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+.help irmatch2d Jan90 noao.nproto
+.ih
+NAME
+irmatch2d -- align and match the elements of the mosaiced image
+.ih
+USAGE
+irmatch2d 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 and matched image produced by IRMATCH2D.
+.le
+.ls database
+The database file from the IRMOSAIC task.
+.le
+.ls coords
+If \fIalignment\fR = "coords", then \fBcoords\fR is
+the 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 the 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 IRMATCH2D by editing the computed shifts slightly and rerunning
+IRMATCH2D with the new shifts.
+.le
+.ls xshift
+The x shift in pixel units if \fIalignment\fR = "shifts".
+.le
+.ls yshift
+The x 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 two dimensions, first
+in the order in which they
+were placed in the output image and then in the orthogonal dimension.
+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, nyrsub = INDEF
+The column and row 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 reference subraster in the output image. By default
+the reference subraster is placed in the same position in the output image
+that it occupied in the input image.
+.le
+.ls trimlimits = "[1:1,1:1]"
+The number of rows and columns to be trimmed off each input subraster
+before it is copied to the output image in section notation.
+The default is to trim 1 row and column off each edge of the input
+subraster.
+.le
+.ls nimcols = INDEF, nimlines = INDEF
+The number of columns and lines in the output image. The default is the
+number of lines and columns 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 = yes
+Print messages on the terminal describing the progress of the task.
+.le
+.ih
+DESCRIPTION
+IRMATCH2D 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", IRMATCH2D 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, IRMATCH2D 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 for 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.
+Subrasters are inserted into 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 subraster
+in the output image can be shifted by setting the parameters \fIxref\fR and
+\fIyref\fR. The \fItrimlimits\fR parameter can be used to trim each
+input subraster before it is inserted into the output image.
+
+Intensities of adjacent subrasters can be matched using the \fImatch\fR
+parameter. 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 two dimensions,  first along the direction in which subrasters
+were inserted into the mosaic and then in the orthogonal dimension.
+For example if IRMOSAIC was run with \fIcorner\fR = "ll", \fIdirection\fR =
+"row" and \fIraster\fR = "no", then the matching would proceed along
+each row starting with the lower-left hand corner and then along
+each column beginning again in the lower-left corner.
+
+.ih
+EXAMPLES
+
+1. Align an 8 by 8 mosaic with respect to subraster 6, 5.
+
+.nf
+    pr> irmatch2d 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> irmatch2d 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> irmatch2d 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 irmatch2d with the
+new shifts.
+
+.nf
+    pr> irmatch2d 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> irmatch2d 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, irmatch1d, apphot.center, apphot.apselect
+.endhelp