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()