def run_analysis(config): print('Running analysis...') gta = GTAnalysis(config) gta.setup() gta.optimize() gta.print_roi() # Localize and generate SED for first source in ROI srcname = gta.roi.sources[0].name gta.free_source(srcname) gta.fit() gta.localize(srcname) gta.sed(srcname) gta.write_roi('roi', make_plots=True) gta.tsmap(make_plots=True) gta.residmap(make_plots=True)
class ExtensionFit: def __init__(self, configFile): self.gta = GTAnalysis(configFile, logging={'verbosity': 3}) self.target = None self.targetRadius = None self.distance = None self.catalog = fits.getdata('/users-data/mfalxa/code/gll_psch_v13.fit', 1) def setSourceName(self, sourceObject, newName): self.gta.delete_source(sourceObject['name']) self.gta.add_source(newName, sourceObject) ''' INITIALIZE ''' def initialize(self, sizeROI, rInner, addToROI, TSMin, debug): self.gta.setup() if self.gta.config['selection']['emin'] >= 10000: self.gta.set_parameter('galdiff', 'Scale', 30000) if debug == True: self.gta.make_plots('startAll') self.gta.residmap(prefix='startAll', make_plots=True) # Get model source names sourceList = self.gta.get_sources(exclude=['isodiff', 'galdiff']) # Delete sources unassociated with TS < 50 for i in range(len(sourceList)): if sourceList[i]['catalog']['TS_value'] < TSMin and self.catalog[ 'CLASS'][self.catalog['Source_Name'] == sourceList[i] ['name']][0] == '': self.gta.delete_source(sourceList[i]['name']) closests = self.gta.get_sources(distance=rInner, exclude=['isodiff', 'galdiff']) # Delete all unidentified sources for i in range(len(closests)): if self.catalog['CLASS'][self.catalog['Source_Name'] == closests[i] ['name']][0].isupper() == False: self.gta.delete_source(closests[i]['name']) if self.catalog['CLASS'][self.catalog['Source_Name'] == closests[i] ['name']][0] == 'SFR': self.target = closests[i] self.setSourceName(self.target, 'TESTSOURCE') # If debug, save ROI and make plots if debug == True: self.gta.write_roi('startModel') self.gta.residmap(prefix='start', make_plots=True) self.gta.make_plots('start') # Optmize spectral parameters for sources with npred > 1 self.gta.optimize(npred_threshold=1, skip=['isodiff']) # Get model source names sourceList = self.gta.get_sources(distance=sizeROI + addToROI, square=True, exclude=['isodiff', 'galdiff']) # Iterate source localizing on source list for i in range(len(sourceList)): if sourceList[i].extended == False: self.gta.localize(sourceList[i]['name'], write_fits=False, write_npy=False, update=True) # Free sources within ROI size + extra distance from center self.gta.free_sources(distance=sizeROI + addToROI, square=True) # Re-optimize ROI self.gta.optimize(skip=['isodiff']) # Save and make plots if debug if debug == True: self.gta.write_roi('modelInitialized') self.gta.residmap(prefix='initialized', make_plots=True) self.gta.make_plots('initialized') # Lock sources self.gta.free_sources(free=False) ''' OUTER REGION ''' def outerRegionAnalysis(self, sizeROI, rInner, sqrtTsThreshold, minSeparation, debug): self.gta.free_sources(distance=sizeROI, pars='norm', square=True, free=True) self.gta.free_sources(distance=rInner, free=False) self.gta.free_source('galdiff', free=True) self.gta.free_source('isodiff', free=False) # Seek new sources until none are found sourceModel = { 'SpectrumType': 'PowerLaw', 'Index': 2.0, 'Scale': 30000, 'Prefactor': 1.e-15, 'SpatialModel': 'PointSource' } newSources = self.gta.find_sources(sqrt_ts_threshold=sqrtTsThreshold, min_separation=minSeparation, model=sourceModel, **{ 'search_skydir': self.gta.roi.skydir, 'search_minmax_radius': [rInner, sizeROI] }) if len(newSources) > 0: for i in range(len(newSources)): if newSources['sources'][i]['ts'] > 100.: self.gta.set_source_spectrum( newSources['sources'][i]['name'], spectrum_type='LogParabola') self.gta.free_source(newSources['sources'][i]['name']) self.gta.fit() self.gta.free_source(newSources['sources'][i]['name'], free=False) # Optimize all ROI self.gta.optimize(skip=['isodiff']) # Save sources found if debug == True: self.gta.residmap(prefix='outer', make_plots=True) self.gta.write_roi('outerAnalysisROI') self.gta.make_plots('outer') ''' INNER REGION ''' def innerRegionAnalysis(self, sizeROI, rInner, maxIter, sqrtTsThreshold, minSeparation, dmMin, TSm1Min, TSextMin, debug): self.gta.free_sources(distance=sizeROI, square=True, free=False) self.gta.free_sources(distance=rInner, free=True, exclude=['isodiff']) # Keep closest source if identified with star forming region in catalog or look for new source closest to center within Rinner if self.target != None: print('Closest source identified with star forming region : ', self.target['name']) self.gta.set_source_morphology('TESTSOURCE', **{'spatial_model': 'PointSource'}) else: closeSources = self.gta.find_sources(sqrt_ts_threshold=2., min_separation=minSeparation, max_iter=1, **{ 'search_skydir': self.gta.roi.skydir, 'search_minmax_radius': [0., rInner] }) dCenter = np.array([]) for i in range(len(closeSources['sources'])): dCenter = np.append( dCenter, self.gta.roi.skydir.separation( closeSources['sources'][i].skydir).value) self.target = closeSources['sources'][np.argmin(dCenter)] print('Target name : ', self.target['name']) self.setSourceName(self.target, 'TESTSOURCE') for i in [ x for x in range(len(closeSources['sources'])) if x != (np.argmin(dCenter)) ]: self.gta.delete_source(closeSources['sources'][i]['name']) self.gta.optimize(skip=['isodiff']) # Initialize n sources array nSources = [] # Save ROI without extension fit self.gta.write_roi('nSourcesFit') if debug == True: self.gta.make_plots('innerInit') self.gta.residmap(prefix='innerInit', make_plots=True) # Test for extension extensionTest = self.gta.extension('TESTSOURCE', make_plots=True, write_npy=debug, write_fits=debug, spatial_model='RadialDisk', update=True, free_background=True, fit_position=True) extLike = extensionTest['loglike_ext'] TSext = extensionTest['ts_ext'] print('TSext : ', TSext) extAIC = 2 * (len(self.gta.get_free_param_vector()) - self.gta._roi_data['loglike']) self.gta.write_roi('extFit') if debug == True: self.gta.residmap(prefix='ext0', make_plots=True) self.gta.make_plots('ext0') self.gta.load_roi('nSourcesFit', reload_sources=True) for i in range(1, maxIter + 1): # Test for n point sources nSourcesTest = self.gta.find_sources( sources_per_iter=1, sqrt_ts_threshold=sqrtTsThreshold, min_separation=minSeparation, max_iter=1, **{ 'search_skydir': self.gta.roi.skydir, 'search_minmax_radius': [0., rInner] }) if len(nSourcesTest['sources']) > 0: if nSourcesTest['sources'][0]['ts'] > 100.: self.gta.set_source_spectrum( nSourcesTest['sources'][0]['name'], spectrum_type='LogParabola') self.gta.free_source(nSourcesTest['sources'][0]['name']) self.gta.fit() self.gta.free_source(nSourcesTest['sources'][0]['name'], free=False) if debug == True: self.gta.make_plots('nSources' + str(i)) nSources.append(nSourcesTest['sources']) self.gta.localize(nSourcesTest['sources'][0]['name'], write_npy=debug, write_fits=debug, update=True) nAIC = 2 * (len(self.gta.get_free_param_vector()) - self.gta._roi_data['loglike']) self.gta.free_source(nSourcesTest['sources'][0]['name'], free=True) self.gta.residmap(prefix='nSources' + str(i), make_plots=True) self.gta.write_roi('n1SourcesFit') # Estimate Akaike Information Criterion difference between both models dm = extAIC - nAIC print('AIC difference between both models = ', dm) # Estimate TS_m+1 extensionTestPlus = self.gta.extension( 'TESTSOURCE', make_plots=True, write_npy=debug, write_fits=debug, spatial_model='RadialDisk', update=True, free_background=True, fit_position=True) TSm1 = 2 * (extensionTestPlus['loglike_ext'] - extLike) print('TSm+1 = ', TSm1) if debug == True: self.gta.residmap(prefix='ext' + str(i), make_plots=True) self.gta.make_plots('ext' + str(i)) if dm < dmMin and TSm1 < TSm1Min: self.gta.load_roi('extFit', reload_sources=True) break else: # Set extension test to current state and save current extension fit ROI and load previous nSources fit ROI extensionTest = extensionTestPlus extLike = extensionTestPlus['loglike_ext'] TSext = extensionTestPlus['ts_ext'] print('TSext : ', TSext) extAIC = 2 * (len(self.gta.get_free_param_vector()) - self.gta._roi_data['loglike']) self.gta.write_roi('extFit') self.gta.load_roi('n1SourcesFit', reload_sources=True) self.gta.write_roi('nSourcesFit') else: if TSext > TSextMin: self.gta.load_roi('extFit', reload_sources=True) break else: self.gta.load_roi('nSourcesFit', reload_sources=True) break self.gta.fit() # Get source radius depending on spatial model endSources = self.gta.get_sources() for i in range(len(endSources)): if endSources[i]['name'] == 'TESTSOURCE': self.target = endSources[i] self.distance = self.gta.roi.skydir.separation( endSources[i].skydir).value if endSources[i].extended == True: self.targetRadius = endSources[i]['SpatialWidth'] else: self.targetRadius = endSources[i]['pos_r95'] ''' CHECK OVERLAP ''' def overlapDisk(self, rInner, radiusCatalog): print('Target radius : ', self.targetRadius) # Check radius sizes if radiusCatalog < self.targetRadius: r = float(radiusCatalog) R = float(self.targetRadius) else: r = float(self.targetRadius) R = float(radiusCatalog) # Estimating overlapping area d = self.distance print('Distance from center : ', d) if d < (r + R): if R < (r + d): area = r**2 * np.arccos( (d**2 + r**2 - R**2) / (2 * d * r)) + R**2 * np.arccos( (d**2 + R**2 - r**2) / (2 * d * R)) - 0.5 * np.sqrt( (-d + r + R) * (d + r - R) * (d - r + R) * (d + r + R)) overlap = round((area / (np.pi * r**2)) * 100, 2) else: area = np.pi * r**2 overlap = 100.0 else: area = 0. overlap = 0. print('Overlapping surface : ', area) print('Overlap : ', overlap) if overlap > 68. and self.distance < rInner: associated = True else: associated = False return associated ''' CHECK UPPER LIMIT ''' def upperLimit(self, name, radius): sourceModel = { 'SpectrumType': 'PowerLaw', 'Index': 2.0, 'Scale': 30000, 'Prefactor': 1.e-15, 'SpatialModel': 'RadialDisk', 'SpatialWidth': radius, 'glon': self.gta.config['selection']['glon'], 'glat': self.gta.config['selection']['glat'] } self.gta.add_source(name, sourceModel, free=True) self.gta.fit() self.gta.residmap(prefix='upperLimit', make_plots=True) print('Upper limit : ', self.gta.get_sources()[0]['flux_ul95'])
config['fileio']['outdir'] = cwd+'/fits' config['fileio']['logfile'] = cwd+'/fits/fermipy.log' config['data']['ltcube'] = cwd+'/fits/ltcube_00.fits' config['model']['galdiff'] = path_to_conda+'/share/fermitools/refdata/fermi/galdiffuse/gll_iem_v07.fits' config['model']['isodiff'] = path_to_conda+'/share/fermitools/refdata/fermi/galdiffuse/iso_P8R3_SOURCE_V3_v1.txt' config['logging']['verbosity'] = 4 source = config['selection']['target'] with open(cwd+'/config_modified.yaml', 'w') as o: yaml.dump(config, o) likelihoods = np.zeros((5)) gta = GTAnalysis(config='config_modified.yaml') gta.setup() model = {'Index' : 2.0, 'SpatialModel' : 'PointSource'} for i in range(1,6): gta.optimize() gta.free_sources(free=False) gta.free_source(source) gta.free_source('galdiff') gta.free_source('isodiff') gta.free_sources(distance=3, pars='norm') gta.free_sources(minmax_ts=[100, None], pars='norm') gta.fit(optimizer='NEWMINUIT', reoptimize=True) maps = gta.residmap(f'../maps/opt_alternating{i}', model=model, make_plots=True) maps = gta.tsmap(f'../maps/opt_alternating_{i}', model=model, make_plots=True) gta.write_roi(f'opt_{i}', make_plots=True) likelihoods[i-1] = - gta.like() np.savetxt('optimization_process_likes_alternating.dat', likelihoods)
def FGES_BinnedAnalysis(prefix, ANALYSISDIR, numsources, xmlsources, spectrum, spectrumpoints, spectrumpointsUL, spectrum_mev_or_erg, spectrum_mev_or_tev, configfile): ANALYSISDIR = ANALYSISDIR + prefix + '/' i = numsources #number of sources sources_names = '' for x in range(0, i): sources_names += str(xmlsources[x]) #Run the likelihood analysis up to doing the fit gta = GTAnalysis(ANALYSISDIR + configfile, logging={'verbosity': 3}) gta.setup() #Print the pre likelihood fit parameters gta.print_roi() for x in range(0, i): print(gta.roi[xmlsources[x]]) #Do an initial optimization of parameters gta.optimize() gta.print_roi() #Prepare to get the likelihood #Free the normalizations of sources within 7 degrees of the center of the field of view gta.free_sources(distance=7.0, pars='norm') gta.free_source('galdiff') gta.free_source('isodiff') for x in range(0, i): gta.free_source(xmlsources[x]) #LIKELIHOOD ANALYSIS fit_results = gta.fit() #print out and return the results print('Fit Quality: ', fit_results['fit_quality']) for x in range(0, i): print(gta.roi[xmlsources[x]]) gta.write_roi(sources_names + 'fit') #RESIDUAL MAP model = {'Index': 2.0, 'SpatialModel': 'PointSource'} maps = gta.residmap('residual', model=model, make_plots=True) # Generate residual map with source of interest removed from the model model_nosource = {'Index': 2.0, 'SpatialModel': 'PointSource'} maps_nosource = gta.residmap('residual_wsource', model=model_nosource, exclude=xmlsources, make_plots=True) #TS Map tsmap = gta.tsmap('tsmap', model={ 'SpatialModel': 'PointSource', 'Index': 2.0 }, exclude=xmlsources, make_plots=True) tsmap_wSNR = gta.tsmap('tsmap_wSNR', model={ 'SpatialModel': 'PointSource', 'Index': 2.0 }, make_plots=True) #PLOT SEDs for x in range(0, i): c = np.load('10to500gev/' + sources_names + 'fit.npy').flat[0] sorted(c['sources'].keys()) c['sources'][xmlsources[x]]['flux'] print(c['sources'][xmlsources[x]]['param_names'][:4]) print(c['sources'][xmlsources[x]]['param_values'][:4]) c['sources'][xmlsources[x]]['ts'] E = np.array(c['sources'][xmlsources[x]]['model_flux']['energies']) dnde = np.array(c['sources'][xmlsources[x]]['model_flux']['dnde']) dnde_hi = np.array( c['sources'][xmlsources[x]]['model_flux']['dnde_hi']) dnde_lo = np.array( c['sources'][xmlsources[x]]['model_flux']['dnde_lo']) if spectrum_mev_or_erg == "erg": suffix = 'erg' mult = 0.00000160218 elif spectrum_mev_or_erg == "mev": suffix = 'MeV' mult = 1 if spectrum_mev_or_tev == "mev": xaxis = 'MeV' denominator = 1 elif spectrum_mev_or_tev == "tev": xaxis = 'TeV' denominator = 1000000 if spectrum: plt.loglog(E, (E**2) * dnde, 'k--') plt.loglog(E, (E**2) * dnde_hi, 'k') plt.loglog(E, (E**2) * dnde_lo, 'k') plt.xlabel('E [MeV]') plt.ylabel(r'E$^2$ dN/dE [MeV cm$^{-2}$ s$^{-1}$]') plt.savefig('spectrum_' + xmlsources[x] + '.png') #GET SED POINTS if spectrumpoints: sed = gta.sed(xmlsources[x], make_plots=True) #sed = gta.sed(xmlsource,prefix=xmlsource + 'spectrum',loge_bins=) src = gta.roi[xmlsources[x]] #Plot without upper limits plt.loglog(E, (E**2) * dnde, 'k--') plt.loglog(E, (E**2) * dnde_hi, 'k') plt.loglog(E, (E**2) * dnde_lo, 'k') plt.errorbar(np.array(sed['e_ctr']), sed['e2dnde'], yerr=sed['e2dnde_err'], fmt='o') plt.xlabel('E [MeV]') plt.ylabel(r'E$^{2}$ dN/dE [MeV cm$^{-2}$ s$^{-1}$]') #plt.show() plt.savefig('spectrumpoints_' + xmlsources[x] + '.png') #Plot with upper limits, last 5 points plt.loglog(E, (E**2) * dnde, 'k--') plt.loglog(E, (E**2) * dnde_hi, 'k') plt.loglog(E, (E**2) * dnde_lo, 'k') plt.errorbar(sed['e_ctr'][:-5], sed['e2dnde'][:-5], yerr=sed['e2dnde_err'][:-5], fmt='o') plt.errorbar(np.array(sed['e_ctr'][-5:]), sed['e2dnde_ul95'][-5:], yerr=0.2 * sed['e2dnde_ul95'][-5:], fmt='o', uplims=True) plt.xlabel('E [MeV]') plt.ylabel(r'E$^{2}$ dN/dE [MeV cm$^{-2}$ s$^{-1}$]') plt.savefig('spectrumpointsUL_' + xmlsources[x] + '.png') plt.clf()
def main(): usage = "usage: %(prog)s [config file]" description = "Run fermipy analysis chain." parser = argparse.ArgumentParser(usage=usage, description=description) parser.add_argument('--config', default='sample_config.yaml') parser.add_argument('--source', default=None) args = parser.parse_args() gta = GTAnalysis(args.config, logging={'verbosity': 3}, fileio={'workdir_regex': '\.xml$|\.npy$'}) model0 = {'SpatialModel': 'PointSource', 'Index': 1.5} model1 = {'SpatialModel': 'PointSource', 'Index': 2.0} model2 = {'SpatialModel': 'PointSource', 'Index': 2.7} src_name = gta.config['selection']['target'] gta.setup(overwrite=True) gta.free_sources(False) gta.print_roi() gta.optimize() gta.print_roi() exclude = [] # Localize all point sources for s in sorted(gta.roi.sources, key=lambda t: t['ts'], reverse=True): # for s in gta.roi.sources: if not s['SpatialModel'] == 'PointSource': continue if s['offset_roi_edge'] > -0.1: continue if s.name in exclude: continue if not '3FGL' in s.name: continue if s.name == src_name: continue gta.localize(s.name, nstep=5, dtheta_max=0.5, update=True, prefix='base', make_plots=True) gta.optimize() gta.print_roi() gta.write_roi('base_roi', make_plots=True) exclude = [src_name] if not 'carina_2' in exclude: exclude += ['carina_2'] if not 'carina_3' in exclude: exclude += ['carina_3'] gta.tsmap('base', model=model0, make_plots=True, exclude=exclude) gta.residmap('base', model=model0, make_plots=True, exclude=exclude) gta.tsmap('base', model=model1, make_plots=True, exclude=exclude) gta.residmap('base', model=model1, make_plots=True, exclude=exclude) gta.tsmap('base', model=model2, make_plots=True, exclude=exclude) gta.residmap('base', model=model2, make_plots=True, exclude=exclude) gta.find_sources(sqrt_ts_threshold=5.0) gta.optimize() gta.print_roi() gta.print_params() gta.free_sources(skydir=gta.roi.skydir, distance=1.0, pars='norm') gta.fit() gta.print_roi() gta.print_params() gta.write_roi('fit0_roi', make_plots=True) m = gta.tsmap('fit0', model=model0, make_plots=True, exclude=exclude) gta.plotter.make_tsmap_plots(m, gta.roi, zoom=2, suffix='tsmap_zoom') gta.residmap('fit0', model=model0, make_plots=True, exclude=exclude) gta.tsmap('fit0', model=model1, make_plots=True, exclude=exclude) gta.plotter.make_tsmap_plots(m, gta.roi, zoom=2, suffix='tsmap_zoom') gta.residmap('fit0', model=model1, make_plots=True, exclude=exclude) gta.tsmap('fit0', model=model2, make_plots=True, exclude=exclude) gta.plotter.make_tsmap_plots(m, gta.roi, zoom=2, suffix='tsmap_zoom') gta.residmap('fit0', model=model2, make_plots=True, exclude=exclude) gta.sed(src_name, prefix='fit0', make_plots=True, free_radius=1.0) gta.free_source(src_name) gta.fit(reoptimize=True) gta.print_roi() gta.print_params() gta.write_roi('fit1_roi', make_plots=True)