From b51f0037c41428b13ea48b4d4d4fd331ca3d0783 Mon Sep 17 00:00:00 2001 From: paoloserra Date: Wed, 19 Jun 2024 19:08:40 +0200 Subject: [PATCH] improve help and usage info --- README.rst | 93 +++++++++++++++++++++++++++++++++++++++++++++ mosaicqueen/main.py | 6 ++- 2 files changed, 97 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 6ff5131..66e6c28 100755 --- a/README.rst +++ b/README.rst @@ -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. + diff --git a/mosaicqueen/main.py b/mosaicqueen/main.py index e1a24e0..fc77254 100755 --- a/mosaicqueen/main.py +++ b/mosaicqueen/main.py @@ -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",