From fa080de7afc95aa1c19a6e6fc0e0708ced2eadc4 Mon Sep 17 00:00:00 2001
From: Joseph Hunkeler <jhunkeler@gmail.com>
Date: Wed, 8 Jul 2015 20:46:52 -0400
Subject: Initial commit

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+.help sensfunc Mar93 noao.onedspec
+.ih
+NAME
+sensfunc -- Determine sensitivity and extinction functions
+.ih
+USAGE
+sensfunc standards sensitivity
+.ih
+PARAMETERS
+.ls standards = "std"
+Input standard star data file created by the task \fBstandard\fR.
+.le
+.ls sensitivity = "sens"
+Output sensitivity function image name or rootname.  Generally each
+aperture results in an independent sensitivity function with the
+aperture number appended to the rootname.  If the parameter \fIignoreaps\fR
+is set, however, the aperture numbers are ignored and a single sensitivity
+function is determined with the output image having the specified name
+with no extension.
+.le
+.ls apertures = ""
+List of apertures to be selected from the input file.  All other apertures
+are ignored.  If no list is specified then all apertures are selected.
+See \fBranges\fR for the syntax.
+.le
+.ls ignoreaps = no
+Ignore aperture numbers and create a single sensitivity function?  Normally
+each aperture produces an independent sensitivity function.  If the
+apertures are ignored then all the observations are combined into
+a single sensitivity function.
+.le
+.ls logfile = "logfile"
+Output log filename for statistical information about the stars used
+and the sensitivity function and extinction function.
+If no filename is given then no file is written.
+.le
+.ls extinction = <no default>
+Input extinction file.  Any extinction determination made will be
+relative to this extinction.  If no file is given then no extinction
+correction is applied and any extinction determination from the
+standard star data will be an absolute determination of the
+extinction.  The default value is redirected to the package parameter
+of the same name.  The extinction file is generally one of the standard
+extinctions in the calibration directory "onedstds$".
+
+If extinction corrected spectra were used as input to \fBstandard\fR
+then it is important that the same extinction file be used here.
+This includes using no extinction file in both tasks.
+.le
+.ls newextinction = "extinct.dat"
+Output revised extinction file.  If the extinction is revised and an
+output filename is given then a revised extinction file is written.  It
+has the same format as the standard extinction files.
+.le
+.ls observatory = ")_.observatory"
+Observatory at which the spectra were obtained if not specified in the
+image header by the keyword OBSERVAT.  The default is a redirection to look
+in the parameters for the parent package for a value.  This is only used
+when graphing flux calibrated data of spectra which do not include the
+airmass in the image header.  The observatory may be one of the
+observatories in the observatory database, "observatory" to select the
+observatory defined by the environment variable "observatory" or the
+parameter \fBobservatory.observatory\fR, or "obspars" to select the current
+parameters set in the \fBobservatory\fR task.  See help for
+\fBobservatory\fR for additional information.
+.le
+.ls function = "spline3"
+Function used to fit the sensitivity data.  The function types are
+"chebyshev" polynomial, "legendre" polynomial, "spline3" cubic spline,
+and "spline1" linear spline.  The default value may be changed interactively.
+.le
+.ls order = 6
+Order of the sensitivity fitting function.  The value corresponds to the
+number of polynomial terms or the number of spline pieces.  The default
+value may be changed interactively.
+.le
+.ls interactive = yes
+Determine the sensitivity function interactively?  If yes the user
+graphically interacts with the data, modifies data and parameters
+affecting the sensitivity function, and determines a residual extinction.
+.le
+.ls graphs = "sr"
+Graphs to be displayed per frame.  From one to four graphs may be displayed
+per frame.  The graph types are selected by single characters and are:
+
+.nf
+a - residual sensitivity vs airmass
+c - composite residual sensitivity and error bars vs wavelength
+e - input extinction and revised extinction vs wavelength
+i - Flux calibrated spectrum vs wavelength
+r - residual sensitivity vs wavelength
+s - sensitivity vs wavelength
+.fi
+
+All other characters including whitespace and commas are ignored.  The order
+and number of graphs determines the positions of the graphs.
+.le
+.ls marks = "plus cross box"
+Symbols used to mark included, deleted, and added data respectively.
+The available mark types are point, box, plus, cross, diamond, hline
+(horizontal line), vline (vertical line), hebar (horizontal error bar),
+vebar (vertical error bar), and circle.
+.le
+.ls colors = "2 1 3 4"
+Colors to use for "lines", "marks", "deleted" data, and "added" data.
+The colors associated with the numbers is graphics device dependent.
+For example in XGTERM they are defined by resources while on other
+devices that don't support colors only one color will appear.
+.le
+.ls cursor = ""
+Graphics cursor input list.  If not specified as a file then standard
+graphics cursor is read.
+.le
+.ls device = "stdgraph"
+Graphics output device.
+.le
+.ls answer
+Query parameter for selecting whether to fit apertures interactively.
+.le
+.ih
+CURSOR COMMANDS
+
+.nf
+?	Print help
+a	Add a point at the cursor position
+c	Toggle use of composite points
+d	Delete point, star, or wavelength nearest the cursor
+e	Toggle residual extinction correction
+f	Fit data with a sensitivity function and overplot
+g	Fit data with a sensitivity function and redraw the graph(s)
+i	Print information about point nearest the cursor
+m	Move point, star, wavelength nearest the cursor to new sensitivity
+o	Reset to original data
+q	Quit and write sensitivity function for current aperture
+r	Redraw graph(s)
+s	Toggle shift of standard stars to eliminate mean deviations
+u	Undelete point, star, or wavelength nearest the cursor
+w	Change weights of point, star, or wavelength nearest the cursor
+
+:flux [min] [max]  Limits for flux calibrated graphs (INDEF for autoscale)
+:function [type]   Function to be fit to sensitivity data:
+			chebyshev - Chebyshev polynomial
+			legendre  - Legendre polynomial
+			spline1   - Linear spline
+			spline3   - Cubic spline
+:graphs [types]    Graphs to be displayed (up to four):
+		a - Residual sensitivity vs airmass
+		c - Composite residuals and error bars vs wavelength
+		e - Extinction (and revised extinction) vs wavelength
+		i - Flux calibrated image vs wavelength
+		l - Log of flux calibrated image vs wavelength
+		r - Residual sensitivity vs wavelength
+		s - Sensitivity vs wavelength
+:images [images]   Images to flux calibrate and plot (up to four)
+:marks marks       Mark types to use for included, delete, and added points:
+			point, box, plus, cross, diamond, hline,
+			vline, hebar, vebar, circle
+:order [order]     Order of function
+:skys [images]     Sky images for flux calibration (up to four)
+:stats [file]      Statistics about stars and sensitivity fit
+:vstats [file]     Verbose statistics about sensitivity fit
+.fi
+.ih
+DESCRIPTION
+Standard star calibration measurements are used to determine the system
+sensitivity as a function of wavelength for each independent aperture.
+If the parameter \fIignoreaps\fR is set then the aperture numbers are
+ignored and a single sensitivity function is determined from all the
+observations.  Using measurements spanning a range of airmass it is
+also possible to derive an adjustment to the standard extinction curve
+or even an absolute determination.  Extinction determination requires
+that the observations span a good range of airmass during photometric
+conditions.  When conditions are poor and standard star observations
+are obtained during periods of variable transparency, the entire
+sensitivity curve may vary by a constant factor, assuming that the
+cause of the variations has no color effect.  This is often the case
+during periods of thin clouds.  In this case the mean sensitivity of
+each observation may be shifted to match the observation of greatest
+sensitivity.  This allows for the possibility of deriving correct
+absolute fluxes if one observation of a standard was obtained during a
+clear period.
+
+The input data is a file of calibration information produced by the
+task \fBstandard\fR.  The data consists of a spectrum identification
+line containing the spectrum image name, the sky image name if beam
+switching, the aperture number, the length of the spectrum, the
+exposure time, airmass, wavelength range, and title.  Following the
+identification line are calibration lines consisting of the central
+bandpass wavelengths, the tabulated fluxes in the bandpasses, the
+bandpass widths, and the observed counts in the bandpasses.  The
+spectrum identification and calibration lines repeat for each standard
+star observation.  The parameter \fIapertures\fR may be used to select
+only specific apertures from the input data.  This parameter is in the
+form of a range list (see help for \fBranges\fR) and if no list is
+given (specified by the null string "") then all apertures are selected.
+
+An input extinction file may also be specified.  Any extinction
+determinations are then residuals to this input extinction table.
+The format of this table is described in \fBlcalib\fR.
+
+The calibration factor at each point is computed as
+
+	(1) C = 2.5 log (O / (T B F)) + A E
+
+where O is the observed counts in a bandpass of an observation,
+T is the exposure time of the observation, B is the bandpass width,
+F is the flux per Angstrom at the bandpass for the standard star,
+A is the airmass of the observation, and E is the extinction
+at the bandpass.  Thus, C is the ratio of the observed count rate per
+Angstrom corrected to some extinction curve to the expected flux
+expressed in magnitudes.  The goal of the task is to fit the observations
+to the relation
+
+	(2) C = S(W) + AE(W)
+
+where W is wavelength, S(W) is the sensitivity function, and E(W) is
+a residual extinction function relative to the extinction used in (1).
+In later discussion we will also refer to the residual sensitivity which
+is defined by
+
+	(3) R = C - S(W) - AE(W)
+
+The sensitivity function S(W) is output as an one dimensional image
+much like the spectra.  The sensitivities are in magnitude units to
+better judge the variations and because the interpolation is smoother
+in the logarithmic space (mags = 2.5 log10[sensitivity]).  There is one
+sensitivity function for each aperture unless the parameter
+\fIignoreaps\fR is set.  In the first case the image names are formed
+from the specified rootname with the aperture number as a four digit
+numerical extension.  In the latter case a single sensitivity function
+is determined from all data, ignoring the aperture numbers, and the
+specified output image is created without an extension.  These images
+are used by \fBcalibrate\fR to correct observations to a relative of
+absolute flux scale.  If no sensitivity function image rootname is
+specified then the sensitivity curves are not output.
+
+If a revised extinction function E(W) has been determined for one or
+more of the apertures then the functions are averaged over all
+apertures, added to the original extinction, and written to the
+specified extinction table.  The format of this table is the same as
+the standard extinction tables and are, thus, interchangeable.  If no
+new extinction filename is specified then no extinction table is
+recorded.
+
+If a log filename is given then statistical information about the
+sensitivity function determinations are recorded.  This includes the
+names of the input standard star observations and the tabulated
+sensitivity, extinction, and error information.
+
+Some points to note are that if no input extinction is given then the
+E in (1) are zero and the E determined in (2) is the absolute extinction.
+If the data are not good enough to determine extinction then using one
+of the standard extinction curves the problem reduces to fitting
+
+	(4) C = S(W)
+
+The sensitivity and extinction functions are determined as fitted
+curves.  The curves are defined by a function type and order.  There
+are four function types and the order specifies either the number of
+terms in the polynomial or the number of pieces in the spline.  The
+order is automatically reduced to the largest
+value which produces a nonsingular result.  In this case the function
+will attempt to pass through every calibration point.  Lower orders
+provide for a smoother representation of the function.  The latter
+is generally more appropriate for a detector.  The initial function
+type and order for the sensitivity function is specified by the
+parameters \fIfunction\fR and \fIorder\fR.
+
+If the \fIinteractive\fR flag is no then the default function and order
+is fit to equation (4) (i.e. there is no residual extinction determination
+or manipulation of the data).  The sensitivity functions are output
+if an image rootname is given and the log information is output if a
+log filename is given.
+
+When the sensitivity is determined interactively a query is given for
+each aperture.  The responses "no" and "yes" select fitting the sensitivity
+interactively or not for the specified aperture.  The responses "NO" and
+"YES" apply to all apertures and no further queries will be given.
+When interactive fitting is selected the data are graphed
+on the specified graphics device and input is through the specified
+cursor list.  The graphics output consists of from one to four graphs.
+The user selects how many and which types of graphs to display.  The
+graph types and their single character code used to select them are:
+
+.nf
+   a - residual sensitivity vs airmass
+   c - composite residual sensitivity and error bars vs wavelength
+   e - input extinction and revised extinction vs wavelength
+   i - Flux calibrated spectrum vs wavelength
+   r - residual sensitivity vs wavelength
+   s - sensitivity vs wavelength
+.fi
+
+The initial graphs are selected with the parameter \fBgraphs\fR and changed
+interactively with the colon command ':graphs \fItypes\fR'.  The ability
+to view a variety of graphs allows evaluating the effects of the
+sensitivity curve and extinction in various ways.  The flux calibrated
+spectrum graph uses the current sensitivity function and checks for
+possible wiggles in the sensitivity curve which affect the shape of the
+continuum.  The choice of graphs also allows the
+user to trade off plotting speed and resolution against the amount of
+information available simultaneously.  Thus, with some graphics devices
+or over a slow line one can reduce the number of graphs for greater speed
+while on very fast devices with large screens one can look at more
+data.  The parameter \fImarks\fR and the associated colon command
+':marks \fItypes\fR' also let the user define the symbols used to mark
+included, deleted, and added data points.
+
+The list of interactive commands in given in the section on CURSOR COMMANDS.
+The commands include deleting, undeleting, adding, moving, and identifying
+individual data points, whole stars, or all points at the same wavelength.
+Some other commands include 'c' to create composite points by averaging
+all points at the same wavelength (this requires exact overlap in the
+bandpasses) which then replace the individual data points in the fit.
+This is different than the composite point graph which displays the
+residual in the mean sensitivity
+and error \fIin the mean\fR but uses the input data in the fitting.
+The 's' command shifts the data so that the mean sensitivity of each
+star is the same as the star with the greatest mean sensitivity.
+This compensates for variable grey extinction due to clouds.  Note
+that delete points are excluded from the shift calculation and a
+deleted star will not be used as the star of greatest sensitivity.
+Another useful command is 'o' to recover the original data.  This cancels
+all changes made due to shifting, extinction corrections, deleting points,
+creating composite points, etc.
+
+The 'e' command attempts to compute a residual extinction by finding
+correlations between the sensitivity points at different airmass.
+Note that this is not iterative so that repeating this after having
+added an extinction correction simply redetermines the correction.
+At each wavelength or wavelength regions having multiple observations at
+different airmass a slope with airmass is determined.  This slope is
+the residual extinction at that wavelength.  A plot of the residual
+extinctions at each wavelength is made using the ICFIT procedure.
+The user may then examine and fit a curve through the residual extinction
+estimates as a function of wavelength (see \fBicfit\fR for a description
+of the commands).  The user must decide how much wavelength dependence
+is derivable from the data.  In many cases only a constant fit
+to a "gray extinction" or possibly a linear fit is realistic.
+The fitting is exited by the key 'q'.
+
+To help evaluate how important the residual extinction determination
+is a t-statistic significance is computed.  This statistic is defined by
+
+	(5) t = sqrt (r**2 * (N - 2) / (1 - r**2))
+
+where the correlation coefficient
+
+	(6) r = RMS with correction / RMS without correction
+
+is the fractional improvement in the RMS due to the added extinction
+correction and N is the number of wavelength points.  For large
+N this approaches a gaussian sigma but a more precise significance
+requires the t-distribution for N-2 degrees of freedom.  Basically this
+asks, was the improvement in the RMS significantly more than would
+occur with random errors?  A value greater than 3 is good while
+a value less than 1 is not significant.  The user may then accept the
+revised extinction and apply it to the data.
+
+Note that when there are multiple apertures used each aperture has an
+independent system sensitivity but the residual extinction is the same.
+Therefore, the residual extinctions from each aperture are averaged at
+the end.  If one determines a new extinction then one may replace the
+original input extinction by the new extinction and rederive the
+sensitivity.
+.ih
+EXAMPLES
+1.  The following command generates sensitivity spectra
+
+	cl> sensfunc std sens
+
+This command uses the data from the \fBstandard\fR output
+file "std" to create sensitivity functions with rootname "sens".
+If not interactive the task will produce the output with some
+progress messages being printed.  If it is interactive the graphics
+device will be used to display the data and the fit and user can
+change the function and order of the fit, delete bad points, shift
+data to correct for clouds or bandpass errors, and possibly determine
+a revised extinction function.  The statistics of the
+sensitivity determination are written to the logfile ("logfile" by
+default).
+
+2. The following examples illustrate the colon command syntax.  Generally
+if no argument is given the current value is displayed.  For the statistics
+commands an optional output file may be given to record the information.
+
+.nf
+:flux 1e-12 INDEF    Set lower limit for flux plots
+:flux INDEF INDEF    Restore autoscaling in flux plots
+:func spline3	     Select cubic spline function
+:g srae		     Graph sensitivity, residuals, airmass,
+		     and extinction
+:g sii		     Graph sensitivity and two images
+:i n1.0004 n1.0008   Set first two images to graph (the defaults
+		     are taken from the standard star list)
+:skys n1.0005	     Subtract this sky image from first image
+		     for flux calibrated spectrum
+:m plus		     Change the mark type for included points and
+		     don't change the deleted or added point mark type
+:stats		     Print statistics to terminal
+:vstats stdstats     Print verbose statistics to file
+.fi
+.ih
+REVISIONS
+.ls SENSFUNC V2.10.3+
+Deleted points and stars are now ignored from the grey shift calculation.
+.le
+.ls SENSFUNC V2.10.3
+A color parameter was added for graphics terminals supporting color.
+.le
+.ls SENSFUNC V2.10
+The latitude parameter has been replaced by the observatory parameter.
+The 'i' flux calibrated graph type now shows flux in linear scaling 
+while the new graph type 'l' shows flux in log scaling.  A new colon
+command allows fixing the flux limits for the flux calibrated graphs.
+.le
+.ls SENSFUNC V2.8
+This task has been completely rewritten from that of versions 2.5 and
+earlier.
+
+.nf
+1. The input standard data format is different.
+2. Extinction corrections beyond a grey term are now supported.
+3. Weighting by the counts is not supported.
+4. Tabular input is not supported.
+5. The data which can be displayed is greatly improved.
+6. The fitting options have been greatly enhanced.
+7. The fitting function types available have been extended.
+8. One or more flux calibrated images may be displayed using the
+   current sensitivity function.
+9. Additional flexibility is provided for treating apertures.
+.fi
+.le
+.ih
+BUGS
+If the flux points do not span the wavelength range, set by the
+standard star observations, then the fitting may fail at some maximum
+order.  When it fails there is no message but the highest order which
+can be successfully fit is used.  To work around this one can either
+add fake points, truncate the wavelength range in the first line of each
+tabulated object in the file produced by \fBstandard\fR, or exclude the
+part of the image data which cannot be uncalibrated (using
+\fBscopy\fR or \fBdispcor\fR).
+.ih
+SEE ALSO
+standard, lcalib, calibrate, observatory, icfit, ranges, scopy, dispcor
+.endhelp
-- 
cgit 

