def collate(configOpts, fluxtable, hidata, dd0, sdd0, rhoHI, srho, G0, contr):
print "Re-organizing & tabulating ..."
print "PDRID, RA, DEC, pRA, pDEC, NHI, sNHI, dd0, sdd0, rhoHI, srho, net flux, sflux, mean_at_r, ntot, sntot"
data = [[] for dummy in range(20)]
data_full = configOpts['data_full']
ntot = np.zeros(np.size(hidata.PDRID))
sntot = np.zeros(np.size(hidata.PDRID))
#Add ntot and sntot for later
with open(data_full, 'w') as fullfile: #no close file needed this way
for i in range(np.size(hidata.PDRID)):
#There can be no duplicate PDRIDs in fluxtable or this will yield incorrect results
#for legibility:
uv_idx = np.where(fluxtable.PDRID == hidata.PDRID[i])[0][0] #expect only one value - problem if there are more HI PDRIDs than UV PDRIDs
#hack: 'g' does not take [number] so have to convert again with [0]. Need to 'fix' fluxtable. Same problem with G0
#print "{0:>3}, {1:12s}, {2:12s}, {3:8g}, {4:6g}, {5:.3f}, {6:f}, {7:.3f}, {8:.3f}, {9:g}, {10:.3g}, {11:g}".format(hidata.PDRID[i], fluxtable.RA[uv_idx], fluxtable.DEC[uv_idx], hidata.NHI[i], hidata.sNHI[i], dd0[i], sdd0[i], rhoHI[i], srho[i], fluxtable.netflux[uv_idx], fluxtable.sflux[uv_idx], fluxtable.mean_at_r[uv_idx])
#Patch RAs, DECs not written here
#fullfile.write("{0:>3}, {1:12s}, {2:12s}, {3:8g}, {4:6g}, {5:.3f}, {6:f}, {7:.3f}, {8:.3f}, {9:g}, {10:.3g}, {11:g}\n".format(hidata.PDRID[i], fluxtable.RA[uv_idx], fluxtable.DEC[uv_idx], hidata.NHI[i], hidata.sNHI[i], dd0[i], sdd0[i], rhoHI[i], srho[i], fluxtable.netflux[uv_idx], fluxtable.sflux[uv_idx], fluxtable.mean_at_r[uv_idx]))
#Fedora bug: need to type cast the variables
fullfile.write("{0:>3}, {1:12s}, {2:12s}, {3:8g}, {4:6g}, {5:.3f}, {6:f}, {7:.3f}, {8:.3f}, {9:g}, {10:.3g}, {11:g}\n".format(
int(hidata.PDRID[i]),
fluxtable.RA[uv_idx], fluxtable.DEC[uv_idx],
hidata.NHI[i], hidata.sNHI[i],
dd0[i], sdd0[i], rhoHI[i], srho[i],
fluxtable.netflux[uv_idx], fluxtable.sflux[uv_idx],
fluxtable.mean_at_r[uv_idx]))
for m, n in enumerate((hidata.PDRID[i], fluxtable.RA[uv_idx], fluxtable.DEC[uv_idx], hidata.RA[i], hidata.DEC[i], Rgal[uv_idx], hidata.NHI[i], hidata.sNHI[i], dd0[i], sdd0[i], rhoHI[i], srho[i], fluxtable.netflux[uv_idx], fluxtable.sflux[uv_idx], fluxtable.mean_at_r[uv_idx], fluxtable.aperture[uv_idx], G0[i], contr[i], ntot[i], sntot[i])):
#print m, n
data[m].append(n)
labels = 'PDRID, RA, DEC, pRA, pDEC, Rgal, NHI, sNHI, dd0, sdd0, rhoHI, srho, flux, sflux, mean_at_r, aperture, G0, contr, ntot, sntot'
data = pdr.records(data, labels) #transform into rec.array
#print data #instead of the print earlier, for testing
print "Wrote to file {0}".format(data_full)
print "... done"
print
return data
def getHI(configOpts, fluxtable):
print "Identifying HI patches ..."
data_hi = configOpts['data_hi']
hiImage = configOpts['hiImage']
hi_baselist = "{0}_Regions/{0}_Reg".format(os.path.splitext(hiImage)[0])
hi_logsbase = "{0}_Regions/{1}".format(os.path.splitext(hiImage)[0], configOpts['hi_logsbase'])
try:
dummy = file(data_hi, 'r')
print "... HI patch data read from file {0}".format(data_hi)
#Read: HI data (if already there); note that if the read fails, patches will be re-measured also
columns = np.dtype([('PDRID', 'int',), ('RA', '|S14'), ('DEC', '|S14'), ('NHI', 'float'), ('sNHI', 'float')])
hidata = pdr.read_array(data_hi, columns)
print " {0} records read".format(np.size(hidata))
#Very simple and incomplete check for enough data:
if (np.size(np.unique(hidata.PDRID)) != np.size(np.unique(fluxtable.PDRID))):
print "Fatal error: number of UV and HI PDRIDs do not match. Try regenerating the HI files."
exit(0)
except:
#File does not exist, so process HI postage stamp regions.
#Must have regions with names matching the PDRIDs
scale = configOpts['HIscale'] # 2.896e19 for NGC 628 (m?)Jy/beam to cm-2
hi_bg = configOpts['hiBackground']
print "Using map scaling of {0} cm-2".format(scale)
hiresults = [[] for dummy in xrange(5)] #PDRID, ra, dec, NHI, sNHI
#Warning: up to 999 files
for i in range(np.size(fluxtable.PDRID)):
fitsfile = hi_baselist + "{0:03d}.fits".format(int(fluxtable.PDRID[i]))
print "Calling SExtractor with file {0}".format(fitsfile)
catfile = pdr.call_SEx(fitsfile)
if catfile==1:
print "Fatal error: SExtractor call failed."
exit(0)
else:
logfile = hi_logsbase + "{0:03}.txt".format(int(fluxtable.PDRID[i]))
patches = pdr.read_secat(catfile, fitsfile, logfile, wcs=True)
#Patches are not background-subtracted, that will happen now:
for n in range(len(patches[0])):
if patches[2][n] > (hi_bg*2.):
#subtract the background and ignore patches that are fainter than hi_bg
hiresults[0].append(fluxtable.PDRID[i])
hiresults[1].append(patches[0][n])
hiresults[2].append(patches[1][n])
hiresults[3].append((patches[2][n]-hi_bg)*scale)
hiresults[4].append(hi_bg * scale * 0.5) #fix sN_HI to half the background value
else:
print "Patch too faint: ", patches[2][n]
if not np.size(np.where(hiresults[0] == fluxtable.PDRID[i])):
print "No suitable patches were found for PDRID ", fluxtable.PDRID[i], "; creating empty entry."
#With SExtractor, this is unlikely since it does not pick up the faintest patches
hiresults[0].append(fluxtable.PDRID[i])
hiresults[1].append(0)
hiresults[2].append(0)
hiresults[3].append(0)
hiresults[4].append(0)
#End for
#Finally, convert the results into a rec array and save the results
labels = 'PDRID, RA, DEC, NHI, sNHI'
hidata = pdr.records(hiresults, labels)
#Write: HI patches
hifile = fancyPrint(writeLog=True, logFile=data_hi, verbose=True)
print "HI patches:"
#print "#PDRID, RA, DEC, NHI, sNHI"
hifile.write("#PDRID, RA, DEC, NHI, sNHI\n")
for n in range(len(hidata)):
#print type(hidata[n].NHI)
#Apparently python 2.6 needs explicit conversion from numpy.float32, so workaround
#fedora bug: changed PDRID:>3 to PDRID:3g
#print "{0.PDRID:3g}, {0.RA:14s}, {0.DEC:14s}, {1:7.5g}, {2:7.5g}".format(hidata[n], float(hidata[n].NHI), float(hidata[n].sNHI))
hifile.write("{0.PDRID:3g}, {0.RA:14s}, {0.DEC:14s}, {1:7.5g}, {2:7.5g}\n".format(hidata[n], float(hidata[n].NHI), float(hidata[n].sNHI)))
#hifile.close()
#End of try/except
print
return hidata
