def launch(self,
uploaded,
surface_type,
zero_based_triangles=False,
should_center=False):
"""
Execute import operations: unpack ZIP and build Surface object as result.
:param uploaded: an archive containing the Surface data to be imported
:param surface_type: a string from the following\: \
"Skin Air", "Skull Skin", "Brain Skull", "Cortical Surface", "EEG Cap", "Face"
:returns: a subclass of `Surface` DataType
:raises LaunchException: when
* `uploaded` is missing
* `surface_type` is invalid
:raises RuntimeError: when triangles contain an invalid vertex index
"""
if uploaded is None:
raise LaunchException(
"Please select ZIP file which contains data to import")
self.logger.debug("Start to import surface: '%s' from file: %s" %
(surface_type, uploaded))
try:
zip_surface = ZipSurfaceParser(uploaded)
except IOError:
exception_str = "Did not find the specified ZIP at %s" % uploaded
raise LaunchException(exception_str)
# Detect and instantiate correct surface type
self.logger.debug("Create surface instance")
surface = self._make_surface(surface_type)
surface.storage_path = self.storage_path
surface.zero_based_triangles = zero_based_triangles
if should_center:
vertices = center_vertices(zip_surface.vertices)
else:
vertices = zip_surface.vertices
surface.vertices = vertices
if len(zip_surface.normals) != 0:
surface.vertex_normals = zip_surface.normals
if zero_based_triangles:
surface.triangles = zip_surface.triangles
else:
surface.triangles = zip_surface.triangles - 1
if zip_surface.bi_hemispheric:
self.logger.info("Hemispheres detected")
surface.hemisphere_mask = zip_surface.hemisphere_mask
surface.triangle_normals = None
# Now check if the triangles of the surface are valid
triangles_min_vertex = numpy.amin(surface.triangles)
if triangles_min_vertex < 0:
if triangles_min_vertex == -1 and not zero_based_triangles:
raise LaunchException(
"Triangles contain a negative vertex index. Maybe you have a ZERO based surface."
)
else:
raise LaunchException(
"Your triangles contain a negative vertex index: %d" %
triangles_min_vertex)
no_of_vertices = len(surface.vertices)
triangles_max_vertex = numpy.amax(surface.triangles)
if triangles_max_vertex >= no_of_vertices:
if triangles_max_vertex == no_of_vertices and zero_based_triangles:
raise LaunchException(
"Your triangles contain an invalid vertex index: %d. "
"Maybe your surface is NOT ZERO Based." %
triangles_max_vertex)
else:
raise LaunchException(
"Your triangles contain an invalid vertex index: %d." %
triangles_max_vertex)
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
self.logger.debug("Surface ready to be stored")
return surface
def launch(self, view_model):
# type: (ZIPSurfaceImporterModel) -> [SurfaceIndex]
"""
Execute import operations: unpack ZIP and build Surface object as result
:raises LaunchException: when
* `uploaded` is missing
* `surface_type` is invalid
:raises RuntimeError: when triangles contain an invalid vertex index
"""
if view_model.uploaded is None:
raise LaunchException(
"Please select ZIP file which contains data to import")
self.logger.debug("Start to import surface: '%s' from file: %s" %
(view_model.surface_type, view_model.uploaded))
try:
zip_surface = ZipSurfaceParser(view_model.uploaded)
except IOError:
exception_str = "Did not find the specified ZIP at %s" % view_model.uploaded
raise LaunchException(exception_str)
# Detect and instantiate correct surface type
self.logger.debug("Create surface instance")
surface = self._make_surface(view_model.surface_type)
surface.zero_based_triangles = view_model.zero_based_triangles
if view_model.should_center:
vertices = center_vertices(zip_surface.vertices)
else:
vertices = zip_surface.vertices
surface.vertices = vertices
if len(zip_surface.normals) != 0:
surface.vertex_normals = zip_surface.normals
if view_model.zero_based_triangles:
surface.triangles = zip_surface.triangles
else:
surface.triangles = zip_surface.triangles - 1
if zip_surface.bi_hemispheric:
self.logger.info("Hemispheres detected")
surface.hemisphere_mask = zip_surface.hemisphere_mask
surface.compute_triangle_normals()
# Now check if the triangles of the surface are valid
triangles_min_vertex = numpy.amin(surface.triangles)
if triangles_min_vertex < 0:
if triangles_min_vertex == -1 and not view_model.zero_based_triangles:
raise LaunchException(
"Triangles contain a negative vertex index. Maybe you have a ZERO based surface."
)
else:
raise LaunchException(
"Your triangles contain a negative vertex index: %d" %
triangles_min_vertex)
no_of_vertices = len(surface.vertices)
triangles_max_vertex = numpy.amax(surface.triangles)
if triangles_max_vertex >= no_of_vertices:
if triangles_max_vertex == no_of_vertices and view_model.zero_based_triangles:
raise LaunchException(
"Your triangles contain an invalid vertex index: %d. "
"Maybe your surface is NOT ZERO Based." %
triangles_max_vertex)
else:
raise LaunchException(
"Your triangles contain an invalid vertex index: %d." %
triangles_max_vertex)
validation_result = surface.validate()
if validation_result.warnings:
self.add_operation_additional_info(validation_result.summary())
surface.configure()
self.logger.debug("Surface ready to be stored")
surf_idx = h5.store_complete(surface, self.storage_path)
self.generic_attributes.user_tag_1 = surface.surface_type
return surf_idx