def imsubimage(
imagename, outfile, box, region, chans, stokes, mask, dropdeg,
overwrite, verbose, stretch, keepaxes
):
casalog.origin('imsubimage')
myia = iatool()
myia.dohistory(False)
outia = None
try:
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
if (len(outfile) == 0):
raise Exception, "outfile must be specified."
xregion = region
if (type(region) != type({})):
xregion = _rg.frombcs(
csys=myia.coordsys().torecord(), shape=myia.shape(), box=box,
chans=chans, stokes=stokes, stokescontrol="a", region=region
)
outia = myia.subimage(
outfile=outfile, region=xregion, mask=mask, dropdeg=dropdeg,
overwrite=overwrite, list=verbose, stretch=stretch, keepaxes=keepaxes
)
try:
param_names = imsubimage.func_code.co_varnames[:imsubimage.func_code.co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(
outia, sys._getframe().f_code.co_name,
param_names, param_vals, casalog
)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance), 'WARN')
return True
def imcollapse(imagename=None,
function=None,
axes=None,
outfile=None,
box=None,
region=None,
chans=None,
stokes=None,
mask=None,
overwrite=None,
stretch=None):
casalog.origin('imcollapse')
try:
if (len(outfile) == 0):
raise Exception, "oufile must be specified"
myia = iatool()
myia.dohistory(False)
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
outia = myia.collapse(function, axes, outfile, region, box, chans,
stokes, mask, overwrite, stretch)
try:
param_names = imcollapse.func_code.co_varnames[:imcollapse.
func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(outia,
sys._getframe().f_code.co_name, param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
outia.done()
return True
def impbcor(
imagename=None, pbimage=None, outfile=None, overwrite=None,
box=None, region=None, chans=None, stokes=None, mask=None,
mode=None, cutoff=None, stretch=None
):
casalog.origin('impbcor')
myia = iatool()
try:
myia.dohistory(False)
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
if (len(outfile) == 0):
raise Exception, "outfile must be specified"
outia = myia.pbcor(
pbimage=pbimage, outfile=outfile, overwrite=overwrite,
box=box, region=region, chans=chans, stokes=stokes,
mask=mask, mode=mode, cutoff=cutoff, stretch=stretch
)
try:
param_names = impbcor.func_code.co_varnames[:impbcor.func_code.co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(
outia, sys._getframe().f_code.co_name,
param_names, param_vals, casalog
)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance), 'WARN')
outia.done()
return True
def rmfit(
imagename,
rm,
rmerr,
pa0,
pa0err,
nturns,
chisq,
sigma,
rmfg,
rmmax,
maxpaerr,
):
casalog.origin('prom')
myia = iatool()
myia.dohistory(False)
mypo = potool()
tmpim = ""
try:
if len(imagename) == 0:
raise Exception, "imagename must be specified."
if type(imagename) == type(['s']):
# negative axis value means concatenate along spectral axis
tmpim = tempfile.mkdtemp(suffix=".im", prefix="_rmfit_concat")
myia = myia.imageconcat(outfile=tmpim,
infiles=imagename,
relax=True,
axis=-1,
overwrite=True)
if not myia:
raise Exception("Unable to concatenate images.")
myia.done()
mypo.open(tmpim)
else:
if (not mypo.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
mypo.rotationmeasure(rm=rm,
rmerr=rmerr,
pa0=pa0,
pa0err=pa0err,
nturns=nturns,
chisq=chisq,
sigma=sigma,
rmfg=rmfg,
rmmax=rmmax,
maxpaerr=maxpaerr)
try:
param_names = rmfit.func_code.co_varnames[:rmfit.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
for im in [rm, rmerr, pa0, pa0err, nturns, chisq]:
write_image_history(im,
sys._getframe().f_code.co_name,
param_names, param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return True
def imrebin(imagename, outfile, factor, region, box, chans, stokes, mask,
dropdeg, overwrite, stretch, crop):
casalog.origin('imrebin')
valid = True
# because there is a bug in the tasking layer that allows float
# arrays through when the spec is for intArray
for x in factor:
if x != int(x):
valid = False
break
if not valid:
for i in range(len(factor)):
factor[i] = int(factor[i])
casalog.post(
"factor is not an int array, it will be adjusted to " +
str(factor), 'WARN')
myia = iatool()
myia.dohistory(False)
outia = None
try:
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
if (len(outfile) == 0):
raise Exception, "outfile must be specified."
if (type(region) != type({})):
myrg = rgtool()
reg = myrg.frombcs(csys=myia.coordsys().torecord(),
shape=myia.shape(),
box=box,
chans=chans,
stokes=stokes,
stokescontrol="a",
region=region)
else:
reg = region
outia = myia.rebin(outfile=outfile,
bin=factor,
region=reg,
mask=mask,
dropdeg=dropdeg,
overwrite=overwrite,
stretch=stretch,
crop=crop)
try:
param_names = imrebin.func_code.co_varnames[:imrebin.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(outia,
sys._getframe().f_code.co_name, param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return True
def immoments(imagename, moments, axis, region, box, chans, stokes, mask,
includepix, excludepix, outfile, stretch):
retValue = None
casalog.origin('immoments')
_myia = iatool()
try:
_myia.dohistory(False)
# First check to see if the output file exists. If it
# does then we abort. CASA doesn't allow files to be
# over-written, just a policy.
if (len(outfile) > 0 and os.path.exists(outfile)):
raise Exception, 'Output file, '+outfile+\
' exists. immoment can not proceed, please\n'\
'remove it or change the output file name.'
elif (len(outfile) == 1):
raise Exception, 'outfile is not specified but must be'
_myia.open(imagename)
reg = _rg.frombcs(csys=_myia.coordsys().torecord(),
shape=_myia.shape(),
box=box,
chans=chans,
stokes=stokes,
stokescontrol="a",
region=region)
if isinstance(axis, str):
axis = _myia.coordsys().findaxisbyname(axis)
outia = _myia.moments(moments=moments,
axis=int(axis),
mask=mask,
region=reg,
includepix=includepix,
excludepix=excludepix,
outfile=outfile,
drop=False,
stretch=stretch)
created_images = _immoments_get_created_images(outia.name(), outfile)
created_images.append(outia)
try:
param_names = immoments.func_code.co_varnames[:immoments.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
method = sys._getframe().f_code.co_name
for im in created_images:
write_image_history(im, method, param_names, param_vals,
casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return True
def impv(
imagename, outfile, mode, start, end, center, length, pa, width,
unit, overwrite, region, chans, stokes, mask, stretch
):
casalog.origin('impv')
try:
if len(outfile) == 0:
raise Exception, "outfile must be specified."
mymode = mode.lower()
if mymode.startswith('c'):
if len(start) == 0 or len(end) == 0:
raise Exception, "When mode='coords', start and end must both be specified."
center = ""
length = ""
pa = ""
elif mymode.startswith('l'):
if (
len(center) == 0
or (
not isinstance(length, (int, long, float))
and len(length) == 0
)
or len(pa) == 0
):
raise Exception, "When mode='length', center, length, and pa must all be specified."
start = ""
end = ""
else:
raise Exception, "Unsupported value for mode."
myia = iatool()
myia.dohistory(False)
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
outia = myia.pv(
outfile=outfile, start=start, end=end, center=center,
length=length, pa=pa, width=width, unit=unit,
overwrite=overwrite, region=region, chans=chans,
stokes=stokes, mask=mask, stretch=stretch, wantreturn=True
)
try:
param_names = impv.func_code.co_varnames[:impv.func_code.co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(
outia, sys._getframe().f_code.co_name,
param_names, param_vals, casalog
)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance), 'WARN')
return True
def imfit(imagename, box, region, chans, stokes, mask, includepix, excludepix,
residual, model, estimates, logfile, append, newestimates, complist,
overwrite, dooff, offset, fixoffset, stretch, rms, noisefwhm,
summary):
casalog.origin('imfit')
myia = iatool()
try:
myia.dohistory(False)
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
result_dict = myia.fitcomponents(box=box,
region=region,
chans=chans,
stokes=stokes,
mask=mask,
includepix=includepix,
excludepix=excludepix,
residual=residual,
model=model,
estimates=estimates,
logfile=logfile,
append=append,
newestimates=newestimates,
complist=complist,
overwrite=overwrite,
dooff=dooff,
offset=offset,
fixoffset=fixoffset,
stretch=stretch,
rms=rms,
noisefwhm=noisefwhm,
summary=summary)
try:
param_names = imfit.func_code.co_varnames[:imfit.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
for im in [residual, model]:
write_image_history(im,
sys._getframe().f_code.co_name,
param_names, param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return result_dict
def imdev(imagename, outfile, region, box, chans, stokes, mask, overwrite,
stretch, grid, anchor, xlength, ylength, interp, stattype, statalg,
zscore, maxiter):
_myia = iatool()
_myrg = rgtool()
_mycs = cstool()
try:
casalog.origin('imdev')
_myia.open(imagename)
_mycs = _myia.coordsys()
csrec = _mycs.torecord()
shape = _myia.shape()
reg = _myrg.frombcs(csrec, shape, box, chans, stokes, "a", region)
outia = _myia.deviation(outfile=outfile,
region=reg,
mask=mask,
overwrite=overwrite,
stretch=stretch,
grid=grid,
anchor=anchor,
xlength=xlength,
ylength=ylength,
interp=interp,
stattype=stattype,
statalg=statalg,
zscore=zscore,
maxiter=maxiter)
try:
param_names = imdev.func_code.co_varnames[:imdev.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(outia,
sys._getframe().f_code.co_name, param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
outia.done()
return True
def imtrans(imagename, outfile, order):
casalog.origin('imtrans')
myia = iatool()
myia.dohistory(False)
outia = None
try:
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
if (len(outfile) == 0):
raise Exception, "outfile parameter must be specified."
outia = myia.transpose(outfile=outfile, order=order)
try:
param_names = imtrans.func_code.co_varnames[:imtrans.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(outia,
sys._getframe().f_code.co_name, param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return True
def immath(imagename, mode, outfile, expr, varnames, sigma, polithresh, mask,
region, box, chans, stokes, stretch, imagemd):
# Tell CASA who will be reporting
casalog.origin('immath')
tmpFilePrefix = '_immath_tmp' + str(os.getpid()) + '_'
_myia = iatool()
_myia.dohistory(False)
outia = iatool()
try:
_immath_initial_cleanup(tmpFilePrefix)
outfile = _immath_check_outfile(outfile)
# Find the list of filenames in the expression
# also do a quick check to see if all of the files
# exist
tmpfilenames = ''
filenames = imagename
if mode == 'evalexpr':
tmpfilenames = _immath_parse(expr)
if isinstance(filenames, str):
filenames = [filenames]
varnames = _immath_varnames(varnames, filenames, tmpfilenames)
filenames = _immath_filenames(filenames, tmpfilenames, varnames, mode)
expr = expr.replace(' ', '')
if mode == 'spix':
expr = _immath_dospix(len(filenames), varnames)
elif mode == 'pola':
_immath_new_pola(filenames, outfile, tmpFilePrefix, mask, region,
box, chans, stokes, stretch, polithresh, _myia)
return True
elif mode == 'poli':
_immath_new_poli(filenames, outfile, tmpFilePrefix, mask, region,
box, chans, stokes, stretch, sigma, _myia)
return True
if box or chans or stokes or region or mask:
(subImages,
file_map) = _immath_createsubimages(box, chans, stokes, region,
mask, stretch, filenames,
_myia, tmpFilePrefix)
if imagemd:
casalog.post(
"Specifying region, box, chan, or stokes will " +
"create smaller sub-images. The image " +
"metadata specified in imagemd will have to " +
"conform to the output, not the input image " +
"dimensions. Please check your output image " +
"for accurate header definition.", 'WARN')
(expr, varnames,
subImages) = _immath_updateexpr(expr, varnames, subImages,
filenames, file_map)
outia = _immath_compute(imagename, expr, outfile, imagemd, _myia)
else:
# If the user didn't give any region or mask information
# then just evaluated the expression with the filenames in it.
outia = _immath_dofull(imagename, imagemd, outfile, mode, expr,
varnames, filenames, _myia)
try:
param_names = immath.func_code.co_varnames[:immath.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(outia,
sys._getframe().f_code.co_name, param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return True
def imsmooth(imagename, kernel, major, minor, pa, targetres, kimage, scale,
region, box, chans, stokes, mask, outfile, stretch, overwrite,
beam):
casalog.origin('imsmooth')
ikernel = kernel.startswith('i')
ckernel = kernel.startswith('c')
bkernel = kernel.startswith('b')
gkernel = kernel.startswith('g')
if (not (gkernel or bkernel or ckernel or ikernel)):
casalog.post('Unsupported kernel, ' + kernel, 'SEVERE')
return False
if (not ikernel and type(beam) == str):
if len(beam) != 0:
err = "beam cannot be a non-empty string"
casalog.post(err, "SEVERE")
raise Exception(err)
beam = {}
# First check to see if the output file exists. If it
# does then we abort. CASA doesn't allow files to be
# over-written, just a policy.
if (len(outfile) < 1):
outfile = 'imsmooth_results.im'
casalog.post( "The outfile paramter is empty, consequently the" \
+" smoothed image will be\nsaved on disk in file, " \
+ outfile, 'WARN')
_myia = iatool()
_myia.dohistory(False)
retia = iatool()
_myia.open(imagename)
mycsys = _myia.coordsys()
myrg = rgtool()
reg = myrg.frombcs(mycsys.torecord(), _myia.shape(), box, chans, stokes,
"a", region)
myrg.done()
mycsys.done()
_myia.done()
# If the values given are integers we assume they are given in
# arcsecs and alter appropriately
if not ikernel:
if isinstance(major, (int, long, float)):
major = str(major) + 'arcsec'
if isinstance(minor, (int, long, float)):
minor = str(minor) + 'arcsec'
if isinstance(pa, (int, long, float)):
pa = str(pa) + 'deg'
try:
if (gkernel or ckernel):
_myia.open(imagename)
if ckernel:
beam = _myia.commonbeam()
# add a small epsilon to avoid convolving with a null beam to reach
# a target resolution that already exists
beam['major'] = qa.mul(beam['major'], 1 + 1e-10)
beam['minor'] = qa.mul(beam['minor'], 1 + 1e-10)
major = ""
minor = ""
pa = ""
targetres = True
if (beam and (major or minor or pa)):
raise Exception, "You may specify only beam or the set of major/minor/pa"
if not beam:
if not major:
raise Exception, "Major axis must be specified"
if not minor:
raise Exception, "Minor axis must be specified"
if not pa:
raise Exception, "Position angle must be specified"
outia = _myia.convolve2d(axes=[0, 1],
region=reg,
major=major,
minor=minor,
pa=pa,
outfile=outfile,
mask=mask,
stretch=stretch,
targetres=targetres,
overwrite=overwrite,
beam=beam)
elif (bkernel):
if not major or not minor:
raise Exception, "Both major and minor must be specified."
# BOXCAR KERNEL
#
# Until convolve2d supports boxcar we will need to
# use sepconvolve to do this.
#
# BIG NOTE!!!!!
# According to Gaussian2D documentation the default position
# angle aligns the major axis along the y-axis, which typically
# be lat. So this means that we need to use the major quantity
# on the y axis (or 1) for sepconvolve.
_myia.open(imagename)
casalog.post( "ia.sepconvolve( axes=[0,1],"+\
"types=['boxcar','boxcar' ],"+\
"widths=[ "+str(minor)+", "+str(major)+" ],"+ \
"region="+str(reg)+",outfile="+outfile+" )",\
'DEBUG2' )
#retValue = ia.sepconvolve( axes=[0,1], types=['box','box' ],\
# widths=[ minor, major ], \
# region=reg,outfile=outfile )
outia = _myia.sepconvolve(axes=[0, 1],
types=['box', 'box'],
widths=[minor, major],
region=reg,
outfile=outfile,
mask=mask,
stretch=stretch,
overwrite=overwrite)
elif ikernel:
_myia.open(imagename)
outia = _myia.convolve(outfile=outfile,
kernel=kimage,
scale=scale,
region=reg,
mask=mask,
overwrite=overwrite,
stretch=stretch)
else:
casalog.post('Unrecognized kernel type: ' + kernel, 'SEVERE')
return False
try:
param_names = imsmooth.func_code.co_varnames[:imsmooth.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(outia,
sys._getframe().f_code.co_name, param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return True
def importfits(fitsimage, imagename, whichrep, whichhdu, zeroblanks, overwrite,
defaultaxes, defaultaxesvalues, beam):
"""Convert an image FITS file into a CASA image:
Keyword arguments:
fitsimage -- Name of input image FITS file
default: none; example='3C273XC1.fits'
imagename -- Name of output CASA image
default: none; example: imagename='3C273XC1.image'
whichrep -- If fits image has multiple coordinate reps, choose one.
default: 0 means first; example: whichrep=1
whichhdu -- If its file contains multiple images, choose one (0 = first HDU, -1 = first valid image)
default=-1 ; example: whichhdu=1
zeroblanks -- Set blanked pixels to zero (not NaN)
default=True; example: zeroblanks=True
overwrite -- Overwrite pre-existing imagename
default=False; example: overwrite=True
defaultaxes -- Add the default 4D coordinate axes where they are missing
default=False, example: defaultaxes=True
defaultaxesvalues -- List of values to assign to added degenerate axes when defaultaxes==True (ra,dec,freq,stokes)
default = [], example: defaultaxesvalues=['13.5h', '-2.5deg', '88.5GHz', 'Q']
beam -- List of values to be used to define the synthesized beam [BMAJ,BMIN,BPA] (as in the FITS keywords)
default = [] (i.e. take from FITS file), example: beam=['0.35arcsec', '0.24arcsec', '25deg']
"""
#Python script
casalog.origin('importfits')
_myia = iatool()
tmpname = imagename
reorder = False
addaxes = False
adddir = False
addstokes = False
addfreq = False
defaultorder = ['Right Ascension', 'Declination', 'Stokes', 'Frequency']
addbeam = False
try:
_myia.dohistory(False)
if os.path.exists(imagename):
if not overwrite:
raise RuntimeError, 'Output image exists already and you did not set overwrite to True.'
else:
os.system('rm -rf ' + imagename)
if defaultaxes:
if len(defaultaxesvalues) != 4:
raise TypeError, 'When defaultaxes==True, parameter defaultaxesvalues must be provided as a list of 4 values: RA, Dec, Freq, Stokes,\n e.g. [\'13.5h\', \'-2.5deg\', \'88.5GHz\', \'I\']\nFor existing axes, empty strings can be given as values.'
_myia.open(fitsimage)
_mycs = _myia.coordsys()
acts = _mycs.axiscoordinatetypes()
cnames = _mycs.names()
_myia.close()
if ('Direction' in acts and not ('Right Ascension' in cnames
and 'Declination' in cnames)):
raise RuntimeError, 'Non-standard direction axes. Cannot add default axes.'
if ('Spectral' in acts and not 'Frequency' in cnames):
raise RuntimeError, 'Non-standard spectral axis. Cannot add default axes.'
if ('Stokes' in acts and not 'Stokes' in cnames):
raise RuntimeError, 'Non-standard Stokes axis. Cannot add default axes.'
if not ('Right Ascension' in cnames and 'Declination' in cnames):
addaxes = True
adddir = True
if not ('Frequency' in cnames):
addaxes = True
addfreq = True
if not ('Stokes' in cnames):
addaxes = True
addstokes = True
if not addaxes and cnames != defaultorder:
reorder = True
if addaxes or reorder:
tmpname = imagename + '.tmp'
os.system('rm -rf ' + tmpname)
if beam != []: # user has set beam
if type(beam) != list or len(beam) != 3 or not (type(
beam[0]) == str and type(beam[1]) == str
and type(beam[2])):
raise TypeError, "Parameter beam is invalid (should be list of 3 strings or empty): " + str(
beam)
qabeam = []
for i in range(0, 3):
try:
qabeam.append(qa.quantity(beam[i]))
tmp = qa.toangle(qabeam[i])
except:
raise TypeError, "Parameter beam[" + str(
i) + "] is invalid (should be an angle): " + str(
beam[i])
if (qa.convert(qabeam[0], 'arcsec') >= qa.convert(
qabeam[1], 'arcsec')):
addbeam = True
else:
raise TypeError, "Parameter beam[" + str(
i
) + "] is invalid (major axis must be >= minor axis): " + str(
beam)
_myia.fromfits(tmpname, fitsimage, whichrep, whichhdu, zeroblanks)
_myia.close()
if addaxes:
casalog.post('Adding missing coodinate axes ...', 'INFO')
tmpname2 = imagename + '.tmp2'
os.system('rm -rf ' + tmpname2)
_myia.open(tmpname)
ia2 = _myia.adddegaxes(outfile=tmpname2,
direction=True,
spectral=True,
stokes=defaultaxesvalues[3],
silent=True)
_myia.close()
os.system('rm -rf ' + tmpname)
ia2.close()
ia2.open(tmpname2)
# set the right reference values in the added axes
_mynewcs = ia2.coordsys()
raval = 0.
decval = 0.
freqval = 0.
if adddir:
ra = defaultaxesvalues[0]
if type(ra) == int or type(ra) == float:
raval = ra
else:
qara = qa.quantity(qa.angle(ra)[0])
if qara['unit'].find('deg') < 0:
raise TypeError, "RA default value is not a valid angle quantity " % ra
raval = qara['value']
dec = defaultaxesvalues[1]
if type(dec) == int or type(dec) == float:
decval = dec
else:
qadec = qa.quantity(qa.angle(dec)[0])
if qadec['unit'].find('deg') < 0:
raise TypeError, "DEC default value is not a valid angle quantity " % dec
decval = qadec['value']
_mynewcs.setunits(value='deg deg', type='direction')
_mynewcs.setreferencevalue(type='direction',
value=[raval, decval])
if addfreq:
freq = defaultaxesvalues[2]
if type(freq) == int or type(freq) == float:
freqval = freq
else:
qafreq = qa.quantity(freq)
if qafreq['unit'].find('Hz') < 0:
raise TypeError, "Freq default value is not a valid frequency quantity " % freq
freqval = qa.convertfreq(qafreq, 'Hz')['value']
_mynewcs.setunits(value='Hz', type='spectral')
_mynewcs.setreferencevalue(type='spectral', value=freqval)
_mynewcs.setrestfrequency(freqval)
# Note: stokes default value was already set in adddegaxes
if adddir or addfreq:
ia2.setcoordsys(_mynewcs.torecord())
ia2.close()
cnames = _mynewcs.names()
if len(cnames) == 4 and not (cnames == defaultorder):
# need to reorder
reorder = True
tmpname = tmpname2
else:
os.system('mv ' + tmpname2 + ' ' + imagename)
if reorder:
casalog.post('Transposing coodinate axes ...', 'INFO')
_myia.open(tmpname)
ia2 = _myia.transpose(outfile=imagename, order=defaultorder)
_myia.close()
ia2.close()
os.system('rm -rf ' + tmpname)
_myia.open(imagename)
if addbeam:
_myia.setrestoringbeam(beam[0], beam[1], beam[2])
else:
mybeam = _myia.restoringbeam()
if mybeam == {}: # the fits image had no beam
casalog.post(
"This image has no beam or angular resolution provided, so you will not receive warnings from\n"
"tasks such as imregrid if your image pixels do not sample the the angular resolution well.\n"
"(This only affects warnings, not any functionality).\n"
"Providing a beam and brightness units in an image can also be useful for flux calculations.\n"
"If you wish to add a beam or brightness units to your image, please use\n"
"the \"beam\" parameter or ia.setrestoringbeam() and ia.setbrightnessunit()",
'WARN')
try:
param_names = importfits.func_code.co_varnames[:importfits.
func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(_myia,
sys._getframe().f_code.co_name, param_names,
param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return True
def specfit(imagename, box, region, chans, stokes, axis, mask, ngauss, poly,
estimates, minpts, multifit, model, residual, amp, amperr, center,
centererr, fwhm, fwhmerr, integral, integralerr, wantreturn,
stretch, logresults, pampest, pcenterest, pfwhmest, pfix, gmncomps,
gmampcon, gmcentercon, gmfwhmcon, gmampest, gmcenterest, gmfwhmest,
gmfix, logfile, append, pfunc, goodamprange, goodcenterrange,
goodfwhmrange, sigma, outsigma):
casalog.origin('specfit')
retval = None
myia = iatool()
myia.dohistory(False)
try:
if (not myia.open(imagename)):
raise Exception, "Cannot create image analysis tool using " + imagename
target_time = time.time()
retval = myia.fitprofile(box=box,
region=region,
chans=chans,
stokes=stokes,
axis=axis,
mask=mask,
ngauss=ngauss,
poly=poly,
estimates=estimates,
minpts=minpts,
multifit=multifit,
model=model,
residual=residual,
amp=amp,
amperr=amperr,
center=center,
centererr=centererr,
fwhm=fwhm,
fwhmerr=fwhmerr,
integral=integral,
integralerr=integralerr,
stretch=stretch,
logresults=logresults,
pampest=pampest,
pcenterest=pcenterest,
pfwhmest=pfwhmest,
pfix=pfix,
gmncomps=gmncomps,
gmampcon=gmampcon,
gmcentercon=gmcentercon,
gmfwhmcon=gmfwhmcon,
gmampest=gmampest,
gmcenterest=gmcenterest,
gmfwhmest=gmfwhmest,
gmfix=gmfix,
logfile=logfile,
append=append,
pfunc=pfunc,
goodamprange=goodamprange,
goodcenterrange=goodcenterrange,
goodfwhmrange=goodfwhmrange,
sigma=sigma,
outsigma=outsigma)
try:
param_names = specfit.func_code.co_varnames[:specfit.func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
ims = [model, residual]
for x in [
amp, amperr, center, centererr, fwhm, fwhmerr, integral,
integralerr
]:
if x:
ims.extend(get_created_images(x, target_time))
for im in ims:
write_image_history(im,
sys._getframe().f_code.co_name,
param_names, param_vals, casalog)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
except Exception, instance:
casalog.post('*** Error *** ' + str(instance), 'SEVERE')
retval = None
def imcontsub(
imagename, linefile, contfile, fitorder,
region, box, chans, stokes
):
casalog.origin('imcontsub')
filesExist=False
if ( len( linefile ) > 0 ):
if ( os.path.exists( linefile ) ):
casalog.post('Error: file ' + linefile
+' already exists, please delete before continuing.',\
'SEVERE' )
filesExist=True
else:
casalog.post("The linefile parameter is empty, consequently the"
+" spectral line image will NOT be\nsaved on disk.", \
'WARN')
if ( len( contfile ) > 0 ):
if ( os.path.exists( contfile ) ):
casalog.post( 'Error: Unable to continue file '+contfile\
+' already exists, please delete before continuing.',\
'SEVERE' )
filesExist=True
else:
casalog.post("The contfile parameter is empty, consequently the"
+" continuum image will NOT be\nsaved on disk.", \
'WARN')
if ( filesExist ):
return False
_myia = iatool()
_myia.dohistory(False)
_myia.open(imagename)
mycsys = _myia.coordsys()
if isinstance(box, list):
box = ', '.join([str(b) for b in box])
# Don't mix chans up with reg! reg selects a subset for output, and chans
# selects a subset to define the line-free channels.
myrg = rgtool()
reg = myrg.frombcs(
csys=mycsys.torecord(), shape=_myia.shape(),
box=box, stokes=stokes, stokescontrol="f",
region=region
)
channels = []
if chans != None and len(chans) > 0:
channels = myrg.selectedchannels(chans, _myia.shape())
try:
# Now do the continuum subtraction.
lineim = _myia.continuumsub(
outline=linefile, outcont=contfile, region=reg,
channels=channels, fitorder=fitorder,
overwrite=False
)
if not lineim:
raise Exception("ia.continuumsub did not complete successfully")
try:
param_names = imcontsub.func_code.co_varnames[:imcontsub.func_code.co_argcount]
param_vals = [eval(p) for p in param_names]
for x in [lineim, contfile]:
write_image_history(
x, sys._getframe().f_code.co_name,
param_names, param_vals, casalog
)
except Exception, instance:
casalog.post("*** Error \'%s\' updating HISTORY" % (instance), 'WARN')
lineim.done()
return True
res = myimd.add(hdkey, hdvalue)
elif mode.startswith('d'):
res = myimd.remove(hdkey, hdvalue)
elif mode.startswith('g'):
return myimd.get(hdkey)
elif mode.startswith('l'):
return myimd.list(True)
elif mode.startswith('p'):
res = myimd.set(hdkey, hdvalue)
if res:
try:
param_names = imhead.func_code.co_varnames[:imhead.
func_code.
co_argcount]
param_vals = [eval(p) for p in param_names]
write_image_history(imagename,
sys._getframe().f_code.co_name,
param_names, param_vals, casalog)
except Exception, instance:
casalog.post(
"*** Error \'%s\' updating HISTORY" % (instance),
'WARN')
return res
except Exception, instance:
casalog.post(str('*** Error *** ') + str(instance), 'SEVERE')
return False
finally:
myimd.done()
casalog.post('Unknown imhead mode ' + str(mode), 'SEVERE')
return False