcsobj.wcs.cd[0,0]**2 + lin_wcsobj.wcs.cd[1,0]**2)*3600. - lin_wcsobj.wcs.crval = np.array([0.,0.]) - lin_wcsobj.wcs.crpix = np.array([0.,0.]) - lin_wcsobj.wcs.ctype = ['RA---TAN', 'DEC--TAN'] - lin_wcsobj.wcs.set() - - return lin_wcsobj - -def undistortWCS(wcsobj): - """ - Creates an undistorted linear WCS by applying the IDCTAB distortion model - to a 3-point square. The new ORIENTAT angle is calculated as well as the - plate scale in the undistorted frame. - """ - assert isinstance(wcsobj, pywcs.WCS) - from . import coeff_converter - - cx, cy = coeff_converter.sip2idc(wcsobj) - # cx, cy can be None because either there is no model available - # or updatewcs was not run. - if cx is None or cy is None: - if foundIDCTAB(wcsobj.idctab): - m = """IDCTAB is present but distortion model is missing. - Run updatewcs() to update the headers or - pass 'undistort=False' keyword to output_wcs().\n - """ - raise RuntimeError(m) - else: - print('Distortion model is not available, using input reference image for output WCS.\n') - return wcsobj.copy() - crpix1 = wcsobj.wcs.crpix[0] - crpix2 = wcsobj.wcs.crpix[1] - xy = np.array([(crpix1,crpix2),(crpix1+1.,crpix2),(crpix1,crpix2+1.)],dtype=np.double) - offsets = np.array([wcsobj.ltv1, wcsobj.ltv2]) - px = xy + offsets - #order = wcsobj.sip.a_order - pscale = wcsobj.idcscale - #pixref = np.array([wcsobj.sip.SIPREF1, wcsobj.sip.SIPREF2]) - - tan_pix = apply_idc(px, cx, cy, wcsobj.wcs.crpix, pscale, order=1) - xc = tan_pix[:,0] - yc = tan_pix[:,1] - am = xc[1] - xc[0] - bm = xc[2] - xc[0] - cm = yc[1] - yc[0] - dm = yc[2] - yc[0] - cd_mat = np.array([[am,bm],[cm,dm]],dtype=np.double) - - # Check the determinant for singularity - _det = (am * dm) - (bm * cm) - if ( _det == 0.0): - print('Singular matrix in updateWCS, aborting ...') - return - - lin_wcsobj = pywcs.WCS() - cd_inv = np.linalg.inv(cd_mat) - cd = np.dot(wcsobj.wcs.cd, cd_inv).astype(np.float64) - lin_wcsobj.wcs.cd = cd - lin_wcsobj.wcs.set() - lin_wcsobj.orientat = arctan2(lin_wcsobj.wcs.cd[0,1],lin_wcsobj.wcs.cd[1,1]) * 180./np.pi - lin_wcsobj.pscale = sqrt(lin_wcsobj.wcs.cd[0,0]**2 + lin_wcsobj.wcs.cd[1,0]**2)*3600. - lin_wcsobj.wcs.crval = np.array([0.,0.]) - lin_wcsobj.wcs.crpix = np.array([0.,0.]) - lin_wcsobj.wcs.ctype = ['RA---TAN', 'DEC--TAN'] - lin_wcsobj.wcs.set() - return lin_wcsobj - -def apply_idc(pixpos, cx, cy, pixref, pscale= None, order=None): - """ - Apply the IDCTAB polynomial distortion model to pixel positions. - pixpos must be already corrected for ltv1/2. - - Parameters - ---------- - pixpos: a 2D numpy array of (x,y) pixel positions to be distortion corrected - cx, cy: IDC model distortion coefficients - pixref: reference opixel position - - """ - if cx is None: - return pixpos - - if order is None: - print('Unknown order of distortion model \n') - return pixpos - if pscale is None: - print('Unknown model plate scale\n') - return pixpos - - # Apply in the same way that 'drizzle' would... - _cx = cx/pscale - _cy = cy/ pscale - _p = pixpos - - # Do NOT include any zero-point terms in CX,CY here - # as they should not be scaled by plate-scale like rest - # of coeffs... This makes the computations consistent - # with 'drizzle'. WJH 17-Feb-2004 - _cx[0,0] = 0. - _cy[0,0] = 0. - - dxy = _p - pixref - # Apply coefficients from distortion model here... - - c = _p * 0. - for i in range(order+1): - for j in range(i+1): - c[:,0] = c[:,0] + _cx[i][j] * pow(dxy[:,0],j) * pow(dxy[:,1],(i-j)) - c[:,1] = c[:,1] + _cy[i][j] * pow(dxy[:,0],j) * pow(dxy[:,1],(i-j)) - - return c - -def foundIDCTAB(idctab): - idctab_found = True - try: - idctab = fileutil.osfn(idctab) - if idctab == 'N/A' or idctab == "": - idctab_found = False - if os.path.exists(idctab): - idctab_found = True - else: - idctab_found = False - except KeyError: - idctab_found = False - return idctab_found diff --git a/lib/stwcs/gui/__init__.py b/lib/stwcs/gui/__init__.py deleted file mode 100644 index cd21bf6..0000000 --- a/lib/stwcs/gui/__init__.py +++ /dev/null @@ -1,19 +0,0 @@ -""" STWCS.GUI - -This package defines the TEAL interfaces for public, file-based operations -provided by the STWCS package. - -""" -from __future__ import absolute_import # confidence high -__docformat__ = 'restructuredtext' - -# import modules which define the TEAL interfaces -from . import write_headerlet -from . import extract_headerlet -from . import attach_headerlet -from . import delete_headerlet -from . import headerlet_summary -from . import archive_headerlet -from . import restore_headerlet -from . import apply_headerlet -from . import updatewcs diff --git a/lib/stwcs/gui/apply_headerlet.help b/lib/stwcs/gui/apply_headerlet.help deleted file mode 100644 index f701b52..0000000 --- a/lib/stwcs/gui/apply_headerlet.help +++ /dev/null @@ -1,38 +0,0 @@ -This task applies a headerlet to a science observation to update either the -PRIMARY WCS or to add it as an alternate WCS. - -filename = "" -hdrlet = "" -attach = True -primary = True -archive = True -force = False -wcskey = "" -wcsname = "" -verbose = False - -Parameters ----------- -filename: string, @-file or wild-card name - File name(s) of science observation whose WCS solution will be updated -hdrlet: string, @-file or wild-card name - Headerlet file(s), must match input filenames 1-to-1 -attach: boolean - True (default): append headerlet to FITS file as a new extension. -primary: boolean - Specify whether or not to replace PRIMARY WCS with WCS from headerlet. -archive: boolean - True (default): before updating, create a headerlet with the - WCS old solution. -force: boolean - If True, this will cause the headerlet to replace the current PRIMARY - WCS even if it has a different distortion model. [Default: False] -wcskey: string - Key value (A-Z, except O) for this alternate WCS - If None, the next available key will be used -wcsname: string - Name to be assigned to this alternate WCS - WCSNAME is a required keyword in a Headerlet but this allows the - user to change it as desired. -logging: boolean - enable file logging diff --git a/lib/stwcs/gui/apply_headerlet.py b/lib/stwcs/gui/apply_headerlet.py deleted file mode 100644 index d517e9f..0000000 --- a/lib/stwcs/gui/apply_headerlet.py +++ /dev/null @@ -1,54 +0,0 @@ -import os -from stsci.tools import teal, parseinput - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - # start by interpreting filename and hdrlet inputs - filename = parseinput.parseinput(configObj['filename'])[0] - hdrlet = parseinput.parseinput(configObj['hdrlet'])[0] - - if configObj['primary']: - # Call function with properly interpreted input parameters - # Syntax: apply_headerlet_as_primary(filename, hdrlet, attach=True, - # archive=True, force=False, verbose=False) - headerlet.apply_headerlet_as_primary(filename, - hdrlet,attach=configObj['attach'], - archive=configObj['archive'],force=configObj['force'], - logging=configObj['logging']) - else: - wcsname = configObj['wcsname'] - if wcsname in ['',' ','INDEF']: wcsname = None - wcskey = configObj['wcskey'] - if wcskey == '': wcskey = None - # Call function with properly interpreted input parameters - # apply_headerlet_as_alternate(filename, hdrlet, attach=True, - # wcskey=None, wcsname=None, verbose=False) - headerlet.apply_headerlet_as_alternate(filename, - hdrlet, attach=configObj['attach'], - wcsname=wcsname, wcskey=wcskey, - logging=configObj['logging']) diff --git a/lib/stwcs/gui/archive_headerlet.py b/lib/stwcs/gui/archive_headerlet.py deleted file mode 100644 index 7ad3d4d..0000000 --- a/lib/stwcs/gui/archive_headerlet.py +++ /dev/null @@ -1,69 +0,0 @@ -from __future__ import print_function -import os - -from astropy.io import fits -from stsci.tools import teal - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString += headerlet.archive_as_headerlet.__doc__ - - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - if configObj['hdrname'] in ['',' ','INDEF']: - print('='*60) - print('ERROR:') - print(' No valid "hdrname" parameter value provided!') - print(' Please restart this task and provide a value for this parameter.') - print('='*60) - return - - str_kw = ['wcsname','destim','sipname','npolfile','d2imfile', - 'descrip','history','author'] - - # create dictionary of remaining parameters, deleting extraneous ones - # such as those above - cdict = configObj.dict() - # remove any rules defined for the TEAL interface - if "_RULES_" in cdict: del cdict['_RULES_'] - del cdict['_task_name_'] - del cdict['filename'] - del cdict['hdrname'] - - # Convert blank string input as None - for kw in str_kw: - if cdict[kw] == '': cdict[kw] = None - if cdict['wcskey'].lower() == 'primary': cdict['wcskey'] = ' ' - - # Call function with properly interpreted input parameters - # Syntax: archive_as_headerlet(filename, sciext='SCI', wcsname=None, wcskey=None, - # hdrname=None, destim=None, - # sipname=None, npolfile=None, d2imfile=None, - # author=None, descrip=None, history=None, - # hdrlet=None, clobber=False) - headerlet.archive_as_headerlet(configObj['filename'], configObj['hdrname'], - **cdict) diff --git a/lib/stwcs/gui/attach_headerlet.py b/lib/stwcs/gui/attach_headerlet.py deleted file mode 100644 index 873c549..0000000 --- a/lib/stwcs/gui/attach_headerlet.py +++ /dev/null @@ -1,36 +0,0 @@ -import os - -from stsci.tools import teal - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString += eval('.'.join([__package__,__taskname__,'__doc__'])) - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - headerlet.attach_headerlet(configObj['filename'],configObj['hdrlet'], - configObj['logging']) - diff --git a/lib/stwcs/gui/delete_headerlet.py b/lib/stwcs/gui/delete_headerlet.py deleted file mode 100644 index b3df5a7..0000000 --- a/lib/stwcs/gui/delete_headerlet.py +++ /dev/null @@ -1,52 +0,0 @@ -from __future__ import print_function -import os - -from stsci.tools import teal -from stsci.tools import parseinput - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString += eval('.'.join([__package__,__taskname__,'__doc__'])) - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - if configObj['hdrname'] == '' and configObj['hdrext'] is None and \ - configObj['distname'] == '': - print('='*60) - print('ERROR:') - print(' No valid "hdrname", "hdrext" or "distname" parameter value provided!') - print(' Please restart this task and provide a value for one of these parameters.') - print('='*60) - return - filename = parseinput.parseinput(configObj['filename'])[0] - # Call function with properly interpreted input parameters - # Syntax: delete_headerlet(filename, hdrname=None, hdrext=None, distname=None) - headerlet.delete_headerlet(filename, - hdrname = configObj['hdrname'], - hdrext = configObj['hdrext'], - distname = configObj['distname'], - logging = configObj['logging']) - diff --git a/lib/stwcs/gui/extract_headerlet.py b/lib/stwcs/gui/extract_headerlet.py deleted file mode 100644 index 02ecd7a..0000000 --- a/lib/stwcs/gui/extract_headerlet.py +++ /dev/null @@ -1,58 +0,0 @@ -from __future__ import print_function -import os - -from stsci.tools import teal - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString += eval('.'.join([__package__,__taskname__,'__doc__'])) - - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - if configObj['output'] in ['',' ',None]: - print('='*60) - print('ERROR:') - print(' No valid "output" parameter value provided!') - print(' Please restart this task and provide a value for this parameter.') - print('='*60) - return - - # create dictionary of remaining parameters, deleting extraneous ones - # such as those above - cdict = configObj.dict() - # remove any rules defined for the TEAL interface - if "_RULES_" in cdict: del cdict['_RULES_'] - del cdict['_task_name_'] - del cdict['filename'] - del cdict['output'] - - # Call function with properly interpreted input parameters - # Syntax: extract_headerlet(filename, output, extnum=None, hdrname=None, - # clobber=False, verbose=100) - headerlet.extract_headerlet(configObj['filename'], configObj['output'], - **cdict) - diff --git a/lib/stwcs/gui/headerlet_summary.py b/lib/stwcs/gui/headerlet_summary.py deleted file mode 100644 index 82a3e0c..0000000 --- a/lib/stwcs/gui/headerlet_summary.py +++ /dev/null @@ -1,47 +0,0 @@ -import os -from stsci.tools import teal - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString += eval('.'.join([__package__,__taskname__,'__doc__'])) - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - # create dictionary of remaining parameters, deleting extraneous ones - # such as those above - cdict = configObj.dict() - # remove any rules defined for the TEAL interface - if "_RULES_" in cdict: del cdict['_RULES_'] - del cdict['_task_name_'] - del cdict['filename'] - if headerlet.is_par_blank(cdict['columns']): - cdict['columns'] = None - # Call function with properly interpreted input parameters - - # Syntax: headerlet_summary(filename,columns=None,pad=2,maxwidth=None, - # output=None,clobber=True,quiet=False) - headerlet.headerlet_summary(configObj['filename'],**cdict) - diff --git a/lib/stwcs/gui/pars/apply_headerlet.cfg b/lib/stwcs/gui/pars/apply_headerlet.cfg deleted file mode 100644 index 06d6daf..0000000 --- a/lib/stwcs/gui/pars/apply_headerlet.cfg +++ /dev/null @@ -1,10 +0,0 @@ -_task_name_ = apply_headerlet -filename = "" -hdrlet = "" -attach = True -primary = True -archive = True -force = False -wcskey = "" -wcsname = "" -logging = False diff --git a/lib/stwcs/gui/pars/apply_headerlet.cfgspc b/lib/stwcs/gui/pars/apply_headerlet.cfgspc deleted file mode 100644 index 648e562..0000000 --- a/lib/stwcs/gui/pars/apply_headerlet.cfgspc +++ /dev/null @@ -1,12 +0,0 @@ -_task_name_ = string_kw(default="apply_headerlet") -filename = string_kw(default="", comment="Input file name") -hdrlet = string_kw(default="", comment="Headerlet FITS filename") -attach = boolean_kw(default=True, comment= "Append headerlet to FITS file as new extension?") -primary = boolean_kw(default=True, triggers="_rule1_", comment="Replace PRIMARY WCS with headerlet WCS?") -archive = boolean_kw(default=True, active_if="_rule1_", comment="Save PRIMARY WCS as new headerlet extension?") -force = boolean_kw(default=False, active_if="_rule1_", comment="If distortions do not match, force update anyway?") -wcskey = option_kw("A","B","C","D","E","F","G","H","I","J","K","L","M","N","P","Q","R","S","T","U","V","W","X","Y","Z","", default="", inactive_if="_rule1_", comment="Apply headerlet as alternate WCS with this letter") -wcsname = string_kw(default="", inactive_if="_rule1_", comment="Apply headerlet as alternate WCS with this name") -logging = boolean_kw(default=False, comment= "Enable logging to a file") -[ _RULES_ ] -_rule1_ = string_kw(default=True, code='tyfn={"yes":True, "no":False}; OUT = tyfn[VAL]') diff --git a/lib/stwcs/gui/pars/archive_headerlet.cfg b/lib/stwcs/gui/pars/archive_headerlet.cfg deleted file mode 100644 index 97cd7ef..0000000 --- a/lib/stwcs/gui/pars/archive_headerlet.cfg +++ /dev/null @@ -1,14 +0,0 @@ -_task_name_ = archive_headerlet -filename = "" -hdrname = "" -sciext = "SCI" -wcsname = "" -wcskey = "PRIMARY" -destim = "" -sipname = "" -npolfile = "" -d2imfile = "" -author = "" -descrip = "" -history = "" -logging = False
\ No newline at end of file diff --git a/lib/stwcs/gui/pars/archive_headerlet.cfgspc b/lib/stwcs/gui/pars/archive_headerlet.cfgspc deleted file mode 100644 index 03e67f0..0000000 --- a/lib/stwcs/gui/pars/archive_headerlet.cfgspc +++ /dev/null @@ -1,14 +0,0 @@ -_task_name_ = string_kw(default="archive_headerlet") -filename = string_kw(default="", comment="Input file name") -hdrname = string_kw(default="", comment="Unique name(HDRNAME) for headerlet") -sciext = string_kw(default="SCI", comment="EXTNAME of extension with WCS") -wcsname = string_kw(default="", comment="Name of WCS to be archived") -wcskey = option_kw("A","B","C","D","E","F","G","H","I","J","K","L","M","N","P","Q","R","S","T","U","V","W","X","Y","Z","PRIMARY", default="PRIMARY", comment="Archive the WCS with this letter") -destim = string_kw(default="", comment="Rootname of image to which this headerlet applies ") -sipname = string_kw(default="", comment="Name for source of polynomial distortion keywords") -npolfile = string_kw(default="", comment="Name for source of non-polynomial residuals") -d2imfile = string_kw(default="", comment="Name for source of detector correction table") -author = string_kw(default="", comment="Author name for creator of headerlet") -descrip = string_kw(default="", comment="Short description of headerlet solution") -history = string_kw(default="", comment="Name of ASCII file containing history for headerlet") -logging = boolean_kw(default=False, comment= "Enable logging to a file")
\ No newline at end of file diff --git a/lib/stwcs/gui/pars/attach_headerlet.cfg b/lib/stwcs/gui/pars/attach_headerlet.cfg deleted file mode 100644 index d131a70..0000000 --- a/lib/stwcs/gui/pars/attach_headerlet.cfg +++ /dev/null @@ -1,4 +0,0 @@ -_task_name_ = attach_headerlet -filename = "" -hdrlet = "" -logging = False diff --git a/lib/stwcs/gui/pars/attach_headerlet.cfgspc b/lib/stwcs/gui/pars/attach_headerlet.cfgspc deleted file mode 100644 index bc91bca..0000000 --- a/lib/stwcs/gui/pars/attach_headerlet.cfgspc +++ /dev/null @@ -1,4 +0,0 @@ -_task_name_ = string_kw(default="attach_headerlet") -filename = string_kw(default="", comment="FITS image file name") -hdrlet = string_kw(default="", comment="Headerlet FITS filename") -logging = boolean_kw(default=False, comment= "Enable logging to a file")
\ No newline at end of file diff --git a/lib/stwcs/gui/pars/delete_headerlet.cfg b/lib/stwcs/gui/pars/delete_headerlet.cfg deleted file mode 100644 index d156937..0000000 --- a/lib/stwcs/gui/pars/delete_headerlet.cfg +++ /dev/null @@ -1,6 +0,0 @@ -_task_name_ = delete_headerlet -filename = "" -hdrname = "" -hdrext = None -distname = "" -logging = False
\ No newline at end of file diff --git a/lib/stwcs/gui/pars/delete_headerlet.cfgspc b/lib/stwcs/gui/pars/delete_headerlet.cfgspc deleted file mode 100644 index 43790b1..0000000 --- a/lib/stwcs/gui/pars/delete_headerlet.cfgspc +++ /dev/null @@ -1,6 +0,0 @@ -_task_name_ = string_kw(default="delete_headerlet") -filename = string_kw(default="", comment="FITS image file name(s), list or wild-card") -hdrname = string_kw(default="", comment="Delete headerlet with this HDRNAME") -hdrext = integer_or_none_kw(default=None, comment="Delete headerlet from this extension") -distname = string_kw(default="", comment="Delete *ALL* with this DISTNAME") -logging = boolean_kw(default=False, comment= "Enable logging to a file") diff --git a/lib/stwcs/gui/pars/extract_headerlet.cfg b/lib/stwcs/gui/pars/extract_headerlet.cfg deleted file mode 100644 index 3dd0a7a..0000000 --- a/lib/stwcs/gui/pars/extract_headerlet.cfg +++ /dev/null @@ -1,7 +0,0 @@ -_task_name_ = extract_headerlet -filename = "" -output = "" -extnum = None -hdrname = "" -clobber = True -logging = False diff --git a/lib/stwcs/gui/pars/extract_headerlet.cfgspc b/lib/stwcs/gui/pars/extract_headerlet.cfgspc deleted file mode 100644 index b50d4bf..0000000 --- a/lib/stwcs/gui/pars/extract_headerlet.cfgspc +++ /dev/null @@ -1,7 +0,0 @@ -_task_name_ = string_kw(default="extract_headerlet") -filename = string_kw(default="", comment="Input file name") -output = string_kw(default="", comment="Output headerlet FITS filename") -extnum = integer_or_none_kw(default=None, comment="FITS extension number of headerlet") -hdrname = string_kw(default="", comment="Unique name(HDRNAME) for headerlet") -clobber = boolean_kw(default=True, comment= "Overwrite existing headerlet FITS file?") -logging = boolean_kw(default=False, comment= "Enable logging to a file") diff --git a/lib/stwcs/gui/pars/headerlet_summary.cfg b/lib/stwcs/gui/pars/headerlet_summary.cfg deleted file mode 100644 index 7203552..0000000 --- a/lib/stwcs/gui/pars/headerlet_summary.cfg +++ /dev/null @@ -1,8 +0,0 @@ -_task_name_ = headerlet_summary -filename = "" -columns = None -pad = 2 -maxwidth = None -output = "" -clobber = True -quiet = False diff --git a/lib/stwcs/gui/pars/headerlet_summary.cfgspc b/lib/stwcs/gui/pars/headerlet_summary.cfgspc deleted file mode 100644 index ce65930..0000000 --- a/lib/stwcs/gui/pars/headerlet_summary.cfgspc +++ /dev/null @@ -1,8 +0,0 @@ -_task_name_ = string_kw(default="headerlet_summary") -filename = string_kw(default="", comment="FITS image file name") -columns = string_kw(default="", comment="Headerlet keyword(s) to be reported") -pad = integer_kw(default=2, comment="Number of spaces between output columns") -maxwidth = integer_or_none_kw(default=None, comment="Max width for each column") -output = string_kw(default="", comment="Name of output file for summary") -clobber = boolean_kw(default=True, comment="Overwrite previously written summary?") -quiet = boolean_kw(default=False, comment="Suppress output of summary to STDOUT?") diff --git a/lib/stwcs/gui/pars/restore_headerlet.cfg b/lib/stwcs/gui/pars/restore_headerlet.cfg deleted file mode 100644 index b0ec427..0000000 --- a/lib/stwcs/gui/pars/restore_headerlet.cfg +++ /dev/null @@ -1,10 +0,0 @@ -_task_name_ = restore_headerlet -filename = "" -archive = True -force = False -distname = "" -primary = None -sciext = "SCI" -hdrname = "" -hdrext = None -logging = False
\ No newline at end of file diff --git a/lib/stwcs/gui/pars/restore_headerlet.cfgspc b/lib/stwcs/gui/pars/restore_headerlet.cfgspc deleted file mode 100644 index df47e3f..0000000 --- a/lib/stwcs/gui/pars/restore_headerlet.cfgspc +++ /dev/null @@ -1,12 +0,0 @@ -_task_name_ = string_kw(default="restore_headerlet") -filename = string_kw(default="", comment="Input file name") -archive = boolean_kw(default=True, comment= "Create headerlets from WCSs being replaced?") -force = boolean_kw(default=False, comment="If distortions do not match, force update anyway?") -distname = string_kw(default="", triggers="_rule1_", comment="Restore ALL headerlet extensions with this DISTNAME") -primary = integer_or_none_kw(default=None, inactive_if="_rule1_", comment="Headerlet extension to restore as new primary WCS") -sciext = string_kw(default="SCI", inactive_if="_rule1_", comment="EXTNAME of extension with WCS") -hdrname = string_kw(default="", active_if="_rule1_", comment="HDRNAME of headerlet extension to be restored") -hdrext = integer_or_none_kw(default=None, active_if="_rule1_", comment="Extension number for headerlet to be restored") -logging = boolean_kw(default=False, comment= "Enable logging to a file") -[ _RULES_ ] -_rule1_ = string_kw(default=True, code='from stwcs import wcsutil;from stwcs.wcsutil import headerlet;OUT = headerlet.is_par_blank(VAL)') diff --git a/lib/stwcs/gui/pars/updatewcs.cfg b/lib/stwcs/gui/pars/updatewcs.cfg deleted file mode 100644 index 35360f2..0000000 --- a/lib/stwcs/gui/pars/updatewcs.cfg +++ /dev/null @@ -1,8 +0,0 @@ -_task_name_ = updatewcs -input = "*flt.fits" -extname = "SCI" -vacorr = True -tddcorr = True -npolcorr = True -d2imcorr = True -checkfiles = True diff --git a/lib/stwcs/gui/pars/updatewcs.cfgspc b/lib/stwcs/gui/pars/updatewcs.cfgspc deleted file mode 100644 index a3a3fb5..0000000 --- a/lib/stwcs/gui/pars/updatewcs.cfgspc +++ /dev/null @@ -1,8 +0,0 @@ -_task_name_ = string_kw(default="updatewcs") -input = string_kw(default="", comment="Input files (name, suffix, or @list)") -extname = string_kw(default="SCI", comment="EXTNAME of extensions to be archived") -vacorr = boolean_kw(default=True, comment= "Apply velocity aberration correction?") -tddcorr = boolean_kw(default=True, comment= "Apply time dependent distortion correction?") -npolcorr = boolean_kw(default=True, comment= "Apply lookup table distortion?") -d2imcorr = boolean_kw(default=True, comment= "Apply detector to image correction?") -checkfiles = boolean_kw(default=True, comment= "Check format of input files?") diff --git a/lib/stwcs/gui/pars/write_headerlet.cfg b/lib/stwcs/gui/pars/write_headerlet.cfg deleted file mode 100644 index 9eb4592..0000000 --- a/lib/stwcs/gui/pars/write_headerlet.cfg +++ /dev/null @@ -1,18 +0,0 @@ -_task_name_ = write_headerlet -filename = "" -output = "" -clobber = True -hdrname = "" -wcskey = "PRIMARY" -wcsname = "" -author = "" -descrip = "" -catalog = "" -history = "" -sciext = "SCI" -destim = "" -sipname = "" -npolfile = "" -d2imfile = "" -attach = True -logging = False
\ No newline at end of file diff --git a/lib/stwcs/gui/pars/write_headerlet.cfgspc b/lib/stwcs/gui/pars/write_headerlet.cfgspc deleted file mode 100644 index ba28b05..0000000 --- a/lib/stwcs/gui/pars/write_headerlet.cfgspc +++ /dev/null @@ -1,18 +0,0 @@ -_task_name_ = string_kw(default="write_headerlet") -filename = string_kw(default="", comment="Input file name") -output = string_kw(default="", comment="Filename for headerlet FITS file") -clobber = boolean_kw(default=True, comment= "Overwrite existing headerlet FITS file?") -hdrname = string_kw(default="", comment="Unique name(HDRNAME) for headerlet[REQUIRED]") -wcskey = option_kw("A","B","C","D","E","F","G","H","I","J","K","L","M","N","P","Q","R","S","T","U","V","W","X","Y","Z","PRIMARY", default="PRIMARY", comment="Create headerlet from WCS with this letter") -wcsname = string_kw(default="", comment="Create headerlet from WCS with this name") -author = string_kw(default="", comment="Author name for creator of headerlet") -descrip = string_kw(default="", comment="Short description of headerlet solution") -catalog = string_kw(default="", comment="Reference frame for headerlet solution") -history = string_kw(default="", comment="Name of ASCII file containing history for headerlet") -sciext = string_kw(default="SCI", comment="EXTNAME of extension with WCS") -destim = string_kw(default="", comment="Rootname of image to which this headerlet applies ") -sipname = string_kw(default="", comment="Name for source of polynomial distortion keywords") -npolfile = string_kw(default="", comment="Name for source of non-polynomial residuals") -d2imfile = string_kw(default="", comment="Name for source of detector correction table") -attach = boolean_kw(default=True, comment="Create headerlet FITS extension?") -logging = boolean_kw(default=False, comment= "Enable logging to a file")
\ No newline at end of file diff --git a/lib/stwcs/gui/restore_headerlet.help b/lib/stwcs/gui/restore_headerlet.help deleted file mode 100644 index fe07a15..0000000 --- a/lib/stwcs/gui/restore_headerlet.help +++ /dev/null @@ -1,43 +0,0 @@ -Restore headerlet extension(s) as either a primary WCS or as alternate WCSs - -This task can restore a WCS solution stored in a headerlet extension or -restore all WCS solutions from all headerlet extensions with the same -distortion model. - -Parameters ----------- -filename: string or HDUList - Either a filename or PyFITS HDUList object for the input science file - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - -archive: boolean (default True) - flag indicating if HeaderletHDUs should be created from the - primary and alternate WCSs in fname before restoring all matching - headerlet extensions - -force: boolean (default:False) - When the distortion models of the headerlet and the primary do - not match, and archive is False, this flag forces an update of - the primary. - -distname: string - distortion model as represented by a DISTNAME keyword - -primary: int or string or None - HeaderletHDU to be restored as primary - if int - a fits extension - if string - HDRNAME - if None - use first HeaderletHDU - -sciext: string (default: SCI) - EXTNAME value of FITS extensions with WCS keywords - -hdrname: string - HDRNAME keyword of HeaderletHDU - -hdrext: int or tuple - Headerlet extension number of tuple ('HDRLET',2) - -logging: boolean - enable file logging
\ No newline at end of file diff --git a/lib/stwcs/gui/restore_headerlet.py b/lib/stwcs/gui/restore_headerlet.py deleted file mode 100644 index 7570d76..0000000 --- a/lib/stwcs/gui/restore_headerlet.py +++ /dev/null @@ -1,48 +0,0 @@ -import os - -from stsci.tools import teal - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - if configObj['distname'] not in ['',' ','INDEF']: - # Call function with properly interpreted input parameters - # Syntax: restore_all_with_distname(filename, distname, primary, - # archive=True, sciext='SCI', verbose=False) - headerlet.restore_all_with_distname(configObj['filename'], - configObj['distname'],configObj['primary'], - archive=configObj['archive'],sciext=configObj['sciext'], - logging=configObj['logging']) - else: - # Call function with properly interpreted input parameters - # restore_from_headerlet(filename, hdrname=None, hdrext=None, - # archive=True, force=False) - headerlet.restore_from_headerlet(configObj['filename'], - hdrname=configObj['hdrname'],hdrext=configObj['hdrext'], - archive=configObj['archive'], force=configObj['force'], - logging=configObj['logging']) - diff --git a/lib/stwcs/gui/updatewcs.py b/lib/stwcs/gui/updatewcs.py deleted file mode 100644 index 3dacb67..0000000 --- a/lib/stwcs/gui/updatewcs.py +++ /dev/null @@ -1,90 +0,0 @@ -from __future__ import print_function -import os - -from astropy.io import fits -from stsci.tools import parseinput -from stsci.tools import fileutil -from stsci.tools import teal -import stwcs -from stwcs import updatewcs -from stwcs.wcsutil import convertwcs - -allowed_corr_dict = {'vacorr':'VACorr','tddcorr':'TDDCorr','npolcorr':'NPOLCorr','d2imcorr':'DET2IMCorr'} - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = updatewcs.__name__ -__version__ = stwcs.__version__ - -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString += eval('.'.join([__package__,__taskname__,'__doc__'])) - - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - - # Interpret primary parameters from configObj instance - extname = configObj['extname'] - input = configObj['input'] - - # create dictionary of remaining parameters, deleting extraneous ones - # such as those above - cdict = configObj.dict() - # remove any rules defined for the TEAL interface - if "_RULES_" in cdict: del cdict['_RULES_'] - del cdict['_task_name_'] - del cdict['input'] - del cdict['extname'] - - # parse input - input,altfiles = parseinput.parseinput(configObj['input']) - - # Insure that all input files have a correctly archived - # set of OPUS WCS keywords - # Legacy files from OTFR, like all WFPC2 data from OTFR, will only - # have the OPUS WCS keywords archived using a prefix of 'O' - # These keywords need to be converted to the Paper I alternate WCS - # standard using a wcskey (suffix) of 'O' - # If an alternate WCS with wcskey='O' already exists, this will copy - # the values from the old prefix-'O' WCS keywords to insure the correct - # OPUS keyword values get archived for use with updatewcs. - # - for file in input: - # Check to insure that there is a valid reference file to be used - idctab = fits.getval(file, 'idctab') - if not os.path.exists(fileutil.osfn(idctab)): - print('No valid distortion reference file ',idctab,' found in ',file,'!') - raise ValueError - - # Re-define 'cdict' to only have switches for steps supported by that instrument - # the set of supported steps are defined by the dictionary - # updatewcs.apply_corrections.allowed_corrections - # - for file in input: - # get instrument name from input file - instr = fits.getval(file,'INSTRUME') - # make copy of input parameters dict for this file - fdict = cdict.copy() - # Remove any parameter that is not part of this instrument's allowed corrections - for step in allowed_corr_dict: - if allowed_corr_dict[step] not in updatewcs.apply_corrections.allowed_corrections[instr]: - fdict[step] - # Call 'updatewcs' on correctly archived file - updatewcs.updatewcs(file,**fdict) - diff --git a/lib/stwcs/gui/write_headerlet.py b/lib/stwcs/gui/write_headerlet.py deleted file mode 100644 index e18bed8..0000000 --- a/lib/stwcs/gui/write_headerlet.py +++ /dev/null @@ -1,80 +0,0 @@ -from __future__ import print_function -import os - -from stsci.tools import teal -from stsci.tools import parseinput - -import stwcs -from stwcs.wcsutil import headerlet - -__taskname__ = __name__.split('.')[-1] # needed for help string -__package__ = headerlet.__name__ -__version__ = stwcs.__version__ -# -#### Interfaces used by TEAL -# -def getHelpAsString(docstring=False): - """ - return useful help from a file in the script directory called __taskname__.help - """ - install_dir = os.path.dirname(__file__) - htmlfile = os.path.join(install_dir,'htmlhelp',__taskname__+'.html') - helpfile = os.path.join(install_dir,__taskname__+'.help') - if docstring or (not docstring and not os.path.exists(htmlfile)): - helpString = __taskname__+' Version '+__version__+'\n\n' - if os.path.exists(helpfile): - helpString += teal.getHelpFileAsString(__taskname__,__file__) - else: - helpString += headerlet.write_headerlet.__doc__ - - else: - helpString = 'file://'+htmlfile - - return helpString - -def run(configObj=None): - flist,oname = parseinput.parseinput(configObj['filename']) - if len(flist) == 0: - print('='*60) - print('ERROR:') - print(' No valid "filename" parameter value provided!') - print(' Please check the working directory and restart this task.') - print('='*60) - return - - if configObj['hdrname'] in ['',' ','INDEF']: - print('='*60) - print('ERROR:') - print(' No valid "hdrname" parameter value provided!') - print(' Please restart this task and provide a value for this parameter.') - print('='*60) - return - - if configObj['output'] in ['',' ','INDEF']: - configObj['output'] = None - - str_kw = ['wcsname','destim','sipname','npolfile','d2imfile', - 'descrip','history','author','output','catalog'] - - # create dictionary of remaining parameters, deleting extraneous ones - # such as those above - cdict = configObj.dict() - # remove any rules defined for the TEAL interface - if "_RULES_" in cdict: del cdict['_RULES_'] - del cdict['_task_name_'] - del cdict['filename'] - del cdict['hdrname'] - - # Convert blank string input as None - for kw in str_kw: - if cdict[kw] == '': cdict[kw] = None - if cdict['wcskey'].lower() == 'primary': cdict['wcskey'] = ' ' - - # Call function with properly interpreted input parameters - # Syntax: write_headerlet(filename, hdrname, output, sciext='SCI', - # wcsname=None, wcskey=None, destim=None, - # sipname=None, npolfile=None, d2imfile=None, - # author=None, descrip=None, history=None, - # attach=True, clobber=False) - headerlet.write_headerlet(flist, configObj['hdrname'], - **cdict) diff --git a/lib/stwcs/updatewcs/__init__.py b/lib/stwcs/updatewcs/__init__.py deleted file mode 100644 index eb5e850..0000000 --- a/lib/stwcs/updatewcs/__init__.py +++ /dev/null @@ -1,376 +0,0 @@ -from __future__ import absolute_import, division, print_function # confidence high - -from astropy.io import fits -from stwcs import wcsutil -from stwcs.wcsutil import HSTWCS -import stwcs - -from astropy import wcs as pywcs -import astropy - -from . import utils, corrections, makewcs -from . import npol, det2im -from stsci.tools import parseinput, fileutil -from . import apply_corrections - -import time -import logging -logger = logging.getLogger('stwcs.updatewcs') - -import atexit -atexit.register(logging.shutdown) - -#Note: The order of corrections is important - -def updatewcs(input, vacorr=True, tddcorr=True, npolcorr=True, d2imcorr=True, - checkfiles=True, verbose=False): - """ - - Updates HST science files with the best available calibration information. - This allows users to retrieve from the archive self contained science files - which do not require additional reference files. - - Basic WCS keywords are updated in the process and new keywords (following WCS - Paper IV and the SIP convention) as well as new extensions are added to the science files. - - - Example - ------- - >>>from stwcs import updatewcs - >>>updatewcs.updatewcs(filename) - - Dependencies - ------------ - `stsci.tools` - `astropy.io.fits` - `astropy.wcs` - - Parameters - ---------- - input: a python list of file names or a string (wild card characters allowed) - input files may be in fits, geis or waiver fits format - vacorr: boolean - If True, vecocity aberration correction will be applied - tddcorr: boolean - If True, time dependent distortion correction will be applied - npolcorr: boolean - If True, a Lookup table distortion will be applied - d2imcorr: boolean - If True, detector to image correction will be applied - checkfiles: boolean - If True, the format of the input files will be checked, - geis and waiver fits files will be converted to MEF format. - Default value is True for standalone mode. - """ - if verbose == False: - logger.setLevel(100) - else: - formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") - log_filename = 'stwcs.log' - fh = logging.FileHandler(log_filename, mode='w') - fh.setLevel(logging.DEBUG) - fh.setFormatter(formatter) - logger.addHandler(fh) - logger.setLevel(verbose) - args = "vacorr=%s, tddcorr=%s, npolcorr=%s, d2imcorr=%s, checkfiles=%s, \ - " % (str(vacorr), str(tddcorr), str(npolcorr), - str(d2imcorr), str(checkfiles)) - logger.info('\n\tStarting UPDATEWCS: %s', time.asctime()) - - files = parseinput.parseinput(input)[0] - logger.info("\n\tInput files: %s, " % [i for i in files]) - logger.info("\n\tInput arguments: %s" %args) - if checkfiles: - files = checkFiles(files) - if not files: - print('No valid input, quitting ...\n') - return - - for f in files: - acorr = apply_corrections.setCorrections(f, vacorr=vacorr, \ - tddcorr=tddcorr,npolcorr=npolcorr, d2imcorr=d2imcorr) - if 'MakeWCS' in acorr and newIDCTAB(f): - logger.warning("\n\tNew IDCTAB file detected. All current WCSs will be deleted") - cleanWCS(f) - - makecorr(f, acorr) - - return files - -def makecorr(fname, allowed_corr): - """ - Purpose - ======= - Applies corrections to the WCS of a single file - - :Parameters: - `fname`: string - file name - `acorr`: list - list of corrections to be applied - """ - logger.info("Allowed corrections: {0}".format(allowed_corr)) - f = fits.open(fname, mode='update') - #Determine the reference chip and create the reference HSTWCS object - nrefchip, nrefext = getNrefchip(f) - wcsutil.restoreWCS(f, nrefext, wcskey='O') - rwcs = HSTWCS(fobj=f, ext=nrefext) - rwcs.readModel(update=True,header=f[nrefext].header) - - if 'DET2IMCorr' in allowed_corr: - kw2update = det2im.DET2IMCorr.updateWCS(f) - for kw in kw2update: - f[1].header[kw] = kw2update[kw] - - for i in range(len(f))[1:]: - extn = f[i] - - if 'extname' in extn.header: - extname = extn.header['extname'].lower() - if extname == 'sci': - wcsutil.restoreWCS(f, ext=i, wcskey='O') - sciextver = extn.header['extver'] - ref_wcs = rwcs.deepcopy() - hdr = extn.header - ext_wcs = HSTWCS(fobj=f, ext=i) - ### check if it exists first!!! - # 'O ' can be safely archived again because it has been restored first. - wcsutil.archiveWCS(f, ext=i, wcskey="O", wcsname="OPUS", reusekey=True) - ext_wcs.readModel(update=True,header=hdr) - for c in allowed_corr: - if c != 'NPOLCorr' and c != 'DET2IMCorr': - corr_klass = corrections.__getattribute__(c) - kw2update = corr_klass.updateWCS(ext_wcs, ref_wcs) - for kw in kw2update: - hdr[kw] = kw2update[kw] - # give the primary WCS a WCSNAME value - idcname = f[0].header.get('IDCTAB', " ") - if idcname.strip() and 'idc.fits' in idcname: - wname = ''.join(['IDC_', - utils.extract_rootname(idcname,suffix='_idc')]) - else: wname = " " - hdr['WCSNAME'] = wname - - elif extname in ['err', 'dq', 'sdq', 'samp', 'time']: - cextver = extn.header['extver'] - if cextver == sciextver: - hdr = f[('SCI',sciextver)].header - w = pywcs.WCS(hdr, f) - copyWCS(w, extn.header) - - else: - continue - - if 'NPOLCorr' in allowed_corr: - kw2update = npol.NPOLCorr.updateWCS(f) - for kw in kw2update: - f[1].header[kw] = kw2update[kw] - # Finally record the version of the software which updated the WCS - if 'HISTORY' in f[0].header: - f[0].header.set('UPWCSVER', value=stwcs.__version__, - comment="Version of STWCS used to updated the WCS", - before='HISTORY') - f[0].header.set('PYWCSVER', value=astropy.__version__, - comment="Version of PYWCS used to updated the WCS", - before='HISTORY') - elif 'ASN_MTYP' in f[0].header: - f[0].header.set('UPWCSVER', value=stwcs.__version__, - comment="Version of STWCS used to updated the WCS", - after='ASN_MTYP') - f[0].header.set('PYWCSVER', value=astropy.__version__, - comment="Version of PYWCS used to updated the WCS", - after='ASN_MTYP') - else: - # Find index of last non-blank card, and insert this new keyword after that card - for i in range(len(f[0].header) - 1, 0, -1): - if f[0].header[i].strip() != '': - break - f[0].header.set('UPWCSVER', stwcs.__version__, - "Version of STWCS used to updated the WCS", - after=i) - f[0].header.set('PYWCSVER', astropy.__version__, - "Version of PYWCS used to updated the WCS", - after=i) - # add additional keywords to be used by headerlets - distdict = utils.construct_distname(f,rwcs) - f[0].header['DISTNAME'] = distdict['DISTNAME'] - f[0].header['SIPNAME'] = distdict['SIPNAME'] - # Make sure NEXTEND keyword remains accurate - f[0].header['NEXTEND'] = len(f)-1 - f.close() - -def copyWCS(w, ehdr): - """ - This is a convenience function to copy a WCS object - to a header as a primary WCS. It is used only to copy the - WCS of the 'SCI' extension to the headers of 'ERR', 'DQ', 'SDQ', - 'TIME' or 'SAMP' extensions. - """ - hwcs = w.to_header() - - if w.wcs.has_cd(): - wcsutil.pc2cd(hwcs) - for k in hwcs.keys(): - key = k[:7] - ehdr[key] = hwcs[k] - -def getNrefchip(fobj): - """ - - Finds which FITS extension holds the reference chip. - - The reference chip has EXTNAME='SCI', can be in any extension and - is instrument specific. This functions provides mappings between - sci extensions, chips and fits extensions. - In the case of a subarray when the reference chip is missing, the - first 'SCI' extension is the reference chip. - - Parameters - ---------- - fobj: `astropy.io.fits.HDUList` object - """ - nrefext = 1 - nrefchip = 1 - instrument = fobj[0].header['INSTRUME'] - - if instrument == 'WFPC2': - chipkw = 'DETECTOR' - extvers = [("SCI",img.header['EXTVER']) for img in - fobj[1:] if img.header['EXTNAME'].lower()=='sci'] - detectors = [img.header[chipkw] for img in fobj[1:] if - img.header['EXTNAME'].lower()=='sci'] - fitsext = [i for i in range(len(fobj))[1:] if - fobj[i].header['EXTNAME'].lower()=='sci'] - det2ext=dict(list(zip(detectors, extvers))) - ext2det=dict(list(zip(extvers, detectors))) - ext2fitsext=dict(list(zip(extvers, fitsext))) - - if 3 not in detectors: - nrefchip = ext2det.pop(extvers[0]) - nrefext = ext2fitsext.pop(extvers[0]) - else: - nrefchip = 3 - extname = det2ext.pop(nrefchip) - nrefext = ext2fitsext.pop(extname) - - elif (instrument == 'ACS' and fobj[0].header['DETECTOR'] == 'WFC') or \ - (instrument == 'WFC3' and fobj[0].header['DETECTOR'] == 'UVIS'): - chipkw = 'CCDCHIP' - extvers = [("SCI",img.header['EXTVER']) for img in - fobj[1:] if img.header['EXTNAME'].lower()=='sci'] - detectors = [img.header[chipkw] for img in fobj[1:] if - img.header['EXTNAME'].lower()=='sci'] - fitsext = [i for i in range(len(fobj))[1:] if - fobj[i].header['EXTNAME'].lower()=='sci'] - det2ext=dict(list(zip(detectors, extvers))) - ext2det=dict(list(zip(extvers, detectors))) - ext2fitsext=dict(list(zip(extvers, fitsext))) - - if 2 not in detectors: - nrefchip = ext2det.pop(extvers[0]) - nrefext = ext2fitsext.pop(extvers[0]) - else: - nrefchip = 2 - extname = det2ext.pop(nrefchip) - nrefext = ext2fitsext.pop(extname) - else: - for i in range(len(fobj)): - extname = fobj[i].header.get('EXTNAME', None) - if extname != None and extname.lower == 'sci': - nrefext = i - break - - return nrefchip, nrefext - -def checkFiles(input): - """ - Checks that input files are in the correct format. - Converts geis and waiver fits files to multiextension fits. - """ - from stsci.tools.check_files import geis2mef, waiver2mef, checkFiles - logger.info("\n\tChecking files %s" % input) - removed_files = [] - newfiles = [] - if not isinstance(input, list): - input=[input] - - for file in input: - try: - imgfits,imgtype = fileutil.isFits(file) - except IOError: - logger.warning( "\n\tFile %s could not be found, removing it from the input list.\n" %file) - removed_files.append(file) - continue - # Check for existence of waiver FITS input, and quit if found. - # Or should we print a warning and continue but not use that file - if imgfits: - if imgtype == 'waiver': - newfilename = waiver2mef(file, convert_dq=True) - if newfilename == None: - logger.warning("\n\tRemoving file %s from input list - could not convert waiver to mef" %file) - removed_files.append(file) - else: - newfiles.append(newfilename) - else: - newfiles.append(file) - - # If a GEIS image is provided as input, create a new MEF file with - # a name generated using 'buildFITSName()' - # Convert the corresponding data quality file if present - if not imgfits: - newfilename = geis2mef(file, convert_dq=True) - if newfilename == None: - logger.warning("\n\tRemoving file %s from input list - could not convert geis to mef" %file) - removed_files.append(file) - else: - newfiles.append(newfilename) - if removed_files: - logger.warning('\n\tThe following files will be removed from the list of files to be processed %s' % removed_files) - - newfiles = checkFiles(newfiles)[0] - logger.info("\n\tThese files passed the input check and will be processed: %s" % newfiles) - return newfiles - -def newIDCTAB(fname): - #When this is called we know there's a kw IDCTAB in the header - hdul = fits.open(fname) - idctab = fileutil.osfn(hdul[0].header['IDCTAB']) - try: - #check for the presence of IDCTAB in the first extension - oldidctab = fileutil.osfn(hdul[1].header['IDCTAB']) - except KeyError: - return False - if idctab == oldidctab: - return False - else: - return True - -def cleanWCS(fname): - # A new IDCTAB means all previously computed WCS's are invalid - # We are deleting all of them except the original OPUS WCS. - f = fits.open(fname, mode='update') - keys = wcsutil.wcskeys(f[1].header) - # Remove the primary WCS from the list - try: - keys.remove(' ') - except ValueError: - pass - fext = list(range(1, len(f))) - for key in keys: - try: - wcsutil.deleteWCS(fname, ext=fext, wcskey=key) - except KeyError: - # Some extensions don't have the alternate (or any) WCS keywords - continue - -def getCorrections(instrument): - """ - Print corrections available for an instrument - - :Parameters: - `instrument`: string, one of 'WFPC2', 'NICMOS', 'STIS', 'ACS', 'WFC3' - """ - acorr = apply_corrections.allowed_corrections[instrument] - - print("The following corrections will be performed for instrument %s\n" % instrument) - for c in acorr: print(c,': ' , apply_corrections.cnames[c]) diff --git a/lib/stwcs/updatewcs/apply_corrections.py b/lib/stwcs/updatewcs/apply_corrections.py deleted file mode 100644 index 86b623a..0000000 --- a/lib/stwcs/updatewcs/apply_corrections.py +++ /dev/null @@ -1,248 +0,0 @@ -from __future__ import division, print_function # confidence high - -import os -from astropy.io import fits -import time -from stsci.tools import fileutil -import os.path -from stwcs.wcsutil import altwcs -from . import utils -from . import wfpc2_dgeo - -import logging -logger = logging.getLogger("stwcs.updatewcs.apply_corrections") - -#Note: The order of corrections is important - - -# A dictionary which lists the allowed corrections for each instrument. -# These are the default corrections applied also in the pipeline. - -allowed_corrections={'WFPC2': ['DET2IMCorr', 'MakeWCS','CompSIP', 'VACorr'], - 'ACS': ['DET2IMCorr', 'TDDCorr', 'MakeWCS', 'CompSIP','VACorr', 'NPOLCorr'], - 'STIS': ['MakeWCS', 'CompSIP','VACorr'], - 'NICMOS': ['MakeWCS', 'CompSIP','VACorr'], - 'WFC3': ['DET2IMCorr', 'MakeWCS', 'CompSIP','VACorr', 'NPOLCorr'], - } - -cnames = {'DET2IMCorr': 'Detector to Image Correction', - 'TDDCorr': 'Time Dependent Distortion Correction', - 'MakeWCS': 'Recalculate basic WCS keywords based on the distortion model', - 'CompSIP': 'Given IDCTAB distortion model calculate the SIP coefficients', - 'VACorr': 'Velocity Aberration Correction', - 'NPOLCorr': 'Lookup Table Distortion' - } - -def setCorrections(fname, vacorr=True, tddcorr=True, npolcorr=True, d2imcorr=True): - """ - Creates a list of corrections to be applied to a file - based on user input paramters and allowed corrections - for the instrument. - """ - instrument = fits.getval(fname, 'INSTRUME') - # make a copy of this list ! - acorr = allowed_corrections[instrument][:] - - # For WFPC2 images, the old-style DGEOFILE needs to be - # converted on-the-fly into a proper D2IMFILE here... - if instrument == 'WFPC2': - # check for DGEOFILE, and convert it to D2IMFILE if found - d2imfile = wfpc2_dgeo.update_wfpc2_d2geofile(fname) - # Check if idctab is present on disk - # If kw IDCTAB is present in the header but the file is - # not found on disk, do not run TDDCorr, MakeCWS and CompSIP - if not foundIDCTAB(fname): - if 'TDDCorr' in acorr: acorr.remove('TDDCorr') - if 'MakeWCS' in acorr: acorr.remove('MakeWCS') - if 'CompSIP' in acorr: acorr.remove('CompSIP') - - if 'VACorr' in acorr and vacorr==False: acorr.remove('VACorr') - if 'TDDCorr' in acorr: - tddcorr = applyTDDCorr(fname, tddcorr) - if tddcorr == False: acorr.remove('TDDCorr') - - if 'NPOLCorr' in acorr: - npolcorr = applyNpolCorr(fname, npolcorr) - if npolcorr == False: acorr.remove('NPOLCorr') - if 'DET2IMCorr' in acorr: - d2imcorr = applyD2ImCorr(fname, d2imcorr) - if d2imcorr == False: acorr.remove('DET2IMCorr') - logger.info("\n\tCorrections to be applied to %s: %s " % (fname, str(acorr))) - return acorr - - -def foundIDCTAB(fname): - """ - This functions looks for an "IDCTAB" keyword in the primary header. - - Returns - ------- - status : bool - If False : MakeWCS, CompSIP and TDDCorr should not be applied. - If True : there's no restriction on corrections, they all should be applied. - - Raises - ------ - IOError : If IDCTAB file not found on disk. - """ - - try: - idctab = fits.getval(fname, 'IDCTAB').strip() - if idctab == 'N/A' or idctab == "": - return False - except KeyError: - return False - idctab = fileutil.osfn(idctab) - if os.path.exists(idctab): - return True - else: - raise IOError("IDCTAB file {0} not found".format(idctab)) - - -def applyTDDCorr(fname, utddcorr): - """ - The default value of tddcorr for all ACS images is True. - This correction will be performed if all conditions below are True: - - the user did not turn it off on the command line - - the detector is WFC - - the idc table specified in the primary header is available. - """ - - phdr = fits.getheader(fname) - instrument = phdr['INSTRUME'] - try: - detector = phdr['DETECTOR'] - except KeyError: - detector = None - try: - tddswitch = phdr['TDDCORR'] - except KeyError: - tddswitch = 'PERFORM' - - if instrument == 'ACS' and detector == 'WFC' and utddcorr == True and tddswitch == 'PERFORM': - tddcorr = True - try: - idctab = phdr['IDCTAB'] - except KeyError: - tddcorr = False - #print "***IDCTAB keyword not found - not applying TDD correction***\n" - if os.path.exists(fileutil.osfn(idctab)): - tddcorr = True - else: - tddcorr = False - #print "***IDCTAB file not found - not applying TDD correction***\n" - else: - tddcorr = False - return tddcorr - -def applyNpolCorr(fname, unpolcorr): - """ - Determines whether non-polynomial distortion lookup tables should be added - as extensions to the science file based on the 'NPOLFILE' keyword in the - primary header and NPOLEXT kw in the first extension. - This is a default correction and will always run in the pipeline. - The file used to generate the extensions is - recorded in the NPOLEXT keyword in the first science extension. - If 'NPOLFILE' in the primary header is different from 'NPOLEXT' in the - extension header and the file exists on disk and is a 'new type' npolfile, - then the lookup tables will be updated as 'WCSDVARR' extensions. - """ - applyNPOLCorr = True - try: - # get NPOLFILE kw from primary header - fnpol0 = fits.getval(fname, 'NPOLFILE') - if fnpol0 == 'N/A': - utils.remove_distortion(fname, "NPOLFILE") - return False - fnpol0 = fileutil.osfn(fnpol0) - if not fileutil.findFile(fnpol0): - msg = """\n\tKw "NPOLFILE" exists in primary header but file %s not found - Non-polynomial distortion correction will not be applied\n - """ % fnpol0 - logger.critical(msg) - raise IOError("NPOLFILE {0} not found".format(fnpol0)) - try: - # get NPOLEXT kw from first extension header - fnpol1 = fits.getval(fname, 'NPOLEXT', ext=1) - fnpol1 = fileutil.osfn(fnpol1) - if fnpol1 and fileutil.findFile(fnpol1): - if fnpol0 != fnpol1: - applyNPOLCorr = True - else: - msg = """\n\tNPOLEXT with the same value as NPOLFILE found in first extension. - NPOL correction will not be applied.""" - logger.info(msg) - applyNPOLCorr = False - else: - # npl file defined in first extension may not be found - # but if a valid kw exists in the primary header, non-polynomial - #distortion correction should be applied. - applyNPOLCorr = True - except KeyError: - # the case of "NPOLFILE" kw present in primary header but "NPOLEXT" missing - # in first extension header - applyNPOLCorr = True - except KeyError: - logger.info('\n\t"NPOLFILE" keyword not found in primary header') - applyNPOLCorr = False - return applyNPOLCorr - - if isOldStyleDGEO(fname, fnpol0): - applyNPOLCorr = False - return (applyNPOLCorr and unpolcorr) - -def isOldStyleDGEO(fname, dgname): - # checks if the file defined in a NPOLFILE kw is a full size - # (old style) image - - sci_hdr = fits.getheader(fname, ext=1) - dgeo_hdr = fits.getheader(dgname, ext=1) - sci_naxis1 = sci_hdr['NAXIS1'] - sci_naxis2 = sci_hdr['NAXIS2'] - dg_naxis1 = dgeo_hdr['NAXIS1'] - dg_naxis2 = dgeo_hdr['NAXIS2'] - if sci_naxis1 <= dg_naxis1 or sci_naxis2 <= dg_naxis2: - msg = """\n\tOnly full size (old style) DGEO file was found.\n - Non-polynomial distortion correction will not be applied.""" - logger.critical(msg) - return True - else: - return False - -def applyD2ImCorr(fname, d2imcorr): - applyD2IMCorr = True - try: - # get D2IMFILE kw from primary header - fd2im0 = fits.getval(fname, 'D2IMFILE') - if fd2im0 == 'N/A': - utils.remove_distortion(fname, "D2IMFILE") - return False - fd2im0 = fileutil.osfn(fd2im0) - if not fileutil.findFile(fd2im0): - msg = """\n\tKw D2IMFILE exists in primary header but file %s not found\n - Detector to image correction will not be applied\n""" % fd2im0 - logger.critical(msg) - print(msg) - raise IOError("D2IMFILE {0} not found".format(fd2im0)) - try: - # get D2IMEXT kw from first extension header - fd2imext = fits.getval(fname, 'D2IMEXT', ext=1) - fd2imext = fileutil.osfn(fd2imext) - if fd2imext and fileutil.findFile(fd2imext): - if fd2im0 != fd2imext: - applyD2IMCorr = True - else: - applyD2IMCorr = False - else: - # D2IM file defined in first extension may not be found - # but if a valid kw exists in the primary header, - # detector to image correction should be applied. - applyD2IMCorr = True - except KeyError: - # the case of D2IMFILE kw present in primary header but D2IMEXT missing - # in first extension header - applyD2IMCorr = True - except KeyError: - print('D2IMFILE keyword not found in primary header') - applyD2IMCorr = False - return applyD2IMCorr diff --git a/lib/stwcs/updatewcs/corrections.py b/lib/stwcs/updatewcs/corrections.py deleted file mode 100644 index d3641eb..0000000 --- a/lib/stwcs/updatewcs/corrections.py +++ /dev/null @@ -1,326 +0,0 @@ -from __future__ import division, print_function # confidence high - -import copy -import datetime -import logging, time -import numpy as np -from numpy import linalg -from stsci.tools import fileutil - -from . import npol -from . import makewcs -from .utils import diff_angles - -logger=logging.getLogger('stwcs.updatewcs.corrections') - -MakeWCS = makewcs.MakeWCS -NPOLCorr = npol.NPOLCorr - -class TDDCorr(object): - """ - Apply time dependent distortion correction to distortion coefficients and basic - WCS keywords. This correction **must** be done before any other WCS correction. - - Parameters - ---------- - ext_wcs: HSTWCS object - An HSTWCS object to be modified - ref_wcs: HSTWCS object - A reference HSTWCS object - - Notes - ----- - Compute the ACS/WFC time dependent distortion terms as described - in [1]_ and apply the correction to the WCS of the observation. - - The model coefficients are stored in the primary header of the IDCTAB. - :math:`D_{ref}` is the reference date. The computed corrections are saved - in the science extension header as TDDALPHA and TDDBETA keywords. - - .. math:: TDDALPHA = A_{0} + {A_{1}*(obsdate - D_{ref})} - - .. math:: TDDBETA = B_{0} + B_{1}*(obsdate - D_{ref}) - - - The time dependent distortion affects the IDCTAB coefficients, and the - relative location of the two chips. Because the linear order IDCTAB - coefficients ar eused in the computatuion of the NPOL extensions, - the TDD correction affects all components of the distortion model. - - Application of TDD to the IDCTAB polynomial coefficients: - The TDD model is computed in Jay's frame, while the IDCTAB coefficients - are in the HST V2/V3 frame. The coefficients are transformed to Jay's frame, - TDD is applied and they are transformed back to the V2/V3 frame. This - correction is performed in this class. - - Application of TDD to the relative location of the two chips is - done in `makewcs`. - - References - ---------- - .. [1] Jay Anderson, "Variation of the Distortion Solution of the WFC", ACS ISR 2007-08. - - """ - def updateWCS(cls, ext_wcs, ref_wcs): - """ - - Calculates alpha and beta for ACS/WFC data. - - Writes 2 new kw to the extension header: TDDALPHA and TDDBETA - """ - logger.info("\n\tStarting TDDCorr: %s" % time.asctime()) - ext_wcs.idcmodel.ocx = copy.deepcopy(ext_wcs.idcmodel.cx) - ext_wcs.idcmodel.ocy = copy.deepcopy(ext_wcs.idcmodel.cy) - - newkw = {'TDDALPHA': None, 'TDDBETA':None, - 'OCX10':ext_wcs.idcmodel.ocx[1,0], - 'OCX11':ext_wcs.idcmodel.ocx[1,1], - 'OCY10':ext_wcs.idcmodel.ocy[1,0], - 'OCY11':ext_wcs.idcmodel.ocy[1,1], - 'TDD_CTA':None, 'TDD_CTB':None, - 'TDD_CYA':None, 'TDD_CYB':None, - 'TDD_CXA':None, 'TDD_CXB':None} - - if ext_wcs.idcmodel.refpix['skew_coeffs']is not None and \ - ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CTB'] is not None: - cls.apply_tdd2idc2015(ref_wcs) - cls.apply_tdd2idc2015(ext_wcs) - - newkw.update({ - 'TDD_CTA':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CTA'], - 'TDD_CYA':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CYA'], - 'TDD_CXA':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CXA'], - 'TDD_CTB':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CTB'], - 'TDD_CYB':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CYB'], - 'TDD_CXB':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CXB']}) - - elif ext_wcs.idcmodel.refpix['skew_coeffs']is not None and \ - ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CY_BETA'] is not None: - logger.info("\n\t Applying 2014-calibrated TDD: %s" % time.asctime()) - # We have 2014-calibrated TDD, not J.A.-style TDD - cls.apply_tdd2idc2(ref_wcs) - cls.apply_tdd2idc2(ext_wcs) - newkw.update({'TDD_CYA':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CY_ALPHA'], - 'TDD_CYB':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CY_BETA'], - 'TDD_CXA':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CX_ALPHA'], - 'TDD_CXB':ext_wcs.idcmodel.refpix['skew_coeffs']['TDD_CX_BETA']}) - - else: - alpha, beta = cls.compute_alpha_beta(ext_wcs) - cls.apply_tdd2idc(ref_wcs, alpha, beta) - cls.apply_tdd2idc(ext_wcs, alpha, beta) - ext_wcs.idcmodel.refpix['TDDALPHA'] = alpha - ext_wcs.idcmodel.refpix['TDDBETA'] = beta - ref_wcs.idcmodel.refpix['TDDALPHA'] = alpha - ref_wcs.idcmodel.refpix['TDDBETA'] = beta - - newkw.update( {'TDDALPHA': alpha, 'TDDBETA':beta} ) - - return newkw - updateWCS = classmethod(updateWCS) - - def apply_tdd2idc2015(cls, hwcs): - """ Applies 2015-calibrated TDD correction to a couple of IDCTAB - coefficients for ACS/WFC observations. - """ - if not isinstance(hwcs.date_obs,float): - year,month,day = hwcs.date_obs.split('-') - rdate = datetime.datetime(int(year),int(month),int(day)) - rday = float(rdate.strftime("%j"))/365.25 + rdate.year - else: - rday = hwcs.date_obs - - skew_coeffs = hwcs.idcmodel.refpix['skew_coeffs'] - delta_date = rday - skew_coeffs['TDD_DATE'] - - if skew_coeffs['TDD_CXB'] is not None: - hwcs.idcmodel.cx[1,1] += skew_coeffs['TDD_CXB']*delta_date - if skew_coeffs['TDD_CTB'] is not None: - hwcs.idcmodel.cy[1,1] += skew_coeffs['TDD_CTB']*delta_date - if skew_coeffs['TDD_CYB'] is not None: - hwcs.idcmodel.cy[1,0] += skew_coeffs['TDD_CYB']*delta_date - #print("CX[1,1]_TDD={}, CY[1,1]_TDD={}, CY[1,0]_TDD={}".format(hwcs.idcmodel.cx[1,1],hwcs.idcmodel.cy[1,1],hwcs.idcmodel.cy[1,0])) - - apply_tdd2idc2015 = classmethod(apply_tdd2idc2015) - - def apply_tdd2idc2(cls, hwcs): - """ Applies 2014-calibrated TDD correction to single IDCTAB coefficient - of an ACS/WFC observation. - """ - if not isinstance(hwcs.date_obs,float): - year,month,day = hwcs.date_obs.split('-') - rdate = datetime.datetime(int(year),int(month),int(day)) - rday = float(rdate.strftime("%j"))/365.25 + rdate.year - else: - rday = hwcs.date_obs - - skew_coeffs = hwcs.idcmodel.refpix['skew_coeffs'] - cy_beta = skew_coeffs['TDD_CY_BETA'] - cy_alpha = skew_coeffs['TDD_CY_ALPHA'] - delta_date = rday - skew_coeffs['TDD_DATE'] - print("DELTA_DATE: {0} based on rday: {1}, TDD_DATE: {2}".format(delta_date,rday,skew_coeffs['TDD_DATE'])) - - if cy_alpha is None: - hwcs.idcmodel.cy[1,1] += cy_beta*delta_date - else: - new_beta = cy_alpha + cy_beta*delta_date - hwcs.idcmodel.cy[1,1] = new_beta - print("CY11: {0} based on alpha: {1}, beta: {2}".format(hwcs.idcmodel.cy[1,1],cy_alpha,cy_beta)) - - cx_beta = skew_coeffs['TDD_CX_BETA'] - cx_alpha = skew_coeffs['TDD_CX_ALPHA'] - if cx_alpha is not None: - new_beta = cx_alpha + cx_beta*delta_date - hwcs.idcmodel.cx[1,1] = new_beta - print("CX11: {0} based on alpha: {1}, beta: {2}".format(new_beta,cx_alpha,cx_beta)) - - apply_tdd2idc2 = classmethod(apply_tdd2idc2) - - def apply_tdd2idc(cls, hwcs, alpha, beta): - """ - Applies TDD to the idctab coefficients of a ACS/WFC observation. - This should be always the first correction. - """ - theta_v2v3 = 2.234529 - mrotp = fileutil.buildRotMatrix(theta_v2v3) - mrotn = fileutil.buildRotMatrix(-theta_v2v3) - tdd_mat = np.array([[1+(beta/2048.), alpha/2048.],[alpha/2048.,1-(beta/2048.)]],np.float64) - abmat1 = np.dot(tdd_mat, mrotn) - abmat2 = np.dot(mrotp,abmat1) - xshape, yshape = hwcs.idcmodel.cx.shape, hwcs.idcmodel.cy.shape - icxy = np.dot(abmat2,[hwcs.idcmodel.cx.ravel(), hwcs.idcmodel.cy.ravel()]) - hwcs.idcmodel.cx = icxy[0] - hwcs.idcmodel.cy = icxy[1] - hwcs.idcmodel.cx.shape = xshape - hwcs.idcmodel.cy.shape = yshape - - apply_tdd2idc = classmethod(apply_tdd2idc) - - def compute_alpha_beta(cls, ext_wcs): - """ - Compute the ACS time dependent distortion skew terms - as described in ACS ISR 07-08 by J. Anderson. - - Jay's code only computes the alpha/beta values based on a decimal year - with only 3 digits, so this line reproduces that when needed for comparison - with his results. - rday = float(('%0.3f')%rday) - - The zero-point terms account for the skew accumulated between - 2002.0 and 2004.5, when the latest IDCTAB was delivered. - alpha = 0.095 + 0.090*(rday-dday)/2.5 - beta = -0.029 - 0.030*(rday-dday)/2.5 - """ - if not isinstance(ext_wcs.date_obs,float): - year,month,day = ext_wcs.date_obs.split('-') - rdate = datetime.datetime(int(year),int(month),int(day)) - rday = float(rdate.strftime("%j"))/365.25 + rdate.year - else: - rday = ext_wcs.date_obs - - skew_coeffs = ext_wcs.idcmodel.refpix['skew_coeffs'] - if skew_coeffs is None: - # Only print out warning for post-SM4 data where this may matter - if rday > 2009.0: - err_str = "------------------------------------------------------------------------ \n" - err_str += "WARNING: the IDCTAB geometric distortion file specified in the image \n" - err_str += " header did not have the time-dependent distortion coefficients. \n" - err_str += " The pre-SM4 time-dependent skew solution will be used by default.\n" - err_str += " Please update IDCTAB with new reference file from HST archive. \n" - err_str += "------------------------------------------------------------------------ \n" - print(err_str) - # Using default pre-SM4 coefficients - skew_coeffs = {'TDD_A':[0.095,0.090/2.5], - 'TDD_B':[-0.029,-0.030/2.5], - 'TDD_DATE':2004.5,'TDDORDER':1} - - alpha = 0 - beta = 0 - # Compute skew terms, allowing for non-linear coefficients as well - for c in range(skew_coeffs['TDDORDER']+1): - alpha += skew_coeffs['TDD_A'][c]* np.power((rday-skew_coeffs['TDD_DATE']),c) - beta += skew_coeffs['TDD_B'][c]*np.power((rday-skew_coeffs['TDD_DATE']),c) - - return alpha,beta - compute_alpha_beta = classmethod(compute_alpha_beta) - - -class VACorr(object): - """ - Apply velocity aberation correction to WCS keywords. - - Notes - ----- - Velocity Aberration is stored in the extension header keyword 'VAFACTOR'. - The correction is applied to the CD matrix and CRVALs. - - """ - def updateWCS(cls, ext_wcs, ref_wcs): - logger.info("\n\tStarting VACorr: %s" % time.asctime()) - if ext_wcs.vafactor != 1: - ext_wcs.wcs.cd = ext_wcs.wcs.cd * ext_wcs.vafactor - crval0 = ref_wcs.wcs.crval[0] + ext_wcs.vafactor*diff_angles(ext_wcs.wcs.crval[0], - ref_wcs.wcs.crval[0]) - crval1 = ref_wcs.wcs.crval[1] + ext_wcs.vafactor*diff_angles(ext_wcs.wcs.crval[1], - ref_wcs.wcs.crval[1]) - crval = np.array([crval0,crval1]) - ext_wcs.wcs.crval = crval - ext_wcs.wcs.set() - else: - pass - kw2update={'CD1_1': ext_wcs.wcs.cd[0,0], 'CD1_2':ext_wcs.wcs.cd[0,1], - 'CD2_1':ext_wcs.wcs.cd[1,0], 'CD2_2':ext_wcs.wcs.cd[1,1], - 'CRVAL1':ext_wcs.wcs.crval[0], 'CRVAL2':ext_wcs.wcs.crval[1]} - return kw2update - - updateWCS = classmethod(updateWCS) - - -class CompSIP(object): - """ - Compute Simple Imaging Polynomial (SIP) coefficients as defined in [2]_ - from IDC table coefficients. - - This class transforms the TDD corrected IDCTAB coefficients into SIP format. - It also applies a binning factor to the coefficients if the observation was - binned. - - References - ---------- - .. [2] David Shupe, et al, "The SIP Convention of representing Distortion - in FITS Image headers", Astronomical Data Analysis Software And Systems, ASP - Conference Series, Vol. 347, 2005 - - """ - def updateWCS(cls, ext_wcs, ref_wcs): - logger.info("\n\tStarting CompSIP: %s" %time.asctime()) - kw2update = {} - if not ext_wcs.idcmodel: - logger.info("IDC model not found, SIP coefficient will not be computed") - return kw2update - order = ext_wcs.idcmodel.norder - kw2update['A_ORDER'] = order - kw2update['B_ORDER'] = order - pscale = ext_wcs.idcmodel.refpix['PSCALE'] - - cx = ext_wcs.idcmodel.cx - cy = ext_wcs.idcmodel.cy - - matr = np.array([[cx[1,1],cx[1,0]], [cy[1,1],cy[1,0]]], dtype=np.float64) - imatr = linalg.inv(matr) - akeys1 = np.zeros((order+1,order+1), dtype=np.float64) - bkeys1 = np.zeros((order+1,order+1), dtype=np.float64) - for n in range(order+1): - for m in range(order+1): - if n >= m and n>=2: - idcval = np.array([[cx[n,m]],[cy[n,m]]]) - sipval = np.dot(imatr, idcval) - akeys1[m,n-m] = sipval[0] - bkeys1[m,n-m] = sipval[1] - Akey="A_%d_%d" % (m,n-m) - Bkey="B_%d_%d" % (m,n-m) - kw2update[Akey] = sipval[0,0] * ext_wcs.binned - kw2update[Bkey] = sipval[1,0] * ext_wcs.binned - kw2update['CTYPE1'] = 'RA---TAN-SIP' - kw2update['CTYPE2'] = 'DEC--TAN-SIP' - return kw2update - - updateWCS = classmethod(updateWCS) diff --git a/lib/stwcs/updatewcs/det2im.py b/lib/stwcs/updatewcs/det2im.py deleted file mode 100644 index bddb37b..0000000 --- a/lib/stwcs/updatewcs/det2im.py +++ /dev/null @@ -1,299 +0,0 @@ -from __future__ import absolute_import, division # confidence high - -import numpy as np -from astropy.io import fits -from stsci.tools import fileutil - -from . import utils - -import logging, time -logger = logging.getLogger('stwcs.updatewcs.d2im') - -class DET2IMCorr(object): - """ - Defines a Lookup table prior distortion correction as per WCS paper IV. - It uses a reference file defined by the D2IMFILE (suffix 'd2im') keyword - in the primary header. - - Notes - ----- - - Using extensions in the reference file create a WCSDVARR extensions - and add them to the science file. - - Add record-valued keywords to the science extension header to describe - the lookup tables. - - Add a keyword 'D2IMEXT' to the science extension header to store - the name of the reference file used to create the WCSDVARR extensions. - - If WCSDVARR extensions exist and `D2IMFILE` is different from `D2IMEXT`, - a subsequent update will overwrite the existing extensions. - If WCSDVARR extensions were not found in the science file, they will be added. - - """ - - def updateWCS(cls, fobj): - """ - Parameters - ---------- - fobj: `astropy.io.fits.HDUList` object - Science file, for which a distortion correction in a NPOLFILE is available - - """ - logger.info("\n\tStarting DET2IM: %s" %time.asctime()) - try: - assert isinstance(fobj, fits.HDUList) - except AssertionError: - logger.exception('\n\tInput must be a fits.HDUList object') - raise - - cls.applyDet2ImCorr(fobj) - d2imfile = fobj[0].header['D2IMFILE'] - - new_kw = {'D2IMEXT': d2imfile} - return new_kw - - updateWCS = classmethod(updateWCS) - - def applyDet2ImCorr(cls, fobj): - """ - For each science extension in a fits file object: - - create a WCSDVARR extension - - update science header - - add/update D2IMEXT keyword - """ - d2imfile = fileutil.osfn(fobj[0].header['D2IMFILE']) - # Map D2IMARR EXTVER numbers to FITS extension numbers - wcsdvarr_ind = cls.getWCSIndex(fobj) - d2im_num_ext = 1 - for ext in fobj: - try: - extname = ext.header['EXTNAME'].lower() - except KeyError: - continue - if extname == 'sci': - extversion = ext.header['EXTVER'] - ccdchip = cls.get_ccdchip(fobj, extname='SCI', extver=extversion) - header = ext.header - # get the data arrays from the reference file - dx, dy = cls.getData(d2imfile, ccdchip) - # Determine EXTVER for the D2IMARR extension from the D2I file (EXTNAME, EXTVER) kw. - # This is used to populate DPj.EXTVER kw - for ename in zip(['DX', 'DY'], [dx, dy]): - if ename[1] is not None: - error_val = ename[1].max() - cls.addSciExtKw(header, wdvarr_ver=d2im_num_ext, d2im_extname=ename[0], error_val=error_val) - hdu = cls.createD2ImHDU(header, d2imfile=d2imfile, - wdvarr_ver=d2im_num_ext, - d2im_extname=ename[0], - data=ename[1],ccdchip=ccdchip) - if wcsdvarr_ind and d2im_num_ext in wcsdvarr_ind: - fobj[wcsdvarr_ind[d2im_num_ext]] = hdu - else: - fobj.append(hdu) - d2im_num_ext = d2im_num_ext + 1 - applyDet2ImCorr = classmethod(applyDet2ImCorr) - - def getWCSIndex(cls, fobj): - - """ - If fobj has WCSDVARR extensions: - returns a mapping of their EXTVER kw to file object extension numbers - if fobj does not have WCSDVARR extensions: - an empty dictionary is returned - """ - wcsd = {} - for e in range(len(fobj)): - try: - ename = fobj[e].header['EXTNAME'] - except KeyError: - continue - if ename == 'D2IMARR': - wcsd[fobj[e].header['EXTVER']] = e - logger.debug("A map of D2IMARR extensions %s" % wcsd) - return wcsd - - getWCSIndex = classmethod(getWCSIndex) - - def addSciExtKw(cls, hdr, wdvarr_ver=None, d2im_extname=None, error_val=0.0): - """ - Adds kw to sci extension to define WCSDVARR lookup table extensions - - """ - if d2im_extname =='DX': - j=1 - else: - j=2 - - d2imerror = 'D2IMERR%s' %j - d2imdis = 'D2IMDIS%s' %j - d2imext = 'D2IM%s.' %j + 'EXTVER' - d2imnaxes = 'D2IM%s.' %j +'NAXES' - d2imaxis1 = 'D2IM%s.' %j+'AXIS.1' - d2imaxis2 = 'D2IM%s.' %j+'AXIS.2' - keys = [d2imerror, d2imdis, d2imext, d2imnaxes, d2imaxis1, d2imaxis2] - values = {d2imerror: error_val, - d2imdis: 'Lookup', - d2imext: wdvarr_ver, - d2imnaxes: 2, - d2imaxis1: 1, - d2imaxis2: 2} - - comments = {d2imerror: 'Maximum error of NPOL correction for axis %s' % j, - d2imdis: 'Detector to image correction type', - d2imext: 'Version number of WCSDVARR extension containing d2im lookup table', - d2imnaxes: 'Number of independent variables in d2im function', - d2imaxis1: 'Axis number of the jth independent variable in a d2im function', - d2imaxis2: 'Axis number of the jth independent variable in a d2im function' - } - # Look for HISTORY keywords. If present, insert new keywords before them - before_key = 'HISTORY' - if before_key not in hdr: - before_key = None - - for key in keys: - hdr.set(key, value=values[key], comment=comments[key], before=before_key) - - addSciExtKw = classmethod(addSciExtKw) - - def getData(cls,d2imfile, ccdchip): - """ - Get the data arrays from the reference D2I files - Make sure 'CCDCHIP' in the npolfile matches "CCDCHIP' in the science file. - """ - xdata, ydata = (None, None) - d2im = fits.open(d2imfile) - for ext in d2im: - d2imextname = ext.header.get('EXTNAME',"") - d2imccdchip = ext.header.get('CCDCHIP',1) - if d2imextname == 'DX' and d2imccdchip == ccdchip: - xdata = ext.data.copy() - continue - elif d2imextname == 'DY' and d2imccdchip == ccdchip: - ydata = ext.data.copy() - continue - else: - continue - d2im.close() - return xdata, ydata - getData = classmethod(getData) - - def createD2ImHDU(cls, sciheader, d2imfile=None, wdvarr_ver=1, - d2im_extname=None,data = None, ccdchip=1): - """ - Creates an HDU to be added to the file object. - """ - hdr = cls.createD2ImHdr(sciheader, d2imfile=d2imfile, - wdvarr_ver=wdvarr_ver, d2im_extname=d2im_extname, - ccdchip=ccdchip) - hdu = fits.ImageHDU(header=hdr, data=data) - return hdu - - createD2ImHDU = classmethod(createD2ImHDU) - - def createD2ImHdr(cls, sciheader, d2imfile, wdvarr_ver, d2im_extname, ccdchip): - """ - Creates a header for the D2IMARR extension based on the D2I reference file - and sci extension header. The goal is to always work in image coordinates - (also for subarrays and binned images). The WCS for the D2IMARR extension - is such that a full size d2im table is created and then shifted or scaled - if the science image is a subarray or binned image. - """ - d2im = fits.open(d2imfile) - d2im_phdr = d2im[0].header - for ext in d2im: - try: - d2imextname = ext.header['EXTNAME'] - d2imextver = ext.header['EXTVER'] - except KeyError: - continue - d2imccdchip = cls.get_ccdchip(d2im, extname=d2imextname, extver=d2imextver) - if d2imextname == d2im_extname and d2imccdchip == ccdchip: - d2im_header = ext.header - break - else: - continue - d2im.close() - - naxis = d2im[1].header['NAXIS'] - ccdchip = d2imextname - - kw = { 'NAXIS': 'Size of the axis', - 'CDELT': 'Coordinate increment along axis', - 'CRPIX': 'Coordinate system reference pixel', - 'CRVAL': 'Coordinate system value at reference pixel', - } - - kw_comm1 = {} - kw_val1 = {} - for key in kw.keys(): - for i in range(1, naxis+1): - si = str(i) - kw_comm1[key+si] = kw[key] - - for i in range(1, naxis+1): - si = str(i) - kw_val1['NAXIS'+si] = d2im_header.get('NAXIS'+si) - kw_val1['CDELT'+si] = d2im_header.get('CDELT'+si, 1.0) * sciheader.get('LTM'+si+'_'+si, 1) - kw_val1['CRPIX'+si] = d2im_header.get('CRPIX'+si, 0.0) - kw_val1['CRVAL'+si] = (d2im_header.get('CRVAL'+si, 0.0) - \ - sciheader.get('LTV'+str(i), 0)) - kw_comm0 = {'XTENSION': 'Image extension', - 'BITPIX': 'IEEE floating point', - 'NAXIS': 'Number of axes', - 'EXTNAME': 'WCS distortion array', - 'EXTVER': 'Distortion array version number', - 'PCOUNT': 'Special data area of size 0', - 'GCOUNT': 'One data group', - } - - kw_val0 = { 'XTENSION': 'IMAGE', - 'BITPIX': -32, - 'NAXIS': naxis, - 'EXTNAME': 'D2IMARR', - 'EXTVER': wdvarr_ver, - 'PCOUNT': 0, - 'GCOUNT': 1, - 'CCDCHIP': ccdchip, - } - cdl = [] - for key in kw_comm0.keys(): - cdl.append((key, kw_val0[key], kw_comm0[key])) - for key in kw_comm1.keys(): - cdl.append((key, kw_val1[key], kw_comm1[key])) - # Now add keywords from NPOLFILE header to document source of calibration - # include all keywords after and including 'FILENAME' from header - start_indx = -1 - end_indx = 0 - for i, c in enumerate(d2im_phdr): - if c == 'FILENAME': - start_indx = i - if c == '': # remove blanks from end of header - end_indx = i+1 - break - if start_indx >= 0: - for card in d2im_phdr.cards[start_indx:end_indx]: - cdl.append(card) - - hdr = fits.Header(cards=cdl) - - return hdr - - createD2ImHdr = classmethod(createD2ImHdr) - - def get_ccdchip(cls, fobj, extname, extver): - """ - Given a science file or npol file determine CCDCHIP - """ - ccdchip = 1 - if fobj[0].header['INSTRUME'] == 'ACS' and fobj[0].header['DETECTOR'] == 'WFC': - ccdchip = fobj[extname, extver].header['CCDCHIP'] - elif fobj[0].header['INSTRUME'] == 'WFC3' and fobj[0].header['DETECTOR'] == 'UVIS': - ccdchip = fobj[extname, extver].header['CCDCHIP'] - elif fobj[0].header['INSTRUME'] == 'WFPC2': - ccdchip = fobj[extname, extver].header['DETECTOR'] - elif fobj[0].header['INSTRUME'] == 'STIS': - ccdchip = fobj[extname, extver].header['DETECTOR'] - elif fobj[0].header['INSTRUME'] == 'NICMOS': - ccdchip = fobj[extname, extver].header['CAMERA'] - return ccdchip - - get_ccdchip = classmethod(get_ccdchip) diff --git a/lib/stwcs/updatewcs/makewcs.py b/lib/stwcs/updatewcs/makewcs.py deleted file mode 100644 index 06c6f9c..0000000 --- a/lib/stwcs/updatewcs/makewcs.py +++ /dev/null @@ -1,273 +0,0 @@ -from __future__ import absolute_import, division # confidence high - -import datetime - -import numpy as np -import logging, time -from math import sin, sqrt, pow, cos, asin, atan2,pi - -from stsci.tools import fileutil -from . import utils - -logger = logging.getLogger(__name__) - -class MakeWCS(object): - """ - Recompute basic WCS keywords based on PA_V3 and distortion model. - - Notes - ----- - - Compute the reference chip WCS: - - -- CRVAL: transform the model XREF/YREF to the sky - -- PA_V3 is calculated at the target position and adjusted - for each chip orientation - -- CD: PA_V3 and the model scale are used to cnstruct a CD matrix - - - Compute the second chip WCS: - - -- CRVAL: - the distance between the zero points of the two - chip models on the sky - -- CD matrix: first order coefficients are added to the components - of this distance and transfered on the sky. The difference - between CRVAL and these vectors is the new CD matrix for each chip. - -- CRPIX: chip's model zero point in pixel space (XREF/YREF) - - - Time dependent distortion correction is applied to both chips' V2/V3 values. - - """ - tdd_xyref = {1: [2048, 3072], 2:[2048, 1024]} - def updateWCS(cls, ext_wcs, ref_wcs): - """ - recomputes the basic WCS kw - """ - logger.info("\n\tStarting MakeWCS: %s" % time.asctime()) - if not ext_wcs.idcmodel: - logger.info("IDC model not found, turning off Makewcs") - return {} - ltvoff, offshift = cls.getOffsets(ext_wcs) - - v23_corr = cls.zero_point_corr(ext_wcs) - rv23_corr = cls.zero_point_corr(ref_wcs) - - cls.uprefwcs(ext_wcs, ref_wcs, rv23_corr, ltvoff, offshift) - cls.upextwcs(ext_wcs, ref_wcs, v23_corr, rv23_corr, ltvoff, offshift) - - kw2update = {'CD1_1': ext_wcs.wcs.cd[0,0], - 'CD1_2': ext_wcs.wcs.cd[0,1], - 'CD2_1': ext_wcs.wcs.cd[1,0], - 'CD2_2': ext_wcs.wcs.cd[1,1], - 'CRVAL1': ext_wcs.wcs.crval[0], - 'CRVAL2': ext_wcs.wcs.crval[1], - 'CRPIX1': ext_wcs.wcs.crpix[0], - 'CRPIX2': ext_wcs.wcs.crpix[1], - 'IDCTAB': ext_wcs.idctab, - 'OCX10' : ext_wcs.idcmodel.cx[1,0], - 'OCX11' : ext_wcs.idcmodel.cx[1,1], - 'OCY10' : ext_wcs.idcmodel.cy[1,0], - 'OCY11' : ext_wcs.idcmodel.cy[1,1] - } - return kw2update - - updateWCS = classmethod(updateWCS) - - def upextwcs(cls, ext_wcs, ref_wcs, v23_corr, rv23_corr, loff, offsh): - """ - updates an extension wcs - """ - ltvoffx, ltvoffy = loff[0], loff[1] - offshiftx, offshifty = offsh[0], offsh[1] - ltv1 = ext_wcs.ltv1 - ltv2 = ext_wcs.ltv2 - if ltv1 != 0. or ltv2 != 0.: - offsetx = ext_wcs.wcs.crpix[0] - ltv1 - ext_wcs.idcmodel.refpix['XREF'] - offsety = ext_wcs.wcs.crpix[1] - ltv2 - ext_wcs.idcmodel.refpix['YREF'] - ext_wcs.idcmodel.shift(offsetx,offsety) - - fx, fy = ext_wcs.idcmodel.cx, ext_wcs.idcmodel.cy - - ext_wcs.setPscale() - tddscale = (ref_wcs.pscale/fx[1,1]) - v2 = ext_wcs.idcmodel.refpix['V2REF'] + v23_corr[0,0] * tddscale - v3 = ext_wcs.idcmodel.refpix['V3REF'] - v23_corr[1,0] * tddscale - v2ref = ref_wcs.idcmodel.refpix['V2REF'] + rv23_corr[0,0] * tddscale - v3ref = ref_wcs.idcmodel.refpix['V3REF'] - rv23_corr[1,0] * tddscale - - R_scale = ref_wcs.idcmodel.refpix['PSCALE']/3600.0 - off = sqrt((v2-v2ref)**2 + (v3-v3ref)**2)/(R_scale*3600.0) - - if v3 == v3ref: - theta=0.0 - else: - theta = atan2(ext_wcs.parity[0][0]*(v2-v2ref), ext_wcs.parity[1][1]*(v3-v3ref)) - - if ref_wcs.idcmodel.refpix['THETA']: theta += ref_wcs.idcmodel.refpix['THETA']*pi/180.0 - - dX=(off*sin(theta)) + offshiftx - dY=(off*cos(theta)) + offshifty - - px = np.array([[dX,dY]]) - newcrval = ref_wcs.wcs.p2s(px, 1)['world'][0] - newcrpix = np.array([ext_wcs.idcmodel.refpix['XREF'] + ltvoffx, - ext_wcs.idcmodel.refpix['YREF'] + ltvoffy]) - ext_wcs.wcs.crval = newcrval - ext_wcs.wcs.crpix = newcrpix - ext_wcs.wcs.set() - - # Create a small vector, in reference image pixel scale - delmat = np.array([[fx[1,1], fy[1,1]], \ - [fx[1,0], fy[1,0]]]) / R_scale/3600. - - # Account for subarray offset - # Angle of chip relative to chip - if ext_wcs.idcmodel.refpix['THETA']: - dtheta = ext_wcs.idcmodel.refpix['THETA'] - ref_wcs.idcmodel.refpix['THETA'] - else: - dtheta = 0.0 - - rrmat = fileutil.buildRotMatrix(dtheta) - # Rotate the vectors - dxy = np.dot(delmat, rrmat) - wc = ref_wcs.wcs.p2s((px + dxy), 1)['world'] - - # Calculate the new CDs and convert to degrees - cd11 = utils.diff_angles(wc[0,0],newcrval[0])*cos(newcrval[1]*pi/180.0) - cd12 = utils.diff_angles(wc[1,0],newcrval[0])*cos(newcrval[1]*pi/180.0) - cd21 = utils.diff_angles(wc[0,1],newcrval[1]) - cd22 = utils.diff_angles(wc[1,1],newcrval[1]) - cd = np.array([[cd11, cd12], [cd21, cd22]]) - ext_wcs.wcs.cd = cd - ext_wcs.wcs.set() - - upextwcs = classmethod(upextwcs) - - def uprefwcs(cls, ext_wcs, ref_wcs, rv23_corr_tdd, loff, offsh): - """ - Updates the reference chip - """ - ltvoffx, ltvoffy = loff[0], loff[1] - ltv1 = ref_wcs.ltv1 - ltv2 = ref_wcs.ltv2 - if ref_wcs.ltv1 != 0. or ref_wcs.ltv2 != 0.: - offsetx = ref_wcs.wcs.crpix[0] - ltv1 - ref_wcs.idcmodel.refpix['XREF'] - offsety = ref_wcs.wcs.crpix[1] - ltv2 - ref_wcs.idcmodel.refpix['YREF'] - ref_wcs.idcmodel.shift(offsetx,offsety) - - rfx, rfy = ref_wcs.idcmodel.cx, ref_wcs.idcmodel.cy - - offshift = offsh - dec = ref_wcs.wcs.crval[1] - tddscale = (ref_wcs.pscale/ref_wcs.idcmodel.cx[1,1]) - rv23 = [ref_wcs.idcmodel.refpix['V2REF'] + (rv23_corr_tdd[0,0] *tddscale), - ref_wcs.idcmodel.refpix['V3REF'] - (rv23_corr_tdd[1,0] * tddscale)] - # Get an approximate reference position on the sky - rref = np.array([[ref_wcs.idcmodel.refpix['XREF']+ltvoffx , - ref_wcs.idcmodel.refpix['YREF']+ltvoffy]]) - - crval = ref_wcs.wcs.p2s(rref, 1)['world'][0] - # Convert the PA_V3 orientation to the orientation at the aperture - # This is for the reference chip only - we use this for the - # reference tangent plane definition - # It has the same orientation as the reference chip - pv = troll(ext_wcs.pav3,dec,rv23[0], rv23[1]) - # Add the chip rotation angle - if ref_wcs.idcmodel.refpix['THETA']: - pv += ref_wcs.idcmodel.refpix['THETA'] - - - # Set values for the rest of the reference WCS - ref_wcs.wcs.crval = crval - ref_wcs.wcs.crpix = np.array([0.0,0.0])+offsh - parity = ref_wcs.parity - R_scale = ref_wcs.idcmodel.refpix['PSCALE']/3600.0 - cd11 = parity[0][0] * cos(pv*pi/180.0)*R_scale - cd12 = parity[0][0] * -sin(pv*pi/180.0)*R_scale - cd21 = parity[1][1] * sin(pv*pi/180.0)*R_scale - cd22 = parity[1][1] * cos(pv*pi/180.0)*R_scale - - rcd = np.array([[cd11, cd12], [cd21, cd22]]) - ref_wcs.wcs.cd = rcd - ref_wcs.wcs.set() - - uprefwcs = classmethod(uprefwcs) - - def zero_point_corr(cls,hwcs): - if hwcs.idcmodel.refpix['skew_coeffs'] is not None and 'TDD_CY_BETA' in hwcs.idcmodel.refpix['skew_coeffs']: - v23_corr = np.array([[0.],[0.]]) - return v23_corr - else: - try: - alpha = hwcs.idcmodel.refpix['TDDALPHA'] - beta = hwcs.idcmodel.refpix['TDDBETA'] - except KeyError: - alpha = 0.0 - beta = 0.0 - v23_corr = np.array([[0.],[0.]]) - logger.debug("\n\tTDD Zero point correction for chip %s defaulted to: %s" % (hwcs.chip, v23_corr)) - return v23_corr - - tdd = np.array([[beta, alpha], [alpha, -beta]]) - mrotp = fileutil.buildRotMatrix(2.234529)/2048. - xy0 = np.array([[cls.tdd_xyref[hwcs.chip][0]-2048.], [cls.tdd_xyref[hwcs.chip][1]-2048.]]) - v23_corr = np.dot(mrotp,np.dot(tdd,xy0)) * 0.05 - logger.debug("\n\tTDD Zero point correction for chip %s: %s" % (hwcs.chip, v23_corr)) - return v23_corr - - zero_point_corr = classmethod(zero_point_corr) - - def getOffsets(cls, ext_wcs): - ltv1 = ext_wcs.ltv1 - ltv2 = ext_wcs.ltv2 - - offsetx = ext_wcs.wcs.crpix[0] - ltv1 - ext_wcs.idcmodel.refpix['XREF'] - offsety = ext_wcs.wcs.crpix[1] - ltv2 - ext_wcs.idcmodel.refpix['YREF'] - - shiftx = ext_wcs.idcmodel.refpix['XREF'] + ltv1 - shifty = ext_wcs.idcmodel.refpix['YREF'] + ltv2 - if ltv1 != 0. or ltv2 != 0.: - ltvoffx = ltv1 + offsetx - ltvoffy = ltv2 + offsety - offshiftx = offsetx + shiftx - offshifty = offsety + shifty - else: - ltvoffx = 0. - ltvoffy = 0. - offshiftx = 0. - offshifty = 0. - - ltvoff = np.array([ltvoffx, ltvoffy]) - offshift = np.array([offshiftx, offshifty]) - return ltvoff, offshift - - getOffsets = classmethod(getOffsets) - - -def troll(roll, dec, v2, v3): - """ Computes the roll angle at the target position based on: - the roll angle at the V1 axis(roll), - the dec of the target(dec), and - the V2/V3 position of the aperture (v2,v3) in arcseconds. - - Based on algorithm provided by Colin Cox and used in - Generic Conversion at STScI. - """ - # Convert all angles to radians - _roll = np.deg2rad(roll) - _dec = np.deg2rad(dec) - _v2 = np.deg2rad(v2 / 3600.) - _v3 = np.deg2rad(v3 / 3600.) - - # compute components - sin_rho = sqrt((pow(sin(_v2),2)+pow(sin(_v3),2)) - (pow(sin(_v2),2)*pow(sin(_v3),2))) - rho = asin(sin_rho) - beta = asin(sin(_v3)/sin_rho) - if _v2 < 0: beta = pi - beta - gamma = asin(sin(_v2)/sin_rho) - if _v3 < 0: gamma = pi - gamma - A = pi/2. + _roll - beta - B = atan2( sin(A)*cos(_dec), (sin(_dec)*sin_rho - cos(_dec)*cos(rho)*cos(A))) - - # compute final value - troll = np.rad2deg(pi - (gamma+B)) - - return troll diff --git a/lib/stwcs/updatewcs/npol.py b/lib/stwcs/updatewcs/npol.py deleted file mode 100644 index 33579f0..0000000 --- a/lib/stwcs/updatewcs/npol.py +++ /dev/null @@ -1,343 +0,0 @@ -from __future__ import absolute_import, division # confidence high - -import logging, time - -import numpy as np -from astropy.io import fits - -from stsci.tools import fileutil -from . import utils - -logger = logging.getLogger('stwcs.updatewcs.npol') - -class NPOLCorr(object): - """ - Defines a Lookup table prior distortion correction as per WCS paper IV. - It uses a reference file defined by the NPOLFILE (suffix 'NPL') keyword - in the primary header. - - Notes - ----- - - Using extensions in the reference file create a WCSDVARR extensions - and add them to the science file. - - Add record-valued keywords to the science extension header to describe - the lookup tables. - - Add a keyword 'NPOLEXT' to the science extension header to store - the name of the reference file used to create the WCSDVARR extensions. - - If WCSDVARR extensions exist and `NPOLFILE` is different from `NPOLEXT`, - a subsequent update will overwrite the existing extensions. - If WCSDVARR extensions were not found in the science file, they will be added. - - It is assumed that the NPL reference files were created to work with IDC tables - but will be applied with SIP coefficients. A transformation is applied to correct - for the fact that the lookup tables will be applied before the first order coefficients - which are in the CD matrix when the SIP convention is used. - """ - - def updateWCS(cls, fobj): - """ - Parameters - ---------- - fobj : `astropy.io.fits.HDUList` object - Science file, for which a distortion correction in a NPOLFILE is available - - """ - logger.info("\n\tStarting NPOL: %s" %time.asctime()) - try: - assert isinstance(fobj, fits.HDUList) - except AssertionError: - logger.exception('\n\tInput must be a fits.HDUList object') - raise - - cls.applyNPOLCorr(fobj) - nplfile = fobj[0].header['NPOLFILE'] - - new_kw = {'NPOLEXT': nplfile} - return new_kw - - updateWCS = classmethod(updateWCS) - - def applyNPOLCorr(cls, fobj): - """ - For each science extension in a fits file object: - - create a WCSDVARR extension - - update science header - - add/update NPOLEXT keyword - """ - nplfile = fileutil.osfn(fobj[0].header['NPOLFILE']) - # Map WCSDVARR EXTVER numbers to extension numbers - wcsdvarr_ind = cls.getWCSIndex(fobj) - for ext in fobj: - try: - extname = ext.header['EXTNAME'].lower() - except KeyError: - continue - if extname == 'sci': - extversion = ext.header['EXTVER'] - ccdchip = cls.get_ccdchip(fobj, extname='SCI', extver=extversion) - header = ext.header - # get the data arrays from the reference file and transform - # them for use with SIP - dx,dy = cls.getData(nplfile, ccdchip) - idccoeffs = cls.getIDCCoeffs(header) - - if idccoeffs is not None: - dx, dy = cls.transformData(dx,dy, idccoeffs) - - # Determine EXTVER for the WCSDVARR extension from the - # NPL file (EXTNAME, EXTVER) kw. - # This is used to populate DPj.EXTVER kw - wcsdvarr_x_version = 2 * extversion -1 - wcsdvarr_y_version = 2 * extversion - for ename in zip(['DX', 'DY'], [wcsdvarr_x_version,wcsdvarr_y_version],[dx, dy]): - error_val = ename[2].max() - cls.addSciExtKw(header, wdvarr_ver=ename[1], npol_extname=ename[0], error_val=error_val) - hdu = cls.createNpolHDU(header, npolfile=nplfile, \ - wdvarr_ver=ename[1], npl_extname=ename[0], data=ename[2],ccdchip=ccdchip) - if wcsdvarr_ind: - fobj[wcsdvarr_ind[ename[1]]] = hdu - else: - fobj.append(hdu) - - - applyNPOLCorr = classmethod(applyNPOLCorr) - - def getWCSIndex(cls, fobj): - - """ - If fobj has WCSDVARR extensions: - returns a mapping of their EXTVER kw to file object extension numbers - if fobj does not have WCSDVARR extensions: - an empty dictionary is returned - """ - wcsd = {} - for e in range(len(fobj)): - try: - ename = fobj[e].header['EXTNAME'] - except KeyError: - continue - if ename == 'WCSDVARR': - wcsd[fobj[e].header['EXTVER']] = e - logger.debug("A map of WSCDVARR externsions %s" % wcsd) - return wcsd - - getWCSIndex = classmethod(getWCSIndex) - - def addSciExtKw(cls, hdr, wdvarr_ver=None, npol_extname=None, error_val=0.0): - """ - Adds kw to sci extension to define WCSDVARR lookup table extensions - - """ - if npol_extname =='DX': - j=1 - else: - j=2 - - cperror = 'CPERR%s' %j - cpdis = 'CPDIS%s' %j - dpext = 'DP%s.' %j + 'EXTVER' - dpnaxes = 'DP%s.' %j +'NAXES' - dpaxis1 = 'DP%s.' %j+'AXIS.1' - dpaxis2 = 'DP%s.' %j+'AXIS.2' - keys = [cperror, cpdis, dpext, dpnaxes, dpaxis1, dpaxis2] - values = {cperror: error_val, - cpdis: 'Lookup', - dpext: wdvarr_ver, - dpnaxes: 2, - dpaxis1: 1, - dpaxis2: 2} - - comments = {cperror: 'Maximum error of NPOL correction for axis %s' % j, - cpdis: 'Prior distortion function type', - dpext: 'Version number of WCSDVARR extension containing lookup distortion table', - dpnaxes: 'Number of independent variables in distortion function', - dpaxis1: 'Axis number of the jth independent variable in a distortion function', - dpaxis2: 'Axis number of the jth independent variable in a distortion function' - } - # Look for HISTORY keywords. If present, insert new keywords before them - before_key = 'HISTORY' - if before_key not in hdr: - before_key = None - - for key in keys: - hdr.set(key, value=values[key], comment=comments[key], before=before_key) - - addSciExtKw = classmethod(addSciExtKw) - - def getData(cls,nplfile, ccdchip): - """ - Get the data arrays from the reference NPOL files - Make sure 'CCDCHIP' in the npolfile matches "CCDCHIP' in the science file. - """ - npl = fits.open(nplfile) - for ext in npl: - nplextname = ext.header.get('EXTNAME',"") - nplccdchip = ext.header.get('CCDCHIP',1) - if nplextname == 'DX' and nplccdchip == ccdchip: - xdata = ext.data.copy() - continue - elif nplextname == 'DY' and nplccdchip == ccdchip: - ydata = ext.data.copy() - continue - else: - continue - npl.close() - return xdata, ydata - getData = classmethod(getData) - - def transformData(cls, dx, dy, coeffs): - """ - Transform the NPOL data arrays for use with SIP - """ - ndx, ndy = np.dot(coeffs, [dx.ravel(), dy.ravel()]).astype(np.float32) - ndx.shape = dx.shape - ndy.shape=dy.shape - return ndx, ndy - - transformData = classmethod(transformData) - - def getIDCCoeffs(cls, header): - """ - Return a matrix of the scaled first order IDC coefficients. - """ - try: - ocx10 = header['OCX10'] - ocx11 = header['OCX11'] - ocy10 = header['OCY10'] - ocy11 = header['OCY11'] - coeffs = np.array([[ocx11, ocx10], [ocy11,ocy10]], dtype=np.float32) - except KeyError: - logger.exception('\n\tFirst order IDCTAB coefficients are not available. \n\ - Cannot convert SIP to IDC coefficients.') - return None - try: - idcscale = header['IDCSCALE'] - except KeyError: - logger.exception("IDCSCALE not found in header - setting it to 1.") - idcscale = 1 - - return np.linalg.inv(coeffs/idcscale) - - getIDCCoeffs = classmethod(getIDCCoeffs) - - def createNpolHDU(cls, sciheader, npolfile=None, wdvarr_ver=1, npl_extname=None,data = None, ccdchip=1): - """ - Creates an HDU to be added to the file object. - """ - hdr = cls.createNpolHdr(sciheader, npolfile=npolfile, wdvarr_ver=wdvarr_ver, npl_extname=npl_extname, ccdchip=ccdchip) - hdu = fits.ImageHDU(header=hdr, data=data) - return hdu - - createNpolHDU = classmethod(createNpolHDU) - - def createNpolHdr(cls, sciheader, npolfile, wdvarr_ver, npl_extname, ccdchip): - """ - Creates a header for the WCSDVARR extension based on the NPOL reference file - and sci extension header. The goal is to always work in image coordinates - (also for subarrays and binned images. The WCS for the WCSDVARR extension - i ssuch that a full size npol table is created and then shifted or scaled - if the science image is a subarray or binned image. - """ - npl = fits.open(npolfile) - npol_phdr = npl[0].header - for ext in npl: - try: - nplextname = ext.header['EXTNAME'] - nplextver = ext.header['EXTVER'] - except KeyError: - continue - nplccdchip = cls.get_ccdchip(npl, extname=nplextname, extver=nplextver) - if nplextname == npl_extname and nplccdchip == ccdchip: - npol_header = ext.header - break - else: - continue - npl.close() - - naxis = npl[1].header['NAXIS'] - ccdchip = nplextname #npol_header['CCDCHIP'] - - kw = { 'NAXIS': 'Size of the axis', - 'CDELT': 'Coordinate increment along axis', - 'CRPIX': 'Coordinate system reference pixel', - 'CRVAL': 'Coordinate system value at reference pixel', - } - - kw_comm1 = {} - kw_val1 = {} - for key in kw.keys(): - for i in range(1, naxis+1): - si = str(i) - kw_comm1[key+si] = kw[key] - - for i in range(1, naxis+1): - si = str(i) - kw_val1['NAXIS'+si] = npol_header.get('NAXIS'+si) - kw_val1['CDELT'+si] = npol_header.get('CDELT'+si, 1.0) * \ - sciheader.get('LTM'+si+'_'+si, 1) - kw_val1['CRPIX'+si] = npol_header.get('CRPIX'+si, 0.0) - kw_val1['CRVAL'+si] = (npol_header.get('CRVAL'+si, 0.0) - \ - sciheader.get('LTV'+str(i), 0)) - - kw_comm0 = {'XTENSION': 'Image extension', - 'BITPIX': 'IEEE floating point', - 'NAXIS': 'Number of axes', - 'EXTNAME': 'WCS distortion array', - 'EXTVER': 'Distortion array version number', - 'PCOUNT': 'Special data area of size 0', - 'GCOUNT': 'One data group', - } - - kw_val0 = { 'XTENSION': 'IMAGE', - 'BITPIX': -32, - 'NAXIS': naxis, - 'EXTNAME': 'WCSDVARR', - 'EXTVER': wdvarr_ver, - 'PCOUNT': 0, - 'GCOUNT': 1, - 'CCDCHIP': ccdchip, - } - cdl = [] - for key in kw_comm0.keys(): - cdl.append((key, kw_val0[key], kw_comm0[key])) - for key in kw_comm1.keys(): - cdl.append((key, kw_val1[key], kw_comm1[key])) - # Now add keywords from NPOLFILE header to document source of calibration - # include all keywords after and including 'FILENAME' from header - start_indx = -1 - end_indx = 0 - for i, c in enumerate(npol_phdr): - if c == 'FILENAME': - start_indx = i - if c == '': # remove blanks from end of header - end_indx = i+1 - break - if start_indx >= 0: - for card in npol_phdr.cards[start_indx:end_indx]: - cdl.append(card) - - hdr = fits.Header(cards=cdl) - - return hdr - - createNpolHdr = classmethod(createNpolHdr) - - def get_ccdchip(cls, fobj, extname, extver): - """ - Given a science file or npol file determine CCDCHIP - """ - ccdchip = 1 - if fobj[0].header['INSTRUME'] == 'ACS' and fobj[0].header['DETECTOR'] == 'WFC': - ccdchip = fobj[extname, extver].header['CCDCHIP'] - elif fobj[0].header['INSTRUME'] == 'WFC3' and fobj[0].header['DETECTOR'] == 'UVIS': - ccdchip = fobj[extname, extver].header['CCDCHIP'] - elif fobj[0].header['INSTRUME'] == 'WFPC2': - ccdchip = fobj[extname, extver].header['DETECTOR'] - elif fobj[0].header['INSTRUME'] == 'STIS': - ccdchip = fobj[extname, extver].header['DETECTOR'] - elif fobj[0].header['INSTRUME'] == 'NICMOS': - ccdchip = fobj[extname, extver].header['CAMERA'] - return ccdchip - - get_ccdchip = classmethod(get_ccdchip) diff --git a/lib/stwcs/updatewcs/utils.py b/lib/stwcs/updatewcs/utils.py deleted file mode 100644 index 1214199..0000000 --- a/lib/stwcs/updatewcs/utils.py +++ /dev/null @@ -1,264 +0,0 @@ -from __future__ import division # confidence high -import os -from astropy.io import fits -from stsci.tools import fileutil - -import logging -logger = logging.getLogger("stwcs.updatewcs.utils") - - -def diff_angles(a,b): - """ - Perform angle subtraction a-b taking into account - small-angle differences across 360degree line. - """ - - diff = a - b - - if diff > 180.0: - diff -= 360.0 - - if diff < -180.0: - diff += 360.0 - - return diff - -def getBinning(fobj, extver=1): - # Return the binning factor - binned = 1 - if fobj[0].header['INSTRUME'] == 'WFPC2': - mode = fobj[0].header.get('MODE', "") - if mode == 'AREA': binned = 2 - else: - binned = fobj['SCI', extver].header.get('BINAXIS',1) - return binned - -def updateNEXTENDKw(fobj): - """ - Updates PRIMARY header with correct value for NEXTEND, if present. - - Parameters - ----------- - fobj : `astropy.io.fits.HDUList` - The FITS object for file opened in `update` mode - - """ - if 'nextend' in fobj[0].header: - fobj[0].header['nextend'] = len(fobj) -1 - -def extract_rootname(kwvalue,suffix=""): - """ Returns the rootname from a full reference filename - - If a non-valid value (any of ['','N/A','NONE','INDEF',None]) is input, - simply return a string value of 'NONE' - - This function will also replace any 'suffix' specified with a blank. - """ - # check to see whether a valid kwvalue has been provided as input - if kwvalue.strip() in ['','N/A','NONE','INDEF',None]: - return 'NONE' # no valid value, so return 'NONE' - - # for a valid kwvalue, parse out the rootname - # strip off any environment variable from input filename, if any are given - if '$' in kwvalue: - fullval = kwvalue[kwvalue.find('$')+1:] - else: - fullval = kwvalue - # Extract filename without path from kwvalue - fname = os.path.basename(fullval).strip() - - # Now, rip out just the rootname from the full filename - rootname = fileutil.buildNewRootname(fname) - - # Now, remove any known suffix from rootname - rootname = rootname.replace(suffix,'') - return rootname.strip() - -def construct_distname(fobj,wcsobj): - """ - This function constructs the value for the keyword 'DISTNAME'. - It relies on the reference files specified by the keywords 'IDCTAB', - 'NPOLFILE', and 'D2IMFILE'. - - The final constructed value will be of the form: - <idctab rootname>-<npolfile rootname>-<d2imfile rootname> - and have a value of 'NONE' if no reference files are specified. - """ - idcname = extract_rootname(fobj[0].header.get('IDCTAB', "NONE"), - suffix='_idc') - if (idcname is None or idcname=='NONE') and wcsobj.sip is not None: - idcname = 'UNKNOWN' - - npolname, npolfile = build_npolname(fobj) - if npolname is None and wcsobj.cpdis1 is not None: - npolname = 'UNKNOWN' - - d2imname, d2imfile = build_d2imname(fobj) - if d2imname is None and wcsobj.det2im is not None: - d2imname = 'UNKNOWN' - - sipname, idctab = build_sipname(fobj) - - distname = build_distname(sipname,npolname,d2imname) - return {'DISTNAME':distname,'SIPNAME':sipname} - -def build_distname(sipname,npolname,d2imname): - """ - Core function to build DISTNAME keyword value without the HSTWCS input. - """ - - distname = sipname.strip() - if npolname != 'NONE' or d2imname != 'NONE': - if d2imname != 'NONE': - distname+= '-'+npolname.strip() + '-'+d2imname.strip() - else: - distname+='-'+npolname.strip() - - return distname - -def build_default_wcsname(idctab): - - idcname = extract_rootname(idctab,suffix='_idc') - wcsname = 'IDC_' + idcname - return wcsname - -def build_sipname(fobj, fname=None, sipname=None): - """ - Build a SIPNAME from IDCTAB - - Parameters - ---------- - fobj : `astropy.io.fits.HDUList` - file object - fname : string - science file name (to be used if ROOTNAME is not present - sipname : string - user supplied SIPNAME keyword - - Returns - ------- - sipname, idctab - """ - try: - idctab = fobj[0].header['IDCTAB'] - idcname = extract_rootname(idctab,suffix='_idc') - except KeyError: - idctab = 'N/A' - idcname= 'N/A' - if not fname: - try: - fname = fobj.filename() - except: - fname = " " - if not sipname: - try: - sipname = fobj[0].header["SIPNAME"] - if idcname == 'N/A' or idcname not in sipname: - raise KeyError - except KeyError: - if idcname != 'N/A': - try: - rootname = fobj[0].header['rootname'] - except KeyError: - rootname = fname - sipname = rootname +'_'+ idcname - else: - if 'A_ORDER' in fobj[1].header or 'B_ORDER' in fobj[1].header: - sipname = 'UNKNOWN' - else: - idcname = 'NOMODEL' - - return sipname, idctab - -def build_npolname(fobj, npolfile=None): - """ - Build a NPOLNAME from NPOLFILE - - Parameters - ---------- - fobj : `astropy.io.fits.HDUList` - file object - npolfile : string - user supplied NPOLFILE keyword - - Returns - ------- - npolname, npolfile - """ - if not npolfile: - try: - npolfile = fobj[0].header["NPOLFILE"] - except KeyError: - npolfile = ' ' - if fileutil.countExtn(fobj, 'WCSDVARR'): - npolname = 'UNKNOWN' - else: - npolname = 'NOMODEL' - npolname = extract_rootname(npolfile, suffix='_npl') - if npolname == 'NONE': - npolname = 'NOMODEL' - else: - npolname = extract_rootname(npolfile, suffix='_npl') - if npolname == 'NONE': - npolname = 'NOMODEL' - return npolname, npolfile - -def build_d2imname(fobj, d2imfile=None): - """ - Build a D2IMNAME from D2IMFILE - - Parameters - ---------- - fobj : `astropy.io.fits.HDUList` - file object - d2imfile : string - user supplied NPOLFILE keyword - - Returns - ------- - d2imname, d2imfile - """ - if not d2imfile: - try: - d2imfile = fobj[0].header["D2IMFILE"] - except KeyError: - d2imfile = 'N/A' - if fileutil.countExtn(fobj, 'D2IMARR'): - d2imname = 'UNKNOWN' - else: - d2imname = 'NOMODEL' - d2imname = extract_rootname(d2imfile,suffix='_d2i') - if d2imname == 'NONE': - d2imname = 'NOMODEL' - else: - d2imname = extract_rootname(d2imfile,suffix='_d2i') - if d2imname == 'NONE': - d2imname = 'NOMODEL' - return d2imname, d2imfile - - -def remove_distortion(fname, dist_keyword): - logger.info("Removing distortion {0} from file {0}".format(dist_keyword, fname)) - from ..wcsutil import altwcs - if dist_keyword == "NPOLFILE": - extname = "WCSDVARR" - keywords = ["CPERR*", "DP1.*", "DP2.*", "CPDIS*", "NPOLEXT"] - elif dist_keyword == "D2IMFILE": - extname = "D2IMARR" - keywords = ["D2IMERR*", "D2IM1.*", "D2IM2.*", "D2IMDIS*", "D2IMEXT"] - else: - raise AttributeError("Unrecognized distortion keyword " - "{0} when attempting to remove distortion".format(dist_keyword)) - ext_mapping = altwcs.mapFitsExt2HDUListInd(fname, "SCI").values() - f = fits.open(fname, mode="update") - for hdu in ext_mapping: - for kw in keywords: - try: - del f[hdu].header[kw] - except KeyError: - pass - ext_mapping = altwcs.mapFitsExt2HDUListInd(fname, extname).values() - ext_mapping.sort() - for hdu in ext_mapping[::-1]: - del f[hdu] - f.close() diff --git a/lib/stwcs/updatewcs/wfpc2_dgeo.py b/lib/stwcs/updatewcs/wfpc2_dgeo.py deleted file mode 100644 index e57bb5c..0000000 --- a/lib/stwcs/updatewcs/wfpc2_dgeo.py +++ /dev/null @@ -1,123 +0,0 @@ -""" wfpc2_dgeo - Functions to convert WFPC2 DGEOFILE into D2IMFILE - -""" -import os -import datetime - -import astropy -from astropy.io import fits -import numpy as np - -from stsci.tools import fileutil - -import logging -logger = logging.getLogger("stwcs.updatewcs.apply_corrections") - -def update_wfpc2_d2geofile(filename, fhdu=None): - """ - Creates a D2IMFILE from the DGEOFILE for a WFPC2 image (input), and - modifies the header to reflect the new usage. - - Parameters - ---------- - filename: string - Name of WFPC2 file to be processed. This file will be updated - to delete any reference to a DGEOFILE and add a D2IMFILE to replace - that correction when running updatewcs. - fhdu: object - FITS object for WFPC2 image. If user has already opened the WFPC2 - file, they can simply pass that FITS object in for direct processing. - - Returns - ------- - d2imfile: string - Name of D2IMFILE created from DGEOFILE. The D2IMFILE keyword in the - image header will be updated/added to point to this newly created file. - - """ - - close_fhdu = False - if fhdu is None: - fhdu = fileutil.openImage(filename, mode='update') - close_fhdu = True - - dgeofile = fhdu['PRIMARY'].header.get('DGEOFILE', None) - already_converted = dgeofile not in [None, "N/A", "", " "] - if already_converted or 'ODGEOFIL' in fhdu['PRIMARY'].header: - if not already_converted: - dgeofile = fhdu['PRIMARY'].header.get('ODGEOFIL', None) - logger.info('Converting DGEOFILE %s into D2IMFILE...' % dgeofile) - rootname = filename[:filename.find('.fits')] - d2imfile = convert_dgeo_to_d2im(dgeofile,rootname) - fhdu['PRIMARY'].header['ODGEOFIL'] = dgeofile - fhdu['PRIMARY'].header['DGEOFILE'] = 'N/A' - fhdu['PRIMARY'].header['D2IMFILE'] = d2imfile - else: - d2imfile = None - fhdu['PRIMARY'].header['DGEOFILE'] = 'N/A' - if 'D2IMFILE' not in fhdu['PRIMARY'].header: - fhdu['PRIMARY'].header['D2IMFILE'] = 'N/A' - - # Only close the file handle if opened in this function - if close_fhdu: - fhdu.close() - - # return the d2imfile name so that calling routine can keep - # track of the new file created and delete it later if necessary - # (multidrizzle clean=True mode of operation) - return d2imfile - -def convert_dgeo_to_d2im(dgeofile,output,clobber=True): - """ Routine that converts the WFPC2 DGEOFILE into a D2IMFILE. - """ - dgeo = fileutil.openImage(dgeofile) - outname = output+'_d2im.fits' - - removeFileSafely(outname) - data = np.array([dgeo['dy',1].data[:,0]]) - scihdu = fits.ImageHDU(data=data) - dgeo.close() - # add required keywords for D2IM header - scihdu.header['EXTNAME'] = ('DY', 'Extension name') - scihdu.header['EXTVER'] = (1, 'Extension version') - fits_str = 'PYFITS Version '+str(astropy.__version__) - scihdu.header['ORIGIN'] = (fits_str, 'FITS file originator') - scihdu.header['INHERIT'] = (False, 'Inherits global header') - - dnow = datetime.datetime.now() - scihdu.header['DATE'] = (str(dnow).replace(' ','T'), - 'Date FITS file was generated') - - scihdu.header['CRPIX1'] = (0, 'Distortion array reference pixel') - scihdu.header['CDELT1'] = (1, 'Grid step size in first coordinate') - scihdu.header['CRVAL1'] = (0, 'Image array pixel coordinate') - scihdu.header['CRPIX2'] = (0, 'Distortion array reference pixel') - scihdu.header['CDELT2'] = (1, 'Grid step size in second coordinate') - scihdu.header['CRVAL2'] = (0, 'Image array pixel coordinate') - - phdu = fits.PrimaryHDU() - phdu.header['INSTRUME'] = 'WFPC2' - d2imhdu = fits.HDUList() - d2imhdu.append(phdu) - scihdu.header['DETECTOR'] = (1, 'CCD number of the detector: PC 1, WFC 2-4 ') - d2imhdu.append(scihdu.copy()) - scihdu.header['EXTVER'] = (2, 'Extension version') - scihdu.header['DETECTOR'] = (2, 'CCD number of the detector: PC 1, WFC 2-4 ') - d2imhdu.append(scihdu.copy()) - scihdu.header['EXTVER'] = (3, 'Extension version') - scihdu.header['DETECTOR'] = (3, 'CCD number of the detector: PC 1, WFC 2-4 ') - d2imhdu.append(scihdu.copy()) - scihdu.header['EXTVER'] = (4, 'Extension version') - scihdu.header['DETECTOR'] = (4, 'CCD number of the detector: PC 1, WFC 2-4 ') - d2imhdu.append(scihdu.copy()) - d2imhdu.writeto(outname) - d2imhdu.close() - - return outname - - -def removeFileSafely(filename,clobber=True): - """ Delete the file specified, but only if it exists and clobber is True. - """ - if filename is not None and filename.strip() != '': - if os.path.exists(filename) and clobber: os.remove(filename) diff --git a/lib/stwcs/wcsutil/__init__.py b/lib/stwcs/wcsutil/__init__.py deleted file mode 100644 index 65280be..0000000 --- a/lib/stwcs/wcsutil/__init__.py +++ /dev/null @@ -1,34 +0,0 @@ -from __future__ import absolute_import, print_function # confidence high - -from .altwcs import * -from .hstwcs import HSTWCS - - -def help(): - doc = """ \ - 1. Using a `astropy.io.fits.HDUList` object and an extension number \n - Example:\n - from astropy.io improt fits - fobj = fits.open('some_file.fits')\n - w = wcsutil.HSTWCS(fobj, 3)\n\n - - 2. Create an HSTWCS object using a qualified file name. \n - Example:\n - w = wcsutil.HSTWCS('j9irw4b1q_flt.fits[sci,1]')\n\n - - 3. Create an HSTWCS object using a file name and an extension number. \n - Example:\n - w = wcsutil.HSTWCS('j9irw4b1q_flt.fits', ext=2)\n\n - - 4. Create an HSTWCS object from WCS with key 'O'.\n - Example:\n - - w = wcsutil.HSTWCS('j9irw4b1q_flt.fits', ext=2, wcskey='O')\n\n - - 5. Create a template HSTWCS object for a DEFAULT object.\n - Example:\n - w = wcsutil.HSTWCS(instrument='DEFAULT')\n\n - """ - - print('How to create an HSTWCS object:\n\n') - print(doc) diff --git a/lib/stwcs/wcsutil/altwcs.py b/lib/stwcs/wcsutil/altwcs.py deleted file mode 100644 index aae1a9f..0000000 --- a/lib/stwcs/wcsutil/altwcs.py +++ /dev/null @@ -1,758 +0,0 @@ -from __future__ import division, print_function # confidence high -import os -import string - -import numpy as np -from astropy import wcs as pywcs -from astropy.io import fits -from stsci.tools import fileutil as fu - -altwcskw = ['WCSAXES', 'CRVAL', 'CRPIX', 'PC', 'CDELT', 'CD', 'CTYPE', 'CUNIT', - 'PV', 'PS'] -altwcskw_extra = ['LATPOLE','LONPOLE','RESTWAV','RESTFRQ'] - -# file operations -def archiveWCS(fname, ext, wcskey=" ", wcsname=" ", reusekey=False): - """ - Copy the primary WCS to the header as an alternate WCS - with wcskey and name WCSNAME. It loops over all extensions in 'ext' - - Parameters - ---------- - fname : string or `astropy.io.fits.HDUList` - file name or a file object - ext : int, tuple, str, or list of integers or tuples (e.g.('sci',1)) - fits extensions to work with - If a string is provided, it should specify the EXTNAME of extensions - with WCSs to be archived - wcskey : string "A"-"Z" or " " - if " ": get next available key if wcsname is also " " or try - to get a key from WCSNAME value - wcsname : string - Name of alternate WCS description - reusekey : boolean - if True - overwrites a WCS with the same key - - Examples - -------- - Copy the primary WCS of an in memory headrlet object to an - alternate WCS with key 'T' - - >>> hlet=headerlet.createHeaderlet('junk.fits', 'hdr1.fits') - >>> altwcs.wcskeys(hlet[1].header) - ['A'] - >>> altwcs.archiveWCS(hlet, ext=[('SIPWCS',1),('SIPWCS',2)], wcskey='T') - >>> altwcs.wcskeys(hlet[1].header) - ['A', 'T'] - - - See Also - -------- - wcsutil.restoreWCS: Copy an alternate WCS to the primary WCS - - """ - - if isinstance(fname, str): - f = fits.open(fname, mode='update') - else: - f = fname - - if not _parpasscheck(f, ext, wcskey, wcsname): - closefobj(fname, f) - raise ValueError("Input parameters problem") - - # Interpret input 'ext' value to get list of extensions to process - ext = _buildExtlist(f, ext) - - if not wcskey and not wcsname: - raise KeyError("Either wcskey or wcsname should be specified") - - if wcsname.strip() == "": - try: - wcsname = readAltWCS(f, ext[0], wcskey=" ")['WCSNAME'] - except KeyError: - pass - wcsext = ext[0] - if wcskey != " " and wcskey in wcskeys(f[wcsext].header) and not reusekey: - closefobj(fname, f) - raise KeyError("Wcskey %s is aready used. \ - Run archiveWCS() with reusekey=True to overwrite this alternate WCS. \ - Alternatively choose another wcskey with altwcs.available_wcskeys()." %wcskey) - elif wcskey == " ": - # wcsname exists, overwrite it if reuse is True or get the next key - if wcsname.strip() in wcsnames(f[wcsext].header).values(): - if reusekey: - # try getting the key from an existing WCS with WCSNAME - wkey = getKeyFromName(f[wcsext].header, wcsname) - wname = wcsname - if wkey == ' ': - wkey = next_wcskey(f[wcsext].header) - elif wkey is None: - closefobj(fname, f) - raise KeyError("Could not get a valid wcskey from wcsname %s" %wcsname) - else: - closefobj(fname, f) - raise KeyError("Wcsname %s is aready used. \ - Run archiveWCS() with reusekey=True to overwrite this alternate WCS. \ - Alternatively choose another wcskey with altwcs.available_wcskeys() or\ - choose another wcsname." %wcsname) - else: - wkey = next_wcskey(f[wcsext].header) - if wcsname.strip(): - wname = wcsname - else: - # determine which WCSNAME needs to be replicated in archived WCS - wnames = wcsnames(f[wcsext].header) - if 'O' in wnames: del wnames['O'] # we don't want OPUS/original - if len(wnames) > 0: - if ' ' in wnames: - wname = wnames[' '] - else: - akeys = string.uppercase - wname = "DEFAULT" - for key in akeys[-1::]: - if key in wnames: - wname = wnames - break - else: - wname = "DEFAULT" - else: - wkey = wcskey - wname = wcsname - - for e in ext: - hwcs = readAltWCS(f,e,wcskey=' ') - if hwcs is None: - continue - - wcsnamekey = 'WCSNAME' + wkey - f[e].header[wcsnamekey] = wname - - try: - old_wcsname=hwcs.pop('WCSNAME') - except: - pass - - for k in hwcs.keys(): - key = k[:7] + wkey - f[e].header[key] = hwcs[k] - closefobj(fname, f) - -def restore_from_to(f, fromext=None, toext=None, wcskey=" ", wcsname=" "): - """ - Copy an alternate WCS from one extension as a primary WCS of another extension - - Reads in a WCS defined with wcskey and saves it as the primary WCS. - Goes sequentially through the list of extensions in ext. - Alternatively uses 'fromext' and 'toext'. - - - Parameters - ---------- - f: string or `astropy.io.fits.HDUList` - a file name or a file object - fromext: string - extname from which to read in the alternate WCS, for example 'SCI' - toext: string or python list - extname or a list of extnames to which the WCS will be copied as - primary, for example ['SCI', 'ERR', 'DQ'] - wcskey: a charater - "A"-"Z" - Used for one of 26 alternate WCS definitions. - or " " - find a key from WCSNAMe value - wcsname: string (optional) - if given and wcskey is " ", will try to restore by WCSNAME value - - See Also - -------- - archiveWCS - copy the primary WCS as an alternate WCS - restoreWCS - Copy a WCS with key "WCSKEY" to the primary WCS - - """ - if isinstance(f, str): - fobj = fits.open(f, mode='update') - else: - fobj = f - - if not _parpasscheck(fobj, ext=None, wcskey=wcskey, fromext=fromext, toext=toext): - closefobj(f, fobj) - raise ValueError("Input parameters problem") - - # Interpret input 'ext' value to get list of extensions to process - #ext = _buildExtlist(fobj, ext) - - if isinstance(toext, str): - toext = [toext] - - # the case of an HDUList object in memory without an associated file - - #if fobj.filename() is not None: - # name = fobj.filename() - - simplefits = fu.isFits(fobj)[1] is 'simple' - if simplefits: - wcskeyext = 0 - else: - wcskeyext = 1 - - if wcskey == " ": - if wcsname.strip(): - wkey = getKeyFromName(fobj[wcskeyext].header, wcsname) - if not wkey: - closefobj(f, fobj) - raise KeyError("Could not get a key from wcsname %s ." % wcsname) - else: - if wcskey not in wcskeys(fobj, ext=wcskeyext): - print("Could not find alternate WCS with key %s in this file" % wcskey) - closefobj(f, fobj) - return - wkey = wcskey - - countext = fu.countExtn(fobj, fromext) - if not countext: - raise KeyError("File does not have extension with extname %s", fromext) - else: - for i in range(1, countext+1): - for toe in toext: - _restore(fobj, fromextnum=i, fromextnam=fromext, toextnum=i, toextnam=toe, ukey=wkey) - - if fobj.filename() is not None: - #fobj.writeto(name) - closefobj(f, fobj) - -def restoreWCS(f, ext, wcskey=" ", wcsname=" "): - """ - Copy a WCS with key "WCSKEY" to the primary WCS - - Reads in a WCS defined with wcskey and saves it as the primary WCS. - Goes sequentially through the list of extensions in ext. - Alternatively uses 'fromext' and 'toext'. - - - Parameters - ---------- - f : str or `astropy.io.fits.HDUList` - file name or a file object - ext : int, tuple, str, or list of integers or tuples (e.g.('sci',1)) - fits extensions to work with - If a string is provided, it should specify the EXTNAME of extensions - with WCSs to be archived - wcskey : str - "A"-"Z" - Used for one of 26 alternate WCS definitions. - or " " - find a key from WCSNAMe value - wcsname : str - (optional) if given and wcskey is " ", will try to restore by WCSNAME value - - See Also - -------- - archiveWCS - copy the primary WCS as an alternate WCS - restore_from_to - - """ - if isinstance(f, str): - fobj = fits.open(f, mode='update') - else: - fobj = f - - if not _parpasscheck(fobj, ext=ext, wcskey=wcskey): - closefobj(f, fobj) - raise ValueError("Input parameters problem") - - # Interpret input 'ext' value to get list of extensions to process - ext = _buildExtlist(fobj, ext) - - - # the case of an HDUList object in memory without an associated file - - #if fobj.filename() is not None: - # name = fobj.filename() - - simplefits = fu.isFits(fobj)[1] is 'simple' - if simplefits: - wcskeyext = 0 - else: - wcskeyext = 1 - - if wcskey == " ": - if wcsname.strip(): - wkey = getKeyFromName(fobj[wcskeyext].header, wcsname) - if not wkey: - closefobj(f, fobj) - raise KeyError("Could not get a key from wcsname %s ." % wcsname) - else: - if wcskey not in wcskeys(fobj, ext=wcskeyext): - #print "Could not find alternate WCS with key %s in this file" % wcskey - closefobj(f, fobj) - return - wkey = wcskey - - for e in ext: - _restore(fobj, wkey, fromextnum=e, verbose=False) - - if fobj.filename() is not None: - #fobj.writeto(name) - closefobj(f, fobj) - -def deleteWCS(fname, ext, wcskey=" ", wcsname=" "): - """ - Delete an alternate WCS defined with wcskey. - If wcskey is " " try to get a key from WCSNAME. - - Parameters - ---------- - fname : str or a `astropy.io.fits.HDUList` - ext : int, tuple, str, or list of integers or tuples (e.g.('sci',1)) - fits extensions to work with - If a string is provided, it should specify the EXTNAME of extensions - with WCSs to be archived - wcskey : str - one of 'A'-'Z' or " " - wcsname : str - Name of alternate WCS description - """ - if isinstance(fname, str): - fobj = fits.open(fname, mode='update') - else: - fobj = fname - - if not _parpasscheck(fobj, ext, wcskey, wcsname): - closefobj(fname, fobj) - raise ValueError("Input parameters problem") - - # Interpret input 'ext' value to get list of extensions to process - ext = _buildExtlist(fobj, ext) - # Do not allow deleting the original WCS. - if wcskey == 'O': - print("Wcskey 'O' is reserved for the original WCS and should not be deleted.") - closefobj(fname, fobj) - return - - wcskeyext = ext[0] - - if not wcskeys and not wcsname: - raise KeyError("Either wcskey or wcsname should be specified") - - if wcskey == " ": - # try getting the key from WCSNAME - wkey = getKeyFromName(fobj[wcskeyext].header, wcsname) - if not wkey: - closefobj(fname, fobj) - raise KeyError("Could not get a key: wcsname '%s' not found in header." % wcsname) - else: - if wcskey not in wcskeys(fobj[wcskeyext].header): - closefobj(fname, fobj) - raise KeyError("Could not find alternate WCS with key %s in this file" % wcskey) - wkey = wcskey - - prexts = [] - for i in ext: - hdr = fobj[i].header - hwcs = readAltWCS(fobj,i,wcskey=wkey) - if hwcs is None: - continue - for k in hwcs[::-1]: - del hdr[k] - #del hdr['ORIENT'+wkey] - prexts.append(i) - if prexts != []: - print('Deleted all instances of WCS with key %s in extensions' % wkey, prexts) - else: - print("Did not find WCS with key %s in any of the extensions" % wkey) - closefobj(fname, fobj) - -def _buildExtlist(fobj, ext): - """ - Utility function to interpret the provided value of 'ext' and return a list - of 'valid' values which can then be used by the rest of the functions in - this module. - - Parameters - ---------- - fobj: HDUList - file to be examined - ext: an int, a tuple, string, list of integers or tuples (e.g.('sci',1)) - fits extensions to work with - If a string is provided, it should specify the EXTNAME of extensions - with WCSs to be archived - """ - if not isinstance(ext,list): - if isinstance(ext,str): - extstr = ext - ext = [] - for extn in range(1, len(fobj)): - if 'extname' in fobj[extn].header and fobj[extn].header['extname'] == extstr: - ext.append(extn) - elif isinstance(ext, int) or isinstance(ext, tuple): - ext = [ext] - else: - raise KeyError("Valid extensions in 'ext' parameter need to be specified.") - return ext - -def _restore(fobj, ukey, fromextnum, - toextnum=None, fromextnam=None, toextnam=None, verbose=True): - """ - fobj: string of HDUList - ukey: string 'A'-'Z' - wcs key - fromextnum: int - extver of extension from which to copy WCS - fromextnam: string - extname of extension from which to copy WCS - toextnum: int - extver of extension to which to copy WCS - toextnam: string - extname of extension to which to copy WCS - """ - # create an extension tuple, e.g. ('SCI', 2) - if fromextnam: - fromextension = (fromextnam, fromextnum) - else: - fromextension = fromextnum - if toextnum: - if toextnam: - toextension = (toextnam, toextnum) - else: - toextension =toextnum - else: - toextension = fromextension - - hwcs = readAltWCS(fobj,fromextension,wcskey=ukey,verbose=verbose) - if hwcs is None: - return - - for k in hwcs.keys(): - key = k[:-1] - if key in fobj[toextension].header: - #fobj[toextension].header.update(key=key, value = hwcs[k]) - fobj[toextension].header[key] = hwcs[k] - else: - continue - if key == 'O' and 'TDDALPHA' in fobj[toextension].header: - fobj[toextension].header['TDDALPHA'] = 0.0 - fobj[toextension].header['TDDBETA'] = 0.0 - if 'ORIENTAT' in fobj[toextension].header: - norient = np.rad2deg(np.arctan2(hwcs['CD1_2'+'%s' %ukey], hwcs['CD2_2'+'%s' %ukey])) - fobj[toextension].header['ORIENTAT'] = norient - # Reset 2014 TDD keywords prior to computing new values (if any are computed) - for kw in ['TDD_CYA','TDD_CYB','TDD_CXA','TDD_CXB']: - if kw in fobj[toextension].header: - fobj[toextension].header[kw] = 0.0 - -#header operations -def _check_headerpars(fobj, ext): - if not isinstance(fobj, fits.Header) and not isinstance(fobj, fits.HDUList) \ - and not isinstance(fobj, str): - raise ValueError("Expected a file name, a file object or a header\n") - - if not isinstance(fobj, fits.Header): - #raise ValueError("Expected a valid ext parameter when input is a file") - if not isinstance(ext, int) and not isinstance(ext, tuple): - raise ValueError("Expected ext to be a number or a tuple, e.g. ('SCI', 1)\n") - -def _getheader(fobj, ext): - if isinstance(fobj, str): - hdr = fits.getheader(fobj,ext) - elif isinstance(fobj, fits.Header): - hdr = fobj - else: - hdr = fobj[ext].header - return hdr - -def readAltWCS(fobj, ext, wcskey=' ',verbose=False): - """ Reads in alternate WCS from specified extension - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList` - fits filename or fits file object - containing alternate/primary WCS(s) to be converted - wcskey : str - [" ",A-Z] - alternate/primary WCS key that will be replaced by the new key - ext : int - fits extension number - - Returns - ------- - hdr: fits.Header - header object with ONLY the keywords for specified alternate WCS - """ - if isinstance(fobj, str): - fobj = fits.open(fobj) - - hdr = _getheader(fobj,ext) - try: - nwcs = pywcs.WCS(hdr, fobj=fobj, key=wcskey) - except KeyError: - if verbose: - print('readAltWCS: Could not read WCS with key %s' %wcskey) - print(' Skipping %s[%s]' % (fobj.filename(), str(ext))) - return None - hwcs = nwcs.to_header() - - if nwcs.wcs.has_cd(): - hwcs = pc2cd(hwcs, key=wcskey) - - return hwcs - -def convertAltWCS(fobj,ext,oldkey=" ",newkey=' '): - """ - Translates the alternate/primary WCS with one key to an alternate/primary WCS with - another key. - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList`, or `astropy.io.fits.Header` - fits filename, fits file object or fits header - containing alternate/primary WCS(s) to be converted - ext : int - extension number - oldkey : str - [" ",A-Z] - alternate/primary WCS key that will be replaced by the new key - newkey : str - [" ",A-Z] - new alternate/primary WCS key - - Returns - ------- - hdr: `astropy.io.fits.Header` - header object with keywords renamed from oldkey to newkey - """ - hdr = readAltWCS(fobj,ext,wcskey=oldkey) - if hdr is None: - return None - # Converting WCS to new key - for card in hdr: - if oldkey == ' ' or oldkey == '': - cname = card - else: - cname = card.rstrip(oldkey) - hdr.rename_key(card,cname+newkey,force=True) - - return hdr - -def wcskeys(fobj, ext=None): - """ - Returns a list of characters used in the header for alternate - WCS description with WCSNAME keyword - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` - fits file name, fits file object or fits header - ext : int or None - extension number - if None, fobj must be a header - """ - _check_headerpars(fobj, ext) - hdr = _getheader(fobj, ext) - names = hdr["WCSNAME*"] - d = [] - for key in names: - wkey = key.replace('WCSNAME','') - if wkey == '': wkey = ' ' - d.append(wkey) - return d - -def wcsnames(fobj, ext=None): - """ - Returns a dictionary of wcskey: WCSNAME pairs - - Parameters - ---------- - fobj : stri, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` - fits file name, fits file object or fits header - ext : int or None - extension number - if None, fobj must be a header - - """ - _check_headerpars(fobj, ext) - hdr = _getheader(fobj, ext) - names = hdr["WCSNAME*"] - d = {} - for keyword, value in names.items(): - wkey = keyword.replace('WCSNAME','') - if wkey == '': wkey = ' ' - d[wkey] = value - return d - -def available_wcskeys(fobj, ext=None): - """ - Returns a list of characters which are not used in the header - with WCSNAME keyword. Any of them can be used to save a new - WCS. - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` - fits file name, fits file object or fits header - ext : int or None - extension number - if None, fobj must be a header - """ - _check_headerpars(fobj, ext) - hdr = _getheader(fobj, ext) - all_keys = list(string.ascii_uppercase) - used_keys = wcskeys(hdr) - try: - used_keys.remove(" ") - except ValueError: - pass - [all_keys.remove(key) for key in used_keys] - return all_keys - -def next_wcskey(fobj, ext=None): - """ - Returns next available character to be used for an alternate WCS - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` - fits file name, fits file object or fits header - ext : int or None - extension number - if None, fobj must be a header - """ - _check_headerpars(fobj, ext) - hdr = _getheader(fobj, ext) - allkeys = available_wcskeys(hdr) - if allkeys != []: - return allkeys[0] - else: - return None - -def getKeyFromName(header, wcsname): - """ - If WCSNAME is found in header, return its key, else return - None. This is used to update an alternate WCS - repeatedly and not generate new keys every time. - - Parameters - ---------- - header : `astropy.io.fits.Header` - wcsname : str - value of WCSNAME - """ - wkey = None - names = wcsnames(header) - wkeys = [] - for item in names.items(): - if item[1].lower() == wcsname.lower(): - wkeys.append(item[0]) - wkeys.sort() - if len(wkeys) > 0: - wkey = wkeys[-1] - else: - wkey = None - return wkey - -def pc2cd(hdr, key=' '): - """ - Convert a CD PC matrix to a CD matrix. - - WCSLIB (and PyWCS) recognizes CD keywords as input - but converts them and works internally with the PC matrix. - to_header() returns the PC matrix even if the i nput was a - CD matrix. To keep input and output consistent we check - for has_cd and convert the PC back to CD. - - Parameters - ---------- - hdr: `astropy.io.fits.Header` - - """ - for c in ['1_1', '1_2', '2_1', '2_2']: - try: - val = hdr['PC'+c+'%s' % key] - del hdr['PC'+c+ '%s' % key] - except KeyError: - if c=='1_1' or c == '2_2': - val = 1. - else: - val = 0. - #hdr.update(key='CD'+c+'%s' %key, value=val) - hdr['CD{0}{1}'.format(c, key)] = val - return hdr - -def _parpasscheck(fobj, ext, wcskey, fromext=None, toext=None, reusekey=False): - """ - Check input parameters to altwcs functions - - fobj : str or `astropy.io.fits.HDUList` object - a file name or a file object - ext : int, a tuple, a python list of integers or a python list - of tuples (e.g.('sci',1)) - fits extensions to work with - wcskey : str - "A"-"Z" or " "- Used for one of 26 alternate WCS definitions - wcsname : str - (optional) - if given and wcskey is " ", will try to restore by WCSNAME value - reusekey : bool - A flag which indicates whether to reuse a wcskey in the header - """ - if not isinstance(fobj, fits.HDUList): - print("First parameter must be a fits file object or a file name.") - return False - - # first one covers the case of an object created in memory - # (e.g. headerlet) for which fileinfo returns None - if fobj.fileinfo(0) is None: - pass - else: - # an HDUList object with associated file - if fobj.fileinfo(0)['filemode'] is not 'update': - print("First parameter must be a file name or a file object opened in 'update' mode.") - return False - - if not isinstance(ext, int) and not isinstance(ext, tuple) \ - and not isinstance(ext,str) \ - and not isinstance(ext, list) and ext is not None: - print("Ext must be integer, tuple, string,a list of int extension numbers, \n\ - or a list of tuples representing a fits extension, for example ('sci', 1).") - return False - - if not isinstance(fromext, str) and fromext is not None: - print("fromext must be a string representing a valid extname") - return False - - if not isinstance(toext, list) and not isinstance(toext, str) and \ - toext is not None : - print("toext must be a string or a list of strings representing extname") - return False - - if len(wcskey) != 1: - print('Parameter wcskey must be a character - one of "A"-"Z" or " "') - return False - - return True - -def closefobj(fname, f): - """ - Functions in this module accept as input a file name or a file object. - If the input was a file name (string) we close the object. If the user - passed a file object we leave it to the user to close it. - """ - if isinstance(fname, str): - f.close() - -def mapFitsExt2HDUListInd(fname, extname): - """ - Map FITS extensions with 'EXTNAME' to HDUList indexes. - """ - - if not isinstance(fname, fits.HDUList): - f = fits.open(fname) - close_file = True - else: - f = fname - close_file = False - d = {} - for hdu in f: - if 'EXTNAME' in hdu.header and hdu.header['EXTNAME'] == extname: - extver = hdu.header['EXTVER'] - d[(extname, extver)] = f.index_of((extname, extver)) - if close_file: - f.close() - return d diff --git a/lib/stwcs/wcsutil/convertwcs.py b/lib/stwcs/wcsutil/convertwcs.py deleted file mode 100644 index a384eb1..0000000 --- a/lib/stwcs/wcsutil/convertwcs.py +++ /dev/null @@ -1,118 +0,0 @@ -from __future__ import print_function -try: - import stwcs - from stwcs import wcsutil -except: - stwcs = None - -from stsci.tools import fileutil - -OPUS_WCSKEYS = ['OCRVAL1','OCRVAL2','OCRPIX1','OCRPIX2', - 'OCD1_1','OCD1_2','OCD2_1','OCD2_2', - 'OCTYPE1','OCTYPE2'] - - -def archive_prefix_OPUS_WCS(fobj,extname='SCI'): - """ Identifies WCS keywords which were generated by OPUS and archived - using a prefix of 'O' for all 'SCI' extensions in the file - - Parameters - ---------- - fobj : str or `astropy.io.fits.HDUList` - Filename or fits object of a file - - """ - if stwcs is None: - print('=====================') - print('The STWCS package is needed to convert an old-style OPUS WCS to an alternate WCS') - print('=====================') - raise ImportError - - - closefits = False - if isinstance(fobj,str): - # A filename was provided as input - fobj = fits.open(fobj,mode='update') - closefits=True - - # Define the header - ext = ('sci',1) - hdr = fobj[ext].header - - numextn = fileutil.countExtn(fobj) - extlist = [] - for e in range(1,numextn+1): - extlist.append(('sci',e)) - - # Insure that the 'O' alternate WCS is present - if 'O' not in wcsutil.wcskeys(hdr): - # if not, archive the Primary WCS as the default OPUS WCS - wcsutil.archiveWCS(fobj,extlist, wcskey='O', wcsname='OPUS') - - # find out how many SCI extensions are in the image - numextn = fileutil.countExtn(fobj,extname=extname) - if numextn == 0: - extname = 'PRIMARY' - - # create HSTWCS object from PRIMARY WCS - wcsobj = wcsutil.HSTWCS(fobj,ext=ext,wcskey='O') - # get list of WCS keywords - wcskeys = list(wcsobj.wcs2header().keys()) - - # For each SCI extension... - for e in range(1,numextn+1): - # Now, look for any WCS keywords with a prefix of 'O' - for key in wcskeys: - okey = 'O'+key[:7] - hdr = fobj[(extname,e)].header - if okey in hdr: - # Update alternate WCS keyword with prefix-O OPUS keyword value - hdr[key] = hdr[okey] - - if closefits: - fobj.close() - -def create_prefix_OPUS_WCS(fobj,extname='SCI'): - """ Creates alternate WCS with a prefix of 'O' for OPUS generated WCS values - to work with old MultiDrizzle. - - Parameters - ---------- - fobj : str or `astropy.io.fits.HDUList` - Filename or fits object of a file - - Raises - ------ - IOError: - if input FITS object was not opened in 'update' mode - - """ - # List of O-prefix keywords to create - owcskeys = OPUS_WCSKEYS - - closefits = False - if isinstance(fobj,str): - # A filename was provided as input - fobj = fits.open(fobj, mode='update') - closefits=True - else: - # check to make sure this FITS obj has been opened in update mode - if fobj.fileinfo(0)['filemode'] != 'update': - print('File not opened with "mode=update". Quitting...') - raise IOError - - # check for existance of O-prefix WCS - if owcskeys[0] not in fobj['sci',1].header: - - # find out how many SCI extensions are in the image - numextn = fileutil.countExtn(fobj,extname=extname) - if numextn == 0: - extname = '' - for extn in range(1,numextn+1): - hdr = fobj[(extname,extn)].header - for okey in owcskeys: - hdr[okey] = hdr[okey[1:]+'O'] - - # Close FITS image if we had to open it... - if closefits: - fobj.close() diff --git a/lib/stwcs/wcsutil/getinput.py b/lib/stwcs/wcsutil/getinput.py deleted file mode 100644 index 8ee1123..0000000 --- a/lib/stwcs/wcsutil/getinput.py +++ /dev/null @@ -1,62 +0,0 @@ -from astropy.io import fits -from stsci.tools import irafglob, fileutil, parseinput - -def parseSingleInput(f=None, ext=None): - if isinstance(f, str): - # create an HSTWCS object from a filename - if ext != None: - filename = f - if isinstance(ext,tuple): - if ext[0] == '': - extnum = ext[1] # handle ext=('',1) - else: - extnum = ext - else: - extnum = int(ext) - elif ext == None: - filename, ext = fileutil.parseFilename(f) - ext = fileutil.parseExtn(ext) - if ext[0] == '': - extnum = int(ext[1]) #handle ext=('',extnum) - else: - extnum = ext - phdu = fits.open(filename) - hdr0 = phdu[0].header - try: - ehdr = phdu[extnum].header - except (IndexError, KeyError) as e: - raise e.__class__('Unable to get extension %s.' % extnum) - - elif isinstance(f, fits.HDUList): - phdu = f - if ext == None: - extnum = 0 - else: - extnum = ext - ehdr = f[extnum].header - hdr0 = f[0].header - filename = hdr0.get('FILENAME', "") - - else: - raise ValueError('Input must be a file name string or a' - '`astropy.io.fits.HDUList` object') - - return filename, hdr0, ehdr, phdu - - -def parseMultipleInput(input): - if isinstance(input, str): - if input[0] == '@': - # input is an @ file - filelist = irafglob.irafglob(input) - else: - try: - filelist, output = parseinput.parseinput(input) - except IOError: raise - elif isinstance(input, list): - if isinstance(input[0], wcsutil.HSTWCS): - # a list of HSTWCS objects - return input - else: - filelist = input[:] - return filelist diff --git a/lib/stwcs/wcsutil/headerlet.py b/lib/stwcs/wcsutil/headerlet.py deleted file mode 100644 index c0dd9b0..0000000 --- a/lib/stwcs/wcsutil/headerlet.py +++ /dev/null @@ -1,2754 +0,0 @@ -""" -This module implements headerlets. - -A headerlet serves as a mechanism for encapsulating WCS information -which can be used to update the WCS solution of an image. The idea -came up first from the desire for passing improved astrometric -solutions for HST data and provide those solutions in a manner -that would not require getting entirely new images from the archive -when only the WCS information has been updated. - -""" - -from __future__ import absolute_import, division, print_function -import os -import sys -import functools -import logging -import textwrap -import copy -import time - -import numpy as np -from astropy.io import fits -#import pywcs -from astropy import wcs as pywcs -from astropy.utils import lazyproperty - -from stsci.tools.fileutil import countExtn -from stsci.tools import fileutil as fu -from stsci.tools import parseinput - -from stwcs.updatewcs import utils -from . import altwcs -from . import wcscorr -from .hstwcs import HSTWCS -from .mappings import basic_wcs - -#### Logging support functions -class FuncNameLoggingFormatter(logging.Formatter): - def __init__(self, fmt=None, datefmt=None): - if '%(funcName)s' not in fmt: - fmt = '%(funcName)s' + fmt - logging.Formatter.__init__(self, fmt=fmt, datefmt=datefmt) - - def format(self, record): - record = copy.copy(record) - if hasattr(record, 'funcName') and record.funcName == 'init_logging': - record.funcName = '' - else: - record.funcName += ' ' - return logging.Formatter.format(self, record) - - -logger = logging.getLogger(__name__) -formatter = FuncNameLoggingFormatter("%(levelname)s: %(message)s") -ch = logging.StreamHandler() -ch.setFormatter(formatter) -ch.setLevel(logging.CRITICAL) -logger.addHandler(ch) -logger.setLevel(logging.DEBUG) - -FITS_STD_KW = ['XTENSION', 'BITPIX', 'NAXIS', 'PCOUNT', - 'GCOUNT', 'EXTNAME', 'EXTVER', 'ORIGIN', - 'INHERIT', 'DATE', 'IRAF-TLM'] - -DEFAULT_SUMMARY_COLS = ['HDRNAME', 'WCSNAME', 'DISTNAME', 'AUTHOR', 'DATE', - 'SIPNAME', 'NPOLFILE', 'D2IMFILE', 'DESCRIP'] -COLUMN_DICT = {'vals': [], 'width': []} -COLUMN_FMT = '{:<{width}}' - - -def init_logging(funcname=None, level=100, mode='w', **kwargs): - """ - - Initialize logging for a function - - Parameters - ---------- - funcname: string - Name of function which will be recorded in log - level: int, or bool, or string - int or string : Logging level - bool: False - switch off logging - Text logging level for the message ("DEBUG", "INFO", - "WARNING", "ERROR", "CRITICAL") - mode: 'w' or 'a' - attach to logfile ('a' or start a new logfile ('w') - - """ - for hndl in logger.handlers: - if isinstance(hndl, logging.FileHandler): - has_file_handler = True - else: - has_file_handler = False - if level: - if not has_file_handler: - logname = 'headerlet.log' - fh = logging.FileHandler(logname, mode=mode) - fh.setFormatter(formatter) - fh.setLevel(logging.DEBUG) - logger.addHandler(fh) - logger.info("%s: Starting %s with arguments:\n\t %s" % - (time.asctime(), funcname, kwargs)) - - -def with_logging(func): - @functools.wraps(func) - def wrapped(*args, **kw): - level = kw.get('logging', 100) - mode = kw.get('logmode', 'w') - func_args = kw.copy() - if sys.version_info[0] >= 3: - argnames = func.__code__.co_varnames - else: - argnames = func.func_code.co_varnames - - for argname, arg in zip(argnames, args): - func_args[argname] = arg - - init_logging(func.__name__, level, mode, **func_args) - return func(*args, **kw) - return wrapped - -#### Utility functions -def is_par_blank(par): - return par in ['', ' ', 'INDEF', "None", None] - -def parse_filename(fname, mode='readonly'): - """ - Interprets the input as either a filename of a file that needs to be opened - or a PyFITS object. - - Parameters - ---------- - fname : str, `astropy.io.fits.HDUList` - Input pointing to a file or `astropy.io.fits.HDUList` object. - An input filename (str) will be expanded as necessary to - interpret any environmental variables - included in the filename. - - mode : string - Specifies what mode to use when opening the file, if it needs - to open the file at all [Default: 'readonly'] - - Returns - ------- - fobj : `astropy.io.fits.HDUList` - FITS file handle for input - - fname : str - Name of input file - - close_fobj : bool - Flag specifying whether or not fobj needs to be closed since it was - opened by this function. This allows a program to know whether they - need to worry about closing the FITS object as opposed to letting - the higher level interface close the object. - - """ - close_fobj = False - if not isinstance(fname, list): - if sys.version_info[0] >= 3: - is_string = isinstance(fname, str) - else: - is_string = isinstance(fname, basestring) - if is_string: - fname = fu.osfn(fname) - fobj = fits.open(fname, mode=mode) - close_fobj = True - else: - fobj = fname - if hasattr(fobj, 'filename'): - fname = fobj.filename() - else: - fname = '' - return fobj, fname, close_fobj - -def get_headerlet_kw_names(fobj, kw='HDRNAME'): - """ - Returns a list of specified keywords from all HeaderletHDU - extensions in a science file. - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList` - kw : str - Name of keyword to be read and reported - """ - - fobj, fname, open_fobj = parse_filename(fobj) - - hdrnames = [] - for ext in fobj: - if isinstance(ext, fits.hdu.base.NonstandardExtHDU): - hdrnames.append(ext.header[kw]) - - if open_fobj: - fobj.close() - - return hdrnames - -def get_header_kw_vals(hdr, kwname, kwval, default=0): - if kwval is None: - if kwname in hdr: - kwval = hdr[kwname] - else: - kwval = default - return kwval - -@with_logging -def find_headerlet_HDUs(fobj, hdrext=None, hdrname=None, distname=None, - strict=True, logging=False, logmode='w'): - """ - Returns all HeaderletHDU extensions in a science file that matches - the inputs specified by the user. If no hdrext, hdrname or distname are - specified, this function will return a list of all HeaderletHDU objects. - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList` - Name of FITS file or open fits object (`astropy.io.fits.HDUList` instance) - hdrext : int, tuple or None - index number(EXTVER) or extension tuple of HeaderletHDU to be returned - hdrname : string - value of HDRNAME for HeaderletHDU to be returned - distname : string - value of DISTNAME for HeaderletHDUs to be returned - strict : bool [Default: True] - Specifies whether or not at least one parameter needs to be provided - If False, all extension indices returned if hdrext, hdrname and distname - are all None. If True and hdrext, hdrname, and distname are all None, - raise an Exception requiring one to be specified. - logging : boolean - enable logging to a file called headerlet.log - logmode : 'w' or 'a' - log file open mode - - Returns - ------- - hdrlets : list - A list of all matching HeaderletHDU extension indices (could be just one) - - """ - - get_all = False - if hdrext is None and hdrname is None and distname is None: - if not strict: - get_all = True - else: - mess = """\n - ===================================================== - No valid Headerlet extension specified. - Either "hdrname", "hdrext", or "distname" needs to be specified. - ===================================================== - """ - logger.critical(mess) - raise ValueError - - fobj, fname, open_fobj = parse_filename(fobj) - - hdrlets = [] - if hdrext is not None and isinstance(hdrext, int): - if hdrext in range(len(fobj)): # insure specified hdrext is in fobj - if isinstance(fobj[hdrext], fits.hdu.base.NonstandardExtHDU) and \ - fobj[hdrext].header['EXTNAME'] == 'HDRLET': - hdrlets.append(hdrext) - else: - for ext in fobj: - if isinstance(ext, fits.hdu.base.NonstandardExtHDU): - if get_all: - hdrlets.append(fobj.index(ext)) - else: - if hdrext is not None: - if isinstance(hdrext, tuple): - hdrextname = hdrext[0] - hdrextnum = hdrext[1] - else: - hdrextname = 'HDRLET' - hdrextnum = hdrext - hdrext_match = ((hdrext is not None) and - (hdrextnum == ext.header['EXTVER']) and - (hdrextname == ext.header['EXTNAME'])) - hdrname_match = ((hdrname is not None) and - (hdrname == ext.header['HDRNAME'])) - distname_match = ((distname is not None) and - (distname == ext.header['DISTNAME'])) - if hdrext_match or hdrname_match or distname_match: - hdrlets.append(fobj.index(ext)) - - if open_fobj: - fobj.close() - - if len(hdrlets) == 0: - if hdrname: - kwerr = 'hdrname' - kwval = hdrname - elif hdrext: - kwerr = 'hdrext' - kwval = hdrext - else: - kwerr = 'distname' - kwval = distname - message = """\n - ===================================================== - No valid Headerlet extension found!' - "%s" = %s not found in %s.' % (kwerr, kwval, fname) - ===================================================== - """ - logger.critical(message) - raise ValueError - - return hdrlets - -def verify_hdrname_is_unique(fobj, hdrname): - """ - Verifies that no other HeaderletHDU extension has the specified hdrname. - - Parameters - ---------- - fobj : str, `astropy.io.fits.HDUList` - Name of FITS file or open fits file object - hdrname : str - value of HDRNAME for HeaderletHDU to be compared as unique - - Returns - ------- - unique: bool - If True, no other HeaderletHDU has the specified HDRNAME value - """ - hdrnames_list = get_headerlet_kw_names(fobj) - unique = not(hdrname in hdrnames_list) - - return unique - -def update_versions(sourcehdr, desthdr): - """ - Update keywords which store version numbers - """ - phdukw = {'PYWCSVER': 'Version of PYWCS used to updated the WCS', - 'UPWCSVER': 'Version of STWCS used to updated the WCS' - } - for key in phdukw: - try: - desthdr[key] = (sourcehdr[key], sourcehdr.comments[key]) - except KeyError: - desthdr[key] = (" ", phdukw[key]) - -def update_ref_files(source, dest): - """ - Update the reference files name in the primary header of 'dest' - using values from 'source' - - Parameters - ---------- - source : `astropy.io.fits.Header` - dest : `astropy.io.fits.Header` - """ - logger.info("Updating reference files") - phdukw = {'NPOLFILE': True, - 'IDCTAB': True, - 'D2IMFILE': True, - 'SIPNAME': True, - 'DISTNAME': True} - - for key in phdukw: - try: - try: - del dest[key] - except: - pass - dest.set(key, source[key], source.comments[key]) - except KeyError: - phdukw[key] = False - return phdukw - -def print_summary(summary_cols, summary_dict, pad=2, maxwidth=None, idcol=None, - output=None, clobber=True, quiet=False ): - """ - Print out summary dictionary to STDOUT, and possibly an output file - - """ - nrows = None - if idcol: - nrows = len(idcol['vals']) - - # Find max width of each column - column_widths = {} - for kw in summary_dict: - colwidth = np.array(summary_dict[kw]['width']).max() - if maxwidth: - colwidth = min(colwidth, maxwidth) - column_widths[kw] = colwidth + pad - if nrows is None: - nrows = len(summary_dict[kw]['vals']) - - # print rows now - outstr = '' - # Start with column names - if idcol: - outstr += COLUMN_FMT.format(idcol['name'], width=idcol['width'] + pad) - for kw in summary_cols: - outstr += COLUMN_FMT.format(kw, width=column_widths[kw]) - outstr += '\n' - # Now, add a row for each headerlet - for row in range(nrows): - if idcol: - outstr += COLUMN_FMT.format(idcol['vals'][row], - width=idcol['width']+pad) - for kw in summary_cols: - val = summary_dict[kw]['vals'][row][:(column_widths[kw]-pad)] - outstr += COLUMN_FMT.format(val, width=column_widths[kw]) - outstr += '\n' - if not quiet: - print(outstr) - - # If specified, write info to separate text file - write_file = False - if output: - output = fu.osfn(output) # Expand any environment variables in filename - write_file = True - if os.path.exists(output): - if clobber: - os.remove(output) - else: - print('WARNING: Not writing results to file!') - print(' Output text file ', output, ' already exists.') - print(' Set "clobber" to True or move file before trying again.') - write_file = False - if write_file: - fout = open(output, mode='w') - fout.write(outstr) - fout.close() - -#### Private utility functions -def _create_primary_HDU(fobj, fname, wcsext, destim, hdrname, wcsname, - sipname, npolfile, d2imfile, - nmatch,catalog, wcskey, - author, descrip, history): - # convert input values into valid FITS kw values - if author is None: - author = '' - if descrip is None: - descrip = '' - - sipname, idctab = utils.build_sipname(fobj, fname, sipname) - logger.info("Setting sipname value to %s" % sipname) - - npolname, npolfile = utils.build_npolname(fobj, npolfile) - logger.info("Setting npolfile value to %s" % npolname) - - d2imname, d2imfile = utils.build_d2imname(fobj,d2imfile) - logger.info("Setting d2imfile value to %s" % d2imname) - - distname = utils.build_distname(sipname, npolname, d2imname) - logger.info("Setting distname to %s" % distname) - - # open file and parse comments - if history not in ['', ' ', None, 'INDEF'] and os.path.isfile(history): - f = open(fu.osfn(history)) - history = f.readlines() - f.close() - else: - history = '' - - rms_ra = fobj[wcsext].header.get("CRDER1"+wcskey, 0) - rms_dec = fobj[wcsext].header.get("CRDER2"+wcskey, 0) - if not nmatch: - nmatch = fobj[wcsext].header.get("NMATCH"+wcskey, 0) - if not catalog: - catalog = fobj[wcsext].header.get('CATALOG'+wcskey, "") - # get the version of STWCS used to create the WCS of the science file. - #try: - #upwcsver = fobj[0].header.cards[fobj[0].header.index('UPWCSVER')] - #except KeyError: - #upwcsver = pyfits.Card("UPWCSVER", " ", - #"Version of STWCS used to update the WCS") - #try: - #pywcsver = fobj[0].header.cards[fobj[0].header.index('PYWCSVER')] - #except KeyError: - #pywcsver = pyfits.Card("PYWCSVER", " ", - #"Version of PYWCS used to update the WCS") - upwcsver = fobj[0].header.get('UPWCSVER', "") - pywcsver = fobj[0].header.get('PYWCSVER', "") - # build Primary HDU - phdu = fits.PrimaryHDU() - phdu.header['DESTIM'] = (destim, 'Destination observation root name') - phdu.header['HDRNAME'] = (hdrname, 'Headerlet name') - fmt = "%Y-%m-%dT%H:%M:%S" - phdu.header['DATE'] = (time.strftime(fmt), 'Date FITS file was generated') - phdu.header['WCSNAME'] = (wcsname, 'WCS name') - phdu.header['DISTNAME'] = (distname, 'Distortion model name') - phdu.header['SIPNAME'] = (sipname, - 'origin of SIP polynomial distortion model') - phdu.header['NPOLFILE'] = (npolfile, - 'origin of non-polynmial distortion model') - phdu.header['D2IMFILE'] = (d2imfile, - 'origin of detector to image correction') - phdu.header['IDCTAB'] = (idctab, - 'origin of Polynomial Distortion') - phdu.header['AUTHOR'] = (author, 'headerlet created by this user') - phdu.header['DESCRIP'] = (descrip, - 'Short description of headerlet solution') - phdu.header['RMS_RA'] = (rms_ra, - 'RMS in RA at ref pix of headerlet solution') - phdu.header['RMS_DEC'] = (rms_dec, - 'RMS in Dec at ref pix of headerlet solution') - phdu.header['NMATCH'] = (nmatch, - 'Number of sources used for headerlet solution') - phdu.header['CATALOG'] = (catalog, - 'Astrometric catalog used for headerlet ' - 'solution') - phdu.header['UPWCSVER'] = (upwcsver, "Version of STWCS used to update the WCS") - phdu.header['PYWCSVER'] = (pywcsver, "Version of PYWCS used to update the WCS") - - # clean up history string in order to remove whitespace characters that - # would cause problems with FITS - if isinstance(history, list): - history_str = '' - for line in history: - history_str += line - else: - history_str = history - history_lines = textwrap.wrap(history_str, width=70) - for hline in history_lines: - phdu.header.add_history(hline) - - return phdu - - -#### Public Interface functions -@with_logging -def extract_headerlet(filename, output, extnum=None, hdrname=None, - clobber=False, logging=True): - """ - Finds a headerlet extension in a science file and writes it out as - a headerlet FITS file. - - If both hdrname and extnum are given they should match, if not - raise an Exception - - Parameters - ---------- - filename: string or HDUList or Python list - This specifies the name(s) of science file(s) from which headerlets - will be extracted. - - String input formats supported include use of wild-cards, IRAF-style - '@'-files (given as '@<filename>') and comma-separated list of names. - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - If a list of filenames has been specified, it will extract a - headerlet from the same extnum from all filenames. - output: string - Filename or just rootname of output headerlet FITS file - If string does not contain '.fits', it will create a filename with - '_hlet.fits' suffix - extnum: int - Extension number which contains the headerlet to be written out - hdrname: string - Unique name for headerlet, stored as the HDRNAME keyword - It stops if a value is not provided and no extnum has been specified - clobber: bool - If output file already exists, this parameter specifies whether or not - to overwrite that file [Default: False] - logging: boolean - enable logging to a file - - """ - - if isinstance(filename, fits.HDUList): - filename = [filename] - else: - filename, oname = parseinput.parseinput(filename) - - for f in filename: - fobj, fname, close_fobj = parse_filename(f) - frootname = fu.buildNewRootname(fname) - if hdrname in ['', ' ', None, 'INDEF'] and extnum is None: - if close_fobj: - fobj.close() - logger.critical("Expected a valid extnum or hdrname parameter") - raise ValueError - if hdrname is not None: - extn_from_hdrname = find_headerlet_HDUs(fobj, hdrname=hdrname)[0] - if extn_from_hdrname != extnum: - logger.critical("hdrname and extnmu should refer to the same FITS extension") - raise ValueError - else: - hdrhdu = fobj[extn_from_hdrname] - else: - hdrhdu = fobj[extnum] - - if not isinstance(hdrhdu, HeaderletHDU): - logger.critical("Specified extension is not a headerlet") - raise ValueError - - hdrlet = hdrhdu.headerlet - - if output is None: - output = frootname - - if '.fits' in output: - outname = output - else: - outname = '%s_hlet.fits' % output - - hdrlet.tofile(outname, clobber=clobber) - - if close_fobj: - fobj.close() - - -@with_logging -def write_headerlet(filename, hdrname, output=None, sciext='SCI', - wcsname=None, wcskey=None, destim=None, - sipname=None, npolfile=None, d2imfile=None, - author=None, descrip=None, history=None, - nmatch=None, catalog=None, - attach=True, clobber=False, logging=False): - - """ - Save a WCS as a headerlet FITS file. - - This function will create a headerlet, write out the headerlet to a - separate headerlet file, then, optionally, attach it as an extension - to the science image (if it has not already been archived) - - Either wcsname or wcskey must be provided; if both are given, they must - match a valid WCS. - - Updates wcscorr if necessary. - - Parameters - ---------- - filename: string or HDUList or Python list - This specifies the name(s) of science file(s) from which headerlets - will be created and written out. - String input formats supported include use of wild-cards, IRAF-style - '@'-files (given as '@<filename>') and comma-separated list of names. - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - hdrname: string - Unique name for this headerlet, stored as HDRNAME keyword - output: string or None - Filename or just rootname of output headerlet FITS file - If string does not contain '.fits', it will create a filename - starting with the science filename and ending with '_hlet.fits'. - If None, a default filename based on the input filename will be - generated for the headerlet FITS filename - sciext: string - name (EXTNAME) of extension that contains WCS to be saved - wcsname: string - name of WCS to be archived, if " ": stop - wcskey: one of A...Z or " " or "PRIMARY" - if " " or "PRIMARY" - archive the primary WCS - destim: string - DESTIM keyword - if NOne, use ROOTNAME or science file name - sipname: string or None (default) - Name of unique file where the polynomial distortion coefficients were - read from. If None, the behavior is: - The code looks for a keyword 'SIPNAME' in the science header - If not found, for HST it defaults to 'IDCTAB' - If there is no SIP model the value is 'NOMODEL' - If there is a SIP model but no SIPNAME, it is set to 'UNKNOWN' - npolfile: string or None (default) - Name of a unique file where the non-polynomial distortion was stored. - If None: - The code looks for 'NPOLFILE' in science header. - If 'NPOLFILE' was not found and there is no npol model, it is set to 'NOMODEL' - If npol model exists, it is set to 'UNKNOWN' - d2imfile: string - Name of a unique file where the detector to image correction was - stored. If None: - The code looks for 'D2IMFILE' in the science header. - If 'D2IMFILE' is not found and there is no d2im correction, - it is set to 'NOMODEL' - If d2im correction exists, but 'D2IMFILE' is missing from science - header, it is set to 'UNKNOWN' - author: string - Name of user who created the headerlet, added as 'AUTHOR' keyword - to headerlet PRIMARY header - descrip: string - Short description of the solution provided by the headerlet - This description will be added as the single 'DESCRIP' keyword - to the headerlet PRIMARY header - history: filename, string or list of strings - Long (possibly multi-line) description of the solution provided - by the headerlet. These comments will be added as 'HISTORY' cards - to the headerlet PRIMARY header - If filename is specified, it will format and attach all text from - that file as the history. - attach: bool - Specify whether or not to attach this headerlet as a new extension - It will verify that no other headerlet extension has been created with - the same 'hdrname' value. - clobber: bool - If output file already exists, this parameter specifies whether or not - to overwrite that file [Default: False] - logging: boolean - enable file logging - """ - - if isinstance(filename, fits.HDUList): - filename = [filename] - else: - filename, oname = parseinput.parseinput(filename) - - for f in filename: - if isinstance(f, str): - fname = f - else: - fname = f.filename() - - if wcsname in [None, ' ', '', 'INDEF'] and wcskey is None: - message = """\n - No valid WCS found found in %s. - A valid value for either "wcsname" or "wcskey" - needs to be specified. - """ % fname - logger.critical(message) - raise ValueError - - # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' - if wcskey == 'PRIMARY': - wcskey = ' ' - - if attach: - umode = 'update' - else: - umode = 'readonly' - - fobj, fname, close_fobj = parse_filename(f, mode=umode) - - # Interpret sciext input for this file - if isinstance(sciext, int): - sciextlist = [sciext] # allow for specification of simple FITS header - elif isinstance(sciext, str): - numsciext = countExtn(fobj, sciext) - if numsciext > 0: - sciextlist = [tuple((sciext,i)) for i in range(1, numsciext+1)] - else: - sciextlist = [0] - elif isinstance(sciext, list): - sciextlist = sciext - else: - errstr = "Expected sciext to be a list of FITS extensions with science data\n"+\ - " a valid EXTNAME string, or an integer." - logger.critical(errstr) - raise ValueError - - wnames = altwcs.wcsnames(fobj,ext=sciextlist[0]) - - # Insure that WCSCORR table has been created with all original - # WCS's recorded prior to adding the headerlet WCS - wcscorr.init_wcscorr(fobj) - - if wcsname is None: - scihdr = fobj[sciextlist[0]].header - wname = scihdr['wcsname'+wcskey] - else: - wname = wcsname - if hdrname in [None, ' ', '']: - hdrname = wcsname - - logger.critical('Creating the headerlet from image %s' % fname) - hdrletobj = create_headerlet(fobj, sciext=sciextlist, - wcsname=wname, wcskey=wcskey, - hdrname=hdrname, - sipname=sipname, npolfile=npolfile, - d2imfile=d2imfile, author=author, - descrip=descrip, history=history, - nmatch=nmatch, catalog=catalog, - logging=False) - - if attach: - # Check to see whether or not a HeaderletHDU with - #this hdrname already exists - hdrnames = get_headerlet_kw_names(fobj) - if hdrname not in hdrnames: - hdrlet_hdu = HeaderletHDU.fromheaderlet(hdrletobj) - - if destim is not None: - hdrlet_hdu.header['destim'] = destim - - fobj.append(hdrlet_hdu) - - # Update the WCSCORR table with new rows from the headerlet's WCSs - wcscorr.update_wcscorr(fobj, source=hdrletobj, - extname='SIPWCS', wcs_id=wname) - - utils.updateNEXTENDKw(fobj) - fobj.flush() - else: - message = """ - Headerlet with hdrname %s already archived for WCS %s. - No new headerlet appended to %s. - """ % (hdrname, wname, fname) - logger.critical(message) - - if close_fobj: - logger.info('Closing image in write_headerlet()...') - fobj.close() - - frootname = fu.buildNewRootname(fname) - - if output is None: - # Generate default filename for headerlet FITS file - outname = '{0}_hlet.fits'.format(frootname) - else: - outname = output - - if not outname.endswith('.fits'): - outname = '{0}_{1}_hlet.fits'.format(frootname,outname) - - # If user specifies an output filename for headerlet, write it out - hdrletobj.tofile(outname, clobber=clobber) - logger.critical( 'Created Headerlet file %s ' % outname) - - del hdrletobj - -@with_logging -def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, - wcskey=" ", wcsname=None, - sipname=None, npolfile=None, d2imfile=None, - author=None, descrip=None, history=None, - nmatch=None, catalog=None, - logging=False, logmode='w'): - """ - Create a headerlet from a WCS in a science file - If both wcskey and wcsname are given they should match, if not - raise an Exception - - Parameters - ---------- - filename: string or HDUList - Either a filename or PyFITS HDUList object for the input science file - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - sciext: string or python list (default: 'SCI') - Extension in which the science data with the linear WCS is. - The headerlet will be created from these extensions. - If string - a valid EXTNAME is expected - If int - specifies an extension with a valid WCS, such as 0 for a - simple FITS file - If list - a list of FITS extension numbers or strings representing - extension tuples, e.g. ('SCI, 1') is expected. - hdrname: string - value of HDRNAME keyword - Takes the value from the HDRNAME<wcskey> keyword, if not available from WCSNAME<wcskey> - It stops if neither is found in the science file and a value is not provided - destim: string or None - name of file this headerlet can be applied to - if None, use ROOTNAME keyword - wcskey: char (A...Z) or " " or "PRIMARY" or None - a char representing an alternate WCS to be used for the headerlet - if " ", use the primary (default) - if None use wcsname - wcsname: string or None - if wcskey is None use wcsname specified here to choose an alternate WCS for the headerlet - sipname: string or None (default) - Name of unique file where the polynomial distortion coefficients were - read from. If None, the behavior is: - The code looks for a keyword 'SIPNAME' in the science header - If not found, for HST it defaults to 'IDCTAB' - If there is no SIP model the value is 'NOMODEL' - If there is a SIP model but no SIPNAME, it is set to 'UNKNOWN' - npolfile: string or None (default) - Name of a unique file where the non-polynomial distortion was stored. - If None: - The code looks for 'NPOLFILE' in science header. - If 'NPOLFILE' was not found and there is no npol model, it is set to 'NOMODEL' - If npol model exists, it is set to 'UNKNOWN' - d2imfile: string - Name of a unique file where the detector to image correction was - If None: - The code looks for 'D2IMFILE' in the science header. - If 'D2IMFILE' is not found and there is no d2im correction, - it is set to 'NOMODEL' - If d2im correction exists, but 'D2IMFILE' is missing from science - header, it is set to 'UNKNOWN' - author: string - Name of user who created the headerlet, added as 'AUTHOR' keyword - to headerlet PRIMARY header - descrip: string - Short description of the solution provided by the headerlet - This description will be added as the single 'DESCRIP' keyword - to the headerlet PRIMARY header - history: filename, string or list of strings - Long (possibly multi-line) description of the solution provided - by the headerlet. These comments will be added as 'HISTORY' cards - to the headerlet PRIMARY header - If filename is specified, it will format and attach all text from - that file as the history. - nmatch: int (optional) - Number of sources used in the new solution fit - catalog: string (optional) - Astrometric catalog used for headerlet solution - logging: boolean - enable file logging - logmode: 'w' or 'a' - log file open mode - - Returns - ------- - Headerlet object - - """ - if wcskey == 'O': - message = "Warning: 'O' is a reserved key for the original WCS. Quitting..." - logger.info(message) - return None - - fobj, fname, close_file = parse_filename(filename) - # based on `sciext` create a list of (EXTNAME, EXTVER) tuples - # of extensions with WCS to be saved in a headerlet - sciext = get_extname_extver_list(fobj, sciext) - logger.debug("Data extensions from which to create headerlet:\n\t %s" - % (str(sciext))) - if not sciext: - logger.critical("No valid target extensions found in file %s" % fname) - raise ValueError - - # Define extension to evaluate for verification of input parameters - wcsext = sciext[0] - logger.debug("sciext in create_headerlet is %s" % str(sciext)) - # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' - if wcskey == 'PRIMARY': - wcskey = ' ' - logger.info("wcskey reset from 'PRIMARY' to ' '") - wcskey = wcskey.upper() - wcsnamekw = "".join(["WCSNAME", wcskey.upper()]).rstrip() - hdrnamekw = "".join(["HDRNAME", wcskey.upper()]).rstrip() - - wnames = altwcs.wcsnames(fobj, ext=wcsext) - if not wcsname: - # User did not specify a value for 'wcsname' - if wcsnamekw in fobj[wcsext].header: - #check if there's a WCSNAME for this wcskey in the header - wcsname = fobj[wcsext].header[wcsnamekw] - logger.info("Setting wcsname from header[%s] to %s" % (wcsnamekw, wcsname)) - else: - if hdrname not in ['', ' ', None, "INDEF"]: - """ - If wcsname for this wcskey was not provided - and WCSNAME<wcskey> does not exist in the header - and hdrname is provided, then - use hdrname as WCSNAME for the headerlet. - """ - wcsname = hdrname - logger.debug("Setting wcsname from hdrname to %s" % hdrname) - else: - if hdrnamekw in fobj[wcsext].header: - wcsname = fobj[wcsext].header[hdrnamekw] - logger.debug("Setting wcsname from header[%s] to %s" % (hdrnamekw, wcsname)) - else: - message = """ - Required keywords 'HDRNAME' or 'WCSNAME' not found! - Please specify a value for parameter 'hdrname' - or update header with 'WCSNAME' keyword. - """ - logger.critical(message) - raise KeyError - else: - # Verify that 'wcsname' and 'wcskey' values specified by user reference - # the same WCS - wname = fobj[wcsext].header[wcsnamekw] - if wcsname != wname: - message = "\tInconsistent values for 'wcskey' and 'wcsname' specified!\n" - message += " 'wcskey' = %s and 'wcsname' = %s. \n" % (wcskey, wcsname) - message += "Actual value of %s found to be %s. \n" % (wcsnamekw, wname) - logger.critical(message) - raise KeyError - wkeys = altwcs.wcskeys(fobj, ext=wcsext) - if wcskey != ' ': - if wcskey not in wkeys: - logger.critical('No WCS with wcskey=%s found in extension %s. Skipping...' % (wcskey, str(wcsext))) - raise ValueError("No WCS with wcskey=%s found in extension %s. Skipping...' % (wcskey, str(wcsext))") - - # get remaining required keywords - if destim is None: - if 'ROOTNAME' in fobj[0].header: - destim = fobj[0].header['ROOTNAME'] - logger.info("Setting destim to rootname of the science file") - else: - destim = fname - logger.info('DESTIM not provided') - logger.info('Keyword "ROOTNAME" not found') - logger.info('Using file name as DESTIM') - - if not hdrname: - # check if HDRNAME<wcskey> is in header - if hdrnamekw in fobj[wcsext].header: - hdrname = fobj[wcsext].header[hdrnamekw] - else: - if wcsnamekw in fobj[wcsext].header: - hdrname = fobj[wcsext].header[wcsnamekw] - message = """ - Using default value for HDRNAME of "%s" derived from %s. - """ % (hdrname, wcsnamekw) - logger.info(message) - logger.info("Setting hdrname to %s from header[%s]" - % (hdrname, wcsnamekw)) - else: - message = "Required keywords 'HDRNAME' or 'WCSNAME' not found" - logger.critical(message) - raise KeyError - - - - hdul = [] - phdu = _create_primary_HDU(fobj, fname, wcsext, destim, hdrname, wcsname, - sipname, npolfile, d2imfile, - nmatch, catalog, wcskey, - author, descrip, history) - hdul.append(phdu) - wcsdvarr_extns = [] - """ - nd2i is a counter for d2i extensions to be used when the science file - has an old d2i correction format. The old format did not write EXTVER - kw for the d2i correction in the science header bu tthe new format expects - them. - """ - nd2i_extver = 1 - for ext in sciext: - wkeys = altwcs.wcskeys(fobj, ext=ext) - if wcskey != ' ': - if wcskey not in wkeys: - logger.debug( - 'No WCS with wcskey=%s found in extension %s. ' - 'Skipping...' % (wcskey, str(ext))) - raise ValueError("") - - hwcs = HSTWCS(fobj, ext=ext, wcskey=wcskey) - - whdul = hwcs.to_fits(relax=True, key=" ") - if hasattr(hwcs, 'orientat'): - orient_comment = "positions angle of image y axis (deg. e of n)" - whdul[0].header['ORIENTAT'] = (hwcs.orientat, orient_comment) - - whdul[0].header.append(('TG_ENAME', ext[0], 'Target science data extname')) - whdul[0].header.append(('TG_EVER', ext[1], 'Target science data extver')) - - if hwcs.wcs.has_cd(): - whdul[0].header = altwcs.pc2cd(whdul[0].header) - - idckw = hwcs._idc2hdr() - whdul[0].header.extend(idckw) - - if hwcs.det2im1 or hwcs.det2im2: - try: - whdul[0].header.append(fobj[ext].header.cards['D2IMEXT']) - except KeyError: - pass - whdul[0].header.extend(fobj[ext].header.cards['D2IMERR*']) - if 'D2IM1.EXTVER' in whdul[0].header: - try: - whdul[0].header['D2IM1.EXTVER'] = fobj[ext].header['D2IM1.EXTVER'] - except KeyError: - whdul[0].header['D2IM1.EXTVER'] = nd2i_extver - nd2i_extver += 1 - if 'D2IM2.EXTVER' in whdul[0].header: - try: - whdul[0].header['D2IM2.EXTVER'] = fobj[ext].header['D2IM2.EXTVER'] - except KeyError: - whdul[0].header['D2IM2.EXTVER'] = nd2i_extver - nd2i_extver += 1 - - if hwcs.cpdis1 or hwcs.cpdis2: - whdul[0].header.extend(fobj[ext].header.cards['CPERR*']) - try: - whdul[0].header.append(fobj[ext].header.cards['NPOLEXT']) - except KeyError: - pass - if 'DP1.EXTVER' in whdul[0].header: - whdul[0].header['DP1.EXTVER'] = fobj[ext].header['DP1.EXTVER'] - if 'DP2.EXTVER' in whdul[0].header: - whdul[0].header['DP2.EXTVER'] = fobj[ext].header['DP2.EXTVER'] - ihdu = fits.ImageHDU(header=whdul[0].header, name='SIPWCS') - - if ext[0] != "PRIMARY": - ihdu.update_ext_version(fobj[ext].header['EXTVER'], comment='Extension version') - - hdul.append(ihdu) - - if hwcs.cpdis1: - whdu = whdul[('WCSDVARR', 1)].copy() - whdu.update_ext_version(fobj[ext].header['DP1.EXTVER']) - hdul.append(whdu) - if hwcs.cpdis2: - whdu = whdul[('WCSDVARR', 2)].copy() - whdu.update_ext_version(fobj[ext].header['DP2.EXTVER']) - hdul.append(whdu) - - if hwcs.det2im1: - whdu = whdul[('D2IMARR', 1)].copy() - whdu.update_ext_version(ihdu.header['D2IM1.EXTVER']) - hdul.append(whdu) - if hwcs.det2im2: - whdu = whdul[('D2IMARR', 2)].copy() - whdu.update_ext_version(ihdu.header['D2IM2.EXTVER']) - hdul.append(whdu) - - - #if hwcs.det2im1 or hwcs.det2im2: - #try: - #darr = hdul[('D2IMARR', 1)] - #except KeyError: - #whdu = whdul[('D2IMARR')] - #whdu.update_ext_version(1) - #hdul.append(whdu) - if close_file: - fobj.close() - - hlet = Headerlet(hdul, logging=logging, logmode='a') - hlet.init_attrs() - return hlet - -@with_logging -def apply_headerlet_as_primary(filename, hdrlet, attach=True, archive=True, - force=False, logging=False, logmode='a'): - """ - Apply headerlet 'hdrfile' to a science observation 'destfile' as the primary WCS - - Parameters - ---------- - filename: string or list of strings - File name(s) of science observation whose WCS solution will be updated - hdrlet: string or list of strings - Headerlet file(s), must match 1-to-1 with input filename(s) - attach: boolean - True (default): append headerlet to FITS file as a new extension. - archive: boolean - True (default): before updating, create a headerlet with the - WCS old solution. - force: boolean - If True, this will cause the headerlet to replace the current PRIMARY - WCS even if it has a different distortion model. [Default: False] - logging: boolean - enable file logging - logmode: 'w' or 'a' - log file open mode - """ - if not isinstance(filename, list): - filename = [filename] - if not isinstance(hdrlet, list): - hdrlet = [hdrlet] - if len(hdrlet) != len(filename): - logger.critical("Filenames must have matching headerlets. " - "{0:d} filenames and {1:d} headerlets specified".format(len(filename),len(hdrlet))) - - for fname,h in zip(filename,hdrlet): - print("Applying {0} as Primary WCS to {1}".format(h,fname)) - hlet = Headerlet.fromfile(h, logging=logging, logmode=logmode) - hlet.apply_as_primary(fname, attach=attach, archive=archive, - force=force) - - -@with_logging -def apply_headerlet_as_alternate(filename, hdrlet, attach=True, wcskey=None, - wcsname=None, logging=False, logmode='w'): - """ - Apply headerlet to a science observation as an alternate WCS - - Parameters - ---------- - filename: string or list of strings - File name(s) of science observation whose WCS solution will be updated - hdrlet: string or list of strings - Headerlet file(s), must match 1-to-1 with input filename(s) - attach: boolean - flag indicating if the headerlet should be attached as a - HeaderletHDU to fobj. If True checks that HDRNAME is unique - in the fobj and stops if not. - wcskey: string - Key value (A-Z, except O) for this alternate WCS - If None, the next available key will be used - wcsname: string - Name to be assigned to this alternate WCS - WCSNAME is a required keyword in a Headerlet but this allows the - user to change it as desired. - logging: boolean - enable file logging - logmode: 'a' or 'w' - """ - if not isinstance(filename, list): - filename = [filename] - if not isinstance(hdrlet, list): - hdrlet = [hdrlet] - if len(hdrlet) != len(filename): - logger.critical("Filenames must have matching headerlets. " - "{0:d} filenames and {1:d} headerlets specified".format(len(filename),len(hdrlet))) - - for fname,h in zip(filename,hdrlet): - print('Applying {0} as an alternate WCS to {1}'.format(h,fname)) - hlet = Headerlet.fromfile(h, logging=logging, logmode=logmode) - hlet.apply_as_alternate(fname, attach=attach, - wcsname=wcsname, wcskey=wcskey) - - -@with_logging -def attach_headerlet(filename, hdrlet, logging=False, logmode='a'): - """ - Attach Headerlet as an HeaderletHDU to a science file - - Parameters - ---------- - filename: HDUList or list of HDULists - science file(s) to which the headerlet should be applied - hdrlet: string, Headerlet object or list of strings or Headerlet objects - string representing a headerlet file(s), must match 1-to-1 input filename(s) - logging: boolean - enable file logging - logmode: 'a' or 'w' - """ - if not isinstance(filename, list): - filename = [filename] - if not isinstance(hdrlet, list): - hdrlet = [hdrlet] - if len(hdrlet) != len(filename): - logger.critical("Filenames must have matching headerlets. " - "{0:d} filenames and {1:d} headerlets specified".format(len(filename),len(hdrlet))) - - for fname,h in zip(filename,hdrlet): - print('Attaching {0} as Headerlet extension to {1}'.format(h,fname)) - hlet = Headerlet.fromfile(h, logging=logging, logmode=logmode) - hlet.attach_to_file(fname,archive=True) - - -@with_logging -def delete_headerlet(filename, hdrname=None, hdrext=None, distname=None, - logging=False, logmode='w'): - """ - Deletes HeaderletHDU(s) with same HDRNAME from science files - - Notes - ----- - One of hdrname, hdrext or distname should be given. - If hdrname is given - delete a HeaderletHDU with a name HDRNAME from fobj. - If hdrext is given - delete HeaderletHDU in extension. - If distname is given - deletes all HeaderletHDUs with a specific distortion model from fobj. - Updates wcscorr - - Parameters - ---------- - filename: string, HDUList or list of strings - Filename can be specified as a single filename or HDUList, or - a list of filenames - Each input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - hdrname: string or None - HeaderletHDU primary header keyword HDRNAME - hdrext: int, tuple or None - HeaderletHDU FITS extension number - tuple has the form ('HDRLET', 1) - distname: string or None - distortion model as specified in the DISTNAME keyword - logging: boolean - enable file logging - logmode: 'a' or 'w' - """ - if not isinstance(filename, list): - filename = [filename] - - for f in filename: - print("Deleting Headerlet from ",f) - _delete_single_headerlet(f, hdrname=hdrname, hdrext=hdrext, - distname=distname, logging=logging, logmode='a') - -def _delete_single_headerlet(filename, hdrname=None, hdrext=None, distname=None, - logging=False, logmode='w'): - """ - Deletes HeaderletHDU(s) from a SINGLE science file - - Notes - ----- - One of hdrname, hdrext or distname should be given. - If hdrname is given - delete a HeaderletHDU with a name HDRNAME from fobj. - If hdrext is given - delete HeaderletHDU in extension. - If distname is given - deletes all HeaderletHDUs with a specific distortion model from fobj. - Updates wcscorr - - Parameters - ---------- - filename: string or HDUList - Either a filename or PyFITS HDUList object for the input science file - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - hdrname: string or None - HeaderletHDU primary header keyword HDRNAME - hdrext: int, tuple or None - HeaderletHDU FITS extension number - tuple has the form ('HDRLET', 1) - distname: string or None - distortion model as specified in the DISTNAME keyword - logging: boolean - enable file logging - logmode: 'a' or 'w' - """ - hdrlet_ind = find_headerlet_HDUs(filename, hdrname=hdrname, hdrext=hdrext, - distname=distname, logging=logging, logmode='a') - if len(hdrlet_ind) == 0: - message = """ - No HDUs deleted... No Headerlet HDUs found with ' - hdrname = %s - hdrext = %s - distname = %s - Please review input parameters and try again. - """ % (hdrname, str(hdrext), distname) - logger.critical(message) - return - - fobj, fname, close_fobj = parse_filename(filename, mode='update') - - # delete row(s) from WCSCORR table now... - # - # - if hdrname not in ['', ' ', None, 'INDEF']: - selections = {'hdrname': hdrname} - elif hdrname in ['', ' ', None, 'INDEF'] and hdrext is not None: - selections = {'hdrname': fobj[hdrext].header['hdrname']} - else: - selections = {'distname': distname} - wcscorr.delete_wcscorr_row(fobj['WCSCORR'].data, selections) - - # delete the headerlet extension now - for hdrind in hdrlet_ind: - del fobj[hdrind] - - utils.updateNEXTENDKw(fobj) - # Update file object with changes - fobj.flush() - # close file, if was opened by this function - if close_fobj: - fobj.close() - logger.critical('Deleted headerlet from extension(s) %s ' % str(hdrlet_ind)) - - -def headerlet_summary(filename, columns=None, pad=2, maxwidth=None, - output=None, clobber=True, quiet=False): - """ - - Print a summary of all HeaderletHDUs in a science file to STDOUT, and - optionally to a text file - The summary includes: - HDRLET_ext_number HDRNAME WCSNAME DISTNAME SIPNAME NPOLFILE D2IMFILE - - Parameters - ---------- - filename: string or HDUList - Either a filename or PyFITS HDUList object for the input science file - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - columns: list - List of headerlet PRIMARY header keywords to report in summary - By default (set to None), it will use the default set of keywords - defined as the global list DEFAULT_SUMMARY_COLS - pad: int - Number of padding spaces to put between printed columns - [Default: 2] - maxwidth: int - Maximum column width(not counting padding) for any column in summary - By default (set to None), each column's full width will be used - output: string (optional) - Name of optional output file to record summary. This filename - can contain environment variables. - [Default: None] - clobber: bool - If True, will overwrite any previous output file of same name - quiet: bool - If True, will NOT report info to STDOUT - - """ - if columns is None: - summary_cols = DEFAULT_SUMMARY_COLS - else: - summary_cols = columns - - summary_dict = {} - for kw in summary_cols: - summary_dict[kw] = copy.deepcopy(COLUMN_DICT) - - # Define Extension number column - extnums_col = copy.deepcopy(COLUMN_DICT) - extnums_col['name'] = 'EXTN' - extnums_col['width'] = 6 - - fobj, fname, close_fobj = parse_filename(filename) - # find all HDRLET extensions and combine info into a single summary - for extn in fobj: - if 'extname' in extn.header and extn.header['extname'] == 'HDRLET': - hdrlet_indx = fobj.index_of(('hdrlet', extn.header['extver'])) - try: - ext_cols, ext_summary = extn.headerlet.summary(columns=summary_cols) - extnums_col['vals'].append(hdrlet_indx) - for kw in summary_cols: - for key in COLUMN_DICT: - summary_dict[kw][key].extend(ext_summary[kw][key]) - except: - print("Skipping headerlet") - print("Could not read Headerlet from extension ", hdrlet_indx) - - if close_fobj: - fobj.close() - - # Print out the summary dictionary - print_summary(summary_cols, summary_dict, pad=pad, maxwidth=maxwidth, - idcol=extnums_col, output=output, - clobber=clobber, quiet=quiet) - - -@with_logging -def restore_from_headerlet(filename, hdrname=None, hdrext=None, archive=True, - force=False, logging=False, logmode='w'): - """ - Restores a headerlet as a primary WCS - - Parameters - ---------- - filename: string or HDUList - Either a filename or PyFITS HDUList object for the input science file - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - hdrname: string - HDRNAME keyword of HeaderletHDU - hdrext: int or tuple - Headerlet extension number of tuple ('HDRLET',2) - archive: boolean (default: True) - When the distortion model in the headerlet is the same as the distortion model of - the science file, this flag indicates if the primary WCS should be saved as an alternate - nd a headerlet extension. - When the distortion models do not match this flag indicates if the current primary and - alternate WCSs should be archived as headerlet extensions and alternate WCS. - force: boolean (default:False) - When the distortion models of the headerlet and the primary do not match, and archive - is False, this flag forces an update of the primary. - logging: boolean - enable file logging - logmode: 'a' or 'w' - """ - - hdrlet_ind = find_headerlet_HDUs(filename, hdrext=hdrext, hdrname=hdrname) - - fobj, fname, close_fobj = parse_filename(filename, mode='update') - - if len(hdrlet_ind) > 1: - if hdrext: - kwerr = 'hdrext' - kwval = hdrext - else: - kwerr = 'hdrname' - kwval = hdrname - message = """ - Multiple Headerlet extensions found with the same name. - %d Headerlets with "%s" = %s found in %s. - """% (len(hdrlet_ind), kwerr, kwval, fname) - if close_fobj: - fobj.close() - logger.critical(message) - raise ValueError - - hdrlet_indx = hdrlet_ind[0] - - # read headerlet from HeaderletHDU into memory - if hasattr(fobj[hdrlet_ind[0]], 'hdulist'): - hdrlet = fobj[hdrlet_indx].hdulist - else: - hdrlet = fobj[hdrlet_indx].headerlet # older convention in PyFITS - - # read in the names of the extensions which HeaderletHDU updates - extlist = [] - for ext in hdrlet: - if 'extname' in ext.header and ext.header['extname'] == 'SIPWCS': - # convert from string to tuple or int - sciext = eval(ext.header['sciext']) - extlist.append(fobj[sciext]) - # determine whether distortion is the same - current_distname = hdrlet[0].header['distname'] - same_dist = True - if current_distname != fobj[0].header['distname']: - same_dist = False - if not archive and not force: - if close_fobj: - fobj.close() - message = """ - Headerlet does not have the same distortion as image! - Set "archive"=True to save old distortion model, or - set "force"=True to overwrite old model with new. - """ - logger.critical(message) - raise ValueError - - # check whether primary WCS has been archived already - # Use information from first 'SCI' extension - priwcs_name = None - - scihdr = extlist[0].header - sci_wcsnames = altwcs.wcsnames(scihdr).values() - if 'hdrname' in scihdr: - priwcs_hdrname = scihdr['hdrname'] - else: - if 'wcsname' in scihdr: - priwcs_hdrname = priwcs_name = scihdr['wcsname'] - else: - if 'idctab' in scihdr: - priwcs_hdrname = ''.join(['IDC_', - utils.extract_rootname(scihdr['idctab'], suffix='_idc')]) - else: - priwcs_hdrname = 'UNKNOWN' - priwcs_name = priwcs_hdrname - scihdr['WCSNAME'] = priwcs_name - - priwcs_unique = verify_hdrname_is_unique(fobj, priwcs_hdrname) - if archive and priwcs_unique: - if priwcs_unique: - newhdrlet = create_headerlet(fobj, sciext=scihdr['extname'], - hdrname=priwcs_hdrname) - newhdrlet.attach_to_file(fobj) - # - # copy hdrlet as a primary - # - hdrlet.apply_as_primary(fobj, attach=False, archive=archive, force=force) - - utils.updateNEXTENDKw(fobj) - fobj.flush() - if close_fobj: - fobj.close() - - -@with_logging -def restore_all_with_distname(filename, distname, primary, archive=True, - sciext='SCI', logging=False, logmode='w'): - """ - Restores all HeaderletHDUs with a given distortion model as alternate WCSs and a primary - - Parameters - -------------- - filename: string or HDUList - Either a filename or PyFITS HDUList object for the input science file - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - distname: string - distortion model as represented by a DISTNAME keyword - primary: int or string or None - HeaderletHDU to be restored as primary - if int - a fits extension - if string - HDRNAME - if None - use first HeaderletHDU - archive: boolean (default True) - flag indicating if HeaderletHDUs should be created from the - primary and alternate WCSs in fname before restoring all matching - headerlet extensions - logging: boolean - enable file logging - logmode: 'a' or 'w' - """ - - fobj, fname, close_fobj = parse_filename(filename, mode='update') - - hdrlet_ind = find_headerlet_HDUs(fobj, distname=distname) - if len(hdrlet_ind) == 0: - message = """ - No Headerlet extensions found with - - DISTNAME = %s in %s. - - For a full list of DISTNAMEs found in all headerlet extensions: - - get_headerlet_kw_names(fobj, kw='DISTNAME') - """ % (distname, fname) - if close_fobj: - fobj.close() - logger.critical(message) - raise ValueError - - # Interpret 'primary' parameter input into extension number - if primary is None: - primary_ind = hdrlet_ind[0] - elif isinstance(primary, int): - primary_ind = primary - else: - primary_ind = None - for ind in hdrlet_ind: - if fobj[ind].header['hdrname'] == primary: - primary_ind = ind - break - if primary_ind is None: - if close_fobj: - fobj.close() - message = """ - No Headerlet extensions found with DISTNAME = %s in %s. - """ % (primary, fname) - logger.critical(message) - raise ValueError - # Check to see whether 'primary' HeaderletHDU has same distname as user - # specified on input - - # read headerlet from HeaderletHDU into memory - if hasattr(fobj[primary_ind], 'hdulist'): - primary_hdrlet = fobj[primary_ind].hdulist - else: - primary_hdrlet = fobj[primary_ind].headerlet # older convention in PyFITS - pri_distname = primary_hdrlet[0].header['distname'] - if pri_distname != distname: - if close_fobj: - fobj.close() - message = """ - Headerlet extension to be used as PRIMARY WCS - has "DISTNAME" = %s - "DISTNAME" = %s was specified on input. - All updated WCSs must have same DISTNAME. Quitting...' - """ % (pri_distname, distname) - logger.critical(message) - raise ValueError - - # read in the names of the WCSs which the HeaderletHDUs will update - wnames = altwcs.wcsnames(fobj[sciext, 1].header) - - # work out how many HeaderletHDUs will be used to update the WCSs - numhlt = len(hdrlet_ind) - hdrnames = get_headerlet_kw_names(fobj, kw='wcsname') - - # read in headerletHDUs and update WCS keywords - for hlet in hdrlet_ind: - if fobj[hlet].header['distname'] == distname: - if hasattr(fobj[hlet], 'hdulist'): - hdrlet = fobj[hlet].hdulist - else: - hdrlet = fobj[hlet].headerlet # older convention in PyFITS - if hlet == primary_ind: - hdrlet.apply_as_primary(fobj, attach=False, - archive=archive, force=True) - else: - hdrlet.apply_as_alternate(fobj, attach=False, - wcsname=hdrlet[0].header['wcsname']) - - utils.updateNEXTENDKw(fobj) - fobj.flush() - if close_fobj: - fobj.close() - - -@with_logging -def archive_as_headerlet(filename, hdrname, sciext='SCI', - wcsname=None, wcskey=None, destim=None, - sipname=None, npolfile=None, d2imfile=None, - author=None, descrip=None, history=None, - nmatch=None, catalog=None, - logging=False, logmode='w'): - """ - Save a WCS as a headerlet extension and write it out to a file. - - This function will create a headerlet, attach it as an extension to the - science image (if it has not already been archived) then, optionally, - write out the headerlet to a separate headerlet file. - - Either wcsname or wcskey must be provided, if both are given, they must match a valid WCS - Updates wcscorr if necessary. - - Parameters - ---------- - filename: string or HDUList - Either a filename or PyFITS HDUList object for the input science file - An input filename (str) will be expanded as necessary to interpret - any environmental variables included in the filename. - hdrname: string - Unique name for this headerlet, stored as HDRNAME keyword - sciext: string - name (EXTNAME) of extension that contains WCS to be saved - wcsname: string - name of WCS to be archived, if " ": stop - wcskey: one of A...Z or " " or "PRIMARY" - if " " or "PRIMARY" - archive the primary WCS - destim: string - DESTIM keyword - if NOne, use ROOTNAME or science file name - sipname: string or None (default) - Name of unique file where the polynomial distortion coefficients were - read from. If None, the behavior is: - The code looks for a keyword 'SIPNAME' in the science header - If not found, for HST it defaults to 'IDCTAB' - If there is no SIP model the value is 'NOMODEL' - If there is a SIP model but no SIPNAME, it is set to 'UNKNOWN' - npolfile: string or None (default) - Name of a unique file where the non-polynomial distortion was stored. - If None: - The code looks for 'NPOLFILE' in science header. - If 'NPOLFILE' was not found and there is no npol model, it is set to 'NOMODEL' - If npol model exists, it is set to 'UNKNOWN' - d2imfile: string - Name of a unique file where the detector to image correction was - stored. If None: - The code looks for 'D2IMFILE' in the science header. - If 'D2IMFILE' is not found and there is no d2im correction, - it is set to 'NOMODEL' - If d2im correction exists, but 'D2IMFILE' is missing from science - header, it is set to 'UNKNOWN' - author: string - Name of user who created the headerlet, added as 'AUTHOR' keyword - to headerlet PRIMARY header - descrip: string - Short description of the solution provided by the headerlet - This description will be added as the single 'DESCRIP' keyword - to the headerlet PRIMARY header - history: filename, string or list of strings - Long (possibly multi-line) description of the solution provided - by the headerlet. These comments will be added as 'HISTORY' cards - to the headerlet PRIMARY header - If filename is specified, it will format and attach all text from - that file as the history. - logging: boolean - enable file folling - logmode: 'w' or 'a' - log file open mode - """ - - fobj, fname, close_fobj = parse_filename(filename, mode='update') - - if wcsname in [None, ' ', '', 'INDEF'] and wcskey is None: - message = """ - No valid WCS found found in %s. - A valid value for either "wcsname" or "wcskey" - needs to be specified. - """ % fname - if close_fobj: - fobj.close() - logger.critical(message) - raise ValueError - - # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' - if wcskey == 'PRIMARY': - wcskey = ' ' - wcskey = wcskey.upper() - - numhlt = countExtn(fobj, 'HDRLET') - - if wcsname is None: - scihdr = fobj[sciext, 1].header - wcsname = scihdr['wcsname'+wcskey] - - if hdrname in [None, ' ', '']: - hdrname = wcsname - - # Check to see whether or not a HeaderletHDU with this hdrname already - # exists - hdrnames = get_headerlet_kw_names(fobj) - if hdrname not in hdrnames: - hdrletobj = create_headerlet(fobj, sciext=sciext, - wcsname=wcsname, wcskey=wcskey, - hdrname=hdrname, - sipname=sipname, npolfile=npolfile, - d2imfile=d2imfile, author=author, - descrip=descrip, history=history, - nmatch=nmatch, catalog=catalog, - logging=False) - hlt_hdu = HeaderletHDU.fromheaderlet(hdrletobj) - - if destim is not None: - hlt_hdu[0].header['destim'] = destim - - fobj.append(hlt_hdu) - - utils.updateNEXTENDKw(fobj) - fobj.flush() - else: - message = """ - Headerlet with hdrname %s already archived for WCS %s - No new headerlet appended to %s . - """ % (hdrname, wcsname, fname) - logger.critical(message) - - if close_fobj: - fobj.close() - -#### Headerlet Class definitions -class Headerlet(fits.HDUList): - """ - A Headerlet class - Ref: http://mediawiki.stsci.edu/mediawiki/index.php/Telescopedia:Headerlets - """ - - def __init__(self, hdus=[], file=None, logging=False, logmode='w'): - """ - Parameters - ---------- - hdus : list - List of HDUs to be used to create the headerlet object itself - file: string - File-like object from which HDUs should be read - logging: boolean - enable file logging - logmode: 'w' or 'a' - for internal use only, indicates whether the log file - should be open in attach or write mode - """ - self.logging = logging - init_logging('class Headerlet', level=logging, mode=logmode) - - super(Headerlet, self).__init__(hdus, file=file) - - def init_attrs(self): - self.fname = self.filename() - self.hdrname = self[0].header["HDRNAME"] - self.wcsname = self[0].header["WCSNAME"] - self.upwcsver = self[0].header.get("UPWCSVER", "") - self.pywcsver = self[0].header.get("PYWCSVER", "") - self.destim = self[0].header["DESTIM"] - self.sipname = self[0].header["SIPNAME"] - self.idctab = self[0].header["IDCTAB"] - self.npolfile = self[0].header["NPOLFILE"] - self.d2imfile = self[0].header["D2IMFILE"] - self.distname = self[0].header["DISTNAME"] - - try: - self.vafactor = self[("SIPWCS", 1)].header.get("VAFACTOR", 1) #None instead of 1? - except (IndexError, KeyError): - self.vafactor = self[0].header.get("VAFACTOR", 1) #None instead of 1? - self.author = self[0].header["AUTHOR"] - self.descrip = self[0].header["DESCRIP"] - - self.fit_kws = ['HDRNAME', 'NMATCH', 'CATALOG'] - self.history = '' - # header['HISTORY'] returns an iterable of all HISTORY values - if 'HISTORY' in self[0].header: - for hist in self[0].header['HISTORY']: - self.history += hist + '\n' - - self.d2imerr = 0 - self.axiscorr = 1 - - # Overridden to support the Headerlet logging features - @classmethod - def fromfile(cls, fileobj, mode='readonly', memmap=False, - save_backup=False, logging=False, logmode='w', **kwargs): - hlet = super(cls, cls).fromfile(fileobj, mode, memmap, save_backup, - **kwargs) - if len(hlet) > 0: - hlet.init_attrs() - hlet.logging = logging - init_logging('class Headerlet', level=logging, mode=logmode) - return hlet - - @classmethod - def fromstring(cls, data, **kwargs): - hlet = super(cls, cls).fromstring(data, **kwargs) - hlet.logging = logging - init_logging('class Headerlet', level=logging, mode=logmode) - return hlet - - def apply_as_primary(self, fobj, attach=True, archive=True, force=False): - """ - Copy this headerlet as a primary WCS to fobj - - Parameters - ---------- - fobj: string, HDUList - science file to which the headerlet should be applied - attach: boolean - flag indicating if the headerlet should be attached as a - HeaderletHDU to fobj. If True checks that HDRNAME is unique - in the fobj and stops if not. - archive: boolean (default is True) - When the distortion model in the headerlet is the same as the - distortion model of the science file, this flag indicates if - the primary WCS should be saved as an alternate and a headerlet - extension. - When the distortion models do not match this flag indicates if - the current primary and alternate WCSs should be archived as - headerlet extensions and alternate WCS. - force: boolean (default is False) - When the distortion models of the headerlet and the primary do - not match, and archive is False this flag forces an update - of the primary - """ - self.hverify() - fobj, fname, close_dest = parse_filename(fobj, mode='update') - if not self.verify_dest(fobj, fname): - if close_dest: - fobj.close() - raise ValueError("Destination name does not match headerlet" - "Observation %s cannot be updated with headerlet %s" % (fname, self.hdrname)) - - # Check to see whether the distortion model in the destination - # matches the distortion model in the headerlet being applied - - dname = self.get_destination_model(fobj) - dist_models_equal = self.equal_distmodel(dname) - if not dist_models_equal and not force: - raise ValueError("Distortion models do not match" - " To overwrite the distortion model, set force=True") - - orig_hlt_hdu = None - numhlt = countExtn(fobj, 'HDRLET') - hdrlet_extnames = get_headerlet_kw_names(fobj) - - # Insure that WCSCORR table has been created with all original - # WCS's recorded prior to adding the headerlet WCS - wcscorr.init_wcscorr(fobj) - - - ### start archive - # If archive has been specified - # regardless of whether or not the distortion models are equal... - - numsip = countExtn(self, 'SIPWCS') - sciext_list = [] - alt_hlethdu = [] - for i in range(1, numsip+1): - sipheader = self[('SIPWCS', i)].header - sciext_list.append((sipheader['TG_ENAME'], sipheader['TG_EVER'])) - target_ext = sciext_list[0] - if archive: - if 'wcsname' in fobj[target_ext].header: - hdrname = fobj[target_ext].header['WCSNAME'] - wcsname = hdrname - else: - hdrname = fobj[0].header['ROOTNAME'] + '_orig' - wcsname = None - if hdrname not in hdrlet_extnames: - # - if WCS has not been saved, write out WCS as headerlet extension - # Create a headerlet for the original Primary WCS data in the file, - # create an HDU from the original headerlet, and append it to - # the file - orig_hlt = create_headerlet(fobj, sciext=sciext_list, #[target_ext], - wcsname=wcsname, - hdrname=hdrname, - logging=self.logging) - orig_hlt_hdu = HeaderletHDU.fromheaderlet(orig_hlt) - numhlt += 1 - orig_hlt_hdu.header['EXTVER'] = numhlt - logger.info("Created headerlet %s to be attached to file" % hdrname) - else: - logger.info("Headerlet with name %s is already attached" % hdrname) - - - if dist_models_equal: - # Use the WCSNAME to determine whether or not to archive - # Primary WCS as altwcs - # wcsname = hwcs.wcs.name - scihdr = fobj[target_ext].header - if 'hdrname' in scihdr: - priwcs_name = scihdr['hdrname'] - else: - if 'wcsname' in scihdr: - priwcs_name = scihdr['wcsname'] - else: - if 'idctab' in scihdr: - priwcs_name = ''.join(['IDC_', - utils.extract_rootname(scihdr['idctab'], - suffix='_idc')]) - else: - priwcs_name = 'UNKNOWN' - nextkey = altwcs.next_wcskey(fobj, ext=target_ext) - altwcs.archiveWCS(fobj, ext=sciext_list, wcskey=nextkey, - wcsname=priwcs_name) - else: - - for hname in altwcs.wcsnames(fobj, ext=target_ext).values(): - if hname != 'OPUS' and hname not in hdrlet_extnames: - # get HeaderletHDU for alternate WCS as well - alt_hlet = create_headerlet(fobj, sciext=sciext_list, - wcsname=hname, wcskey=wcskey, - hdrname=hname, sipname=None, - npolfile=None, d2imfile=None, - author=None, descrip=None, history=None, - logging=self.logging) - numhlt += 1 - alt_hlet_hdu = HeaderletHDU.fromheaderlet(alt_hlet) - alt_hlet_hdu.header['EXTVER'] = numhlt - alt_hlethdu.append(alt_hlet_hdu) - hdrlet_extnames.append(hname) - - self._del_dest_WCS_ext(fobj) - for i in range(1, numsip+1): - target_ext = sciext_list[i-1] - self._del_dest_WCS(fobj, target_ext) - sipwcs = HSTWCS(self, ('SIPWCS', i)) - idckw = sipwcs._idc2hdr() - priwcs = sipwcs.to_fits(relax=True) - numnpol = 1 - numd2im = 1 - if sipwcs.wcs.has_cd(): - priwcs[0].header = altwcs.pc2cd(priwcs[0].header) - priwcs[0].header.extend(idckw) - if 'crder1' in sipheader: - for card in sipheader['crder*'].cards: - priwcs[0].header.set(card.keyword, card.value, card.comment, - after='WCSNAME') - # Update WCS with HDRNAME as well - - for kw in ['SIMPLE', 'BITPIX', 'NAXIS', 'EXTEND']: - try: - priwcs[0].header.remove(kw) - except ValueError: - pass - - priwcs[0].header.set('WCSNAME', self[0].header['WCSNAME'], "") - priwcs[0].header.set('WCSAXES', self[('SIPWCS', i)].header['WCSAXES'], "") - priwcs[0].header.set('HDRNAME', self[0].header['HDRNAME'], "") - if sipwcs.det2im1 or sipwcs.det2im2: - try: - d2imerr = self[('SIPWCS', i)].header['D2IMERR*'] - priwcs[0].header.extend(d2imerr) - except KeyError: - pass - try: - priwcs[0].header.append(self[('SIPWCS', i)].header.cards['D2IMEXT']) - except KeyError: - pass - if 'D2IM1.EXTVER' in priwcs[0].header: - priwcs[0].header['D2IM1.EXTVER'] = self[('SIPWCS', i)].header['D2IM1.EXTVER'] - priwcs[('D2IMARR', 1)].header['EXTVER'] = self[('SIPWCS', i)].header['D2IM1.EXTVER'] - if 'D2IM2.EXTVER' in priwcs[0].header: - priwcs[0].header['D2IM2.EXTVER'] = self[('SIPWCS', i)].header['D2IM2.EXTVER'] - priwcs[('D2IMARR', 2)].header['EXTVER'] = self[('SIPWCS', i)].header['D2IM2.EXTVER'] - # D2IM1 will NOT exist for WFPC2 data... - if 'D2IM1.EXTVER' in priwcs[0].header: - # only set number of D2IM extensions to 2 if D2IM1 exists - numd2im = 2 - - if sipwcs.cpdis1 or sipwcs.cpdis2: - try: - cperr = self[('SIPWCS', i)].header['CPERR*'] - priwcs[0].header.extend(cperr) - except KeyError: - pass - try: - priwcs[0].header.append(self[('SIPWCS', i)].header.cards['NPOLEXT']) - except KeyError: - pass - if 'DP1.EXTVER' in priwcs[0].header: - priwcs[0].header['DP1.EXTVER'] = self[('SIPWCS', i)].header['DP1.EXTVER'] - priwcs[('WCSDVARR', 1)].header['EXTVER'] = self[('SIPWCS', i)].header['DP1.EXTVER'] - if 'DP2.EXTVER' in priwcs[0].header: - priwcs[0].header['DP2.EXTVER'] = self[('SIPWCS', i)].header['DP2.EXTVER'] - priwcs[('WCSDVARR', 2)].header['EXTVER'] = self[('SIPWCS', i)].header['DP2.EXTVER'] - numnpol = 2 - - fobj[target_ext].header.extend(priwcs[0].header) - if sipwcs.cpdis1: - whdu = priwcs[('WCSDVARR', (i-1)*numnpol+1)].copy() - whdu.update_ext_version(self[('SIPWCS', i)].header['DP1.EXTVER']) - fobj.append(whdu) - if sipwcs.cpdis2: - whdu = priwcs[('WCSDVARR', i*numnpol)].copy() - whdu.update_ext_version(self[('SIPWCS', i)].header['DP2.EXTVER']) - fobj.append(whdu) - if sipwcs.det2im1: #or sipwcs.det2im2: - whdu = priwcs[('D2IMARR', (i-1)*numd2im+1)].copy() - whdu.update_ext_version(self[('SIPWCS', i)].header['D2IM1.EXTVER']) - fobj.append(whdu) - if sipwcs.det2im2: - whdu = priwcs[('D2IMARR', i*numd2im)].copy() - whdu.update_ext_version(self[('SIPWCS', i)].header['D2IM2.EXTVER']) - fobj.append(whdu) - - update_versions(self[0].header, fobj[0].header) - refs = update_ref_files(self[0].header, fobj[0].header) - # Update the WCSCORR table with new rows from the headerlet's WCSs - wcscorr.update_wcscorr(fobj, self, 'SIPWCS') - - # Append the original headerlet - if archive and orig_hlt_hdu: - fobj.append(orig_hlt_hdu) - # Append any alternate WCS Headerlets - if len(alt_hlethdu) > 0: - for ahdu in alt_hlethdu: - fobj.append(ahdu) - if attach: - # Finally, append an HDU for this headerlet - self.attach_to_file(fobj) - utils.updateNEXTENDKw(fobj) - if close_dest: - fobj.close() - - - def apply_as_alternate(self, fobj, attach=True, wcskey=None, wcsname=None): - """ - Copy this headerlet as an alternate WCS to fobj - - Parameters - ---------- - fobj: string, HDUList - science file/HDUList to which the headerlet should be applied - attach: boolean - flag indicating if the headerlet should be attached as a - HeaderletHDU to fobj. If True checks that HDRNAME is unique - in the fobj and stops if not. - wcskey: string - Key value (A-Z, except O) for this alternate WCS - If None, the next available key will be used - wcsname: string - Name to be assigned to this alternate WCS - WCSNAME is a required keyword in a Headerlet but this allows the - user to change it as desired. - - """ - self.hverify() - fobj, fname, close_dest = parse_filename(fobj, mode='update') - if not self.verify_dest(fobj, fname): - if close_dest: - fobj.close() - raise ValueError("Destination name does not match headerlet" - "Observation %s cannot be updated with headerlet %s" % (fname, self.hdrname)) - - # Verify whether this headerlet has the same distortion - #found in the image being updated - dname = self.get_destination_model(fobj) - dist_models_equal = self.equal_distmodel(dname) - if not dist_models_equal: - raise ValueError("Distortion models do not match \n" - "Headerlet: %s \n" - "Destination file: %s\n" - "attach_to_file() can be used to append this headerlet" %(self.distname, dname)) - - # Insure that WCSCORR table has been created with all original - # WCS's recorded prior to adding the headerlet WCS - wcscorr.init_wcscorr(fobj) - - # determine value of WCSNAME to be used - if wcsname is not None: - wname = wcsname - else: - wname = self[0].header['WCSNAME'] - tg_ename = self[('SIPWCS', 1)].header['TG_ENAME'] - tg_ever = self[('SIPWCS', 1)].header['TG_EVER'] - # determine what alternate WCS this headerlet will be assigned to - if wcskey is None: - wkey = altwcs.next_wcskey(fobj[(tg_ename, tg_ever)].header) - else: - wcskey = wcskey.upper() - available_keys = altwcs.available_wcskeys(fobj[(tg_ename, tg_ever)].header) - if wcskey in available_keys: - wkey = wcskey - else: - mess = "Observation %s already contains alternate WCS with key %s" % (fname, wcskey) - logger.critical(mess) - if close_dest: - fobj.close() - raise ValueError(mess) - numsip = countExtn(self, 'SIPWCS') - for idx in range(1, numsip + 1): - siphdr = self[('SIPWCS', idx)].header - tg_ext = (siphdr['TG_ENAME'], siphdr['TG_EVER']) - - fhdr = fobj[tg_ext].header - hwcs = pywcs.WCS(siphdr, self) - hwcs_header = hwcs.to_header(key=wkey) - _idc2hdr(siphdr, fhdr, towkey=wkey) - if hwcs.wcs.has_cd(): - hwcs_header = altwcs.pc2cd(hwcs_header, key=wkey) - - fhdr.extend(hwcs_header) - fhdr['WCSNAME' + wkey] = wname - # also update with HDRNAME (a non-WCS-standard kw) - for kw in self.fit_kws: - #fhdr.insert(wind, pyfits.Card(kw + wkey, - # self[0].header[kw])) - fhdr.append(fits.Card(kw + wkey, self[0].header[kw])) - # Update the WCSCORR table with new rows from the headerlet's WCSs - wcscorr.update_wcscorr(fobj, self, 'SIPWCS') - - if attach: - self.attach_to_file(fobj) - utils.updateNEXTENDKw(fobj) - - if close_dest: - fobj.close() - - def attach_to_file(self, fobj, archive=False): - """ - Attach Headerlet as an HeaderletHDU to a science file - - Parameters - ---------- - fobj: string, HDUList - science file/HDUList to which the headerlet should be applied - archive: string - Specifies whether or not to update WCSCORR table when attaching - - Notes - ----- - The algorithm used by this method: - - verify headerlet can be applied to this file (based on DESTIM) - - verify that HDRNAME is unique for this file - - attach as HeaderletHDU to fobj - - """ - self.hverify() - fobj, fname, close_dest = parse_filename(fobj, mode='update') - destver = self.verify_dest(fobj, fname) - hdrver = self.verify_hdrname(fobj) - if destver and hdrver: - - numhlt = countExtn(fobj, 'HDRLET') - new_hlt = HeaderletHDU.fromheaderlet(self) - new_hlt.header['extver'] = numhlt + 1 - fobj.append(new_hlt) - utils.updateNEXTENDKw(fobj) - else: - message = "Headerlet %s cannot be attached to" % (self.hdrname) - message += "observation %s" % (fname) - if not destver: - message += " * Image %s keyword ROOTNAME not equal to " % (fname) - message += " DESTIM = '%s'\n" % (self.destim) - if not hdrver: - message += " * Image %s already has headerlet " % (fname) - message += "with HDRNAME='%s'\n" % (self.hdrname) - logger.critical(message) - if close_dest: - fobj.close() - - def info(self, columns=None, pad=2, maxwidth=None, - output=None, clobber=True, quiet=False): - """ - Prints a summary of this headerlet - The summary includes: - HDRNAME WCSNAME DISTNAME SIPNAME NPOLFILE D2IMFILE - - Parameters - ---------- - columns: list - List of headerlet PRIMARY header keywords to report in summary - By default (set to None), it will use the default set of keywords - defined as the global list DEFAULT_SUMMARY_COLS - pad: int - Number of padding spaces to put between printed columns - [Default: 2] - maxwidth: int - Maximum column width(not counting padding) for any column in summary - By default (set to None), each column's full width will be used - output: string (optional) - Name of optional output file to record summary. This filename - can contain environment variables. - [Default: None] - clobber: bool - If True, will overwrite any previous output file of same name - quiet: bool - If True, will NOT report info to STDOUT - - """ - summary_cols, summary_dict = self.summary(columns=columns) - print_summary(summary_cols, summary_dict, pad=pad, maxwidth=maxwidth, - idcol=None, output=output, clobber=clobber, quiet=quiet) - - def summary(self, columns=None): - """ - Returns a summary of this headerlet as a dictionary - - The summary includes a summary of the distortion model as : - HDRNAME WCSNAME DISTNAME SIPNAME NPOLFILE D2IMFILE - - Parameters - ---------- - columns: list - List of headerlet PRIMARY header keywords to report in summary - By default(set to None), it will use the default set of keywords - defined as the global list DEFAULT_SUMMARY_COLS - - Returns - ------- - summary: dict - Dictionary of values for summary - """ - if columns is None: - summary_cols = DEFAULT_SUMMARY_COLS - else: - summary_cols = columns - - # Initialize summary dict based on requested columns - summary = {} - for kw in summary_cols: - summary[kw] = copy.deepcopy(COLUMN_DICT) - - # Populate the summary with headerlet values - for kw in summary_cols: - if kw in self[0].header: - val = self[0].header[kw] - else: - val = 'INDEF' - summary[kw]['vals'].append(val) - summary[kw]['width'].append(max(len(val), len(kw))) - - return summary_cols, summary - - def hverify(self): - """ - Verify the headerlet file is a valid fits file and has - the required Primary Header keywords - """ - self.verify() - header = self[0].header - assert('DESTIM' in header and header['DESTIM'].strip()) - assert('HDRNAME' in header and header['HDRNAME'].strip()) - assert('UPWCSVER' in header) - - def verify_hdrname(self, dest): - """ - Verifies that the headerlet can be applied to the observation - - Reports whether or not this file already has a headerlet with this - HDRNAME. - """ - unique = verify_hdrname_is_unique(dest, self.hdrname) - logger.debug("verify_hdrname() returned %s"%unique) - return unique - - def get_destination_model(self, dest): - """ - Verifies that the headerlet can be applied to the observation - - Determines whether or not the file specifies the same distortion - model/reference files. - """ - destim_opened = False - if not isinstance(dest, fits.HDUList): - destim = fits.open(dest) - destim_opened = True - else: - destim = dest - dname = destim[0].header['DISTNAME'] if 'distname' in destim[0].header \ - else self.build_distname(dest) - if destim_opened: - destim.close() - return dname - - def equal_distmodel(self, dmodel): - if dmodel != self[0].header['DISTNAME']: - if self.logging: - message = """ - Distortion model in headerlet not the same as destination model - Headerlet model : %s - Destination model: %s - """ % (self[0].header['DISTNAME'], dmodel) - logger.critical(message) - return False - else: - return True - - def verify_dest(self, dest, fname): - """ - verifies that the headerlet can be applied to the observation - - DESTIM in the primary header of the headerlet must match ROOTNAME - of the science file (or the name of the destination file) - """ - try: - if not isinstance(dest, fits.HDUList): - droot = fits.getval(dest, 'ROOTNAME') - else: - droot = dest[0].header['ROOTNAME'] - except KeyError: - logger.debug("Keyword 'ROOTNAME' not found in destination file") - droot = dest.split('.fits')[0] - if droot == self.destim: - logger.debug("verify_destim() returned True") - return True - else: - logger.debug("verify_destim() returned False") - logger.critical("Destination name does not match headerlet. " - "Observation %s cannot be updated with headerlet %s" % (fname, self.hdrname)) - return False - - def build_distname(self, dest): - """ - Builds the DISTNAME for dest based on reference file names. - """ - - try: - npolfile = dest[0].header['NPOLFILE'] - except KeyError: - npolfile = None - try: - d2imfile = dest[0].header['D2IMFILE'] - except KeyError: - d2imfile = None - - sipname, idctab = utils.build_sipname(dest, dest, None) - npolname, npolfile = utils.build_npolname(dest, npolfile) - d2imname, d2imfile = utils.build_d2imname(dest, d2imfile) - dname = utils.build_distname(sipname,npolname,d2imname) - return dname - - def tofile(self, fname, destim=None, hdrname=None, clobber=False): - """ - Write this headerlet to a file - - Parameters - ---------- - fname: string - file name - destim: string (optional) - provide a value for DESTIM keyword - hdrname: string (optional) - provide a value for HDRNAME keyword - clobber: boolean - a flag which allows to overwrte an existing file - """ - if not destim or not hdrname: - self.hverify() - self.writeto(fname, clobber=clobber) - - def _del_dest_WCS(self, dest, ext=None): - """ - Delete the WCS of a science file extension - """ - - logger.info("Deleting all WCSs of file %s" % dest.filename()) - numext = len(dest) - - if ext: - fext = dest[ext] - self._remove_d2im(fext) - self._remove_sip(fext) - self._remove_lut(fext) - self._remove_primary_WCS(fext) - self._remove_idc_coeffs(fext) - self._remove_fit_values(fext) - else: - for idx in range(numext): - # Only delete WCS from extensions which may have WCS keywords - if ('XTENSION' in dest[idx].header and - dest[idx].header['XTENSION'] == 'IMAGE'): - self._remove_d2im(dest[idx]) - self._remove_sip(dest[idx]) - self._remove_lut(dest[idx]) - self._remove_primary_WCS(dest[idx]) - self._remove_idc_coeffs(dest[idx]) - self._remove_fit_values(dest[idx]) - self._remove_ref_files(dest[0]) - """ - if not ext: - self._remove_alt_WCS(dest, ext=range(numext)) - else: - self._remove_alt_WCS(dest, ext=ext) - """ - def _del_dest_WCS_ext(self, dest): - numwdvarr = countExtn(dest, 'WCSDVARR') - numd2im = countExtn(dest, 'D2IMARR') - if numwdvarr > 0: - for idx in range(1, numwdvarr + 1): - del dest[('WCSDVARR', idx)] - if numd2im > 0: - for idx in range(1, numd2im + 1): - del dest[('D2IMARR', idx)] - - def _remove_ref_files(self, phdu): - """ - phdu: Primary HDU - """ - refkw = ['IDCTAB', 'NPOLFILE', 'D2IMFILE', 'SIPNAME', 'DISTNAME'] - for kw in refkw: - try: - del phdu.header[kw] - except KeyError: - pass - - def _remove_fit_values(self, ext): - """ - Remove the any existing astrometric fit values from a FITS extension - """ - - logger.debug("Removing astrometric fit values from (%s, %s)"% - (ext.name, ext.ver)) - dkeys = altwcs.wcskeys(ext.header) - if 'O' in dkeys: dkeys.remove('O') # Do not remove wcskey='O' values - for fitkw in ['NMATCH', 'CATALOG']: - for k in dkeys: - fkw = (fitkw+k).rstrip() - if fkw in ext.header: - del ext.header[fkw] - - def _remove_sip(self, ext): - """ - Remove the SIP distortion of a FITS extension - """ - - logger.debug("Removing SIP distortion from (%s, %s)" - % (ext.name, ext.ver)) - for prefix in ['A', 'B', 'AP', 'BP']: - try: - order = ext.header[prefix + '_ORDER'] - del ext.header[prefix + '_ORDER'] - except KeyError: - continue - for i in range(order + 1): - for j in range(order + 1): - key = prefix + '_%d_%d' % (i, j) - try: - del ext.header[key] - except KeyError: - pass - try: - del ext.header['IDCTAB'] - except KeyError: - pass - - def _remove_lut(self, ext): - """ - Remove the Lookup Table distortion of a FITS extension - """ - - logger.debug("Removing LUT distortion from (%s, %s)" - % (ext.name, ext.ver)) - try: - cpdis = ext.header['CPDIS*'] - except KeyError: - return - try: - for c in range(1, len(cpdis) + 1): - del ext.header['DP%s*...' % c] - del ext.header[cpdis.cards[c - 1].keyword] - del ext.header['CPERR*'] - del ext.header['NPOLFILE'] - del ext.header['NPOLEXT'] - except KeyError: - pass - - def _remove_d2im(self, ext): - """ - Remove the Detector to Image correction of a FITS extension - """ - - logger.debug("Removing D2IM correction from (%s, %s)" - % (ext.name, ext.ver)) - try: - d2imdis = ext.header['D2IMDIS*'] - except KeyError: - return - try: - for c in range(1, len(d2imdis) + 1): - del ext.header['D2IM%s*...' % c] - del ext.header[d2imdis.cards[c - 1].keyword] - del ext.header['D2IMERR*'] - del ext.header['D2IMFILE'] - del ext.header['D2IMEXT'] - except KeyError: - pass - - def _remove_alt_WCS(self, dest, ext): - """ - Remove Alternate WCSs of a FITS extension. - A WCS with wcskey 'O' is never deleted. - """ - dkeys = altwcs.wcskeys(dest[('SCI', 1)].header) - for val in ['O', '', ' ']: - if val in dkeys: - dkeys.remove(val) # Never delete WCS with wcskey='O' - - logger.debug("Removing alternate WCSs with keys %s from %s" - % (dkeys, dest.filename())) - for k in dkeys: - altwcs.deleteWCS(dest, ext=ext, wcskey=k) - - def _remove_primary_WCS(self, ext): - """ - Remove the primary WCS of a FITS extension - """ - - logger.debug("Removing Primary WCS from (%s, %s)" - % (ext.name, ext.ver)) - naxis = ext.header['NAXIS'] - for key in basic_wcs: - for i in range(1, naxis + 1): - try: - del ext.header[key + str(i)] - except KeyError: - pass - try: - del ext.header['WCSAXES'] - except KeyError: - pass - try: - del ext.header['WCSNAME'] - except KeyError: - pass - - def _remove_idc_coeffs(self, ext): - """ - Remove IDC coefficients of a FITS extension - """ - - logger.debug("Removing IDC coefficient from (%s, %s)" - % (ext.name, ext.ver)) - coeffs = ['OCX10', 'OCX11', 'OCY10', 'OCY11', 'IDCSCALE'] - for k in coeffs: - try: - del ext.header[k] - except KeyError: - pass - -@with_logging -def _idc2hdr(fromhdr, tohdr, towkey=' '): - """ - Copy the IDC (HST specific) keywords from one header to another - - """ - # save some of the idc coefficients - coeffs = ['OCX10', 'OCX11', 'OCY10', 'OCY11', 'IDCSCALE'] - for c in coeffs: - try: - tohdr[c+towkey] = fromhdr[c] - logger.debug("Copied %s to header") - except KeyError: - continue - - -def get_extname_extver_list(fobj, sciext): - """ - Create a list of (EXTNAME, EXTVER) tuples - - Based on sciext keyword (see docstring for create_headerlet) - walk throughh the file and convert extensions in `sciext` to - valid (EXTNAME, EXTVER) tuples. - """ - extlist = [] - if isinstance(sciext, int): - if sciext == 0: - extname = 'PRIMARY' - extver = 1 - else: - try: - extname = fobj[sciext].header['EXTNAME'] - except KeyError: - extname = "" - try: - extver = fobj[sciext].header['EXTVER'] - except KeyError: - extver = 1 - extlist.append((extname, extver)) - elif isinstance(sciext, str): - if sciext == 'PRIMARY': - extname = "PRIMARY" - extver = 1 - extlist.append((extname, extver)) - else: - for ext in fobj: - try: - extname = ext.header['EXTNAME'] - except KeyError: - continue - if extname.upper() == sciext.upper(): - try: - extver = ext.header['EXTVER'] - except KeyError: - extver = 1 - extlist.append((extname, extver)) - elif isinstance(sciext, list): - if isinstance(sciext[0], int): - for i in sciext: - try: - extname = fobj[i].header['EXTNAME'] - except KeyError: - if i == 0: - extname = "PRIMARY" - extver = 1 - else: - extname = "" - try: - extver = fobj[i].header['EXTVER'] - except KeyError: - extver = 1 - extlist.append((extname, extver)) - else: - extlist = sciext[:] - else: - errstr = "Expected sciext to be a list of FITS extensions with science data\n"+\ - " a valid EXTNAME string, or an integer." - logger.critical(errstr) - raise ValueError - return extlist - - -class HeaderletHDU(fits.hdu.nonstandard.FitsHDU): - """ - A non-standard extension HDU for encapsulating Headerlets in a file. These - HDUs have an extension type of HDRLET and their EXTNAME is derived from the - Headerlet's HDRNAME. - - The data itself is a FITS file embedded within the HDU data. The file name - is derived from the HDRNAME keyword, and should be in the form - `<HDRNAME>_hdr.fits`. If the COMPRESS keyword evaluates to `True`, the tar - file is compressed with gzip compression. - - The structure of this HDU is the same as that proposed for the 'FITS' - extension type proposed here: - http://listmgr.cv.nrao.edu/pipermail/fitsbits/2002-April/thread.html - - The Headerlet contained in the HDU's data can be accessed by the - `headerlet` attribute. - """ - - _extension = 'HDRLET' - - @lazyproperty - def headerlet(self): - """Return the encapsulated headerlet as a Headerlet object. - - This is similar to the hdulist property inherited from the FitsHDU - class, though the hdulist property returns a normal HDUList object. - """ - - return Headerlet(self.hdulist) - - @classmethod - def fromheaderlet(cls, headerlet, compress=False): - """ - Creates a new HeaderletHDU from a given Headerlet object. - - Parameters - ---------- - headerlet : `Headerlet` - A valid Headerlet object. - - compress : bool, optional - Gzip compress the headerlet data. - - Returns - ------- - hlet : `HeaderletHDU` - A `HeaderletHDU` object for the given `Headerlet` that can be - attached as an extension to an existing `HDUList`. - """ - - # TODO: Perhaps check that the given object is in fact a valid - # Headerlet - hlet = cls.fromhdulist(headerlet, compress) - - # Add some more headerlet-specific keywords to the header - phdu = headerlet[0] - - if 'SIPNAME' in phdu.header: - sipname = phdu.header['SIPNAME'] - else: - sipname = phdu.header['WCSNAME'] - - hlet.header['HDRNAME'] = (phdu.header['HDRNAME'], - phdu.header.comments['HDRNAME']) - hlet.header['DATE'] = (phdu.header['DATE'], - phdu.header.comments['DATE']) - hlet.header['SIPNAME'] = (sipname, 'SIP distortion model name') - hlet.header['WCSNAME'] = (phdu.header['WCSNAME'], 'WCS name') - hlet.header['DISTNAME'] = (phdu.header['DISTNAME'], - 'Distortion model name') - hlet.header['NPOLFILE'] = (phdu.header['NPOLFILE'], - phdu.header.comments['NPOLFILE']) - hlet.header['D2IMFILE'] = (phdu.header['D2IMFILE'], - phdu.header.comments['D2IMFILE']) - hlet.header['EXTNAME'] = (cls._extension, 'Extension name') - - return hlet - - -fits.register_hdu(HeaderletHDU) diff --git a/lib/stwcs/wcsutil/hstwcs.py b/lib/stwcs/wcsutil/hstwcs.py deleted file mode 100644 index bfebcfc..0000000 --- a/lib/stwcs/wcsutil/hstwcs.py +++ /dev/null @@ -1,988 +0,0 @@ -from __future__ import absolute_import, division, print_function # confidence high - -import os -from astropy.wcs import WCS -from astropy.io import fits -from stwcs.distortion import models, coeff_converter -import numpy as np -from stsci.tools import fileutil - -from . import altwcs -from . import getinput -from . import mappings -from . import instruments -from .mappings import inst_mappings, ins_spec_kw -from .mappings import basic_wcs - -__docformat__ = 'restructuredtext' - -# -#### Utility functions copied from 'updatewcs.utils' to avoid circular imports -# -def extract_rootname(kwvalue,suffix=""): - """ Returns the rootname from a full reference filename - - If a non-valid value (any of ['','N/A','NONE','INDEF',None]) is input, - simply return a string value of 'NONE' - - This function will also replace any 'suffix' specified with a blank. - """ - # check to see whether a valid kwvalue has been provided as input - if kwvalue.strip() in ['','N/A','NONE','INDEF',None]: - return 'NONE' # no valid value, so return 'NONE' - - # for a valid kwvalue, parse out the rootname - # strip off any environment variable from input filename, if any are given - if '$' in kwvalue: - fullval = kwvalue[kwvalue.find('$')+1:] - else: - fullval = kwvalue - # Extract filename without path from kwvalue - fname = os.path.basename(fullval).strip() - - # Now, rip out just the rootname from the full filename - rootname = fileutil.buildNewRootname(fname) - - # Now, remove any known suffix from rootname - rootname = rootname.replace(suffix,'') - return rootname.strip() - -def build_default_wcsname(idctab): - - idcname = extract_rootname(idctab,suffix='_idc') - wcsname = 'IDC_' + idcname - return wcsname - - -class NoConvergence(Exception): - """ - An error class used to report non-convergence and/or divergence of - numerical methods. It is used to report errors in the iterative solution - used by the :py:meth:`~stwcs.hstwcs.HSTWCS.all_world2pix`\ . - - Attributes - ---------- - - best_solution : numpy.array - Best solution achieved by the method. - - accuracy : float - Accuracy of the :py:attr:`best_solution`\ . - - niter : int - Number of iterations performed by the numerical method to compute - :py:attr:`best_solution`\ . - - divergent : None, numpy.array - Indices of the points in :py:attr:`best_solution` array for which the - solution appears to be divergent. If the solution does not diverge, - `divergent` will be set to `None`. - - failed2converge : None, numpy.array - Indices of the points in :py:attr:`best_solution` array for which the - solution failed to converge within the specified maximum number - of iterations. If there are no non-converging poits (i.e., if - the required accuracy has been achieved for all points) then - `failed2converge` will be set to `None`. - - """ - def __init__(self, *args, **kwargs): - super(NoConvergence, self).__init__(*args) - - self.best_solution = kwargs.pop('best_solution', None) - self.accuracy = kwargs.pop('accuracy', None) - self.niter = kwargs.pop('niter', None) - self.divergent = kwargs.pop('divergent', None) - self.failed2converge= kwargs.pop('failed2converge', None) - - -# -#### HSTWCS Class definition -# -class HSTWCS(WCS): - - def __init__(self, fobj=None, ext=None, minerr=0.0, wcskey=" "): - """ - Create a WCS object based on the instrument. - - In addition to basic WCS keywords this class provides - instrument specific information needed in distortion computation. - - Parameters - ---------- - fobj : str or `astropy.io.fits.HDUList` object or None - file name, e.g j9irw4b1q_flt.fits - fully qualified filename[EXTNAME,EXTNUM], e.g. j9irw4b1q_flt.fits[sci,1] - `astropy.io.fits` file object, e.g fits.open('j9irw4b1q_flt.fits'), in which case the - user is responsible for closing the file object. - ext : int, tuple or None - extension number - if ext is tuple, it must be ("EXTNAME", EXTNUM), e.g. ("SCI", 2) - if ext is None, it is assumed the data is in the primary hdu - minerr : float - minimum value a distortion correction must have in order to be applied. - If CPERRja, CQERRja are smaller than minerr, the corersponding - distortion is not applied. - wcskey : str - A one character A-Z or " " used to retrieve and define an - alternate WCS description. - """ - - self.inst_kw = ins_spec_kw - self.minerr = minerr - self.wcskey = wcskey - - if fobj is not None: - filename, hdr0, ehdr, phdu = getinput.parseSingleInput(f=fobj, - ext=ext) - self.filename = filename - instrument_name = hdr0.get('INSTRUME', 'DEFAULT') - if instrument_name == 'DEFAULT' or instrument_name not in list(inst_mappings.keys()): - #['IRAF/ARTDATA','',' ','N/A']: - self.instrument = 'DEFAULT' - else: - self.instrument = instrument_name - # Set the correct reference frame - refframe = determine_refframe(hdr0) - ehdr['RADESYS'] = refframe - - WCS.__init__(self, ehdr, fobj=phdu, minerr=self.minerr, - key=self.wcskey) - if self.instrument == 'DEFAULT': - self.pc2cd() - # If input was a `astropy.io.fits.HDUList` object, it's the user's - # responsibility to close it, otherwise, it's closed here. - if not isinstance(fobj, fits.HDUList): - phdu.close() - self.setInstrSpecKw(hdr0, ehdr) - self.readIDCCoeffs(ehdr) - extname = ehdr.get('EXTNAME', '') - extnum = ehdr.get('EXTVER', None) - self.extname = (extname, extnum) - else: - # create a default HSTWCS object - self.instrument = 'DEFAULT' - WCS.__init__(self, minerr=self.minerr, key=self.wcskey) - self.pc2cd() - self.setInstrSpecKw() - self.setPscale() - self.setOrient() - - @property - def naxis1(self): - return self._naxis1 - - @naxis1.setter - def naxis1(self, value): - self._naxis1 = value - - @property - def naxis2(self): - return self._naxis2 - - @naxis2.setter - def naxis2(self, value): - self._naxis2 = value - - def readIDCCoeffs(self, header): - """ - Reads in first order IDCTAB coefficients if present in the header - """ - coeffs = ['ocx10', 'ocx11', 'ocy10', 'ocy11', 'idcscale', - 'idcv2ref','idcv3ref', 'idctheta'] - for c in coeffs: - self.__setattr__(c, header.get(c, None)) - - def setInstrSpecKw(self, prim_hdr=None, ext_hdr=None): - """ - Populate the instrument specific attributes: - - These can be in different headers but each instrument class has knowledge - of where to look for them. - - Parameters - ---------- - prim_hdr : `astropy.io.fits.Header` - primary header - ext_hdr : `astropy.io.fits.Header` - extension header - - """ - if self.instrument in list(inst_mappings.keys()): - inst_kl = inst_mappings[self.instrument] - inst_kl = instruments.__dict__[inst_kl] - insobj = inst_kl(prim_hdr, ext_hdr) - - for key in self.inst_kw: - try: - self.__setattr__(key, insobj.__getattribute__(key)) - except AttributeError: - # Some of the instrument's attributes are recorded in the primary header and - # were already set, (e.g. 'DETECTOR'), the code below is a check for that case. - if not self.__getattribute__(key): - raise - else: - pass - - else: - raise KeyError("Unsupported instrument - %s" %self.instrument) - - def setPscale(self): - """ - Calculates the plate scale from the CD matrix - """ - try: - cd11 = self.wcs.cd[0][0] - cd21 = self.wcs.cd[1][0] - self.pscale = np.sqrt(np.power(cd11,2)+np.power(cd21,2)) * 3600. - except AttributeError: - if self.wcs.has_cd(): - print("This file has a PC matrix. You may want to convert it \n \ - to a CD matrix, if reasonable, by running pc2.cd() method.\n \ - The plate scale can be set then by calling setPscale() method.\n") - self.pscale = None - - def setOrient(self): - """ - Computes ORIENTAT from the CD matrix - """ - try: - cd12 = self.wcs.cd[0][1] - cd22 = self.wcs.cd[1][1] - self.orientat = np.rad2deg(np.arctan2(cd12,cd22)) - except AttributeError: - if self.wcs.has_cd(): - print("This file has a PC matrix. You may want to convert it \n \ - to a CD matrix, if reasonable, by running pc2.cd() method.\n \ - The orientation can be set then by calling setOrient() method.\n") - self.pscale = None - - def updatePscale(self, scale): - """ - Updates the CD matrix with a new plate scale - """ - self.wcs.cd = self.wcs.cd/self.pscale*scale - self.setPscale() - - def readModel(self, update=False, header=None): - """ - Reads distortion model from IDCTAB. - - If IDCTAB is not found ('N/A', "", or not found on disk), then - if SIP coefficients and first order IDCTAB coefficients are present - in the header, restore the idcmodel from the header. - If not - assign None to self.idcmodel. - - Parameters - ---------- - header : `astropy.io.fits.Header` - fits extension header - update : bool (False) - if True - record the following IDCTAB quantities as header keywords: - CX10, CX11, CY10, CY11, IDCSCALE, IDCTHETA, IDCXREF, IDCYREF, - IDCV2REF, IDCV3REF - """ - if self.idctab in [None, '', ' ','N/A']: - #Keyword idctab is not present in header - check for sip coefficients - if header is not None and 'IDCSCALE' in header: - self._readModelFromHeader(header) - else: - print("Distortion model is not available: IDCTAB=None\n") - self.idcmodel = None - elif not os.path.exists(fileutil.osfn(self.idctab)): - if header is not None and 'IDCSCALE' in header: - self._readModelFromHeader(header) - else: - print('Distortion model is not available: IDCTAB file %s not found\n' % self.idctab) - self.idcmodel = None - else: - self.readModelFromIDCTAB(header=header, update=update) - - def _readModelFromHeader(self, header): - # Recreate idc model from SIP coefficients and header kw - print('Restoring IDC model from SIP coefficients\n') - model = models.GeometryModel() - cx, cy = coeff_converter.sip2idc(self) - model.cx = cx - model.cy = cy - model.name = "sip" - model.norder = header['A_ORDER'] - - refpix = {} - refpix['XREF'] = header['IDCXREF'] - refpix['YREF'] = header['IDCYREF'] - refpix['PSCALE'] = header['IDCSCALE'] - refpix['V2REF'] = header['IDCV2REF'] - refpix['V3REF'] = header['IDCV3REF'] - refpix['THETA'] = header['IDCTHETA'] - model.refpix = refpix - - self.idcmodel = model - - - def readModelFromIDCTAB(self, header=None, update=False): - """ - Read distortion model from idc table. - - Parameters - ---------- - header : `astropy.io.fits.Header` - fits extension header - update : booln (False) - if True - save teh following as header keywords: - CX10, CX11, CY10, CY11, IDCSCALE, IDCTHETA, IDCXREF, IDCYREF, - IDCV2REF, IDCV3REF - - """ - if self.date_obs == None: - print('date_obs not available\n') - self.idcmodel = None - return - if self.filter1 == None and self.filter2 == None: - 'No filter information available\n' - self.idcmodel = None - return - - self.idcmodel = models.IDCModel(self.idctab, - chip=self.chip, direction='forward', date=self.date_obs, - filter1=self.filter1, filter2=self.filter2, - offtab=self.offtab, binned=self.binned) - - if self.ltv1 != 0. or self.ltv2 != 0.: - self.resetLTV() - - if update: - if header==None: - print('Update header with IDC model kw requested but header was not provided\n.') - else: - self._updatehdr(header) - - def resetLTV(self): - """ - Reset LTV values for polarizer data - - The polarizer field is smaller than the detector field. - The distortion coefficients are defined for the entire - polarizer field and the LTV values are set as with subarray - data. This may also be true for other special filters. - This is a special case when the observation is considered - a subarray in terms of detector field but a full frame in - terms of distortion model. - To avoid shifting the distortion coefficients the LTV values - are reset to 0. - """ - if self.naxis1 == self.idcmodel.refpix['XSIZE'] and \ - self.naxis2 == self.idcmodel.refpix['YSIZE']: - self.ltv1 = 0. - self.ltv2 = 0. - - def wcs2header(self, sip2hdr=False, idc2hdr=True, wcskey=None, relax=False): - """ - Create a `astropy.io.fits.Header` object from WCS keywords. - - If the original header had a CD matrix, return a CD matrix, - otherwise return a PC matrix. - - Parameters - ---------- - sip2hdr : bool - If True - include SIP coefficients - """ - - h = self.to_header(key=wcskey, relax=relax) - if not wcskey: - wcskey = self.wcs.alt - if self.wcs.has_cd(): - h = altwcs.pc2cd(h, key=wcskey) - - if 'wcsname' not in h: - if self.idctab is not None: - wname = build_default_wcsname(self.idctab) - else: - wname = 'DEFAULT' - h['wcsname{0}'.format(wcskey)] = wname - - if idc2hdr: - for card in self._idc2hdr(): - h[card.keyword + wcskey] = (card.value, card.comment) - try: - del h['RESTFRQ'] - del h['RESTWAV'] - except KeyError: pass - - if sip2hdr and self.sip: - for card in self._sip2hdr('a'): - h[card.keyword] = (card.value, card.comment) - for card in self._sip2hdr('b'): - h[card.keyword] = (card.value, card.comment) - - try: - ap = self.sip.ap - except AssertionError: - ap = None - try: - bp = self.sip.bp - except AssertionError: - bp = None - - if ap: - for card in self._sip2hdr('ap'): - h[card.keyword] = (card.value, card.comment) - if bp: - for card in self._sip2hdr('bp'): - h[card.keyword] = (card.value, card.comment) - return h - - def _sip2hdr(self, k): - """ - Get a set of SIP coefficients in the form of an array - and turn them into a `astropy.io.fits.Cardlist`. - k - one of 'a', 'b', 'ap', 'bp' - """ - - cards = [] #fits.CardList() - korder = self.sip.__getattribute__(k+'_order') - cards.append(fits.Card(keyword=k.upper()+'_ORDER', value=korder)) - coeffs = self.sip.__getattribute__(k) - ind = coeffs.nonzero() - for i in range(len(ind[0])): - card = fits.Card(keyword=k.upper()+'_'+str(ind[0][i])+'_'+str(ind[1][i]), - value=coeffs[ind[0][i], ind[1][i]]) - cards.append(card) - return cards - - def _idc2hdr(self): - # save some of the idc coefficients - coeffs = ['ocx10', 'ocx11', 'ocy10', 'ocy11', 'idcscale'] - cards = [] #fits.CardList() - for c in coeffs: - try: - val = self.__getattribute__(c) - except AttributeError: - continue - if val: - cards.append(fits.Card(keyword=c, value=val)) - return cards - - def pc2cd(self): - if not self.wcs.has_pc(): - self.wcs.pc = self.wcs.get_pc() - self.wcs.cd = self.wcs.pc * self.wcs.cdelt[1] - - def all_world2pix(self, *args, **kwargs): - """ - all_world2pix(*arg, accuracy=1.0e-4, maxiter=20, adaptive=False, \ -detect_divergence=True, quiet=False) - - Performs full inverse transformation using iterative solution - on full forward transformation with complete distortion model. - - Parameters - ---------- - accuracy : float, optional (Default = 1.0e-4) - Required accuracy of the solution. Iteration terminates when the - correction to the solution found during the previous iteration - is smaller (in the sence of the L2 norm) than `accuracy`\ . - - maxiter : int, optional (Default = 20) - Maximum number of iterations allowed to reach the solution. - - adaptive : bool, optional (Default = False) - Specifies whether to adaptively select only points that did not - converge to a solution whithin the required accuracy for the - next iteration. Default is recommended for HST as well as most - other instruments. - - .. note:: - The :py:meth:`all_world2pix` uses a vectorized implementation - of the method of consecutive approximations (see `Notes` - section below) in which it iterates over *all* input poits - *regardless* until the required accuracy has been reached for - *all* input points. In some cases it may be possible that - *almost all* points have reached the required accuracy but - there are only a few of input data points left for which - additional iterations may be needed (this depends mostly on the - characteristics of the geometric distortions for a given - instrument). In this situation it may be - advantageous to set `adaptive` = `True`\ in which - case :py:meth:`all_world2pix` will continue iterating *only* over - the points that have not yet converged to the required - accuracy. However, for the HST's ACS/WFC detector, which has - the strongest distortions of all HST instruments, testing has - shown that enabling this option would lead to a about 10-30\% - penalty in computational time (depending on specifics of the - image, geometric distortions, and number of input points to be - converted). Therefore, for HST instruments, - it is recommended to set `adaptive` = `False`\ . The only - danger in getting this setting wrong will be a performance - penalty. - - .. note:: - When `detect_divergence` is `True`\ , :py:meth:`all_world2pix` \ - will automatically switch to the adaptive algorithm once - divergence has been detected. - - detect_divergence : bool, optional (Default = True) - Specifies whether to perform a more detailed analysis of the - convergence to a solution. Normally :py:meth:`all_world2pix` - may not achieve the required accuracy - if either the `tolerance` or `maxiter` arguments are too low. - However, it may happen that for some geometric distortions - the conditions of convergence for the the method of consecutive - approximations used by :py:meth:`all_world2pix` may not be - satisfied, in which case consecutive approximations to the - solution will diverge regardless of the `tolerance` or `maxiter` - settings. - - When `detect_divergence` is `False`\ , these divergent points - will be detected as not having achieved the required accuracy - (without further details). In addition, if `adaptive` is `False` - then the algorithm will not know that the solution (for specific - points) is diverging and will continue iterating and trying to - "improve" diverging solutions. This may result in NaN or Inf - values in the return results (in addition to a performance - penalties). Even when `detect_divergence` is - `False`\ , :py:meth:`all_world2pix`\ , at the end of the iterative - process, will identify invalid results (NaN or Inf) as "diverging" - solutions and will raise :py:class:`NoConvergence` unless - the `quiet` parameter is set to `True`\ . - - When `detect_divergence` is `True`\ , :py:meth:`all_world2pix` will - detect points for - which current correction to the coordinates is larger than - the correction applied during the previous iteration **if** the - requested accuracy **has not yet been achieved**\ . In this case, - if `adaptive` is `True`, these points will be excluded from - further iterations and if `adaptive` - is `False`\ , :py:meth:`all_world2pix` will automatically - switch to the adaptive algorithm. - - .. note:: - When accuracy has been achieved, small increases in - current corrections may be possible due to rounding errors - (when `adaptive` is `False`\ ) and such increases - will be ignored. - - .. note:: - Setting `detect_divergence` to `True` will incurr about 5-10\% - performance penalty (in our testing on ACS/WFC images). - Because the benefits of enabling this feature outweigh - the small performance penalty, it is recommended to set - `detect_divergence` to `True`\ , unless extensive testing - of the distortion models for images from specific - instruments show a good stability of the numerical method - for a wide range of coordinates (even outside the image - itself). - - .. note:: - Indices of the diverging inverse solutions will be reported - in the `divergent` attribute of the - raised :py:class:`NoConvergence` object. - - quiet : bool, optional (Default = False) - Do not throw :py:class:`NoConvergence` exceptions when the method - does not converge to a solution with the required accuracy - within a specified number of maximum iterations set by `maxiter` - parameter. Instead, simply return the found solution. - - Raises - ------ - NoConvergence - The method does not converge to a - solution with the required accuracy within a specified number - of maximum iterations set by the `maxiter` parameter. - - Notes - ----- - Inputs can either be (RA, Dec, origin) or (RADec, origin) where RA - and Dec are 1-D arrays/lists of coordinates and RADec is an - array/list of pairs of coordinates. - - Using the method of consecutive approximations we iterate starting - with the initial approximation, which is computed using the - non-distorion-aware :py:meth:`wcs_world2pix` (or equivalent). - - The :py:meth:`all_world2pix` function uses a vectorized implementation - of the method of consecutive approximations and therefore it is - highly efficient (>30x) when *all* data points that need to be - converted from sky coordinates to image coordinates are passed at - *once*\ . Therefore, it is advisable, whenever possible, to pass - as input a long array of all points that need to be converted - to :py:meth:`all_world2pix` instead of calling :py:meth:`all_world2pix` - for each data point. Also see the note to the `adaptive` parameter. - - Examples - -------- - >>> import stwcs - >>> from astropy.io import fits - >>> hdulist = fits.open('j94f05bgq_flt.fits') - >>> w = stwcs.wcsutil.HSTWCS(hdulist, ext=('sci',1)) - >>> hdulist.close() - - >>> ra, dec = w.all_pix2world([1,2,3],[1,1,1],1); print(ra); print(dec) - [ 5.52645241 5.52649277 5.52653313] - [-72.05171776 -72.05171295 -72.05170814] - >>> radec = w.all_pix2world([[1,1],[2,1],[3,1]],1); print(radec) - [[ 5.52645241 -72.05171776] - [ 5.52649277 -72.05171295] - [ 5.52653313 -72.05170814]] - >>> x, y = w.all_world2pix(ra,dec,1) - >>> print(x) - [ 1.00000233 2.00000232 3.00000233] - >>> print(y) - [ 0.99999997 0.99999997 0.99999998] - >>> xy = w.all_world2pix(radec,1) - >>> print(xy) - [[ 1.00000233 0.99999997] - [ 2.00000232 0.99999997] - [ 3.00000233 0.99999998]] - >>> xy = w.all_world2pix(radec,1, maxiter=3, accuracy=1.0e-10, \ -quiet=False) - NoConvergence: 'HSTWCS.all_world2pix' failed to converge to requested \ -accuracy after 3 iterations. - - >>> - Now try to use some diverging data: - >>> divradec = w.all_pix2world([[1.0,1.0],[10000.0,50000.0],\ -[3.0,1.0]],1); print(divradec) - [[ 5.52645241 -72.05171776] - [ 7.15979392 -70.81405561] - [ 5.52653313 -72.05170814]] - - >>> try: - >>> xy = w.all_world2pix(divradec,1, maxiter=20, accuracy=1.0e-4, \ -adaptive=False, detect_divergence=True, quiet=False) - >>> except stwcs.wcsutil.hstwcs.NoConvergence as e: - >>> print("Indices of diverging points: {}".format(e.divergent)) - >>> print("Indices of poorly converging points: {}".format(e.failed2converge)) - >>> print("Best solution: {}".format(e.best_solution)) - >>> print("Achieved accuracy: {}".format(e.accuracy)) - >>> raise e - Indices of diverging points: - [1] - Indices of poorly converging points: - None - Best solution: - [[ 1.00006219e+00 9.99999288e-01] - [ -1.99440907e+06 1.44308548e+06] - [ 3.00006257e+00 9.99999316e-01]] - Achieved accuracy: - [[ 5.98554253e-05 6.79918148e-07] - [ 8.59514088e+11 6.61703754e+11] - [ 6.02334592e-05 6.59713067e-07]] - Traceback (innermost last): - File "<console>", line 8, in <module> - NoConvergence: 'HSTWCS.all_world2pix' failed to converge to the requested accuracy. - After 5 iterations, the solution is diverging at least for one input point. - - >>> try: - >>> xy = w.all_world2pix(divradec,1, maxiter=20, accuracy=1.0e-4, \ -adaptive=False, detect_divergence=False, quiet=False) - >>> except stwcs.wcsutil.hstwcs.NoConvergence as e: - >>> print("Indices of diverging points: {}".format(e.divergent)) - >>> print("Indices of poorly converging points: {}".format(e.failed2converge)) - >>> print("Best solution: {}".format(e.best_solution)) - >>> print("Achieved accuracy: {}".format(e.accuracy)) - >>> raise e - Indices of diverging points: - [1] - Indices of poorly converging points: - None - Best solution: - [[ 1. 1.] - [ nan nan] - [ 3. 1.]] - Achieved accuracy: - [[ 0. 0.] - [ nan nan] - [ 0. 0.]] - Traceback (innermost last): - File "<console>", line 8, in <module> - NoConvergence: 'HSTWCS.all_world2pix' failed to converge to the requested accuracy. - After 20 iterations, the solution is diverging at least for one input point. - - """ - ##################################################################### - ## PROCESS ARGUMENTS: ## - ##################################################################### - nargs = len(args) - - if nargs == 3: - try: - ra = np.asarray(args[0], dtype=np.float64) - dec = np.asarray(args[1], dtype=np.float64) - #assert( len(ra.shape) == 1 and len(dec.shape) == 1 ) - origin = int(args[2]) - vect1D = True - except: - raise TypeError("When providing three arguments, they must " \ - "be (Ra, Dec, origin) where Ra and Dec are " \ - "Nx1 vectors.") - elif nargs == 2: - try: - rd = np.asarray(args[0], dtype=np.float64) - #assert( rd.shape[1] == 2 ) - ra = rd[:,0] - dec = rd[:,1] - origin = int(args[1]) - vect1D = False - except: - raise TypeError("When providing two arguments, they must " \ - "be (RaDec, origin) where RaDec is a Nx2 array.") - else: - raise TypeError("Expected 2 or 3 arguments, {:d} given." \ - .format(nargs)) - - # process optional arguments: - accuracy = kwargs.pop('accuracy', 1.0e-4) - maxiter = kwargs.pop('maxiter', 20) - adaptive = kwargs.pop('adaptive', False) - detect_divergence = kwargs.pop('detect_divergence', True) - quiet = kwargs.pop('quiet', False) - - ##################################################################### - ## INITIALIZE ITERATIVE PROCESS: ## - ##################################################################### - x0, y0 = self.wcs_world2pix(ra, dec, origin) # <-- initial approximation - # (WCS based only) - - # see if an iterative solution is required (when any of the - # non-CD-matrix corrections are present). If not required - # return initial approximation (x0, y0). - if self.sip is None and \ - self.cpdis1 is None and self.cpdis2 is None and \ - self.det2im1 is None and self.det2im2 is None: - # no non-WCS corrections are detected - return - # initial approximation - if vect1D: - return [x0, y0] - else: - return np.dstack([x0,y0])[0] - - x = x0.copy() # 0-order solution - y = y0.copy() # 0-order solution - - # initial correction: - dx, dy = self.pix2foc(x, y, origin) - # If pix2foc does not apply all the required distortion - # corrections then replace the above line with: - #r0, d0 = self.all_pix2world(x, y, origin) - #dx, dy = self.wcs_world2pix(r0, d0, origin ) - dx -= x0 - dy -= y0 - - # update initial solution: - x -= dx - y -= dy - - # norn (L2) squared of the correction: - dn2prev = dx**2+dy**2 - dn2 = dn2prev - - # prepare for iterative process - iterlist = list(range(1, maxiter+1)) - accuracy2 = accuracy**2 - ind = None - inddiv = None - - npts = x.shape[0] - - # turn off numpy runtime warnings for 'invalid' and 'over': - old_invalid = np.geterr()['invalid'] - old_over = np.geterr()['over'] - np.seterr(invalid = 'ignore', over = 'ignore') - - ##################################################################### - ## NON-ADAPTIVE ITERATIONS: ## - ##################################################################### - if not adaptive: - for k in iterlist: - # check convergence: - if np.max(dn2) < accuracy2: - break - - # find correction to the previous solution: - dx, dy = self.pix2foc(x, y, origin) - # If pix2foc does not apply all the required distortion - # corrections then replace the above line with: - #r0, d0 = self.all_pix2world(x, y, origin) - #dx, dy = self.wcs_world2pix(r0, d0, origin ) - dx -= x0 - dy -= y0 - - # update norn (L2) squared of the correction: - dn2 = dx**2+dy**2 - - # check for divergence (we do this in two stages - # to optimize performance for the most common - # scenario when succesive approximations converge): - if detect_divergence: - ind, = np.where(dn2 <= dn2prev) - if ind.shape[0] < npts: - inddiv, = np.where( - np.logical_and(dn2 > dn2prev, dn2 >= accuracy2)) - if inddiv.shape[0] > 0: - # apply correction only to the converging points: - x[ind] -= dx[ind] - y[ind] -= dy[ind] - # switch to adaptive iterations: - ind, = np.where((dn2 >= accuracy2) & \ - (dn2 <= dn2prev) & np.isfinite(dn2)) - iterlist = iterlist[k:] - adaptive = True - break - #dn2prev[ind] = dn2[ind] - dn2prev = dn2 - - # apply correction: - x -= dx - y -= dy - - ##################################################################### - ## ADAPTIVE ITERATIONS: ## - ##################################################################### - if adaptive: - if ind is None: - ind = np.asarray(list(range(npts)), dtype=np.int64) - - for k in iterlist: - # check convergence: - if ind.shape[0] == 0: - break - - # find correction to the previous solution: - dx[ind], dy[ind] = self.pix2foc(x[ind], y[ind], origin) - # If pix2foc does not apply all the required distortion - # corrections then replace the above line with: - #r0[ind], d0[ind] = self.all_pix2world(x[ind], y[ind], origin) - #dx[ind], dy[ind] = self.wcs_world2pix(r0[ind], d0[ind], origin) - dx[ind] -= x0[ind] - dy[ind] -= y0[ind] - - # update norn (L2) squared of the correction: - dn2 = dx**2+dy**2 - - # update indices of elements that still need correction: - if detect_divergence: - ind, = np.where((dn2 >= accuracy2) & (dn2 <= dn2prev)) - #ind = ind[np.where((dn2[ind] >= accuracy2) & (dn2[ind] <= dn2prev))] - dn2prev[ind] = dn2[ind] - else: - ind, = np.where(dn2 >= accuracy2) - #ind = ind[np.where(dn2[ind] >= accuracy2)] - - # apply correction: - x[ind] -= dx[ind] - y[ind] -= dy[ind] - - ##################################################################### - ## FINAL DETECTION OF INVALID, DIVERGING, ## - ## AND FAILED-TO-CONVERGE POINTS ## - ##################################################################### - # Identify diverging and/or invalid points: - invalid = (((~np.isfinite(y)) | (~np.isfinite(x)) | \ - (~np.isfinite(dn2))) & \ - (np.isfinite(ra)) & (np.isfinite(dec))) - # When detect_divergence==False, dn2prev is outdated (it is the - # norm^2 of the very first correction). Still better than nothing... - inddiv, = np.where(((dn2 >= accuracy2) & (dn2 > dn2prev)) | invalid) - if inddiv.shape[0] == 0: - inddiv = None - # identify points that did not converge within - # 'maxiter' iterations: - if k >= maxiter: - ind,= np.where((dn2 >= accuracy2) & (dn2 <= dn2prev) & (~invalid)) - if ind.shape[0] == 0: - ind = None - else: - ind = None - - ##################################################################### - ## RAISE EXCEPTION IF DIVERGING OR TOO SLOWLY CONVERGING ## - ## DATA POINTS HAVE BEEN DETECTED: ## - ##################################################################### - # raise exception if diverging or too slowly converging - if (ind is not None or inddiv is not None) and not quiet: - if vect1D: - sol = [x, y] - err = [np.abs(dx), np.abs(dy)] - else: - sol = np.dstack( [x, y] )[0] - err = np.dstack( [np.abs(dx), np.abs(dy)] )[0] - - # restore previous numpy error settings: - np.seterr(invalid = old_invalid, over = old_over) - - if inddiv is None: - raise NoConvergence("'HSTWCS.all_world2pix' failed to " \ - "converge to the requested accuracy after {:d} " \ - "iterations.".format(k), best_solution = sol, \ - accuracy = err, niter = k, failed2converge = ind, \ - divergent = None) - else: - raise NoConvergence("'HSTWCS.all_world2pix' failed to " \ - "converge to the requested accuracy.{0:s}" \ - "After {1:d} iterations, the solution is diverging " \ - "at least for one input point." \ - .format(os.linesep, k), best_solution = sol, \ - accuracy = err, niter = k, failed2converge = ind, \ - divergent = inddiv) - - ##################################################################### - ## FINALIZE AND FORMAT DATA FOR RETURN: ## - ##################################################################### - # restore previous numpy error settings: - np.seterr(invalid = old_invalid, over = old_over) - - if vect1D: - return [x, y] - else: - return np.dstack( [x, y] )[0] - - def _updatehdr(self, ext_hdr): - #kw2add : OCX10, OCX11, OCY10, OCY11 - # record the model in the header for use by pydrizzle - ext_hdr['OCX10'] = self.idcmodel.cx[1,0] - ext_hdr['OCX11'] = self.idcmodel.cx[1,1] - ext_hdr['OCY10'] = self.idcmodel.cy[1,0] - ext_hdr['OCY11'] = self.idcmodel.cy[1,1] - ext_hdr['IDCSCALE'] = self.idcmodel.refpix['PSCALE'] - ext_hdr['IDCTHETA'] = self.idcmodel.refpix['THETA'] - ext_hdr['IDCXREF'] = self.idcmodel.refpix['XREF'] - ext_hdr['IDCYREF'] = self.idcmodel.refpix['YREF'] - ext_hdr['IDCV2REF'] = self.idcmodel.refpix['V2REF'] - ext_hdr['IDCV3REF'] = self.idcmodel.refpix['V3REF'] - - def printwcs(self): - """ - Print the basic WCS keywords. - """ - print('WCS Keywords\n') - print('CD_11 CD_12: %r %r' % (self.wcs.cd[0,0], self.wcs.cd[0,1])) - print('CD_21 CD_22: %r %r' % (self.wcs.cd[1,0], self.wcs.cd[1,1])) - print('CRVAL : %r %r' % (self.wcs.crval[0], self.wcs.crval[1])) - print('CRPIX : %r %r' % (self.wcs.crpix[0], self.wcs.crpix[1])) - print('NAXIS : %d %d' % (self.naxis1, self.naxis2)) - print('Plate Scale : %r' % self.pscale) - print('ORIENTAT : %r' % self.orientat) - - -def determine_refframe(phdr): - """ - Determine the reference frame in standard FITS WCS terms. - - Parameters - ---------- - phdr : `astropy.io.fits.Header` - Primary Header of an HST observation - - In HST images the reference frame is recorded in the primary extension as REFFRAME. - Values are "GSC1" which means FK5 or ICRS (for GSC2 observations). - """ - try: - refframe = phdr['REFFRAME'] - except KeyError: - refframe = " " - if refframe == "GSC1": - refframe = "FK5" - return refframe diff --git a/lib/stwcs/wcsutil/instruments.py b/lib/stwcs/wcsutil/instruments.py deleted file mode 100644 index f662513..0000000 --- a/lib/stwcs/wcsutil/instruments.py +++ /dev/null @@ -1,320 +0,0 @@ -from __future__ import absolute_import, division, print_function # confidence high - -from .mappings import ins_spec_kw - -class InstrWCS(object): - """ - A base class for instrument specific keyword definition. - It prvides a default implementation (modeled by ACS) for - all set_kw methods. - """ - def __init__(self, hdr0=None, hdr=None): - self.exthdr = hdr - self.primhdr = hdr0 - self.set_ins_spec_kw() - - def set_ins_spec_kw(self): - """ - This method MUST call all set_kw methods. - There should be a set_kw method for all kw listed in - mappings.ins_spec_kw. TypeError handles the case when - fobj='DEFAULT'. - """ - self.set_idctab() - self.set_offtab() - self.set_date_obs() - self.set_ra_targ() - self.set_dec_targ() - self.set_pav3() - self.set_detector() - self.set_filter1() - self.set_filter2() - self.set_vafactor() - self.set_naxis1() - self.set_naxis2() - self.set_ltv1() - self.set_ltv2() - self.set_binned() - self.set_chip() - self.set_parity() - - def set_idctab(self): - try: - self.idctab = self.primhdr['IDCTAB'] - except (KeyError, TypeError): - self.idctab = None - - def set_offtab(self): - try: - self.offtab = self.primhdr['OFFTAB'] - except (KeyError, TypeError): - self.offtab = None - - def set_date_obs(self): - try: - self.date_obs = self.primhdr['DATE-OBS'] - except (KeyError, TypeError): - self.date_obs = None - - def set_ra_targ(self): - try: - self.ra_targ = self.primhdr['RA-TARG'] - except (KeyError, TypeError): - self.ra_targ = None - - def set_dec_targ(self): - try: - self.dec_targ = self.primhdr['DEC-TARG'] - except (KeyError, TypeError): - self.dec_targ = None - - def set_pav3(self): - try: - self.pav3 = self.primhdr['PA_V3'] - except (KeyError, TypeError): - self.pav3 = None - - def set_filter1(self): - try: - self.filter1 = self.primhdr['FILTER1'] - except (KeyError, TypeError): - self.filter1 = None - - def set_filter2(self): - try: - self.filter2 = self.primhdr['FILTER2'] - except (KeyError, TypeError): - self.filter2 = None - - def set_vafactor(self): - try: - self.vafactor = self.exthdr['VAFACTOR'] - except (KeyError, TypeError): - self.vafactor = 1 - - def set_naxis1(self): - try: - self.naxis1 = self.exthdr['naxis1'] - except (KeyError, TypeError): - try: - self.naxis1 = self.exthdr['npix1'] - except (KeyError, TypeError): - self.naxis1 = None - - def set_naxis2(self): - try: - self.naxis2 = self.exthdr['naxis2'] - except (KeyError, TypeError): - try: - self.naxis2 = self.exthdr['npix2'] - except (KeyError, TypeError): - self.naxis2 = None - - def set_ltv1(self): - try: - self.ltv1 = self.exthdr['LTV1'] - except (KeyError, TypeError): - self.ltv1 = 0.0 - - def set_ltv2(self): - try: - self.ltv2 = self.exthdr['LTV2'] - except (KeyError, TypeError): - self.ltv2 = 0.0 - - def set_binned(self): - try: - self.binned = self.exthdr['BINAXIS1'] - except (KeyError, TypeError): - self.binned = 1 - - def set_chip(self): - try: - self.chip = self.exthdr['CCDCHIP'] - except (KeyError, TypeError): - self.chip = 1 - - def set_parity(self): - self.parity = [[1.0,0.0],[0.0,-1.0]] - - def set_detector(self): - # each instrument has a different kw for detector and it can be - # in a different header, so this is to be handled by the instrument classes - self.detector = 'DEFAULT' - -class ACSWCS(InstrWCS): - """ - get instrument specific kw - """ - - def __init__(self, hdr0, hdr): - self.primhdr = hdr0 - self.exthdr = hdr - InstrWCS.__init__(self,hdr0, hdr) - self.set_ins_spec_kw() - - def set_detector(self): - try: - self.detector = self.primhdr['DETECTOR'] - except KeyError: - print('ERROR: Detector kw not found.\n') - raise - - def set_parity(self): - parity = {'WFC':[[1.0,0.0],[0.0,-1.0]], - 'HRC':[[-1.0,0.0],[0.0,1.0]], - 'SBC':[[-1.0,0.0],[0.0,1.0]]} - - if self.detector not in list(parity.keys()): - parity = InstrWCS.set_parity(self) - else: - self.parity = parity[self.detector] - - -class WFPC2WCS(InstrWCS): - - - def __init__(self, hdr0, hdr): - self.primhdr = hdr0 - self.exthdr = hdr - InstrWCS.__init__(self,hdr0, hdr) - self.set_ins_spec_kw() - - def set_filter1(self): - self.filter1 = self.primhdr.get('FILTNAM1', None) - if self.filter1 == " " or self.filter1 == None: - self.filter1 = 'CLEAR1' - - def set_filter2(self): - self.filter2 = self.primhdr.get('FILTNAM2', None) - if self.filter2 == " " or self.filter2 == None: - self.filter2 = 'CLEAR2' - - - def set_binned(self): - mode = self.primhdr.get('MODE', 1) - if mode == 'FULL': - self.binned = 1 - elif mode == 'AREA': - self.binned = 2 - - def set_chip(self): - self.chip = self.exthdr.get('DETECTOR', 1) - - def set_parity(self): - self.parity = [[-1.0,0.],[0.,1.0]] - - def set_detector(self): - try: - self.detector = self.exthdr['DETECTOR'] - except KeyError: - print('ERROR: Detector kw not found.\n') - raise - - -class WFC3WCS(InstrWCS): - """ - Create a WFC3 detector specific class - """ - - def __init__(self, hdr0, hdr): - self.primhdr = hdr0 - self.exthdr = hdr - InstrWCS.__init__(self,hdr0, hdr) - self.set_ins_spec_kw() - - def set_detector(self): - try: - self.detector = self.primhdr['DETECTOR'] - except KeyError: - print('ERROR: Detector kw not found.\n') - raise - - def set_filter1(self): - self.filter1 = self.primhdr.get('FILTER', None) - if self.filter1 == " " or self.filter1 == None: - self.filter1 = 'CLEAR' - - def set_filter2(self): - #Nicmos idc tables do not allow 2 filters. - self.filter2 = 'CLEAR' - - def set_parity(self): - parity = {'UVIS':[[-1.0,0.0],[0.0,1.0]], - 'IR':[[-1.0,0.0],[0.0,1.0]]} - - if self.detector not in list(parity.keys()): - parity = InstrWCS.set_parity(self) - else: - self.parity = parity[self.detector] - -class NICMOSWCS(InstrWCS): - """ - Create a NICMOS specific class - """ - - def __init__(self, hdr0, hdr): - self.primhdr = hdr0 - self.exthdr = hdr - InstrWCS.__init__(self,hdr0, hdr) - self.set_ins_spec_kw() - - def set_parity(self): - self.parity = [[-1.0,0.],[0.,1.0]] - - def set_filter1(self): - self.filter1 = self.primhdr.get('FILTER', None) - if self.filter1 == " " or self.filter1 == None: - self.filter1 = 'CLEAR' - - def set_filter2(self): - #Nicmos idc tables do not allow 2 filters. - self.filter2 = 'CLEAR' - - def set_chip(self): - self.chip = self.detector - - def set_detector(self): - try: - self.detector = self.primhdr['CAMERA'] - except KeyError: - print('ERROR: Detector kw not found.\n') - raise - -class STISWCS(InstrWCS): - """ - A STIS specific class - """ - - def __init__(self, hdr0, hdr): - self.primhdr = hdr0 - self.exthdr = hdr - InstrWCS.__init__(self,hdr0, hdr) - self.set_ins_spec_kw() - - def set_parity(self): - self.parity = [[-1.0,0.],[0.,1.0]] - - def set_filter1(self): - self.filter1 = self.exthdr.get('OPT_ELEM', None) - if self.filter1 == " " or self.filter1 == None: - self.filter1 = 'CLEAR1' - - def set_filter2(self): - self.filter2 = self.exthdr.get('FILTER', None) - if self.filter2 == " " or self.filter2 == None: - self.filter2 = 'CLEAR2' - - def set_detector(self): - try: - self.detector = self.primhdr['DETECTOR'] - except KeyError: - print('ERROR: Detector kw not found.\n') - raise - - def set_date_obs(self): - try: - self.date_obs = self.exthdr['DATE-OBS'] - except (KeyError, TypeError): - self.date_obs = None - diff --git a/lib/stwcs/wcsutil/mappings.py b/lib/stwcs/wcsutil/mappings.py deleted file mode 100644 index 24038bf..0000000 --- a/lib/stwcs/wcsutil/mappings.py +++ /dev/null @@ -1,29 +0,0 @@ -from __future__ import division # confidence high - -# This dictionary maps an instrument into an instrument class -# The instrument class handles instrument specific keywords - -inst_mappings={'WFPC2': 'WFPC2WCS', - 'ACS': 'ACSWCS', - 'NICMOS': 'NICMOSWCS', - 'STIS': 'STISWCS', - 'WFC3': 'WFC3WCS', - 'DEFAULT': 'InstrWCS' - } - - -# A list of instrument specific keywords -# Every instrument class must have methods which define each of these -# as class attributes. -ins_spec_kw = [ 'idctab', 'offtab', 'date_obs', 'ra_targ', 'dec_targ', 'pav3', \ - 'detector', 'ltv1', 'ltv2', 'parity', 'binned','vafactor', \ - 'chip', 'naxis1', 'naxis2', 'filter1', 'filter2'] - -# A list of keywords defined in the primary header. -# The HSTWCS class sets this as attributes -prim_hdr_kw = ['detector', 'offtab', 'idctab', 'date-obs', - 'pa_v3', 'ra_targ', 'dec_targ'] - -# These are the keywords which are archived before MakeWCS is run -basic_wcs = ['CD1_', 'CD2_', 'CRVAL', 'CTYPE', 'CRPIX', 'CTYPE', 'CDELT', 'CUNIT'] - diff --git a/lib/stwcs/wcsutil/mosaic.py b/lib/stwcs/wcsutil/mosaic.py deleted file mode 100644 index 9d2d0a3..0000000 --- a/lib/stwcs/wcsutil/mosaic.py +++ /dev/null @@ -1,183 +0,0 @@ -from __future__ import division, print_function -import numpy as np -from matplotlib import pyplot as plt -from astropy.io import fits -import string - -from stsci.tools import parseinput, irafglob -from stwcs.distortion import utils -from stwcs import updatewcs, wcsutil -from stwcs.wcsutil import altwcs - -def vmosaic(fnames, outwcs=None, ref_wcs=None, ext=None, extname=None, undistort=True, wkey='V', wname='VirtualMosaic', plot=False, clobber=False): - """ - Create a virtual mosaic using the WCS of the input images. - - Parameters - ---------- - fnames: a string or a list - a string or a list of filenames, or a list of wcsutil.HSTWCS objects - outwcs: an HSTWCS object - if given, represents the output tangent plane - if None, the output WCS is calculated from the input observations. - ref_wcs: an HSTWCS object - if output wcs is not given, this will be used as a reference for the - calculation of the output WCS. If ref_wcs is None and outwcs is None, - then the first observation in th einput list is used as reference. - ext: an int, a tuple or a list - an int - represents a FITS extension, e.g. 0 is the primary HDU - a tuple - uses the notation (extname, extver), e.g. ('sci',1) - Can be a list of integers or tuples representing FITS extensions - extname: string - the value of the EXTNAME keyword for the extensions to be used in the mosaic - undistort: boolean (default: True) - undistort (or not) the output WCS - wkey: string - default: 'V' - one character A-Z to be used to record the virtual mosaic WCS as - an alternate WCS in the headers of the input files. - wname: string - default: 'VirtualMosaic - a string to be used as a WCSNAME value for the alternate WCS representign - the virtual mosaic - plot: boolean - if True and matplotlib is installed will make a plot of the tangent plane - and the location of the input observations. - clobber: boolean - This covers the case when an alternate WCS with the requested key - already exists in the header of the input files. - if clobber is True, it will be overwritten - if False, it will compute the new one but will not write it to the headers. - - Notes - ----- - The algorithm is: - 1. If output WCS is not given it is calculated from the input WCSes. - The first image is used as a reference, if no reference is given. - This represents the virtual mosaic WCS. - 2. For each input observation/chip, an HSTWCS object is created - and its footprint on the sky is calculated (using only the four corners). - 3. For each input observation the footprint is projected on the output - tangent plane and the virtual WCS is recorded in the header. - """ - wcsobjects = readWCS(fnames, ext, extname) - if outwcs != None: - outwcs = outwcs.deepcopy() - else: - if ref_wcs != None: - outwcs = utils.output_wcs(wcsobjects, ref_wcs=ref_wcs, undistort=undistort) - else: - outwcs = utils.output_wcs(wcsobjects, undistort=undistort) - if plot: - outc=np.array([[0.,0], [outwcs._naxis1, 0], - [outwcs._naxis1, outwcs._naxis2], - [0, outwcs._naxis2], [0, 0]]) - plt.plot(outc[:,0], outc[:,1]) - for wobj in wcsobjects: - outcorners = outwcs.wcs_world2pix(wobj.calc_footprint(),1) - if plot: - plt.plot(outcorners[:,0], outcorners[:,1]) - objwcs = outwcs.deepcopy() - objwcs.wcs.crpix = objwcs.wcs.crpix - (outcorners[0]) - updatehdr(wobj.filename, objwcs,wkey=wkey, wcsname=wname, ext=wobj.extname, clobber=clobber) - return outwcs - -def updatehdr(fname, wcsobj, wkey, wcsname, ext=1, clobber=False): - hdr = fits.getheader(fname, ext=ext) - all_keys = list(string.ascii_uppercase) - if wkey.upper() not in all_keys: - raise KeyError("wkey must be one character: A-Z") - if wkey not in altwcs.available_wcskeys(hdr): - if not clobber: - raise ValueError("wkey %s is already in use. Use clobber=True to overwrite it or specify a different key." %wkey) - else: - altwcs.deleteWCS(fname, ext=ext, wcskey='V') - f = fits.open(fname, mode='update') - - hwcs = wcs2header(wcsobj) - wcsnamekey = 'WCSNAME' + wkey - f[ext].header[wcsnamekey] = wcsname - for k in hwcs: - f[ext].header[k[:7]+wkey] = hwcs[k] - - f.close() - -def wcs2header(wcsobj): - - h = wcsobj.to_header() - - if wcsobj.wcs.has_cd(): - altwcs.pc2cd(h) - h['CTYPE1'] = 'RA---TAN' - h['CTYPE2'] = 'DEC--TAN' - norient = np.rad2deg(np.arctan2(h['CD1_2'],h['CD2_2'])) - #okey = 'ORIENT%s' % wkey - okey = 'ORIENT' - h[okey] = norient - return h - -def readWCS(input, exts=None, extname=None): - if isinstance(input, str): - if input[0] == '@': - # input is an @ file - filelist = irafglob.irafglob(input) - else: - try: - filelist, output = parseinput.parseinput(input) - except IOError: raise - elif isinstance(input, list): - if isinstance(input[0], wcsutil.HSTWCS): - # a list of HSTWCS objects - return input - else: - filelist = input[:] - wcso = [] - fomited = [] - # figure out which FITS extension(s) to use - if exts == None and extname == None: - #Assume it's simple FITS and the data is in the primary HDU - for f in filelist: - try: - wcso = wcsutil.HSTWCS(f) - except AttributeError: - fomited.append(f) - continue - elif exts != None and validateExt(exts): - exts = [exts] - for f in filelist: - try: - wcso.extend([wcsutil.HSTWCS(f, ext=e) for e in exts]) - except KeyError: - fomited.append(f) - continue - elif extname != None: - for f in filelist: - fobj = fits.open(f) - for i in range(len(fobj)): - try: - ename = fobj[i].header['EXTNAME'] - except KeyError: - continue - if ename.lower() == extname.lower(): - wcso.append(wcsutil.HSTWCS(f,ext=i)) - else: - continue - fobj.close() - if fomited != []: - print("These files were skipped:") - for f in fomited: - print(f) - return wcso - - -def validateExt(ext): - if not isinstance(ext, int) and not isinstance(ext, tuple) \ - and not isinstance(ext, list): - print("Ext must be integer, tuple, a list of int extension numbers, \ - or a list of tuples representing a fits extension, for example ('sci', 1).") - return False - else: - return True - - - diff --git a/lib/stwcs/wcsutil/wcscorr.py b/lib/stwcs/wcsutil/wcscorr.py deleted file mode 100644 index 3f9b7d5..0000000 --- a/lib/stwcs/wcsutil/wcscorr.py +++ /dev/null @@ -1,668 +0,0 @@ -from __future__ import absolute_import, division, print_function - -import os,copy -import numpy as np -from astropy.io import fits - -import stwcs -from stwcs.wcsutil import altwcs -from stwcs.updatewcs import utils -from stsci.tools import fileutil -from . import convertwcs - -DEFAULT_WCS_KEYS = ['CRVAL1','CRVAL2','CRPIX1','CRPIX2', - 'CD1_1','CD1_2','CD2_1','CD2_2', - 'CTYPE1','CTYPE2','ORIENTAT'] -DEFAULT_PRI_KEYS = ['HDRNAME','SIPNAME','NPOLNAME','D2IMNAME','DESCRIP'] -COL_FITSKW_DICT = {'RMS_RA':'sci.crder1','RMS_DEC':'sci.crder2', - 'NMatch':'sci.nmatch','Catalog':'sci.catalog'} - -### -### WCSEXT table related keyword archive functions -### -def init_wcscorr(input, force=False): - """ - This function will initialize the WCSCORR table if it is not already present, - and look for WCS keywords with a prefix of 'O' as the original OPUS - generated WCS as the initial row for the table or use the current WCS - keywords as initial row if no 'O' prefix keywords are found. - - This function will NOT overwrite any rows already present. - - This function works on all SCI extensions at one time. - """ - # TODO: Create some sort of decorator or (for Python2.5) context for - # opening a FITS file and closing it when done, if necessary - if not isinstance(input, fits.HDUList): - # input must be a filename, so open as `astropy.io.fits.HDUList` object - fimg = fits.open(input, mode='update') - need_to_close = True - else: - fimg = input - need_to_close = False - - # Do not try to generate a WCSCORR table for a simple FITS file - numsci = fileutil.countExtn(fimg) - if len(fimg) == 1 or numsci == 0: - return - - enames = [] - for e in fimg: enames.append(e.name) - if 'WCSCORR' in enames: - if not force: - return - else: - del fimg['wcscorr'] - print('Initializing new WCSCORR table for ',fimg.filename()) - - used_wcskeys = altwcs.wcskeys(fimg['SCI', 1].header) - - # define the primary columns of the WCSEXT table with initial rows for each - # SCI extension for the original OPUS solution - numwcs = len(used_wcskeys) - if numwcs == 0: numwcs = 1 - - # create new table with more rows than needed initially to make it easier to - # add new rows later - wcsext = create_wcscorr(descrip=True,numrows=numsci, padding=(numsci*numwcs) + numsci * 4) - # Assign the correct EXTNAME value to this table extension - wcsext.header['TROWS'] = (numsci * 2, 'Number of updated rows in table') - wcsext.header['EXTNAME'] = ('WCSCORR', 'Table with WCS Update history') - wcsext.header['EXTVER'] = 1 - - # define set of WCS keywords which need to be managed and copied to the table - wcs1 = stwcs.wcsutil.HSTWCS(fimg,ext=('SCI',1)) - idc2header = True - if wcs1.idcscale is None: - idc2header = False - wcs_keywords = list(wcs1.wcs2header(idc2hdr=idc2header).keys()) - - prihdr = fimg[0].header - prihdr_keys = DEFAULT_PRI_KEYS - pri_funcs = {'SIPNAME':stwcs.updatewcs.utils.build_sipname, - 'NPOLNAME':stwcs.updatewcs.utils.build_npolname, - 'D2IMNAME':stwcs.updatewcs.utils.build_d2imname} - - # Now copy original OPUS values into table - for extver in range(1, numsci + 1): - rowind = find_wcscorr_row(wcsext.data, - {'WCS_ID': 'OPUS', 'EXTVER': extver, - 'WCS_key':'O'}) - # There should only EVER be a single row for each extension with OPUS values - rownum = np.where(rowind)[0][0] - #print 'Archiving OPUS WCS in row number ',rownum,' in WCSCORR table for SCI,',extver - - hdr = fimg['SCI', extver].header - # define set of WCS keywords which need to be managed and copied to the table - if used_wcskeys is None: - used_wcskeys = altwcs.wcskeys(hdr) - # Check to see whether or not there is an OPUS alternate WCS present, - # if so, get its values directly, otherwise, archive the PRIMARY WCS - # as the OPUS values in the WCSCORR table - if 'O' not in used_wcskeys: - altwcs.archiveWCS(fimg,('SCI',extver),wcskey='O', wcsname='OPUS') - wkey = 'O' - - wcs = stwcs.wcsutil.HSTWCS(fimg, ext=('SCI', extver), wcskey=wkey) - wcshdr = wcs.wcs2header(idc2hdr=idc2header) - - if wcsext.data.field('CRVAL1')[rownum] != 0: - # If we find values for these keywords already in the table, do not - # overwrite them again - print('WCS keywords already updated...') - break - for key in wcs_keywords: - if key in wcsext.data.names: - wcsext.data.field(key)[rownum] = wcshdr[(key+wkey)[:8]] - # Now get any keywords from PRIMARY header needed for WCS updates - for key in prihdr_keys: - if key in prihdr: - val = prihdr[key] - else: - val = '' - wcsext.data.field(key)[rownum] = val - - # Now that we have archived the OPUS alternate WCS, remove it from the list - # of used_wcskeys - if 'O' in used_wcskeys: - used_wcskeys.remove('O') - - # Now copy remaining alternate WCSs into table - # TODO: Much of this appears to be redundant with update_wcscorr; consider - # merging them... - for uwkey in used_wcskeys: - for extver in range(1, numsci + 1): - hdr = fimg['SCI', extver].header - wcs = stwcs.wcsutil.HSTWCS(fimg, ext=('SCI', extver), - wcskey=uwkey) - wcshdr = wcs.wcs2header() - if 'WCSNAME' + uwkey not in wcshdr: - wcsid = utils.build_default_wcsname(fimg[0].header['idctab']) - else: - wcsid = wcshdr['WCSNAME' + uwkey] - - # identify next empty row - rowind = find_wcscorr_row(wcsext.data, - selections={'wcs_id':['','0.0']}) - rows = np.where(rowind) - if len(rows[0]) > 0: - rownum = np.where(rowind)[0][0] - else: - print('No available rows found for updating. ') - - # Update selection columns for this row with relevant values - wcsext.data.field('WCS_ID')[rownum] = wcsid - wcsext.data.field('EXTVER')[rownum] = extver - wcsext.data.field('WCS_key')[rownum] = uwkey - - # Look for standard WCS keyword values - for key in wcs_keywords: - if key in wcsext.data.names: - wcsext.data.field(key)[rownum] = wcshdr[key + uwkey] - # Now get any keywords from PRIMARY header needed for WCS updates - for key in prihdr_keys: - if key in pri_funcs: - val = pri_funcs[key](fimg)[0] - else: - if key in prihdr: - val = prihdr[key] - else: - val = '' - wcsext.data.field(key)[rownum] = val - - # Append this table to the image FITS file - fimg.append(wcsext) - # force an update now - # set the verify flag to 'warn' so that it will always succeed, but still - # tell the user if PyFITS detects any problems with the file as a whole - utils.updateNEXTENDKw(fimg) - - fimg.flush('warn') - - if need_to_close: - fimg.close() - - -def find_wcscorr_row(wcstab, selections): - """ - Return an array of indices from the table (NOT HDU) 'wcstab' that matches the - selections specified by the user. - - The row selection criteria must be specified as a dictionary with - column name as key and value(s) representing the valid desired row values. - For example, {'wcs_id':'OPUS','extver':2}. - """ - - mask = None - for i in selections: - icol = wcstab.field(i) - if isinstance(icol,np.chararray): icol = icol.rstrip() - selecti = selections[i] - if not isinstance(selecti,list): - if isinstance(selecti,str): - selecti = selecti.rstrip() - bmask = (icol == selecti) - if mask is None: - mask = bmask.copy() - else: - mask = np.logical_and(mask,bmask) - del bmask - else: - for si in selecti: - if isinstance(si,str): - si = si.rstrip() - bmask = (icol == si) - if mask is None: - mask = bmask.copy() - else: - mask = np.logical_or(mask,bmask) - del bmask - - return mask - - -def archive_wcs_file(image, wcs_id=None): - """ - Update WCSCORR table with rows for each SCI extension to record the - newly updated WCS keyword values. - """ - - if not isinstance(image, fits.HDUList): - fimg = fits.open(image, mode='update') - close_image = True - else: - fimg = image - close_image = False - - update_wcscorr(fimg, wcs_id=wcs_id) - - if close_image: - fimg.close() - - -def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): - """ - Update WCSCORR table with a new row or rows for this extension header. It - copies the current set of WCS keywords as a new row of the table based on - keyed WCSs as per Paper I Multiple WCS standard). - - Parameters - ---------- - dest : HDUList - The HDU list whose WCSCORR table should be appended to (the WCSCORR HDU - must already exist) - source : HDUList, optional - The HDU list containing the extension from which to extract the WCS - keywords to add to the WCSCORR table. If None, the dest is also used - as the source. - extname : str, optional - The extension name from which to take new WCS keywords. If there are - multiple extensions with that name, rows are added for each extension - version. - wcs_id : str, optional - The name of the WCS to add, as in the WCSNAMEa keyword. If - unspecified, all the WCSs in the specified extensions are added. - active: bool, optional - When True, indicates that the update should reflect an update of the - active WCS information, not just appending the WCS to the file as a - headerlet - """ - if not isinstance(dest, fits.HDUList): - dest = fits.open(dest,mode='update') - fname = dest.filename() - - if source is None: - source = dest - - if extname == 'PRIMARY': - return - - numext = fileutil.countExtn(source, extname) - if numext == 0: - raise ValueError('No %s extensions found in the source HDU list.' - % extname) - # Initialize the WCSCORR table extension in dest if not already present - init_wcscorr(dest) - try: - dest.index_of('WCSCORR') - except KeyError: - return - - # check to see whether or not this is an up-to-date table - # replace with newly initialized table with current format - old_table = dest['WCSCORR'] - wcscorr_cols = ['WCS_ID','EXTVER', 'SIPNAME', - 'HDRNAME', 'NPOLNAME', 'D2IMNAME'] - - for colname in wcscorr_cols: - if colname not in old_table.data.columns.names: - print("WARNING: Replacing outdated WCSCORR table...") - outdated_table = old_table.copy() - del dest['WCSCORR'] - init_wcscorr(dest) - old_table = dest['WCSCORR'] - break - - # Current implementation assumes the same WCS keywords are in each - # extension version; if this should not be assumed then this can be - # modified... - wcs_keys = altwcs.wcskeys(source[(extname, 1)].header) - wcs_keys = [kk for kk in wcs_keys if kk] - if ' ' not in wcs_keys: wcs_keys.append(' ') # Insure that primary WCS gets used - # apply logic for only updating WCSCORR table with specified keywords - # corresponding to the WCS with WCSNAME=wcs_id - if wcs_id is not None: - wnames = altwcs.wcsnames(source[(extname, 1)].header) - wkeys = [] - for letter in wnames: - if wnames[letter] == wcs_id: - wkeys.append(letter) - if len(wkeys) > 1 and ' ' in wkeys: - wkeys.remove(' ') - wcs_keys = wkeys - wcshdr = stwcs.wcsutil.HSTWCS(source, ext=(extname, 1)).wcs2header() - wcs_keywords = list(wcshdr.keys()) - - if 'O' in wcs_keys: - wcs_keys.remove('O') # 'O' is reserved for original OPUS WCS - - # create new table for hdr and populate it with the newly updated values - new_table = create_wcscorr(descrip=True,numrows=0, padding=len(wcs_keys)*numext) - prihdr = source[0].header - - # Get headerlet related keywords here - sipname, idctab = utils.build_sipname(source, fname, "None") - npolname, npolfile = utils.build_npolname(source, None) - d2imname, d2imfile = utils.build_d2imname(source, None) - if 'hdrname' in prihdr: - hdrname = prihdr['hdrname'] - else: - hdrname = '' - - idx = -1 - for wcs_key in wcs_keys: - for extver in range(1, numext + 1): - extn = (extname, extver) - if 'SIPWCS' in extname and not active: - tab_extver = 0 # Since it has not been added to the SCI header yet - else: - tab_extver = extver - hdr = source[extn].header - if 'WCSNAME'+wcs_key in hdr: - wcsname = hdr['WCSNAME' + wcs_key] - else: - wcsname = utils.build_default_wcsname(hdr['idctab']) - - selection = {'WCS_ID': wcsname, 'EXTVER': tab_extver, - 'SIPNAME':sipname, 'HDRNAME': hdrname, - 'NPOLNAME': npolname, 'D2IMNAME':d2imname - } - - # Ensure that an entry for this WCS is not already in the dest - # table; if so just skip it - rowind = find_wcscorr_row(old_table.data, selection) - if np.any(rowind): - continue - - idx += 1 - - wcs = stwcs.wcsutil.HSTWCS(source, ext=extn, wcskey=wcs_key) - wcshdr = wcs.wcs2header() - - # Update selection column values - for key, val in selection.items(): - if key in new_table.data.names: - new_table.data.field(key)[idx] = val - - for key in wcs_keywords: - if key in new_table.data.names: - new_table.data.field(key)[idx] = wcshdr[key + wcs_key] - - for key in DEFAULT_PRI_KEYS: - if key in new_table.data.names and key in prihdr: - new_table.data.field(key)[idx] = prihdr[key] - # Now look for additional, non-WCS-keyword table column data - for key in COL_FITSKW_DICT: - fitkw = COL_FITSKW_DICT[key] - # Interpret any 'pri.hdrname' or - # 'sci.crpix1' formatted keyword names - if '.' in fitkw: - srchdr,fitkw = fitkw.split('.') - if 'pri' in srchdr.lower(): srchdr = prihdr - else: srchdr = source[extn].header - else: - srchdr = source[extn].header - - if fitkw+wcs_key in srchdr: - new_table.data.field(key)[idx] = srchdr[fitkw+wcs_key] - - - # If idx was never incremented, no rows were added, so there's nothing else - # to do... - if idx < 0: - return - - # Now, we need to merge this into the existing table - rowind = find_wcscorr_row(old_table.data, {'wcs_id':['','0.0']}) - old_nrows = np.where(rowind)[0][0] - new_nrows = new_table.data.shape[0] - - # check to see if there is room for the new row - if (old_nrows + new_nrows) > old_table.data.shape[0]-1: - pad_rows = 2 * new_nrows - # if not, create a new table with 'pad_rows' new empty rows - upd_table = fits.new_table(old_table.columns,header=old_table.header, - nrows=old_table.data.shape[0]+pad_rows) - else: - upd_table = old_table - pad_rows = 0 - # Now, add - for name in old_table.columns.names: - if name in new_table.data.names: - # reset the default values to ones specific to the row definitions - for i in range(pad_rows): - upd_table.data.field(name)[old_nrows+i] = old_table.data.field(name)[-1] - # Now populate with values from new table - upd_table.data.field(name)[old_nrows:old_nrows + new_nrows] = \ - new_table.data.field(name) - upd_table.header['TROWS'] = old_nrows + new_nrows - - # replace old extension with newly updated table extension - dest['WCSCORR'] = upd_table - - -def restore_file_from_wcscorr(image, id='OPUS', wcskey=''): - """ Copies the values of the WCS from the WCSCORR based on ID specified by user. - The default will be to restore the original OPUS-derived values to the Primary WCS. - If wcskey is specified, the WCS with that key will be updated instead. - """ - - if not isinstance(image, fits.HDUList): - fimg = fits.open(image, mode='update') - close_image = True - else: - fimg = image - close_image = False - numsci = fileutil.countExtn(fimg) - wcs_table = fimg['WCSCORR'] - orig_rows = (wcs_table.data.field('WCS_ID') == 'OPUS') - # create an HSTWCS object to figure out what WCS keywords need to be updated - wcsobj = stwcs.wcsutil.HSTWCS(fimg,ext=('sci',1)) - wcshdr = wcsobj.wcs2header() - for extn in range(1,numsci+1): - # find corresponding row from table - ext_rows = (wcs_table.data.field('EXTVER') == extn) - erow = np.where(np.logical_and(ext_rows,orig_rows))[0][0] - for key in wcshdr: - if key in wcs_table.data.names: # insure that keyword is column in table - tkey = key - - if 'orient' in key.lower(): - key = 'ORIENT' - if wcskey == '': - skey = key - else: - skey = key[:7]+wcskey - fimg['sci',extn].header[skey] = wcs_table.data.field(tkey)[erow] - for key in DEFAULT_PRI_KEYS: - if key in wcs_table.data.names: - if wcskey == '': - pkey = key - else: - pkey = key[:7]+wcskey - fimg[0].header[pkey] = wcs_table.data.field(key)[erow] - - utils.updateNEXTENDKw(fimg) - - # close the image now that the update has been completed. - if close_image: - fimg.close() - - -def create_wcscorr(descrip=False, numrows=1, padding=0): - """ - Return the basic definitions for a WCSCORR table. - The dtype definitions for the string columns are set to the maximum allowed so - that all new elements will have the same max size which will be automatically - truncated to this limit upon updating (if needed). - - The table is initialized with rows corresponding to the OPUS solution - for all the 'SCI' extensions. - """ - - trows = numrows + padding - # define initialized arrays as placeholders for column data - # TODO: I'm certain there's an easier way to do this... for example, simply - # define the column names and formats, then create an empty array using - # them as a dtype, then create the new table from that array. - def_float64_zeros = np.array([0.0] * trows, dtype=np.float64) - def_float64_ones = def_float64_zeros + 1.0 - def_float_col = {'format': 'D', 'array': def_float64_zeros.copy()} - def_float1_col = {'format': 'D', 'array':def_float64_ones.copy()} - def_str40_col = {'format': '40A', - 'array': np.array([''] * trows, dtype='S40')} - def_str24_col = {'format': '24A', - 'array': np.array([''] * trows, dtype='S24')} - def_int32_col = {'format': 'J', - 'array': np.array([0]*trows,dtype=np.int32)} - - # If more columns are needed, simply add their definitions to this list - col_names = [('HDRNAME', def_str24_col), ('SIPNAME', def_str24_col), - ('NPOLNAME', def_str24_col), ('D2IMNAME', def_str24_col), - ('CRVAL1', def_float_col), ('CRVAL2', def_float_col), - ('CRPIX1', def_float_col), ('CRPIX2', def_float_col), - ('CD1_1', def_float_col), ('CD1_2', def_float_col), - ('CD2_1', def_float_col), ('CD2_2', def_float_col), - ('CTYPE1', def_str24_col), ('CTYPE2', def_str24_col), - ('ORIENTAT', def_float_col), ('PA_V3', def_float_col), - ('RMS_RA', def_float_col), ('RMS_Dec', def_float_col), - ('NMatch', def_int32_col), ('Catalog', def_str40_col)] - - # Define selector columns - id_col = fits.Column(name='WCS_ID', format='40A', - array=np.array(['OPUS'] * numrows + [''] * padding, - dtype='S24')) - extver_col = fits.Column(name='EXTVER', format='I', - array=np.array(list(range(1, numrows + 1)), - dtype=np.int16)) - wcskey_col = fits.Column(name='WCS_key', format='A', - array=np.array(['O'] * numrows + [''] * padding, - dtype='S')) - # create list of remaining columns to be added to table - col_list = [id_col, extver_col, wcskey_col] # start with selector columns - - for c in col_names: - cdef = copy.deepcopy(c[1]) - col_list.append(fits.Column(name=c[0], format=cdef['format'], - array=cdef['array'])) - - if descrip: - col_list.append( - fits.Column(name='DESCRIP', format='128A', - array=np.array( - ['Original WCS computed by OPUS'] * numrows, - dtype='S128'))) - - # Now create the new table from the column definitions - newtab = fits.new_table(fits.ColDefs(col_list), nrows=trows) - # The fact that setting .name is necessary should be considered a bug in - # pyfits. - # TODO: Make sure this is fixed in pyfits, then remove this - newtab.name = 'WCSCORR' - - return newtab - -def delete_wcscorr_row(wcstab,selections=None,rows=None): - """ - Sets all values in a specified row or set of rows to default values - - This function will essentially erase the specified row from the table - without actually removing the row from the table. This avoids the problems - with trying to resize the number of rows in the table while preserving the - ability to update the table with new rows again without resizing the table. - - Parameters - ---------- - wcstab: object - PyFITS binTable object for WCSCORR table - selections: dict - Dictionary of wcscorr column names and values to be used to select - the row or set of rows to erase - rows: int, list - If specified, will specify what rows from the table to erase regardless - of the value of 'selections' - """ - - if selections is None and rows is None: - print('ERROR: Some row selection information must be provided!') - print(' Either a row numbers or "selections" must be provided.') - raise ValueError - - delete_rows = None - if rows is None: - if 'wcs_id' in selections and selections['wcs_id'] == 'OPUS': - delete_rows = None - print('WARNING: OPUS WCS information can not be deleted from WCSCORR table.') - print(' This row will not be deleted!') - else: - rowind = find_wcscorr_row(wcstab, selections=selections) - delete_rows = np.where(rowind)[0].tolist() - else: - if not isinstance(rows,list): - rows = [rows] - delete_rows = rows - - # Insure that rows pointing to OPUS WCS do not get deleted, even by accident - for row in delete_rows: - if wcstab['WCS_key'][row] == 'O' or wcstab['WCS_ID'][row] == 'OPUS': - del delete_rows[delete_rows.index(row)] - - if delete_rows is None: - return - - # identify next empty row - rowind = find_wcscorr_row(wcstab, selections={'wcs_id':['','0.0']}) - last_blank_row = np.where(rowind)[0][-1] - - # copy values from blank row into user-specified rows - for colname in wcstab.names: - wcstab[colname][delete_rows] = wcstab[colname][last_blank_row] - -def update_wcscorr_column(wcstab, column, values, selections=None, rows=None): - """ - Update the values in 'column' with 'values' for selected rows - - Parameters - ---------- - wcstab: object - PyFITS binTable object for WCSCORR table - column: string - Name of table column with values that need to be updated - values: string, int, or list - Value or set of values to copy into the selected rows for the column - selections: dict - Dictionary of wcscorr column names and values to be used to select - the row or set of rows to erase - rows: int, list - If specified, will specify what rows from the table to erase regardless - of the value of 'selections' - """ - if selections is None and rows is None: - print('ERROR: Some row selection information must be provided!') - print(' Either a row numbers or "selections" must be provided.') - raise ValueError - - if not isinstance(values, list): - values = [values] - - update_rows = None - if rows is None: - if 'wcs_id' in selections and selections['wcs_id'] == 'OPUS': - update_rows = None - print('WARNING: OPUS WCS information can not be deleted from WCSCORR table.') - print(' This row will not be deleted!') - else: - rowind = find_wcscorr_row(wcstab, selections=selections) - update_rows = np.where(rowind)[0].tolist() - else: - if not isinstance(rows,list): - rows = [rows] - update_rows = rows - - if update_rows is None: - return - - # Expand single input value to apply to all selected rows - if len(values) > 1 and len(values) < len(update_rows): - print('ERROR: Number of new values',len(values)) - print(' does not match number of rows',len(update_rows),' to be updated!') - print(' Please enter either 1 value or the same number of values') - print(' as there are rows to be updated.') - print(' Table will not be updated...') - raise ValueError - - if len(values) == 1 and len(values) < len(update_rows): - values = values * len(update_rows) - # copy values from blank row into user-specified rows - for row in update_rows: - wcstab[column][row] = values[row] diff --git a/lib/stwcs/wcsutil/wcsdiff.py b/lib/stwcs/wcsutil/wcsdiff.py deleted file mode 100644 index cfc2d66..0000000 --- a/lib/stwcs/wcsutil/wcsdiff.py +++ /dev/null @@ -1,150 +0,0 @@ -from __future__ import print_function -from astropy import wcs as pywcs -from collections import OrderedDict -from astropy.io import fits -from .headerlet import parse_filename -import numpy as np - -def is_wcs_identical(scifile, file2, sciextlist, fextlist, scikey=" ", - file2key=" ", verbose=False): - """ - Compares the WCS solution of 2 files. - - Parameters - ---------- - scifile: string - name of file1 (usually science file) - IRAF style extension syntax is accepted as well - for example scifile[1] or scifile[sci,1] - file2: string - name of second file (for example headerlet) - sciextlist - list - a list of int or tuple ('SCI', 1), extensions in the first file - fextlist - list - a list of int or tuple ('SIPWCS', 1), extensions in the second file - scikey: string - alternate WCS key in scifile - file2key: string - alternate WCS key in file2 - verbose: boolean - True: print to stdout - - Notes - ----- - These can be 2 science observations or 2 headerlets - or a science observation and a headerlet. The two files - have the same WCS solution if the following are the same: - - - rootname/destim - - primary WCS - - SIP coefficients - - NPOL distortion - - D2IM correction - - """ - result = True - diff = OrderedDict() - fobj, fname, close_file = parse_filename(file2) - sciobj, sciname, close_scifile = parse_filename(scifile) - diff['file_names'] = [scifile, file2] - if get_rootname(scifile) != get_rootname(file2): - #logger.info('Rootnames do not match.') - diff['rootname'] = ("%s: %s", "%s: %s") % (sciname, get_rootname(scifile), file2, get_rootname(file2)) - result = False - for i, j in zip(sciextlist, fextlist): - w1 = pywcs.WCS(sciobj[i].header, sciobj, key=scikey) - w2 = pywcs.WCS(fobj[j].header, fobj, key=file2key) - diff['extension'] = [get_extname_extnum(sciobj[i]), get_extname_extnum(fobj[j])] - if not np.allclose(w1.wcs.crval, w2.wcs.crval, rtol=10**(-7)): - #logger.info('CRVALs do not match') - diff['CRVAL'] = w1.wcs.crval, w2.wcs.crval - result = False - if not np.allclose(w1.wcs.crpix, w2.wcs.crpix, rtol=10**(-7)): - #logger.info('CRPIX do not match') - diff ['CRPIX'] = w1.wcs.crpix, w2.wcs.crpix - result = False - if not np.allclose(w1.wcs.cd, w2.wcs.cd, rtol=10**(-7)): - #logger.info('CDs do not match') - diff ['CD'] = w1.wcs.cd, w2.wcs.cd - result = False - if not (np.array(w1.wcs.ctype) == np.array(w2.wcs.ctype)).all(): - #logger.info('CTYPEs do not match') - diff ['CTYPE'] = w1.wcs.ctype, w2.wcs.ctype - result = False - if w1.sip or w2.sip: - if (w2.sip and not w1.sip) or (w1.sip and not w2.sip): - diff['sip'] = 'one sip extension is missing' - result = False - if not np.allclose(w1.sip.a, w2.sip.a, rtol=10**(-7)): - diff['SIP_A'] = 'SIP_A differ' - result = False - if not np.allclose(w1.sip.b, w2.sip.b, rtol=10**(-7)): - #logger.info('SIP coefficients do not match') - diff ['SIP_B'] = (w1.sip.b, w2.sip.b) - result = False - if w1.cpdis1 or w2.cpdis1: - if w1.cpdis1 and not w2.cpdis1 or w2.cpdis1 and not w1.cpdis1: - diff['CPDIS1'] = "CPDIS1 missing" - result=False - if w1.cpdis2 and not w2.cpdis2 or w2.cpdis2 and not w1.cpdis2: - diff['CPDIS2'] = "CPDIS2 missing" - result = False - if not np.allclose(w1.cpdis1.data, w2.cpdis1.data, rtol=10**(-7)): - #logger.info('NPOL distortions do not match') - diff ['CPDIS1_data'] = (w1.cpdis1.data, w2.cpdis1.data) - result = False - if not np.allclose(w1.cpdis2.data, w2.cpdis2.data, rtol=10**(-7)): - #logger.info('NPOL distortions do not match') - diff ['CPDIS2_data'] = (w1.cpdis2.data, w2.cpdis2.data) - result = False - if w1.det2im1 or w2.det2im1: - if w1.det2im1 and not w2.det2im1 or \ - w2.det2im1 and not w1.det2im1: - diff['DET2IM'] = "Det2im1 missing" - result = False - if not np.allclose(w1.det2im1.data, w2.det2im1.data, rtol=10**(-7)): - #logger.info('Det2Im corrections do not match') - diff ['D2IM1_data'] = (w1.det2im1.data, w2.det2im1.data) - result = False - if w1.det2im2 or w2.det2im2: - if w1.det2im2 and not w2.det2im2 or \ - w2.det2im2 and not w1.det2im2: - diff['DET2IM2'] = "Det2im2 missing" - result = False - if not np.allclose(w1.det2im2.data, w2.det2im2.data, rtol=10**(-7)): - #logger.info('Det2Im corrections do not match') - diff ['D2IM2_data'] = (w1.det2im2.data, w2.det2im2.data) - result = False - if not result and verbose: - for key in diff: - print(key, ":\t", diff[key][0], "\t", diff[key][1]) - if close_file: - fobj.close() - if close_scifile: - sciobj.close() - return result, diff - -def get_rootname(fname): - """ - Returns the value of ROOTNAME or DESTIM - """ - - hdr = fits.getheader(fname) - try: - rootname = hdr['ROOTNAME'] - except KeyError: - try: - rootname = hdr['DESTIM'] - except KeyError: - rootname = fname - return rootname - -def get_extname_extnum(ext): - """ - Return (EXTNAME, EXTNUM) of a FITS extension - """ - extname = "" - extnum=1 - extname = ext.header.get('EXTNAME', extname) - extnum = ext.header.get('EXTVER', extnum) - return (extname, extnum) |