def launch(self, data_file, **kwargs):
try:
parser = NetworkxParser(self.storage_path, **kwargs)
net = networkx.read_gpickle(data_file)
connectivity = parser.parse(net)
return [connectivity]
except ParseException, excep:
self.log.exception("Could not process Connectivity")
raise LaunchException(excep)
def launch(self, data_file, **kwargs):
try:
parser = NetworkxParser(self.storage_path, **kwargs)
net = networkx.read_gpickle(data_file)
connectivity = parser.parse(net)
return [connectivity]
except ParseException as excep:
self.log.exception("Could not process Connectivity")
raise LaunchException(excep)
def launch(self, view_model):
# type: (NetworkxImporterModel) -> [ConnectivityIndex]
try:
parser = NetworkxParser(view_model)
net = pandas.read_pickle(view_model.data_file)
connectivity = parser.parse(net)
return h5.store_complete(connectivity, self.storage_path)
except ParseException as excep:
self.log.exception("Could not process Connectivity")
raise LaunchException(excep)
def get_upload_input_tree(self):
tree = [{'name': 'data_file', 'type': 'upload', 'required_type': '.gpickle',
'label': 'Please select file to import', 'required': True}]
tree.extend(NetworkxParser.prepare_input_params_tree())
return tree
def get_upload_input_tree(self):
tree = [{'name': 'data_file', 'type': 'upload', 'required_type': '.gpickle',
'label': 'Please select file to import', 'required': True}]
tree.extend(NetworkxParser.prepare_input_params_tree())
return tree
def get_upload_input_tree(self):
"""
Define as input parameter, a CFF archive.
"""
tree = [{
'name': 'cff',
'type': 'upload',
'required_type': '.cff',
'label': 'CFF archive',
'required': True,
'description': 'Connectome File Format archive expected'
}]
tree.extend(
NetworkxParser.prepare_input_params_tree(prefix="CNetwork: "))
tree.append({
'name':
'should_center',
'type':
'bool',
'default':
False,
'label':
'CSurface: Center surfaces',
'description':
'Center surfaces using vertices positions mean along axes'
})
return tree
def _parse_connectome_network(self, connectome_network, warning_message, **kwargs):
"""
Parse data from a NetworkX object and save it in Connectivity DataTypes.
"""
connectivities = []
parser = NetworkxParser(self.storage_path, **kwargs)
for net in connectome_network:
try:
net.load()
connectivity = parser.parse(net.data)
connectivity.user_tag_1 = str(connectivity.weights.shape[0]) + " regions"
connectivities.append(connectivity)
except ParseException:
self.logger.exception("Could not process Connectivity")
warning_message += "Problem when importing Connectivities!! \n"
return connectivities
def _parse_connectome_network(self, connectome_network, warning_message, **kwargs):
"""
Parse data from a NetworkX object and save it in Connectivity DataTypes.
"""
connectivities = []
parser = NetworkxParser(self.storage_path, **kwargs)
for net in connectome_network:
try:
net.load()
connectivity = parser.parse(net.data)
connectivity.user_tag_1 = connectivity.weights.shape[0]
connectivities.append(connectivity)
except ParseException:
self.logger.exception("Could not process Connectivity")
warning_message += "Problem when importing Connectivities!! \n"
return connectivities
def get_upload_input_tree(self):
"""
Define as input parameter, a CFF archive.
"""
tree = [{'name': 'cff', 'type': 'upload', 'required_type': '.cff',
'label': 'CFF archive', 'required': True,
'description': 'Connectome File Format archive expected'}]
tree.extend(NetworkxParser.prepare_input_params_tree(prefix="CNetwork: "))
tree.append({'name': 'should_center', 'type': 'bool', 'default': False, 'label': 'CSurface: Center surfaces',
'description': 'Center surfaces using vertices positions mean along axes'})
return tree
def get_upload_input_tree(self):
tree = [
{
"name": "data_file",
"type": "upload",
"required_type": ".gpickle",
"label": "Please select file to import",
"required": True,
}
]
tree.extend(NetworkxParser.prepare_input_params_tree())
return tree
