def build_manifest(self, file_name):
'''Creation of default path specifications.
Parameters
----------
file_name : string
where to save it
'''
manifest_builder = ManifestBuilder()
manifest_builder.set_version(self.MANIFEST_VERSION)
manifest_builder = self.add_manifest_paths(manifest_builder)
manifest_builder.write_json_file(file_name)
def build_manifest(self, file_name):
'''Creation of default path specifications.
Parameters
----------
file_name : string
where to save it
'''
manifest_builder = ManifestBuilder()
manifest_builder.set_version(self.MANIFEST_VERSION)
manifest_builder = self.add_manifest_paths(manifest_builder)
manifest_builder.write_json_file(file_name)
def build_manifest(self, file_name):
"""
Construct a manifest for this Cache class and save it in a file.
Parameters
----------
file_name: string
File location to save the manifest.
"""
mb = ManifestBuilder()
mb.set_version(self.MANIFEST_VERSION)
mb.add_path('BASEDIR', '.')
mb.add_path(self.CELLS_KEY, 'cells.json',
typename='file', parent_key='BASEDIR')
mb.add_path(self.EPHYS_DATA_KEY, 'specimen_%d/ephys.nwb',
typename='file', parent_key='BASEDIR')
mb.add_path(self.EPHYS_FEATURES_KEY, 'ephys_features.csv',
typename='file', parent_key='BASEDIR')
mb.add_path(self.MORPHOLOGY_FEATURES_KEY, 'morphology_features.csv',
typename='file', parent_key='BASEDIR')
mb.add_path(self.RECONSTRUCTION_KEY, 'specimen_%d/reconstruction.swc',
typename='file', parent_key='BASEDIR')
mb.add_path(self.MARKER_KEY, 'specimen_%d/reconstruction.marker',
typename='file', parent_key='BASEDIR')
mb.add_path(self.EPHYS_SWEEPS_KEY, 'specimen_%d/ephys_sweeps.json',
typename='file', parent_key='BASEDIR')
mb.write_json_file(file_name)
def build_manifest(self, file_name):
manifest_builder = ManifestBuilder()
manifest_builder.set_version(DummyCache.VERSION)
manifest_builder.write_json_file(file_name)
def build_manifest(self, file_name):
"""
Construct a manifest for this Cache class and save it in a file.
Parameters
----------
file_name: string
File location to save the manifest.
"""
mb = ManifestBuilder()
mb.set_version(self.MANIFEST_VERSION)
mb.add_path('BASEDIR', '.')
mb.add_path(self.EXPERIMENT_CONTAINERS_KEY,
'experiment_containers.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EXPERIMENTS_KEY,
'ophys_experiments.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EXPERIMENT_DATA_KEY,
'ophys_experiment_data/%d.nwb',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.ANALYSIS_DATA_KEY,
'ophys_experiment_analysis/%d_%s_analysis.h5',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EVENTS_DATA_KEY,
'ophys_experiment_events/%d_events.npz',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.CELL_SPECIMENS_KEY,
'cell_specimens.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.STIMULUS_MAPPINGS_KEY,
'stimulus_mappings.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(
self.EYE_GAZE_DATA_KEY,
'ophys_eye_gaze_mapping/%d_eyetracking_dlc_to_screen_mapping.h5',
typename='file',
parent_key='BASEDIR')
mb.write_json_file(file_name)
def build_manifest(self, file_name):
"""
Construct a manifest for this Cache class and save it in a file.
Parameters
----------
file_name: string
File location to save the manifest.
"""
manifest_builder = ManifestBuilder()
manifest_builder.add_path('BASEDIR', '.')
manifest_builder.add_path(self.EXPERIMENTS_KEY,
'experiments.json',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.STRUCTURES_KEY,
'structures.csv',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.STRUCTURE_UNIONIZES_KEY,
'experiment_%d/structure_unionizes.csv',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.ANNOTATION_KEY,
'annotation_%d.nrrd',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.TEMPLATE_KEY,
'average_template_%d.nrrd',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.INJECTION_DENSITY_KEY,
'experiment_%d/injection_density_%d.nrrd',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.INJECTION_FRACTION_KEY,
'experiment_%d/injection_fraction_%d.nrrd',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.DATA_MASK_KEY,
'experiment_%d/data_mask_%d.nrrd',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.PROJECTION_DENSITY_KEY,
'experiment_%d/projection_density_%d.nrrd',
parent_key='BASEDIR',
typename='file')
manifest_builder.add_path(self.STRUCTURE_MASK_KEY,
'structure_masks/structure_%d.nrrd',
parent_key='BASEDIR',
typename='file')
manifest_builder.write_json_file(file_name)
def build_manifest(self, file_name):
"""
Construct a manifest for this Cache class and save it in a file.
Parameters
----------
file_name: string
File location to save the manifest.
"""
manifest_builder = ManifestBuilder()
manifest_builder.add_path("BASEDIR", ".")
manifest_builder.add_path(self.EXPERIMENTS_KEY, "experiments.json", parent_key="BASEDIR", typename="file")
manifest_builder.add_path(self.STRUCTURES_KEY, "structures.csv", parent_key="BASEDIR", typename="file")
manifest_builder.add_path(
self.STRUCTURE_UNIONIZES_KEY, "experiment_%d/structure_unionizes.csv", parent_key="BASEDIR", typename="file"
)
manifest_builder.add_path(self.CCF_VERSION_KEY, "%s", parent_key="BASEDIR", typename="dir")
manifest_builder.add_path(
self.ANNOTATION_KEY, "annotation_%d.nrrd", parent_key=self.CCF_VERSION_KEY, typename="file"
)
manifest_builder.add_path(self.TEMPLATE_KEY, "average_template_%d.nrrd", parent_key="BASEDIR", typename="file")
manifest_builder.add_path(
self.INJECTION_DENSITY_KEY, "experiment_%d/injection_density_%d.nrrd", parent_key="BASEDIR", typename="file"
)
manifest_builder.add_path(
self.INJECTION_FRACTION_KEY,
"experiment_%d/injection_fraction_%d.nrrd",
parent_key="BASEDIR",
typename="file",
)
manifest_builder.add_path(
self.DATA_MASK_KEY, "experiment_%d/data_mask_%d.nrrd", parent_key="BASEDIR", typename="file"
)
manifest_builder.add_path(
self.PROJECTION_DENSITY_KEY,
"experiment_%d/projection_density_%d.nrrd",
parent_key="BASEDIR",
typename="file",
)
manifest_builder.add_path(
self.STRUCTURE_MASK_KEY, "structure_masks/structure_%d.nrrd", parent_key="BASEDIR", typename="file"
)
manifest_builder.write_json_file(file_name)
def build_manifest(self, file_name):
"""
Construct a manifest for this Cache class and save it in a file.
Parameters
----------
file_name: string
File location to save the manifest.
"""
mb = ManifestBuilder()
mb.set_version(self.MANIFEST_VERSION)
mb.add_path('BASEDIR', '.')
mb.add_path(self.CELLS_KEY,
'cells.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EPHYS_DATA_KEY,
'specimen_%d/ephys.nwb',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EPHYS_FEATURES_KEY,
'ephys_features.csv',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.MORPHOLOGY_FEATURES_KEY,
'morphology_features.csv',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.RECONSTRUCTION_KEY,
'specimen_%d/reconstruction.swc',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.MARKER_KEY,
'specimen_%d/reconstruction.marker',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EPHYS_SWEEPS_KEY,
'specimen_%d/ephys_sweeps.json',
typename='file',
parent_key='BASEDIR')
mb.write_json_file(file_name)
def build_manifest(self, file_name):
"""
Construct a manifest for this Cache class and save it in a file.
Parameters
----------
file_name: string
File location to save the manifest.
"""
mb = ManifestBuilder()
mb.add_path('BASEDIR', '.')
mb.add_path(self.EXPERIMENT_CONTAINERS_KEY,
'experiment_containers.json', typename='file', parent_key='BASEDIR')
mb.add_path(self.EXPERIMENTS_KEY, 'ophys_experiments.json',
typename='file', parent_key='BASEDIR')
mb.add_path(self.EXPERIMENT_DATA_KEY, 'ophys_experiment_data/%d.nwb',
typename='file', parent_key='BASEDIR')
mb.add_path(self.CELL_SPECIMENS_KEY, 'cell_specimens.json',
typename='file', parent_key='BASEDIR')
mb.add_path(self.STIMULUS_MAPPINGS_KEY, 'stimulus_mappings.json',
typename='file', parent_key='BASEDIR')
mb.write_json_file(file_name)
def builder():
b = ManifestBuilder()
b.add_path('BASEDIR', '/home/username/example')
return b
def build_manifest(self, file_name):
"""
Construct a manifest for this Cache class and save it in a file.
Parameters
----------
file_name: string
File location to save the manifest.
"""
mb = ManifestBuilder()
mb.add_path('BASEDIR', '.')
mb.add_path(self.EXPERIMENT_CONTAINERS_KEY,
'experiment_containers.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EXPERIMENTS_KEY,
'ophys_experiments.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.EXPERIMENT_DATA_KEY,
'ophys_experiment_data/%d.nwb',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.CELL_SPECIMENS_KEY,
'cell_specimens.json',
typename='file',
parent_key='BASEDIR')
mb.add_path(self.STIMULUS_MAPPINGS_KEY,
'stimulus_mappings.json',
typename='file',
parent_key='BASEDIR')
mb.write_json_file(file_name)
def to_manifest(self, manifest_path=None):
b = ManifestBuilder()
b.add_path('BASEDIR', os.path.realpath(os.curdir))
b.add_path('WORKDIR', os.path.realpath(os.curdir))
b.add_path('MORPHOLOGY', self.morphology_path(), typename='file')
b.add_path('CODE_DIR', 'templates')
b.add_path('MODFILE_DIR', 'modfiles')
for modfile in self.mod_file_entries():
b.add_path('MOD_FILE_%s' %
(os.path.splitext(modfile['filename'])[0]),
os.path.join(modfile['storage_directory'],
modfile['filename']),
typename='file',
format='MODFILE')
b.add_path('neuronal_model_run_data', self.lims_path, typename='file')
b.add_path('stimulus_path',
self.stimulus_path(),
typename='file',
format='NWB')
b.add_path('manifest',
os.path.join(os.path.realpath(os.curdir), manifest_path),
typename='file')
neuronal_model_run_id = self.lims_data['id']
nwb_file_name, extension = \
os.path.splitext(os.path.basename(self.stimulus_path()))
b.add_path('output_path',
'%d_virtual_experiment%s' %
(neuronal_model_run_id, extension),
typename='file',
parent_key='WORKDIR',
format='NWB')
b.add_path('fit_parameters', self.fit_parameters_path())
b.add_section(
'biophys', {
"biophys": [{
"model_file": [manifest_path,
self.fit_parameters_path()],
"model_type":
self.model_type()
}]
})
b.add_section(
'stimulus_conf', {
"runs": [{
"neuronal_model_run_id": neuronal_model_run_id,
"sweeps": self.sweep_numbers(),
"sweeps_by_type": self.sweep_numbers_by_type()
}]
})
b.add_section(
'hoc_conf',
{"neuron": [{
"hoc": ["stdgui.hoc", "import3d.hoc", "cell.hoc"]
}]})
m = Manifest(config=b.path_info)
if manifest_path != None:
b.write_json_file(manifest_path, overwrite=True)
return m
def builder():
b = ManifestBuilder()
b.add_path('BASEDIR', '/home/username/example')
return b
def build_manifest(self, manifest_path=None):
b = ManifestBuilder()
b.add_path('BASEDIR', os.path.realpath(os.curdir))
b.add_path('WORKDIR', self.output_directory())
b.add_path('MORPHOLOGY', self.morphology_path(), typename='file')
b.add_path('MODFILE_DIR', 'modfiles')
for modfile in self.mod_file_entries():
b.add_path('MOD_FILE_%s' %
(os.path.splitext(modfile['filename'])[0]),
os.path.join(modfile['storage_directory'],
modfile['filename']),
typename='file',
format='MODFILE')
b.add_path('stimulus_path',
self.stimulus_path(),
typename='file',
format='NWB')
b.add_path('manifest',
os.path.join(os.path.realpath(os.curdir), manifest_path),
typename='file')
b.add_path('output',
os.path.basename(self.stimulus_path()),
typename='file',
parent_key='WORKDIR',
format='NWB')
b.add_path('neuronal_model_data', self.lims_path, typename='file')
b.add_path('upfile',
'upbase.dat',
typename='file',
parent_key='WORKDIR')
b.add_path('downfile',
'downbase.dat',
typename='file',
parent_key='WORKDIR')
b.add_path('passive_fit_data',
'passive_fit_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('stage_1_jobs',
'stage_1_jobs.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_1_file',
'fit_1_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_2_file',
'fit_2_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_3_file',
'fit_3_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_type_path',
typename='file',
spec='%s',
parent_key='WORKDIR')
b.add_path('target_path',
typename='file',
spec='target.json',
parent_key='WORKDIR')
b.add_path('fit_config_json',
typename='file',
spec='%s/config.json',
parent_key='WORKDIR')
b.add_path('final_hof_fit',
typename='file',
spec='%s/s%d/final_hof_fit.txt',
parent_key='WORKDIR')
b.add_path('final_hof',
typename='file',
spec='%s/s%d/final_hof.txt',
parent_key='WORKDIR')
b.add_path('output_fit_file', typename='file', spec='fit_%s_%s.json')
b.add_section('biophys',
{"biophys": [{
"model_file": [manifest_path]
}]})
b.add_section(
'stimulus_conf', {
"runs": [{
"sweeps": self.sweep_numbers(),
"specimen_id": self.lims_data['specimen_id']
}]
})
b.add_section(
'hoc_conf',
{"neuron": [{
"hoc": ["stdgui.hoc", "import3d.hoc", "cell.hoc"]
}]})
return b
