def load_manifest(self, file_name, version=None):
'''Read a keyed collection of path specifications.
Parameters
----------
file_name : string
path to the manifest file
Returns
-------
Manifest
'''
if file_name is not None:
if not os.path.exists(file_name):
# make the directory if it doesn't exist already
dirname = os.path.dirname(file_name)
if dirname:
Manifest.safe_mkdir(dirname)
self.build_manifest(file_name)
try:
self.manifest = Manifest(
ju.read(file_name)['manifest'],
os.path.dirname(file_name),
version=version)
except ManifestVersionError as e:
raise ManifestVersionError(("Your manifest file (%s) is out of date" +
" (version '%s' vs '%s'). Please remove this file" +
" and it will be regenerated for you the next"
" time you instantiate this class.") % (file_name, e.found_version, e.version),
e.version, e.found_version)
else:
self.manifest = None
def load_manifest(self, file_name):
'''Read a keyed collection of path specifications.
Parameters
----------
file_name : string
path to the manifest file
Returns
-------
Manifest
'''
if file_name is not None:
if not os.path.exists(file_name):
# make the directory if it doesn't exist already
dirname = os.path.dirname(file_name)
if dirname:
Manifest.safe_mkdir(dirname)
self.build_manifest(file_name)
self.manifest = Manifest(
ju.read(file_name)['manifest'], os.path.dirname(file_name))
else:
self.manifest = None
def main():
parser = argparse.ArgumentParser()
parser.add_argument('cells_csv', help='CSV containing cell metadata')
parser.add_argument('connections_h5',
help='HDF5 file containing cell connectivity')
parser.add_argument('network_vtk_file', help='.vtk output file')
parser.add_argument('--manifest')
parser.add_argument('--morphology_vtk_file')
args = parser.parse_args()
# read in the cell CSV
with open(args.cells_csv, 'r') as f:
r = csv.DictReader(f)
cells = list(r)
# read in the connections from the H5 file
h5u = Hdf5Util()
connections = h5u.read(args.connections_h5)
# write out the results
write_network_vtk(args.network_vtk_file, cells, connections)
if args.manifest:
config = ju.read(args.manifest)
manifest = Manifest(config['manifest'],
relative_base_dir=os.path.dirname(args.manifest))
write_morphology_vtk(args.morphology_vtk_file, cells, manifest)
def load_manifest(self, file_name, version=None):
'''Read a keyed collection of path specifications.
Parameters
----------
file_name : string
path to the manifest file
Returns
-------
Manifest
'''
if file_name is not None:
if not os.path.exists(file_name):
# make the directory if it doesn't exist already
dirname = os.path.dirname(file_name)
if dirname:
Manifest.safe_mkdir(dirname)
self.build_manifest(file_name)
try:
self.manifest = Manifest(
ju.read(file_name)['manifest'],
os.path.dirname(file_name),
version=version)
except ManifestVersionError as e:
if e.outdated is True:
intro = "is out of date"
elif e.outdated is False:
intro = "was made with a newer version of the AllenSDK"
elif e.outdated is None:
intro = "version did not match the expected version"
ref_url = "https://github.com/alleninstitute/allensdk/wiki"
raise ManifestVersionError(("Your manifest file (%s) %s" +
" (its version is '%s', but" +
" version '%s' is expected). " +
" Please remove this file" +
" and it will be regenerated for" +
" you the next time you" +
" instantiate this class." +
" WARNING: There may be new data" +
" files available that replace" +
" the ones you already have" +
" downloaded. Read the notes" +
" for this release for more" +
" details on what has changed" +
" (%s).") %
(file_name, intro,
e.found_version, e.version,
ref_url),
e.version, e.found_version)
self.manifest_path = file_name
else:
self.manifest = None
def to_manifest(self, manifest_path=None):
b = self.build_manifest(manifest_path)
m = Manifest(config=b.path_info)
if manifest_path != None:
b.write_json_file(manifest_path, overwrite=True)
return m
def load_manifest(self, file_name, version=None):
'''Read a keyed collection of path specifications.
Parameters
----------
file_name : string
path to the manifest file
Returns
-------
Manifest
'''
if file_name is not None:
if not os.path.exists(file_name):
# make the directory if it doesn't exist already
dirname = os.path.dirname(file_name)
if dirname:
Manifest.safe_mkdir(dirname)
self.build_manifest(file_name)
try:
self.manifest = Manifest(ju.read(file_name)['manifest'],
os.path.dirname(file_name),
version=version)
except ManifestVersionError as e:
if e.outdated is True:
intro = "is out of date"
elif e.outdated is False:
intro = "was made with a newer version of the AllenSDK"
elif e.outdated is None:
intro = "version did not match the expected version"
raise ManifestVersionError((
"Your manifest file (%s) %s" +
" (its version is '%s', but version '%s' is expected). Please remove this file"
+ " and it will be regenerated for you the next"
" time you instantiate this class.") %
(file_name, intro, e.found_version,
e.version), e.version,
e.found_version)
self.manifest_path = file_name
else:
self.manifest = None
def __init__(self):
self.data = {}
self.reserved_data = []
self.manifest = Manifest()
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 get_manifest(self):
return Manifest(self.path_info)
