def get_sources(self,skydir,radius=15):
""" Returns a list of ExtendedSource objects from the extended source
catalog that have a center withing a distance radius of the
position skydir.
Note that if there are none, it returns an empty list.
"""
from uw.utilities.xml_parsers import parse_sources
diffs = np.degrees(np.asarray([skydir.difference(d) for d in self.dirs]))
mask = diffs < radius
if sum(mask)==0: return []
diffs = diffs[mask]
sorting = np.argsort(diffs)
names = self.names[mask][sorting]
xmls = self.xmls[mask][sorting]
spatials = self.spatial_models[mask][sorting]
sources = []
failed=False
for name,xml,spatial in zip(names,xmls,spatials):
full_xml=os.path.join(self.archive_directory,'XML',os.path.basename(xml))
# Use the built in xml parser to load the extended source.
xmlfile=full_xml.replace(' ', '')
ps,ds=parse_sources(xmlfile=xmlfile)
# try:
# ps,ds=parse_sources(xmlfile=xmlfile)
# except Exception, msg:
# print 'Source {}: Fail: {}'.format(name, msg)
# failed=True
# continue
if len(ps) > 0:
raise Exception("A point source was found in the extended source file %s" % xmlfile)
if len(ds) > 1:
raise Exception("No diffuse sources were found in the extended soruce file %s" % xmlfile)
if len(ds) < 1:
raise Exception("More than one diffuse source was found in the extended source file %s" % xmlfile)
source=ds[0]
if False: # don't support analytic maps spatial is not None:
# replace the SpatialMap extended source with an analytic one.
analytic_source = ExtendedSource(name=source.name,model=source.model,
spatial_model=spatial)
analytic_source.original_template = source.spatial_model.file # for reference
sources.append(analytic_source)
else:
sources.append(source)
if failed:
raise Exception('Could not parse file')
return sources
def get_sources(self,
roi_dir,
point_sources=[],
diffuse_sources=[],
xmlfile=None,
diffdir=None,
catalogs=[],
include_radius=None):
""" Create a list of PointSource and ROIDiffuseModel objects
that are needed for the ROI. """
for ps in point_sources:
if not isinstance(ps, PointSource):
raise PointlikeException("Source %s is not a point source" %
ps.name)
if diffuse_sources is not None:
for ds in diffuse_sources:
if not isinstance(ds, DiffuseSource):
raise PointlikeException(
"Source %s is not a diffuse source" % ds.name)
if xmlfile is not None:
ps, ds = parse_sources(
xmlfile,
diffdir=diffdir,
roi_dir=roi_dir,
max_roi=self.maxROI +
5 if include_radius is None else include_radius)
point_sources += ps
diffuse_sources += ds
if not isinstance(catalogs,collections.Iterable) or \
isinstance(catalogs,types.StringType):
catalogs = [catalogs]
for cat in catalogs:
if not isinstance(cat, PointSourceCatalog):
raise PointlikeException(
"Catalog %s must be of type PointSourceCatalog" % cat)
point_sources, diffuse_sources = cat.merge_lists(
roi_dir,
self.maxROI + 5 if include_radius is None else include_radius,
point_sources, diffuse_sources)
if point_sources == [] and not self.quiet:
print 'WARNING! No point sources are included in the model.'
if diffuse_sources == [] and not self.quiet:
print 'WARNING! No diffuse sources are included in the model.'
return point_sources, diffuse_sources
def prepareIC(roi,j,mass,final_state,tmpdir,specDir):
if not final_state in ["ee","mumu"]:
raise Exception("IC only implemented for ee, mumu")
### assembles the necessary file spectrum for IC emission! ###
# first bit: build sources
from uw.utilities.xml_parsers import parse_sources, write_sources
from uw.like.scalemodels import ScaleFactorFileFunction
ps,ds=parse_sources(roi.modelxml) # requires to pass the sources into the pointlike format!
# get rid of virgo in the source model
# is in the ds section
new_ds = [s for s in ds if not s.name == "Virgo"]
virgo = [s for s in ds if s.name == "Virgo"][0]
# now modify the virgo source
# that way the scale factor can be identified as <sigmav>
filename = None
if final_state in ["ee","mumu"]:
if final_state == "ee":
# e+/e- final state
if not mass in eeIC.keys():
raise Exception("Could not find mass point")
filename = os.path.join(specDir,eeIC[mass])
elif final_state == "mumu":
# mu+/mu- final state
if not mass in mumuIC.keys():
raise Exception("Could not find mass point")
filename = os.path.join(specDir,mumuIC[mass])
j*=effectiveJ(mass,finalState=final_state) # include the IC correction
if not os.path.isfile(filename):
raise IOError("could not find file spectrum %s"%filename)
if filename is None:
raise Exception("could not find associated file")
model = ScaleFactorFileFunction(ScaleFactor=1,normalization=norm(mass,j),file=filename)
model.set_limits("Normalization",0,1e30)
model.set_limits("ScaleFactor",0,1e8)
model.setp(0,1)
model.setp(1,norm(mass,j))
model.free = np.array([True,False])
virgo.model = model # replace DMFit model with file spectrum
ds = new_ds
ds.append(virgo)
ofile = os.path.join(tmpdir,"%s_%s_%sGeV.xml"%(roi.name,final_state,"%1.0f"%mass))
write_sources(ps,ds, ofile, strict=True,
convert_extended=False,
extended_dir_name=None,
expand_env_vars=True)
print '*INF* wrote temporary xml with IC: %s'%ofile
return ofile
def convert(input, output, emin, emax):
if (output == 'None'):
output = input[:-4] + '_simlibrary.xml'
print 'Using default output name:', output
ps, ds = parse_sources(input)
sources = ps
sources.extend(ds)
directory = os.path.dirname(output)
if (directory == ''):
directory = os.path.abspath('.')
else:
directory = os.path.abspath(directory)
pass
mc = uw.like.roi_monte_carlo.MCModelBuilder(sources,
savedir=directory,
emin=float(emin),
emax=float(emax))
mc.build(output)
print 'File saved as', output
return output
def main(inputfile,tag,idstart=None,idstop=None,debug=False,diffdir=None,tstart=0, tstop=8000, ft2file='None', emin=100, emax=1e5, seed=1000,irf='P7SOURCE_V6', dry_run=True, gtifile=None, zmax=None):
if not diffdir is None:
diffdir = diffdir.replace("~",os.getenv('HOME'))
fid = verifyFile(inputfile)
catalogxml = None
if fid == 1:
catalogxml = inputfile
elif fid == 2:
catalogxml = cFITS2XML(inputfile)
if not os.getenv("LSB_JOBID")==None:
Outdir = NamedTemporaryFile(dir='/scratch/').name # data is stored in Outdir/raw
else:
Outdir = NamedTemporaryFile(dir='/tmp/').name # data is stored in Outdir/raw
print '*OUTDIR* %s'%Outdir
Emin = 10
Emax = 1e6
print '*INFO*: current pfile settings',os.getenv('PFILES');
# AllSky by default, need a ROI object to proceed
os.mkdir(Outdir)
modXML = AddCatalog(inputfile,idstart,idstop,Outdir,diffdir=diffdir)
# now we check whether we have files that refer to nowhere
checkXML(modXML)
ps,ds = None,None
ps,ds=parse_sources(modXML)
sources = ps+ds
# this is only necessary to make use of the roi_montecarlo.py code
montecarlo_object = MonteCarlo(
# ST-09-29-00
sources = sources,
gtifile=gtifile,
zmax = zmax,
tempbase = Outdir,
irf = irf,
ft1 = Outdir+'/raw/ft1.fits',
ft2 = ft2file,
tstart = tstart,
tstop = tstop,
emin = emin,
emax = emax,
seed = seed,
savedir = Outdir+'/raw/'
)
montecarlo_object.simulate(dry_run=dry_run)
# now assemble list of files
# check if we have parts
tags = tag.split(";")
storedir = os.getenv("SKYMODEL_DIR")+"/"
for t in tags:
storedir+="/"+t
print '*INFO* store data here: %s'%storedir
files = os.listdir(os.path.join(Outdir,'raw'))
try:
os.mkdir(storedir)
except OSError:
print '*WARNING* dir %s exists already, overwriting'%storedir
removePath(storedir)
# now move
for f in files:
infile = os.path.join(Outdir+'/raw/',f)
outfile= os.path.join(storedir,f)
move(infile,outfile)
# finally, clean up
removePath(Outdir)
class ExtendedCatalog(ExtendedSourceCatalog):
""" subclass to add this lookup function
TODO: merge, keeping only needed features
if a folder 'XML2' is found, add sources to it. Must be analytic I guess.
"""
def __init__(self, extended_catalog_name, force_map=False, **kwargs):
""" initialize by also filling an array with all source spectral models"""
self.alias = kwargs.pop('alias', dict())
self.quiet = kwargs.pop('quiet', True)
self.catname = extended_catalog_name
if os.path.isabs(self.catname):
extended_catalog_name = self.catname
else:
extended_catalog_name = \
os.path.expandvars(os.path.join('$FERMI','catalog',extended_catalog_name))
if not os.path.exists(extended_catalog_name):
raise Exception('extended source folder "%s" not found' %
extended_catalog_name)
if not self.quiet:
print 'Loaded extended catalog %s' % extended_catalog_name
super(ExtendedCatalog, self).__init__(extended_catalog_name,
force_map=force_map) #**kwargs)
# create list of sources using superclass, for lookup by name
self.sources = [
self.get_sources(self.dirs[i], 0.1)[0]
for i in range(len(self.names))
]
fail = False
for source, spatial_model in zip(self.sources, self.spatial_models):
model = source.model
try:
if model.mappers[0].__class__.__name__ == 'LimitMapper':
#print 'converting mappers for model for source %s, model %s' % (source.name, model.name)
source.model = eval(
'Models.%s(p=%s)' %
(model.name, list(model.get_all_parameters())))
except Exception, msg:
fail = True
print 'Failed to parse {} spectrum : {}'.format(
source.name, msg)
# Replace the spatial model with the one specified by the FITS catalog list
dmodel = source.dmodel
if spatial_model.name != 'SpatialMap':
assert spatial_model.center.difference(dmodel[0].center)<0.001,\
'Center discrepance for {}: {},{}'.format(source.name, spatial_model.center, dmodel[0].center)
source.dmodel[0] = source.spatial_model = spatial_model
if fail:
raise Exception('Parse error(s)')
# Now check for XML2
ff = glob.glob('{}/XML2/*.xml'.format(extended_catalog_name))
#print '{} sources found in folder {}:'.format(len(ff), 'XML2')
if len(ff) == 0: return
for f in ff:
ps, ds = parse_sources(f)
assert len(ps) == 0 and len(
ds
) == 1, 'expected a single extended source in file {}'.format(f)
s = ds[0]
name = s.name
if name[4] == 'J': # insert space
name = name[:4] + ' ' + name[4:]
s.name = name
i = self.lookup(name)
if i is not None:
if not self.quiet:
print 'replacing spectral model for {}'.format(name)
self.sources[i].dmodel = s.dmodel
else:
if not self.quiet:
print 'adding extended source {} at {}'.format(
s.name, s.skydir)
self.names = np.append(self.names, name)
self.sources.append(s)
def run(**kwargs):
if (not available):
raise RuntimeError(
"The command gtconvertxmlmodel.py is not currently usable with public Science Tools"
)
if (len(kwargs.keys()) == 0):
#Nothing specified, the user needs just help!
thisCommand.getHelp()
return
pass
#Get parameters values
thisCommand.setParValuesFromDictionary(kwargs)
try:
xmlmodel = thisCommand.getParValue('likexmlresults')
Emin = float(thisCommand.getParValue('emin'))
Emax = float(thisCommand.getParValue('emax'))
xmlsimmodel = thisCommand.getParValue('xmlsimmodel')
clobber = _yesOrNoToBool(thisCommand.getParValue('clobber'))
verbose = _yesOrNoToBool(thisCommand.getParValue('verbose'))
except KeyError as err:
print("\n\nERROR: Parameter %s not found or incorrect! \n\n" %
(err.args[0]))
#Print help
print thisCommand.getHelp()
return
from GtBurst import dataHandling
irf = dataHandling._getParamFromXML(xmlmodel, 'IRF')
ra = dataHandling._getParamFromXML(xmlmodel, 'RA')
dec = dataHandling._getParamFromXML(xmlmodel, 'DEC')
name = dataHandling._getParamFromXML(xmlmodel, 'OBJECT')
if (irf == None):
print(
"\n\nWARNING: could not read IRF from XML file. Be sure you know what you are doing..."
)
sourceList = xmlmodel.replace('.xml', '.txt')
#Quick fix: MCModelBuilder cannot integrate a isotropic model if it has not a normalization of 1
#We will edit the XML model, put temporarily the normalization of the IsotropicTemplate to 1,
#convert the XML, then multiply the output normalization by the factor contained at the beginning
tmpxml = "__temp__xmlmodel.xml"
shutil.copy(xmlmodel, tmpxml)
originalNorm = dataHandling.getIsotropicTemplateNormalization(xmlmodel)
if (originalNorm != None or originalNorm != 1):
dataHandling.setIsotropicTemplateNormalization(tmpxml, 1)
else:
#Either the template is not in the XML file (possibly because the user used Transient class),
#or it is already 1, nothing to do
originalNorm = 1
pass
ps, ds = parse_sources(tmpxml)
sources = ps
sources.extend(ds)
mc = uw.like.roi_monte_carlo.MCModelBuilder(sources,
savedir='.',
emin=Emin,
emax=Emax)
mc.build(xmlsimmodel)
dataHandling.multiplyIsotropicTemplateFluxSim(xmlsimmodel, originalNorm)
os.remove(tmpxml)
txt = ''
for x in sources:
txt += x.name.replace('2FGL ', '_2FGL_').replace('-', 'm').replace(
'.', '') + '\n'
file(sourceList, 'w').writelines(txt)
lines = file(xmlsimmodel, 'r').readlines()
newlines = ''
pwd = os.environ['PWD']
for l in lines:
newlines += l.replace('$($SIMDIR)', pwd)
pass
file(xmlsimmodel, 'w').writelines(newlines)
if (irf != None):
dataHandling._writeParamIntoXML(xmlsimmodel,
IRF=irf,
OBJECT=name,
RA=ra,
DEC=dec)
pass
return 'xmlsimmodel', xmlsimmodel, 'srclist', sourceList
def run(**kwargs):
if(not available):
raise RuntimeError("The command gtconvertxmlmodel.py is not currently usable with public Science Tools")
if(len(kwargs.keys())==0):
#Nothing specified, the user needs just help!
thisCommand.getHelp()
return
pass
#Get parameters values
thisCommand.setParValuesFromDictionary(kwargs)
try:
xmlmodel = thisCommand.getParValue('likexmlresults')
Emin = float(thisCommand.getParValue('emin'))
Emax = float(thisCommand.getParValue('emax'))
xmlsimmodel = thisCommand.getParValue('xmlsimmodel')
clobber = _yesOrNoToBool(thisCommand.getParValue('clobber'))
verbose = _yesOrNoToBool(thisCommand.getParValue('verbose'))
except KeyError as err:
print("\n\nERROR: Parameter %s not found or incorrect! \n\n" %(err.args[0]))
#Print help
print thisCommand.getHelp()
return
from GtBurst import dataHandling
irf = dataHandling._getParamFromXML(xmlmodel,'IRF')
ra = dataHandling._getParamFromXML(xmlmodel,'RA')
dec = dataHandling._getParamFromXML(xmlmodel,'DEC')
name = dataHandling._getParamFromXML(xmlmodel,'OBJECT')
if(irf is None):
print("\n\nWARNING: could not read IRF from XML file. Be sure you know what you are doing...")
sourceList = xmlmodel.replace('.xml','.txt')
#Quick fix: MCModelBuilder cannot integrate a isotropic model if it has not a normalization of 1
#We will edit the XML model, put temporarily the normalization of the IsotropicTemplate to 1,
#convert the XML, then multiply the output normalization by the factor contained at the beginning
tmpxml = "__temp__xmlmodel.xml"
shutil.copy(xmlmodel,tmpxml)
originalNorm = dataHandling.getIsotropicTemplateNormalization(xmlmodel)
if(originalNorm is not None or originalNorm!=1):
dataHandling.setIsotropicTemplateNormalization(tmpxml,1)
else:
#Either the template is not in the XML file (possibly because the user used Transient class),
#or it is already 1, nothing to do
originalNorm = 1
pass
ps,ds = parse_sources(tmpxml)
sources = ps
sources.extend(ds)
mc = uw.like.roi_monte_carlo.MCModelBuilder(sources,savedir='.',emin=Emin,emax=Emax)
mc.build(xmlsimmodel)
dataHandling.multiplyIsotropicTemplateFluxSim(xmlsimmodel,originalNorm)
os.remove(tmpxml)
txt=''
for x in sources:
txt += x.name.replace('2FGL ','_2FGL_').replace('-','m').replace('.','')+'\n'
file(sourceList,'w').writelines(txt)
lines = file(xmlsimmodel,'r').readlines()
newlines =''
pwd = os.environ['PWD']
for l in lines:
newlines += l.replace('$($SIMDIR)',pwd)
pass
file(xmlsimmodel,'w').writelines(newlines)
if(irf is not None):
dataHandling._writeParamIntoXML(xmlsimmodel,IRF=irf,OBJECT=name,RA=ra,DEC=dec)
pass
return 'xmlsimmodel', xmlsimmodel, 'srclist', sourceList