How to use enable_interactive method in Slash

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imaging_observation.py

Source:imaging_observation.py

1#!/usr/bin/env python2##################################################3###          MODULE IMPORT4##################################################5## STANDARD MODULES6import os7import sys8import subprocess9import string10import time11import signal12from threading import Thread13import datetime14import numpy as np15import random16import math17import errno18## ASTRO MODULES19from astropy.io import fits20## COMMAND-LINE ARG MODULES21import getopt22import argparse23import collections24#### GET SCRIPT ARGS ####25def str2bool(v):26	if v.lower() in ('yes', 'true', 't', 'y', '1'):27		return True28	elif v.lower() in ('no', 'false', 'f', 'n', '0'):29		return False30	else:31		raise argparse.ArgumentTypeError('Boolean value expected.')32def get_args():33	"""This function parses and return arguments passed in"""34	parser = argparse.ArgumentParser(description="Parse args.")35	36	# - MANDATORY OPTIONS37	parser.add_argument('-vis', '--vis', dest='vis', required=True, type=str,action='store',help='Input visibility CASA table name produced by simobserve')38	parser.add_argument('-mapsize', '--mapsize', dest='mapsize', required=True, type=int,action='store',help='Map size in pixels')39	40	# OPTIONAL OPTIONS	41	parser.add_argument('-outimage', '--outimage', dest='outimage', required=False, type=str, default='mosaic',action='store',help='Output mosaic image')42	parser.add_argument('-mask', '--mask', dest='mask', required=False, type=str, default='',action='store',help='Mask file (default=none)')43	parser.add_argument('-outproject', '--outproject', dest='outproject', required=False, type=str, default='rec',action='store',help='Output project name (default=rec)')44	parser.add_argument('-pixsize', '--pixsize', dest='pixsize', required=False, type=str, default='1arcsec',action='store',help='Pixel size (default=1 arcsec)')45	parser.add_argument('-phasecenter', '--phasecenter', dest='phasecenter', required=False, type=str, default='J2000 254.85067091580214deg -41.47631111052697deg',action='store',help='Map phase center')46	parser.add_argument('-deconvolver', '--deconvolver', dest='deconvolver', required=False, type=str, default='clark',action='store',help='Deconvolver (default=clark)')47	parser.add_argument('-gridder', '--gridder', dest='gridder', required=False, type=str, default='standard',action='store',help='Gridder (default=standard)')48	parser.add_argument('-weighting', '--weighting', dest='weighting', required=False, type=str, default='briggs',action='store',help='weighting (default=briggs)')49	parser.add_argument('-projection', '--projection', dest='projection', required=False, type=str, default='SIN',action='store',help='projection (default=SIN)')50	51	parser.add_argument('-niter', '--niter', dest='niter', required=False, type=int, default=1000,action='store',help='Clean tot number of iterations (default=1000)')52	parser.add_argument('-cycleniter', '--cycleniter', dest='cycleniter', required=False, type=int, default=-1,action='store',help='Max cycle niter (default=-1)')53	parser.add_argument('-threshold', '--threshold', dest='threshold', required=False, type=float, default=0,action='store',help='Stopping threshold in Jy (default=0)')54	##parser.add_argument('--mosaic', dest='enable_mosaic', action='store_true')		55	parser.add_argument('--no-mosaic', dest='enable_mosaic', action='store_false')56	parser.set_defaults(enable_mosaic=True)57	##parser.add_argument('--fitsout', dest='enable_fitsout', action='store_true')		58	parser.add_argument('--no-fitsout', dest='enable_fitsout', action='store_false')	59	parser.set_defaults(enable_fitsout=True)60	parser.add_argument('-fitsout', '--fitsout', dest='fitsout', required=False, type=str, default='output.fits',action='store',help='Output FITS file (default=output.fits)')61	parser.add_argument('-scales', '--scales', dest='scales', required=False, type=str, default='0',action='store',help='List of scales (in pixels) for multiscale deconvolver (comma separated) (default=0)')62	parser.add_argument('-restoringbeam', '--restoringbeam', dest='restoringbeam', required=False, type=str, default='common',action='store',help='Restoring beam to be used (default=common)')63	64	parser.add_argument('--interactive', dest='enable_interactive', action='store_true')	65	parser.set_defaults(enable_interactive=False)66	67	parser.add_argument('-c', dest='scriptname', required=False, type=str, default='',action='store',help='Script name')68	args = parser.parse_args()	69	return args70def clean_observation(vis,image_size,niter=1000,cycleniter=-1,threshold=0,mask='',imagename='',field='',cell_size='1arcsec',phase_center='',weighting='briggs',projection='SIN',deconvolver='clark',gridder='standard',scales=[0],restoringbeam='common',savefits=True,fitsout='output.fits',interactive=False):71	""" Clean observation """72	73	## Set image name if empty74	if not imagename:75		project_name= 'rec'76		recimg= 'recmap'77		imagename=project_name + '/' + recimg	78	## Cleaning79	print ('INFO: Cleaning simulated data and produce final image...')80	tclean(81		imagename=imagename,82		vis=vis,83		field=field, 84		mask=mask,85		imsize=image_size,86		phasecenter=phase_center,87		projection=projection,88		cell=cell_size,	89		niter=niter,90		cycleniter=cycleniter,91		threshold=threshold,92		deconvolver=deconvolver,93		gridder=gridder,94		weighting=weighting,95		scales=scales,96		interactive=interactive97	)98	## Exporting to FITS99	if savefits:100		exported_map= imagename + '.image' 101		print ('INFO: Exporting CASA map %s to FITS...' % exported_map)102		exportfits(imagename=exported_map, fitsimage=fitsout, history=False, overwrite=True)103##############104##   MAIN   ##105##############106def main():107	"""Main function"""108	## Get script args109	print 'INFO: #%d arguments found: %s' % (len(sys.argv),str(sys.argv))110	try:111		args= get_args()112	except Exception as ex:113		print("ERROR: Failed to get and parse options (err=%s)",str(ex))114		return 1115	vis= args.vis116	niter= args.niter117	mask= args.mask118	mapsize= args.mapsize	119	outproject= args.outproject120	pixsize= args.pixsize121	phasecenter= args.phasecenter122	deconvolver= args.deconvolver123	gridder= args.gridder124	weighting= args.weighting125	projection= args.projection126	outimage= args.outimage127	cycleniter= args.cycleniter128	threshold= args.threshold129	enable_mosaic= args.enable_mosaic130	##mosaicimage= outproject + '_' + outimage131	mosaicimage= outproject + '/' + outimage132	133	enable_fitsout= args.enable_fitsout	134	fitsout= args.fitsout135	136	enable_interactive= args.enable_interactive137	scales_str = [str(item) for item in args.scales.split(',')]138	scales= []139	for item in scales_str:140		scale_int= int(item)141		scales.append(scale_int)142	restoringbeam= args.restoringbeam143	print("*** ARGS ***")144	print 'vis: ', vis145	print 'niter: ', niter146	print 'cycleniter: ', cycleniter147	print 'threshold: ', threshold148	print 'mask: ', mask149	print 'mapsize: ', mapsize150	print 'outproject: ', outproject151	print 'pixsize: ', pixsize152	print 'phasecenter: ', phasecenter153	print 'deconvolver: ', deconvolver154	print 'gridder: ', gridder155	print 'weighting: ', weighting156	print 'scales: ', scales157	print 'projection: ', projection158	print 'restoringbeam: ', restoringbeam159	print 'outimage: ', outimage160	print 'mosaicimage: ', mosaicimage161	print 'fitsout: ', fitsout162	print("************")163	164	# Retrieve number of pointings in simulation165	#tb= casac.table()	166	tb.open(vis + '/FIELD')167	npointings= tb.nrows()168	tb.close()169	print 'INFO: #' + str(npointings) + ' pointings present in input data...'170	171	## Image each pointing172	print ("INFO: Starting imaging pointing-by-pointing...")173	t_start = time.time()174	weightmap_list= []175	cleanmap_list= []176	bmaj_list= []177	bmin_list= []178	bpa_list= []179	bunit_list= []180	for field in range(0,npointings):181		182		imgname= outproject + '_field' + str(field) + '/recmap'183		##imgname= outproject + '/field' + str(field) + '/recmap'184		weightmap= imgname + '.pb'185		cleanmap= imgname + '.image'186		weightmap_list.append(weightmap) 187		cleanmap_list.append(cleanmap) 188		print 'INFO: Imaging field no. ', field189		clean_observation(190			vis=vis,191			niter=niter,192			cycleniter=cycleniter,193			threshold=threshold,194			mask=mask,195			imagename=imgname,196			field=str(field),197			image_size=mapsize,198			cell_size=pixsize,199			phase_center=phasecenter,200			weighting=weighting,201			projection=projection,	202			deconvolver=deconvolver,203			gridder=gridder,204			restoringbeam=restoringbeam,205			scales=scales,206			savefits=False,207			fitsout='tmpfield.fits',208			interactive=enable_interactive209		)210		211		## Retrieve beam information per each cleaned map212		print 'INFO: Get CASA image header...'213		imghead= imhead(imagename=cleanmap,mode='list')214		bunit= imghead['bunit']215		bmaj= imghead['beammajor']['value']216		bmin= imghead['beamminor']['value']217		bpa= imghead['beampa']['value']218		bmaj_list.append(bmaj)219		bmin_list.append(bmin)220		bpa_list.append(bpa)221		bunit_list.append(bunit)222	223	print 'weightmap_list=',weightmap_list224	print 'cleanmap_list=',cleanmap_list225	print 'bmaj_list=',bmaj_list226	print 'bmin_list=',bmin_list227	print 'bpa_list=',bpa_list228	print 'bunit_list=',bunit_list229	230	## Make linear mosaic with all fields231	if enable_mosaic:232		lm= casac.linearmosaic()233		lm.defineoutputimage(nx=mapsize,ny=mapsize,cellx=pixsize,celly=pixsize, imagecenter=phasecenter,outputimage=mosaicimage)234		lm.setlinmostype('optimal')235		##lm.makemosaic(images=['rec_field0/recmap.image','rec_field1/recmap.image'],weightimages=['rec_field0/recmap.pb','rec_field1/recmap.pb'])236		lm.makemosaic(images=cleanmap_list,weightimages=weightmap_list)237		#lm.saultweightimage('test_sault.linmos') 238		## Set missing field in mosaic image header239		## NB: beam info are missing. Each field has its own restoring beam info. Which one to use? Using the largest bmaj. Alternatively one can set the restoring beam in tclean (FIX ME)240		largest_bmaj_index= bmaj_list.index(max(bmaj_list))	241		cleanmap_head= imhead(imagename=cleanmap_list[largest_bmaj_index],mode='list')242		imhead(mosaicimage, mode="put", hdkey='beammajor', hdvalue=str(cleanmap_head['beammajor']['value']) + cleanmap_head['beammajor']['unit'])243		imhead(mosaicimage, mode="put", hdkey='beamminor', hdvalue=str(cleanmap_head['beamminor']['value']) + cleanmap_head['beamminor']['unit'])244		imhead(mosaicimage, mode="put", hdkey='beampa', hdvalue=str(cleanmap_head['beampa']['value']) + cleanmap_head['beampa']['unit'])245		imhead(mosaicimage, mode="put", hdkey='bunit', hdvalue=cleanmap_head['bunit'])246		## Exporting to FITS247		if enable_fitsout:248			exported_map= mosaicimage 249			print ('INFO: Exporting mosaic map %s to FITS...' % exported_map)250			exportfits(imagename=exported_map, fitsimage=fitsout, history=False, overwrite=True)251	252	t_stop = time.time()253	t_elapsed = t_stop - t_start254	## Print performance info255	print ('INFO: Imaging completed after dt(s)=%s' % str(t_elapsed))256	257###################258##   MAIN EXEC   ##259###################260if __name__ == "__main__":...

__init__.py

Source:__init__.py

...10    for extract source code, assembly, etc.11    """12    set_config("Executable_type", FullyInstrumentedExecutable) 13    set_config("ProgressBar", tqdm)...

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