def pixelmask2cleanmask(imagename='',
maskname='mask0',
maskimage='',
usemasked=False):
"""
convert pixel(T/F) mask (in a CASA image) to a mask image (1/0)
used for clean
imagename - input imagename that contain a mask to be used
maskname - mask name in the image (default: mask0)
maskimage - output mask image name
usemasked - if True use masked region as a valid region
"""
ia.open(imagename)
masks = ia.maskhandler('get')
ia.close()
inmaskname = ''
if type(masks) != list:
masks = [masks]
for msk in masks:
if maskname == msk:
inmaskname = msk
break
if inmaskname == '':
raise Exception, "mask %s does not exist. Available masks are: %s" % (
maskname, masks)
tb.open(imagename + '/' + maskname)
dat0 = tb.getcol('PagedArray')
tb.close()
#os.system('cp -r %s %s' % (imagename, maskimage))
shutil.copytree(imagename, maskimage)
ia.open(maskimage)
# to unset mask
ia.maskhandler('set', [''])
# make all valid
if (usemasked):
ia.set(1)
else:
ia.set(0)
ia.close()
#
tb.open(maskimage, nomodify=False)
imd = tb.getcol('map')
# maybe shape check here
#by default use True part of bool mask
masked = 1
if (usemasked): masked = 0
imd[dat0] = masked
tb.putcol('map', imd)
tb.close()
def pixelmask2cleanmask(imagename='',maskname='mask0',maskimage='',usemasked=False):
"""
convert pixel(T/F) mask (in a CASA image) to a mask image (1/0)
used for clean
imagename - input imagename that contain a mask to be used
maskname - mask name in the image (default: mask0)
maskimage - output mask image name
usemasked - if True use masked region as a valid region
"""
ia.open(imagename)
masks=ia.maskhandler('get')
ia.close()
inmaskname=''
if type(masks)!=list:
masks=[masks]
for msk in masks:
if maskname == msk:
inmaskname=msk
break
if inmaskname=='':
raise Exception, "mask %s does not exist. Available masks are: %s" % (maskname,masks)
tb.open(imagename+'/'+maskname)
dat0=tb.getcol('PagedArray')
tb.close()
#os.system('cp -r %s %s' % (imagename, maskimage))
shutil.copytree(imagename,maskimage)
ia.open(maskimage)
# to unset mask
ia.maskhandler('set',[''])
# make all valid
if (usemasked):
ia.set(1)
else:
ia.set(0)
ia.close()
#
tb.open(maskimage,nomodify=False)
imd=tb.getcol('map')
# maybe shape check here
#by default use True part of bool mask
masked=1
if (usemasked): masked=0
imd[dat0]=masked
tb.putcol('map',imd)
tb.close()
def blankcube(image,
dummyMS,
smooth=True,
verbose=True,
region='centerbox[[10h21m45s,18.05.14.9],[15arcmin,15arcmin]]',
ruthless=False,
extension='.image',
beamround='int',
blankThreshold=2.5,
moments=[0]):
'''
Parameters
----------
image : string
Base name of image. If target image has extension other than '.image',
change the extension keyword.
dummyMS : string
MS file required for blanking process in CASA
smooth : bool, optional
Smooth the image to a circular beam before blanking?
Default True
verbose : bool, optional
region : string, optional
region parameter featured in CASA
ruthless : bool, optional
Delete previous outputs from blankcube
extension : string, optional
Extension of the target image. Must include the '.', e.g., '.restored'
Default '.image'
beamround : string,float
P
blankThreshold : float, optional
Initial blanking threshold of all pixels scaled by the standard
deviation times the blankingthreshold
Default = 2.5 (Walter et al. 2008)
moments : list, optional
Moments to calculate from cube. Options are 0,1,2.
Example: [0,1,2]
Default: [0]
Returns
-------
out : null
Examples
--------
'''
from casa import immath, imsmooth, immoments
from casa import image as ia
from casa import imager as im
from casa import quanta as qa
import os
import numpy as np
# Delete files associated with previous runs
if ruthless:
os.system('rm -rf ' + image + '.smooth.blk.image')
os.system('rm -rf ' + image + '.smooth.image')
os.system('rm -rf ' + image + '.blk.image')
os.system('rm -rf ' + image + '.mask')
imageDir = './'
# Create moment maps
mom0, mom1, mom2 = False, False, False
if len(moments) > 0:
for i, moment in enumerate(moments):
if moment == 0:
mom0 = True
if moment == 1:
mom1 = True
if moment == 2:
mom2 = True
if mom1 == True or mom2 == True:
beamScale = 1.01
elif mom0 == True:
beamScale = 2.
# determine beamsize of cube
ia.open(imageDir + image + extension)
beamsizes = np.zeros(ia.shape()[2])
for i in range(ia.shape()[2]):
beamsizes[i] = ia.restoringbeam(channel=i)['major']['value']
beamsizeUnit = ia.restoringbeam(channel=i)['major']['unit']
beamsize = qa.convert(str(beamsizes.max()) + beamsizeUnit,
'arcsec')['value']
if type(beamround) == float:
beamsize_smooth = beamround * beamsize
else:
beamsize_smooth = np.ceil(beamsize) #beamsize_smooth = 1.01 * beamsize
ia.close()
if verbose:
print 'Max beamsize is ' + str(beamsize) + '"'
if not os.path.exists(image + '.blk.image'):
# create cube for blanking
if smooth: # smooth to a larger beam if the user desires
if verbose:
print 'Convolving to ' + str(beamsize_smooth) + '"'
imsmooth(imagename=image + extension,
outfile=image + '.blk.image',
major=str(beamsize_smooth) + 'arcsec',
minor=str(beamsize_smooth) + 'arcsec',
region=region,
pa='0deg',
targetres=True)
else: # do no smooth
immath(imagename=image + extension,
outfile=image + '.blk.image',
mode='evalexpr',
region=region,
expr='IM0')
if not os.path.exists(image + '.smooth.image'):
# convolve cube to 2X beam for blanking
imsmooth(imagename=image + extension,
outfile=image + '.smooth.image',
major=str(beamsize * beamScale) + 'arcsec',
minor=str(beamsize * beamScale) + 'arcsec',
pa='0deg',
region=region,
targetres=True)
# determine threshold of cube
ia.open(image + '.smooth.image')
threshold = ia.statistics()['sigma'][0] * blankThreshold
ia.close()
# blank the cube at threshold*sigma
ia.open(image + '.smooth.image')
ia.calcmask(mask=image + '.smooth.image > ' + str(threshold), name='mask1')
wait = 'waits for calcmask to close'
ia.close()
# hand blank the cube
im.open(dummyMS)
pause = None
while pause is None:
im.drawmask(image=image + '.smooth.image', mask=image + '.mask')
pause = 0
im.close
# mask contains values of 0 and 1, change to a mask with only values of 1
ia.open(image + '.mask')
ia.calcmask(image + '.mask' + '>0.5')
ia.close()
# apply mask on smoothed image
immath(imagename=image + '.smooth.image',
outfile=image + '.smooth.blk.image',
mode='evalexpr',
mask='mask(' + image + '.mask)',
expr='IM0')
# apply mask on image
ia.open(imageDir + image + '.blk.image')
ia.maskhandler('copy', [image + '.smooth.blk.image:mask0', 'newmask'])
ia.maskhandler('set', 'newmask')
ia.done()
cube = '.blk.image' # specify name of cube for moment calculation
# create moment 0 map
if mom0:
if ruthless:
os.system('rm -rf ' + image + '.mom0.image')
immoments(imagename=image + cube,
moments=[0],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom0.image')
# create moment 1 map
if mom1:
if ruthless:
os.system('rm -rf ' + image + '.mom1.image')
immoments(imagename=image + cube,
moments=[1],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom1.image')
# create moment 2 map
if mom2:
if ruthless:
os.system('rm -rf ' + image + '.mom2.image')
immoments(imagename=image + cube,
moments=[2],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom2.image')
if verbose and mom0:
from casa import imstat
flux = imstat(image + '.mom0.image')['flux'][0]
ia.open(image + '.mom0.image')
beammaj = ia.restoringbeam(channel=0)['major']['value']
beammin = ia.restoringbeam(channel=0)['minor']['value']
beamsizeUnit = ia.restoringbeam(channel=0)['major']['unit']
ia.close()
print 'Moment Image: ' + str(image) + '.mom0.image'
print 'Beamsize: ' + str(beammaj) + '" X ' + str(beammin) + '"'
print 'Flux: ' + str(flux) + ' Jy km/s'
def blankcube(image,
dummyMS,
smooth=True,
verbose=True,
region='centerbox[[10h21m45s,18.05.14.9],[15arcmin,15arcmin]]',
ruthless=False,
extension='.image',
beamround='int',
blankThreshold=2.5,
moments=[0]):
'''
Parameters
----------
image : string
Base name of image. If target image has extension other than '.image',
change the extension keyword.
dummyMS : string
MS file required for blanking process in CASA
smooth : bool, optional
Smooth the image to a circular beam before blanking?
Default True
verbose : bool, optional
region : string, optional
region parameter featured in CASA
ruthless : bool, optional
Delete previous outputs from blankcube
extension : string, optional
Extension of the target image. Must include the '.', e.g., '.restored'
Default '.image'
beamround : string,float
P
blankThreshold : float, optional
Initial blanking threshold of all pixels scaled by the standard
deviation times the blankingthreshold
Default = 2.5 (Walter et al. 2008)
moments : list, optional
Moments to calculate from cube. Options are 0,1,2.
Example: [0,1,2]
Default: [0]
Returns
-------
out : null
Examples
--------
'''
from casa import immath,imsmooth,immoments
from casa import image as ia
from casa import imager as im
from casa import quanta as qa
import os
import numpy as np
# Delete files associated with previous runs
if ruthless:
os.system('rm -rf ' + image + '.smooth.blk.image')
os.system('rm -rf ' + image + '.smooth.image')
os.system('rm -rf ' + image + '.blk.image')
os.system('rm -rf ' + image + '.mask')
imageDir = './'
# Create moment maps
mom0,mom1,mom2 = False,False,False
if len(moments) > 0:
for i, moment in enumerate(moments):
if moment == 0:
mom0 = True
if moment == 1:
mom1 = True
if moment == 2:
mom2 = True
if mom1 == True or mom2 == True:
beamScale = 1.01
elif mom0 == True:
beamScale = 2.
# determine beamsize of cube
ia.open(imageDir + image + extension)
beamsizes = np.zeros(ia.shape()[2])
for i in range(ia.shape()[2]):
beamsizes[i] = ia.restoringbeam(channel=i)['major']['value']
beamsizeUnit = ia.restoringbeam(channel=i)['major']['unit']
beamsize = qa.convert(str(beamsizes.max()) + beamsizeUnit,'arcsec')['value']
if type(beamround) == float:
beamsize_smooth = beamround*beamsize
else:
beamsize_smooth = np.ceil(beamsize) #beamsize_smooth = 1.01 * beamsize
ia.close()
if verbose:
print 'Max beamsize is ' + str(beamsize) + '"'
if not os.path.exists(image + '.blk.image'):
# create cube for blanking
if smooth: # smooth to a larger beam if the user desires
if verbose:
print 'Convolving to ' + str(beamsize_smooth) + '"'
imsmooth(imagename=image + extension,
outfile=image + '.blk.image',
major=str(beamsize_smooth) + 'arcsec',
minor=str(beamsize_smooth) + 'arcsec',
region=region,
pa='0deg',
targetres=True)
else: # do no smooth
immath(imagename=image + extension,
outfile=image + '.blk.image',
mode='evalexpr',
region=region,
expr='IM0')
if not os.path.exists(image + '.smooth.image'):
# convolve cube to 2X beam for blanking
imsmooth(imagename=image + extension,
outfile=image + '.smooth.image',
major=str(beamsize*beamScale) + 'arcsec',
minor=str(beamsize*beamScale) + 'arcsec',
pa='0deg',
region=region,
targetres=True)
# determine threshold of cube
ia.open(image + '.smooth.image')
threshold = ia.statistics()['sigma'][0] * blankThreshold
ia.close()
# blank the cube at threshold*sigma
ia.open(image + '.smooth.image')
ia.calcmask(mask=image + '.smooth.image > ' + str(threshold),
name='mask1')
wait = 'waits for calcmask to close'
ia.close()
# hand blank the cube
im.open(dummyMS)
pause = None
while pause is None:
im.drawmask(image=image + '.smooth.image',
mask=image + '.mask')
pause = 0
im.close
# mask contains values of 0 and 1, change to a mask with only values of 1
ia.open(image + '.mask')
ia.calcmask(image + '.mask' + '>0.5')
ia.close()
# apply mask on smoothed image
immath(imagename=image + '.smooth.image',
outfile=image + '.smooth.blk.image',
mode='evalexpr',
mask='mask(' + image + '.mask)',
expr='IM0')
# apply mask on image
ia.open(imageDir + image + '.blk.image')
ia.maskhandler('copy',[image + '.smooth.blk.image:mask0', 'newmask'])
ia.maskhandler('set','newmask')
ia.done()
cube = '.blk.image' # specify name of cube for moment calculation
# create moment 0 map
if mom0:
if ruthless:
os.system('rm -rf ' + image + '.mom0.image')
immoments(imagename=image + cube,
moments=[0],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom0.image')
# create moment 1 map
if mom1:
if ruthless:
os.system('rm -rf ' + image + '.mom1.image')
immoments(imagename=image + cube,
moments=[1],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom1.image')
# create moment 2 map
if mom2:
if ruthless:
os.system('rm -rf ' + image + '.mom2.image')
immoments(imagename=image + cube,
moments=[2],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom2.image')
if verbose and mom0:
from casa import imstat
flux = imstat(image + '.mom0.image')['flux'][0]
ia.open(image + '.mom0.image')
beammaj = ia.restoringbeam(channel=0)['major']['value']
beammin = ia.restoringbeam(channel=0)['minor']['value']
beamsizeUnit = ia.restoringbeam(channel=0)['major']['unit']
ia.close()
print 'Moment Image: ' + str(image) + '.mom0.image'
print 'Beamsize: ' + str(beammaj) + '" X ' + str(beammin) + '"'
print 'Flux: ' + str(flux) + ' Jy km/s'
