def save_events(self, events_to_save):
'''Save the particular events, identified during the classification process.
Args:
events_to_save (list of strs) : What events to save to the file.
'''
# Open up the file to save the data in.
events_filename = 'events_{}.hdf5'.format(self.tag)
self.events_filepath = os.path.join(self.out_dir, events_filename)
f = h5py.File(self.events_filepath, 'a')
# Save the data
for event_type in events_to_save:
data = getattr(self, event_type)
f.create_dataset(event_type, data=data)
utilities.save_parameters(self, f)
# Save the current code versions
f.attrs['linefinder_version'] = utilities.get_code_version(self)
f.attrs['galaxy_dive_version'] = utilities.get_code_version(
read_ahf, instance_type='module')
f.close()
def save_classifications(self, classifications_to_save):
'''Save the results of running the classifier.
Args:
classifications_to_save (list of strs) :
What classifications to save to the file.
'''
# Open up the file to save the data in.
classification_filename = 'classifications_{}.hdf5'.format(self.tag)
self.classification_filepath = os.path.join(
self.out_dir,
classification_filename,
)
f = h5py.File(self.classification_filepath, 'a')
# Save the data
for classification in classifications_to_save:
data = getattr(self, classification)
f.create_dataset(classification, data=data)
utilities.save_parameters(self, f)
# Save the current code versions
f.attrs['linefinder_version'] = utilities.get_code_version(self)
f.attrs['galaxy_dive_version'] = utilities.get_code_version(
read_ahf, instance_type='module')
# Save the snapshot number when the main halo is first resolved.
f.attrs['main_mt_halo_first_snap'] = self.main_mt_halo_first_snap
f.attrs['ind_first_snap'] = self.ind_first_snap
f.close()
def test_works_for_modules(self):
actual = utilities.get_code_version(utilities, instance_type='module')
expected = subprocess.check_output(['git', 'describe', '--always'])
assert actual == expected
def save_selected_ids(self, selected_ids_formatted, data_filters):
# Open up the file to save the data in.
ids_filename = 'ids_full_{}.hdf5'.format(self.tag)
self.ids_filepath = os.path.join(self.out_dir, ids_filename)
f = h5py.File(self.ids_filepath, 'a')
# Save the data
if isinstance(selected_ids_formatted, tuple):
ids, child_ids = selected_ids_formatted
f.create_dataset('target_ids', data=ids)
f.create_dataset('target_child_ids', data=child_ids)
else:
ids = selected_ids_formatted
f.create_dataset('target_ids', data=ids)
# Create groups for the parameters
grp = f.create_group('parameters')
subgrp = f.create_group('parameters/snapshot_parameters')
data_filter_subgrp = f.create_group('parameters/data_filters')
# Save the data parameters
for parameter in self.stored_parameters:
if parameter != 'snapshot_kwargs':
grp.attrs[parameter] = getattr(self, parameter)
# Save the snapshot parameters too
for key in self.snapshot_kwargs.keys():
subgrp.attrs[key] = self.snapshot_kwargs[key]
# Save the data filter values
for key, data_filter in data_filters.items():
df_subgrp = data_filter_subgrp.create_group(key)
for inner_key, value in data_filter.items():
df_subgrp.attrs[inner_key] = value
# Save how many processors we used.
grp.attrs['n_processors'] = self.n_processors
# Save the current code versions
f.attrs['linefinder_version'] = utilities.get_code_version(self)
f.attrs['galaxy_dive_version'] = utilities.get_code_version(
particle_data, instance_type='module')
f.close()
def write_tracked_data(self, formatted_data):
'''Write tracks to a file.
Args:
formatted_data (dict) :
Formatted particle track data.
attrs (dict):
Particle track data attributes.
'''
ptrack, attrs = formatted_data
# Make sure the output location exists
if not os.path.exists(self.out_dir):
os.mkdir(self.out_dir)
self.outname = 'ptracks_{}.hdf5'.format(self.tag)
outpath = os.path.join(self.out_dir, self.outname)
f = h5py.File(outpath, 'w')
# Save data
for keyname in ptrack.keys():
f.create_dataset(keyname, data=ptrack[keyname])
# Save the attributes
for key in attrs.keys():
f.attrs[key] = attrs[key]
# Save the code of the custom_fns as a string too.
if self.custom_fns is not None:
self.custom_fns_str = [
inspect.getsource(_) for _ in self.custom_fns
]
utilities.save_parameters(self, f)
# Save the current code version
f.attrs['linefinder_version'] = utilities.get_code_version(self)
f.attrs['galaxy_dive_version'] = utilities.get_code_version(
read_snapshot, instance_type='module')
f.close()
def write_galaxy_identifications(self, ptrack_gal_ids):
'''Write the data, close the file, and print out information.'''
# Get the number of particles, for use in reporting the time
self.n_particles = self.ptrack['Den'][...].shape[0]
# Close the old dataset
self.ptrack.close()
# Save the data.
save_filename = 'galids_{}.hdf5'.format(self.tag)
self.save_filepath = os.path.join(self.out_dir, save_filename)
f = h5py.File(self.save_filepath, 'w')
for key in ptrack_gal_ids.keys():
f.create_dataset(key, data=ptrack_gal_ids[key])
# Store the main mt halo id
# (as identified by the larges value at the lowest redshift)
if self.main_mt_halo_id is None:
try:
indice = self.halo_data.mtree_halos[0].index.max()
except AttributeError:
self.halo_data.get_mtree_halos(self.mtree_halos_index,
self.halo_file_tag)
indice = self.halo_data.mtree_halos[0].index.max()
m_vir_z0 = self.halo_data.get_mtree_halo_quantity(
quantity='Mvir',
indice=indice,
index=self.mtree_halos_index,
tag=self.halo_file_tag)
f.attrs['main_mt_halo_id'] = m_vir_z0.argmax()
else:
f.attrs['main_mt_halo_id'] = self.main_mt_halo_id
utilities.save_parameters(self, f)
# Save the current code version
f.attrs['linefinder_version'] = utilities.get_code_version(self)
f.attrs['galaxy_dive_version'] = utilities.get_code_version(
galaxy_linker, instance_type='module')
f.close()
def test_works_in_otherdir(self):
cwd = os.getcwd()
# Change directories
os.chdir('../')
result = utilities.get_code_version(self)
assert result is not None
# Change back
os.chdir(cwd)
def test_doesnt_change_dir_upon_failing(self):
true_cwd = os.getcwd()
# Change to a dir that should not be a repository
os.chdir(os.path.expanduser('~'))
cwd = os.getcwd()
result = utilities.get_code_version(self)
now_cwd = os.getcwd()
assert cwd == now_cwd
# Change back
os.chdir(true_cwd)
def test_default(self):
result = utilities.get_code_version(self)
assert result is not None
