def fatalError(self, ex):
""" Method called when a fata error is encountered
Parameters
----------
ex : exception
The error encountered
Returns
-------
None
"""
logging.error("Fatal error encountered.")
raise ex
def test_error(self):
msg = "unit_test_error_message"
Alogging.error(msg)
found = False
r = open(self.logfile, 'r')
for line in r.readlines():
if msg in line:
if(self.verbose):
print "\nFound message > ", line
found = True
r.close()
break
self.assertTrue(found)
def run(self):
""" The run method creates the BDP
Parameters
----------
None
Returns
-------
None
"""
self._summary = {}
dt = utils.Dtime("Smooth")
dt.tag("start")
# get the input keys
bmaj = self.getkey("bmaj")
bmin = self.getkey("bmin")
bpa = self.getkey("bpa")
velres = self.getkey("velres")
# take care of potential issues in the unit strings
# @todo if not provided?
bmaj['unit'] = bmaj['unit'].lower()
bmin['unit'] = bmin['unit'].lower()
velres['unit'] = velres['unit'].lower()
taskargs = "bmaj=%s bmin=%s bpa=%s velres=%s" % (bmaj, bmin, bpa,
velres)
bdpnames = []
for ibdp in self._bdp_in:
istem = ibdp.getimagefile(bt.CASA)
image_in = ibdp.baseDir() + istem
bdp_name = self.mkext(istem, 'sim')
image_out = self.dir(bdp_name)
taskinit.ia.open(image_in)
h = casa.imhead(image_in, mode='list')
pix_scale = np.abs(h['cdelt1'] *
206265.0) # pix scale in asec @todo QA ?
CC = 299792458.0 # speed of light @todo somewhere else [utils.c , but in km/s]
rest_freq = h['crval3']
# frequency pixel scale in km/s
vel_scale = np.abs(CC * h['cdelt3'] / rest_freq / 1000.0)
# unit conversion to arcsec (spatial) or km/s
# (velocity) or some flavor of Hz.
if (bmaj['unit'] == 'pixel'):
bmaj = bmaj['value'] * pix_scale
else:
bmaj = bmaj['value']
if (bmin['unit'] == 'pixel'):
bmin = bmin['value'] * pix_scale
else:
bmin = bmin['value']
hertz_input = False
if velres['unit'] == 'pixel':
velres['value'] = velres['value'] * vel_scale
velres['unit'] = 'km/s'
elif velres['unit'] == 'm/s':
velres['value'] = velres['value'] / 1000.0
velres['unit'] = 'km/s'
elif velres['unit'][-2:] == 'hz':
hertz_input = True
elif velres['unit'] == 'km/s':
pass
else:
logging.error("Unknown units in velres=%s" % velres['unit'])
rdata = bmaj
# we smooth in velocity first. if smoothing in velocity
# the cube apparently must be closed afterwards and
# then reopened if spatial smoothing is to be done.
if velres['value'] > 0:
# handle the different units allowed. CASA doesn't
# like lowercase for hz units...
if not hertz_input:
freq_res = str(
velres['value'] * 1000.0 / CC * rest_freq) + 'Hz'
else:
freq_res = str(velres['value'])
# try to convert velres to km/s for debug purposes
velres['value'] = velres['value'] / rest_freq * CC / 1000.0
if (velres['unit'] == 'khz'):
velres['value'] = velres['value'] * 1000.0
velres['unit'] = 'kHz'
elif (velres['unit'] == 'mhz'):
velres['value'] = velres['value'] * 1E6
velres['unit'] = 'MHz'
elif (velres['unit'] == 'ghz'):
velres['value'] = velres['value'] * 1E9
velres['unit'] = 'GHz'
freq_res = freq_res + velres['unit']
# NB: there is apparently a bug in CASA. only smoothing along the frequency
# axis does not work. sepconvolve gives a unit error (says axis unit is radian rather
# than Hz). MUST smooth in 2+ dimensions if you want this to work.
if (velres['value'] < vel_scale):
raise Exception, "Desired velocity resolution %g less than pixel scale %g" % (
velres['value'], vel_scale)
image_tmp = self.dir('tmp.smooth')
im2=taskinit.ia.sepconvolve(outfile=image_tmp,axes=[0,1,2], types=["boxcar","boxcar","gauss"],\
widths=['1pix','1pix',freq_res], overwrite=True)
im2.done()
logging.debug("sepconvolve to %s" % image_out)
# for some reason, doing this in memory does not seem to work, so outfile must be specified.
logging.info(
"Smoothing cube to a velocity resolution of %s km/s" %
str(velres['value']))
logging.info("Smoothing cube to a frequency resolution of %s" %
freq_res)
taskinit.ia.close()
taskinit.ia.open(image_tmp)
dt.tag("sepconvolve")
else:
image_tmp = image_out
# now do the spatial smoothing
convolve_to_min_beam = True # default is to convolve to a min enclosing beam
if bmaj > 0 and bmin > 0:
# form qa objects out of these so that casa can understand
bmaj = taskinit.qa.quantity(bmaj, 'arcsec')
bmin = taskinit.qa.quantity(bmin, 'arcsec')
bpa = taskinit.qa.quantity(bpa, 'deg')
target_res = {}
target_res['major'] = bmaj
target_res['minor'] = bmin
target_res['positionangle'] = bpa
# throw an exception if cannot be convolved
try:
# for whatever reason, if you give convolve2d a beam parameter,
# it complains ...
im2=taskinit.ia.convolve2d(outfile=image_out,major = bmaj,\
minor = bmin, pa = bpa,\
targetres=True,overwrite=True)
im2.done()
logging.info(
"Smoothing cube to a resolution of %s by %s at a PA of %s"
% (str(bmaj['value']), str(
bmin['value']), str(bpa['value'])))
convolve_to_min_beam = False
achieved_res = target_res
except:
# @todo remind what you need ?
logging.error("Warning: Could not convolve to requested resolution of "\
+str(bmaj['value']) + " by " + str(bmin['value']) + \
" at a PA of "+ str(bpa['value']))
raise Exception, "Could not convolve to beam given!"
dt.tag("convolve2d-1")
if convolve_to_min_beam:
restoring_beams = taskinit.ia.restoringbeam()
commonbeam = taskinit.ia.commonbeam()
# for whatever reason, setrestoringbeam does not use the same set of hashes...
commonbeam['positionangle'] = commonbeam['pa']
del commonbeam['pa']
# if there's one beam, apparently the beams keyword does not exist
if 'beams' in restoring_beams:
print "Smoothing cube to a resolution of "+ \
str(commonbeam['major']['value']) +" by "+ \
str(commonbeam['minor']['value'])+" at a PA of "\
+str(commonbeam['pa']['value'])
target_res = commonbeam
im2=taskinit.ia.convolve2d(outfile=image_out,major=commonbeam['major'],\
minor=commonbeam['minor'],\
pa=commonbeam['positionangle'],\
targetres=True,overwrite=True)
im2.done()
achieved_res = commonbeam
dt.tag("convolve2d-2")
else:
print "One beam for all planes. Smoothing to common beam redundant."
achieved_res = commonbeam
if velres['value'] < 0:
taskinit.ia.fromimage(outfile=image_out,
infile=image_in)
# not really doing anything
# else, we've already done what we needed to
taskinit.ia.setrestoringbeam(beam=achieved_res)
rdata = achieved_res['major']['value']
# else do no smoothing and just close the image
taskinit.ia.close()
dt.tag("close")
b1 = SpwCube_BDP(bdp_name)
self.addoutput(b1)
# need to update for multiple images.
b1.setkey("image", Image(images={bt.CASA: bdp_name}))
bdpnames = bdpnames.append(bdp_name)
# and clean up the temp image before the next image
if velres['value'] > 0:
utils.remove(image_tmp)
# thes are task arguments not summary entries.
_bmaj = taskinit.qa.convert(achieved_res['major'], 'rad')['value']
_bmin = taskinit.qa.convert(achieved_res['minor'], 'rad')['value']
_bpa = taskinit.qa.convert(achieved_res['positionangle'],
'deg')['value']
vres = "%.2f %s" % (velres['value'], velres['unit'])
logging.regression("SMOOTH: %f %f" % (rdata, velres['value']))
self._summary["smooth"] = SummaryEntry(
[bdp_name, convolve_to_min_beam, _bmaj, _bmin, _bpa, vres],
"Smooth_AT", self.id(True), taskargs)
dt.tag("done")
dt.end()
def run(self):
""" The run method creates the BDP
Parameters
----------
None
Returns
-------
None
"""
self._summary = {}
dt = utils.Dtime("Smooth")
dt.tag("start")
# get the input keys
bmaj = self.getkey("bmaj")
bmin = self.getkey("bmin")
bpa = self.getkey("bpa")
velres = self.getkey("velres")
# take care of potential issues in the unit strings
# @todo if not provided?
bmaj['unit'] = bmaj['unit'].lower()
bmin['unit'] = bmin['unit'].lower()
velres['unit'] = velres['unit'].lower()
taskargs = "bmaj=%s bmin=%s bpa=%s velres=%s" % (bmaj,bmin,bpa,velres)
bdpnames=[]
for ibdp in self._bdp_in:
istem = ibdp.getimagefile(bt.CASA)
image_in = ibdp.baseDir() + istem
bdp_name = self.mkext(istem,'sim')
image_out = self.dir(bdp_name)
taskinit.ia.open(image_in)
h = casa.imhead(image_in, mode='list')
pix_scale = np.abs(h['cdelt1'] * 206265.0) # pix scale in asec @todo QA ?
CC = 299792458.0 # speed of light @todo somewhere else [utils.c , but in km/s]
rest_freq = h['crval3']
# frequency pixel scale in km/s
vel_scale = np.abs(CC*h['cdelt3']/rest_freq/1000.0)
# unit conversion to arcsec (spatial) or km/s
# (velocity) or some flavor of Hz.
if(bmaj['unit'] == 'pixel'):
bmaj = bmaj['value']*pix_scale
else:
bmaj = bmaj['value']
if(bmin['unit'] == 'pixel'):
bmin = bmin['value']*pix_scale
else:
bmin = bmin['value']
hertz_input = False
if velres['unit'] == 'pixel':
velres['value'] = velres['value']*vel_scale
velres['unit'] = 'km/s'
elif velres['unit'] == 'm/s':
velres['value'] = velres['value']/1000.0
velres['unit'] = 'km/s'
elif velres['unit'][-2:] == 'hz':
hertz_input = True
elif velres['unit'] == 'km/s':
pass
else:
logging.error("Unknown units in velres=%s" % velres['unit'])
rdata = bmaj
# we smooth in velocity first. if smoothing in velocity
# the cube apparently must be closed afterwards and
# then reopened if spatial smoothing is to be done.
if velres['value'] > 0:
# handle the different units allowed. CASA doesn't
# like lowercase for hz units...
if not hertz_input:
freq_res = str(velres['value']*1000.0/CC *rest_freq )+'Hz'
else:
freq_res = str(velres['value'])
# try to convert velres to km/s for debug purposes
velres['value'] = velres['value']/rest_freq*CC / 1000.0
if(velres['unit'] == 'khz'):
velres['value'] = velres['value']*1000.0
velres['unit'] = 'kHz'
elif(velres['unit']=='mhz'):
velres['value'] = velres['value']*1E6
velres['unit'] = 'MHz'
elif(velres['unit']=='ghz'):
velres['value'] = velres['value']*1E9
velres['unit'] = 'GHz'
freq_res = freq_res + velres['unit']
# NB: there is apparently a bug in CASA. only smoothing along the frequency
# axis does not work. sepconvolve gives a unit error (says axis unit is radian rather
# than Hz). MUST smooth in 2+ dimensions if you want this to work.
if(velres['value'] < vel_scale):
raise Exception,"Desired velocity resolution %g less than pixel scale %g" % (velres['value'],vel_scale)
image_tmp = self.dir('tmp.smooth')
im2=taskinit.ia.sepconvolve(outfile=image_tmp,axes=[0,1,2], types=["boxcar","boxcar","gauss"],\
widths=['1pix','1pix',freq_res], overwrite=True)
im2.done()
logging.debug("sepconvolve to %s" % image_out)
# for some reason, doing this in memory does not seem to work, so outfile must be specified.
logging.info("Smoothing cube to a velocity resolution of %s km/s" % str(velres['value']))
logging.info("Smoothing cube to a frequency resolution of %s" % freq_res)
taskinit.ia.close()
taskinit.ia.open(image_tmp)
dt.tag("sepconvolve")
else:
image_tmp = image_out
# now do the spatial smoothing
convolve_to_min_beam = True # default is to convolve to a min enclosing beam
if bmaj > 0 and bmin > 0:
# form qa objects out of these so that casa can understand
bmaj = taskinit.qa.quantity(bmaj,'arcsec')
bmin = taskinit.qa.quantity(bmin,'arcsec')
bpa = taskinit.qa.quantity(bpa,'deg')
target_res={}
target_res['major'] = bmaj
target_res['minor'] = bmin
target_res['positionangle'] = bpa
# throw an exception if cannot be convolved
try:
# for whatever reason, if you give convolve2d a beam parameter,
# it complains ...
im2=taskinit.ia.convolve2d(outfile=image_out,major = bmaj,\
minor = bmin, pa = bpa,\
targetres=True,overwrite=True)
im2.done()
logging.info("Smoothing cube to a resolution of %s by %s at a PA of %s" %
(str(bmaj['value']), str(bmin['value']), str(bpa['value'])))
convolve_to_min_beam = False
achieved_res = target_res
except:
# @todo remind what you need ?
logging.error("Warning: Could not convolve to requested resolution of "\
+str(bmaj['value']) + " by " + str(bmin['value']) + \
" at a PA of "+ str(bpa['value']))
raise Exception,"Could not convolve to beam given!"
dt.tag("convolve2d-1")
if convolve_to_min_beam:
restoring_beams = taskinit.ia.restoringbeam()
commonbeam = taskinit.ia.commonbeam()
# for whatever reason, setrestoringbeam does not use the same set of hashes...
commonbeam['positionangle']=commonbeam['pa']
del commonbeam['pa']
# if there's one beam, apparently the beams keyword does not exist
if 'beams' in restoring_beams:
print "Smoothing cube to a resolution of "+ \
str(commonbeam['major']['value']) +" by "+ \
str(commonbeam['minor']['value'])+" at a PA of "\
+str(commonbeam['pa']['value'])
target_res = commonbeam
im2=taskinit.ia.convolve2d(outfile=image_out,major=commonbeam['major'],\
minor=commonbeam['minor'],\
pa=commonbeam['positionangle'],\
targetres=True,overwrite=True)
im2.done()
achieved_res = commonbeam
dt.tag("convolve2d-2")
else:
print "One beam for all planes. Smoothing to common beam redundant."
achieved_res = commonbeam
if velres['value'] < 0:
taskinit.ia.fromimage(outfile=image_out, infile=image_in)
# not really doing anything
# else, we've already done what we needed to
taskinit.ia.setrestoringbeam(beam = achieved_res)
rdata = achieved_res['major']['value']
# else do no smoothing and just close the image
taskinit.ia.close()
dt.tag("close")
b1 = SpwCube_BDP(bdp_name)
self.addoutput(b1)
# need to update for multiple images.
b1.setkey("image", Image(images={bt.CASA:bdp_name}))
bdpnames = bdpnames.append(bdp_name)
# and clean up the temp image before the next image
if velres['value'] > 0:
utils.remove(image_tmp)
# thes are task arguments not summary entries.
_bmaj = taskinit.qa.convert(achieved_res['major'],'rad')['value']
_bmin = taskinit.qa.convert(achieved_res['minor'],'rad')['value']
_bpa = taskinit.qa.convert(achieved_res['positionangle'],'deg')['value']
vres = "%.2f %s" % (velres['value'],velres['unit'])
logging.regression("SMOOTH: %f %f" % (rdata,velres['value']))
self._summary["smooth"] = SummaryEntry([bdp_name,convolve_to_min_beam,_bmaj,_bmin,_bpa,vres],"Smooth_AT",self.id(True),taskargs)
dt.tag("done")
dt.end()
