def launch(self, data_file):
if data_file is None:
raise LaunchException(
"Please select ZIP file which contains data to import")
#todo warn: all in memory, this is memory hungry; at least twice the tractografy
tracts = []
max_tract_count = 0
with TvbZip(data_file) as zipf:
# todo sort tract8 before tract74 parse ints out of file names
for tractf in zipf.namelist():
vertices_file = zipf.open(tractf)
tract_vertices = numpy.loadtxt(vertices_file,
dtype=numpy.float32)
tracts.append(tract_vertices)
max_tract_count = max(max_tract_count, len(tract_vertices))
vertices_file.close()
vertices_arr = numpy.zeros((len(tracts), max_tract_count, 3))
counts_arr = numpy.zeros((len(tracts), ))
for i, tr in enumerate(tracts):
vertices_arr[i, :len(tr)] = tr
counts_arr[i] = len(tr)
datatype = Tracts()
datatype.storage_path = self.storage_path
datatype.vertices = vertices_arr
datatype.vertex_counts = counts_arr
return datatype
def launch(self, data_file):
if data_file is None:
raise LaunchException("Please select ZIP file which contains data to import")
# todo warn: all in memory, this is memory hungry; at least twice the tractografy
tracts = []
max_tract_count = 0
with TvbZip(data_file) as zipf:
# todo sort tract8 before tract74 parse ints out of file names
for tractf in zipf.namelist():
vertices_file = zipf.open(tractf)
tract_vertices = numpy.loadtxt(vertices_file, dtype=numpy.float32)
tracts.append(tract_vertices)
max_tract_count = max(max_tract_count, len(tract_vertices))
vertices_file.close()
vertices_arr = numpy.zeros((len(tracts), max_tract_count, 3))
counts_arr = numpy.zeros((len(tracts),))
for i, tr in enumerate(tracts):
vertices_arr[i, : len(tr)] = tr
counts_arr[i] = len(tr)
datatype = Tracts()
datatype.storage_path = self.storage_path
datatype.vertices = vertices_arr
datatype.vertex_counts = counts_arr
return datatype
def _base_before_launch(self, data_file, region_volume_gid):
if data_file is None:
raise LaunchException("Please select a file to import!")
if region_volume_gid is not None:
rvm_h5 = h5.h5_file_for_gid(region_volume_gid)
self._attempt_to_cache_regionmap(rvm_h5)
self.region_volume_shape = rvm_h5.read_data_shape()
self.region_volume_h5 = rvm_h5
datatype = Tracts()
dummy_rvm = RegionVolumeMapping()
dummy_rvm.gid = region_volume_gid
datatype.region_volume_map = dummy_rvm
return datatype
def _base_before_launch(self, data_file, region_volume):
if data_file is None:
raise LaunchException("Please select a file to import")
self.region_volume = region_volume
if region_volume is not None:
self._attempt_to_cache_regionmap(region_volume)
# this is called here and not in _get_tract_region because it goes to disk to get this info
# which would massively dominate the runtime of the import
self.region_volume_shape = region_volume.read_data_shape()
datatype = Tracts()
datatype.storage_path = self.storage_path
datatype.region_volume_map = region_volume
return datatype
def _base_before_launch(self, data_file, region_volume):
if data_file is None:
raise LaunchException("Please select a file to import")
self.region_volume = region_volume
if region_volume is not None:
self._attempt_to_cache_regionmap(region_volume)
# this is called here and not in _get_tract_region because it goes to disk to get this info
# which would massively dominate the runtime of the import
self.region_volume_shape = region_volume.read_data_shape()
datatype = Tracts()
datatype.storage_path = self.storage_path
datatype.region_volume_map = region_volume
return datatype