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Diffstat (limited to 'pkg/images/imfit/doc')
| -rw-r--r-- | pkg/images/imfit/doc/fit1d.hlp | 177 | ||||
| -rw-r--r-- | pkg/images/imfit/doc/imsurfit.hlp | 226 | ||||
| -rw-r--r-- | pkg/images/imfit/doc/lineclean.hlp | 129 |
3 files changed, 532 insertions, 0 deletions
diff --git a/pkg/images/imfit/doc/fit1d.hlp b/pkg/images/imfit/doc/fit1d.hlp new file mode 100644 index 00000000..5b49f45f --- /dev/null +++ b/pkg/images/imfit/doc/fit1d.hlp @@ -0,0 +1,177 @@ +.help fit1d Jul85 images.imfit +.ih +NAME +fit1d -- fit a function to image lines +.ih +USAGE +.nf +fit1d input output type +.fi +.ih +PARAMETERS +.ls input +Images to be fit. The images may contain image sections. Only the region +covered by the section will be modified in the output image. +.le +.ls output +Output images to be created or modified. The number of output images +must match the number of input images. If an output image does not exist +it is first created and initialized to zero for fit types "fit" and +"difference" and to one for fit type "ratio". +.le +.ls type +Type of output. The choices are: +.ls fit +An image created from the function fits to the image lines. +.le +.ls difference +The difference between the image and the fit (i.e. residuals). +.le +.ls ratio +The ratio of the image and fit. +.le +.le +.ls bpm = "" +List of bad pixel masks. This may be a null string to not use a +bad pixel mask, a single mask that applies to all input images, or +a matching list. The value may also be !<keyword> to specify a keyword whose +value is the mask to use. +.le +.ls axis = 1 +Axis along which the one dimensional fitting is done. Axis 1 corresponds +to fitting the image lines and axis 2 corresponds to fitting the columns. +.le +.ls interactive = yes +If \fBinteractive\fR is set to yes, a plot of the fit is drawn and the +cursor is available for interactively examining and adjusting the fit. +.le +.ls sample = "*" +Lines or columns to be used in the fits. +.le +.ls naverage = 1 +Number of sample points to combined to create a fitting point. +A positive value specifies an average and a negative value specifies +a median. +.le +.ls function = spline3 +Function to be fit to the image lines or columns. The functions are +"legendre" (legendre polynomial), "chebyshev" (chebyshev polynomial), +"spline1" (linear spline), and "spline3" (cubic spline). The functions +may be abbreviated. +.le +.ls order = 1 +The order of the polynomials or the number of spline pieces. +.le +.ls low_reject = 0., high_reject = 0. +Rejection limits below and above the fit in units of the residual sigma. +.le +.ls niterate = 1 +Number of rejection iterations. +.le +.ls grow = 0. +When a pixel is rejected, pixels within this distance of the rejected pixel +are also rejected. +.le +.ls graphics = "stdgraph" +Graphics output device for interactive graphics. +.le +.ls cursor = "stdgcur" +Graphics cursor input. +.le +.ih +DESCRIPTION +A one dimensional function is fit to each line or column of the input images. +The function may be a legendre polynomial, chebyshev polynomial, +linear spline, or cubic spline of a given order or number of spline pieces. +The output image is of pixel type real and is formed from the fitted +function values, the difference or residuals of the fit (pixel value - +fitted value), or the ratio between the pixel values and the fitted values. + +The output image may exist in which case a section in the input image is +applied to the output image. Thus, a section on the input image causes only +that part of the output image to be changed. If the output image does not +exist it is first created with a size given by the full (without a section) +input image and initialized to zero for fit and difference output types +and one for ratio output types. + +A bad pixel mask may be specified to exclude data from the fitting. Any +non-zero value in the mask is excluded. It appears in the interactive +fitting in the same way as manually deleted points. The mask is matched to +the input image(s) as described by \fBpmmatch\fR. The default is matching +in physical coordinates. + +The points fit are determined by selecting a sample of lines or columns +specified by the parameter \fIsample\fR and taking either the average or +median of the number of points specified by the parameter \fInaverage\fR. +The type of averaging is selected by the sign of the parameter and the number +of points is selected by the absolute value of the parameter. +The sample points are specified relative to any image sections. + +If \fIlow_reject\fR and/or \fIhigh_reject\fR are greater than zero the sigma +of the residuals between the fitted points and the fitted function is computed +and those points whose residuals are less than \fI-low_reject\fR * sigma +and greater than \fIhigh_reject\fR * sigma are excluded from the fit. +Points within a distance of \fIgrow\fR pixels of a rejected pixel are also +excluded from the fit. The function is then refit without the rejected points. +This rejection procedure may be iterated a number of times given by the +parameter \fIniterate\fR. + +The fitting parameters (\fIsample, naverage, function, order, low_reject, +high_reject, niterate, grow\fR) +may be adjusted interactively if the parameter \fIinteractive\fR is yes. +Lines or columns from the image are selected to be fit with the \fBicfit\fR +package. A single column or line may be chosen or a blank-separated range +may be averaged. Note that the averaging applies only to the graphed +data used to set the fitting parameters. The actual image lines and columns +are fit individually. The interactive cursor mode commands for this package +are described in a separate help entry under "icfit". Line 1 is automatically +selected for one dimensional images and any number of lines or columns may be +selected for two dimensional images. Note that the lines or columns are +relative to the input image section; for example line 1 is the first line of +the image section and not the first line of the image. When an end-of-file or +no line(s) or column(s) are given then the last selected fitting parameters +are used on each line or column of the image. This step is repeated for +each image in the input list. +.ih +EXAMPLES +1. To create a smoothed version of an image by fitting the image lines: + + cl> fit1d image fitimage fit + +If the interactive flag is set and the image is two dimensional then a prompt +for an image line is printed: + + image: Fit line = 100 200 + +The selected lines are averaged, graphed, and the interactive options for +setting and fitting the line are used. Exiting with 'q' or return prompts for +another line if the image is two dimensional. When the fitting parameters +are suitably set then respond with end-of-file or return to fit all the lines +of the image and create the output image. + +2. To subtract a linear function fit to columns 10 to 20 and 80 to 100 from +columns 10 to 100 and to subtract another linear function fit to lines +110 to 120 and 180 to 200 from columns 110 to 200: + +.nf + cl> fit1d image1[10:100,*] output diff axis=2 sample="1:11,71:91" + cl> fit1d image1[110:200,*] output diff axis=2 sample="1:11,71:91" +.fi + +Pixels outside columns 10 to 100 and 110 to 200 are not affected. Note that the +sample points are specified relative to the image sections. The script +\fBbackground\fR is available in other packages for doing background +subtractions. + +3. To determine a small scale response image: + + cl> fit1d image1 flat ratio + +The task \fBimred.generic.flat1d\fR is available for making flat field images +by this method with the addition of an extra parameter to limit the data values +for which the ratio is computed. +.ih +SEE ALSO +imred.generic.background, imred.generic.flat1d +xtools.icfit, lineclean, imsurfit +.endhelp diff --git a/pkg/images/imfit/doc/imsurfit.hlp b/pkg/images/imfit/doc/imsurfit.hlp new file mode 100644 index 00000000..0aa46a97 --- /dev/null +++ b/pkg/images/imfit/doc/imsurfit.hlp @@ -0,0 +1,226 @@ +.help imsurfit Feb88 images.imfit +.ih +NAME +imsurfit -- fit a surface function to an image +.ih +USAGE +imsurfit input, output, xorder, yorder +.ih +PARAMETERS +.ls input +List of images to be fit. +.le +.ls output +Output image(s) of \fItype_output\fR. +.le +.ls xorder +The order in x of the polynomials (1 = constant) or the number of polynomial +pieces for the bicubic spline. +.le +.ls yorder +The order in y of the polynomials (1 = constant) or the number of polynomial +pieces for the bicubic spline. +.le +.ls cross_terms = yes +Cross terms for the polynomials. For example, if \fIxorder\fR = 2 and +\fIyorder\fR = 2 +then a function of the form z = a + b * x + c * y + d * x * y will be fit. +.le +.ls function = "leg" +Functional for of surface to be fit to the image. The available functions +(with minimum match abbreviation) are: +.ls legendre +.le +.ls chebyshev +.le +.ls spline3 +.le +.ls spline1 +.le +.le +.ls type_output = "fit" +The type of output image. The allowed types (with minimum match abbreviation) +are: +.ls clean +The input image with deviant pixels in the good regions replaced by the +fitted value. +.le +.ls fit +An image created from the surface fits to the image. +.le +.ls residual +The difference of the input image and the fitted image. +.le +.ls response +The ratio of the input image to the fitted image. +All fitted (denominator) pixels below \fIdiv_min\fR are given a value of 1. +.le +.le +.ls xmedian = 1, ymedian = 1 +The x and y dimensions of the box used for median processing. +If \fIxmedian\fR > 1 or \fIymedian\fR is > 1, +then the median is calculated for each box and used in the surface +fit instead of the individual pixels. +.le +.ls median_percent = 50. +If the number of pixels in the median box is less than \fImedian_percent\fR * +\fIxmedian\fR * \fIymedian\fR the box will be omitted from the fit. +.le +.ls upper = 0., lower = 0. +The number of sigma limits for pixel rejection. If \fIupper\fR > 0. or +\fIlower\fR > 0. and median processing is turned off, +pixel rejection is enabled. +.le +.ls ngrow = 0 +The radius in pixels for region growing. +Pixels within a distance of \fIngrow\fR pixels of +a rejected pixel are also rejected. +.le +.ls niter = 0 +The maximum number of iterations in the rejection cycle. +Rejection will be terminated if the number of rejected pixels is zero +or the number of iterations equals \fIniter\fR. +.le +.ls regions = "all" +The available options (with minimum match abbreviation) are: +.ls all +All points in the image are fit. +.le +.ls rows +The fit is performed on the image rows specified by \fIrows\fR. +.le +.ls columns +The fit is performed on the image columns specified by \fIcolumns\fR. +.le +.ls border +The fit is performed on a border around the image whose width is specified +by \fIborder\fR. +.le +.ls sections +The fit is performed on image sections listed in the file specified +by \fIsections\fR. +.le +.ls circle +The fit is performed on a circular region whose parameters are specified by +\fIcircle\fR. +.le +.ls invcircle +The fit is performed on a region exterior to the circular region whose +parameters are specified by \fIcircle\fR. +.le +.le +.ls rows = "*" +When \fIregion_type\fR = 'rows', the string parameter \fIrows\fR specifies +the rows to be fit. +.le +.ls columns = "*" +When \fIregion_type\fR = 'columns', the string parameter \fIcolumns\fR +specifies the columns to be fit. +.le +.ls border = "50" +When \fIregion_type\fR = 'border', the +string parameter \fIborder\fR specifies the width of the border to be fit. +.le +.ls sections = "" +When \fIregion_type\fR = 'sections', the +string parameter \fIsections\fR is the name of the file containing the list of +image sections to be fit, where \fISections\fR may be the standard +input (STDIN). +The sections must be listed one per line in the following form: x1 x2 y1 y2. +.le +.ls circle = "" +The string parameter \fIcircle\fR lists the parameter needed to specify +the circle in the following format: xcenter ycenter radius. The three +parameters must be integers. +.le +.ls div_min = INDEF +When \fItype_output\fR = 'response' all divisions in which the fitted value +is below \fIdiv_min\fR are set to the value 1. +.le +.ih +DESCRIPTION +A surface is fit to selected portions of the input image. +The user may elect to fit the whole image, \fIregion_type\fR = 'all', +selected rows, \fIregion_type\fR = 'rows', selected columns, +\fIregion_type\fR = 'columns', a +border around the image, \fIregion_type\fR = 'border' or image sections, +\fIregion_type\fR = 'sections'. If the sections option is enabled the user +must supply the name of the file containing a list of sections, +\fIsections\fR = 'list', or enter them from the standard input. In either case +the sections must be listed one per line in the following form: x1 x2 y1 y2. + +The parameter \fIsurface_type\fR may be a +"legendre" polynomial, "chebyshev" polynomial, +a cubic spline ("spline3") or a linear spline ("spline1"). +The order of the polynomials is selected in both x and y. +Cross terms for the polynomial surfaces are optional. +For the cubic spline the parameters \fIxorder\fR and \fIyorder\fR specify +the number of polynomial pieces to be fit to the surface in +each direction. + +The output image may be the fitted image, the difference between the +input and the fitted image, the ratio of the input to the fitted image +or the input image with deviant pixels in the fitted regions replaced +with the fitted values, according to whether \fItype_output\fR = +'fit', 'residual', +'response' or 'clean'. If \fItype_output\fR = 'response' then pixels in the +fitted image with values < \fIdiv_min\fR are replaced by 1. +If \fItype_output\fR = +'clean' then at least one of \fIupper\fR or \fIlower\fR must be > 0. + +Pixel rejection is enabled if median processing is turned off, +\fIniter\fR > 0, +and at least one of the parameters \fIupper\fR and \fIlower\fR is > 0. +Region growing +can be turned on by setting \fIngrow\fR > 0, in which case all pixels within +a radius ngrow of a deviant pixel will be rejected. + +.ih +EXAMPLES +1. To create a smoothed version of an image: + +.nf + cl> imsurfit m74 m74smooth 5 10 function=spline3 +.fi + +2. To create a smoothed version of an image using median processing: + +.nf + cl> imsurfit m74 m74med 5 10 function=spline3 \ + >>> xmed=5 ymed=5 +.fi + +3. To subtract a constant background from an image: + +.nf + cl> imsurfit abell30 abell30bck 1 1 function=leg \ + >>> type=resid +.fi + +4. To make a ratio image using signals above 1000 units: + +.nf + cl> imsurfit n7006 n7006ratio 20 20 function=spline3 \ + >>> type=response div_min=1000 +.fi + +.ih +TIMINGS +Fitting and subtracting a constant from a 512 by 512 IRAF image requires +~35 cpu seconds. Approximately 130 cpu seconds are required to fit a +second degree polynomial in x and y (including cross-terms) to a +100 pixel wide border around a 512 by +512 IRAF image, and to subtract the fitted image from the input image. +To produce a smooth 512 by 512 IRAF image using a 10 by 10 bicubic spline +requires ~300 cpu seconds. Timings refer to a VAX 11/750 + fpa. + +.ih +NOTES +The surface fitting code uses the IRAF SURFIT math routines, +which have been optimized for image fitting . +The routines which fit selected portions +of the image, perform pixel rejection and region growing, and create and +maintain a list of rejected pixels utilize the ranges and pixlist packages +of routines currently maintained in the images directory. These will be +replaced by more general ranges and image masking routines in the future. +.endhelp diff --git a/pkg/images/imfit/doc/lineclean.hlp b/pkg/images/imfit/doc/lineclean.hlp new file mode 100644 index 00000000..9ce2b95f --- /dev/null +++ b/pkg/images/imfit/doc/lineclean.hlp @@ -0,0 +1,129 @@ +.help lineclean May85 images.imfit +.ih +NAME +lineclean -- replace deviant pixels in image lines +.ih +USAGE +.nf +lineclean input output +.fi +.ih +PARAMETERS +.ls input +Input images to be cleaned. +.le +.ls output +Output cleaned images. The number of output images must be the same as the +number of input images. +.le +.ls sample = "*" +Columns to be used in fitting the cleaning function. +.le +.ls naverage = 1 +Number of sample points to combined to create a fitting point. +A positive value specifies an average and a negative value specifies +a median. +.le +.ls function = spline3 +Cleaning function to be fit to the image lines. The functions are: +.ls legendre +Legendre polynomial of the specified order. +.le +.ls chebyshev +Chebyshev polynomial of the specified order. +.le +.ls spline1 +Linear spline of the specified number of pieces. +.le +.ls spline3 +Cubic spline of the specified number of pieces. +.le +.le +.ls order = 1 +The order of the polynomials or the number of spline pieces. +.le +.ls low_reject = 2.5, high_reject = 2.5 +Rejection limits below and above the fit in units of the residual sigma. +.le +.ls niterate = 1 +Number of rejection iterations. +.le +.ls grow = 1. +When a pixel is rejected, pixels within this distance of the rejected pixel +are also rejected. +.le +.ls graphics = "stdgraph" +Graphics output device for interactive graphics. +.le +.ls cursor = "stdgcur" +Graphics cursor input. +.le +.ih +DESCRIPTION +A one dimensional function is fit to each line of the input images. +The function may be a legendre polynomial, chebyshev polynomial, +linear spline, or cubic spline of a given order or number of spline pieces. +If \fIlow_reject\fR and/or \fIhigh_reject\fR are greater than zero the sigma +of the residuals between the fitted points and the fitted function is computed +and those points whose residuals are less than \fI-low_reject\fR * sigma +and greater than \fIhigh_reject\fR * sigma are excluded from the fit. +Points within a distance of \fIgrow\fR pixels of a rejected pixel are also +excluded from the fit. The function is then refit without the rejected points. +This rejection procedure may be iterated a number of times given by the +parameter \fIniterate\fR. Finally, the +rejected points in the input image are replaced by the fitted values +to create the output image lines. + +The output image may exist in which case a section in the input image is +applied to the output image. Thus, a section on the input image causes only +that part of the output image to be cleaned. If the output image does not +exist it is first created by making a copy of the full (without a section) +input image. + +The points fit are determined by selecting a sample of columns specified by +the parameter \fIsample\fR and taking either the average or median of +the number of points specified by the parameter \fInaverage\fR. +The type of averaging is selected by the sign of the parameter and the number +of points is selected by the absolute value of the parameter. +The sample points are specified relative to any image section. + +The fitting parameters (\fIsample, naverage, function, order, low_reject, +high_reject, niterate, grow\fR) +may be adjusted interactively if the parameter \fIinteractive\fR is yes. +Lines from the image are selected to be fit with the \fBicfit\fR package. +For images of greater than two dimensions sets of numbers giving the +2nd, 3rd, etc. coordinates are entered. +The image lines are specified relative to any image section. +When an end-of-file or no line is given then the last selected fitting +parameters are used on each line of the image. This step is repeated for +each image in the input list. The interactive options are described +in the help information \fBicfit\fR. +.ih +EXAMPLES +1. To clean pixels deviating by more than 2.5 sigma: + + cl> lineclean image cleanimage + +If the interactive flag is set then a prompt for an image line is +printed: + + image: Fit line = 100 + +For a one or two dimensional image the line number is entered (1 for a one +dimensional image). For a three dimensional image two numbers are entered. +For example: + + image: Fit line = 10 2 + +for line 10 of the second image plane. + +The selected line is graphed and the interactive options for setting and +fitting the line are used. Data points marked with diamonds indicate +points to be replaced by the fitted value. Exiting with 'q' or return +prompts for another line. When the fitting parameters are suitably set +then respond with end-of-file or return to fit all the lines of the image +and create the output image. +.ih +SEE ALSO +fit1d, xtools.icfit, imsurfit +.endhelp |