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+.help iralign Sep93 noao.nproto
+.ih
+NAME
+iralign -- align the elements of the mosaiced image
+.ih
+USAGE
+iralign input output database coords
+.ih
+PARAMETERS
+.ls input
+The mosaiced image written by IRMOSAIC.
+.le
+.ls output
+The output aligned image.
+.le
+.ls database
+The database file written by IRMOSAIC.
+.le
+.ls coords
+If \fIalignment\fR = "coords", then \fBcoords\fR is
+a text file containing the x and y coordinates, measured in the input
+mosaiced image, of reference objects common
+to adjacent subrasters in the input mosaiced
+image. The reference coordinates are written with the following format:
+line 1) the x and y coordinates of an object in the any subraster,
+line 2) the x and y coordinates of the same object in any adjacent subraster,
+line 3) the x and y coordinates of another object in the any subraster,
+line 4) the x and y coordinates of the same object in any adjacent subraster,
+etc.
+If \fIalignment\fR = "file", then \fBcoords\fR is a text file containing
+the x and y shifts in columns 1 and 2 respectively,
+of each subraster relative to the reference subraster, in the order
+in which the subrasters were written into the mosaiced input image.
+This option can be used to make fine adjustments to the output aligned image
+by manually editing the computed shifts and rerunning
+IRALIGN with the new shifts.
+.le
+.ls xshift
+The x shift in pixels used if \fIalignment\fR = "shifts".
+.le
+.ls yshift
+The y shift in pixels used if \fIalignment\fR = "shifts".
+.le
+.ls alignment = "coords"
+The method of aligning the subraster.
+.ls coords
+The x and y positions of the reference points common to adjacent subrasters
+in the input mosaiced image are listed in a text file as described
+under the help for the  \fIcoords\fR parameter.
+.le
+.ls shifts
+The x and y shifts of each subraster with respect to its neighbour are
+set to \fIxshift\fR and \fIyshift\fR.
+.le
+.ls file
+The x and y  shifts of each input subraster with respect to the
+reference subraster image are listed in a text file as described
+under the help for the \fIcoords\fR parameter.
+.le
+.le
+.ls nxrsub = INDEF, ls nyrsub = INDEF
+The column and row index of the reference subraster.
+The default reference subraster is the central subraster.
+.le
+.ls xref = 0, yref = 0
+The x and y offset of the reference
+subraster in the output aligned image.
+By default the reference subraster occupies the same position in
+the output image that it does in the input image.
+.le
+.ls trimlimits = "[1:1,1:1]"
+The number of columns or rows to trim off each edge of each input subraster
+before inserting it in the output image, specified in image section notation.
+The default action is to trim 1 column or line at each edge of the subraster.
+.le
+.ls nimcols = INDEF, nimlines = INDEF
+The number of columns and lines in the output image. The defaults are  the
+number of columns and lines in the input image.
+.le
+.ls oval = INDEF
+The value of undefined pixels in the output image. The default is the value
+stored in the database file written by 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
+IRALIGN takes the mosaiced image \fIinput\fR and database
+\fIdatabase\fR files
+written by IRMOSAIC, and a list of reference object
+coordinates \fIcoords\fR created by the user, and writes
+an output image \fIoutput\fR in which all the subrasters are aligned
+with respect to a reference subraster.
+
+If \fIalignment\fR = "coords", IRALIGN accumulates the relative shifts
+between adjacent subrasters defined by the data in \fIcoords\fR,
+into a total shift for each subraster with respect to the reference subraster.
+Relative shifts defined for non-adjacent subrasters are ignored.
+For those subrasters which have no relative shift information,
+IRALIGN makes a best guess at the relative x and y shifts
+based on the relative x andy shifts of nearby subrasters
+which do have relative shift information.  If the x and y shifts
+are sufficiently uniform over the whole input image the user may set
+\fIalignment\fR to  "shifts" and supply values for
+\fIxshift\fR and \fIyshift\fR.
+Alternatively the total shifts may be read directly from the  file \fIcoords\fR
+if \fIalignment\fR = "file".
+
+Coordinate lists for the \fIalignment\fR = "coords" option,
+may be generated interactively using the RIMCURSOR, 
+or APPHOT package CENTER and APSELECT tasks. For example a coordinate list
+written by RIMCURSOR for a 
+4 by 4 mosaic of 51 by 51 pixel square images containing a single
+reference object common to all the subrasters might look like the following.
+
+.nf
+41.3   42.6     1 \40 	# coordinates of ref object in subraster 1
+62.0   38.5	1 \40   # coordinates of ref object in subraster 2
+41.3   42.6     1 \40   # coordinates of ref object in subraster 1
+38.1   95.8     1 \40   # coordinates of ref object in subraster 3
+62.0   38.5     1 \40   # coordinates of ref object in subraster 2
+70.3   89.0     1 \40   # coordinates of ref object in subraster 4
+38.1   95.8     1 \40   # coordinates of ref object in subraster 3
+70.3   89.0     1 \40   # coordinates of ref object in subraster 4
+.fi
+
+In this example subrasters 1 and 2 are in the lower-left and
+lower-right hand corners of
+the mosaiced image respectively, while subrasters 3 and 4 are in the
+upper-left and upper- right hand corner of the mosaiced image.
+Any number of reference objects may be used.
+
+The subrasters are inserted into the output image using the
+interpolation scheme defined by
+\fIinterpolant\fR, and aligned with reference to the subraster defined
+by \fInxrsub\fR and \fInyrsub\fR, using the shifts defined by
+the data in the file \fIcoords\fR or defined by \fIxshift\fR and
+\fIyshift\fR. Subrasters are inserted into the output image in the order
+they were placed in the original mosaic with pixels in the most recently
+placed subrasters replacing those in earlier placed ones in the overlap regions.
+Undefined pixels in the output image
+are assigned the value \fIoval\fR. The position of the reference subraster
+in the output image may be adjusted by setting the offset 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.
+
+.ih
+EXAMPLES
+
+1. Align an 8 by 8 mosaic with respect to subraster 6, 5.
+
+.nf
+    pr> iralign mosaic mosaic.al mosaic.db coords nxrsub=6 \
+	nyrsub=5
+.fi
+
+2. Align an 8 by 8 mosaic as in example 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> iralign 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 subraster before inserting it into the output image.
+
+.nf
+    pr> iralign 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 manually and rerun IRALIGN with the
+new shifts.
+
+.nf
+    pr> iralign 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> iralign mosaic mosaic.al.2 mosaic.db shifts2 align=file \
+	nxrsub=6 nyrsub=5 trimlimits="[2:2,2:2]"
+.fi
+
+.ih
+TIME REQUIREMENTS
+.ih
+BUGS
+.ih
+SEE ALSO
+irmosaic, apphot.center, apphot.apselect, irmatch1d, irmatch2d
+.endhelp