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@AlecThomson
AlecThomson committed Apr 18, 2024
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Expand Up @@ -21,77 +21,86 @@ This can be run using:
.. code-block::
$ spice_image -h
usage: spice_image [-h] [--temp_dir TEMP_DIR] [--psf_cutoff PSF_CUTOFF] [--robust ROBUST] [--nchan NCHAN] [--pols POLS] [--size SIZE]
[--scale SCALE] [--mgain MGAIN] [--niter NITER] [--nmiter NMITER] [--auto_mask AUTO_MASK]
[--auto_threshold AUTO_THRESHOLD] [--local_rms] [--local_rms_window LOCAL_RMS_WINDOW]
[--force_mask_rounds FORCE_MASK_ROUNDS] [--gridder {direct-ft,idg,wgridder,tuned-wgridder,wstacking}] [--taper TAPER]
[--minuv MINUV] [--parallel PARALLEL] [--purge] [--mpi] [--multiscale] [--multiscale_scale_bias MULTISCALE_SCALE_BIAS]
[--multiscale_scales MULTISCALE_SCALES] [--absmem ABSMEM] [--make_residual_cubes] [--ms_glob_pattern MS_GLOB_PATTERN]
[--data_column DATA_COLUMN] [--no_mf_weighting] [--skip_fix_ms]
[--hosted-wsclean HOSTED_WSCLEAN | --local_wsclean LOCAL_WSCLEAN]
msdir outdir
mmm mmm mmm mmm mmm
)-( )-( )-( )-( )-(
( S ) ( P ) ( I ) ( C ) ( E )
| | | | | | | | | |
|___| |___| |___| |___| |___|
mmm mmm mmm mmm
)-( )-( )-( )-(
( R ) ( A ) ( C ) ( S )
| | | | | | | |
|___| |___| |___| |___|
usage: spice_image [-h] [--temp_dir_wsclean TEMP_DIR_WSCLEAN] [--temp_dir_images TEMP_DIR_IMAGES]
[--psf_cutoff PSF_CUTOFF] [--robust ROBUST] [--nchan NCHAN] [--pols POLS] [--size SIZE] [--scale SCALE]
[--mgain MGAIN] [--niter NITER] [--nmiter NMITER] [--auto_mask AUTO_MASK]
[--auto_threshold AUTO_THRESHOLD] [--local_rms] [--local_rms_window LOCAL_RMS_WINDOW]
[--force_mask_rounds FORCE_MASK_ROUNDS] [--gridder {direct-ft,idg,wgridder,tuned-wgridder,wstacking}]
[--taper TAPER] [--minuv MINUV] [--parallel PARALLEL] [--purge] [--mpi] [--multiscale]
[--multiscale_scale_bias MULTISCALE_SCALE_BIAS] [--multiscale_scales MULTISCALE_SCALES]
[--absmem ABSMEM] [--make_residual_cubes] [--ms_glob_pattern MS_GLOB_PATTERN]
[--data_column DATA_COLUMN] [--no_mf_weighting] [--skip_fix_ms] [--num_beams NUM_BEAMS]
[--hosted-wsclean HOSTED_WSCLEAN | --local_wsclean LOCAL_WSCLEAN]
msdir datadir
mmm mmm mmm mmm mmm
)-( )-( )-( )-( )-(
( S ) ( P ) ( I ) ( C ) ( E )
| | | | | | | | | |
|___| |___| |___| |___| |___|
mmm mmm mmm mmm
)-( )-( )-( )-(
( R ) ( A ) ( C ) ( S )
| | | | | | | |
|___| |___| |___| |___|
Arrkis imager
options:
-h, --help show this help message and exit
-h, --help show this help message and exit
--hosted-wsclean HOSTED_WSCLEAN
Docker or Singularity image for wsclean (default: docker://alecthomson/wsclean:latest)
--local_wsclean LOCAL_WSCLEAN
Path to local wsclean Singularity image (default: None)
imaging arguments:
msdir Directory containing MS files
outdir Directory to output images
--temp_dir TEMP_DIR Temporary directory to store intermediate files (default: None)
--psf_cutoff PSF_CUTOFF
msdir Directory containing MS files
--temp_dir_wsclean TEMP_DIR_WSCLEAN
Temporary directory for WSClean to store intermediate files (default: None)
--temp_dir_images TEMP_DIR_IMAGES
Temporary directory for to store intermediate image files (default: None)
--psf_cutoff PSF_CUTOFF
Cutoff for smoothing in units of arcseconds. (default: None)
--robust ROBUST
--nchan NCHAN
--pols POLS
--size SIZE
--scale SCALE
--mgain MGAIN
--niter NITER
--nmiter NMITER
--auto_mask AUTO_MASK
--auto_threshold AUTO_THRESHOLD
--local_rms
--local_rms_window LOCAL_RMS_WINDOW
--force_mask_rounds FORCE_MASK_ROUNDS
--gridder {direct-ft,idg,wgridder,tuned-wgridder,wstacking}
--taper TAPER
--minuv MINUV
--parallel PARALLEL
--purge Purge intermediate files (default: False)
--mpi Use MPI (default: False)
--multiscale Use multiscale clean (default: False)
--multiscale_scale_bias MULTISCALE_SCALE_BIAS
--robust ROBUST
--nchan NCHAN
--pols POLS
--size SIZE
--scale SCALE
--mgain MGAIN
--niter NITER
--nmiter NMITER
--auto_mask AUTO_MASK
--auto_threshold AUTO_THRESHOLD
--local_rms
--local_rms_window LOCAL_RMS_WINDOW
--force_mask_rounds FORCE_MASK_ROUNDS
--gridder {direct-ft,idg,wgridder,tuned-wgridder,wstacking}
--taper TAPER
--minuv MINUV
--parallel PARALLEL
--purge Purge intermediate files (default: False)
--mpi Use MPI (default: False)
--multiscale Use multiscale clean (default: False)
--multiscale_scale_bias MULTISCALE_SCALE_BIAS
The multiscale scale bias term provided to wsclean. (default: None)
--multiscale_scales MULTISCALE_SCALES
--multiscale_scales MULTISCALE_SCALES
The scales used in the multiscale clean. (default: 0,2,4,8,16,32,64,128)
--absmem ABSMEM Absolute memory limit in GB (default: None)
--make_residual_cubes
--absmem ABSMEM Absolute memory limit in GB (default: None)
--make_residual_cubes
Create residual cubes as well as cubes from restored images. (default: False)
--ms_glob_pattern MS_GLOB_PATTERN
--ms_glob_pattern MS_GLOB_PATTERN
The pattern used to search for measurement sets. (default: scienceData*_averaged_cal.leakage.ms)
--data_column DATA_COLUMN
--data_column DATA_COLUMN
Which column in the measurement set to image. (default: CORRECTED_DATA)
--no_mf_weighting Do not use multi-frequency weighting. (default: False)
--skip_fix_ms Do not apply the ASKAP MS corrections from the package fixms. (default: False)
--hosted-wsclean HOSTED_WSCLEAN
Docker or Singularity image for wsclean [docker://alecthomson/wsclean:latest] (default: docker://alecthomson/wsclean:latest)
--local_wsclean LOCAL_WSCLEAN
Path to local wsclean Singularity image (default: None)
--no_mf_weighting Do not use multi-frequency weighting. (default: False)
--skip_fix_ms Do not apply the ASKAP MS corrections from the package fixms. (default: False)
--num_beams NUM_BEAMS
Number of beams to image (default: 36)
workdir arguments:
datadir Directory to create/find full-size images and 'cutout' directory
You may instead prefer to use the Python API, which is more flexible and allows for parallel imaging. You will need to set up your own Prefect task-runner for this. Here is a (very) minimal example:
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