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 __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 __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 __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 __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 __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 __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 runInput(self, config):
try:
self.__callCriticalUser(config)
self.__callOptionalUser(config)
self.__calcPrivate()
self.__checkConfig(config)
except (SystemExit, KeyboardInterrupt):
uf.exit(self)
except:
logger.error('Encountered an exception:', exc_info=True)
uf.earlyexit(self)
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 __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 __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 __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 __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 __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 display(self, cat, allflux, extra=None, hide=None):
if cat.uncert == 'y':
uncert = True
else:
uncert = False
try:
self.__read_in_data(cat)
except (SystemExit, KeyboardInterrupt):
uf.exit(cat)
except:
logger.critical('Encountered an error reading in the FITS data.',
exc_info=True)
uf.earlyexit(cat)
try:
self.__readTextData()
except (SystemExit, KeyboardInterrupt):
uf.exit(cat)
except:
logger.critical('Encountered an error reading in the text data.',
exc_info=True)
uf.earlyexit(cat)
try:
self.__printStatistics(uncert, cat, self.spec, self.specuncert,
self.spectralaxis)
except (SystemExit, KeyboardInterrupt):
uf.exit(cat)
except:
logger.critical('Encountered an error printing the results.',
exc_info=True)
uf.earlyexit(cat)
if cat.suppress == 'hide':
logger.info(
'Final plots are not displayed to screen. Check saved data.')
return
else:
try:
self.__displayplots(cat,
uncert,
allflux=allflux,
spec=self.spec,
spectral=self.spectralaxis,
refspec=self.refspec,
specuncert=self.specuncert,
extra=extra)
except (SystemExit, KeyboardInterrupt):
uf.exit(cat)
except:
logger.critical(
'Encountered an error trying to display the plots:',
exc_info=True)
uf.earlyexit(cat)
return
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 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