.TH MSUBCUBE 1 "Dec 2016" "Montage 5" "Montage"
.SH NAME
mSubCube \- Create a subimage of a cube

.SH SYNOPSIS
mSubCube [\-d] [\-D3 \fIindex-selection-string\fP] [\-D4 \fIindex-selection-string\fP] [\-a] [\-h \fIhdu\fP] [\-s \fIstatusfile\fP] in.fits out.fits ra dec xsize [ysize]
.PP
mSubCube \-p [\-d] [\-D3 \fIindex-selection-string\fP] [\-D4 \fIindex-selection-string\fP] [\-h \fIhdu\fP] [\-s \fIstatusfile\fP] in.fits out.fits xstartpix ystartpix xpixsize [ypixsize]

.SH DESCRIPTION
Creates a subimage (or "cutout") of a FITS file.  Note that in "normal" mode,
all the parameters (location and size) are in degrees; in pixel (\-p) mode, all of
them are in pixels.

.SH OPTIONS
.TP
\-d
Turns on debugging.
.TP
\-D3
This argument is a string (quoted if it contain spaces) defining the subset of indices desired.  The string
has the form of an ordered set of comma-separated values, which each value is either an index or a range of indices.
For instance, "2, 4:46, 58, 101:120" would copy dimension three planes 2, 4 through 46, 58 and 101 through 120 to
the output cube.  Note that these numbers refer to indices in a FITS cube, so are one-offset, not zero. Attempts
to go outside the available data result in an error.
.TP
\-D4
The same sort of thing as \-D3, but for the fourth dimension.
.TP
\-a
All pixels \- Force retrieval of whole image (useful to extract an entire HDU)
.TP
\-h \fIhdu\fP
Operate on the specified FITS header extension (HDU)
.TP
\-s \fIstatusfile\fP
Output and errors are sent to \fIstatusfile\fP instead of to stdout
.TP
\-p
Pixel mode \- create subimage using pixel locations, instead of a location on the sky

.SH ARGUMENTS
.TP
in.fits
Input FITS file.
.TP
out.fits
Path to output FITS file.
.TP
ra
In normal mode, RA of center of output image.
.TP
dec
In normal mode, declination of center of output image.
.TP
xstartpix
In pixel mode, pixel along the x-axis where the cutout image will begin
.TP
ystartpix
In pixel mode, pixel along the y-axis where the cutout image will begin
.TP
xsize
In normal mode, width of output image in degrees.
.TP
ysize
In normal mode, height of output image in degrees (default is equal to \fIxsize\fP.
.TP
xpixsize
In pixel mode, width of output image in pixels
.TP
ypixsize
In pixel mode, height of output image in pixels (default is equal to \fIxpixsize\fP

.SH RESULT
\fB[struct stat="OK", content="\fIblank, flat or normal\fP"]\fP
.PP
The content keyword indicates whether all pixels where NaN (blank), all pixels were the same value (flat), or the image appears to be normal.

.SH MESSAGES
.TP
OK
[struct stat="OK", content="\fIblank, flat or normal\fP"]
.TP
ERROR
HDU value (\fIhdu\fP) must be a non-negative integer
.TP
ERROR
Cannot open status file: \fIstatusfile\fP
.TP
ERROR
Center RA string (\fIstring\fP) cannot be interpreted as a real number
.TP
ERROR
Center Dec string (\fIstring\fP) cannot be interpreted as a real number
.TP
ERROR
X size string (\fIstring\fP) cannot be interpreted as a real number
.TP
ERROR
Y size string (\fIstring\fP) cannot be interpreted as a real number
.TP
ERROR
Invalid 'x' size
.TP
ERROR
Invalid 'y' size
.TP
ERROR
Image file \fIfilename\fP missing or invalid FITS
.TP
ERROR
Cannot find HDU \fIhdu\fP
.TP
ERROR
Output wcsinit() failed.
.TP
ERROR
Location is off image
.TP
ERROR
Region outside image
.TP
ERROR
No pixels match area.
.TP
ERROR
Can't create output file: \fIout.fits\fP
.TP
ERROR
\fIFITS library error\fP

.SH EXAMPLES
.TP
$ mSubCube image1.fits subimage.fits 307.9 37.29 .01 .01
[struct stat="OK", content="normal"]

.SH BUGS
The drizzle algorithm has been implemented but has not been tested
in this release.
.PP
If a header template contains carriage returns (i.e., created/modified
on a Windows machine), the cfitsio library will be unable to read it
properly, resulting in the error: [struct stat="ERROR", status=207,
msg="illegal character in keyword"]
.PP
It is best for the background correction algorithms if the area
described in the header template completely encloses all of the input
images in their entirety. If parts of input images are "chopped off"
by the header template, the background correction will be affected. We
recommend you use an expanded header for the reprojection and
background modeling steps, returning to the originally desired header
size for the final coaddition. The default background matching assumes
that there are no non-linear background variations in the individual
images (and therefore in the overlap differences). If there is any
uncertainty in this regard, it is safer to turn on the "level only"
background matching (the "\-l" flag in mBgModel.

.SH COPYRIGHT
2001-2015 California Institute of Technology, Pasadena, California
.PP
If your research uses Montage, please include the following
acknowledgement: "This research made use of Montage. It is funded by
the National Science Foundation under Grant Number ACI-1440620, and
was previously funded by the National Aeronautics and Space
Administration's Earth Science Technology Office, Computation
Technologies Project, under Cooperative Agreement Number NCC5-626
between NASA and the California Institute of Technology."
.PP
The Montage distribution includes an adaptation of the MOPEX algorithm
developed at the Spitzer Science Center.