def launch(self, data_file, surface=None):
"""
Execute import operations:
"""
if surface is None:
raise LaunchException(
"No surface selected. Please initiate upload again and select a brain surface."
)
parser = GIFTIParser(self.storage_path, self.operation_id)
try:
time_series = parser.parse(data_file)
ts_data_shape = time_series.read_data_shape()
if surface.number_of_vertices != ts_data_shape[1]:
msg = "Imported time series doesn't have values for all surface vertices. Surface has %d vertices " \
"while time series has %d values." % (surface.number_of_vertices, ts_data_shape[1])
raise LaunchException(msg)
else:
time_series.surface = surface
return [time_series]
except ParseException, excep:
logger = get_logger(__name__)
logger.exception(excep)
raise LaunchException(excep)
def launch(self, data_file, surface=None):
"""
Execute import operations:
"""
if surface is None:
raise LaunchException("No surface selected. Please initiate upload again and select a brain surface.")
parser = GIFTIParser(self.storage_path, self.operation_id)
try:
time_series = parser.parse(data_file)
ts_data_shape = time_series.read_data_shape()
if surface.number_of_vertices != ts_data_shape[1]:
msg = "Imported time series doesn't have values for all surface vertices. Surface has %d vertices " \
"while time series has %d values." % (surface.number_of_vertices, ts_data_shape[1])
raise LaunchException(msg)
else:
time_series.surface = surface
return [time_series]
except ParseException, excep:
logger = get_logger(__name__)
logger.exception(excep)
raise LaunchException(excep)
def launch(self,
file_type,
data_file,
data_file_part2,
should_center=False):
"""
Execute import operations:
"""
parser = GIFTIParser(self.storage_path, self.operation_id)
try:
surface = parser.parse(data_file,
data_file_part2,
file_type,
should_center=should_center)
surface.compute_triangle_normals()
surface.compute_vertex_normals()
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
self.generic_attributes.user_tag_1 = surface.surface_type
surface_idx = h5.store_complete(surface, self.storage_path)
return [surface_idx]
except ParseException as excep:
logger = get_logger(__name__)
logger.exception(excep)
raise LaunchException(excep)
def _parse_connectome_surfaces(self, connectome_surface, warning_message,
should_center):
"""
Parse data from a CSurface object and save it in our internal Surface DataTypes
"""
surfaces, processed_files = [], []
parser = GIFTIParser(self.storage_path, self.operation_id)
for c_surface in connectome_surface:
if c_surface.src in processed_files:
continue
try:
# create a meaningful but unique temporary path to extract
tmpdir = os.path.join(
gettempdir(), c_surface.parent_cfile.get_unique_cff_name())
self.log.debug("Extracting %s[%s] into %s ..." %
(c_surface.src, c_surface.name, tmpdir))
_zipfile = ZipFile(c_surface.parent_cfile.src, 'r',
ZIP_DEFLATED)
gifti_file_1 = _zipfile.extract(c_surface.src, tmpdir)
gifti_file_2 = None
surface_name, pair_surface = self._find_pair_file(
c_surface, connectome_surface)
if pair_surface:
self.log.debug(
"Extracting pair %s[%s] into %s ..." %
(pair_surface.src, pair_surface.name, tmpdir))
gifti_file_2 = _zipfile.extract(pair_surface.src, tmpdir)
surface_type = self._guess_surface_type(c_surface.src.lower())
self.logger.info("We will import surface %s as type %s" %
(c_surface.src, surface_type))
surface = parser.parse(gifti_file_1, gifti_file_2,
surface_type, should_center)
surface.user_tag_1 = surface_name
validation_result = surface.validate()
if validation_result.warnings:
warning_message += validation_result.summary() + "\n"
surfaces.append(surface)
if pair_surface:
processed_files.append(pair_surface.src)
processed_files.append(c_surface.src)
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
except ParseException:
self.logger.exception("Could not import a Surface entity.")
warning_message += "Problem when importing Surfaces!! \n"
except OSError:
self.log.exception("Could not clean up temporary file(s).")
return surfaces
def launch(self, view_model):
# type: (GIFTITimeSeriesImporterModel) -> [TimeSeriesSurfaceIndex]
"""
Execute import operations:
"""
if view_model.surface is None:
raise LaunchException(
"No surface selected. Please initiate upload again and select a brain surface."
)
parser = GIFTIParser(self.storage_path, self.operation_id)
try:
partial_time_series, gifti_data_arrays = parser.parse(
view_model.data_file)
ts_idx = TimeSeriesSurfaceIndex()
ts_h5_path = h5.path_for(self.storage_path, TimeSeriesSurfaceH5,
ts_idx.gid)
ts_h5 = TimeSeriesSurfaceH5(ts_h5_path)
# todo : make sure that write_time_slice is not required here
for data_array in gifti_data_arrays:
ts_h5.write_data_slice([data_array.data])
ts_h5.store(partial_time_series,
scalars_only=True,
store_references=False)
ts_h5.gid.store(uuid.UUID(ts_idx.gid))
ts_data_shape = ts_h5.read_data_shape()
surface = self.load_entity_by_gid(view_model.surface)
if surface.number_of_vertices != ts_data_shape[1]:
msg = "Imported time series doesn't have values for all surface vertices. Surface has %d vertices " \
"while time series has %d values." % (surface.number_of_vertices, ts_data_shape[1])
raise LaunchException(msg)
else:
ts_h5.surface.store(uuid.UUID(surface.gid))
ts_idx.fk_surface_gid = surface.gid
ts_h5.close()
ts_idx.sample_period_unit = partial_time_series.sample_period_unit
ts_idx.sample_period = partial_time_series.sample_period
ts_idx.sample_rate = partial_time_series.sample_rate
ts_idx.labels_ordering = json.dumps(
partial_time_series.labels_ordering)
ts_idx.labels_dimensions = json.dumps(
partial_time_series.labels_dimensions)
ts_idx.data_ndim = len(ts_data_shape)
ts_idx.data_length_1d, ts_idx.data_length_2d, ts_idx.data_length_3d, ts_idx.data_length_4d = prepare_array_shape_meta(
ts_data_shape)
return [ts_idx]
except ParseException as excep:
logger = get_logger(__name__)
logger.exception(excep)
raise LaunchException(excep)
def test_import_surface_gifti_data(self, operation_factory):
"""
This method tests import of a surface from GIFTI file.
!!! Important: We changed this test to execute only GIFTI parse
because storing surface it takes too long (~ 9min) since
normals needs to be calculated.
"""
operation_id = operation_factory().id
parser = GIFTIParser(operation_id)
surface = parser.parse(self.GIFTI_SURFACE_FILE)
assert 131342 == len(surface.vertices)
assert 262680 == len(surface.triangles)
def _parse_connectome_surfaces(self, connectome_surface, warning_message, should_center):
"""
Parse data from a CSurface object and save it in our internal Surface DataTypes
"""
surfaces, processed_files = [], []
parser = GIFTIParser(self.storage_path, self.operation_id)
for c_surface in connectome_surface:
if c_surface.src in processed_files:
continue
try:
# create a meaningful but unique temporary path to extract
tmpdir = os.path.join(gettempdir(), c_surface.parent_cfile.get_unique_cff_name())
self.log.debug("Extracting %s[%s] into %s ..." % (c_surface.src, c_surface.name, tmpdir))
_zipfile = ZipFile(c_surface.parent_cfile.src, 'r', ZIP_DEFLATED)
gifti_file_1 = _zipfile.extract(c_surface.src, tmpdir)
gifti_file_2 = None
surface_name, pair_surface = self._find_pair_file(c_surface, connectome_surface)
if pair_surface:
self.log.debug("Extracting pair %s[%s] into %s ..." % (pair_surface.src, pair_surface.name, tmpdir))
gifti_file_2 = _zipfile.extract(pair_surface.src, tmpdir)
surface_type = self._guess_surface_type(c_surface.src.lower())
self.logger.info("We will import surface %s as type %s" % (c_surface.src, surface_type))
surface = parser.parse(gifti_file_1, gifti_file_2, surface_type, should_center)
surface.user_tag_1 = surface_name
validation_result = surface.validate()
if validation_result.warnings:
warning_message += validation_result.summary() + "\n"
surfaces.append(surface)
if pair_surface:
processed_files.append(pair_surface.src)
processed_files.append(c_surface.src)
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
except ParseException:
self.logger.exception("Could not import a Surface entity.")
warning_message += "Problem when importing Surfaces!! \n"
except OSError:
self.log.exception("Could not clean up temporary file(s).")
return surfaces
def test_import_surface_gifti_data(self):
"""
This method tests import of a surface from GIFTI file.
!!! Important: We changed this test to execute only GIFTI parse
because storing surface it takes too long (~ 9min) since
normals needs to be calculated.
"""
operation_id = self.datatypeFactory.get_operation().id
storage_path = FilesHelper().get_operation_folder(self.test_project.name, operation_id)
parser = GIFTIParser(storage_path, operation_id)
surface = parser.parse(self.GIFTI_SURFACE_FILE)
assert 131342 == len(surface.vertices)
assert 262680 == len(surface.triangles)
def test_import_timeseries_gifti_data(self, operation_factory):
"""
This method tests import of a time series from GIFTI file.
!!! Important: We changed this test to execute only GIFTI parse
because storing surface it takes too long (~ 9min) since
normals needs to be calculated.
"""
operation_id = operation_factory().id
parser = GIFTIParser(operation_id)
time_series = parser.parse(self.GIFTI_TIME_SERIES_FILE)
data_shape = time_series[1]
assert 135 == len(data_shape)
assert 143479 == data_shape[0].dims[0]
def launch(self, file_type, data_file, data_file_part2, should_center=False):
"""
Execute import operations:
"""
parser = GIFTIParser(self.storage_path, self.operation_id)
try:
surface = parser.parse(data_file, data_file_part2, file_type, should_center=should_center)
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
return [surface]
except ParseException, excep:
logger = get_logger(__name__)
logger.exception(excep)
raise LaunchException(excep)
def test_import_timeseries_gifti_data(self):
"""
This method tests import of a time series from GIFTI file.
!!! Important: We changed this test to execute only GIFTI parse
because storing surface it takes too long (~ 9min) since
normals needs to be calculated.
"""
operation_id = self.datatypeFactory.get_operation().id
storage_path = FilesHelper().get_operation_folder(self.test_project.name, operation_id)
parser = GIFTIParser(storage_path, operation_id)
time_series = parser.parse(self.GIFTI_TIME_SERIES_FILE)
data_shape = time_series.read_data_shape()
assert 135 == data_shape[0]
assert 143479 == data_shape[1]
def launch(self, view_model):
# type: (GIFTISurfaceImporterModel) -> [SurfaceIndex]
"""
Execute import operations:
"""
parser = GIFTIParser(self.storage_path, self.operation_id)
try:
surface = parser.parse(view_model.data_file, view_model.data_file_part2, view_model.file_type,
should_center=view_model.should_center)
surface.compute_triangle_normals()
surface.compute_vertex_normals()
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
surface_idx = h5.store_complete(surface, self.storage_path)
return [surface_idx]
except ParseException as excep:
logger = get_logger(__name__)
logger.exception(excep)
raise LaunchException(excep)
