def initialize_phoebe(output_dir=None, mpi_ncores=0, logger=True):
if output_dir != None:
try:
os.mkdir(output_dir)
except:
shutil.rmtree(output_dir)
os.mkdir(output_dir)
if logger:
sys.stdout = Logger(output_dir)
phoebe.logger(
clevel='ERROR') # ignore warnings - for tqdm to work properly
phoebe.interactive_checks_off()
phoebe.check_visible_off()
phoebe.interactive_constraints_off()
if mpi_ncores != 0:
phoebe.mpi_on(nprocs=mpi_ncores)
return output_dir
#turn off albedos (legacy requirement)
b.set_value_all('irrad_frac_refl_bol', 0.0)
if plot: print("running phoebe2 model...")
b.run_compute(compute='phoebe2', irrad_method='none', model='phoebe2model')
if gen_comp:
if plot: print("running phoebe1 model...")
b.run_compute(compute='phoebe1', refl_num=0, model='phoebe1model')
b.filter(model='phoebe1model').save('test_blackbody.comp.model')
else:
b.import_model(os.path.join(os.path.dirname(__file__),
'test_blackbody.comp.model'),
model='phoebe1model')
phoebe2_val = b.get_value('fluxes@phoebe2model')
phoebe1_val = b.get_value('fluxes@phoebe1model')
if plot:
b.plot(dataset='lc01', show=True)
assert (np.allclose(phoebe2_val, phoebe1_val, rtol=1e-3, atol=0.))
return b
if __name__ == '__main__':
logger = phoebe.logger(clevel='INFO')
b = test_binary(plot=True, gen_comp=True)
# ## Setup
#
# Let's first make sure we have the latest version of PHOEBE 2.3 installed (uncomment this line if running in an online notebook session such as colab).
# In[1]:
#!pip install -I "phoebe>=2.3,<2.4"
# In[2]:
import phoebe
from phoebe import u # units
import numpy as np
logger = phoebe.logger('error')
# We'll then start with the bundle from the end of the [emcee tutorial](./emcee.ipynb). If you're running this notebook locally, you will need to run that first to create the `emcee_advanced_tutorials.bundle` file that we will use here.
# In[3]:
b = phoebe.load('emcee_advanced_tutorials.bundle')
# ## init_from parameter
#
# In cases where [continuing emcee from a previous run](./emcee_continue_from.ipynb) is insufficient, it may be ncessary to resample a new emcee run from the results of a previous run. This can be useful in several scenarios:
#
# * change the number of walkers
# * resample from the "best" branch when other branches are stuck (NOTE: this is making some assumptions and should be used with caution)
# * change the parameters being sampled (in this case, any NEW parameter will need to have initializing distributions created manually or from some other source)
# * "merge" the results from multiple emcee runs (if RV- and LC-sensitive parameters were sampled independently but now you want to resample simultaneously)
get_ipython().system('pip install -I "phoebe>=2.1,<2.2"')
# As always, let's do imports and initialize a logger and a new bundle. See [Building a System](../tutorials/building_a_system.ipynb) for more details.
# In[1]:
get_ipython().run_line_magic('matplotlib', 'inline')
# In[2]:
import phoebe
from phoebe import u # units
import numpy as np
import matplotlib.pyplot as plt
logger = phoebe.logger()
b = phoebe.default_binary()
# In[3]:
b.set_value(qualifier='pitch', component='primary', value=30)
# Model without Spots
# --------------------------
# In[4]:
b.add_dataset('lc', times=phoebe.linspace(0, 1, 101))
# In[5]:
pb.save('my_passband.pb')
# Getting started
# -----------------
#
# Let us start by importing phoebe, numpy and matplotlib:
# In[1]:
get_ipython().run_line_magic('matplotlib', 'inline')
import phoebe
from phoebe import u # units
import numpy as np
import matplotlib.pyplot as plt
logger = phoebe.logger(clevel='WARNING')
# Passband transmission function
# -----------------------------------
#
# The passband transmission function is typically a user-provided two-column file. The first column is wavelength, and the second column is passband transmission. For the purposes of this tutorial, we will simulate the passband as a uniform box.
# In[2]:
wl = np.linspace(300, 360, 61)
ptf = np.zeros(len(wl))
ptf[(wl >= 320) & (wl <= 340)] = 1.0
# Let us plot this simulated passband transmission function to see what it looks like:
# In[3]:
cb.run_compute(compute='phoebe1', refl_num=0, model='phoebe1model')
phoebe2_val_lc = cb.get_value('fluxes@phoebe2model')
phoebe1_val_lc = cb.get_value('fluxes@phoebe1model')
phoebe2_val_rv1 = cb.get_value('rvs@primary@phoebe2model')[2:48]
phoebe1_val_rv1 = cb.get_value('rvs@primary@phoebe1model')[2:48]
phoebe2_val_rv2 = cb.get_value('rvs@secondary@phoebe2model')[2:48]
phoebe1_val_rv2 = cb.get_value('rvs@secondary@phoebe1model')[2:48]
if plot:
print "max lc atol {}: rtol: {}".format(np.max(phoebe2_val_lc - phoebe1_val_lc), np.max((phoebe2_val_lc - phoebe1_val_lc)/phoebe1_val_lc))
print "max rv1 atol: {} rtol: {}".format(np.max(phoebe2_val_rv1 - phoebe1_val_rv1), np.max((phoebe2_val_rv1 - phoebe1_val_rv1)/phoebe1_val_rv1))
print "max rv2 atol: {} rtol: {}".format(np.max(phoebe2_val_rv2 - phoebe1_val_rv2), np.max((phoebe2_val_rv2 - phoebe1_val_rv2)/phoebe1_val_rv2))
cb.plot(dataset='lc01', show=True)
cb.plot(dataset='rv01', show=True)
assert(np.allclose(phoebe2_val_lc, phoebe1_val_lc, rtol=7e-3, atol=0.))
# note we can't use relative tolerances because those blow up near 0, so
# instead we'll fake a relative tolerance by using the amplitude of the RV curve.
rv_ampl = np.max(np.abs(phoebe1_val_rv1))
rtol = 7e-3
assert(np.allclose(phoebe2_val_rv1, phoebe1_val_rv1, rtol=0., atol=rtol*rv_ampl))
assert(np.allclose(phoebe2_val_rv2, phoebe1_val_rv2, rtol=0., atol=rtol*rv_ampl))
return cb
if __name__ == '__main__':
logger = phoebe.logger(clevel='debug')
cb = test_binary(plot=True)
b.set_value_all('ld_coeffs', [0.0, 0.0])
#turn off albedos (legacy requirement)
b.set_value_all('irrad_frac_refl_bol', 0.0)
print("running phoebe2 model...")
b.run_compute(compute='phoebe2', irrad_method='none', model='phoebe2model')
print("running phoebe1 model...")
b.run_compute(compute='phoebe1', refl_num=0, model='phoebe1model')
phoebe2_val = b.get_value('fluxes@phoebe2model')
phoebe1_val = b.get_value('fluxes@phoebe1model')
if plot:
print("rel: ", ((phoebe2_val - phoebe1_val) / phoebe2_val).max())
print("abs: ", (phoebe2_val - phoebe1_val).max())
# b.plot(dataset='mesh01', show=True)
b.plot(dataset='lc01', legend=True, show=True)
assert (np.allclose(phoebe2_val, phoebe1_val, rtol=2e-3, atol=5e-4))
return b
if __name__ == '__main__':
logger = phoebe.logger(clevel='DEBUG')
b = test_binary(plot=True)
if plot:
print("rv@secondary max rel diff: {}".format(
max(np.abs((phoebe1_val - phoebe2_val) / phoebe2_val))))
assert (np.allclose(phoebe2_val, phoebe1_val, rtol=1e-1, atol=0.))
def test_binary(plot=False, gen_comp=False):
## system = [sma (solRad), period (d)]
system1 = [11, 2.575]
system2 = [215., 257.5]
system3 = [8600., 65000.]
ind = 0
for q in [0.5, 1.]:
for system in [system1, system2, system3]:
ind += 1
b = phoebe.Bundle.default_binary()
b.set_value('sma@binary', system[0])
b.set_value('period@binary', system[1])
b.set_value('q', q)
_beta_vs_legacy(b, ind=ind, plot=plot, gen_comp=gen_comp)
if __name__ == '__main__':
logger = phoebe.logger('debug')
test_binary(plot=True, gen_comp=True)
#
# Before starting any script, it is a good habit to initialize a logger and define which levels of information you want printed to the command line (clevel) and dumped to a file (flevel).
#
# The levels from most to least information are:
#
# * DEBUG
# * INFO
# * WARNING
# * ERROR
# * CRITICAL
#
# In[2]:
logger = phoebe.logger(clevel='WARNING',
flevel='DEBUG',
filename='tutorial.log')
# All of these arguments are optional and will default to clevel='WARNING' if not provided. There is therefore no need to provide a filename if you don't provide a value for flevel.
#
# So with this logger, anything with "WARNING, ERROR, or CRITICAL levels will be printed to the screen. All messages of any level will be written to a file named 'tutorial.log' in the current directory.
#
# Note: the logger messages are not included in the outputs shown below.
#
#
#
# Parameters
# ------------------------
#
# Parameters hold a single value, but need to be aware about their own types, limits, and connection with other Parameters (more on this later when we discuss ParameterSets).
# ### Logger # # Before starting any script, it is a good habit to initialize a logger and define which levels of information you want printed to the command line (clevel) and dumped to a file (flevel). A convenience function is provided at the top-level via [phoebe.logger](../api/phoebe.logger.md) to initialize the logger with any desired level. # # The levels from most to least information are: # # * DEBUG # * INFO # * WARNING # * ERROR # * CRITICAL # # In[2]: logger = phoebe.logger(clevel='INFO', flevel='DEBUG', filename='tutorial.log') # All of these arguments are optional and will default to clevel='WARNING' if not provided. There is therefore no need to provide a filename if you don't provide a value for flevel. # # So with this logger, anything with INFO, WARNING, ERROR, or CRITICAL levels will be printed to the screen. All messages of any level will be written to a file named 'tutorial.log' in the current directory. # # Note: the logger messages are not included in the outputs shown below. # # # # Parameters # ------------------------ # # [Parameters](../api/phoebe.parameters.Parameter.md) hold a single value, but need to be aware about their own types, limits, and connection with other Parameters (more on this later when we discuss [ParameterSets](../api/phoebe.parameters.ParameterSet.md)). #
# In[1]:
#!pip install -I "phoebe>=2.3,<2.4"
# In[2]:
import matplotlib.pyplot as plt
plt.rc('font', family='serif', size=14, serif='STIXGeneral')
plt.rc('mathtext', fontset='stix')
# In[3]:
import phoebe
logger = phoebe.logger('warning')
# In[4]:
b = phoebe.default_binary()
# In[5]:
b.set_value('latex_repr', component='binary', value='orb')
b.set_value('latex_repr', component='primary', value='1')
b.set_value('latex_repr', component='secondary', value='2')
# In[6]:
b.add_distribution(
{
"""
"""
import phoebe
from phoebe import u
import numpy as np
import matplotlib.pyplot as plt
from nose.tools import assert_raises
phoebe.logger('DEBUG')
def test_limits():
b = phoebe.Bundle.default_binary()
assert_raises(ValueError, b.set_value, 'teff@primary', -10)
# NOTE: celsius not supported for all supported astropy versions (not 1.0)
#assert_raises(ValueError, b.set_value, 'teff@primary', -10*u.Celsius)
assert_raises(ValueError, b.set_value, 'requiv@primary', -10 * u.km)
assert_raises(ValueError, b.set_value, 'ecc@binary', 1.0)
return b
if __name__ == '__main__':
logger = phoebe.logger(clevel='INFO')
b = test_limits()
fitParams = json.load(open(fitParamsFileName))
#%%######################create output folder #################################
#
outputPath = dataPath + datetime.now().strftime(
'%Y%m%d_%H%M') + '_' + location + '/'
print('output will be written to %s' % outputPath)
logFileName = sysName + '_' + datetime.now().strftime(
'%Y%m%d_%H%M') + '_log.txt'
os.mkdir(outputPath, )
tl = datetime.now().strftime('%Y%m%d_%H%M')
loggerFileName = outputPath + sysName + '_' + tl + '.log'
logger = phoebe.logger(clevel='CRITICAL',
flevel='DEBUG',
filename=loggerFileName)
print(sysConfig)
#if wrt2log: fd.write('Sys. Config.:\n')
#if wrt2log: fd.write(str(sysConfig)+'\n')
#if wrt2log: fd.flush()
#%% set the parameters into the bundle
#k['period@binary@component']=sysConfig['period']
kb = pb.sysConfig2Bundle(sysConfig, kb)
period = sysConfig['period']
sysfm = sysConfig['measMassfn']
initM1 = sysConfig['M1']
initR1 = sysConfig['rp1']
