def create_surface(self):
"""
Create a dummy surface entity.
:return: (Algorithm Identifier, stored Surface entity)
"""
operation, algo_id, storage_path = self.__create_operation()
surface = CorticalSurface(storage_path=storage_path)
surface.vertices = numpy.array(
[[-10, 0, 0], [0, 0, -10], [10, 0, 0], [0, 10, 0]], dtype=float)
surface.triangles = numpy.array(
[[0, 1, 2], [0, 1, 3], [1, 2, 3], [0, 2, 3]], dtype=int)
surface.number_of_triangles = 4
surface.number_of_vertices = 4
surface.triangle_normals = numpy.ones((4, 3))
surface.vertex_normals = numpy.ones((4, 3))
surface.zero_based_triangles = True
adapter_instance = StoreAdapter([surface])
OperationService().initiate_prelaunch(operation, adapter_instance, {})
return algo_id, surface
def create_surface(self):
"""
Create a dummy surface entity.
:returns: (Algorithm Identifier, stored Surface entity)
"""
operation, algo_id, storage_path = self.__create_operation()
surface = CorticalSurface(storage_path=storage_path)
surface.vertices = numpy.array([[-10, 0, 0],
[0, 0, -10],
[10, 0, 0],
[0, 10, 0]], dtype=float)
surface.triangles = numpy.array([[0, 1, 2],
[0, 1, 3],
[1, 2, 3],
[0, 2, 3]], dtype=int)
surface.number_of_triangles = 4
surface.number_of_vertices = 4
surface.triangle_normals = numpy.ones((4, 3))
surface.vertex_normals = numpy.ones((4, 3))
surface.zero_based_triangles = True
surface.validate()
adapter_instance = StoreAdapter([surface])
OperationService().initiate_prelaunch(operation, adapter_instance, {})
return algo_id, surface
def launch(self, uploaded, surface_type, zero_based_triangles = False):
"""
Execute import operations: unpack ZIP and build Surface object as result.
"""
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:
files = FilesHelper().unpack_zip(uploaded, self.storage_path)
except IOError:
exception_str = "Did not find the specified ZIP at %s" % uploaded
raise LaunchException(exception_str)
vertices = []
normals = []
triangles = []
for file_name in files:
if file_name.lower().find(self.VERTICES_TOKEN) >= 0:
vertices.append(file_name)
continue
if file_name.lower().find(self.NORMALS_TOKEN) >= 0:
normals.append(file_name)
continue
if file_name.lower().find(self.TRIANGLES_TOKEN) >= 0:
triangles.append(file_name)
# Now detect and instantiate correct surface type
self.logger.debug("Create surface instance")
if surface_type == CORTICAL:
surface = CorticalSurface()
elif surface_type == INNER_SKULL:
surface = BrainSkull()
elif surface_type == OUTER_SKULL:
surface = SkullSkin()
elif surface_type == OUTER_SKIN:
surface = SkinAir()
elif surface_type == EEG_CAP:
surface = EEGCap()
elif surface_type == FACE:
surface = FaceSurface()
else:
exception_str = "Could not determine surface type (selected option %s)" % surface_type
raise LaunchException(exception_str)
surface.storage_path = self.storage_path
all_vertices, all_normals, all_triangles = self._process_files(vertices, normals, triangles)
FilesHelper.remove_files(files, True)
surface.zero_based_triangles = zero_based_triangles
surface.vertices = all_vertices
surface.vertex_normals = all_normals
if zero_based_triangles:
surface.triangles = all_triangles
else :
surface.triangles = all_triangles - 1
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 RuntimeError("Triangles contain a negative vertex index. Maybe you have a ZERO based surface.")
else:
raise RuntimeError("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 RuntimeError("Your triangles contain an invalid vertex index: %d. \
Maybe your surface is NOT ZERO Based."%triangles_max_vertex)
else:
raise RuntimeError("Your triangles contain an invalid vertex index: %d." %triangles_max_vertex)
self.logger.debug("Surface ready to be stored")
return surface
