def _make_surface(surface_type):
result = make_surface(surface_type)
if result is not None:
return result
exception_str = "Could not determine surface type (selected option %s)" % surface_type
raise LaunchException(exception_str)
def _make_surface(surface_type):
result = make_surface(surface_type)
if result is not None:
return result
exception_str = "Could not determine surface type (selected option %s)" % surface_type
raise LaunchException(exception_str)
def _parse_surface(self, data_arrays, data_arrays_part2, surface_type,
should_center):
meta_dict = self._get_meta_dict(data_arrays[0])
anatomical_structure_primary = meta_dict.get(self.ASP_ATTR)
gid = meta_dict.get(self.UNIQUE_ID_ATTR)
subject = meta_dict.get(self.SUBJECT_ATTR)
title = meta_dict.get(self.NAME_ATTR)
# Now try to determine what type of surface we have
# If a surface type is not explicitly given we use the type specified in the metadata
if surface_type == OPTION_READ_METADATA:
surface_type = anatomical_structure_primary
if surface_type is None:
raise ParseException("Please specify the type of the surface")
surface = make_surface(surface_type)
if surface is None:
raise ParseException("Could not determine surface type! %s" %
surface_type)
# Now fill TVB data type with metadata
if gid is not None:
gid = gid.replace("{", "").replace("}", "")
surface.gid = gid
if subject is not None:
surface.subject = subject
if title is not None:
surface.title = title
surface.storage_path = self.storage_path
surface.zero_based_triangles = True
# Now fill TVB data type with geometry data
vertices = data_arrays[0].data
triangles = data_arrays[1].data
vertices_in_lh = len(vertices)
# If a second file is present append that data
if data_arrays_part2 is not None:
# offset the indices
offset = len(vertices)
vertices = np.vstack([vertices, data_arrays_part2[0].data])
triangles = np.vstack(
[triangles, offset + data_arrays_part2[1].data])
if should_center:
vertices = center_vertices(vertices)
# set hemisphere mask if cortex
if isinstance(surface, CorticalSurface):
# if there was a 2nd file then len(vertices) != vertices_in_lh
surface.hemisphere_mask = np.zeros(len(vertices), dtype=np.bool)
surface.hemisphere_mask[vertices_in_lh:] = 1
surface.vertices = vertices
surface.triangles = triangles
return surface
def _parse_surface(self, data_arrays, data_arrays_part2, surface_type, should_center):
meta_dict = self._get_meta_dict(data_arrays[0])
anatomical_structure_primary = meta_dict.get(self.ASP_ATTR)
gid = meta_dict.get(self.UNIQUE_ID_ATTR)
subject = meta_dict.get(self.SUBJECT_ATTR)
title = meta_dict.get(self.NAME_ATTR)
# Now try to determine what type of surface we have
# If a surface type is not explicitly given we use the type specified in the metadata
if surface_type == OPTION_READ_METADATA:
surface_type = anatomical_structure_primary
if surface_type is None:
raise ParseException("Please specify the type of the surface")
surface = make_surface(surface_type)
if surface is None:
raise ParseException("Could not determine surface type! %s" % surface_type)
# Now fill TVB data type with metadata
if gid is not None:
gid = gid.replace("{", "").replace("}", "")
surface.gid = gid
if subject is not None:
surface.subject = subject
if title is not None:
surface.title = title
surface.storage_path = self.storage_path
surface.set_operation_id(self.operation_id)
surface.zero_based_triangles = True
# Now fill TVB data type with geometry data
vertices = data_arrays[0].data
triangles = data_arrays[1].data
vertices_in_lh = len(vertices)
# If a second file is present append that data
if data_arrays_part2 is not None:
# offset the indices
offset = len(vertices)
vertices = np.vstack([vertices, data_arrays_part2[0].data])
triangles = np.vstack([triangles, offset + data_arrays_part2[1].data])
if should_center:
vertices = center_vertices(vertices)
# set hemisphere mask if cortex
if isinstance(surface, CorticalSurface):
# if there was a 2nd file then len(vertices) != vertices_in_lh
surface.hemisphere_mask = np.zeros(len(vertices), dtype=np.bool)
surface.hemisphere_mask[vertices_in_lh:] = 1
surface.vertices = vertices
surface.triangles = triangles
return surface
def launch(self, view_model):
# type: (ObjSurfaceImporterModel) -> [SurfaceIndex]
"""
Execute import operations:
"""
try:
surface = make_surface(view_model.surface_type)
if surface is None:
raise ParseException("Could not determine surface type! %s" %
view_model.surface_type)
surface.zero_based_triangles = True
with open(view_model.data_file) as f:
obj = ObjSurface(f)
if view_model.should_center:
vertices = center_vertices(obj.vertices)
else:
vertices = obj.vertices
surface.vertices = vertices
surface.triangles = obj.triangles
if obj.have_normals:
self.log.debug("OBJ came with normals included")
surface.vertex_normals = obj.normals
else:
self.log.warning(
"OBJ came without normals. We will try to compute them...")
surface.number_of_vertices = surface.vertices.shape[0]
surface.number_of_triangles = surface.triangles.shape[0]
surface.compute_triangle_normals()
surface.compute_vertex_normals()
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
return h5.store_complete(surface, self.storage_path)
except ParseException as excep:
self.log.exception(excep)
raise LaunchException(excep)
def launch(self, surface_type, data_file, should_center=False):
"""
Execute import operations:
"""
try:
surface = make_surface(surface_type)
if surface is None:
raise ParseException("Could not determine surface type! %s" %
surface_type)
surface.storage_path = self.storage_path
surface.set_operation_id(self.operation_id)
surface.zero_based_triangles = True
with open(data_file) as f:
obj = ObjSurface(f)
if should_center:
vertices = center_vertices(obj.vertices)
else:
vertices = obj.vertices
surface.vertices = vertices
surface.triangles = obj.triangles
if obj.have_normals:
self.log.debug("OBJ came with normals included")
surface.vertex_normals = obj.normals
else:
self.log.warning(
"OBJ came without normals. We will try to compute them...")
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
return [surface]
except ParseException, excep:
self.log.exception(excep)
raise LaunchException(excep)
def launch(self, surface_type, data_file, should_center=False):
"""
Execute import operations:
"""
try:
surface = make_surface(surface_type)
if surface is None:
raise ParseException("Could not determine surface type! %s" % surface_type)
surface.storage_path = self.storage_path
surface.set_operation_id(self.operation_id)
surface.zero_based_triangles = True
with open(data_file) as f:
obj = ObjSurface(f)
if should_center:
vertices = center_vertices(obj.vertices)
else:
vertices = obj.vertices
surface.vertices = vertices
surface.triangles = obj.triangles
if obj.have_normals:
self.log.debug("OBJ came with normals included")
surface.vertex_normals = obj.normals
else:
self.log.warning("OBJ came without normals. We will try to compute them...")
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
return [surface]
except ParseException, excep:
self.log.exception(excep)
raise LaunchException(excep)