def PlotLC(self,show=True,save=True,legend=True,residualscale=False,
xlimits=None,ylimits=None,figsize=(13,8),incl_xrt=False):
'''
show: Plot to screen
save: Save to disk
legend: include a legend
residualscale: BETA. CURRENTLY ONLY FOR USE WITH GRB120119A. HACK.
xlimits: optional tuple of limits (observer frame)
ylimits: optional tuple of limits (flux units)
figsize: figsize tuple in inches
'''
# set font
rc('font', family='Times New Roman')
fig=plt.figure(figsize=figsize)
ax=fig.add_axes([0.1,0.1,0.8,0.8])
ax.loglog()
# Plot the XRT data if desired
if incl_xrt:
obslist = ['BAT_unknown','XRT_unknown']
for obstr in obslist:
ob = self.obsdict[obstr]
label= obstr.replace('_',' ')
label= label.replace(' unknown','')
detectinds = np.array([not a for a in ob.isupperlist])
ax.errorbar(np.array(ob.tmidlist)[detectinds],ob.fluxarr[detectinds],yerr=ob.fluxerrarr[detectinds], color=ob.color, fmt=ob.marker, label=label)
leg=ax.legend(loc=3,borderaxespad=1.2,numpoints=1,frameon=False)
from pylab import setp
setp(leg.get_texts(),fontsize=20)
setp(leg.get_title(),fontsize=20)
## HACK THiS IS AWFUL AND REMOVES DATA. for use ONLY for one time plots
if residualscale:
# first remove the xrt and bat data if it exists
removelist = ['BAT_unknown','XRT_unknown']
for key in removelist:
if key in self.obsdict:
del(self.obsdict[key])
from Modelling.ExtinctModel import CorrectFluxForGalExt
filtlist=['K','H','J',"z'",'I',"i'",'R',"r'",'V','B'] # liverpool are just estimates!
wave_Alist = []
# loop through and grab the wavlengths for each filter
for filttt in filtlist:
for key, ob in self.obsdict.iteritems():
if ob.filtstr == filttt:
if ob.filt.wave_A not in wave_Alist:
wave_Alist.append(ob.filt.wave_A)
wave_Alist = np.array(wave_Alist)
removelist=[]
fluxconv_uncorr = np.array([4312.1,2522.7,1358.6,654.0,456.1,340.6,193.6,160.6,109.9,45])
fluxconv_uncorrerr=np.array([145.,80.,45.,26.,19,16.,8.2,6.7,5.1,2.5])
fluxconv,fluxconverr = CorrectFluxForGalExt(self.galebv,wave_Alist,fluxconv_uncorr,fluxconv_uncorrerr)
fluxconv = list(fluxconv)
sed=zip(filtlist,fluxconv)
for key, ob in self.obsdict.iteritems():
if ob.filtstr not in filtlist:
removelist.append(key)
else:
index = filtlist.index(ob.filtstr)
ob.gcfluxarr*=fluxconv[0]/fluxconv[index]
ob.gcfluxerrarr*=fluxconv[0]/fluxconv[index]
for key in removelist:
del(self.obsdict[key])
##HACK
# get list of all sources of observations for use in legend-making
sources = {}
filters = []
for key, ob in self.obsdict.iteritems():
if ob.filt != None:
if ob.filtstr not in filters:
filters.append(ob.filtstr)
detectinds = np.array([not a for a in ob.isupperlist])
if detectinds.any(): # only plot here if we have at least one detection
if ob.source not in sources:
sources.update({ob.source:1}) #collecting number of detections for each filter for legend
else:
sources[ob.source]+=1
print sources
#HACK to get most number of sources to left. smarts has most. all alphabetical
sourcenames = sources.keys()
sourcenames.sort()
sourcenames = sourcenames[::-1] #reverse; have smarts first
# CAN HACK AS NECESSARY FOR NEW SOURCES - JUST PUT SOURCENAMES IN THE ORDER YOU WANT
nsourcelist = [] # get the maximum number of instances for each source
for nsource in sources.itervalues():
nsourcelist.append(nsource)
maxsource = max(nsourcelist)
for key, nsource in sources.iteritems():
sources[key] = abs(nsource-maxsource) #now the val is how many blank spaces to add for the legend
print sources
print filters
for source in sourcenames: # loop through each source for ordering purposes
i=0
while i < sources[source]:
ax.errorbar((100,100),(100,100),label=' ',color='white',marker=None)
i+=1
ax.errorbar((100,100),(100,100),label=source,color='white',marker=None)
for key, ob in self.obsdict.iteritems():
if ob.filt != None and ob.source == source:
upperinds = np.array(ob.isupperlist)
detectinds = np.array([not a for a in ob.isupperlist])
label = ob.filtstr
if detectinds.any(): # only plot here if we have at least one detection
ax.errorbar(np.array(ob.tmidlist)[detectinds],ob.gcfluxarr[detectinds],yerr=ob.gcfluxerrarr[detectinds], color=ob.color, fmt=ob.marker, label=label)
if upperinds.any(): # only plot here if we have at least one upper limit
ax.errorbar(np.array(ob.tmidlist)[upperinds],ob.gcfluxarr[upperinds],yerr=ob.gcfluxerrarr[upperinds], color=ob.color, fmt='v')
# ax.set_ylim(1,1E5)
if xlimits:
ax.set_xlim(xlimits)
if ylimits:
ax.set_ylim(ylimits)
old_ylim=ax.get_ylim() # saving for later, as gets modified..
ax2=ax.twinx()
ax3=ax.twiny()
ax3.loglog()
xobstime=ax.get_xlim()
xresttime0=xobstime[0]/(1+self.redshift)
xresttime1=xobstime[1]/(1+self.redshift)
xrest=(xresttime0,xresttime1)
ax3.set_xlim(xrest)
# duplicate axis for AB mag
ax.set_ylim(old_ylim)
ylimflux=ax.get_ylim()
ylimmag0=flux2abmag(ylimflux[0])
ylimmag1=flux2abmag(ylimflux[1])
ylimmag=(ylimmag0,ylimmag1)
ax2.set_ylim(ylimmag)
# Label the axes
ax.set_ylabel(r'$F_\nu$ (uJy)', size=20)
zsubscript=str(self.redshift)
topxlabel = r'$t_{z=%s}$ (s)' % zsubscript
ax.set_xlabel(r'$t$ (s)', size=20)
ax2.set_ylabel('AB Mag',size=20)
ax3.set_xlabel(topxlabel,size=20)
for label in ax.xaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
for label in ax.yaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
for label in ax2.yaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
for label in ax3.xaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
acceptlabels=['K','H','J',"z'","I","i'","R","r'","V","g'","B"]
if legend:
# hugely convoluted way to get the legend the way I want
handles, labels = ax.get_legend_handles_labels()
print handles
print labels
newhandles=[]
newlabels=[]
# sort the legend symbols
i=0
strt=0
stop=maxsource+1
fullindices = np.arange(0,len(labels))
while i < len(sources):
newsublabels=[]
sorted_labels=[]
new_lab_ind_tup=[]
sublabels = labels[strt:stop]
indices = np.arange(0,maxsource+1)
lab_ind_tup = zip(sublabels,indices)
for labtup in lab_ind_tup:
if labtup[0] in sources or labtup[0] == ' ': #only deal with filters
new_lab_ind_tup.append(labtup)
else:
print acceptlabels.index(labtup[0])
sorted_labels.append((acceptlabels.index(labtup[0]),labtup))
sorted_labels.sort()
print sorted_labels
for item in sorted_labels:
new_lab_ind_tup.append(item[1])
print lab_ind_tup
print new_lab_ind_tup
for indxx in np.arange(0,maxsource+1):
fullindices[lab_ind_tup[indxx][1]+strt]=new_lab_ind_tup[indxx][1]+strt
print new_lab_ind_tup
strt+=maxsource+1
stop+=maxsource+1
i+=1
print fullindices
for indd in fullindices:
newlabels.append(labels[indd])
newhandles.append(handles[indd])
print newlabels
leg = ax.legend()
from pylab import setp
setp(leg.get_texts(),fontsize=2)
setp(leg.get_title(),fontsize=2)
ax.legend(newhandles,newlabels,loc=3,numpoints=1,frameon=False,ncol=len(sources))
if save:
xrtstr=''
if incl_xrt:
xrtstr = '_xrt'
filepath = storepath + 'LC_' + self.name.replace('\,','') + xrtstr + '.png'
fig.savefig(filepath)
filepath = storepath + 'LC_' + self.name.replace('\,','') + xrtstr + '.pdf'
fig.savefig(filepath)
if show:
fig.show()
def PlotLC(self,
show=True,
save=True,
legend=True,
residualscale=False,
xlimits=None,
ylimits=None,
figsize=(13, 8),
incl_xrt=False):
'''
show: Plot to screen
save: Save to disk
legend: include a legend
residualscale: BETA. CURRENTLY ONLY FOR USE WITH GRB120119A. HACK.
xlimits: optional tuple of limits (observer frame)
ylimits: optional tuple of limits (flux units)
figsize: figsize tuple in inches
'''
# set font
rc('font', family='Times New Roman')
fig = plt.figure(figsize=figsize)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
ax.loglog()
# Plot the XRT data if desired
if incl_xrt:
obslist = ['BAT_unknown', 'XRT_unknown']
for obstr in obslist:
ob = self.obsdict[obstr]
label = obstr.replace('_', ' ')
label = label.replace(' unknown', '')
detectinds = np.array([not a for a in ob.isupperlist])
ax.errorbar(np.array(ob.tmidlist)[detectinds],
ob.fluxarr[detectinds],
yerr=ob.fluxerrarr[detectinds],
color=ob.color,
fmt=ob.marker,
label=label)
leg = ax.legend(loc=3,
borderaxespad=1.2,
numpoints=1,
frameon=False)
from pylab import setp
setp(leg.get_texts(), fontsize=20)
setp(leg.get_title(), fontsize=20)
## HACK THiS IS AWFUL AND REMOVES DATA. for use ONLY for one time plots
if residualscale:
# first remove the xrt and bat data if it exists
removelist = ['BAT_unknown', 'XRT_unknown']
for key in removelist:
if key in self.obsdict:
del (self.obsdict[key])
from Modelling.ExtinctModel import CorrectFluxForGalExt
filtlist = ['K', 'H', 'J', "z'", 'I', "i'", 'R', "r'", 'V',
'B'] # liverpool are just estimates!
wave_Alist = []
# loop through and grab the wavlengths for each filter
for filttt in filtlist:
for key, ob in self.obsdict.iteritems():
if ob.filtstr == filttt:
if ob.filt.wave_A not in wave_Alist:
wave_Alist.append(ob.filt.wave_A)
wave_Alist = np.array(wave_Alist)
removelist = []
fluxconv_uncorr = np.array([
4312.1, 2522.7, 1358.6, 654.0, 456.1, 340.6, 193.6, 160.6,
109.9, 45
])
fluxconv_uncorrerr = np.array(
[145., 80., 45., 26., 19, 16., 8.2, 6.7, 5.1, 2.5])
fluxconv, fluxconverr = CorrectFluxForGalExt(
self.galebv, wave_Alist, fluxconv_uncorr, fluxconv_uncorrerr)
fluxconv = list(fluxconv)
sed = zip(filtlist, fluxconv)
for key, ob in self.obsdict.iteritems():
if ob.filtstr not in filtlist:
removelist.append(key)
else:
index = filtlist.index(ob.filtstr)
ob.gcfluxarr *= fluxconv[0] / fluxconv[index]
ob.gcfluxerrarr *= fluxconv[0] / fluxconv[index]
for key in removelist:
del (self.obsdict[key])
##HACK
# get list of all sources of observations for use in legend-making
sources = {}
filters = []
for key, ob in self.obsdict.iteritems():
if ob.filt != None:
if ob.filtstr not in filters:
filters.append(ob.filtstr)
detectinds = np.array([not a for a in ob.isupperlist])
if detectinds.any(
): # only plot here if we have at least one detection
if ob.source not in sources:
sources.update(
{ob.source: 1}
) #collecting number of detections for each filter for legend
else:
sources[ob.source] += 1
print sources
#HACK to get most number of sources to left. smarts has most. all alphabetical
sourcenames = sources.keys()
sourcenames.sort()
sourcenames = sourcenames[::-1] #reverse; have smarts first
# CAN HACK AS NECESSARY FOR NEW SOURCES - JUST PUT SOURCENAMES IN THE ORDER YOU WANT
nsourcelist = [] # get the maximum number of instances for each source
for nsource in sources.itervalues():
nsourcelist.append(nsource)
maxsource = max(nsourcelist)
for key, nsource in sources.iteritems():
sources[key] = abs(
nsource - maxsource
) #now the val is how many blank spaces to add for the legend
print sources
print filters
for source in sourcenames: # loop through each source for ordering purposes
i = 0
while i < sources[source]:
ax.errorbar((100, 100), (100, 100),
label=' ',
color='white',
marker=None)
i += 1
ax.errorbar((100, 100), (100, 100),
label=source,
color='white',
marker=None)
for key, ob in self.obsdict.iteritems():
if ob.filt != None and ob.source == source:
upperinds = np.array(ob.isupperlist)
detectinds = np.array([not a for a in ob.isupperlist])
label = ob.filtstr
if detectinds.any(
): # only plot here if we have at least one detection
ax.errorbar(np.array(ob.tmidlist)[detectinds],
ob.gcfluxarr[detectinds],
yerr=ob.gcfluxerrarr[detectinds],
color=ob.color,
fmt=ob.marker,
label=label)
if upperinds.any(
): # only plot here if we have at least one upper limit
ax.errorbar(np.array(ob.tmidlist)[upperinds],
ob.gcfluxarr[upperinds],
yerr=ob.gcfluxerrarr[upperinds],
color=ob.color,
fmt='v')
# ax.set_ylim(1,1E5)
if xlimits:
ax.set_xlim(xlimits)
if ylimits:
ax.set_ylim(ylimits)
old_ylim = ax.get_ylim() # saving for later, as gets modified..
ax2 = ax.twinx()
ax3 = ax.twiny()
ax3.loglog()
xobstime = ax.get_xlim()
xresttime0 = xobstime[0] / (1 + self.redshift)
xresttime1 = xobstime[1] / (1 + self.redshift)
xrest = (xresttime0, xresttime1)
ax3.set_xlim(xrest)
# duplicate axis for AB mag
ax.set_ylim(old_ylim)
ylimflux = ax.get_ylim()
ylimmag0 = flux2abmag(ylimflux[0])
ylimmag1 = flux2abmag(ylimflux[1])
ylimmag = (ylimmag0, ylimmag1)
ax2.set_ylim(ylimmag)
# Label the axes
ax.set_ylabel(r'$F_\nu$ (uJy)', size=20)
zsubscript = str(self.redshift)
topxlabel = r'$t_{z=%s}$ (s)' % zsubscript
ax.set_xlabel(r'$t$ (s)', size=20)
ax2.set_ylabel('AB Mag', size=20)
ax3.set_xlabel(topxlabel, size=20)
for label in ax.xaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
for label in ax.yaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
for label in ax2.yaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
for label in ax3.xaxis.get_ticklabels():
# label is a Text instance
# label.set_color('red')
# label.set_rotation(45)
label.set_fontsize(20)
acceptlabels = [
'K', 'H', 'J', "z'", "I", "i'", "R", "r'", "V", "g'", "B"
]
if legend:
# hugely convoluted way to get the legend the way I want
handles, labels = ax.get_legend_handles_labels()
print handles
print labels
newhandles = []
newlabels = []
# sort the legend symbols
i = 0
strt = 0
stop = maxsource + 1
fullindices = np.arange(0, len(labels))
while i < len(sources):
newsublabels = []
sorted_labels = []
new_lab_ind_tup = []
sublabels = labels[strt:stop]
indices = np.arange(0, maxsource + 1)
lab_ind_tup = zip(sublabels, indices)
for labtup in lab_ind_tup:
if labtup[0] in sources or labtup[
0] == ' ': #only deal with filters
new_lab_ind_tup.append(labtup)
else:
print acceptlabels.index(labtup[0])
sorted_labels.append(
(acceptlabels.index(labtup[0]), labtup))
sorted_labels.sort()
print sorted_labels
for item in sorted_labels:
new_lab_ind_tup.append(item[1])
print lab_ind_tup
print new_lab_ind_tup
for indxx in np.arange(0, maxsource + 1):
fullindices[lab_ind_tup[indxx][1] +
strt] = new_lab_ind_tup[indxx][1] + strt
print new_lab_ind_tup
strt += maxsource + 1
stop += maxsource + 1
i += 1
print fullindices
for indd in fullindices:
newlabels.append(labels[indd])
newhandles.append(handles[indd])
print newlabels
leg = ax.legend()
from pylab import setp
setp(leg.get_texts(), fontsize=2)
setp(leg.get_title(), fontsize=2)
ax.legend(newhandles,
newlabels,
loc=3,
numpoints=1,
frameon=False,
ncol=len(sources))
if save:
xrtstr = ''
if incl_xrt:
xrtstr = '_xrt'
filepath = storepath + 'LC_' + self.name.replace(
'\,', '') + xrtstr + '.png'
fig.savefig(filepath)
filepath = storepath + 'LC_' + self.name.replace(
'\,', '') + xrtstr + '.pdf'
fig.savefig(filepath)
if show:
fig.show()
def PlotXRTlc(self,show=True,save=True,legend=True,
obslist=['BAT_unknown','XRT_unknown','PAIRITEL_K'],
xlimits=None,ylimits=None,figsize=None):
'''
show: Plot to screen
save: Save to disk
legend: include a legend
obslist: parameters to plot
xlimits: optional tuple of limits (observer frame)
ylimits: optional tuple of limits (flux units)
figsize: figsize tuple in inches
'''
# set font
# EDIT TO SHOW MORE THAN JUST BAT/XRT/KBAND
rc('font', family='Times New Roman')
if not figsize:
fig=plt.figure()
else:
fig=plt.figure(figsize=figsize)
ax=fig.add_axes([0.1,0.1,0.8,0.8])
ax.loglog()
if not 'XRT_unknown' in self.obsdict:
print 'Cannot find XRT data; skipping plot'
return
for obstr in obslist:
ob = self.obsdict[obstr]
label= obstr.replace('_',' ')
label= label.replace(' unknown','')
detectinds = np.array([not a for a in ob.isupperlist])
ax.errorbar(np.array(ob.tmidlist)[detectinds],ob.fluxarr[detectinds],yerr=ob.fluxerrarr[detectinds], color=ob.color, fmt=ob.marker, label=label)
# COPY FROM PlotLC
old_ylim=ax.get_ylim() # saving for later, as gets modified..
ax2=ax.twinx()
ax3=ax.twiny()
ax3.loglog()
if xlimits:
ax.set_xlim(xlimits)
if ylimits:
ax.set_ylim(ylimits)
xobstime=ax.get_xlim()
xresttime0=xobstime[0]/(1+self.redshift)
xresttime1=xobstime[1]/(1+self.redshift)
xrest=(xresttime0,xresttime1)
ax3.set_xlim(xrest)
# duplicate axis for AB mag
ax.set_ylim(old_ylim)
ylimflux=ax.get_ylim()
ylimmag0=flux2abmag(ylimflux[0])
ylimmag1=flux2abmag(ylimflux[1])
ylimmag=(ylimmag0,ylimmag1)
ax2.set_ylim(ylimmag)
# Label the axes
ax.set_ylabel(r'$F_\nu$ (uJy)',size=16)
zsubscript=str(self.redshift)
topxlabel = r'$t_{z=%s}$ (s)' % zsubscript
ax.set_xlabel(r'$t$ (s)')
ax2.set_ylabel('AB Mag',size=16)
ax3.set_xlabel(topxlabel,size=16)
ax.legend(loc=3,numpoints=1,frameon=False)
if save:
filepath = storepath + 'LCxrt_' + self.name.replace('\,','') + '.png'
fig.savefig(filepath)
filepath = storepath + 'LCxrt_' + self.name.replace('\,','') + '.pdf'
fig.savefig(filepath)
if show:
fig.show()
def PlotXRTlc(self,
show=True,
save=True,
legend=True,
obslist=['BAT_unknown', 'XRT_unknown', 'PAIRITEL_K'],
xlimits=None,
ylimits=None,
figsize=None):
'''
show: Plot to screen
save: Save to disk
legend: include a legend
obslist: parameters to plot
xlimits: optional tuple of limits (observer frame)
ylimits: optional tuple of limits (flux units)
figsize: figsize tuple in inches
'''
# set font
# EDIT TO SHOW MORE THAN JUST BAT/XRT/KBAND
rc('font', family='Times New Roman')
if not figsize:
fig = plt.figure()
else:
fig = plt.figure(figsize=figsize)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
ax.loglog()
if not 'XRT_unknown' in self.obsdict:
print 'Cannot find XRT data; skipping plot'
return
for obstr in obslist:
ob = self.obsdict[obstr]
label = obstr.replace('_', ' ')
label = label.replace(' unknown', '')
detectinds = np.array([not a for a in ob.isupperlist])
ax.errorbar(np.array(ob.tmidlist)[detectinds],
ob.fluxarr[detectinds],
yerr=ob.fluxerrarr[detectinds],
color=ob.color,
fmt=ob.marker,
label=label)
# COPY FROM PlotLC
old_ylim = ax.get_ylim() # saving for later, as gets modified..
ax2 = ax.twinx()
ax3 = ax.twiny()
ax3.loglog()
if xlimits:
ax.set_xlim(xlimits)
if ylimits:
ax.set_ylim(ylimits)
xobstime = ax.get_xlim()
xresttime0 = xobstime[0] / (1 + self.redshift)
xresttime1 = xobstime[1] / (1 + self.redshift)
xrest = (xresttime0, xresttime1)
ax3.set_xlim(xrest)
# duplicate axis for AB mag
ax.set_ylim(old_ylim)
ylimflux = ax.get_ylim()
ylimmag0 = flux2abmag(ylimflux[0])
ylimmag1 = flux2abmag(ylimflux[1])
ylimmag = (ylimmag0, ylimmag1)
ax2.set_ylim(ylimmag)
# Label the axes
ax.set_ylabel(r'$F_\nu$ (uJy)', size=16)
zsubscript = str(self.redshift)
topxlabel = r'$t_{z=%s}$ (s)' % zsubscript
ax.set_xlabel(r'$t$ (s)')
ax2.set_ylabel('AB Mag', size=16)
ax3.set_xlabel(topxlabel, size=16)
ax.legend(loc=3, numpoints=1, frameon=False)
if save:
filepath = storepath + 'LCxrt_' + self.name.replace('\,',
'') + '.png'
fig.savefig(filepath)
filepath = storepath + 'LCxrt_' + self.name.replace('\,',
'') + '.pdf'
fig.savefig(filepath)
if show:
fig.show()
