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improve help and usage info
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@paoloserra
paoloserra committed Jun 19, 2024
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93 changes: 93 additions & 0 deletions README.rst
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Expand Up @@ -28,3 +28,96 @@ Work in progress: convolution of input images to a common synthesised beam befor
.. |Pypi Version| image:: https://img.shields.io/pypi/v/mosaic-queen.svg
:target: https://pypi.org/project/mosaic-queen/
:alt:

=======
Usage
=======

usage: mosaic-queen [-h] -i INPUT -t TARGET_IMAGES [TARGET_IMAGES ...] -o
OUTPUT -n NAME [-j NUM_WORKERS] [-a] [-r] [-f]
[-bc BEAM_CUTOFF] [-mc MOSAIC_CUTOFF] [-u]
[-s {mad,rms,fit}] [-g GUESS_STD] [-ra RA] [-dec DEC]
[-v VELOCITY] [-dra DRA] [-ddec DDEC] [-dv DV]

Run make_mosaic over the targets

optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
The directory that contains the (2D or 3D) images and
beams.
-t TARGET_IMAGES [TARGET_IMAGES ...], --target-images TARGET_IMAGES [TARGET_IMAGES ...]
The filenames of each target/pointing image to be
mosaicked. A suffix of 'image.fits' is expected, and
this is replaced by 'pb.fits' in order to locate the
corresponding beams (which are also required as
input).
-o OUTPUT, --output OUTPUT
The directory for all output files.
-n NAME, --name NAME The prefix to be used for output files.
-j NUM_WORKERS, --num-workers NUM_WORKERS
Number of worker threads. Default=0 means all
available threads.
-a, --associated-mosaics
Also make mosaics of the associated 'model' and
'residual' .fits files.
-r, --regrid Use montage for regridding the images and beams.Also
regrid the 'model' and 'residual' files, if '--
associated-mosaics' is enabled.
-f, --force-regrid If the user wants newly-regridded files, this '--
force-regrid' argument should be enabled.(If '--
regrid' is enabled instead, the package will first
check whether regridded files already exist.If they
are found, regridding will not proceed because this is
a time-consuming step.)
-bc BEAM_CUTOFF, --beam-cutoff BEAM_CUTOFF
The cutoff in the primary beam to use.E.g. The default
of 0.1 means going down to the 10 percent level for
each pointing. Set to zero for no primary beam cutoff.
-mc MOSAIC_CUTOFF, --mosaic-cutoff MOSAIC_CUTOFF
Sensitivity cutoff in the final mosaic. Pixels with a
noise level > minimum mosaic noise / cutoff are
blanked in all final products. E.g. The default of 0.2
means blanking in the mosaic all pixels with a noise
level > 5x the minimum mosaic noise level. Set to zero
for no cutoff (but some cutoff may still result from
the -bc setting).
-u, --unity-weights Build the mosaic using weight=1 instead of
weight=1/noise**2 for the input images.
-s {mad,rms,fit}, --statistic {mad,rms,fit}
State 'mad' (median absolute deviation), 'rms' (root
mean square) or 'fit' (Gaussian fit) as the statistic
to be used for estimating the noise level in the input
images. This will be derived using the negative pixel-
values. The noise levels set the weights=1/noise**2
used when mosaicking. Not used if the '-u' option is
enabled. Default is mad.
-g GUESS_STD, --guess-std GUESS_STD
An initial guess of the noise level in the input
images, if user has set '--statistic' to 'fit'.(This
is to aid a Gaussian fit to the negative pixel-
values.) The default of 0.02 assumes that the pixel
values are in units of Jy/beam, so a std of ~ 20
mJy/beam).
-ra RA Central RA (in degrees) of the output mosaic
image/cube, if the user does not want to image the
entire FoV covered by the input images/cubes.
-dec DEC Central Dec (in degrees) of the output mosaic
image/cube, if the user does not want to image the
entire FoV covered by the input images/cubes.
-v VELOCITY, --velocity VELOCITY
Central velocity/frequency of the output mosaic cube
(in the appropriate units of the input cubes) if the
user does not want to image the entire
velocity/frequency range covered by the input cubes.
-dra DRA RA range of the output mosaic image/cube (in degrees),
if the user does not want to image the entire FoV
covered by the input images/cubes.
-ddec DDEC Dec range of the output mosaic image/cube (in
degrees), if the user does not want to image the
entire FoV covered by the input images/cubes.
-dv DV Velocity/frequency range of the output mosaic cube (in
the unit used by the input images), if the user does
not want to image the entire velocity/frequency range
covered by the input cubes.

6 changes: 4 additions & 2 deletions mosaicqueen/main.py
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Expand Up @@ -75,10 +75,12 @@ def main(argv):
"If they are found, regridding will not proceed because this is a time-consuming step.)")
parser.add_argument("-bc", "--beam-cutoff", type=float, default=0.1,
help="The cutoff in the primary beam to use."
"E.g. The default of 0.1 means going down to the 10 percent level for each pointing.")
"E.g. The default of 0.1 means going down to the 10 percent level for each pointing."
" Set to zero for no primary beam cutoff.")
parser.add_argument("-mc", "--mosaic-cutoff", type=float, default=0.2,
help="Sensitivity cutoff in the final mosaic. Pixels with a noise level > minimum mosaic noise / cutoff are blanked in all final products. "
"E.g. The default of 0.2 means blanking in the mosaic all pixels with a noise level > 5x the minimum mosaic noise level.")
"E.g. The default of 0.2 means blanking in the mosaic all pixels with a noise level > 5x the minimum mosaic noise level."
" Set to zero for no cutoff (but some cutoff may still result from the -bc setting).")
parser.add_argument("-u", "--unity-weights", action="store_true",
help="Build the mosaic using weight=1 instead of weight=1/noise**2 for the input images.")
parser.add_argument("-s", "--statistic", choices= ["mad", "rms", "fit"], required = False, default = "mad",
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