From 40e5a5811c6ffce9b0974e93cdd927cbcf60c157 Mon Sep 17 00:00:00 2001
From: Joe Hunkeler <jhunkeler@gmail.com>
Date: Tue, 11 Aug 2015 16:51:37 -0400
Subject: Repatch (from linux) of OSX IRAF

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+.help irmatch1d Jan90 noao.nproto
+.ih
+NAME
+irmatch1d -- align and match the elements of the mosaiced image
+.ih
+USAGE
+irmatch1d input output database coords
+.ih
+PARAMETERS
+.ls input
+The mosaiced image to be aligned. This image must have been produced by
+the IRMOSAIC task and have an accompanying database file specified by
+\fIdatabase\fR.
+.le
+.ls output
+The aligned image produced by IRMATCH1D.
+.le
+.ls database
+The database file from the IRMOSAIC task.
+.le
+.ls coords
+If \fIalignment\fR = "coords", then \fBcoords\fR is
+a text file listing the coordinates of objects in the input
+image one object per line in the following
+format: 1) the x and y coordinates of the object in the first subraster
+2) the x and y coordinates of the same object in the second subraster
+3) the x and y coordinates of the next object in the first subraster
+etc.
+If \fIalignment\fR = "file", then \fBcoords\fR is a text file listing
+the x, y and intensity shifts in columns 1, 2 and 3 respectively,
+of each input subraster relative to the reference subraster. The
+most common use of this option is to make fine adjustments by hand
+to the output of IRMATCH1D by editing the computed shifts slightly and
+rerunning IRMATCH1D with the new shifts.
+.le
+.ls xshift
+The x shift in pixel units if \fIalignment\fR = "shifts".
+.le
+.ls yshift
+The y shift in pixel units if \fIalignment\fR = "shifts".
+.le
+.ls alignment = "coords"
+The method of aligning the subraster.
+.ls coords
+The x and y positions of the marker points are listed in a file in the
+format specified by the \fIcoords\fR parameter.
+.le
+.ls shifts
+The x and y shifts of a subraster with respect to its neighbour are
+set to \fIxshift\fR and \fIyshift\fR.
+.le
+.ls file
+The x,  y  and intensity shifts of each input subraster with respect to the
+reference subraster image.
+.le
+.le
+.ls match = "*"
+Match intensities using the overlap region between adjacent subrasters. The
+median intensity is computed in the overlap region
+and the intensity scale of the current subraster is scaled to that of
+the previous subraster. Intensities are matched in one dimension in the order
+in which they
+are placed in the output image. The default is match everything.
+Those subrasters to be matched must be listed by number. For example to
+match intensities for subrasters 1 to 5 and 10 to 20 set match = "1-5,10-20".
+To match all the subrasters set match = "1-999" or match="*".
+.le
+.ls nxrsub = INDEF, ls nyrsub = INDEF
+The column and line index of the reference subraster.
+This will default to the central subraster.
+.le
+.ls xref = 0, yref = 0
+The x and y offset of the position of the reference subraster in the
+output image. The default action is to place the reference subraster
+in the same position in the output image as it has in the input image.
+.le
+.ls trimlimits = "[1:1,1:1]"
+The number of columns and rows to be trimmed off each edge of the
+input subraster before it is inserted in the output image in section
+notation. The default is to trim 1 column or row in each direction.
+.le
+.ls nimcols = INDEF, ls nimlines = INDEF
+The number of columns and rows in the output image. The default is the
+number of columns and rows in the input image.
+.le
+.ls oval = INDEF
+The value of undefined pixels in the output image. The default is the value
+in the database file from IRMOSAIC.
+.le
+.ls interpolant = linear
+The type of interpolant used to shift the subrasters. The options are:
+.ls nearest
+Nearest neighbour interpolation.
+.le
+.ls linear
+Bilinear interpolation.
+.le
+.ls poly3
+Bicubic polynomial interpolation.
+.le
+.ls poly5
+Biquintic polynomial interpolation.
+.le
+.ls spline3
+Bicubic spline interpolation.
+.le
+.le
+.ls verbose = no
+Print messages on the terminal describing the progress of the task.
+.le
+.ih
+DESCRIPTION
+IRMATCH1D takes the mosaiced image \fIinput\fR, the database file \fIdatabase\fR
+generated by IRMOSAIC and a list of coordinates \fIcoords\fR and computes
+an output image \fIoutput\fR in which all the individual subrasters are aligned.
+If \fIalignment\fR = "coords", IRMATCH1D accumulates the relative shifts
+between adjacent subrasters
+into a total shift with respect to the reference subraster. Shifts which
+do not correspond to adjacent subrasters are ignored.
+For subrasters which have no direct shift information, IRMATCH1D makes a best
+guess at the x and y shift based on the shifts of nearby subrasters which
+do have direct shift information.
+If the x and y shifts are sufficiently uniform over the whole input image
+the user may set \fIalignment\fR
+= shifts and input values of \fIxshift\fR and \fIyshift\fR.
+Alternatively the shifts may be read from the file \fIcoords\fR if
+\fIalignment\fR = "file".
+
+Coordinate lists may be generated interactively on the Sun workstations
+using the IRAF imtool facility and centered using the APPHOT CENTER
+and APSELECT tasks.
+
+The subrasters are inserted into the output image
+using the interpolation scheme defined by
+\fIinterpolant\fR and is made with reference to the subraster defined
+by \fInxrsub\fR and \fInyrsub\fR, using the shifts defined by
+the coordinates in the file \fIcoords\fR or defined by \fIxshift\fR and
+\fIyshift\fR. Subrasters are placed in the output image in the order
+they were inserted into the original mosaic with pixels in the most
+recently placed subrasters replacing those placed earlier in the overlap
+regions. Undefined pixels in the output image
+are given the value \fIoval\fR. The position of the reference image in the
+output image can be adjusted by setting the parameters \fIxref\fR and
+\fIyref\fR. The edges of each subraster may be trimmed before
+insertion into the output image by setting the \fItrimlimits\fR parameter.
+
+Intensities of adjacent subrasters can be matched using the \fImatch\fR
+parameters. At present matching is done by computing the median in the
+overlap region between adjacent subrasters and applying difference in
+these two numbers to the subraster in question. Intensity matching is
+done in one dimension  only with the direction of matching following
+the order that the individual subrasters were inserted into the mosaic.
+For example if IRMOSAIC was run with \fIcorner\fR = "ll", \fIdirection\fR
+="row" and \fIraster\fR = "no", then the matching would start in the
+lower-left corner, proceed along the first row, move to the star of the
+second row and so on.
+
+.ih
+EXAMPLES
+
+1. Align an 8 by 8 mosaic with respect to subraster 6, 5.
+
+.nf
+    pr> irmatch1d mosaic mosaic.al mosaic.db coords nxrsub=6 \
+	nyrsub=5
+.fi
+
+2. Align an 8 by 8 mosaic as 1 above but shift the position of the
+reference subraster in the output image by 2 pixels in x and 3 pixels
+in y.
+
+.nf
+    pr> irmatch1d mosaic mosaic.al mosaic.db coords nxrsub=6 \
+	nyrsub=5 xref=2 yref=3
+.fi
+
+3. Align an 8 by 8 mosaic as 1 above but trim 2 rows and columns off
+of each input image before inserting into the output image.
+
+.nf
+    pr> irmatch1d mosaic mosaic.al mosaic.db coords nxrsub=6 \
+	nyrsub=5 trimlimits="[2:2,2:2]"
+.fi
+
+4. Rerun the above example saving the verbose output in a file. Use the 
+PROTO package fields task to select the xshift, yshift and intensity
+shift fields, edit the shifts slightly and rerun irmatch1d with the
+new shifts.
+
+.nf
+    pr> irmatch1d mosaic mosaic.al mosaic.db coords nxrsub=6 \
+	nyrsub=5 trimlimits="[2:2,2:2]" > shifts1
+
+    pr> fields shifts1 3,4,6 > shifts2
+
+    pr> edit shifts2
+
+	... make whatever changes are desired
+
+    pr> irmatch1d mosaic mosaic.al mosaic.db shifts2 align=file \
+	nxrsub=6 nyrsub=5 trimlimits="[2:2,2:2]"
+.fi
+
+.ih
+TIME REQUIREMENTS
+.ih
+BUGS
+.ih
+SEE ALSO
+irmosaic, iralign, irmatch2d, apphot.center, apphot.apselect
+.endhelp
-- 
cgit 

