def open_ms(vis):
(ms, ) = gentools(['ms'])
ms.open(vis)
try:
yield ms
finally:
ms.close()
def open_table(vis):
(tb, ) = gentools(['tb'])
tb.open(vis)
try:
yield tb
finally:
tb.close()
def msmoments(infile, moments, antenna, field, spw, includemask, excludemask,
outfile, overwrite):
retms = None
casalog.origin('msmoments')
# CAS-5410 Use private tools inside task scripts
ms = gentools(['ms'])[0]
try:
if ((not overwrite) and (len(moments) == 1)):
if (os.path.exists(outfile)):
raise Exception(outfile + " exists.")
ms.open(infile)
retms = ms.moments(moments=moments,
antenna=antenna,
field=field,
spw=spw,
includemask=includemask,
excludemask=excludemask,
outfile=outfile,
overwrite=overwrite)
ms.close()
retms.close()
except Exception, instance:
ms.close()
if retms: retms.close()
print '*** Error ***', instance
raise Exception, instance
def __execute_imaging(self):
#if pointingcolumn.upper()=="OFFSET":
# pointingcolumn="POINTING_OFFSET"
#print "pointingcolumn=",pointingcolumn
#print "Imaging...."
casalog.post( "pointingcolumn used: %s" % self.pointingcolumn )
casalog.post( "Imaging...." )
self.open_imager(self.infile)
self.imager.selectvis(spw=self.spw, baseline=self.antsel)
#self.imager.selectvis(field=0, spw=self.spw, baseline=self.antsel)
#self.imager.selectvis(vis=infile, field=0, spw=spw, baseline=antsel)
#self.imager.defineimage(nx=nx, ny=ny, cellx=cellx, celly=celly, phasecenter=phasecenter, spw=0, stokes=stokes, movingsource=ephemsrcname)
self.imager.defineimage(nx=self.nx, ny=self.ny, cellx=self.cellx, celly=self.celly, phasecenter=self.phasecenter, spw=self.spw, stokes=self.stokes, movingsource=self.ephemsrcname)
#self.imager.defineimage(nx=nx, ny=ny, cellx=cellx, celly=celly, phasecenter=phasecenter, spw=0, stokes=stokes, movingsource=ephemsrcname,restfreq=1.14e11)
self.imager.setoptions(ftmachine='sd', gridfunction=self.gridfunction)
#self.imager.setsdoptions(convsupport=5)
self.imager.setsdoptions(pointingcolumntouse=self.pointingcolumn, convsupport=-1, truncate=-1, gwidth=-1, jwidth=-1)
self.imager.makeimage(type='singledish-observed', image=self.outfile)
#self.imager.makeimage(type='singledish', image=self.outfile)
# create temporal weight image for masking
weightfile_temp = self.outfile+".weight."+str(time.time()).replace('.', '_')
self.imager.makeimage(type='coverage', image=weightfile_temp)
self.close_imager()
# Handle mask
my_ia = gentools(['ia'])[0]
my_ia.open(self.outfile)
my_ia.calcmask("'%s'>%f" % (weightfile_temp,0.0), asdefault=True)
my_ia.close()
shutil.rmtree(weightfile_temp)
def open_ia(imagename):
(ia, ) = gentools(['ia'])
ia.open(imagename)
try:
yield ia
finally:
ia.close()
def splitant(filename, outprefix='',overwrite=False, getpt=True):
"""
Split Measurement set by antenna name, save data as a scantables,
and return a list of filename. Note that frequency reference frame
is imported as it is in Measurement set.
Notice this method can only be available from CASA.
Prameter
filename: the name of Measurement set to be read.
outprefix: the prefix of output scantable name.
the names of output scantable will be
outprefix.antenna1, outprefix.antenna2, ....
If not specified, outprefix = filename is assumed.
overwrite If the file should be overwritten if it exists.
The default False is to return with warning
without writing the output. USE WITH CARE.
getpt Whether to import direction from MS/POINTING
table or not. Default is True (import direction).
"""
# Import the table toolkit from CASA
from taskinit import gentools
from asap.scantable import is_ms
tb = gentools(['tb'])[0]
# Check the input filename
if isinstance(filename, str):
import os.path
filename = os.path.expandvars(filename)
filename = os.path.expanduser(filename)
if not os.path.exists(filename):
s = "File '%s' not found." % (filename)
raise IOError(s)
# check if input file is MS
if not is_ms(filename):
s = "File '%s' is not a Measurement set." % (filename)
raise IOError(s)
else:
s = "The filename should be string. "
raise TypeError(s)
# Check out put file name
outname=''
if len(outprefix) > 0: prefix=outprefix+'.'
else:
prefix=filename.rstrip('/')
# Now do the actual splitting.
outfiles=[]
tb.open(tablename=filename,nomodify=True)
ant1=tb.getcol('ANTENNA1',0,-1,1)
anttab=tb.getkeyword('ANTENNA').lstrip('Table: ')
tb.close()
tb.open(tablename=anttab,nomodify=True)
nant=tb.nrows()
antnames=tb.getcol('NAME',0,nant,1)
tb.close()
for antid in set(ant1):
scan=scantable(filename,average=False,antenna=int(antid),getpt=getpt)
outname=prefix+antnames[antid]+'.asap'
scan.save(outname,format='ASAP',overwrite=overwrite)
del scan
outfiles.append(outname)
return outfiles
def _is_empty_caltable(self, **params):
(tb, ) = gentools(['tb'])
tb.open(params['outfile'])
try:
nrow = tb.nrows()
finally:
tb.close()
self.assertEqual(nrow, 0)
def _is_empty_caltable(self, **params):
(tb,) = gentools(['tb'])
tb.open(params['outfile'])
try:
nrow = tb.nrows()
finally:
tb.close()
self.assertEqual(nrow, 0)
def generate(self):
# generate Tsys table
from sdcal_cli import sdcal_cli as sdcal
sdcal(infile=self.infile,
outfile=self.tsystable,
calmode='tsys',
overwrite=True)
self.assertTrue(os.path.exists(self.tsystable))
# get information from MS
(tb, ) = gentools(['tb'])
tb.open(self.infile)
s = tb.getcol('FLOAT_DATA', 0, 2)
w = tb.getcol('WEIGHT', 0, 2).reshape((2, 1, 2))
t = tb.getcol('TIME')
tmax = t.max()
tmin = t.min()
tb.close()
# generate sky table based on Tsys table
tb.open(self.tsystable)
t = tb.copy(self.skytable, deep=True)
tb.close()
t.close()
tb.open(self.skytable, nomodify=False)
tb.putkeyword('VisCal', 'SDSKY_PS')
s[:] = w
tb.putcol('WEIGHT', s, 0, 2)
s[:] = 1.0
tb.putcol('FPARAM', s, 0, 2)
tb.close()
with open(self.skytable + '/table.info', 'r') as f:
l = f.read()
#print l
l = l.replace('B TSYS', 'SDSKY_PS')
#print l
with open(self.skytable + '/table.info', 'w') as f:
f.write(l)
self.assertTrue(os.path.exists(self.skytable))
# edit Tsys table
tb.open(self.tsystable, nomodify=False)
spw_id = tb.getcol('SPECTRAL_WINDOW_ID')
spw_id[2:] = spw_id[:2]
tb.putcol('SPECTRAL_WINDOW_ID', spw_id)
time = tb.getcol('TIME')
time[:2] = tmin
time[2:] = tmax
tb.putcol('TIME', time)
param = tb.getcol('FPARAM')
param[:, :, :2] = 100.0
param[:, :, 2:] = 200.0
tb.putcol('FPARAM', param)
param[:] = 1.0
tb.putcol('WEIGHT', param)
tb.close()
def _get_table(self, name=None):
""" A table object """
from taskinit import gentools
tb, = gentools(['tb'])
if name is None:
tb.open('%s' % self.measurement_set)
else:
tb.open('%s/%s' % (self.measurement_set, name))
return tb
def _edit_tsys_spw(self, spwmap):
(tb, ) = gentools(['tb'])
tb.open(self.tsystable, nomodify=False)
spw_id = tb.getcol('SPECTRAL_WINDOW_ID')
print 'before ', spw_id
for i in xrange(len(spw_id)):
spw_id[i] = spwmap[spw_id[i]]
print 'after', spw_id
tb.putcol('SPECTRAL_WINDOW_ID', spw_id)
tb.close()
def _generic_verify(self, **params):
(
tb,
ms,
) = gentools(['tb', 'ms'])
nrow_per_spw = 102
spwsel = params['spw']
if spwsel == '':
nspw = 2
else:
infile = params['infile']
ms.open(infile)
try:
ms.msselect({'spw': spwsel})
mssel = ms.msselectedindices()
nspw = len(mssel['spw'])
finally:
ms.close()
caltable = params['outfile']
tb.open(caltable)
try:
nrow = tb.nrows()
self.assertEqual(nrow, nspw * nrow_per_spw)
spwids = tb.getcol('SPECTRAL_WINDOW_ID')
spwid_list = set(spwids)
for spwid in spwid_list:
self.assertEqual(len(spwids[spwids == spwid]), nrow_per_spw)
# by definition, mean of gain factor becomes almost 1.0
for spwid in spwid_list:
t = tb.query('SPECTRAL_WINDOW_ID == %s' % (spwid))
try:
fparam = t.getcol('CPARAM').real
flag = t.getcol('FLAG')
finally:
t.close()
ma = numpy.ma.masked_array(fparam, flag)
mean_gain = ma.mean(axis=2)
print mean_gain
npol = fparam.shape[0]
for ipol in xrange(npol):
if numpy.any(flag[ipol] == False):
self.assertTrue(abs(mean_gain[ipol] - 1.0) < 0.01)
self._verify_param_and_flag(tb)
finally:
tb.close()
pass
def get_selection_idx_for_ms(self, file_idx):
"""
Returns a dictionary of selection indices for i-th MS in infiles
Argument: file idx in infiles list
"""
if file_idx < len(self.infiles) and file_idx > -1:
vis = self.infiles[file_idx]
field = self.get_selection_param_for_ms(file_idx, self.field)
spw = self.get_selection_param_for_ms(file_idx, self.spw)
spw = self.__format_spw_string(spw)
antenna = self.get_selection_param_for_ms(file_idx, self.antenna)
if antenna == -1: antenna = ''
scan = self.get_selection_param_for_ms(file_idx, self.scanno)
intent = self.get_selection_param_for_ms(file_idx, self.intent)
my_ms = gentools(['ms'])[0]
sel_ids = my_ms.msseltoindex(vis=vis,
spw=spw,
field=field,
baseline=antenna,
scan=scan)
fieldid = list(
sel_ids['field']) if len(sel_ids['field']) > 0 else -1
baseline = self.format_ac_baseline(sel_ids['antenna1'])
scanid = list(sel_ids['scan']) if len(sel_ids['scan']) > 0 else ""
# SPW (need to get a list of valid spws instead of -1)
if len(sel_ids['channel']) > 0:
spwid = [chanarr[0] for chanarr in sel_ids['channel']]
elif spw == "": # No spw selection
my_ms.open(vis)
try:
spwinfo = my_ms.getspectralwindowinfo()
except:
raise
finally:
my_ms.close()
spwid = [int(idx) for idx in spwinfo.keys()]
else:
raise RuntimeError("Invalid spw selction, %s ,for MS %d" (
str(spw), file_idx))
return {
'field': fieldid,
'spw': spwid,
'baseline': baseline,
'scan': scanid,
'intent': intent,
'antenna1': sel_ids['antenna1']
}
else:
raise ValueError, ("Invalid file index, %d" % file_idx)
def purify_image(datatransform, imagename, imsize=(128, 128), overwrite=False,
**kwargs):
""" Creates an image using the Purify method
Parameters:
datatransform: DataTransform derived
Iterator of purify data
imagename: string
Path to output image
imsize: 2-tuple
Width and height of the output image in pixels
overwrite: bool
Whether to overwrite existing image. Defaults to False.
other arguments:
See purify.SDMM
"""
from os.path import exists, abspath
from numpy import array
from taskinit import gentools, casalog
from . import SDMM
# Input sanitizing
if 'image_size' in kwargs:
msg = 'Image size should be given using the imsize argument'
raise ValueError(msg)
imagename = abspath(imagename)
if exists(imagename) and not overwrite:
msg = "File %s already exist. It will not be overwritten.\n" \
"Please delete the file or choose another filename for the" \
" image."
raise IOError(msg % imagename)
casalog.post('Starting Purify task')
scale = kwargs.pop('scale', 'default')
sdmm = SDMM(image_size=imsize, **kwargs)
# Contains images over all dimensions
image = []
for i, data in enumerate(datatransform):
casalog.origin('Purifying plane %s' % str(i))
channel = sdmm(data, scale=scale)
image.append(channel)
image = array(image, order='F')
# Create image
casalog.post('Creating CASA image')
ia, = gentools(['ia'])
ia.newimagefromarray(imagename, image.real, overwrite=overwrite)
def __polynomial_fit_model(self, image=None, model=None, axis=0, order=2):
if not image or not os.path.exists(image):
raise RuntimeError, "No image found to fit."
if os.path.exists(model):
# CAS-5410 Use private tools inside task scripts
cu = utilstool()
cu.removetable([model])
tmpia = gentools(['ia'])[0]
modelimg = tmpia.newimagefromimage(infile=image, outfile=model)
try:
if tmpia.isopen(): tmpia.close()
imshape = modelimg.shape()
# the axis order of [ra, dec, chan(, pol)] is assumed throughout the task.
ndim = len(imshape)
nx = imshape[0]
ny = imshape[1]
# an xy-plane can be fit simultaneously (doing per plane to save memory)
if ndim == 3:
get_blc = lambda i, j: [0, 0, i]
get_trc = lambda i, j: [nx - 1, ny - 1, i]
imshape2 = imshape[2]
imshape3 = 1
elif ndim == 4:
get_blc = lambda i, j: [0, 0, i, j]
get_trc = lambda i, j: [nx - 1, ny - 1, i, j]
imshape2 = imshape[2]
imshape3 = imshape[3]
else: # ndim == 2
get_blc = lambda i, j: [0, 0]
get_trc = lambda i, j: [nx - 1, ny - 1]
imshape2 = 1
imshape3 = 1
for i3 in range(imshape3):
for i2 in range(imshape2):
blc = get_blc(i2, i3)
trc = get_trc(i2, i3)
dslice = modelimg.getchunk(blc, trc)
mslice = modelimg.getchunk(blc, trc, getmask=True)
model = self._get_polyfit_model_array(
dslice.reshape(nx, ny), mslice.reshape(nx, ny), axis,
order)
modelimg.putchunk(model, blc)
# the fit model image itself is free from invalid pixels
modelimg.calcmask('T', asdefault=True)
except:
raise
finally:
modelimg.close()
def __polynomial_fit_model(self, image=None, model=None, axis=0, order=2):
if not image or not os.path.exists(image):
raise RuntimeError, "No image found to fit."
if os.path.exists(model):
# CAS-5410 Use private tools inside task scripts
cu = utilstool()
cu.removetable([model])
tmpia = gentools(['ia'])[0]
modelimg = tmpia.newimagefromimage(infile=image, outfile=model)
try:
if tmpia.isopen(): tmpia.close()
imshape = modelimg.shape()
# the axis order of [ra, dec, chan(, pol)] is assumed throughout the task.
ndim = len(imshape)
nx = imshape[0]
ny = imshape[1]
# an xy-plane can be fit simultaneously (doing per plane to save memory)
if ndim == 3:
for ichan in range(imshape[2]):
dslice = modelimg.getchunk([0, 0, ichan],
[nx - 1, ny - 1, ichan])
mslice = modelimg.getchunk([0, 0, ichan],
[nx - 1, ny - 1, ichan],
getmask=True)
model = self._get_polyfit_model_array(
dslice.reshape(nx, ny), mslice.reshape(nx, ny), axis,
order)
modelimg.putchunk(model, [0, 0, ichan, ipol])
elif ndim == 4:
for ipol in range(imshape[3]):
for ichan in range(imshape[2]):
dslice = modelimg.getchunk(
[0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
mslice = modelimg.getchunk(
[0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol],
getmask=True)
model = self._get_polyfit_model_array(
dslice.reshape(nx, ny), mslice.reshape(nx, ny),
axis, order)
modelimg.putchunk(model, [0, 0, ichan, ipol])
else:
# ndim=2 is not supported in this task.
raise RuntimeError, "image dimension should be 3 or 4"
# the fit model image itself is free from invalid pixels
modelimg.calcmask('T', asdefault=True)
except:
raise
finally:
modelimg.close()
def _generic_verify(self, **params):
(tb,ms,) = gentools(['tb','ms'])
nrow_per_spw = 102
spwsel = params['spw']
if spwsel == '':
nspw = 2
else:
infile = params['infile']
ms.open(infile)
try:
ms.msselect({'spw': spwsel})
mssel = ms.msselectedindices()
nspw = len(mssel['spw'])
finally:
ms.close()
caltable = params['outfile']
tb.open(caltable)
try:
nrow = tb.nrows()
self.assertEqual(nrow, nspw * nrow_per_spw)
spwids = tb.getcol('SPECTRAL_WINDOW_ID')
spwid_list = set(spwids)
for spwid in spwid_list:
self.assertEqual(len(spwids[spwids == spwid]), nrow_per_spw)
# by definition, mean of gain factor becomes almost 1.0
for spwid in spwid_list:
t = tb.query('SPECTRAL_WINDOW_ID == %s'%(spwid))
try:
fparam = t.getcol('CPARAM').real
flag = t.getcol('FLAG')
finally:
t.close()
ma = numpy.ma.masked_array(fparam, flag)
mean_gain = ma.mean(axis=2)
print mean_gain
self.assertTrue(numpy.all((numpy.abs(mean_gain) - 1.0) < 0.01))
self._verify_fparam_and_flag(tb)
finally:
tb.close()
pass
def __polynomial_fit_model(self, image=None, model=None, axis=0, order=2):
if not image or not os.path.exists(image):
raise RuntimeError, "No image found to fit."
if os.path.exists( model ):
# CAS-5410 Use private tools inside task scripts
cu = utilstool()
cu.removetable([model])
tmpia = gentools(['ia'])[0]
modelimg = tmpia.newimagefromimage(infile=image,outfile=model)
try:
if tmpia.isopen(): tmpia.close()
imshape = modelimg.shape()
# the axis order of [ra, dec, chan(, pol)] is assumed throughout the task.
ndim = len(imshape)
nx = imshape[0]
ny = imshape[1]
# an xy-plane can be fit simultaneously (doing per plane to save memory)
if ndim == 3:
get_blc = lambda i, j: [0, 0, i]
get_trc = lambda i, j: [nx-1, ny-1, i]
imshape2 = imshape[2]
imshape3 = 1
elif ndim == 4:
get_blc = lambda i, j: [0, 0, i, j]
get_trc = lambda i, j: [nx-1, ny-1, i, j]
imshape2 = imshape[2]
imshape3 = imshape[3]
else: # ndim == 2
get_blc = lambda i, j: [0,0]
get_trc = lambda i, j: [nx-1, ny-1]
imshape2 = 1
imshape3 = 1
for i3 in range(imshape3):
for i2 in range(imshape2):
blc = get_blc(i2, i3)
trc = get_trc(i2, i3)
dslice = modelimg.getchunk(blc, trc)
mslice = modelimg.getchunk(blc, trc, getmask=True)
model = self._get_polyfit_model_array(dslice.reshape(nx,ny),
mslice.reshape(nx,ny),
axis, order)
modelimg.putchunk(model, blc)
# the fit model image itself is free from invalid pixels
modelimg.calcmask('T', asdefault=True)
except: raise
finally: modelimg.close()
def __init__(self, imagename):
self.imagename = imagename
# read data to storage
ia = gentools(['ia'])[0]
ia.open(self.imagename)
try:
self.image_shape = ia.shape()
self.coordsys = ia.coordsys()
coord_types = self.coordsys.axiscoordinatetypes()
self.units = self.coordsys.units()
self.names = self.coordsys.names()
self.direction_reference = self.coordsys.referencecode('dir')[0]
self.spectral_reference = self.coordsys.referencecode('spectral')[0]
self.id_direction = coord_types.index('Direction')
self.id_direction = [self.id_direction, self.id_direction+1]
self.id_spectral = coord_types.index('Spectral')
self.id_stokes = coord_types.index('Stokes')
casalog.post('id_direction=%s'%(self.id_direction))
casalog.post('id_spectral=%s'%(self.id_spectral))
casalog.post('id_stokes=%s'%(self.id_stokes))
self.data = ia.getchunk()
self.mask = ia.getchunk(getmask=True)
bottom = ia.toworld(numpy.zeros(len(self.image_shape),dtype=int), 'q')['quantity']
top = ia.toworld(self.image_shape-1, 'q')['quantity']
key = lambda x: '*%s'%(x+1)
ra_min = bottom[key(self.id_direction[0])]
ra_max = top[key(self.id_direction[0])]
if ra_min > ra_max:
ra_min,ra_max = ra_max,ra_min
self.ra_min = ra_min
self.ra_max = ra_max
self.dec_min = bottom[key(self.id_direction[1])]
self.dec_max = top[key(self.id_direction[1])]
self._brightnessunit = ia.brightnessunit()
if self.spectral_label == 'Frequency':
refpix, refval, increment = self.spectral_axis(unit='GHz')
self.spectral_data = numpy.array([refval+increment*(i-refpix) for i in xrange(self.nchan)])
elif self.spectral_label == 'Velocity':
refpix, refval, increment = self.spectral_axis(unit='km/s')
self.spectral_data = numpy.array([refval+increment*(i-refpix) for i in xrange(self.nchan)])
self.stokes = self.coordsys.stokes()
finally:
ia.close()
def _verify_param_and_flag(self, table):
(reftable, ) = gentools(['tb'])
reftable.open(self.reffile)
try:
nrow = table.nrows()
ref_nrow = reftable.nrows()
self.assertEqual(nrow, ref_nrow)
for irow in xrange(nrow):
ref_fparam = reftable.getcell('CPARAM', irow).real
fparam = table.getcell('CPARAM', irow).real
self.assertTrue(numpy.all(ref_fparam == fparam))
ref_flag = reftable.getcell('FLAG', irow)
flag = table.getcell('FLAG', irow)
self.assertTrue(numpy.all(ref_flag == flag))
finally:
reftable.close()
def _verify_fparam_and_flag(self, table):
(reftable,) = gentools(['tb'])
reftable.open(self.reffile)
try:
nrow = table.nrows()
ref_nrow = reftable.nrows()
self.assertEqual(nrow, ref_nrow)
for irow in xrange(nrow):
ref_fparam = reftable.getcell('CPARAM', irow).real
fparam = table.getcell('CPARAM', irow).real
self.assertTrue(numpy.all(ref_fparam == fparam))
ref_flag = reftable.getcell('FLAG', irow)
flag = table.getcell('FLAG', irow)
self.assertTrue(numpy.all(ref_flag == flag))
finally:
reftable.close()
def __polynomial_fit_model(self, image=None, model=None, axis=0, order=2):
if not image or not os.path.exists(image):
raise RuntimeError, "No image found to fit."
if os.path.exists(model):
# CAS-5410 Use private tools inside task scripts
cu = utilstool()
cu.removetable([model])
tmpia = gentools(["ia"])[0]
modelimg = tmpia.newimagefromimage(infile=image, outfile=model)
try:
if tmpia.isopen():
tmpia.close()
imshape = modelimg.shape()
# the axis order of [ra, dec, chan(, pol)] is assumed throughout the task.
ndim = len(imshape)
nx = imshape[0]
ny = imshape[1]
# an xy-plane can be fit simultaneously (doing per plane to save memory)
if ndim == 3:
for ichan in range(imshape[2]):
dslice = modelimg.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
mslice = modelimg.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan], getmask=True)
model = self._get_polyfit_model_array(dslice.reshape(nx, ny), mslice.reshape(nx, ny), axis, order)
modelimg.putchunk(model, [0, 0, ichan, ipol])
elif ndim == 4:
for ipol in range(imshape[3]):
for ichan in range(imshape[2]):
dslice = modelimg.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
mslice = modelimg.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol], getmask=True)
model = self._get_polyfit_model_array(
dslice.reshape(nx, ny), mslice.reshape(nx, ny), axis, order
)
modelimg.putchunk(model, [0, 0, ichan, ipol])
else:
# ndim=2 is not supported in this task.
raise RuntimeError, "image dimension should be 3 or 4"
# the fit model image itself is free from invalid pixels
modelimg.calcmask("T", asdefault=True)
except:
raise
finally:
modelimg.close()
def create_4d_image(infile, outfile):
(ia,) = gentools(['ia'])
ia.open(infile)
image_shape = ia.shape()
try:
if len(image_shape) < 4:
# add degenerate axes
axistypes = ia.coordsys().axiscoordinatetypes()
no_stokes = 'Stokes' not in axistypes
no_spectral = 'Spectral' not in axistypes
stokes_axis = 'I' if no_stokes else ''
outimage = ia.adddegaxes(outfile=outfile, spectral=no_spectral,
stokes=stokes_axis)
else:
# generage complete copy of input image using subimage
outimage = ia.subimage(outfile=outfile)
finally:
ia.close()
return outimage
def _updateHistory(self, clrecs, vis):
"""
Update history table when setSolarObjectJy is run
"""
#
from taskinit import gentools
(mytb, ) = gentools(['tb'])
mytb.open(vis + '/HISTORY', nomodify=False)
nrow = mytb.nrows()
lasttime = mytb.getcol('TIME')[nrow - 1]
rown = nrow
#
for ky in clrecs.keys():
# expect only one component for each
comp = clrecs[ky]['component0']
srcn = ky.split('_')[0]
ispw = ky.split('_')[1]
mytb.addrows(1)
appl = 'setjy'
msg = (
" %s: spw %s Flux:[I=%s,Q=%s,U=%s,V=%s] +/- [I=%s,Q=%s,U=%s,V=%s] Jy"
% (srcn, ispw, comp['flux']['value'][0],
comp['flux']['value'][1], comp['flux']['value'][2],
comp['flux']['value'][3], comp['flux']['error'][0],
comp['flux']['error'][1], comp['flux']['error'][2],
comp['flux']['error'][3]))
origin = 'setjy'
priority = 'INFO'
time = lasttime
emptystrarr = numpy.array([''])
mytb.putcell('APP_PARAMS', rown, [''])
mytb.putcell('CLI_COMMAND', rown, [''])
mytb.putcell('APPLICATION', rown, appl)
mytb.putcell('MESSAGE', rown, msg)
mytb.putcell('OBSERVATION_ID', rown, -1)
mytb.putcell('ORIGIN', rown, origin)
mytb.putcell('PRIORITY', rown, priority)
mytb.putcell('TIME', rown, time)
rown += 1
mytb.close()
def msmoments( infile, moments, antenna, field, spw, includemask, excludemask, outfile, overwrite):
retms=None
casalog.origin('msmoments')
# CAS-5410 Use private tools inside task scripts
ms = gentools(['ms'])[0]
try:
if ( (not overwrite) and (len(moments) == 1) ):
if ( os.path.exists(outfile) ):
raise Exception( outfile+" exists." )
ms.open( infile )
retms = ms.moments( moments=moments,antenna=antenna,field=field,spw=spw,includemask=includemask,excludemask=excludemask,outfile=outfile,overwrite=overwrite)
ms.close()
retms.close()
except Exception, instance:
ms.close()
if retms: retms.close()
print '*** Error ***',instance
raise Exception, instance
def _updateHistory(self,clrecs,vis):
"""
Update history table when setSolarObjectJy is run
"""
#
from taskinit import gentools
(mytb,) = gentools(['tb'])
mytb.open(vis+'/HISTORY',nomodify=False)
nrow = mytb.nrows()
lasttime=mytb.getcol('TIME')[nrow-1]
rown=nrow
#
for ky in clrecs.keys():
# expect only one component for each
comp = clrecs[ky]['component0']
srcn = ky.split('_')[0]
ispw = ky.split('_')[1]
mytb.addrows(1)
appl='setjy'
msg = (" %s: spw %s Flux:[I=%s,Q=%s,U=%s,V=%s] +/- [I=%s,Q=%s,U=%s,V=%s] Jy" %
(srcn, ispw, comp['flux']['value'][0], comp['flux']['value'][1],
comp['flux']['value'][2], comp['flux']['value'][3],
comp['flux']['error'][0], comp['flux']['error'][1],comp['flux']['error'][2],
comp['flux']['error'][3]))
origin='setjy'
priority='INFO'
time=lasttime
emptystrarr=numpy.array([''])
mytb.putcell('APP_PARAMS', rown, [''])
mytb.putcell('CLI_COMMAND',rown, [''])
mytb.putcell('APPLICATION',rown, appl)
mytb.putcell('MESSAGE',rown, msg)
mytb.putcell('OBSERVATION_ID',rown, -1)
mytb.putcell('ORIGIN',rown,origin)
mytb.putcell('PRIORITY',rown,priority)
mytb.putcell('TIME',rown, time)
rown += 1
mytb.close()
def inspect_caltable(self, caltable):
# caltable must exist
self.assertTrue(os.path.exists(caltable))
# caltable must be a directory
self.assertTrue(os.path.isdir(caltable))
# caltable must be opened by table tool
(tb, ) = gentools(['tb'])
is_open_successful = tb.open(caltable)
self.assertTrue(is_open_successful)
try:
# caltype must be "G Jones"
caltype = tb.getkeyword('VisCal')
self.assertEqual(caltype, "SDGAIN_OTFD")
# paramter must be Complex
partype = tb.getkeyword('ParType')
self.assertEqual(partype, 'Complex')
self.assertIn('CPARAM', tb.colnames())
finally:
tb.close()
def inspect_caltable(self, caltable):
# caltable must exist
self.assertTrue(os.path.exists(caltable))
# caltable must be a directory
self.assertTrue(os.path.isdir(caltable))
# caltable must be opened by table tool
(tb,) = gentools(['tb'])
is_open_successful = tb.open(caltable)
self.assertTrue(is_open_successful)
try:
# caltype must be "G Jones"
caltype = tb.getkeyword('VisCal')
self.assertEqual(caltype, "G Jones")
# paramter must be Complex
partype = tb.getkeyword('ParType')
self.assertEqual(partype, 'Complex')
self.assertIn('CPARAM', tb.colnames())
finally:
tb.close()
def get_selection_idx_for_ms(self, file_idx):
"""
Returns a dictionary of selection indices for i-th MS in infiles
Argument: file idx in infiles list
"""
if file_idx < len(self.infiles) and file_idx > -1:
vis = self.infiles[file_idx]
field = self.get_selection_param_for_ms(file_idx, self.field)
spw = self.get_selection_param_for_ms(file_idx, self.spw)
spw = self.__format_spw_string(spw)
antenna = self.get_selection_param_for_ms(file_idx, self.antenna)
if antenna == -1: antenna = ''
scan = self.get_selection_param_for_ms(file_idx, self.scanno)
intent = self.get_selection_param_for_ms(file_idx, self.intent)
my_ms = gentools(['ms'])[0]
sel_ids = my_ms.msseltoindex(vis=vis, spw=spw, field=field,
baseline=antenna, scan=scan)
fieldid = list(sel_ids['field']) if len(sel_ids['field']) > 0 else -1
baseline = self.format_ac_baseline(sel_ids['antenna1'])
scanid = list(sel_ids['scan']) if len(sel_ids['scan']) > 0 else ""
# SPW (need to get a list of valid spws instead of -1)
if len(sel_ids['channel']) > 0:
spwid = [ chanarr[0] for chanarr in sel_ids['channel'] ]
elif spw=="": # No spw selection
my_ms.open(vis)
try: spwinfo = my_ms.getspectralwindowinfo()
except: raise
finally: my_ms.close()
spwid = [int(idx) for idx in spwinfo.keys()]
else:
raise RuntimeError("Invalid spw selction, %s ,for MS %d" (str(spw), file_idx))
return {'field': fieldid, 'spw': spwid, 'baseline': baseline, 'scan': scanid, 'intent': intent, 'antenna1': sel_ids['antenna1']}
else:
raise ValueError, ("Invalid file index, %d" % file_idx)
import numpy
import os
import time, datetime
from taskinit import gentools, casalog
import sdutil
ms, sdms, tb = gentools(['ms','sdms','tb'])
from numpy import ma, array, logical_not, logical_and
@sdutil.sdtask_decorator
def sdfit(infile=None, datacolumn=None, antenna=None, field=None, spw=None,
timerange=None, scan=None, pol=None, intent=None,
timeaverage=None, timebin=None, timespan=None,
polaverage=None, polaveragemode=None,
fitfunc=None, fitmode=None, nfit=None, thresh=None, avg_limit=None,
minwidth=None, edge=None, outfile=None, overwrite=None):
casalog.origin('sdfit')
try:
if os.path.exists(outfile):
if overwrite:
os.system('rm -rf %s' % outfile)
else:
raise ValueError(outfile + ' exists.')
if (fitmode not in ['list', 'auto']):
raise ValueError, "fitmode='%s' is not supported yet" % fitmode
if (spw == ''): spw = '*'
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
def setSolarObjectJy(self,
field,
spw,
scalebychan,
timerange,
observation,
scan,
intent,
useephemdir,
usescratch=False):
"""
Set flux density of a solar system object using Bryan Butler's new
python model calculation code.
A single time stamp (first time stamp of MS after selections are applied) is
currently used per execution. For flux observation done in a long time span
may need to run multiple setjy with selections by time range (or scans).
"""
#retval = True
output = {}
cleanupcomps = True # leave generated cl files
#from taskinit import *
from taskinit import gentools
qa = casac.quanta()
(myms, mytb, mycl, myme, mycb,
mymsmd) = gentools(['ms', 'tb', 'cl', 'me', 'cb', 'msmd'])
# prepare parameters need to pass to the Bryan's code
# make ms selections
# get source name
# get time ranges
# get spwused and get frequency ranges
sel = {}
sel['field'] = field
sel['spw'] = spw
sel['timerange'] = timerange
sel['observation'] = str(observation)
sel['scan'] = scan
sel['scanintent'] = intent
measframes = [
'REST', 'LSRK', 'LSRD', 'BARY', 'GEO', 'TOPO', 'GALACTO', 'LGROUP',
'CMB'
]
myms.open(self.vis)
myms.msselect(sel, False)
scansummary = myms.getscansummary()
nscan = len(scansummary.keys())
selectedids = myms.msselectedindices()
fieldids = selectedids['field']
obsids = selectedids['observationid']
myms.close()
mytb.open(self.vis + '/OBSERVATION')
if len(obsids) == 0:
getrow = 0
else:
getrow = obsids[0]
observatory = mytb.getcell('TELESCOPE_NAME', getrow)
mytb.close()
mytb.open(self.vis + '/FIELD')
colnames = mytb.colnames()
if len(fieldids) == 0:
fieldids = range(mytb.nrows())
# frame reference for field position
phdir_info = mytb.getcolkeyword("PHASE_DIR", "MEASINFO")
if phdir_info.has_key('Ref'):
fieldref = phdir_info['Ref']
elif phdir_info.has_key('TabRefTypes'):
colnames = mytb.colnames()
for col in colnames:
if col == 'PhaseDir_Ref':
fieldrefind = mytb.getcell(col, fieldids[0])
fieldref = phdir_info['TabRefTypes'][fieldrefind]
else:
fieldref = ''
srcnames = {}
fielddirs = {}
ftimes = {}
ephemid = {}
for fid in fieldids:
#srcnames.append(mytb.getcell('NAME',int(fid)))
srcnames[fid] = (mytb.getcell('NAME', int(fid)))
#fielddirs[fid]=(mytb.getcell('PHASE_DIR',int(fid)))
ftimes[fid] = (mytb.getcell('TIME', int(fid)))
if colnames.count('EHPHEMERIS_ID'):
ephemid[fid] = (mytb.getcell('EPHEMERIS_ID', int(fid)))
else:
ephemid[fid] = -1
mytb.close() # close FIELD table
# need to get a list of time
# but for now for test just get a time centroid of the all scans
# get time range
# Also, this needs to be done per source
# gather freq info from Spw table
mytb.open(self.vis + '/SPECTRAL_WINDOW')
nspw = mytb.nrows()
freqcol = mytb.getvarcol('CHAN_FREQ')
freqwcol = mytb.getvarcol('CHAN_WIDTH')
fmeasrefcol = mytb.getcol('MEAS_FREQ_REF')
reffreqs = mytb.getcol('REF_FREQUENCY')
mytb.close()
# store all parameters need to call solar_system_fd for all sources
inparams = {}
validfids = [
] # keep track of valid fid that has data (after selection)
# if same source name ....need handle this...
for fid in fieldids:
sel['field'] = str(fid)
myms.open(self.vis)
#reset the selection
try:
status = myms.msselect(sel)
except:
#skip this field
continue
if not status:
continue
validfids.append(fid)
trange = myms.range('time')
#if not inparams.has_key(srcnames[fid]):
# inparams[srcnames[fid]]={}
if not inparams.has_key(fid):
inparams[fid] = {}
inparams[fid]['fieldname'] = srcnames[fid]
#tc = (trange['time'][0]+trange['time'][1])/2. #in sec.
# use first timestamp to be consistent with the ALMA Control
# old setjy (Butler-JPL-Horizons 2010) seems to be using
# time in FIELD... but here is first selected time in main table
if ephemid[fid] == -1: # keep old behavior
tc = trange['time'][0] #in sec.
tmsg = "Time used for the model calculation (=first time stamp of the selected data) for field "
else: # must have ephem table attached...
tc = ftimes[fid] #in sec.
tmsg = "Time used for the model calculation for field "
#if inparams[srcnames[fid]].has_key('mjd'):
# inparams[srcnames[fid]]['mjds'][0].append([myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']])
#else:
# inparams[srcnames[fid]]['mjds']=[myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']]
if inparams[fid].has_key('mjd'):
inparams[fid]['mjds'][0].append(
[myme.epoch('utc', qa.quantity(tc, 's'))['m0']['value']])
else:
inparams[fid]['mjds'] = [
myme.epoch('utc', qa.quantity(tc, 's'))['m0']['value']
]
usedtime = qa.time(qa.quantity(tc, 's'), form='ymd')[0]
self._casalog.post(tmsg + str(fid) + ":" + usedtime)
# get a correct direction measure
mymsmd.open(self.vis)
dirdic = mymsmd.phasecenter(int(fid))
mymsmd.close()
# check if frame is J2000 and if not do the transform
if dirdic['refer'] != 'J2000':
myme.doframe(myme.observatory(observatory))
myme.doframe(myme.epoch('utc', qa.quantity(tc, 's')))
azeldir = myme.measure(dirdic, 'AZELGEO')
dirdic = myme.measure(azeldir, 'J2000')
fielddirs[fid] = (numpy.array([[dirdic['m0']['value']],
[dirdic['m1']['value']]]))
# somehow it gives you duplicated ids .... so need to uniquify
selspws = list(set(myms.msselectedindices()['spw']))
# make sure it is int rather than numpy.int32, etc.
selspws = [int(ispw) for ispw in selspws]
#inparams[srcnames[fid]]['spwids']= selspws if len(selspws)!=0 else range(nspw)
inparams[fid]['spwids'] = selspws if len(selspws) != 0 else range(
nspw)
#create a list of freq ranges with selected spws
# should worry about freq order???
freqlist = []
freqlistraw = []
framelist = []
#for idx in inparams[srcnames[fid]]['spwids']:
for idx in inparams[fid]['spwids']:
freqs = freqcol['r' + str(idx + 1)]
freqws = freqwcol['r' + str(idx + 1)]
fmeasref = fmeasrefcol[idx]
#if scalebychan=T, this has to be min, max determined from
# chan_freq(channel center)+/- chan width.
if scalebychan:
# pack into list of list of list (freqlist[nf][nspw])
perspwfreqlist = []
for nf in range(len(freqs)):
fl = freqs[nf][0] - freqws[nf][0] / 2.
fh = freqs[nf][0] + freqws[nf][0] / 2.
perspwfreqlist.append([fl, fh])
freqlist.append(perspwfreqlist)
else:
if (len(freqs) == 1):
fl = freqs[0][0] - freqws[0][0] / 2.
fh = freqs[0][0] + freqws[0][0] / 2.
freqlist.append([float(fl), float(fh)])
else:
freqlist.append([float(min(freqs)), float(max(freqs))])
framelist.append(measframes[fmeasref])
freqlistraw.append(
freqs.transpose()[0].tolist()) # data chanfreq list
#inparams[srcnames[fid]]['freqlist']=freqlist
#inparams[srcnames[fid]]['freqlistraw']=freqlistraw
#inparams[srcnames[fid]]['framelist']=framelist
#inparams[srcnames[fid]]['reffreqs']=reffreqs
inparams[fid]['freqlist'] = freqlist
inparams[fid]['freqlistraw'] = freqlistraw
inparams[fid]['framelist'] = framelist
inparams[fid]['reffreqs'] = reffreqs
myms.close()
# call Bryan's code
# errcode: list of list - inner list - each values for range of freqs
# flluxes: list of list
# fluxerrs:
# size: [majoraxis, minoraxis, pa]
# direction: direction for each time stamp
#
#import solar_system_setjy as ss_setjy
import solar_system_setjy as SSsetjy
retdict = {} # for returning flux densities?
ss_setjy = SSsetjy.solar_system_setjy()
#for src in srcnames:
self.clnamelist = []
for vfid in validfids:
src = srcnames[vfid]
#mjds=inparams[src]['mjds']
mjds = inparams[vfid]['mjds']
fluxes = []
# call solar_system_fd() per spw (for scalebychan freqlist has an extra dimention)
#nspwused=len(inparams[src]['freqlist'])
nspwused = len(inparams[vfid]['freqlist'])
# warning for many channels but it is really depends on the source
if scalebychan:
maxnf = 0
for ispw in range(nspwused):
#nf = len(inparams[src]['freqlist'][ispw])
nf = len(inparams[vfid]['freqlist'][ispw])
maxnf = max(nf, maxnf)
if maxnf >= 3840 and src.upper(
) != "MARS": # mars shoulde be ok
self._casalog.post(
"Processing %s spw(s) and at least some of them are a few 1000 channels or more. This may take \
many minutes (>3min per spw for 3840 channels) in some cases. Please be patient."
% nspwused, "WARN")
for i in range(nspwused): # corresponds to n spw
if type(freqlist[0][0]) == list:
#infreqs=inparams[src]['freqlist'][i]
infreqs = inparams[vfid]['freqlist'][i]
else:
#infreqs=[inparams[src]['freqlist'][i]]
infreqs = [inparams[vfid]['freqlist'][i]]
self._casalog.post(
"Calling solar_system_fd: %s(%s) for spw%s freqs=%s" %
(src, vfid, i, freqlist[i]), 'DEBUG1')
(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, observatory=observatory, casalog=self._casalog)
# for old code
#(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
# ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, casalog=self._casalog)
# for nf freq ranges, nt mjds
# errcodes[nf][nt], subfluxes[nf][nt], fluxerrs[nf][nt], sizes[nt], dirs[nt]
self._casalog.post(
"+++++ solar_system_fd() returned values +++++", 'DEBUG1')
self._casalog.post(" fluxes(fds)=%s" % subfluxes, 'DEBUG1')
self._casalog.post(" sizes=%s" % sizes, 'DEBUG1')
self._casalog.post(" directions=%s\n" % dirs, 'DEBUG1')
# packed fluxes for all spws
fluxes.append(subfluxes)
# fluxes has fluxesi[nspw][nf][nt]
# ------------------------------------------------------------------------
# For testing with hardcoded values without calling solar_system_fd()...
#errcodes=[[0,0,0,0,0]]
#fluxes=[[26.40653147,65.23839313,65.23382757,65.80638802,69.33396562]]
#fluxerrs=[[0.0,0.0,0.0,0.0,0.0]]
#sizes=[[3.6228991032674371,3.6228991032674371,0.0]]
#dirs=[{'m0': {'unit': 'rad', 'value': 0.0}, 'm1': {'unit': 'rad', 'value': 0.0}, 'refer': 'J2000', 'type': 'direction'}]
# ------------------------------------------------------------------------
# local params for selected src
#framelist=inparams[src]['framelist']
#freqlist=inparams[src]['freqlist']
#freqlistraw=inparams[src]['freqlistraw']
#reffreqs=inparams[src]['reffreqs']
#spwids=inparams[src]['spwids']
framelist = inparams[vfid]['framelist']
freqlist = inparams[vfid]['freqlist']
freqlistraw = inparams[vfid]['freqlistraw']
reffreqs = inparams[vfid]['reffreqs']
spwids = inparams[vfid]['spwids']
clrecs = odict.odict()
labels = []
# loop for over for multiple directions (=multiple MJDs) for a given src
for i in range(
len(dirs)
): # this is currently only length of 1 since no multiple timestamps were used
# check errcode - error code would be there per flux per time (dir)
reterr = testerrs(errcodes[i], src)
if reterr == 2:
continue
#dirstring = [dirs[i]['refer'],qa.tos(dirs[i]['m0']),qa.tos(dirs[i]['m1'])]
if useephemdir:
dirstring = [
dirs[i]['refer'],
qa.tos(dirs[i]['m0']),
qa.tos(dirs[i]['m1'])
]
else:
#dirstring = [fieldref, str(fielddirs[fieldids[0]][0][0])+'rad', str(fielddirs[fieldids[0]][1][0])+'rad']
# extract field direction of first id of the selected field ids
#dirstring = [fieldref, "%.18frad" % (fielddirs[fieldids[0]][0][0]), "%.18frad" % (fielddirs[fieldids[0]][1][0])]
dirstring = [
fieldref,
"%.18frad" % (fielddirs[vfid][0][0]),
"%.18frad" % (fielddirs[vfid][1][0])
]
#print "dirstring=",dirstring
# setup componentlists
# need to set per dir
# if scalebychan=F, len(freqs) corresponds to nspw selected
# Need to put in for-loop to create cl for each time stamp? or scan?
#clpath='/tmp/'
clpath = './'
# construct cl name (multiple spws in one componentlist table)
selreffreqs = [reffreqs[indx] for indx in spwids]
minfreq = min(selreffreqs)
maxfreq = max(selreffreqs)
freqlabel = '%.3f-%.3fGHz' % (minfreq / 1.e9, maxfreq / 1.e9)
#tmlabel = '%.1fd' % (tc/86400.)
mjd = inparams[vfid]['mjds'][0]
tmlabel = '%.1fd' % (mjd)
#clabel = src+'_spw'+str(spwids[j])+'_'+freqlabel+'_'+tmlabel
#clabel0 = src+'_'+freqlabel+'_'+tmlabel
#pid=str(os.getpid())
#clname = clpath+clabel0+"_"+pid+'.cl'
clabel0 = src + '_' + freqlabel + '_' + tmlabel + "_" + os.path.basename(
self.vis)
clname = clpath + clabel0 + '.cl'
#debug
self._casalog.post(
"Create componentlist: %s for vfid=%s" % (clname, vfid),
'DEBUG1')
if (os.path.exists(clname)):
shutil.rmtree(clname)
iiflux = []
iinfreq = []
# for logging/output dict - pack each freq list for each spw
freqsforlog = []
for j in range(len(freqlist)): # loop over nspw
freqlabel = '%.3fGHz' % (reffreqs[int(spwids[j])] / 1.e9)
clabel = src + '_spw' + str(
spwids[j]) + '_' + freqlabel + '_' + tmlabel
#print "addcomponent...for spw=",spwids[j]," i=",i," flux=",fluxes[j][i]
if scalebychan:
index = 2.0
sptype = 'spectral index'
else:
index = 0.0
sptype = 'constant'
# adjust to change in returned flux shape. An extra [] now seems to be gone. 2012-09-27
iflux = fluxes[j][i][0]
#print "addcomponent with flux=%s at frequency=%s" %\
# (iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz')
# i - time stamps = 0 for now, j = a freq range
infreq = freqlist[j][0][0] if type(
freqlist[j][0]) == list else freqlist[j][0]
# for a single CL with multple spws
if j == 0: infreq0 = infreq
# --- version for 'multi-spws in a single comp single CL'
# accumulate all frequencies from all spws to a list
#if not scalebychan:
#freqlist[j] for j spw should contain a list with two freqs (min and max of
# of the spw and the same fluxes should be set for the freqs so that cl.setspectrum
# with tabular would not interpolate inside each spw
##iinfreq.extend(freqlist[j])
# nch = len(freqlistraw[j])
# iinfreq.extend(freqlistraw[j])
# assigning the same flux to the two freqs
##iiflux.extend([iflux,iflux])
# for ich in range(nch):
# iiflux.extend([iflux])
#else:
# iiflux.extend(fluxes[j][i])
# if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# for fr in freqlist[j]:
# iinfreq.append((fr[1]+fr[0])/2)
# else:
# if type(freqlist[j])==list:
# iinfreq.append((freqlist[j][1]+freqlist[j][0])/2)
# else:
# iinfreq.append(freqlist[j])
# freqsforlog.append(iinfreq)
# -----------------------------------------------------------------------------------
self._casalog.post("addcomponent with flux=%s at frequency=%s" %\
# (fluxes[j][i][0],str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
(iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
#
mycl.addcomponent(iflux,
fluxunit='Jy',
polarization="Stokes",
dir=dirstring,
shape='disk',
majoraxis=str(sizes[i][0]) + 'arcsec',
minoraxis=str(sizes[i][1]) + 'arcsec',
positionangle=str(sizes[i][2]) + 'deg',
freq=[framelist[0],
str(infreq) + 'Hz'],
spectrumtype=sptype,
index=index,
label=clabel)
if scalebychan:
# use tabular form to set flux for each channel
# This may be redundant
if type(fluxes[j][i]) == list and len(
fluxes[j][i]) > 1:
if type(freqlist[j][0]) == list and len(
freqlist[j][0]) > 1:
freqs = []
for fr in freqlist[j]:
freqs.append((fr[1] + fr[0]) / 2)
clind = mycl.length() - 1
mycl.setspectrum(which=clind,
type='tabular',
tabularfreqs=freqs,
tabularflux=fluxes[j][0],
tabularframe=framelist[j])
### === per spw process end here
# - version that put all spws into a component -
# set a single component freq set at the the lower edge of first spw
#mycl.addcomponent(iiflux[0],fluxunit='Jy', polarization="Stokes", dir=dirstring,
# shape='disk', majoraxis=str(sizes[i][0])+'arcsec', minoraxis=str(sizes[i][1])+'arcsec',
# positionangle=str(sizes[i][2])+'deg', freq=[framelist[0],str(infreq0)+'Hz'],
# spectrumtype=sptype, index=index, label=clabel)
# if it's list of fluxes try to put in tabular form
#if type(fluxes[j][i]) ==list and len(fluxes[j][i])> 1:
# if len(iiflux)> 1:
#print "framelist[j]=",framelist[j]
#if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# freqs=[]
# for fr in freqlist[j]:
# freqs.append((fr[1]+fr[0])/2)
#else:
# freqs=freqlist[j]
#clind = mycl.length() - 1
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=freqs, tabularflux=fluxes[j][0],
#tabularframe=framelist[j])
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=iinfreq, tabularflux=iiflux,
# tabularframe=framelist[0])
#mycl.rename(clname)
#put in a record for log output
#clrecs[clabel] = mycl.torecord()
clrecs[clabel0] = mycl.torecord()
clrecs[clabel0]['allfluxinfo'] = fluxes
clrecs[clabel0]['allfreqinfo'] = freqsforlog
clrecs[clabel0]['spwids'] = spwids
mycl.rename(clname) # - A CL per field
mycl.close(False) # False for not to send a warning message
mycl.done()
# if scratch=F check if the virtual model already exist
# for the field if it is clear it.
# if j==0 and (not usescratch):
# mytb.open(self.vis, nomodify=False)
# kwds = mytb.getkeywords()
# modelkwd='definedmodel_field_'+str(vfid)
# if kwds.has_key(modelkwd):
# clmodname=kwds[modelkwd]
# mytb.removekeyword(clmodname)
# mytb.removekeyword(modelkwd)
# mytb.close()
mycb.open(self.vis, addcorr=False, addmodel=False)
mycb.delmod(otf=True, field=str(vfid), spw=spwids, scr=False)
mycb.close()
# finally, put the componentlist as model
#tqlstr=''
#if intent!='':
# tqlstr='any(STATE_ID=='+str(stateids.tolist())+')'
# Currently still need to do per spw (see the comment below...)
# assuming CL contains nrow = nspw components
mycl.open(clname)
clinrec = mycl.torecord()
mycl.close(False)
mycl.done()
ncomp = clinrec['nelements']
if ncomp != len(spwids):
raise Exception, "Inconsistency in generated componentlist...Please submit a bug report."
for icomp in range(ncomp):
#self.im.selectvis(spw=spwids[icomp],field=field,observation=observation,time=timerange,intent=intent)
ok = self.im.selectvis(spw=spwids[icomp],
field=vfid,
observation=observation,
time=timerange,
intent=intent)
# for MMS, particular subms may not contain the particular spw, so skip for such a case
if ok:
newclinrec = {}
newclinrec['nelements'] = 1
newclinrec['component0'] = clinrec['component' +
str(icomp)]
mycl.fromrecord(newclinrec)
cdir = os.getcwd()
if os.access(cdir, os.W_OK):
tmpclpath = cdir + "/"
elif os.access("/tmp", os.W_OK):
tmpclpath = "/tmp/"
#tmpclpath=tmpclpath+"_tmp_setjyCLfile_"+pid
tmpclpath = tmpclpath + os.path.basename(
self.vis) + "_tmp_setjyCLfile"
self._casalog.post("tmpclpath=" + tmpclpath)
if os.path.exists(tmpclpath):
shutil.rmtree(tmpclpath)
mycl.rename(tmpclpath)
mycl.close(False)
self._casalog.post("Now tmpclpath=" + tmpclpath)
self.im.ft(complist=tmpclpath)
# --------------------------------------------------------------------------------------------
# Currently this does not work properly for some case. Need ft can handle multi-component CL
# with the way to map which component apply to which spw
# Unable when such functionality is implemented in im.ft()
#self.im.selectvis(spw=spwids,field=field,observation=observation,time=timerange,intent=intent)
#self.im.ft(complist=clname) <= e.g. im.ft(comprec) where comrec = {'spw-mapping':[...],comprecs}..
# --------------------------------------------------------------------------------------------
#debug: set locally saved 2010-version component list instead
#cl2010='mod_setjy_spw0_Titan_230.543GHz55674.1d.cl'
#print "Using complist=",cl2010
#self.im.ft(complist=cl2010)
#if cleanupcomps:
# shutil.rmtree(clname)
#self.clnamelist.append(clname)
self.clnamelist.append(clname)
msg = "Using channel dependent " if scalebychan else "Using spw dependent "
if clrecs == {}:
raise Exception, "No componentlist is generated."
self._casalog.post(msg + " flux densities")
#self._reportoLog(clrecs,self._casalog)
self._reportoLog2(clrecs, self._casalog)
#self._updateHistory(clrecs,self.vis)
self._updateHistory2(clrecs, self.vis)
# dictionary of dictionary for each field
retdict[vfid] = clrecs
# ==== end of for loop over fields
#output=self._makeRetFluxDict(retdict)
output = self._makeRetFluxDict2(retdict)
#return retval
return output
def splitant(filename, outprefix='', overwrite=False, getpt=True):
"""
Split Measurement set by antenna name, save data as a scantables,
and return a list of filename. Note that frequency reference frame
is imported as it is in Measurement set.
Notice this method can only be available from CASA.
Prameter
filename: the name of Measurement set to be read.
outprefix: the prefix of output scantable name.
the names of output scantable will be
outprefix.antenna1, outprefix.antenna2, ....
If not specified, outprefix = filename is assumed.
overwrite If the file should be overwritten if it exists.
The default False is to return with warning
without writing the output. USE WITH CARE.
getpt Whether to import direction from MS/POINTING
table or not. Default is True (import direction).
"""
# Import the table toolkit from CASA
from taskinit import gentools
from asap.scantable import is_ms
tb = gentools(['tb'])[0]
# Check the input filename
if isinstance(filename, str):
import os.path
filename = os.path.expandvars(filename)
filename = os.path.expanduser(filename)
if not os.path.exists(filename):
s = "File '%s' not found." % (filename)
raise IOError(s)
# check if input file is MS
if not is_ms(filename):
s = "File '%s' is not a Measurement set." % (filename)
raise IOError(s)
else:
s = "The filename should be string. "
raise TypeError(s)
# Check out put file name
outname = ''
if len(outprefix) > 0: prefix = outprefix + '.'
else:
prefix = filename.rstrip('/')
# Now do the actual splitting.
outfiles = []
tb.open(tablename=filename, nomodify=True)
ant1 = tb.getcol('ANTENNA1', 0, -1, 1)
anttab = tb.getkeyword('ANTENNA').lstrip('Table: ')
tb.close()
tb.open(tablename=anttab, nomodify=True)
nant = tb.nrows()
antnames = tb.getcol('NAME', 0, nant, 1)
tb.close()
for antid in set(ant1):
scan = scantable(filename,
average=False,
antenna=int(antid),
getpt=getpt)
outname = prefix + antnames[antid] + '.asap'
scan.save(outname, format='ASAP', overwrite=overwrite)
del scan
outfiles.append(outname)
return outfiles
def sdgaincal(infile=None, calmode=None, radius=None, smooth=None,
antenna=None, field=None, spw=None, scan=None, intent=None,
applytable=None, outfile='', overwrite=False):
casalog.origin('sdgaincal')
# Calibrator tool
(mycb,) = gentools(['cb'])
try:
# outfile must be specified
if (outfile == '') or not isinstance(outfile, str):
raise ValueError, "outfile is empty."
# overwrite check
if os.path.exists(outfile) and not overwrite:
raise RuntimeError(outfile + ' exists.')
# TODO: pre-application functionality is not supported yet
if type(applytable) == types.ListType or \
(isinstance(applytable, str) and len(applytable) > 0):
msg = 'Pre-application of calibration solutions is not supported yet.'
casalog.post(msg, priority='SEVERE')
raise RuntimeError(msg)
# open MS
if isinstance(infile, str) and os.path.exists(infile):
mycb.open(filename=infile, compress=False, addcorr=False, addmodel=False)
else:
raise RuntimeError, 'infile not found - please verify the name'
# select data
if isinstance(antenna, str) and len(antenna) > 0:
baseline = '{ant}&&&'.format(ant=antenna)
else:
baseline = ''
mycb.selectvis(spw=spw, scan=scan, field=field, intent=intent, baseline=baseline)
# set solve
if calmode == 'doublecircle':
if radius is None:
raise RuntimeError('radius must be specified.')
elif not isinstance(radius, str):
rcenter = '%sarcsec'%(radius)
else:
try:
# if radius is a string only consists of numeric value without unit,
# it will succeed.
rcenter = '%sarcsec'%(float(radius))
except:
# if the above fails, it may indicate that the string contains unit
rcenter = radius
mycb.setsolve(type='SDGAIN_OTFD', table=outfile, radius=rcenter, smooth=smooth)
else:
raise RuntimeError('Unknown calibration mode: \'{mode}\''.format(mode=calmode))
# solve
mycb.solve()
## reporting calibration solution
#reportsolvestats(mycb.activityrec());
except Exception, e:
import traceback
casalog.post(traceback.format_exc(), priority='DEBUG')
casalog.post(errmsg(e), priority='SEVERE')
raise e
def get_table_cache():
(mytb, ) = gentools(['tb'])
cache = mytb.showcache()
#print 'cache = {}'.format(cache)
return cache
###############################
#
# FLS3a HI Reduction Script
# Frequency-Switched data
# Formatted for wide screen (150
# characters wide)
#
###############################
#
import time
import os
from taskinit import gentools
(myim, myia) = gentools(['im', 'ia'])
os.system('rm -rf FLS3a_HI.image FLS3a_HI.asap FLS3b_HI.asap FLS3a_calfs')
casapath=os.environ['CASAPATH'].split()[0]
datapath=casapath+'/data/regression/ATST5/FLS3/FLS3_all_newcal_SP'
#copystring='cp -r '+datapath+' .'
#os.system(copystring)
startTime=time.time()
startProc=time.clock()
# Project: AGBT02A_007_01
# Observation: GBT(1 antennas)
#
# Telescope Observation Date Observer Project
# GBT [ 4.57539e+09, 4.5754e+09]Lockman AGBT02A_007_01
def __init__( self, filename ):
self.filename = filename.rstrip('/')
self.polno = None
self.beamno = None
self.table = gentools(['tb'])[0]
self.table.open( self.filename, nomodify=False )
from taskinit import casalog, gentools, qa
import pylab as pl
import numpy
import os
import contextlib
import asap as sd
tb = gentools(['tb'])[0]
def asdatestring(mjd, digit, timeonly=False):
datedict = qa.splitdate(qa.quantity(mjd, 'd'))
if digit > 10 : digit = 10
sstr_tmp = str(numpy.round(datedict['s'], digit)).split('.')
sstr = sstr_tmp[0] + '.' + sstr_tmp[1][0:digit]
if timeonly:
return '%s:%s:%s'%(datedict['hour'],datedict['min'],sstr)
else:
return '%s/%s/%s/%s:%s:%s'%(datedict['year'],datedict['month'],datedict['monthday'],datedict['hour'],datedict['min'],sstr)
def astimerange(tmargin, mjd0, mjd1):
digit = numpy.abs(int(numpy.floor(numpy.log10(tmargin))))
if int(mjd0) == int(mjd1): # same date, different time
timeonly=True
else: # different date
timeonly=False
return '%s~%s'%(asdatestring(mjd0,digit), asdatestring(mjd1,digit,timeonly=timeonly))
@contextlib.contextmanager
def selection_manager(scantab, original_selection, **kwargs):
sel = sd.selector(original_selection)
def sdgaincal(infile=None,
calmode=None,
radius=None,
smooth=None,
antenna=None,
field=None,
spw=None,
scan=None,
intent=None,
applytable=None,
interp=None,
spwmap=None,
outfile='',
overwrite=False):
casalog.origin('sdgaincal')
# Calibrator tool
(mycb, ) = gentools(['cb'])
try:
# outfile must be specified
if (outfile == '') or not isinstance(outfile, str):
raise ValueError, "outfile is empty."
# overwrite check
if os.path.exists(outfile) and not overwrite:
raise RuntimeError(outfile + ' exists.')
# open MS
if isinstance(infile, str) and os.path.exists(infile):
#mycb.setvi(old=True)
mycb.open(filename=infile,
compress=False,
addcorr=False,
addmodel=False)
else:
raise RuntimeError, 'infile not found - please verify the name'
# select data
if isinstance(antenna, str) and len(antenna) > 0:
baseline = '{ant}&&&'.format(ant=antenna)
else:
baseline = ''
mycb.selectvis(spw=spw,
scan=scan,
field=field,
intent=intent,
baseline=baseline)
# set apply
casalog.post('interp="{0}" spwmap={1}'.format(interp, spwmap))
if isinstance(applytable, str):
if len(applytable) > 0:
thisinterp = parse_interp(interp, 0)
thisspwmap = parse_spwmap(spwmap, 0)
casalog.post('thisinterp="{0}" thisspwmap={1}'.format(
thisinterp, thisspwmap))
mycb.setapply(table=applytable,
interp=thisinterp,
spwmap=thisspwmap)
elif hasattr(applytable, '__iter__'):
# list type
for i in xrange(len(applytable)):
table = applytable[i]
if isinstance(table, str) and len(table) > 0:
thisinterp = parse_interp(interp, i)
thisspwmap = parse_spwmap(spwmap, i)
casalog.post('thisinterp="{0}" thisspwmap={1}'.format(
thisinterp, thisspwmap))
mycb.setapply(table=table,
interp=thisinterp,
spwmap=thisspwmap)
else:
RuntimeError, 'wrong type of applytable item ({0}). it should be string'.format(
type(table))
else:
raise RuntimeError, 'wrong type of applytable ({0}). it should be string or list'.format(
type(applytable))
# set solve
if calmode == 'doublecircle':
if radius is None:
raise RuntimeError('radius must be specified.')
elif not isinstance(radius, str):
rcenter = '%sarcsec' % (radius)
else:
try:
# if radius is a string only consists of numeric value without unit,
# it will succeed.
rcenter = '%sarcsec' % (float(radius))
except:
# if the above fails, it may indicate that the string contains unit
rcenter = radius
mycb.setsolve(type='SDGAIN_OTFD',
table=outfile,
radius=rcenter,
smooth=smooth)
else:
raise RuntimeError(
'Unknown calibration mode: \'{mode}\''.format(mode=calmode))
# solve
mycb.solve()
## reporting calibration solution
#reportsolvestats(mycb.activityrec());
except Exception, e:
import traceback
casalog.post(traceback.format_exc(), priority='DEBUG')
casalog.post(errmsg(e), priority='SEVERE')
raise e
import numpy
import os
import time, datetime
from taskinit import gentools, casalog
import sdutil
ms, sdms, tb = gentools(['ms','sdms','tb'])
from numpy import ma, array, logical_not, logical_and
@sdutil.sdtask_decorator
def sdfit(infile=None, datacolumn=None, antenna=None, field=None, spw=None,
timerange=None, scan=None, pol=None, intent=None,
timebin=None, timespan=None,
polaverage=None,
fitfunc=None, fitmode=None, nfit=None, thresh=None, avg_limit=None,
minwidth=None, edge=None, outfile=None, overwrite=None):
casalog.origin('sdfit')
try:
if os.path.exists(outfile):
if overwrite:
os.system('rm -rf %s' % outfile)
else:
raise ValueError(outfile + ' exists.')
if (fitmode not in ['list', 'auto']):
raise ValueError, "fitmode='%s' is not supported yet" % fitmode
if (spw == ''): spw = '*'
selection = ms.msseltoindex(vis=infile, spw=spw, field=field,
def compile(self):
# imaging mode
self.imager_param['mode'] = self.mode
# Work on selection of the first table in sorted list
# to get default restfreq and outframe
imhelper = cleanhelper(self.imager, self.infiles, casalog=casalog)
imhelper.sortvislist(self.spw, self.mode, self.width)
self.sorted_idx = imhelper.sortedvisindx
selection_ids = self.get_selection_idx_for_ms(self.sorted_idx[0])
self.__update_subtable_name(self.infiles[self.sorted_idx[0]])
# field
fieldid = selection_ids['field'][0] if type(
selection_ids['field']) != int else selection_ids['field']
sourceid = -1
self.open_table(self.field_table)
source_ids = self.table.getcol('SOURCE_ID')
self.close_table()
if self.field == '' or fieldid == -1:
sourceid = source_ids[0]
elif fieldid >= 0 and fieldid < len(source_ids):
sourceid = source_ids[fieldid]
else:
raise ValueError, "No valid field in the first MS."
# restfreq
if self.restfreq == '' and self.source_table != '':
self.open_table(self.source_table)
source_ids = self.table.getcol('SOURCE_ID')
for i in range(self.table.nrows()):
if sourceid == source_ids[i] \
and self.table.iscelldefined('REST_FREQUENCY',i) \
and (selection_ids['spw'] == -1 or \
self.table.getcell('SPECTRAL_WINDOW_ID', i) in selection_ids['spw']):
rf = self.table.getcell('REST_FREQUENCY', i)
if len(rf) > 0:
self.restfreq = self.table.getcell(
'REST_FREQUENCY', i)[0]
break
self.close_table()
casalog.post("restfreq set to %s" % self.restfreq, "INFO")
# REST_FREQUENCY column is optional (need retry if not exists)
self.imager_param['restfreq'] = self.restfreq
#
# spw (define representative spw id = spwid_ref)
spwid_ref = selection_ids['spw'][0] if type(
selection_ids['spw']) != int else selection_ids['spw']
# Invalid spw selection should have handled at msselectiontoindex().
# -1 means all spw are selected.
self.open_table(self.spw_table)
if spwid_ref < 0:
for id in range(self.table.nrows()):
if self.table.getcell('NUM_CHAN', id) > 0:
spwid_ref = id
break
if spwid_ref < 0:
self.close_table()
msg = 'No valid spw id exists in the first table'
raise ValueError, msg
self.allchannels = self.table.getcell('NUM_CHAN', spwid_ref)
freq_chan0 = self.table.getcell('CHAN_FREQ', spwid_ref)[0]
freq_inc0 = self.table.getcell('CHAN_WIDTH', spwid_ref)[0]
# in case rest frequency is not defined yet.
if self.restfreq == '':
self.restfreq = '%fHz' % self.table.getcell(
'CHAN_FREQ', spwid_ref).mean()
self.imager_param['restfreq'] = self.restfreq
casalog.post(
"Using mean freq of spw %d as restfreq: %s" %
(spwid_ref, self.restfreq), "INFO")
self.close_table()
self.imager_param['spw'] = -1 #spwid_ref
# outframe (force using the current frame)
self.imager_param['outframe'] = self.outframe
if self.outframe == '':
if len(self.infiles) > 1:
# The default will be 'LSRK'
casalog.post(
"Multiple MS inputs. The default outframe is set to 'LSRK'"
)
self.imager_param['outframe'] = 'LSRK'
else:
# get from MS
my_ms = gentools(['ms'])[0]
my_ms.open(self.infiles[0])
spwinfo = my_ms.getspectralwindowinfo()
my_ms.close()
del my_ms
for key, spwval in spwinfo.items():
if spwval['SpectralWindowId'] == spwid_ref:
self.imager_param['outframe'] = spwval['Frame']
casalog.post("Using frequency frame of MS, '%s'" %
self.imager_param['outframe'])
break
if self.imager_param['outframe'] == '':
raise Exception, "Internal error of getting frequency frame of spw=%d." % spwid_ref
else:
casalog.post("Using frequency frame defined by user, '%s'" %
self.imager_param['outframe'])
class sdimaging_worker(sdutil.sdtask_template_imaging):
def __init__(self, **kwargs):
super(sdimaging_worker, self).__init__(**kwargs)
self.imager_param = {}
self.sorted_idx = []
def parameter_check(self):
# outfile check
sdutil.assert_outfile_canoverwrite_or_nonexistent(
self.outfile, 'im', self.overwrite)
sdutil.assert_outfile_canoverwrite_or_nonexistent(
self.outfile + '.weight', 'im', self.overwrite)
# fix spw
if type(self.spw) == str:
self.spw = self.__format_spw_string(self.spw)
# check unit of start and width
# fix default
if self.mode == 'channel':
if self.start == '': self.start = 0
if self.width == '': self.width = 1
else:
if self.start == 0: self.start = ''
if self.width == 1: self.width = ''
# fix unit
if self.mode == 'frequency':
myunit = 'Hz'
elif self.mode == 'velocity':
myunit = 'km/s'
else: # channel
myunit = ''
for name in ['start', 'width']:
param = getattr(self, name)
new_param = self.__format_quantum_unit(param, myunit)
if new_param == None:
raise ValueError, "Invalid unit for %s in mode %s: %s" % \
(name, self.mode, param)
setattr(self, name, new_param)
casalog.post("mode='%s': start=%s, width=%s, nchan=%d" % \
(self.mode, self.start, self.width, self.nchan))
# check length of selection parameters
if is_string_type(self.infiles):
nfile = 1
self.infiles = [self.infiles]
else:
nfile = len(self.infiles)
for name in ['field', 'spw', 'antenna', 'scanno']:
param = getattr(self, name)
if not self.__check_selection_length(param, nfile):
raise ValueError, "Length of %s != infiles." % (name)
# set convsupport default
if self.convsupport >= 0 and self.gridfunction.upper() != 'SF':
casalog.post("user defined convsupport is ignored for %s kernel" %
self.gridfunction,
priority='WARN')
self.convsupport = -1
def __format_spw_string(self, spw):
"""
Returns formatted spw selection string which is accepted by imager.
"""
if type(spw) != str:
raise ValueError, "The parameter should be string."
if spw.strip() == '*': spw = ''
# WORKAROUND for CAS-6422, i.e., ":X~Y" fails while "*:X~Y" works.
if spw.startswith(":"): spw = '*' + spw
return spw
def __format_quantum_unit(self, data, unit):
"""
Returns False if data has an unit which in not a variation of
input unit.
Otherwise, returns input data as a quantum string. The input
unit is added to the return value if no unit is in data.
"""
my_qa = qatool()
if data == '' or my_qa.compare(data, unit):
return data
if my_qa.getunit(data) == '':
casalog.post("No unit specified. Using '%s'" % unit)
return '%f%s' % (data, unit)
return None
def __check_selection_length(self, data, nfile):
"""
Returns true if data is either a string, an array with length
1 or nfile
"""
if not is_string_type(data) and len(data) not in [1, nfile]:
return False
return True
def get_selection_param_for_ms(self, fileid, param):
"""
Returns valid selection string for a certain ms
Arguments
fileid : file idx in infiles list
param : string (array) selection value
"""
if is_string_type(param):
return param
elif len(param) == 1:
return param[0]
else:
return param[fileid]
def get_selection_idx_for_ms(self, file_idx):
"""
Returns a dictionary of selection indices for i-th MS in infiles
Argument: file idx in infiles list
"""
if file_idx < len(self.infiles) and file_idx > -1:
vis = self.infiles[file_idx]
field = self.get_selection_param_for_ms(file_idx, self.field)
spw = self.get_selection_param_for_ms(file_idx, self.spw)
spw = self.__format_spw_string(spw)
antenna = self.get_selection_param_for_ms(file_idx, self.antenna)
if antenna == -1: antenna = ''
scan = self.get_selection_param_for_ms(file_idx, self.scanno)
intent = self.get_selection_param_for_ms(file_idx, self.intent)
my_ms = gentools(['ms'])[0]
sel_ids = my_ms.msseltoindex(vis=vis,
spw=spw,
field=field,
baseline=antenna,
scan=scan)
fieldid = list(
sel_ids['field']) if len(sel_ids['field']) > 0 else -1
baseline = self.format_ac_baseline(sel_ids['antenna1'])
scanid = list(sel_ids['scan']) if len(sel_ids['scan']) > 0 else ""
# SPW (need to get a list of valid spws instead of -1)
if len(sel_ids['channel']) > 0:
spwid = [chanarr[0] for chanarr in sel_ids['channel']]
elif spw == "": # No spw selection
my_ms.open(vis)
try:
spwinfo = my_ms.getspectralwindowinfo()
except:
raise
finally:
my_ms.close()
spwid = [int(idx) for idx in spwinfo.keys()]
else:
raise RuntimeError("Invalid spw selction, %s ,for MS %d" (
str(spw), file_idx))
return {
'field': fieldid,
'spw': spwid,
'baseline': baseline,
'scan': scanid,
'intent': intent,
'antenna1': sel_ids['antenna1']
}
else:
raise ValueError, ("Invalid file index, %d" % file_idx)
def format_ac_baseline(self, in_antenna):
""" format auto-correlation baseline string from antenna idx list """
# exact match string
if is_string_type(in_antenna):
if (len(in_antenna) != 0) and (in_antenna.find('&') == -1) \
and (in_antenna.find(';')==-1):
in_antenna = + '&&&'
return in_antenna
# single integer -> list of int
if type(in_antenna) == int:
if in_antenna >= 0:
in_antenna = [in_antenna]
else:
return -1
# format auto-corr string from antenna idices.
baseline = ''
for idx in in_antenna:
if len(baseline) > 0: baseline += ';'
if idx >= 0:
baseline += (str(idx) + '&&&')
return baseline
def compile(self):
# imaging mode
self.imager_param['mode'] = self.mode
# Work on selection of the first table in sorted list
# to get default restfreq and outframe
imhelper = cleanhelper(self.imager, self.infiles, casalog=casalog)
imhelper.sortvislist(self.spw, self.mode, self.width)
self.sorted_idx = imhelper.sortedvisindx
selection_ids = self.get_selection_idx_for_ms(self.sorted_idx[0])
self.__update_subtable_name(self.infiles[self.sorted_idx[0]])
# field
fieldid = selection_ids['field'][0] if type(
selection_ids['field']) != int else selection_ids['field']
sourceid = -1
self.open_table(self.field_table)
source_ids = self.table.getcol('SOURCE_ID')
self.close_table()
if self.field == '' or fieldid == -1:
sourceid = source_ids[0]
elif fieldid >= 0 and fieldid < len(source_ids):
sourceid = source_ids[fieldid]
else:
raise ValueError, "No valid field in the first MS."
# restfreq
if self.restfreq == '' and self.source_table != '':
self.open_table(self.source_table)
source_ids = self.table.getcol('SOURCE_ID')
for i in range(self.table.nrows()):
if sourceid == source_ids[i] \
and self.table.iscelldefined('REST_FREQUENCY',i) \
and (selection_ids['spw'] == -1 or \
self.table.getcell('SPECTRAL_WINDOW_ID', i) in selection_ids['spw']):
rf = self.table.getcell('REST_FREQUENCY', i)
if len(rf) > 0:
self.restfreq = self.table.getcell(
'REST_FREQUENCY', i)[0]
break
self.close_table()
casalog.post("restfreq set to %s" % self.restfreq, "INFO")
# REST_FREQUENCY column is optional (need retry if not exists)
self.imager_param['restfreq'] = self.restfreq
#
# spw (define representative spw id = spwid_ref)
spwid_ref = selection_ids['spw'][0] if type(
selection_ids['spw']) != int else selection_ids['spw']
# Invalid spw selection should have handled at msselectiontoindex().
# -1 means all spw are selected.
self.open_table(self.spw_table)
if spwid_ref < 0:
for id in range(self.table.nrows()):
if self.table.getcell('NUM_CHAN', id) > 0:
spwid_ref = id
break
if spwid_ref < 0:
self.close_table()
msg = 'No valid spw id exists in the first table'
raise ValueError, msg
self.allchannels = self.table.getcell('NUM_CHAN', spwid_ref)
freq_chan0 = self.table.getcell('CHAN_FREQ', spwid_ref)[0]
freq_inc0 = self.table.getcell('CHAN_WIDTH', spwid_ref)[0]
# in case rest frequency is not defined yet.
if self.restfreq == '':
self.restfreq = '%fHz' % self.table.getcell(
'CHAN_FREQ', spwid_ref).mean()
self.imager_param['restfreq'] = self.restfreq
casalog.post(
"Using mean freq of spw %d as restfreq: %s" %
(spwid_ref, self.restfreq), "INFO")
self.close_table()
self.imager_param['spw'] = -1 #spwid_ref
# outframe (force using the current frame)
self.imager_param['outframe'] = self.outframe
if self.outframe == '':
if len(self.infiles) > 1:
# The default will be 'LSRK'
casalog.post(
"Multiple MS inputs. The default outframe is set to 'LSRK'"
)
self.imager_param['outframe'] = 'LSRK'
else:
# get from MS
my_ms = gentools(['ms'])[0]
my_ms.open(self.infiles[0])
spwinfo = my_ms.getspectralwindowinfo()
my_ms.close()
del my_ms
for key, spwval in spwinfo.items():
if spwval['SpectralWindowId'] == spwid_ref:
self.imager_param['outframe'] = spwval['Frame']
casalog.post("Using frequency frame of MS, '%s'" %
self.imager_param['outframe'])
break
if self.imager_param['outframe'] == '':
raise Exception, "Internal error of getting frequency frame of spw=%d." % spwid_ref
else:
casalog.post("Using frequency frame defined by user, '%s'" %
self.imager_param['outframe'])
# # antenna
# in_antenna = self.antenna # backup for future use
# if type(self.antenna)==int:
# if self.antenna >= 0:
# self.antenna=str(self.antenna)+'&&&'
# else:
# if (len(self.antenna) != 0) and (self.antenna.find('&') == -1) \
# and (self.antenna.find(';')==-1):
# self.antenna = self.antenna + '&&&'
def _configure_map_property(self):
selection_ids = self.get_selection_idx_for_ms(self.sorted_idx[0])
# stokes
if self.stokes == '':
self.stokes = 'I'
self.imager_param['stokes'] = self.stokes
# gridfunction
# outfile
if os.path.exists(self.outfile) and self.overwrite:
os.system('rm -rf %s' % (self.outfile))
if os.path.exists(self.outfile + '.weight') and self.overwrite:
os.system('rm -rf %s' % (self.outfile + '.weight'))
# cell
cell = self.cell
if cell == '' or cell[0] == '':
# Calc PB
grid_factor = 3.
casalog.post(
"The cell size will be calculated using PB size of antennas in the first MS"
)
qPB = self._calc_PB(selection_ids['antenna1'])
cell = '%f%s' % (qPB['value'] / grid_factor, qPB['unit'])
casalog.post("Using cell size = PB/%4.2F = %s" %
(grid_factor, cell))
(cellx, celly) = sdutil.get_cellx_celly(cell, unit='arcmin')
self.imager_param['cellx'] = cellx
self.imager_param['celly'] = celly
# Calculate Pointing center and extent (if necessary)
# return a dictionary with keys 'center', 'width', 'height'
#imsize = self.imsize
imsize = sdutil._to_list(self.imsize, int) or \
sdutil._to_list(self.imsize, numpy.integer)
if imsize is None:
imsize = self.imsize if hasattr(self.imsize,
'__iter__') else [self.imsize]
imsize = [int(numpy.ceil(v)) for v in imsize]
casalog.post(
"imsize is not integers. force converting to integer pixel numbers.",
priority="WARN")
casalog.post("rounded-up imsize: %s --> %s" %
(str(self.imsize), str(imsize)))
phasecenter = self.phasecenter
if self.phasecenter == "" or \
len(imsize) == 0 or imsize[0] < 1:
map_param = self._get_pointing_extent()
# imsize
if len(imsize) == 0 or imsize[0] < 1:
imsize = self._get_imsize(map_param['width'],
map_param['height'], cellx, celly)
if self.phasecenter != "":
casalog.post(
"You defined phasecenter but not imsize. The image will cover as wide area as pointing in MS extends, but be centered at phasecenter. This could result in a strange image if your phasecenter is a part from the center of pointings",
priority='WARN')
if imsize[0] > 1024 or imsize[1] > 1024:
casalog.post(
"The calculated image pixel number is larger than 1024. It could take time to generate the image depending on your computer resource. Please wait...",
priority='WARN')
# phasecenter
# if empty, it should be determined here...
if self.phasecenter == "":
phasecenter = map_param['center']
# imsize
(nx, ny) = sdutil.get_nx_ny(imsize)
self.imager_param['nx'] = nx
self.imager_param['ny'] = ny
# phasecenter
self.imager_param['phasecenter'] = phasecenter
self.imager_param['movingsource'] = self.ephemsrcname
# channel map
imhelper = cleanhelper(self.imager, self.infiles, casalog=casalog)
imhelper.sortvislist(self.spw, self.mode, self.width)
spwsel = str(',').join([str(spwid) for spwid in selection_ids['spw']])
srestf = self.imager_param['restfreq'] if is_string_type(
self.imager_param['restfreq']
) else "%fHz" % self.imager_param['restfreq']
(imnchan, imstart, imwidth) = imhelper.setChannelizeDefault(
self.mode, spwsel, self.field, self.nchan, self.start, self.width,
self.imager_param['outframe'], self.veltype,
self.imager_param['phasecenter'], srestf)
del imhelper
# start and width
if self.mode == 'velocity':
startval = [self.imager_param['outframe'], imstart]
widthval = imwidth
elif self.mode == 'frequency':
startval = [self.imager_param['outframe'], imstart]
widthval = imwidth
else: #self.mode==channel
startval = int(self.start)
widthval = int(self.width)
if self.nchan < 0: self.nchan = self.allchannels
self.imager_param['start'] = startval
self.imager_param['step'] = widthval
self.imager_param['nchan'] = imnchan #self.nchan
def execute(self):
# imaging
casalog.post("Start imaging...", "INFO")
if len(self.infiles) == 1:
self.open_imager(self.infiles[0])
selection_ids = self.get_selection_idx_for_ms(0)
spwsel = self.get_selection_param_for_ms(0, self.spw)
if spwsel.strip() in ['', '*']: spwsel = selection_ids['spw']
### TODO: channel selection based on spw
ok = self.imager.selectvis(
field=selection_ids['field'],
#spw=selection_ids['spw'],
spw=spwsel,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=selection_ids['scan'],
intent=selection_ids['intent'])
if not ok:
raise ValueError, "Selection is empty: you may want to review this MS selection"
else:
self.close_imager()
#self.sorted_idx.reverse()
for idx in self.sorted_idx.__reversed__():
name = self.infiles[idx]
selection_ids = self.get_selection_idx_for_ms(idx)
spwsel = self.get_selection_param_for_ms(idx, self.spw)
if spwsel.strip() in ['', '*']: spwsel = selection_ids['spw']
### TODO: channel selection based on spw
self.imager.selectvis(
vis=name,
field=selection_ids['field'],
#spw=selection_ids['spw'],
spw=spwsel,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=selection_ids['scan'],
intent=selection_ids['intent'])
# need to do this
self.is_imager_opened = True
# it should be called after infiles are registered to imager
self._configure_map_property()
casalog.post(
"Using phasecenter \"%s\"" % (self.imager_param['phasecenter']),
"INFO")
self.imager.defineimage(**self.imager_param) #self.__get_param())
self.imager.setoptions(ftmachine='sd', gridfunction=self.gridfunction)
self.imager.setsdoptions(pointingcolumntouse=self.pointingcolumn,
convsupport=self.convsupport,
truncate=self.truncate,
gwidth=self.gwidth,
jwidth=self.jwidth,
minweight=0.,
clipminmax=self.clipminmax)
self.imager.makeimage(type='singledish', image=self.outfile)
weightfile = self.outfile + ".weight"
self.imager.makeimage(type='coverage', image=weightfile)
self.close_imager()
if not os.path.exists(self.outfile):
raise RuntimeError, "Failed to generate output image '%s'" % self.outfile
if not os.path.exists(weightfile):
raise RuntimeError, "Failed to generate weight image '%s'" % weightfile
# Convert output images to proper output frame
my_ia = gentools(['ia'])[0]
my_ia.open(self.outfile)
csys = my_ia.coordsys()
csys.setconversiontype(spectral=csys.referencecode('spectra')[0])
my_ia.setcoordsys(csys.torecord())
my_ia.close()
# Mask image pixels whose weight are smaller than minweight.
# Weight image should have 0 weight for pixels below < minweight
casalog.post("Start masking the map using minweight = %f" % \
self.minweight, "INFO")
my_ia.open(weightfile)
try:
stat = my_ia.statistics(mask="'" + weightfile + "' > 0.0",
robust=True)
valid_pixels = stat['npts']
except RuntimeError, e:
if e.message.find('No valid data found.') >= 0:
valid_pixels = [0]
else:
raise e
if len(valid_pixels) == 0 or valid_pixels[0] == 0:
my_ia.close()
casalog.post(
"All pixels weight zero. This indicates no data in MS is in image area. Mask will not be set. Please check your image parameters.",
"WARN")
return
median_weight = stat['median'][0]
weight_threshold = median_weight * self.minweight
casalog.post("Median of weight in the map is %f" % median_weight, \
"INFO")
casalog.post("Pixels in map with weight <= median(weight)*minweight = %f will be masked." % \
(weight_threshold),"INFO")
###Leaving the original logic to calculate the number of masked pixels via
###product of median of and min_weight (which i don't understand the logic)
### if one wanted to find how many pixel were masked one could easily count the
### number of pixels set to false
### e.g after masking self.outfile below one could just do this
### nmasked_pixels=tb.calc('[select from "'+self.outfile+'"/mask0'+'" giving [nfalse(PagedArray )]]')
my_tb = gentools(['tb'])[0]
nmask_pixels = 0
nchan = stat['trc'][3] + 1
casalog.filter('ERROR') ### hide the useless message of tb.calc
### doing it by channel to make sure it does not go out of memory
####tab.calc try to load the whole chunk in ram
for k in range(nchan):
nmask_pixels += my_tb.calc('[select from "' + weightfile +
'" giving [ntrue(map[,,,' + str(k) +
'] <=' +
str(median_weight * self.minweight) +
')]]')['0'][0]
casalog.filter() ####set logging back to normal
casalog.filter() ####set logging back to normal
imsize = numpy.product(my_ia.shape())
my_ia.close()
# Modify default mask
my_ia.open(self.outfile)
my_ia.calcmask("'%s'>%f" % (weightfile, weight_threshold),
asdefault=True)
my_ia.close()
masked_fraction = 100. * (
1. - (imsize - nmask_pixels) / float(valid_pixels[0]))
casalog.post("This amounts to %5.1f %% of the area with nonzero weight." % \
( masked_fraction ),"INFO")
casalog.post("The weight image '%s' is returned by this task, if the user wishes to assess the results in detail." \
% (weightfile), "INFO")
# Calculate theoretical beam size
casalog.post("Calculating image beam size.")
if self.gridfunction.upper() not in ['SF']:
casalog.post(
"Beam size definition for '%s' kernel is experimental." %
self.gridfunction,
priority='WARN')
casalog.post(
"You may want to take careful look at the restoring beam in the image.",
priority='WARN')
my_msmd = gentools(['msmd'])[0]
# antenna diameter and blockage
ref_ms_idx = self.sorted_idx[0]
ref_ms_name = self.infiles[ref_ms_idx]
selection_ids = self.get_selection_idx_for_ms(ref_ms_idx)
ant_idx = selection_ids['antenna1']
diameter = self._get_average_antenna_diameter(ant_idx)
my_msmd.open(ref_ms_name)
ant_name = my_msmd.antennanames(ant_idx)
my_msmd.close()
is_alma = False
for name in ant_name:
if name[0:2] in ["PM", "DV", "DA", "CM"]:
is_alma = True
break
blockage = "0.75m" if is_alma else "0.0m" # unknown blockage diameter
# output reference code
my_ia.open(self.outfile)
csys = my_ia.coordsys()
my_ia.close()
outref = csys.referencecode('direction')[0]
cell = list(csys.increment(type='direction', format='s')['string'])
# pointing sampling
ref_ms_spw = self.get_selection_param_for_ms(ref_ms_idx, self.spw)
ref_ms_field = self.get_selection_param_for_ms(ref_ms_idx, self.field)
ref_ms_scan = self.get_selection_param_for_ms(ref_ms_idx, self.scanno)
# xSampling, ySampling, angle = sdutil.get_ms_sampling_arcsec(ref_ms_name, spw=ref_ms_spw,
# antenna=selection_ids['baseline'],
# field=ref_ms_field,
# scan=ref_ms_scan,#timerange='',
# outref=outref)
# obtain sampling interval for beam calculation.
self.open_imager(ref_ms_name)
ok = self.imager.selectvis(
field=ref_ms_field,
#spw=selection_ids['spw'],
spw=ref_ms_spw,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=ref_ms_scan,
intent=selection_ids['intent'])
if len(ant_idx) > 1:
casalog.post(
"Using only antenna %s to calculate sampling interval" %
ant_name[0])
ptg_samp = self.imager.pointingsampling(
pattern='raster',
ref=outref,
movingsource=self.ephemsrcname,
pointingcolumntouse=self.pointingcolumn,
antenna=('%s&&&' % ant_name[0]))
self.close_imager()
my_qa = qatool()
xSampling, ySampling = my_qa.getvalue(
my_qa.convert(ptg_samp['sampling'], 'arcsec'))
angle = my_qa.getvalue(my_qa.convert(ptg_samp['angle'], "deg"))[0]
casalog.post("Detected raster sampling = [%f, %f] arcsec" %
(xSampling, ySampling))
# handling of failed sampling detection
valid_sampling = True
sampling = [xSampling, ySampling]
if abs(xSampling) < 2.2e-3 or not numpy.isfinite(xSampling):
casalog.post(
"Invalid sampling=%s arcsec. Using the value of orthogonal direction=%s arcsec"
% (xSampling, ySampling),
priority="WARN")
sampling = [ySampling]
angle = 0.0
valid_sampling = False
if abs(ySampling) < 1.0e-3 or not numpy.isfinite(ySampling):
if valid_sampling:
casalog.post(
"Invalid sampling=%s arcsec. Using the value of orthogonal direction=%s arcsec"
% (ySampling, xSampling),
priority="WARN")
sampling = [xSampling]
angle = 0.0
valid_sampling = True
# reduce sampling and cell if it's possible
if len(sampling) > 1 and abs(sampling[0] -
sampling[1]) <= 0.01 * abs(sampling[0]):
sampling = [sampling[0]]
angle = 0.0
if cell[0] == cell[1]: cell = [cell[0]]
if valid_sampling:
# actual calculation of beam size
bu = sdbeamutil.TheoreticalBeam()
bu.set_antenna(diameter, blockage)
bu.set_sampling(sampling, "%fdeg" % angle)
bu.set_image_param(cell, self.restfreq, self.gridfunction,
self.convsupport, self.truncate, self.gwidth,
self.jwidth, is_alma)
bu.summary()
imbeam_dict = bu.get_beamsize_image()
casalog.post("Setting image beam: major=%s, minor=%s, pa=%s" % (
imbeam_dict['major'],
imbeam_dict['minor'],
imbeam_dict['pa'],
))
# set beam size to image
my_ia.open(self.outfile)
my_ia.setrestoringbeam(**imbeam_dict)
my_ia.close()
else:
#BOTH sampling was invalid
casalog.post(
"Could not detect valid raster sampling. Exitting without setting beam size to image",
priority='WARN')
def execute(self):
# imaging
casalog.post("Start imaging...", "INFO")
if len(self.infiles) == 1:
self.open_imager(self.infiles[0])
selection_ids = self.get_selection_idx_for_ms(0)
spwsel = self.get_selection_param_for_ms(0, self.spw)
if spwsel.strip() in ['', '*']: spwsel = selection_ids['spw']
### TODO: channel selection based on spw
ok = self.imager.selectvis(
field=selection_ids['field'],
#spw=selection_ids['spw'],
spw=spwsel,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=selection_ids['scan'],
intent=selection_ids['intent'])
if not ok:
raise ValueError, "Selection is empty: you may want to review this MS selection"
else:
self.close_imager()
#self.sorted_idx.reverse()
for idx in self.sorted_idx.__reversed__():
name = self.infiles[idx]
selection_ids = self.get_selection_idx_for_ms(idx)
spwsel = self.get_selection_param_for_ms(idx, self.spw)
if spwsel.strip() in ['', '*']: spwsel = selection_ids['spw']
### TODO: channel selection based on spw
self.imager.selectvis(
vis=name,
field=selection_ids['field'],
#spw=selection_ids['spw'],
spw=spwsel,
nchan=-1,
start=0,
step=1,
baseline=selection_ids['baseline'],
scan=selection_ids['scan'],
intent=selection_ids['intent'])
# need to do this
self.is_imager_opened = True
# it should be called after infiles are registered to imager
self._configure_map_property()
casalog.post(
"Using phasecenter \"%s\"" % (self.imager_param['phasecenter']),
"INFO")
self.imager.defineimage(**self.imager_param) #self.__get_param())
self.imager.setoptions(ftmachine='sd', gridfunction=self.gridfunction)
self.imager.setsdoptions(pointingcolumntouse=self.pointingcolumn,
convsupport=self.convsupport,
truncate=self.truncate,
gwidth=self.gwidth,
jwidth=self.jwidth,
minweight=0.,
clipminmax=self.clipminmax)
self.imager.makeimage(type='singledish', image=self.outfile)
weightfile = self.outfile + ".weight"
self.imager.makeimage(type='coverage', image=weightfile)
self.close_imager()
if not os.path.exists(self.outfile):
raise RuntimeError, "Failed to generate output image '%s'" % self.outfile
if not os.path.exists(weightfile):
raise RuntimeError, "Failed to generate weight image '%s'" % weightfile
# Convert output images to proper output frame
my_ia = gentools(['ia'])[0]
my_ia.open(self.outfile)
csys = my_ia.coordsys()
csys.setconversiontype(spectral=csys.referencecode('spectra')[0])
my_ia.setcoordsys(csys.torecord())
my_ia.close()
# Mask image pixels whose weight are smaller than minweight.
# Weight image should have 0 weight for pixels below < minweight
casalog.post("Start masking the map using minweight = %f" % \
self.minweight, "INFO")
my_ia.open(weightfile)
try:
stat = my_ia.statistics(mask="'" + weightfile + "' > 0.0",
robust=True)
valid_pixels = stat['npts']
except RuntimeError, e:
if e.message.find('No valid data found.') >= 0:
valid_pixels = [0]
else:
raise e
import numpy
import os
from taskinit import gentools, casalog
import sdutil
from collections import Counter
ms,sdms,tb,msmd = gentools(['ms','sdms','tb', 'msmd'])
def tsdbaseline(infile=None, datacolumn=None, antenna=None, field=None, spw=None, timerange=None, scan=None, pol=None, intent=None, maskmode=None, thresh=None, avg_limit=None, minwidth=None, edge=None, blmode=None, dosubtract=None, blformat=None, bloutput=None, bltable=None, blfunc=None, order=None, npiece=None,
applyfft=None, fftmethod=None, fftthresh=None,
addwn=None, rejwn=None, clipthresh=None, clipniter=None, blparam=None, verbose=None, showprogress=None, minnrow=None, outfile=None, overwrite=None):
casalog.origin('tsdbaseline')
try:
if (outfile == '') or not isinstance(outfile, str):
print("type=%s, value=%s" % (type(outfile), str(outfile)))
raise ValueError, "outfile name is empty."
if os.path.exists(outfile) and not overwrite:
raise Exception(outfile + ' exists.')
if (maskmode == 'interact'):
raise ValueError, "maskmode='%s' is not supported yet" % maskmode
if (blfunc == 'variable' and not os.path.exists(blparam)):
raise ValueError, "input file '%s' does not exists" % blparam
if (spw == ''): spw = '*'
if (blmode == 'apply'):
if not os.path.exists(bltable):
raise ValueError, "file specified in bltable '%s' does not exist." % bltable
sorttab_info = remove_sorted_table_keyword(infile)
def __execute_press(self):
###
# Pressed-out method (Sofue & Reich 1979)
###
casalog.post("Apply Pressed-out method")
# CAS-5410 Use private tools inside task scripts
ia = gentools(["ia"])[0]
# mask
self.image = ia.newimagefromimage(infile=self.infiles, outfile=self.tmpmskname)
# back-up original mask name
is_initial_mask = self.image.maskhandler("default")[0] != ""
temp_maskname = "temporal"
imshape = self.image.shape()
nx = imshape[0]
ny = imshape[1]
nchan = imshape[2]
if len(self.thresh) == 0:
casalog.post("Use whole region")
else:
# mask pixels beyond thresholds
maskstr = "mask('%s')" % self.tmpmskname
if self.thresh[0] != self.nolimit:
maskstr += " && '%s'>=%f" % (self.tmpmskname, self.thresh[0])
if self.thresh[1] != self.nolimit:
maskstr += " && '%s'<=%f" % (self.tmpmskname, self.thresh[1])
# Need to flush to image once to calcmask ... sigh
self.image.done()
self.image = ia.newimage(self.tmpmskname)
self.image.calcmask(mask=maskstr, name=temp_maskname, asdefault=True)
# smoothing
# bmajor = 0.0
# bminor = 0.0
# CAS-5410 Use private tools inside task scripts
qa = qatool()
if type(self.beamsize) == str:
qbeamsize = qa.quantity(self.beamsize)
else:
qbeamsize = qa.quantity(self.beamsize, "arcsec")
if type(self.smoothsize) == str:
# bmajor = smoothsize
# bminor = smoothsize
qsmoothsize = qa.quantity(self.smoothsize)
else:
# bmajor = '%sarcsec' % (beamsize*smoothsize)
# bminor = '%sarcsec' % (beamsize*smoothsize)
qsmoothsize = qa.mul(qbeamsize, self.smoothsize)
bmajor = qsmoothsize
bminor = qsmoothsize
# masked channels are replaced by zero and convolved here.
self.convimage = self.image.convolve2d(outfile=self.tmpconvname, major=bmajor, minor=bminor, overwrite=True)
self.convimage.done()
self.convimage = ia.newimage(self.tmpconvname)
# get dTij (original - smoothed)
if len(imshape) == 4:
# with polarization axis
npol = imshape[3]
for ichan in range(nchan):
for ipol in range(npol):
pixmsk = self.image.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
pixsmo = self.convimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
pixsub = pixmsk - pixsmo
self.convimage.putchunk(pixsub, [0, 0, ichan, ipol])
elif len(imshape) == 3:
for ichan in range(nchan):
# no polarization axis
pixmsk = self.image.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
pixsmo = self.convimage.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
pixsub = pixmsk - pixsmo
self.convimage.putchunk(pixsub, [0, 0, ichan])
# polynomial fit
fitaxis = 0
if self.direction == 0.0:
fitaxis = 0
elif self.direction == 90.0:
fitaxis = 1
else:
raise Exception, "Sorry, the task don't support inclined scan with respect to horizontal or vertical axis, right now."
# Replace duplicated method ia.fitpolynomial with
# ia.fitprofile
# polyimage = convimage.fitpolynomial( fitfile=tmppolyname, axis=fitaxis, order=numpoly, overwrite=True )
# polyimage.done()
if os.path.exists(self.tmppolyname):
# CAS-5410 Use private tools inside task scripts
cu = utilstool()
cu.removetable([self.tmppolyname])
self.convimage.setbrightnessunit("K")
# Unfortunately, ia.fitprofile is very fragile.
# Using numpy instead for fitting with masked pixels (KS, 2014/07/02)
# resultdic = self.convimage.fitprofile( model=self.tmppolyname, axis=fitaxis, poly=self.numpoly, ngauss=0, multifit=True, gmncomps=0 )
self.__polynomial_fit_model(image=self.tmpmskname, model=self.tmppolyname, axis=fitaxis, order=self.numpoly)
polyimage = ia.newimage(self.tmppolyname)
# set back defalut mask (need to get from self.image)
avail_mask = polyimage.maskhandler("get")
if is_initial_mask:
casalog.post("copying mask from %s" % (self.infiles))
polyimage.calcmask("mask('%s')" % self.infiles, asdefault=True)
else: # no mask in the original image
polyimage.calcmask("T", asdefault=True)
if temp_maskname in avail_mask:
polyimage.maskhandler("delete", name=temp_maskname)
# subtract fitted image from original map
imageorg = ia.newimage(self.infiles)
if len(imshape) == 4:
# with polarization axis
npol = imshape[3]
for ichan in range(nchan):
for ipol in range(npol):
pixorg = imageorg.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
pixpol = polyimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
pixsub = pixorg - pixpol
polyimage.putchunk(pixsub, [0, 0, ichan, ipol])
elif len(imshape) == 3:
# no polarization axis
for ichan in range(nchan):
pixorg = imageorg.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
pixpol = polyimage.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
pixsub = pixorg - pixpol
polyimage.putchunk(pixsub, [0, 0, ichan])
# output
polyimage.rename(self.outfile, overwrite=self.overwrite)
polyimage.done()
self.convimage.done(remove=True)
self.image.done()
imageorg.done()
def _updateHistory2(self, clrecs, vis):
"""
Update history table when setSolarObjectJy is run
(mulitple comopents in one version)
"""
#
from taskinit import gentools
(mytb, ) = gentools(['tb'])
mytb.open(vis + '/HISTORY', nomodify=False)
nrow = mytb.nrows()
lasttime = mytb.getcol('TIME')[nrow - 1]
rown = nrow
#
clname = clrecs.keys()[0]
#for ky in clrecs.keys():
srcn = clname.split('_')[0]
comprec = clrecs[clname]
nelm = comprec['nelements']
for icomp in range(nelm):
comp = comprec['component' + str(icomp)]
complab = comp['label']
origin = 'setjy'
priority = 'INFO'
time = lasttime
appl = 'setjy'
emptystrarr = numpy.array([''])
if nelm == 1:
for i in range(len(comprec['spwids'])):
mytb.addrows(1)
ispw = comprec['spwids'][i]
iflux = comprec['allfluxinfo'][i][0][0]
msg = (
" %s: spw %s Flux:[I=%s,Q=%s,U=%s,V=%s] +/- [I=%s,Q=%s,U=%s,V=%s] Jy"
%
(srcn, ispw, iflux, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
mytb.putcell('APP_PARAMS', rown, [''])
mytb.putcell('CLI_COMMAND', rown, [''])
mytb.putcell('APPLICATION', rown, appl)
mytb.putcell('MESSAGE', rown, msg)
mytb.putcell('OBSERVATION_ID', rown, -1)
mytb.putcell('ORIGIN', rown, origin)
mytb.putcell('PRIORITY', rown, priority)
mytb.putcell('TIME', rown, time)
rown += 1
else:
ispw = complab.split('_')[1]
mytb.addrows(1)
msg = (
" %s: spw %s Flux:[I=%s,Q=%s,U=%s,V=%s] +/- [I=%s,Q=%s,U=%s,V=%s] Jy"
% (srcn, ispw, comp['flux']['value'][0],
comp['flux']['value'][1], comp['flux']['value'][2],
comp['flux']['value'][3], comp['flux']['error'][0],
comp['flux']['error'][1], comp['flux']['error'][2],
comp['flux']['error'][3]))
mytb.putcell('APP_PARAMS', rown, [''])
mytb.putcell('CLI_COMMAND', rown, [''])
mytb.putcell('APPLICATION', rown, appl)
mytb.putcell('MESSAGE', rown, msg)
mytb.putcell('OBSERVATION_ID', rown, -1)
mytb.putcell('ORIGIN', rown, origin)
mytb.putcell('PRIORITY', rown, priority)
mytb.putcell('TIME', rown, time)
rown += 1
mytb.close()
jplfiles_to_repository() puts it all together, so it is most likely the
function you want.
There are various utilities like convert_radec, datestr*, get_num_from_str,
mean_radius*, and construct_tablepath defined in here as well.
"""
from glob import glob
import os
import re
import scipy.special
import time # We can always use more time.
from taskinit import gentools, qa, casalog
me = gentools(["me"])[0]
from dict_to_table import dict_to_table
# Possible columns, as announced by their column titles.
# The data is scooped up by 'pat'. Either use ONE group named by the column
# key, or mark it as unwanted. '-' is not valid in group names.
# Leading and trailing whitespace will be taken care of later.
# Sample lines:
# Date__(UT)__HR:MN R.A.___(ICRF/J2000.0)___DEC Ob-lon Ob-lat Sl-lon Sl-lat NP.ang NP.dist r rdot delta deldot S-T-O L_s
# 2010-May-01 00:00 09 01 43.1966 +19 04 28.673 286.52 18.22 246.99 25.34 358.6230 3.44 1.661167637023 -0.5303431 1.28664311447968 15.7195833 37.3033 84.50
#
# some mod to label names and comments so that they corresponds to
# JPL-Horizons naming comvension
cols = {
"MJD": {"header": r"Date__\(UT\)__HR:MN", "comment": "date", "pat": r"(?P<MJD>\d+-\w+-\d+ \d+:\d+)"},
def __init__(self, imagename):
self.imagename = imagename
# read data to storage
ia = gentools(['ia'])[0]
ia.open(self.imagename)
try:
self.image_shape = ia.shape()
self.coordsys = ia.coordsys()
coord_types = self.coordsys.axiscoordinatetypes()
self.units = self.coordsys.units()
self.names = self.coordsys.names()
self.direction_reference = self.coordsys.referencecode('dir')[0]
self.spectral_reference = self.coordsys.referencecode('spectral')[0]
self.id_direction = coord_types.index('Direction')
self.id_direction = [self.id_direction, self.id_direction+1]
self.id_spectral = coord_types.index('Spectral')
try:
self.id_stokes = coord_types.index('Stokes')
stokes_axis_exists = True
except:
# if no Stokes axis exists, set dummy axis at the end
self.id_stokes = len(coord_types)
stokes_axis_exists = False
casalog.post('id_direction=%s'%(self.id_direction), priority='DEBUG')
casalog.post('id_spectral=%s'%(self.id_spectral), priority='DEBUG')
casalog.post('id_stokes=%s (%s stokes axis)'%(self.id_stokes,('real' if stokes_axis_exists else 'dummy')),
priority='DEBUG')
self.data = ia.getchunk()
self.mask = ia.getchunk(getmask=True)
if not stokes_axis_exists:
# put degenerate Stokes axis at the end
self.data = numpy.expand_dims(self.data, axis=-1)
self.mask = numpy.expand_dims(self.mask, axis=-1)
casalog.post('add dummy Stokes axis to data and mask since input image doesn\'t have it.')
casalog.post('data.shape={}'.format(self.data.shape), priority='DEBUG')
casalog.post('mask.shape={}'.format(self.mask.shape), priority='DEBUG')
bottom = ia.toworld(numpy.zeros(len(self.image_shape),dtype=int), 'q')['quantity']
top = ia.toworld(self.image_shape-1, 'q')['quantity']
key = lambda x: '*%s'%(x+1)
ra_min = bottom[key(self.id_direction[0])]
ra_max = top[key(self.id_direction[0])]
if ra_min > ra_max:
ra_min,ra_max = ra_max,ra_min
self.ra_min = ra_min
self.ra_max = ra_max
self.dec_min = bottom[key(self.id_direction[1])]
self.dec_max = top[key(self.id_direction[1])]
self._brightnessunit = ia.brightnessunit()
if self.spectral_label == 'Frequency':
refpix, refval, increment = self.spectral_axis(unit='GHz')
self.spectral_data = numpy.array([refval+increment*(i-refpix) for i in xrange(self.nchan)])
elif self.spectral_label == 'Velocity':
refpix, refval, increment = self.spectral_axis(unit='km/s')
self.spectral_data = numpy.array([refval+increment*(i-refpix) for i in xrange(self.nchan)])
if stokes_axis_exists:
self.stokes = self.coordsys.stokes()
else:
# if no Stokes axis exists, set ['I']
self.stokes = ['I']
finally:
ia.close()
def __execute_basket_weaving(self):
###
# Basket-Weaving (Emerson & Grave 1988)
###
casalog.post("Apply Basket-Weaving")
# CAS-5410 Use private tools inside task scripts
ia = gentools(["ia"])[0]
# initial setup
outimage = ia.newimagefromimage(infile=self.infiles[0], outfile=self.outfile, overwrite=self.overwrite)
imshape = outimage.shape()
nx = imshape[0]
ny = imshape[1]
nchan = imshape[2]
tmp = []
nfile = len(self.infiles)
for i in xrange(nfile):
tmp.append(numpy.zeros(imshape, dtype=float))
maskedpixel = numpy.array(tmp)
del tmp
# direction
dirs = []
if len(self.direction) == nfile:
dirs = self.direction
else:
casalog.post("direction information is extrapolated.")
for i in range(nfile):
dirs.append(self.direction[i % len(direction)])
# masklist
masks = []
if type(self.masklist) == float:
for i in range(nfile):
masks.append(self.masklist)
elif type(self.masklist) == list and nfile != len(self.masklist):
for i in range(nfile):
masks.append(self.masklist[i % len(self.masklist)])
for i in range(len(masks)):
masks[i] = 0.01 * masks[i]
# mask
for i in range(nfile):
self.realimage = ia.newimagefromimage(infile=self.infiles[i], outfile=self.tmprealname[i])
self.imagimage = ia.newimagefromimage(infile=self.infiles[i], outfile=self.tmpimagname[i])
# replace masked pixels with 0.0
if not self.realimage.getchunk(getmask=True).all():
casalog.post("Replacing masked pixels with 0.0 in %d-th image" % (i))
self.realimage.replacemaskedpixels(0.0)
self.realimage.close()
self.imagimage.close()
if len(self.thresh) == 0:
casalog.post("Use whole region")
else:
if len(imshape) == 4:
# with polarization axis
npol = imshape[3]
for i in range(nfile):
self.realimage = ia.newimage(self.tmprealname[i])
for ichan in range(nchan):
for ipol in range(npol):
pixmsk = self.realimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
for ix in range(pixmsk.shape[0]):
for iy in range(pixmsk.shape[1]):
if self.thresh[0] == self.nolimit:
if pixmsk[ix][iy] > self.thresh[1]:
maskedpixel[i][ix][iy][ichan][ipol] = pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
elif self.thresh[1] == self.nolimit:
if pixmsk[ix][iy] < self.thresh[0]:
maskedpixel[i][ix][iy][ichan][ipol] = pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
else:
if pixmsk[ix][iy] < self.thresh[0] or pixmsk[ix][iy] > self.thresh[1]:
maskedpixel[i][ix][iy][ichan][ipol] = pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
self.realimage.putchunk(pixmsk, [0, 0, ichan, ipol])
self.realimage.close()
elif len(imshape) == 3:
# no polarization axis
for i in range(nfile):
self.realimage = ia.newimage(self.tmprealname[i])
for ichan in range(nchan):
pixmsk = self.realimage.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
for ix in range(pixmsk.shape[0]):
for iy in range(pixmsk.shape[1]):
if self.thresh[0] == self.nolimit:
if pixmsk[ix][iy] > self.thresh[1]:
maskedpixel[i][ix][iy][ichan] = pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
elif self.thresh[1] == self.nolimit:
if pixmsk[ix][iy] < self.thresh[0]:
maskedpixel[i][ix][iy][ichan] = pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
else:
if pixmsk[ix][iy] < self.thresh[0] or pixmsk[ix][iy] > self.thresh[1]:
maskedpixel[i][ix][iy][ichan] = pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
self.realimage.putchunk(pixmsk, [0, 0, ichan])
self.realimage.close()
maskedvalue = None
if any(maskedpixel.flatten() != 0.0):
maskedvalue = maskedpixel.mean(axis=0)
del maskedpixel
# set weight factor
weights = numpy.ones(shape=(nfile, nx, ny), dtype=float)
eps = 1.0e-5
dtor = numpy.pi / 180.0
for i in range(nfile):
if abs(numpy.sin(dirs[i] * dtor)) < eps:
# direction is around 0 deg
maskw = 0.5 * nx * masks[i]
for ix in range(nx):
for iy in range(ny):
dd = abs(float(ix) - 0.5 * (nx - 1))
if dd < maskw:
cosd = numpy.cos(0.5 * numpy.pi * dd / maskw)
weights[i][ix][iy] = 1.0 - cosd * cosd
if weights[i][ix][iy] == 0.0:
weights[i][ix][iy] += eps * 0.01
elif abs(numpy.cos(dirs[i] * dtor)) < eps:
# direction is around 90 deg
maskw = 0.5 * ny * masks[i]
for ix in range(nx):
for iy in range(ny):
dd = abs(float(iy) - 0.5 * (ny - 1))
if dd < maskw:
cosd = numpy.cos(0.5 * numpy.pi * dd / maskw)
weights[i][ix][iy] = 1.0 - cosd * cosd
if weights[i][ix][iy] == 0.0:
weights[i][ix][iy] += eps * 0.01
else:
maskw = 0.5 * sqrt(nx * ny) * masks[i]
for ix in range(nx):
for iy in range(ny):
tand = numpy.tan((dirs[i] - 90.0) * dtor)
dd = abs(ix * tand - iy - 0.5 * (nx - 1) * tand + 0.5 * (ny - 1))
dd = dd / sqrt(1.0 + tand * tand)
if dd < maskw:
cosd = numpy.cos(0.5 * numpy.pi * dd / maskw)
weights[i][ix][iy] = 1.0 - cosd * cosd
if weights[i][ix][iy] == 0.0:
weights[i][ix][iy] += eps * 0.01
# shift
xshift = -((ny - 1) / 2)
yshift = -((nx - 1) / 2)
for ix in range(xshift, 0, 1):
tmp = weights[i, :, 0].copy()
weights[i, :, 0 : ny - 1] = weights[i, :, 1:ny].copy()
weights[i, :, ny - 1] = tmp
for iy in range(yshift, 0, 1):
tmp = weights[i, 0:1].copy()
weights[i, 0 : nx - 1] = weights[i, 1:nx].copy()
weights[i, nx - 1 : nx] = tmp
# FFT
if len(imshape) == 4:
# with polarization axis
npol = imshape[3]
for i in range(nfile):
self.realimage = ia.newimage(self.tmprealname[i])
self.imagimage = ia.newimage(self.tmpimagname[i])
for ichan in range(nchan):
for ipol in range(npol):
pixval = self.realimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
pixval = pixval.reshape((nx, ny))
pixfft = npfft.fft2(pixval)
pixfft = pixfft.reshape((nx, ny, 1, 1))
self.realimage.putchunk(pixfft.real, [0, 0, ichan, ipol])
self.imagimage.putchunk(pixfft.imag, [0, 0, ichan, ipol])
del pixval, pixfft
self.realimage.close()
self.imagimage.close()
elif len(imshape) == 3:
# no polarization axis
for i in range(nfile):
self.realimage = ia.newimage(self.tmprealname[i])
self.imagimage = ia.newimage(self.tmpimagname[i])
for ichan in range(nchan):
pixval = self.realimage.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
pixval = pixval.reshape((nx, ny))
pixfft = npfft.fft2(pixval)
pixfft = pixfft.reshape((nx, ny, 1))
self.realimage.putchunk(pixfft.real, [0, 0, ichan])
self.imagimage.putchunk(pixfft.imag, [0, 0, ichan])
del pixval, pixfft
self.realimage.close()
self.imagimage.close()
# weighted mean
if len(imshape) == 4:
npol = imshape[3]
for ichan in range(nchan):
for ipol in range(npol):
pixout = numpy.zeros(shape=(nx, ny), dtype=complex)
denom = numpy.zeros(shape=(nx, ny), dtype=float)
for i in range(nfile):
self.realimage = ia.newimage(self.tmprealname[i])
self.imagimage = ia.newimage(self.tmpimagname[i])
pixval = (
self.realimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
+ self.imagimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol]) * 1.0j
)
pixval = pixval.reshape((nx, ny))
pixout = pixout + pixval * weights[i]
denom = denom + weights[i]
self.realimage.close()
self.imagimage.close()
pixout = pixout / denom
pixout = pixout.reshape((nx, ny, 1, 1))
self.realimage = ia.newimage(self.tmprealname[0])
self.imagimage = ia.newimage(self.tmpimagname[0])
self.realimage.putchunk(pixout.real, [0, 0, ichan, ipol])
self.imagimage.putchunk(pixout.imag, [0, 0, ichan, ipol])
self.realimage.close()
self.imagimage.close()
elif len(imshape) == 3:
for ichan in range(nchan):
pixout = numpy.zeros(shape=(nx, ny), dtype=complex)
denom = numpy.zeros(shape=(nx, ny), dtype=float)
for i in range(nfile):
self.realimage = ia.newimage(self.tmprealname[i])
self.imagimage = ia.newimage(self.tmpimagname[i])
pixval = self.realimage.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
pixval = pixval.reshape((nx, ny))
pixout = pixout + pixval * weights[i]
denom = denom + weights[i]
self.realimage.close()
self.imagimage.close()
pixout = pixout / denom
pixout = pixout.reshape((nx, ny, 1))
self.realimage = ia.newimage(self.tmprealname[0])
self.imagimage = ia.newimage(self.tmpimagname[0])
self.realimage.putchunk(pixout.real, [0, 0, ichan])
self.imagimage.putchunk(pixout.imag, [0, 0, ichan])
self.realimage.close()
self.imagimage.close()
# inverse FFT
self.realimage = ia.newimage(self.tmprealname[0])
self.imagimage = ia.newimage(self.tmpimagname[0])
if len(imshape) == 4:
npol = imshape[3]
for ichan in range(nchan):
for ipol in range(npol):
pixval = (
self.realimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol])
+ self.imagimage.getchunk([0, 0, ichan, ipol], [nx - 1, ny - 1, ichan, ipol]) * 1.0j
)
pixval = pixval.reshape((nx, ny))
pixifft = npfft.ifft2(pixval)
pixifft = pixifft.reshape((nx, ny, 1, 1))
outimage.putchunk(pixifft.real, [0, 0, ichan, ipol])
del pixval, pixifft
elif len(imshape) == 3:
for ichan in range(nchan):
pixval = (
self.realimage.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan])
+ self.imagimage.getchunk([0, 0, ichan], [nx - 1, ny - 1, ichan]) * 1.0j
)
pixval = pixval.reshape((nx, ny))
pixifft = npfft.ifft2(pixval)
pixifft = pixifft.reshape((nx, ny, 1))
outimage.putchunk(pixifft.real, [0, 0, ichan])
del pixval, pixifft
if maskedvalue is not None:
outimage.putchunk(outimage.getchunk() + maskedvalue)
# handling of output image mask
maskstr = ""
for name in self.infiles:
if len(maskstr) > 0:
maskstr += " || "
maskstr += "mask('%s')" % (name)
outimage.calcmask(maskstr, name="basketweaving", asdefault=True)
self.realimage.close()
self.imagimage.close()
outimage.close()
import numpy
import os
from taskinit import gentools, casalog
import sdutil
from collections import Counter
ms, sdms, tb, msmd = gentools(['ms', 'sdms', 'tb', 'msmd'])
def sdbaseline(infile=None,
datacolumn=None,
antenna=None,
field=None,
spw=None,
timerange=None,
scan=None,
pol=None,
intent=None,
maskmode=None,
thresh=None,
avg_limit=None,
minwidth=None,
edge=None,
blmode=None,
dosubtract=None,
blformat=None,
bloutput=None,
bltable=None,
blfunc=None,
order=None,
npiece=None,
applyfft=None,
def __execute_basket_weaving(self):
###
# Basket-Weaving (Emerson & Grave 1988)
###
casalog.post( 'Apply Basket-Weaving' )
# CAS-5410 Use private tools inside task scripts
ia = gentools(['ia'])[0]
# initial setup
outimage = ia.newimagefromimage( infile=self.infiles[0], outfile=self.outfile, overwrite=self.overwrite )
imshape_out = outimage.shape()
ndim_out = len(imshape_out)
coordsys = outimage.coordsys()
axis_types = coordsys.axiscoordinatetypes()
# direction axis should always exist
try:
direction_axis0 = axis_types.index('Direction')
direction_axis1 = axis_types[direction_axis0+1:].index('Direction') + direction_axis0 + 1
except IndexError:
raise RuntimeError('Direction axes don\'t exist.')
nx = imshape_out[direction_axis0]
ny = imshape_out[direction_axis1]
tmp=[]
nfile = len(self.infiles)
for i in xrange(nfile):
tmp.append(numpy.zeros(imshape_out,dtype=float))
maskedpixel=numpy.array(tmp)
del tmp
# direction
dirs = []
if len(self.direction) == nfile:
dirs = self.direction
else:
casalog.post( 'direction information is extrapolated.' )
for i in range(nfile):
dirs.append(self.direction[i%len(self.direction)])
# masklist
masks = []
if type(self.masklist) == float:
for i in range(nfile):
masks.append( self.masklist )
elif type(self.masklist) == list and nfile != len(self.masklist):
for i in range(nfile):
masks.append( self.masklist[i%len(self.masklist)] )
for i in range(len(masks)):
masks[i] = 0.01 * masks[i]
# mask
for i in range(nfile):
self.realimage = create_4d_image(self.infiles[i], self.tmprealname[i])
self.imagimage = self.realimage.subimage(outfile=self.tmpimagname[i])
# replace masked pixels with 0.0
if not self.realimage.getchunk(getmask=True).all():
casalog.post("Replacing masked pixels with 0.0 in %d-th image" % (i))
self.realimage.replacemaskedpixels(0.0)
self.realimage.close()
self.imagimage.close()
# Below working images are all 4D regardless of dimension of input images
# image shape for temporary images (always 4D)
ia.open(self.tmprealname[0])
imshape = ia.shape()
ndim = len(imshape)
ia.close()
if len(self.thresh) == 0:
casalog.post( 'Use whole region' )
else:
for i in range(nfile):
self.realimage = ia.newimage( self.tmprealname[i] )
for iaxis2 in range(imshape[2]):
for iaxis3 in range(imshape[3]):
pixmsk = self.realimage.getchunk( [0,0,iaxis2,iaxis3], [nx-1,ny-1,iaxis2,iaxis3])
for ix in range(pixmsk.shape[0]):
for iy in range(pixmsk.shape[1]):
if self.thresh[0] == self.nolimit:
if pixmsk[ix][iy] > self.thresh[1]:
maskedpixel[i][ix][iy][iaxis2][iaxis3]=pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
elif self.thresh[1] == self.nolimit:
if pixmsk[ix][iy] < self.thresh[0]:
maskedpixel[i][ix][iy][iaxis2][iaxis3]=pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
else:
if pixmsk[ix][iy] < self.thresh[0] or pixmsk[ix][iy] > self.thresh[1]:
maskedpixel[i][ix][iy][iaxis2][iaxis3]=pixmsk[ix][iy]
pixmsk[ix][iy] = 0.0
self.realimage.putchunk( pixmsk, [0,0,iaxis2,iaxis3] )
self.realimage.close()
maskedvalue=None
if any(maskedpixel.flatten()!=0.0):
maskedvalue=maskedpixel.mean(axis=0)
del maskedpixel
# set weight factor
weights = numpy.ones( shape=(nfile,nx,ny), dtype=float )
eps = 1.0e-5
dtor = numpy.pi / 180.0
for i in range(nfile):
if abs(numpy.sin(dirs[i]*dtor)) < eps:
# direction is around 0 deg
maskw = 0.5 * nx * masks[i]
for ix in range(nx):
for iy in range(ny):
dd = abs( float(ix) - 0.5 * (nx-1) )
if dd < maskw:
cosd = numpy.cos(0.5*numpy.pi*dd/maskw)
weights[i][ix][iy] = 1.0 - cosd * cosd
if weights[i][ix][iy] == 0.0:
weights[i][ix][iy] += eps*0.01
elif abs(numpy.cos(dirs[i]*dtor)) < eps:
# direction is around 90 deg
maskw = 0.5 * ny * masks[i]
for ix in range(nx):
for iy in range(ny):
dd = abs( float(iy) - 0.5 * (ny-1) )
if dd < maskw:
cosd = numpy.cos(0.5*numpy.pi*dd/maskw)
weights[i][ix][iy] = 1.0 - cosd * cosd
if weights[i][ix][iy] == 0.0:
weights[i][ix][iy] += eps*0.01
else:
maskw = 0.5 * numpy.sqrt( nx * ny ) * masks[i]
for ix in range(nx):
for iy in range(ny):
tand = numpy.tan((dirs[i]-90.0)*dtor)
dd = abs( ix * tand - iy - 0.5 * (nx-1) * tand + 0.5 * (ny-1) )
dd = dd / numpy.sqrt( 1.0 + tand * tand )
if dd < maskw:
cosd = numpy.cos(0.5*numpy.pi*dd/maskw)
weights[i][ix][iy] = 1.0 - cosd * cosd
if weights[i][ix][iy] == 0.0:
weights[i][ix][iy] += eps*0.01
# shift
xshift = -((ny-1)/2)
yshift = -((nx-1)/2)
for ix in range(xshift,0,1):
tmp = weights[i,:,0].copy()
weights[i,:,0:ny-1] = weights[i,:,1:ny].copy()
weights[i,:,ny-1] = tmp
for iy in range(yshift,0,1):
tmp = weights[i,0:1].copy()
weights[i,0:nx-1] = weights[i,1:nx].copy()
weights[i,nx-1:nx] = tmp
# FFT
for i in range(nfile):
self.realimage = ia.newimage( self.tmprealname[i] )
self.imagimage = ia.newimage( self.tmpimagname[i] )
for iaxis2 in range(imshape[2]):
for iaxis3 in range(imshape[3]):
pixval = self.realimage.getchunk( [0,0,iaxis2,iaxis3], [nx-1,ny-1,iaxis2,iaxis3] )
pixval = pixval.reshape((nx,ny))
pixfft = npfft.fft2( pixval )
pixfft = pixfft.reshape((nx,ny,1,1))
self.realimage.putchunk( pixfft.real, [0,0,iaxis2,iaxis3] )
self.imagimage.putchunk( pixfft.imag, [0,0,iaxis2,iaxis3] )
del pixval, pixfft
self.realimage.close()
self.imagimage.close()
# weighted mean
for ichan in range(imshape[2]):
for iaxis3 in range(imshape[3]):
pixout = numpy.zeros( shape=(nx,ny), dtype=complex )
denom = numpy.zeros( shape=(nx,ny), dtype=float )
for i in range(nfile):
self.realimage = ia.newimage( self.tmprealname[i] )
self.imagimage = ia.newimage( self.tmpimagname[i] )
pixval = self.realimage.getchunk( [0,0,ichan,iaxis3], [nx-1,ny-1,ichan,iaxis3] ) \
+ self.imagimage.getchunk( [0,0,ichan,iaxis3], [nx-1,ny-1,ichan,iaxis3] ) * 1.0j
pixval = pixval.reshape((nx,ny))
pixout = pixout + pixval * weights[i]
denom = denom + weights[i]
self.realimage.close()
self.imagimage.close()
pixout = pixout / denom
pixout = pixout.reshape((nx,ny,1,1))
self.realimage = ia.newimage( self.tmprealname[0] )
self.imagimage = ia.newimage( self.tmpimagname[0] )
self.realimage.putchunk( pixout.real, [0,0,ichan,iaxis3] )
self.imagimage.putchunk( pixout.imag, [0,0,ichan,iaxis3] )
self.realimage.close()
self.imagimage.close()
# inverse FFT
self.realimage = ia.newimage( self.tmprealname[0] )
self.imagimage = ia.newimage( self.tmpimagname[0] )
for ichan in range(imshape[2]):
for iaxis3 in range(imshape[3]):
pixval = self.realimage.getchunk( [0,0,ichan,iaxis3], [nx-1,ny-1,ichan,iaxis3] ) \
+ self.imagimage.getchunk( [0,0,ichan,iaxis3], [nx-1,ny-1,ichan,iaxis3] ) * 1.0j
pixval = pixval.reshape((nx,ny))
pixifft = npfft.ifft2( pixval )
pixifft = pixifft.reshape((nx,ny,1,1))
self.realimage.putchunk(pixifft.real, blc=[0,0,ichan,iaxis3])
del pixval, pixifft
if maskedvalue is not None:
self.realimage.putchunk(self.realimage.getchunk()+maskedvalue)
# put result into outimage
chunk = self.realimage.getchunk()
outimage.putchunk(chunk.reshape(imshape_out))
# handling of output image mask
maskstr = ""
for name in self.infiles:
if len(maskstr) > 0: maskstr += " || "
maskstr += ("mask('%s')" % (name))
outimage.calcmask(maskstr,name="basketweaving",asdefault=True)
self.realimage.close()
self.imagimage.close()
outimage.close()
jplfiles_to_repository() puts it all together, so it is most likely the
function you want.
There are various utilities like convert_radec, datestr*, get_num_from_str,
mean_radius*, and construct_tablepath defined in here as well.
"""
from glob import glob
import os
import re
import scipy.special
import time # We can always use more time.
from taskinit import gentools, qa, casalog
me = gentools(['me'])[0]
from dict_to_table import dict_to_table
# Possible columns, as announced by their column titles.
# The data is scooped up by 'pat'. Either use ONE group named by the column
# key, or mark it as unwanted. '-' is not valid in group names.
# Leading and trailing whitespace will be taken care of later.
# Sample lines:
# Date__(UT)__HR:MN R.A.___(ICRF/J2000.0)___DEC Ob-lon Ob-lat Sl-lon Sl-lat NP.ang NP.dist r rdot delta deldot S-T-O L_s
# 2010-May-01 00:00 09 01 43.1966 +19 04 28.673 286.52 18.22 246.99 25.34 358.6230 3.44 1.661167637023 -0.5303431 1.28664311447968 15.7195833 37.3033 84.50
#
# some mod to label names and comments so that they corresponds to
# JPL-Horizons naming comvension
cols = {
'MJD': {
def __execute_press(self):
###
# Pressed-out method (Sofue & Reich 1979)
###
casalog.post( 'Apply Pressed-out method' )
# CAS-5410 Use private tools inside task scripts
ia = gentools(['ia'])[0]
# mask
self.image = ia.newimagefromimage(infile=self.infiles,outfile=self.tmpmskname)
# back-up original mask name
is_initial_mask = (self.image.maskhandler('default')[0] != '')
temp_maskname = "temporal"
imshape = self.image.shape()
ndim = len(imshape)
nx = imshape[0]
ny = imshape[1]
if len(self.thresh) == 0:
casalog.post( 'Use whole region' )
else:
# mask pixels beyond thresholds
maskstr = ("mask('%s')" % self.tmpmskname)
if self.thresh[0] != self.nolimit:
maskstr += (" && '%s'>=%f" % (self.tmpmskname, self.thresh[0]))
if self.thresh[1] != self.nolimit:
maskstr += (" && '%s'<=%f" % (self.tmpmskname, self.thresh[1]))
# Need to flush to image once to calcmask ... sigh
self.image.done()
self.image = ia.newimage( self.tmpmskname )
self.image.calcmask(mask=maskstr, name=temp_maskname, asdefault=True)
# smoothing
#bmajor = 0.0
#bminor = 0.0
# CAS-5410 Use private tools inside task scripts
qa = qatool()
if type(self.beamsize) == str:
qbeamsize = qa.quantity(self.beamsize)
else:
qbeamsize = qa.quantity(self.beamsize,'arcsec')
if type(self.smoothsize) == str:
#bmajor = smoothsize
#bminor = smoothsize
qsmoothsize = qa.quantity(self.smoothsize)
else:
#bmajor = '%sarcsec' % (beamsize*smoothsize)
#bminor = '%sarcsec' % (beamsize*smoothsize)
qsmoothsize = qa.mul(qbeamsize,self.smoothsize)
bmajor = qsmoothsize
bminor = qsmoothsize
pa = qa.quantity(0.0, 'deg')
# masked channels are replaced by zero and convolved here.
self.convimage = self.image.convolve2d( outfile=self.tmppolyname, major=bmajor, minor=bminor, pa=pa,
overwrite=True )
self.convimage.done()
# get dTij (original - smoothed)
self.convimage = ia.imagecalc(outfile=self.tmpconvname,
pixels='"{org}" - "{conv}"'.format(org=self.tmpmskname,
conv=self.tmppolyname),
overwrite=True)
# polynomial fit
fitaxis = 0
if self.direction == 0.0:
fitaxis = 0
elif self.direction == 90.0:
fitaxis = 1
else:
raise Exception, "Sorry, the task don't support inclined scan with respect to horizontal or vertical axis, right now."
# Replace duplicated method ia.fitpolynomial with
# ia.fitprofile
#polyimage = convimage.fitpolynomial( fitfile=tmppolyname, axis=fitaxis, order=numpoly, overwrite=True )
#polyimage.done()
if os.path.exists( self.tmppolyname ):
# CAS-5410 Use private tools inside task scripts
cu = utilstool()
cu.removetable([self.tmppolyname])
self.convimage.setbrightnessunit('K')
# Unfortunately, ia.fitprofile is very fragile.
# Using numpy instead for fitting with masked pixels (KS, 2014/07/02)
#resultdic = self.convimage.fitprofile( model=self.tmppolyname, axis=fitaxis, poly=self.numpoly, ngauss=0, multifit=True, gmncomps=0 )
self.__polynomial_fit_model(image=self.tmpmskname, model=self.tmppolyname,axis=fitaxis, order=self.numpoly)
polyimage = ia.newimage( self.tmppolyname )
# set back defalut mask (need to get from self.image)
avail_mask = polyimage.maskhandler('get')
if is_initial_mask:
casalog.post("copying mask from %s"%(self.infiles))
polyimage.calcmask("mask('%s')"%self.infiles,asdefault=True)
else: #no mask in the original image
polyimage.calcmask('T', asdefault=True)
if temp_maskname in avail_mask:
polyimage.maskhandler('delete', name=temp_maskname)
# subtract fitted image from original map
subtracted = ia.imagecalc(outfile=self.outfile,
pixels='"{org}" - "{fit}"'.format(org=self.infiles,
fit=self.tmppolyname),
overwrite=self.overwrite)
subtracted.done()
# finalization
polyimage.done(remove=True)
self.convimage.done(remove=True)
self.image.done()
def setSolarObjectJy(self,field,spw,scalebychan, timerange,observation, scan, intent, useephemdir, usescratch=False):
"""
Set flux density of a solar system object using Bryan Butler's new
python model calculation code.
A single time stamp (first time stamp of MS after selections are applied) is
currently used per execution. For flux observation done in a long time span
may need to run multiple setjy with selections by time range (or scans).
"""
#retval = True
output = {}
cleanupcomps = True # leave generated cl files
#from taskinit import *
from taskinit import gentools
qa = casac.quanta()
(myms, mytb, mycl, myme, mycb, mymsmd) = gentools(['ms','tb','cl','me', 'cb','msmd'])
# prepare parameters need to pass to the Bryan's code
# make ms selections
# get source name
# get time ranges
# get spwused and get frequency ranges
sel={}
sel['field']=field
sel['spw']=spw
sel['timerange']=timerange
sel['observation']=str(observation)
sel['scan']=scan
sel['scanintent']=intent
measframes=['REST','LSRK','LSRD','BARY','GEO','TOPO','GALACTO','LGROUP','CMB']
myms.open(self.vis)
myms.msselect(sel,False)
scansummary=myms.getscansummary()
nscan=len(scansummary.keys())
selectedids=myms.msselectedindices()
fieldids=selectedids['field']
obsids=selectedids['observationid']
myms.close()
mytb.open(self.vis+'/OBSERVATION')
if len(obsids)==0:
getrow=0
else:
getrow=obsids[0]
observatory=mytb.getcell('TELESCOPE_NAME',getrow)
mytb.close()
mytb.open(self.vis+'/FIELD')
colnames = mytb.colnames()
if len(fieldids)==0:
fieldids = range(mytb.nrows())
# frame reference for field position
phdir_info=mytb.getcolkeyword("PHASE_DIR","MEASINFO")
if phdir_info.has_key('Ref'):
fieldref=phdir_info['Ref']
elif phdir_info.has_key('TabRefTypes'):
colnames=mytb.colnames()
for col in colnames:
if col=='PhaseDir_Ref':
fieldrefind=mytb.getcell(col,fieldids[0])
fieldref=phdir_info['TabRefTypes'][fieldrefind]
else:
fieldref=''
srcnames={}
fielddirs={}
ftimes={}
ephemid={}
for fid in fieldids:
#srcnames.append(mytb.getcell('NAME',int(fid)))
srcnames[fid]=(mytb.getcell('NAME',int(fid)))
#fielddirs[fid]=(mytb.getcell('PHASE_DIR',int(fid)))
ftimes[fid]=(mytb.getcell('TIME',int(fid)))
if colnames.count('EPHEMERIS_ID'):
ephemid[fid]=(mytb.getcell('EPHEMERIS_ID',int(fid)))
else:
ephemid[fid]=-1
mytb.close() # close FIELD table
# need to get a list of time
# but for now for test just get a time centroid of the all scans
# get time range
# Also, this needs to be done per source
# gather freq info from Spw table
mytb.open(self.vis+'/SPECTRAL_WINDOW')
nspw = mytb.nrows()
freqcol=mytb.getvarcol('CHAN_FREQ')
freqwcol=mytb.getvarcol('CHAN_WIDTH')
fmeasrefcol=mytb.getcol('MEAS_FREQ_REF')
reffreqs=mytb.getcol('REF_FREQUENCY')
mytb.close()
# store all parameters need to call solar_system_fd for all sources
inparams={}
validfids = [] # keep track of valid fid that has data (after selection)
# if same source name ....need handle this...
for fid in fieldids:
sel['field']=str(fid)
myms.open(self.vis)
#reset the selection
try:
status=myms.msselect(sel)
except:
#skip this field
continue
if not status:
continue
validfids.append(fid)
trange=myms.range('time')
#if not inparams.has_key(srcnames[fid]):
# inparams[srcnames[fid]]={}
if not inparams.has_key(fid):
inparams[fid]={}
inparams[fid]['fieldname']=srcnames[fid]
#tc = (trange['time'][0]+trange['time'][1])/2. #in sec.
# use first timestamp to be consistent with the ALMA Control
# old setjy (Butler-JPL-Horizons 2010) seems to be using
# time in FIELD... but here is first selected time in main table
if ephemid[fid]==-1: # keep old behavior
tc = trange['time'][0] #in sec.
tmsg = "Time used for the model calculation (=first time stamp of the selected data) for field "
else: # must have ephem table attached...
tc = ftimes[fid]#in sec.
tmsg = "Time used for the model calculation for field "
#if inparams[srcnames[fid]].has_key('mjd'):
# inparams[srcnames[fid]]['mjds'][0].append([myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']])
#else:
# inparams[srcnames[fid]]['mjds']=[myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']]
if inparams[fid].has_key('mjd'):
inparams[fid]['mjds'][0].append([myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']])
else:
inparams[fid]['mjds']=[myme.epoch('utc',qa.quantity(tc,'s'))['m0']['value']]
usedtime = qa.time(qa.quantity(tc,'s'),form='ymd')[0]
self._casalog.post(tmsg+str(fid)+":"+usedtime)
# get a correct direction measure
mymsmd.open(self.vis)
dirdic = mymsmd.phasecenter(int(fid))
mymsmd.close()
# check if frame is J2000 and if not do the transform
if dirdic['refer'] != 'J2000':
myme.doframe(myme.observatory(observatory))
myme.doframe(myme.epoch('utc', qa.quantity(tc,'s')))
azeldir = myme.measure(dirdic,'AZELGEO')
dirdic=myme.measure(azeldir,'J2000')
fielddirs[fid]=(numpy.array([[dirdic['m0']['value']],[dirdic['m1']['value']]]))
# somehow it gives you duplicated ids .... so need to uniquify
selspws= list(set(myms.msselectedindices()['spw']))
# make sure it is int rather than numpy.int32, etc.
selspws = [int(ispw) for ispw in selspws]
#inparams[srcnames[fid]]['spwids']= selspws if len(selspws)!=0 else range(nspw)
inparams[fid]['spwids']= selspws if len(selspws)!=0 else range(nspw)
#create a list of freq ranges with selected spws
# should worry about freq order???
freqlist=[]
freqlistraw=[]
framelist=[]
#for idx in inparams[srcnames[fid]]['spwids']:
for idx in inparams[fid]['spwids']:
freqs=freqcol['r'+str(idx+1)]
freqws=freqwcol['r'+str(idx+1)]
fmeasref=fmeasrefcol[idx]
#if scalebychan=T, this has to be min, max determined from
# chan_freq(channel center)+/- chan width.
if scalebychan:
# pack into list of list of list (freqlist[nf][nspw])
perspwfreqlist=[]
for nf in range(len(freqs)):
fl = freqs[nf][0]-freqws[nf][0]/2.
fh = freqs[nf][0]+freqws[nf][0]/2.
perspwfreqlist.append([fl,fh])
freqlist.append(perspwfreqlist)
else:
if (len(freqs)==1):
fl = freqs[0][0]-freqws[0][0]/2.
fh = freqs[0][0]+freqws[0][0]/2.
freqlist.append([float(fl),float(fh)])
else:
freqlist.append([float(min(freqs)),float(max(freqs))])
framelist.append(measframes[fmeasref])
freqlistraw.append(freqs.transpose()[0].tolist()) # data chanfreq list
#inparams[srcnames[fid]]['freqlist']=freqlist
#inparams[srcnames[fid]]['freqlistraw']=freqlistraw
#inparams[srcnames[fid]]['framelist']=framelist
#inparams[srcnames[fid]]['reffreqs']=reffreqs
inparams[fid]['freqlist']=freqlist
inparams[fid]['freqlistraw']=freqlistraw
inparams[fid]['framelist']=framelist
inparams[fid]['reffreqs']=reffreqs
myms.close()
# call Bryan's code
# errcode: list of list - inner list - each values for range of freqs
# flluxes: list of list
# fluxerrs:
# size: [majoraxis, minoraxis, pa]
# direction: direction for each time stamp
#
#import solar_system_setjy as ss_setjy
import solar_system_setjy as SSsetjy
retdict={} # for returning flux densities?
ss_setjy=SSsetjy.solar_system_setjy()
#for src in srcnames:
self.clnamelist=[]
for vfid in validfids:
src=srcnames[vfid]
#mjds=inparams[src]['mjds']
mjds=inparams[vfid]['mjds']
fluxes=[]
# call solar_system_fd() per spw (for scalebychan freqlist has an extra dimention)
#nspwused=len(inparams[src]['freqlist'])
nspwused=len(inparams[vfid]['freqlist'])
# warning for many channels but it is really depends on the source
if scalebychan:
maxnf=0
for ispw in range(nspwused):
#nf = len(inparams[src]['freqlist'][ispw])
nf = len(inparams[vfid]['freqlist'][ispw])
maxnf = max(nf,maxnf)
if maxnf >= 3840 and src.upper()!="MARS": # mars shoulde be ok
self._casalog.post("Processing %s spw(s) and at least some of them are a few 1000 channels or more. This may take \
many minutes (>3min per spw for 3840 channels) in some cases. Please be patient." % nspwused,"WARN")
for i in range(nspwused): # corresponds to n spw
if type(freqlist[0][0])==list:
#infreqs=inparams[src]['freqlist'][i]
infreqs=inparams[vfid]['freqlist'][i]
else:
#infreqs=[inparams[src]['freqlist'][i]]
infreqs=[inparams[vfid]['freqlist'][i]]
self._casalog.post("Calling solar_system_fd: %s(%s) for spw%s freqs=%s" % (src, vfid,i,freqlist[i]),'DEBUG1')
(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, observatory=observatory, casalog=self._casalog)
# for old code
#(errcodes, subfluxes, fluxerrs, sizes, dirs)=\
# ss_setjy.solar_system_fd(source_name=src, MJDs=mjds, frequencies=infreqs, casalog=self._casalog)
# for nf freq ranges, nt mjds
# errcodes[nf][nt], subfluxes[nf][nt], fluxerrs[nf][nt], sizes[nt], dirs[nt]
self._casalog.post("+++++ solar_system_fd() returned values +++++", 'DEBUG1')
self._casalog.post(" fluxes(fds)=%s" % subfluxes, 'DEBUG1')
self._casalog.post(" sizes=%s" % sizes, 'DEBUG1')
self._casalog.post(" directions=%s\n" % dirs, 'DEBUG1')
# packed fluxes for all spws
fluxes.append(subfluxes)
# fluxes has fluxesi[nspw][nf][nt]
# ------------------------------------------------------------------------
# For testing with hardcoded values without calling solar_system_fd()...
#errcodes=[[0,0,0,0,0]]
#fluxes=[[26.40653147,65.23839313,65.23382757,65.80638802,69.33396562]]
#fluxerrs=[[0.0,0.0,0.0,0.0,0.0]]
#sizes=[[3.6228991032674371,3.6228991032674371,0.0]]
#dirs=[{'m0': {'unit': 'rad', 'value': 0.0}, 'm1': {'unit': 'rad', 'value': 0.0}, 'refer': 'J2000', 'type': 'direction'}]
# ------------------------------------------------------------------------
# local params for selected src
#framelist=inparams[src]['framelist']
#freqlist=inparams[src]['freqlist']
#freqlistraw=inparams[src]['freqlistraw']
#reffreqs=inparams[src]['reffreqs']
#spwids=inparams[src]['spwids']
framelist=inparams[vfid]['framelist']
freqlist=inparams[vfid]['freqlist']
freqlistraw=inparams[vfid]['freqlistraw']
reffreqs=inparams[vfid]['reffreqs']
spwids=inparams[vfid]['spwids']
clrecs=odict.odict()
labels = []
# loop for over for multiple directions (=multiple MJDs) for a given src
for i in range(len(dirs)): # this is currently only length of 1 since no multiple timestamps were used
# check errcode - error code would be there per flux per time (dir)
reterr=testerrs(errcodes[i],src)
if reterr == 2:
continue
#dirstring = [dirs[i]['refer'],qa.tos(dirs[i]['m0']),qa.tos(dirs[i]['m1'])]
if useephemdir:
dirstring = [dirs[i]['refer'],qa.tos(dirs[i]['m0']),qa.tos(dirs[i]['m1'])]
dirmsg = "Using the source position from the ephemeris table in the casa data directory: "
else:
#dirstring = [fieldref, str(fielddirs[fieldids[0]][0][0])+'rad', str(fielddirs[fieldids[0]][1][0])+'rad']
# extract field direction of first id of the selected field ids
#dirstring = [fieldref, "%.18frad" % (fielddirs[fieldids[0]][0][0]), "%.18frad" % (fielddirs[fieldids[0]][1][0])]
#dirstring = [fieldref, "%.18frad" % (fielddirs[vfid][0][0]), "%.18frad" % (fielddirs[vfid][1][0])]
# by now the direction should be in J2000
dirstring = ['J2000', "%.18frad" % (fielddirs[vfid][0][0]), "%.18frad" % (fielddirs[vfid][1][0])]
dirmsg = "Using the source position in the MS (or in the attached ephemeris table, if any): "
self._casalog.post(dirmsg+str(dirstring))
# setup componentlists
# need to set per dir
# if scalebychan=F, len(freqs) corresponds to nspw selected
# Need to put in for-loop to create cl for each time stamp? or scan?
#clpath='/tmp/'
clpath='./'
# construct cl name (multiple spws in one componentlist table)
selreffreqs = [reffreqs[indx] for indx in spwids]
minfreq = min(selreffreqs)
maxfreq = max(selreffreqs)
freqlabel = '%.3f-%.3fGHz' % (minfreq/1.e9, maxfreq/1.e9)
#tmlabel = '%.1fd' % (tc/86400.)
mjd=inparams[vfid]['mjds'][0]
tmlabel = '%.1fd' % (mjd)
#clabel = src+'_spw'+str(spwids[j])+'_'+freqlabel+'_'+tmlabel
#clabel0 = src+'_'+freqlabel+'_'+tmlabel
#pid=str(os.getpid())
#clname = clpath+clabel0+"_"+pid+'.cl'
clabel0 = src+'_'+freqlabel+'_'+tmlabel+"_"+os.path.basename(self.vis)
clname = clpath+clabel0+'.cl'
#debug
self._casalog.post("Create componentlist: %s for vfid=%s" % (clname,vfid),'DEBUG1')
if (os.path.exists(clname)):
shutil.rmtree(clname)
iiflux=[]
iinfreq=[]
# for logging/output dict - pack each freq list for each spw
freqsforlog=[]
for j in range(len(freqlist)): # loop over nspw
freqlabel = '%.3fGHz' % (reffreqs[int(spwids[j])]/1.e9)
clabel=src+'_spw'+str(spwids[j])+'_'+freqlabel+'_'+tmlabel
#print "addcomponent...for spw=",spwids[j]," i=",i," flux=",fluxes[j][i]
if scalebychan:
index= 2.0
sptype = 'spectral index'
else:
index= 0.0
sptype = 'constant'
# adjust to change in returned flux shape. An extra [] now seems to be gone. 2012-09-27
iflux=fluxes[j][i][0]
#print "addcomponent with flux=%s at frequency=%s" %\
# (iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz')
# i - time stamps = 0 for now, j = a freq range
infreq=freqlist[j][0][0] if type(freqlist[j][0])==list else freqlist[j][0]
# for a single CL with multple spws
if j ==0: infreq0=infreq
# --- version for 'multi-spws in a single comp single CL'
# accumulate all frequencies from all spws to a list
#if not scalebychan:
#freqlist[j] for j spw should contain a list with two freqs (min and max of
# of the spw and the same fluxes should be set for the freqs so that cl.setspectrum
# with tabular would not interpolate inside each spw
##iinfreq.extend(freqlist[j])
# nch = len(freqlistraw[j])
# iinfreq.extend(freqlistraw[j])
# assigning the same flux to the two freqs
##iiflux.extend([iflux,iflux])
# for ich in range(nch):
# iiflux.extend([iflux])
#else:
# iiflux.extend(fluxes[j][i])
# if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# for fr in freqlist[j]:
# iinfreq.append((fr[1]+fr[0])/2)
# else:
# if type(freqlist[j])==list:
# iinfreq.append((freqlist[j][1]+freqlist[j][0])/2)
# else:
# iinfreq.append(freqlist[j])
# freqsforlog.append(iinfreq)
# -----------------------------------------------------------------------------------
self._casalog.post("addcomponent with flux=%s at frequency=%s" %\
# (fluxes[j][i][0],str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
(iflux,str(reffreqs[int(spwids[j])]/1.e9)+'GHz'), 'INFO1')
#
mycl.addcomponent(iflux,fluxunit='Jy', polarization="Stokes", dir=dirstring,
shape='disk', majoraxis=str(sizes[i][0])+'arcsec', minoraxis=str(sizes[i][1])+'arcsec',
positionangle=str(sizes[i][2])+'deg', freq=[framelist[0],str(infreq)+'Hz'],
spectrumtype=sptype, index=index, label=clabel)
if scalebychan:
# use tabular form to set flux for each channel
# This may be redundant
if type(fluxes[j][i]) ==list and len(fluxes[j][i])> 1:
if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
freqs=[]
for fr in freqlist[j]:
freqs.append((fr[1]+fr[0])/2)
clind = mycl.length() - 1
mycl.setspectrum(which=clind, type='tabular', tabularfreqs=freqs, tabularflux=fluxes[j][0],
tabularframe=framelist[j])
### === per spw process end here
# - version that put all spws into a component -
# set a single component freq set at the the lower edge of first spw
#mycl.addcomponent(iiflux[0],fluxunit='Jy', polarization="Stokes", dir=dirstring,
# shape='disk', majoraxis=str(sizes[i][0])+'arcsec', minoraxis=str(sizes[i][1])+'arcsec',
# positionangle=str(sizes[i][2])+'deg', freq=[framelist[0],str(infreq0)+'Hz'],
# spectrumtype=sptype, index=index, label=clabel)
# if it's list of fluxes try to put in tabular form
#if type(fluxes[j][i]) ==list and len(fluxes[j][i])> 1:
# if len(iiflux)> 1:
#print "framelist[j]=",framelist[j]
#if type(freqlist[j][0])==list and len(freqlist[j][0])>1:
# freqs=[]
# for fr in freqlist[j]:
# freqs.append((fr[1]+fr[0])/2)
#else:
# freqs=freqlist[j]
#clind = mycl.length() - 1
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=freqs, tabularflux=fluxes[j][0],
#tabularframe=framelist[j])
# mycl.setspectrum(which=clind, type='tabular', tabularfreqs=iinfreq, tabularflux=iiflux,
# tabularframe=framelist[0])
#mycl.rename(clname)
#put in a record for log output
#clrecs[clabel] = mycl.torecord()
clrecs[clabel0] = mycl.torecord()
clrecs[clabel0]['allfluxinfo']=fluxes
clrecs[clabel0]['allfreqinfo']=freqsforlog
clrecs[clabel0]['spwids']=spwids
mycl.rename(clname) # - A CL per field
mycl.close(False) # False for not to send a warning message
mycl.done()
# if scratch=F check if the virtual model already exist
# for the field if it is clear it.
# if j==0 and (not usescratch):
# mytb.open(self.vis, nomodify=False)
# kwds = mytb.getkeywords()
# modelkwd='definedmodel_field_'+str(vfid)
# if kwds.has_key(modelkwd):
# clmodname=kwds[modelkwd]
# mytb.removekeyword(clmodname)
# mytb.removekeyword(modelkwd)
# mytb.close()
mycb.open(self.vis,addcorr=False,addmodel=False)
mycb.delmod(otf=True,field=str(vfid),spw=spwids, scr=False)
mycb.close()
# finally, put the componentlist as model
#tqlstr=''
#if intent!='':
# tqlstr='any(STATE_ID=='+str(stateids.tolist())+')'
# Currently still need to do per spw (see the comment below...)
# assuming CL contains nrow = nspw components
mycl.open(clname)
clinrec = mycl.torecord()
mycl.close(False)
mycl.done()
ncomp = clinrec['nelements']
if ncomp != len(spwids):
raise Exception, "Inconsistency in generated componentlist...Please submit a bug report."
for icomp in range(ncomp):
#self.im.selectvis(spw=spwids[icomp],field=field,observation=observation,time=timerange,intent=intent)
ok = self.im.selectvis(spw=spwids[icomp],field=vfid,observation=observation,time=timerange,intent=intent)
# for MMS, particular subms may not contain the particular spw, so skip for such a case
if ok:
newclinrec = {}
newclinrec['nelements']=1
newclinrec['component0']=clinrec['component'+str(icomp)]
mycl.fromrecord(newclinrec)
cdir = os.getcwd()
if os.access(cdir,os.W_OK):
tmpclpath = cdir+"/"
elif os.access("/tmp",os.W_OK):
tmpclpath = "/tmp/"
#tmpclpath=tmpclpath+"_tmp_setjyCLfile_"+pid
tmpclpath=tmpclpath+os.path.basename(self.vis)+"_tmp_setjyCLfile"
if os.path.exists(tmpclpath):
shutil.rmtree(tmpclpath)
mycl.rename(tmpclpath)
mycl.close(False)
self.im.ft(complist=tmpclpath)
# --------------------------------------------------------------------------------------------
# Currently this does not work properly for some case. Need ft can handle multi-component CL
# with the way to map which component apply to which spw
# Unable when such functionality is implemented in im.ft()
#self.im.selectvis(spw=spwids,field=field,observation=observation,time=timerange,intent=intent)
#self.im.ft(complist=clname) <= e.g. im.ft(comprec) where comrec = {'spw-mapping':[...],comprecs}..
# --------------------------------------------------------------------------------------------
#debug: set locally saved 2010-version component list instead
#cl2010='mod_setjy_spw0_Titan_230.543GHz55674.1d.cl'
#print "Using complist=",cl2010
#self.im.ft(complist=cl2010)
#if cleanupcomps:
# shutil.rmtree(clname)
#self.clnamelist.append(clname)
self.clnamelist.append(clname)
msg="Using channel dependent " if scalebychan else "Using spw dependent "
if clrecs=={}:
raise Exception, "No componentlist is generated."
self._casalog.post(msg+" flux densities")
#self._reportoLog(clrecs,self._casalog)
self._reportoLog2(clrecs,self._casalog)
#self._updateHistory(clrecs,self.vis)
self._updateHistory2(clrecs,self.vis)
# dictionary of dictionary for each field
retdict[vfid]=clrecs
# ==== end of for loop over fields
#output=self._makeRetFluxDict(retdict)
output=self._makeRetFluxDict2(retdict)
#return retval
return output
jplfiles_to_repository() puts it all together, so it is most likely the
function you want.
There are various utilities like convert_radec, datestr*, get_num_from_str,
mean_radius*, and construct_tablepath defined in here as well.
"""
from glob import glob
import os
import re
import scipy.special
import time # We can always use more time.
from taskinit import gentools, qa, casalog
me = gentools(['me'])[0]
from dict_to_table import dict_to_table
# Possible columns, as announced by their column titles.
# The data is scooped up by 'pat'. Either use ONE group named by the column
# key, or mark it as unwanted. '-' is not valid in group names.
# Leading and trailing whitespace will be taken care of later.
# Sample lines:
# Date__(UT)__HR:MN R.A.___(ICRF/J2000.0)___DEC Ob-lon Ob-lat Sl-lon Sl-lat NP.ang NP.dist r rdot delta deldot S-T-O L_s
# 2010-May-01 00:00 09 01 43.1966 +19 04 28.673 286.52 18.22 246.99 25.34 358.6230 3.44 1.661167637023 -0.5303431 1.28664311447968 15.7195833 37.3033 84.50
#
# some mod to label names and comments so that they corresponds to
# JPL-Horizons naming comvension
cols = {
'MJD': {'header': r'Date__\(UT\)__HR:MN',
def _updateHistory2(self,clrecs,vis):
"""
Update history table when setSolarObjectJy is run
(mulitple comopents in one version)
"""
#
from taskinit import gentools
(mytb,) = gentools(['tb'])
mytb.open(vis+'/HISTORY',nomodify=False)
nrow = mytb.nrows()
lasttime=mytb.getcol('TIME')[nrow-1]
rown=nrow
#
clname = clrecs.keys()[0]
#for ky in clrecs.keys():
srcn = clname.split('_')[0]
comprec = clrecs[clname]
nelm = comprec['nelements']
for icomp in range(nelm):
comp = comprec['component'+str(icomp)]
complab = comp['label']
origin='setjy'
priority='INFO'
time=lasttime
appl='setjy'
emptystrarr=numpy.array([''])
if nelm==1:
for i in range(len(comprec['spwids'])):
mytb.addrows(1)
ispw=comprec['spwids'][i]
iflux = comprec['allfluxinfo'][i][0][0]
msg = (" %s: spw %s Flux:[I=%s,Q=%s,U=%s,V=%s] +/- [I=%s,Q=%s,U=%s,V=%s] Jy" %
(srcn, ispw, iflux, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
mytb.putcell('APP_PARAMS', rown, [''])
mytb.putcell('CLI_COMMAND',rown, [''])
mytb.putcell('APPLICATION',rown, appl)
mytb.putcell('MESSAGE',rown, msg)
mytb.putcell('OBSERVATION_ID',rown, -1)
mytb.putcell('ORIGIN',rown,origin)
mytb.putcell('PRIORITY',rown,priority)
mytb.putcell('TIME',rown, time)
rown += 1
else:
ispw = complab.split('_')[1]
mytb.addrows(1)
msg = (" %s: spw %s Flux:[I=%s,Q=%s,U=%s,V=%s] +/- [I=%s,Q=%s,U=%s,V=%s] Jy" %
(srcn, ispw, comp['flux']['value'][0], comp['flux']['value'][1],
comp['flux']['value'][2], comp['flux']['value'][3],
comp['flux']['error'][0], comp['flux']['error'][1],comp['flux']['error'][2],
comp['flux']['error'][3]))
mytb.putcell('APP_PARAMS', rown, [''])
mytb.putcell('CLI_COMMAND',rown, [''])
mytb.putcell('APPLICATION',rown, appl)
mytb.putcell('MESSAGE',rown, msg)
mytb.putcell('OBSERVATION_ID',rown, -1)
mytb.putcell('ORIGIN',rown,origin)
mytb.putcell('PRIORITY',rown,priority)
mytb.putcell('TIME',rown, time)
rown += 1
mytb.close()
import numpy as np
import pdb
from taskinit import gentools
ms = gentools(['ms'])[0]
ia = gentools(['ia'])[0]
#qa = gentools(['qa'])[0]
#execfile('fixImage_fixedcoord.py')
emerlin_ost_dir = '/local/scratch/btunbrid/work/im3shape_work/COSMOS/Radio_noise_simulations/output/'
def rescale_image(image_array,new_max):
image_max = image_array.max()
factor = float( new_max / image_max)
image_array = np.multiply(image_array,factor)
return image_array
def fixImage(datafile,
centre_freq=1.4, #GHz
bandwidth=2., # in fits header 2.5e+07 quoted 25000000
#GHz 37.5 MHz for
n_channels=7,
peakvalue='0.024',#'0.0092034321',
peakunit='Jy',
pixel_scale=0.2, #pixel/arcmin
#Central image is positioned at 150.119166668, 2.20573611111#'0h8m49.4s',
Ra_central='10h02m28.67s',
Dec_central='+02d38m28.64s',
ost_template_image=emerlin_ost_dir+'ost_template.image',
input_casa_image='simulated_VLA_large_casa.image'):
'''Kludgey function to give an image from GalSim the correct co-ordinate
system for observation with CASA.