iralign: Align the image produced by irmosaic
Package: irred
Usage
iralign input output database coords
Parameters
- input
- The mosaiced image written by IRMOSAIC.
- output
- The output aligned image.
- database
- The database file written by IRMOSAIC.
- coords
- If alignment = "coords", then coords 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 alignment = "file", then coords 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.
- xshift
- The x shift in pixels used if alignment = "shifts".
- yshift
- The y shift in pixels used if alignment = "shifts".
- alignment = "coords"
- The method of aligning the subraster.
- 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 coords parameter.
- shifts
- The x and y shifts of each subraster with respect to its neighbour are set to xshift and yshift.
- 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 coords parameter.
- nxrsub = INDEF, ls nyrsub = INDEF
- The column and row index of the reference subraster. The default reference subraster is the central subraster.
- 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.
- 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.
- 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.
- oval = INDEF
- The value of undefined pixels in the output image. The default is the value stored in the database file written by IRMOSAIC.
- interpolant = linear
- The type of interpolant used to shift the subrasters. The options are:
- nearest
- Nearest neighbour interpolation.
- linear
- Bilinear interpolation.
- poly3
- Bicubic polynomial interpolation.
- poly5
- Biquintic polynomial interpolation.
- spline3
- Bicubic spline interpolation.
- verbose = yes
- Print messages on the terminal describing the progress of the task?
Description
IRALIGN takes the mosaiced image input and database database files written by IRMOSAIC, and a list of reference object coordinates coords created by the user, and writes an output image output in which all the subrasters are aligned with respect to a reference subraster.
If alignment = "coords", IRALIGN accumulates the relative shifts between adjacent subrasters defined by the data in coords, 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 alignment to "shifts" and supply values for xshift and yshift. Alternatively the total shifts may be read directly from the file coords if alignment = "file".
Coordinate lists for the alignment = "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.
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
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 interpolant, and aligned with reference to the subraster defined by nxrsub and nyrsub, using the shifts defined by the data in the file coords or defined by xshift and yshift. 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 oval. The position of the reference subraster in the output image may be adjusted by setting the offset parameters xref and yref. The edges of each subraster may be trimmed before insertion into the output image by setting the trimlimits parameter.
Examples
1. Align an 8 by 8 mosaic with respect to subraster 6, 5.
pr> iralign mosaic mosaic.al mosaic.db coords nxrsub=6 \
nyrsub=5
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.
pr> iralign mosaic mosaic.al mosaic.db coords nxrsub=6 \
nyrsub=5 xref=2 yref=3
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.
pr> iralign mosaic mosaic.al mosaic.db coords nxrsub=6 \
nyrsub=5 trimlimits="[2:2,2:2]"
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.
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]"
Time requirements
Bugs
See also
irmosaic, apphot.center, apphot.apselect, irmatch1d, irmatch2d