def setup_pycecream(self,
test_project_folder='test_pycecream_output',
dream=False):
'''
test pycecream using yasamans script
:return:
'''
#instantiate and remove previous test if present
os.system('rm -rf ' + test_project_folder)
a = pycecream.pycecream()
a.project_folder = test_project_folder
#set the hyperparameters
a.p_accretion_rate_step = 0.1
a.bh_mass = self.BHMass
a.p_inclination = self.disk_inc
a.bh_efficieny = self.BHefficiency
a.p_inclination_step = 0.0
a.hi_frequency = 0.5
a.N_iterations = 20
#add the light curves one at a time
previous_wavelength = np.nan
wavelengths = self.datnorm['wavelength']
names = self.datnorm['name']
LightCurveData = self.datnorm['light curve']
if dream is False:
for i in range(len(names)):
wavelength, lc, name = wavelengths[i], LightCurveData[
i], names[i]
if wavelength == previous_wavelength:
share_previous_lag = True
else:
share_previous_lag = False
a.add_lc(lc,
kind='continuum',
name=name,
wavelength=wavelength,
share_previous_lag=share_previous_lag)
previous_wavelength = wavelength
elif dream is True:
wav_tophat = 0.0
for i in range(len(names)):
wavelength, lc, name = wavelengths[i], LightCurveData[
i], names[i]
if wavelength == previous_wavelength:
share_previous_lag = True
else:
share_previous_lag = False
wav_tophat += -1.0
a.add_lc(lc,
kind='line',
name=name,
wavelength=np.round(wav_tophat, 1),
share_previous_lag=share_previous_lag)
previous_wavelength = wavelength
return a
def run_pycecream(self, test_project_folder='test_pycecream_output'):
'''
test pycecream using yasamans script
:return:
'''
cream_lc0, cream_lc1, cream_lc4, cream_lc2, cream_lc3, cream_lc8, cream_lc5, cream_lc6, cream_lc7 = self.dat
#instantiate and remove previous test if present
os.system('rm -rf ' + test_project_folder)
a = pycecream.pycecream()
a.project_folder = test_project_folder
#step accretion rate?
a.p_accretion_rate_step = 0.1
a.bh_mass = 6.6e8
# MgII Line lightcurve
a.add_lc(cream_lc0,
name='line 0 (MgII)',
kind='line',
background_polynomials=[0.1, 0.1])
a.p_linelag_centroids_step = 0.0
# g-band photometric lightcurves
a.add_lc(cream_lc1,
name='continuum (Bok)',
kind='continuum',
wavelength=4680)
a.add_lc(cream_lc2,
name='continuum 4720 (CFHT 1)',
kind='continuum',
wavelength=4720,
share_previous_lag=True)
a.add_lc(cream_lc3,
name='continuum 4720 (CFHT 2)',
kind='continuum',
wavelength=4720,
share_previous_lag=True)
a.add_lc(cream_lc4,
name='continuum 4686 (SynthPhot)',
kind='continuum',
wavelength=4686,
share_previous_lag=True)
# i-band photometric lightcurves
a.add_lc(cream_lc5,
name='continuum (Bok)',
kind='continuum',
wavelength=7760,
share_previous_lag=False)
a.add_lc(cream_lc6,
name='continuum (CFHT 1)',
kind='continuum',
wavelength=7764,
share_previous_lag=True)
a.add_lc(cream_lc7,
name='continuum (CFHT 2)',
kind='continuum',
wavelength=7764,
share_previous_lag=True)
a.add_lc(cream_lc8,
name='continuum (SynthPhot)',
kind='continuum',
wavelength=7480,
share_previous_lag=True)
a.hi_frequency = 0.5
a.N_iterations = 20
a.run(ncores=4)
self.pc = a
def run_pycecream(self):
'''
test pycecream using yasamans script
:return:
'''
cream_lc0, cream_lc1, cream_lc4, cream_lc2, cream_lc3, cream_lc8, cream_lc5, cream_lc6, cream_lc7 = self.dat
a = pycecream.pycecream()
#step accretion rate?
a.p_accretion_rate_step = 0.1
# MgII Line lightcurve
a.add_lc(cream_lc0, name='line 0 (MgII)', kind='line')
a.p_linelag_centroids_step = 0.0
# g-band photometric lightcurves
a.add_lc(cream_lc1,
name='continuum (Bok)',
kind='continuum',
wavelength=4680)
a.add_lc(cream_lc2,
name='continuum 4720 (CFHT 1)',
kind='continuum',
wavelength=4720,
share_previous_lag=True)
a.add_lc(cream_lc3,
name='continuum 4720 (CFHT 2)',
kind='continuum',
wavelength=4720,
share_previous_lag=True)
a.add_lc(cream_lc4,
name='continuum 4686 (SynthPhot)',
kind='continuum',
wavelength=4686,
share_previous_lag=True)
# i-band photometric lightcurves
a.add_lc(cream_lc5,
name='continuum (Bok)',
kind='continuum',
wavelength=7760,
share_previous_lag=True)
a.add_lc(cream_lc6,
name='continuum (CFHT 1)',
kind='continuum',
wavelength=7764,
share_previous_lag=True)
a.add_lc(cream_lc7,
name='continuum (CFHT 2)',
kind='continuum',
wavelength=7764,
share_previous_lag=True)
a.add_lc(cream_lc8,
name='continuum (SynthPhot)',
kind='continuum',
wavelength=7480,
share_previous_lag=True)
a.hi_frequency = 0.5
a.N_iterations = 20
a.run()
self.pc = a
background_data[:,0] = t background_data[:,1] = x background_data[:,2] = sig dat.append(background_data) # # Section 2: Settup and run PyceCREAM # # # In[2]: import pycecream #instantiate a pycecream object a = pycecream.pycecream() ''' If you use a fortran compiler other than gfortran please indicate here. I just re-enter gfortran here for demonstration purposes even though this is unecassary as gfortran is the default argument. ''' a.fortran_caller = 'gfortran' '''Choose an output directory in which to save the results. This will be a new directory that you have not previously created (pycecream will make it automatically). NOTE: Each new cream simulation must have a new name for "output_directory argument below otherwise an excpetion is raised. This is to prevent accidentally overwriting previous simulations.
for lcf in lightcurve_files:
idxrmid = lcf.find('_rm')
filter = lcf[idxrmid+7]
wavelength_list.append(filter_wavelengths[filter])
'''
sort by increasing wavelength (should already be sorted)
'''
idxsort = np.argsort(wavelength_list)
wavelength_list = [wavelength_list[idx] for idx in idxsort]
lightcurve_files = [lightcurve_files[idx] for idx in idxsort]
'''
instantiate pycecream
'''
pcfit = pycecream.pycecream()
'''
customize for current target (set output directory and bh mass)
'''
pcfit.project_folder = pycecream_output_dir+'/'+group_dir+'/'+target.replace(batch_directory+'/','')
idx_bh_mass = np.where(sdssrm_masses[:,0] == rmid)[0]
if len(idx_bh_mass) > 0:
pcfit.bh_mass = sdssrm_masses[idx_bh_mass[0],1]
else:
pcfit.bh_mass = default_bh_mass
'''
iteratively add each lightcurve
'''
previous_wavelength = -999