def run(self):
"""Make the multicolor catalog."""
# define the zero point error
zpoint_err = 0.01
self.logfile.write('Processing catalogs...')
detection_variables = tableio.get_data(self.detCatalog,self.detectionColumns)
nsources = len(detection_variables[0])
ncats = len(self.catalogList)
#Create a series of arrays to keep the relevant data
flux = Numeric.zeros((ncats,nsources))*1.0 # ISO flux ... for now.
fluxerr = Numeric.zeros((ncats,nsources))*1.0 # ISO flux error... for now.
m = Numeric.zeros((ncats,nsources))*1.0 # MAG_ISO
em = Numeric.zeros((ncats,nsources))*1.0 # MAGERR_ISO
m_corr = Numeric.zeros((ncats,nsources))*1.0 # extinction corrected magnitude
em_corr = Numeric.zeros((ncats,nsources))*1.0 # extinction corrected magnitude error
ap_corr = Numeric.zeros((ncats,nsources))*1.0 # aperture correction
m_bpz = Numeric.zeros((ncats,nsources))*1.0 # MAG_BPZ extinction/aperture corrected
em_bpz = Numeric.zeros((ncats,nsources))*1.0 # MAGERR_BPZ extinction/aperture corrected
preds = [os.path.basename(self.detCatalog)]
# this is a list of those indices of the catalogList which raised the filterError exception
# i think i need to know this, but i'm not sure why yet....
self.badcats = []
for i in range(ncats):
selectSet = {}
pardict = {}
imname = os.path.splitext(self.catalogList[i])[0]
basefits= imname + '.fits'
fitsfile= os.path.join(self.obsFits,basefits)
detector= fUtil.getDetector(fitsfile)
try:
imfilter= fUtil.filterResponseName(fitsfile)
except fUtil.filterError:
self.badcats.append(i)
imfilter = fUtil.twoFilterName(fitsfile)
try:
filterXCorr = extinction.filterFactor(imfilter) * self.eBV
filterXCorrError = filterXCorr*0.16
except fUtil.filterError,err:
self.errorList.append(("extintion.py","filterError: "+str(err)))
self.logfile.write("filterError: "+str(err))
filterXCorr = 0.0
filterXCorrError = 0.0
try:
filter = fUtil.filterName(fitsfile)
ap_corr[i,:] = self._apcorr(detector,filter)
except KeyError,err:
print str(err)
self.logfile.write(str(err))
# if we can't do it, well, we can't do it.
pass
def bandcounts(self):
"""Count the filter number in band (['opt','nir','red','uv']) .
"""
# pdb.set_trace()
for fitsfile in self.sciImageList:
# Use user-defined detector for the detection image
det = fUtil.getDetector(os.path.join(self.obsFits, fitsfile))
if det == self.det:
if (self.band == 'red'):
if string.find(fitsfile, '160') > -1 or string.find(
fitsfile, '140') > -1:
yes = 1
self.bandlist.append(fitsfile)
else:
print 'Not including ' + fitsfile + ' in detection image.'
yes = 0
else:
yes = 1
self.bandlist.append(fitsfile)
else:
print 'Not including ' + fitsfile + ' in detection image.'
yes = 0
print len(self.bandlist), ' filters are detected under ' + self.band
print self.bandlist
def getStats(self,Band):
"""Runs SExtractor with phoney pars to get noise and background stats.
Now implement this using the Popen4 class, which sends both stdout
and stderr to the fromchild file object. We suppress stdout from
SExtractor by shunting stuff to /dev/null via the par file, so we
will only get stderr anyway, at least, in theory. The Popen3 class
or rather, the factory function is uses, popen3, has proved
to be buggy at times, so this is an attempt to move away from it.
"""
self.logfile.write('Generating background and noise statistics for fits images')
self.statsList = []
# pdb.set_trace()
for fitsfile in self.sciImageList:
# Use user-defined detector for the detection image
det = fUtil.getDetector(os.path.join(self.obsFits,fitsfile))
if det == self.det:
if (Band =='red'):
if string.find(fitsfile,'160') > -1 or string.find(fitsfile,'140') > -1:
yes = 1
else:
self.logfile.write('Not including '+fitsfile+' in detection image.')
yes = 0
else:
yes = 1
else:
self.logfile.write('Not including '+fitsfile+' in detection image.')
yes = 0
if self.excludeFilters:
# pass on user excluded filters for the detection image
filt = fUtil.getFilter2(os.path.join(self.obsFits,fitsfile))
if filt in self.excludeFilters:
self.logfile.write('User requested exclude filter found in data.')
self.logfile.write('Not including'+filt+' in detection image.')
yes = 0
if (yes == 1):
self.logfile.write('running SExtractor on ' + fitsfile)
cmd = 'sex ' + os.path.join(self.obsFits, fitsfile) + ' -c ' + self.inParFileName
subproc = popen2.Popen4(cmd)
lines = subproc.fromchild.readlines()
self.logfile.write('logging background and noise stats.')
for line in lines:
if string.find(line,'(M+D) Background:') != -1:
# pdb.set_trace()
linef = string.split(line)
self.logfile.write(fitsfile+': '+linef[1]+linef[2]+' '+linef[3]+linef[4])
self.statsList.append((fitsfile,linef[2],linef[4])) # linef[2] is background, linef[4] is noise. ############ attention here by XX
elif string.find(line,'*ERROR*') != -1:
self.errorList.append((self.modName,line))
self.logfile.write('Error in running SExtractor: '+ line)
return
def xmlStartCat(outfile, name, imgfile=None):
"""Initialise the xml header of a catalog file. imgfile is a passed fits file.
"""
xmlcatalog = open(outfile, 'w+')
xmlcatalog.write(
"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n")
xmlcatalog.write('<!DOCTYPE catalog SYSTEM ' +\
'\n\t"http://acs.pha.jhu.edu/science/pipeline/DTD/Catalog.dtd">\n')
if imgfile == None:
xmlcatalog.write("<catalog type=\"xml/text\" dataset=\"" + name +
"\" date=\"" + ptime() + "\">\n")
else:
img = os.path.basename(imgfile)
tel = fUtil.getTel(imgfile)
inst = fUtil.getInstr(imgfile)
det = fUtil.getDetector(imgfile)
filter1 = fUtil.getFilter1(imgfile)
filter2 = fUtil.getFilter2(imgfile)
acs = filters.ACSFilterInfo()
if filter1 and filter2:
if filter1 not in acs.clear and filter2 not in acs.clear:
xmlcatalog.write("<catalog type=\"xml/text\" imgsrc=\"" +img+ \
"\" dataset=\""+name+"\" telescope=\"" +tel+ \
"\" instrument=\""+inst+"\" detector=\"" +det+\
"\" filtername=\""+filter1+"/"+filter2+"\" date=\""+ptime()+"\">\n")
elif filter1 in acs.clear:
xmlcatalog.write("<catalog type=\"xml/text\" imgsrc=\"" +img+ \
"\" dataset=\""+name+"\" telescope=\"" +tel+ \
"\" instrument=\""+inst+"\" detector=\"" +det+\
"\" filtername=\""+filter2+"\" date=\""+ptime()+"\">\n")
elif filter2 in acs.clear:
xmlcatalog.write("<catalog type=\"xml/text\" imgsrc=\"" +img+ \
"\" dataset=\""+name+"\" telescope=\"" +tel+ \
"\" instrument=\""+inst+"\" detector=\"" +det+\
"\" filtername=\""+filter1+"\" date=\""+ptime()+"\">\n")
else:
print "No filters found in image:", img, "for markup."
xmlcatalog.write("<catalog type=\"xml/text\" dataset=\""+name+"\" imgsrc=\"" \
+img+ "\" date=\""+ptime()+"\">\n")
xmlcatalog.close()
return
def run(self, band):
"""Make the multicolor catalog."""
# define the zero point error
zpoint_err = 0.01
self.logfile.write('Processing catalogs...')
detection_variables = tableio.get_data(self.detCatalog,
self.detectionColumns)
nsources = len(detection_variables[0])
# WZ Should be a dimension check here with the filter catalogs before crashing
ncats = len(self.catalogList)
#Create a series of arrays to keep the relevant data
flux = Numeric.zeros((ncats, nsources)) * 1.0 # ISO flux ... for now.
fluxerr = Numeric.zeros(
(ncats, nsources)) * 1.0 # ISO flux error... for now.
m = Numeric.zeros((ncats, nsources)) * 1.0 # MAG_ISO
em = Numeric.zeros((ncats, nsources)) * 1.0 # MAGERR_ISO
m_corr = Numeric.zeros(
(ncats, nsources)) * 1.0 # extinction corrected magnitude
em_corr = Numeric.zeros(
(ncats, nsources)) * 1.0 # extinction corrected magnitude error
ap_corr = Numeric.zeros(
(ncats, nsources)) * 1.0 # aperture correction
m_bpz = Numeric.zeros(
(ncats,
nsources)) * 1.0 # MAG_BPZ extinction/aperture corrected
em_bpz = Numeric.zeros(
(ncats,
nsources)) * 1.0 # MAGERR_BPZ extinction/aperture corrected
preds = [os.path.basename(self.detCatalog)]
# this is a list of those indices of the catalogList which raised the filterError exception
# i think i need to know this, but i'm not sure why yet....
self.badcats = []
for i in range(ncats):
selectSet = {}
pardict = {}
imname = os.path.splitext(self.catalogList[i])[0]
j = string.rfind(imname, '_')
basefits = imname[0:j] + '_sci.fits'
fitsfile = os.path.join(self.obsFits, basefits)
detector = fUtil.getDetector(fitsfile)
try:
imfilter = fUtil.filterResponseName(fitsfile)
except fUtil.filterError:
self.badcats.append(i)
imfilter = fUtil.twoFilterName(fitsfile)
try:
filterXCorr = extinction.filterFactor(imfilter) * self.eBV
filterXCorrError = filterXCorr * 0.16
except fUtil.filterError, err:
self.errorList.append(
("extintion.py", "filterError: " + str(err)))
self.logfile.write("filterError: " + str(err))
filterXCorr = 0.0
filterXCorrError = 0.0
try:
f = pyfits.open(fitsfile) # WZ
instr = f[0].header.get('INSTRUME')
f.close()
del f
if instr == 'ACS':
#filter = 'F814W' #WZ
filter = fUtil.filterNameACS(fitsfile)
elif instr == 'WFC3':
#filter = fUtil.filterName(fitsfile)
filter = fUtil.filterNameWFC3(fitsfile)
if filter:
print "Find filter ", filter
else:
raise filterError, "No filter found for fits image: " + fitsfile
#filter = fUtil.filterName(fitsfile)
ap_corr[i, :] = self._apcorr(detector, filter)
except KeyError, err:
print str(err)
self.logfile.write(str(err))
# if we can't do it, well, we can't do it.
pass