def __getFluxUnits(self, config):
try:
options = [astun.Jy, astun.mJy, astun.uJy]
if uf.checkkeys(config, 'SpectrumFluxUnit'):
choice = config['SpectrumFluxUnit']
else:
print ("\nWhat are the flux denisty units of your spectra?\n\t1. Jansky (Jy)\n\t2. Milli Jansky (mJy)\n\t3. Micro Jansky (uJy)\n\t4. Jansky/beam (Jy/beam)\n\t5. Milli Jansky/beam (mJy/beam)\n\t6. Micro Jansky/beam (uJy/beam)")
choice = input('Please enter the number of the applicable units: ')
if type(choice) != int:
print ('Please only select one unit.')
self.__getFluxUnits(None)
elif choice in [1,2,3]:
self.fluxunit = options[int(choice-1)]
self.convfactor = 1
else:
self.fluxunit = options[int(choice-4)]
if uf.checkkeys(config, 'BeamSize') and uf.checkkeys(config, 'PixelSize'):
pxsize = config['PixelSize']
beamsize = config['BeamSize']
else:
pxsize = input('Please enter pixel size in arcseconds: ')
beamsize = input('Please enter fwhm of beam (in arcseconds): ')
self.convfactor = ( 2.*np.pi*beamsize*beamsize/( 2.*np.sqrt(2.*np.log(2) ) )**2 )/pxsize**2
except KeyboardInterrupt:
raise KeyboardInterrupt
except SystemExit:
uf.exit(self)
except:
logger.error('There was an input error with your unit selection', exc_info=True)
uf.earlyexit(self)
return
def __getSpectralUnits(self, config):
try:
if uf.checkkeys(config, 'SpectralAxisUnit') and uf.checkkeys(
config, 'VelocityType'):
choice = config['SpectralAxisUnit']
self.veltype = config['VelocityType']
else:
print(
"\nWhat are the units of spectral axis of your spectra?\n\t1. Hertz (Hz)\n\t2. Kilo Hertz (kHz)\n\t3. Mega Hertz (MHz)\n\t4. Metres/Second (m/s)\n\t5. Kilometres/Second (km/s)\n\t6. Radio velocity (km/s)"
)
choice = input(
'Please enter the number of the applicable units: ')
if int(choice) in [4, 5]:
self.veltype = input(
'Please enter the velocity type [optical/radio]: '
).lower()
options = [
astun.Hz, astun.kHz, astun.MHz, astun.m / astun.s,
astun.km / astun.s
]
self.spectralunit = options[int(choice) - 1]
except KeyboardInterrupt:
raise KeyboardInterrupt
except SystemExit:
uf.exit(self)
except:
logger.error('There was an input error with your unit selection.',
exc_info=True)
uf.earlyexit(self)
return
def __getClusterStack(self, config):
try:
vals = {'t': True, 'f': False}
if uf.checkkeys(config, 'ClusterStack'):
val = config['ClusterStack']
val = val[0].lower()
self.cluster = vals[val]
else:
val = input('Are you stacking a galaxy cluster [True/False]: ')
val = val.lower()
self.cluster = vals[val]
if self.cluster == True:
if uf.checkkeys(config, 'ClusterRedshift'):
val = config['ClusterRedshift']
if type(val) != float:
val = eval(val)
else: pass
self.clusterZ = val
else:
val = eval(input('Enter the cluster redshift: '))
self.clusterZ = val
self.clusterDL = self.cosmology.luminosity_distance(self.clusterZ)
logger.info('Stacking galaxy cluster at z = %.4f (Dl = %.1f Mpc)'%(self.clusterZ, self.clusterDL.value))
else:
logger.info('No galaxy cluster in this sample.')
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
raise uf.exit(self)
except:
logger.error("Did not understand if there is a galaxy cluster in this sample.", exc_info=True)
uf.earlyexit(self)
def __getCosmology(self, config):
try:
if uf.checkkeys(config, 'H0') and uf.checkkeys(config, 'Om0'):
H0 = config['H0']
Om0 = config['Om0']
else:
print('\nWe assume a Flat Lambda CDM universe')
H0 = input(
'Please enter the Hubble constant (H0) in units of km/s/Mpc: '
)
Om0 = input('Please enter the Omega matter (Om0): ')
self.cosmology = astcos.FlatLambdaCDM(H0, Om0)
logger.info(
'Cosmology: H0 = %.1f %s, Om0 = %.3f' %
(self.cosmology.H0.value, self.cosmology.H0.unit.to_string(),
self.cosmology.Om0))
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
raise uf.exit(self)
except:
logger.error('There was a problem with entering the cosmology.',
exc_info=True)
uf.earlyexit(self)
return
def determineBins(self, config):
if self.config == True:
self.fullfuncnum = config['FittedFunctionNumbers']
self.fulloptnum = config['AnalysisOptions']
self.fullsmoothtype = config['SmoothType']
self.fullsmoothwin = config['SmoothWindow']
self.fullmaxgalw = config['IntegrateGalaxyWidth']
self.fullrebinstatus = config['SmoothStatus']
else:
pass
if uf.checkkeys(config, 'BinInfo') and uf.checkkeys(config, 'Bins'):
colname, binwidth, binstart, binend = config["BinInfo"]
self.bins = config['Bins']
self.binnedtable, self.binpartindicies = self.__bintable(self.fullcatalogue, colname, binwidth, binstart, binend)
return
else:
print ('\n%s\t%s\t%s\t%s\t%s\n'%(self.fullcatalogue.colnames[0], self.fullcatalogue.colnames[1], self.fullcatalogue.colnames[2], self.fullcatalogue.colnames[3], self.fullcatalogue.colnames[4]))
colname = raw_input('Please enter the exact Column name for the column containing the data to be binned: ')
binwidth = input('Please enter the bin width (in same units as the data to be binned): ')
binstart = input('Please enter the start of the bin range (in same units as the data to be binned): ')
binend = input('Please enter the end of the bin range (in same units as the data to be binned): ')
self.binnedtable, self.binpartindicies = self.__bintable(self.fullcatalogue, colname, binwidth, binstart, binend)
return
def __getMaxLenSpectrum(self, config):
try:
if uf.checkkeys(config, 'StackedSpectrumLength'):
maxstackw = config['StackedSpectrumLength'] * astun.km / astun.s
else:
maxstackw = input(
'Please enter the maximum length of the stacked spectrum in km/s: '
) * astun.km / astun.s
if maxstackw < 2.5 * self.maxgalw:
print(
'The stacked spectrum length is too short - we will not be able to have very good noise calculations, etc. Please try again.\n'
)
self.__getMaxLenSpectrum(config=None)
else:
self.maxstackw = maxstackw
logger.info(
'Length of stacked spectrum: %i %s' %
(self.maxstackw.value, self.maxstackw.unit.to_string()))
except (KeyboardInterrupt, SystemExit):
uf.exit(self)
except:
logger.error(
'Could not determine the maximum length of the stacked spectrum.',
exc_info=True)
uf.earlyexit(self)
def __getStackUnits(self, config):
try:
if uf.checkkeys(config, 'StackFluxUnit'):
choice = config['StackFluxUnit']
else:
print(
"\nWhat units do you want your final stacked profile to have?\n\t1. Jansky (Jy)\n\t2. Solar Masses (Msun)\n\t3. Gas Fraction (Msun/Msun)\n\t4. Solar Masses (Msun), stack in Jy [recommend for clusters]"
)
choice = eval(
input('Please enter the number of the applicable units: '))
print(type(choice))
if (type(choice) != int):
print('Please only select one unit.')
self.__getStackUnits(None)
else:
options = [astun.Jy, uf.msun, uf.gasfrac, astun.Jy]
self.stackunit = options[int(choice - 1)]
if choice == 4:
self.cluster = True
else:
pass
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
raise uf.exit(self)
except:
logger.error('There was an input error with your unit selection.',
exc_info=True)
uf.earlyexit(self)
return
def __getWeightingScheme(self, config):
try:
if uf.checkkeys(config, 'WeightOption'):
self.weighting = str(config['WeightOption'])
else:
print(
'\nThe following are options can be used to weight each spectrum:\n\t1. w = 1. [default]\n\t2. w = 1/rms \n\t3. w = 1/rms^2 \n\t4. w = dl^2/rms^2'
)
## TODO: add in option for individual weights from catalogue as well as custom weighting function
weights = input(
'Please enter the number of the scheme you would like to use: '
)
self.weighting = weights[0]
wghts = {
'1': 'w = 1',
'2': 'w = 1/rms',
'3': 'w = 1/rms^2',
'4': 'w = dl^2/rms^2'
}
logger.info('Weighting factor: %s' % wghts[self.weighting])
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
raise uf.exit(self)
except:
logger.error('Could not identify the weighting scheme.',
exc_info=True)
uf.earlyexit(self)
def __getSpectraLocation(self, config):
try:
if uf.checkkeys(config, 'SpectrumLocation'):
self.specloc = config['SpectrumLocation']
else:
self.specloc = input(
'Please enter the full path of the spectra location: ')
if self.specloc[-1] != '/':
self.specloc += '/'
else:
h = 0
if not os.path.exists(self.specloc):
print(
'\nThe spectrum location you have entered does not exist. Please try again.\n'
)
self.__getSpectraLocation(config=None)
else:
print('\nThe spectrum location exists :).\n')
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
uf.exit(self)
except:
logger.error(
'There was an issue with the entered spectrum folder path.',
exc_info=True)
uf.earlyexit(self)
def __checkConfig(self, config): if uf.checkkeys(config, 'IntegrateGalaxyWidth'): intwid = True self.maxgalw = config['IntegrateGalaxyWidth']*astun.km/astun.s else: intwid = False if uf.checkkeys(config, 'SmoothStatus'): self.rebinstatus = config['SmoothStatus'] rebin = True else: rebin = False if uf.checkkeys(config, 'SmoothType'): self.smoothtype = config['SmoothType'] else: pass if uf.checkkeys(config, 'SmoothWindow'): self.smoothwin = config['SmoothWindow'] else: pass if uf.checkkeys(config, 'FittedFunctionNumbers'): self.funcnum = config['FittedFunctionNumbers'] else: pass if uf.checkkeys(config, 'AnalysisOptions'): self.optnum = config['AnalysisOptions'] else: pass if (intwid == True) and (rebin == True): self.config = True else: self.config = False return
def __getSpectrumDelimiter(self, config):
try:
if uf.checkkeys(config, 'RowDelimiter'):
self.rowdelim = config['RowDelimiter']
else:
self.rowdelim = input('Please enter the delimiter used in the spectra files (this must be the same for all spectra): ')
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
uf.exit(self)
except:
logger.error('There was an error with the row delimiter.', exc_info=True)
uf.earlyexit(self)
def __getMaxRedshift(self, config):
try:
if uf.checkkeys(config, 'z_max'):
self.max_redshift = config["z_max"]
else:
self.max_redshift = input('\nPlease enter the maximum redshift value of your sample: ')
except KeyboardInterrupt:
uf.earlyexit(self)
except SystemExit:
uf.exit(self)
except:
logger.critical("There was an error with the maximum redshift value.", exc_info=True)
uf.earlyexit(self)
def __getChannelWidth(self, config):
try:
if uf.checkkeys(config, 'ChannelWidth'):
self.channelwidth = config['ChannelWidth'] * self.spectralunit
else:
self.channelwidth = input('Please enter the channel width (in the same units as the spectral axis): ') * self.spectralunit
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
uf.exit(self)
except:
logger.error('There was an input error with your channel width.', exc_info=True)
uf.earlyexit(self)
def __getMaxGalaxyWidth(self, config):
try:
if uf.checkkeys(config, 'GalaxyWidth'):
self.maxgalw = config['GalaxyWidth'] * astun.km/astun.s
else:
self.maxgalw = input('Enter maximum galaxy width in km/s: ') * astun.km/astun.s
logger.info('Maximum galaxy width = %i %s'%(self.maxgalw.value, self.maxgalw.unit.to_string()))
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
raise uf.exit(self)
except:
logger.error("Did not understand the maximum galaxy width.", exc_info=True)
uf.earlyexit(self)
def __getSpectrumRowStart(self, config):
try:
if uf.checkkeys(config, 'FirstRowInSpectrum'):
self.rowstart = int(config['FirstRowInSpectrum'])
else:
self.rowstart = input('Please enter the row number corresponding to the start of the data in the spectrum files (this number should be the same for every spectrum file).\n(Please note: row numbering starts at 1 - the first row of information is row 1): ')
self.rowstart = int(self.rowstart)
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
uf.exit(self)
except:
logger.error('There was an error with the number of the first row in the spectrum files.', exc_info=True)
uf.earlyexit(self)
def __getUncertType(self, config):
try:
if uf.checkkeys(config, 'UncertaintyMethod'):
self.uncerttype = config['UncertaintyMethod']
else:
untyp = input('Which method of redshift uncertainties should I use? [dagjk/redshift] ')
uncertop = { 'r': 'redshift', 'd': 'dagjk' }
self.uncerttype = uncertop[(untyp.lower())[0]]
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
raise uf.exit(self)
except:
logger.error('There was a problem determining whether or not to perform an uncertainty analysis', exc_info=True)
uf.earlyexit(self)
def __getSpectrumColumns(self, config):
try:
if uf.checkkeys(config, 'SpectrumColumns'):
self.speccol = config['SpectrumColumns']
else:
self.speccol = input("Please enter the column numbers of the spectral axis and flux (the column number of the first column is 0).\nThe numbers should be separated by a ',' e.g. 0,1: ")
if len(self.speccol) != 2:
print ('You need to enter two column numbers. Please try again.\n')
self.__getSpectrumColumns(config=False, data=None)
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit():
raise uf.exit(self)
except:
logger.error('There was an error with the spectrum column numbers.', exc_info=True)
uf.earlyexit(self)
def __getUncertAn(self, config):
try:
if uf.checkkeys(config, 'UncertaintyYN'):
self.uncert = config['UncertaintyYN']
else:
self.uncert = input('Should I calculate uncertainties? ')
if self.uncert.lower() == 'n':
self.mc = 1
else:
self.mc = self.mc
except KeyboardInterrupt:
raise uf.exit(self)
except SystemExit:
raise uf.exit(self)
except:
logger.error('There was a problem determining whether or not to perform an uncertainty analysis.')
uf.earlyexit(self)
def __getOutputLocation(self, config):
try:
if uf.checkkeys(config, 'OutputLocation'):
self.outloc = config['OutputLocation']
else:
self.outloc = input('Enter the full location to where you would like the output saved: ')
if self.outloc[-1] != '/':
self.outloc +='/'
uf.checkpath(self.outloc)
else:
uf.checkpath(self.outloc)
logger.info('Output location: %s'%self.outloc)
except KeyboardInterrupt:
uf.exit(self)
except SystemExit:
uf.exit(self)
except:
print ('There was a problem with entering the output location. Please try again.\n')
self.__getOutputLocation(config=False, data=None)
def pipeline(cat, config, data, binstatus, binno=None, mccount=0):
disp, spectrum, stackspectrum, analysis, analysisfinal = None, None, None, None, None
fig, ax1, ax2, ax3, ax4 = startfigure(cat)
if cat.progress == 'progress':
plt.show(block=False)
else:
pass
## creating the stack objects
xs = cat.spectralaxis.value[0]
xe = cat.spectralaxis.value[-1]
if uf.checkkeys(data, 'StackEntireCatalogueYN'):
stacknoYN = data['StackEntireCatalogueYN']
else:
stacknoYN = raw_input(
'Do you want to stack your entire catalogue? [y/n] ')
if stacknoYN.lower() == 'y':
stackobj = len(cat.catalogue)
else:
if uf.checkkeys(data, 'NumberCatalogueObjects'):
stackobj = int(data['NumberCatalogueObjects'])
else:
stackobj = None
while type(stackobj) != int:
stackobj = int(
input(
'Please enter the number of profiles you want to stack: '
))
if stackobj > cat.numcatspec:
stackobj = len(cat.catalogue)
else:
h = 0
logging.info('Number of objects going into the stack: %i' % stackobj)
if cat.uncert == 'y' and mccount == 0:
if binstatus == 'bin':
print('\nProgress of first round of Bin %i: ' % binno)
logging.info('Starting first round of Bin %i.' % binno)
else:
print('\nProgress of first round: ')
logging.info('Starting stacking first round.')
elif cat.uncert == 'n':
if binstatus == 'bin':
print('\nStacking progress of Bin %i: ' % binno)
logging.info('Starting stacking of Bin %i.' % binno)
else:
print('\nStacking progress: ')
logging.info('Starting stacking.')
else:
h = 0
pbar = ''
if ((mccount == 0) or ((mccount == 1)) and (binstatus == 'bin')):
cat, analysisfinal = stackeverything(pbar, cat, stackobj, binstatus,
'firstcall', binno, mccount, fig,
ax1, ax2, ax3, ax4)
else:
h = 0
if mccount == 0 and cat.uncert == 'y' and binstatus == 'bin':
logging.info('Finished stacking first round of Bin %i.' % binno)
return cat
else:
disp = DD.dispData(cat)
mccount += 1
if cat.uncert == 'y':
if binstatus == 'bin':
print('\n\nUncertainty calculations of Bin %i in progress:' %
binno)
else:
print('\n\nUncertainty calculations in progress:')
pbar = ''
if cat.multiop == 'multi':
results = []
cpu_count = int(multi.cpu_count() / 2)
logging.info(
'Spawning %i processes to run uncertainty calculations.' %
cpu_count)
pool = multi.Pool(processes=cpu_count, maxtasksperchild=1)
else:
h = 0
analysisempty = UA.uncertAnalysis(cat,
analysisfinal,
allspec=[],
allnoise=[],
allrms=[],
middle=[],
allintflux=np.array([[], [], [],
[], [], [],
[], []]))
mccount = 1
suppress = cat.suppress
cat.suppress = 'hide'
fullcatfile = cat.catalogue
logging.info('Starting uncertainty calculations...')
while mccount < (cat.mc + 1):
if cat.uncerttype == 'dagjk':
indices = np.random.randint(low=0,
high=(len(fullcatfile) - 1),
size=int(cat.R *
len(fullcatfile)))
cat.catalogue = fullcatfile[indices]
if stackobj > len(cat.catalogue):
stackobj = len(cat.catalogue)
else:
h = 0
else:
h = 0
if mccount > 0 and cat.multiop != 'multi':
frac = int((mccount) / (cat.mc * 2.) * 100.)
if frac < 2:
frac = 0
else:
h = 0
pbar = uf.progressbar(frac, pbar)
cat = stackeverything(pbar,
cat,
stackobj,
binstatus,
'uncertcall',
binno,
mccount,
fig,
ax1,
ax2,
ax3,
ax4,
analysisfinal=analysisfinal)
else:
result = pool.apply_async(
stackeverything,
args=(pbar, cat, stackobj, binstatus, 'uncertcall',
binno, mccount, fig, ax1, ax2, ax3, ax4,
analysisfinal))
results.append(result)
mccount += 1
if cat.multiop == 'multi':
pool.close()
pbar = ''
for n in range(cat.mc):
frac = int((n + 1.) / cat.mc * 100.)
if frac < 2:
frac = 0
else:
h = 0
pbar = uf.progressbar(frac, pbar)
results[n].get()
analysisfinal = analysisfinal + analysisempty.load(
n + 1, cat)
else:
for n in range(1, cat.mc + 1, 1):
frac = int(float(cat.mc + n) / (cat.mc * 2.) * 100.)
pbar = uf.progressbar(frac, pbar)
analysisfinal = analysisfinal + analysisempty.load(n, cat)
cat.suppress = suppress
analysisfinal.ProcessUncertainties(cat)
pck.dump(
analysisfinal,
open('%sstackedresultsobj_%s.pkl' % (cat.outloc, cat.runtime),
'wb'))
disp.display(cat, analysisfinal.allintflux,
[analysisfinal.middle, analysisfinal.allrms],
args.suppress)
else:
disp.display(cat, None, cat.suppress)
return cat
def main():
fullcat = ID.inputCatalogue(runtime)
fullcat.runInput(data)
fullcat.clean = args.clean
fullcat.suppress = args.suppress
fullcat.progress = args.progress
fullcat.saveprogress = args.saveprogress
fullcat.multiop = args.multiop
fullcat.latex = args.latex
## create a temp file for all object files
uf.checkpath('%sstackertemp/' % fullcat.outloc)
if uf.checkkeys(data, 'BinYN'):
binyn = data["BinYN"]
else:
binyn = raw_input(
'\nWould you like to stack in various bins? [y/n] ').lower()
if binyn == 'y':
bincatalogue = BD.binnedCatalogue(fullcat)
try:
bincatalogue.determineBins(data)
except (SystemExit, KeyboardInterrupt):
uf.exit(fullcat)
except:
logging.warning(
"Couldn't determine the catalogue for the different bins:",
exc_info=True)
uf.earlyexit(fullcat)
if fullcat.uncert == 'y':
repeat = 2
else:
repeat = 1
counter = 0
while counter < repeat:
mccount = counter
for m in range(0, len(bincatalogue.binpartindicies) - 1):
if counter > 0:
bincatalogue = pck.load(
open(
'%sstackertemp/catalogue_obj.pkl' % fullcat.outloc,
'rb'))
else:
h = 0
try:
bincatalogue.createCatalogue(bincatalogue.binpartindicies,
bincatalogue.binnedtable, m,
counter)
except KeyboardInterrupt:
uf.earlyexit(cat)
raise sys.exit()
except SystemExit:
uf.earlyexit(cat)
raise sys.exit()
except:
logger.error(
'Exception occurred trying to create the binned catalogue.',
exc_info=True)
uf.earlyexit(cat)
raise sys.exit()
if len(bincatalogue.catalogue) < 2:
h = 0
else:
catalogue = pipeline(bincatalogue, config, data, 'bin',
m + 1, mccount)
if counter == 0:
bincatalogue = bincatalogue + catalogue
else:
h = 0
if counter == 0:
bincatalogue.outcatalogue[
'Stellar Mass'].unit = bincatalogue.fullcatalogue[
'Stellar Mass'].unit
bincatalogue.outcatalogue[
'Other Data'].unit = bincatalogue.fullcatalogue[
'Other Data'].unit
bincatalogue.outcatalogue[
'Integrated Flux'].unit = astun.Jy * astun.km / astun.s
pck.dump(
bincatalogue,
open(
'%sstackertemp/catalogue_obj.pkl' %
bincatalogue.outloc, 'wb'))
catalogue = uf.maskTable(bincatalogue.outcatalogue)
catalogue = asttab.unique(catalogue, keys='Object ID')
catalogue.sort('Bin Number')
astasc.write(
catalogue,
bincatalogue.outloc +
'Stacked_Catalogue_%s.csv' % bincatalogue.origruntime,
format='ecsv')
fullcat.updateconfig(data, bincatalogue.fullmaxgalw,
bincatalogue.fullrebinstatus,
bincatalogue.fullsmoothtype,
bincatalogue.fullsmoothwin,
bincatalogue.fullfuncnum,
bincatalogue.fulloptnum)
else:
h = 0
saveprogress = None
counter += 1
else:
fullcat.catalogue.add_column(
asttab.Column(name='Bin Number',
data=np.ones(len(fullcat.catalogue), dtype=int)))
fullcat = pipeline(fullcat, config, data, 'normal')
try:
fullcat.updateconfig(data, fullcat.maxgalw.value,
fullcat.rebinstatus, fullcat.smoothtype,
fullcat.smoothwin, fullcat.funcnum,
fullcat.optnum)
fullcat.outcatalogue['Stellar Mass'].unit = fullcat.catalogue[
'Stellar Mass'].unit
fullcat.outcatalogue['Other Data'].unit = fullcat.catalogue[
'Other Data'].unit
fullcat.outcatalogue[
'Integrated Flux'].unit = astun.Jy * astun.km / astun.s
catalogue = uf.maskTable(fullcat.outcatalogue)
catalogue = asttab.unique(catalogue, keys='Object ID')
catalogue.sort('Bin Number')
astasc.write(catalogue,
fullcat.outloc +
'Stacked_Catalogue_%s.csv' % fullcat.runtime,
format='ecsv')
logging.info('Written Stacked Catalogue to file.')
except (SystemExit, KeyboardInterrupt):
uf.exit(fullcat)
except:
logging.warning("Struggled to save the catalogue files.",
exc_info=True)
uf.earlyexit(fullcat)
## inform the user that the stacking has finished
if fullcat.suppress != 'hide':
outloc = uf.bashfriendlypath(fullcat.outloc)
os.system('open ' + outloc)
else:
h = 0
print('\nStacker has finished.\n')
uf.exit(fullcat)
return
def __get_astropy_catalogue(self, config):
print("Initialising the catalogue file.")
logger.info('Initialising the catalogue file.')
if uf.checkkeys(config, 'CatalogueFilename'):
self.catfilename = config['CatalogueFilename']
else:
self.catfilename = input(
'Enter location and filename of catalogue file: ')
while not os.path.isfile(self.catfilename):
print(
'The catalogue filename and location you have given does not exist.\n'
)
self.catfilename = input(
'Enter location and filename of catalogue file: ')
try:
filetable = astasc.read(
self.catfilename
) # [, format='csv'] took out 10/01/19 when line crashed with .dat on JD system
except KeyboardInterrupt:
uf.earlyexit(self)
raise sys.exit()
except:
print(
"Did not recognise the catalogue data type. Please check that your catalogue file is in the same format as the example catalogue file."
)
logger.critical("Did not recognise the catalogue file data type.")
raise sys.exit()
if uf.checkkeys(config, 'CatalogueColumnNumbers'):
catcols = config['CatalogueColumnNumbers']
else:
catcols = None
filetablenames = filetable.colnames
print('\nThe following columns are available:')
for u in range(len(filetablenames)):
print('%i: %s' % (u, filetablenames[u]))
colnames = [
'Object ID', 'Filename', 'Redshift', 'Redshift Uncertainty',
'Stellar Mass', 'Other Data'
]
catalogue = asttab.Table(names=['Dud'],
dtype=['f8'],
masked=True,
data=[np.zeros(len(filetable))])
for o in range(len(colnames)):
try:
self.__fill_catalogue(catalogue, filetable, colnames[o], o,
catcols)
except KeyboardInterrupt:
uf.earlyexit(self)
except SystemExit():
uf.earlyexit(self)
raise sys.exit()
except:
print(
'There was problem with entering the column number, please try again.\n'
)
self.__fill_catalogue(catalogue, filetable, colnames[o], o,
None)
catalogue.remove_column('Dud')
## check units of the stellar mass
if True in catalogue['Stellar Mass'].mask:
if self.stackunit == uf.gasfrac:
print(
"\nTo stack in gas fraction, the catalogue file must include the Stellar Mass for each profile."
)
logger.info(
'To stack in gas fraction, the catalogue file must include the Stellar Mass for each profile.'
)
uf.earlyexit(self)
else:
checkval = str(int(catalogue['Stellar Mass'][0]))
if len(checkval) < 3:
catalogue['Stellar Mass'].unit = astun.dex * uf.msun
else:
catalogue['Stellar Mass'].unit = uf.msun
self.avesm = np.mean(catalogue['Stellar Mass'].data
) * catalogue['Stellar Mass'].unit
uniquecatalogue = asttab.unique(catalogue, keys='Object ID')
self.catalogue = uniquecatalogue
self.medianz = np.median(self.catalogue['Redshift'].data)
logger.info('Catalogue has been read in.')
return