class SimulatorH5(SimulatorConfigurationH5):
def __init__(self, path):
super(SimulatorH5, self).__init__(path)
self.connectivity = Reference(Simulator.connectivity, self)
self.conduction_speed = Scalar(Simulator.conduction_speed, self)
self.coupling = Reference(Simulator.coupling, self)
self.surface = Reference(Simulator.surface, self)
self.stimulus = Reference(Simulator.stimulus, self)
self.model = Reference(Simulator.model, self)
self.integrator = Reference(Simulator.integrator, self)
self.initial_conditions = DataSet(Simulator.initial_conditions, self)
self.monitors = Json(Simulator.monitors, self)
self.simulation_length = Scalar(Simulator.simulation_length, self)
self.simulation_state = Reference(Attr(field_type=uuid.UUID),
self,
name='simulation_state')
def store(self, datatype, scalars_only=False, store_references=False):
# type: (Simulator, bool, bool) -> None
self.gid.store(datatype.gid)
self.connectivity.store(datatype.connectivity)
self.conduction_speed.store(datatype.conduction_speed)
self.initial_conditions.store(datatype.initial_conditions)
self.simulation_length.store(datatype.simulation_length)
integrator_gid = self.store_config_as_reference(datatype.integrator)
self.integrator.store(integrator_gid)
coupling_gid = self.store_config_as_reference(datatype.coupling)
self.coupling.store(coupling_gid)
model_gid = self.store_config_as_reference(datatype.model)
self.model.store(model_gid)
# TODO: handle multiple monitors
monitor_gid = self.store_config_as_reference(datatype.monitors[0])
self.monitors.store([monitor_gid.hex])
if datatype.surface:
cortex_gid = self.store_config_as_reference(datatype.surface)
self.surface.store(cortex_gid)
if datatype.stimulus:
self.stimulus.store(datatype.stimulus)
self.type.store(self.get_full_class_name(type(datatype)))
def load_into(self, datatype):
# type: (Simulator) -> None
datatype.conduction_speed = self.conduction_speed.load()
datatype.initial_conditions = self.initial_conditions.load()
datatype.simulation_length = self.simulation_length.load()
datatype.integrator = self.load_from_reference(self.integrator.load())
datatype.coupling = self.load_from_reference(self.coupling.load())
datatype.model = self.load_from_reference(self.model.load())
# TODO: handle multiple monitors
datatype.monitors = [self.load_from_reference(self.monitors.load()[0])]
if self.surface.load():
datatype.surface = self.load_from_reference(self.surface.load())
class SurfaceH5(H5File):
def __init__(self, path):
super(SurfaceH5, self).__init__(path)
self.vertices = DataSet(Surface.vertices, self)
self.triangles = DataSet(Surface.triangles, self)
self.vertex_normals = DataSet(Surface.vertex_normals, self)
self.triangle_normals = DataSet(Surface.triangle_normals, self)
self.number_of_vertices = Scalar(Surface.number_of_vertices, self)
self.number_of_triangles = Scalar(Surface.number_of_triangles, self)
self.edge_mean_length = Scalar(Surface.edge_mean_length, self)
self.edge_min_length = Scalar(Surface.edge_min_length, self)
self.edge_max_length = Scalar(Surface.edge_max_length, self)
self.zero_based_triangles = Scalar(Surface.zero_based_triangles, self)
self.split_triangles = DataSet(NArray(dtype=int), self, name="split_triangles")
self.number_of_split_slices = Scalar(Int(), self, name="number_of_split_slices")
self.split_slices = Json(Attr(field_type=dict), self, name="split_slices")
self.bi_hemispheric = Scalar(Surface.bi_hemispheric, self)
self.surface_type = Scalar(Surface.surface_type, self)
self.valid_for_simulations = Scalar(Surface.valid_for_simulations, self)
# cached header like information, needed to interpret the rest of the file
# Load the data that is required in order to interpret the file format
# number_of_vertices and split_slices are needed for the get_vertices_slice read call
if not self.is_new_file:
self._split_slices = self.split_slices.load()
self._split_triangles = self.split_triangles.load()
self._number_of_vertices = self.number_of_vertices.load()
self._number_of_triangles = self.number_of_triangles.load()
self._number_of_split_slices = self.number_of_split_slices.load()
self._bi_hemispheric = self.bi_hemispheric.load()
# else: this is a new file
def store(self, datatype, scalars_only=False, store_references=True):
# type: (Surface, bool, bool) -> None
super(SurfaceH5, self).store(datatype, scalars_only=scalars_only, store_references=store_references)
# When any of the header fields change we have to update our cache of them
# As they are an invariant of SurfaceH5 we don't do that in the accessors but here.
# This implies that direct public writes to them via the accessors will break the invariant.
# todo: should we make the accessors private? In complex formats like this one they are private
# for this type direct writes to accessors should not be done
self._number_of_vertices = datatype.number_of_vertices
self._number_of_triangles = datatype.number_of_triangles
self._bi_hemispheric = datatype.bi_hemispheric
self.prepare_slices(datatype)
self.number_of_split_slices.store(self._number_of_split_slices)
self.split_slices.store(self._split_slices)
self.split_triangles.store(self._split_triangles)
def read_subtype_attr(self):
return self.surface_type.load()
def center(self):
"""
Compute the center of the surface as the mean spot on all the three axes.
"""
# is this different from return numpy.mean(self.vertices, axis=0) ?
return [float(numpy.mean(self.vertices[:, 0])),
float(numpy.mean(self.vertices[:, 1])),
float(numpy.mean(self.vertices[:, 2]))]
def get_number_of_split_slices(self):
return self._number_of_split_slices
def prepare_slices(self, datatype):
"""
Before storing Surface in H5, make sure vertices/triangles are split in
slices that are readable by WebGL.
WebGL only supports triangle indices in interval [0.... 2^16]
"""
# Do not split when size is conveniently small:
if self._number_of_vertices <= SPLIT_MAX_SIZE + SPLIT_BUFFER_SIZE and not self._bi_hemispheric:
self._number_of_split_slices = 1
self._split_slices = {0: {KEY_TRIANGLES: {KEY_START: 0, KEY_END: self._number_of_triangles},
KEY_VERTICES: {KEY_START: 0, KEY_END: self._number_of_vertices},
KEY_HEMISPHERE: HEMISPHERE_UNKNOWN}}
self._split_triangles = numpy.array([], dtype=numpy.int32)
return
# Compute the number of split slices:
left_hemisphere_slices = 0
left_hemisphere_vertices_no = 0
if self._bi_hemispheric:
# when more than one hemisphere
right_hemisphere_vertices_no = numpy.count_nonzero(datatype.hemisphere_mask)
left_hemisphere_vertices_no = self._number_of_vertices - right_hemisphere_vertices_no
LOG.debug("Right %d Left %d" % (right_hemisphere_vertices_no, left_hemisphere_vertices_no))
left_hemisphere_slices = self._get_slices_number(left_hemisphere_vertices_no)
self._number_of_split_slices = left_hemisphere_slices
self._number_of_split_slices += self._get_slices_number(right_hemisphere_vertices_no)
LOG.debug("Hemispheres Total %d Left %d" % (self._number_of_split_slices, left_hemisphere_slices))
else:
# when a single hemisphere
self._number_of_split_slices = self._get_slices_number(self._number_of_vertices)
LOG.debug("Start to compute surface split triangles and vertices")
split_triangles = []
ignored_triangles_counter = 0
self._split_slices = {}
for i in range(self._number_of_split_slices):
split_triangles.append([])
if not self._bi_hemispheric:
self._split_slices[i] = {KEY_VERTICES: {KEY_START: i * SPLIT_MAX_SIZE,
KEY_END: min(self._number_of_vertices,
(i + 1) * SPLIT_MAX_SIZE + SPLIT_BUFFER_SIZE)},
KEY_HEMISPHERE: HEMISPHERE_UNKNOWN}
else:
if i < left_hemisphere_slices:
self._split_slices[i] = {KEY_VERTICES: {KEY_START: i * SPLIT_MAX_SIZE,
KEY_END: min(left_hemisphere_vertices_no,
(i + 1) * SPLIT_MAX_SIZE + SPLIT_BUFFER_SIZE)},
KEY_HEMISPHERE: HEMISPHERE_LEFT}
else:
self._split_slices[i] = {KEY_VERTICES: {KEY_START: left_hemisphere_vertices_no +
(i - left_hemisphere_slices) * SPLIT_MAX_SIZE,
KEY_END: min(self._number_of_vertices,
left_hemisphere_vertices_no + SPLIT_MAX_SIZE *
(i + 1 - left_hemisphere_slices)
+ SPLIT_BUFFER_SIZE)},
KEY_HEMISPHERE: HEMISPHERE_RIGHT}
# Iterate Triangles and find the slice where it fits best, based on its vertices indexes:
for i in range(self._number_of_triangles):
current_triangle = [datatype.triangles[i][j] for j in range(3)]
fit_slice, transformed_triangle = self._find_slice(current_triangle)
if fit_slice is not None:
split_triangles[fit_slice].append(transformed_triangle)
else:
# triangle ignored, as it has vertices over multiple slices.
ignored_triangles_counter += 1
continue
final_split_triangles = []
last_triangles_idx = 0
# Concatenate triangles, to be stored in a single HDF5 array.
for slice_idx, split_ in enumerate(split_triangles):
self._split_slices[slice_idx][KEY_TRIANGLES] = {KEY_START: last_triangles_idx,
KEY_END: last_triangles_idx + len(split_)}
final_split_triangles.extend(split_)
last_triangles_idx += len(split_)
self._split_triangles = numpy.array(final_split_triangles, dtype=numpy.int32)
if ignored_triangles_counter > 0:
LOG.warning("Ignored triangles from multiple hemispheres: " + str(ignored_triangles_counter))
LOG.debug("End compute surface split triangles and vertices " + str(self._split_slices))
@staticmethod
def _get_slices_number(vertices_number):
"""
Slices are for vertices [SPLIT_MAX_SIZE * i ... SPLIT_MAX_SIZE * (i + 1) + SPLIT_BUFFER_SIZE]
Slices will overlap :
|........SPLIT_MAX_SIZE|...SPLIT_BUFFER_SIZE| <-- split 1
|......... SPLIT_MAX_SIZE|...SPLIT_BUFFER_SIZE| <-- split 2
If we have trailing data smaller than the SPLIT_BUFFER_SIZE,
then we no longer split but we need to have at least 1 slice.
"""
slices_number, trailing = divmod(vertices_number, SPLIT_MAX_SIZE)
if trailing > SPLIT_BUFFER_SIZE or (slices_number == 0 and trailing > 0):
slices_number += 1
return slices_number
def _find_slice(self, triangle):
mn = min(triangle)
mx = max(triangle)
for i in range(self._number_of_split_slices):
v = self._split_slices[i][KEY_VERTICES] # extracted for performance
slice_start = v[KEY_START]
if slice_start <= mn and mx < v[KEY_END]:
return i, [triangle[j] - slice_start for j in range(3)]
return None, triangle
def get_slice_vertex_boundaries(self, slice_idx):
if str(slice_idx) in self._split_slices:
start_idx = max(0, self._split_slices[str(slice_idx)][KEY_VERTICES][KEY_START])
end_idx = min(self._split_slices[str(slice_idx)][KEY_VERTICES][KEY_END], self._number_of_vertices)
return start_idx, end_idx
else:
LOG.warning("Could not access slice indices, possibly due to an incompatibility with code update!")
return 0, min(SPLIT_BUFFER_SIZE, self._number_of_vertices)
def _get_slice_triangle_boundaries(self, slice_idx):
if str(slice_idx) in self._split_slices:
start_idx = max(0, self._split_slices[str(slice_idx)][KEY_TRIANGLES][KEY_START])
end_idx = min(self._split_slices[str(slice_idx)][KEY_TRIANGLES][KEY_END], self._number_of_triangles)
return start_idx, end_idx
else:
LOG.warn("Could not access slice indices, possibly due to an incompatibility with code update!")
return 0, self._number_of_triangles
def get_vertices_slice(self, slice_number=0):
"""
Read vertices slice, to be used by WebGL visualizer.
"""
slice_number = int(slice_number)
start_idx, end_idx = self.get_slice_vertex_boundaries(slice_number)
return self.vertices[start_idx: end_idx: 1]
def get_vertex_normals_slice(self, slice_number=0):
"""
Read vertex-normal slice, to be used by WebGL visualizer.
"""
slice_number = int(slice_number)
start_idx, end_idx = self.get_slice_vertex_boundaries(slice_number)
return self.vertex_normals[start_idx: end_idx: 1]
def get_triangles_slice(self, slice_number=0):
"""
Read split-triangles slice, to be used by WebGL visualizer.
"""
if self._number_of_split_slices == 1:
return self.triangles.load()
slice_number = int(slice_number)
start_idx, end_idx = self._get_slice_triangle_boundaries(slice_number)
return self._split_triangles[start_idx: end_idx: 1]
def get_lines_slice(self, slice_number=0):
"""
Read the gl lines values for the current slice number.
"""
return Surface._triangles_to_lines(self.get_triangles_slice(slice_number))
def get_slices_to_hemisphere_mask(self):
"""
:return: a vector af length number_of_slices, with 1 when current chunk belongs to the Right hemisphere
"""
if not self._bi_hemispheric or self._split_slices is None:
return None
result = [1] * self._number_of_split_slices
for key, value in self._split_slices.items():
if value[KEY_HEMISPHERE] == HEMISPHERE_LEFT:
result[int(key)] = 0
return result
# todo: many of these do not belong in the data access layer but higher, adapter or gui layer
####################################### Split for Picking
#######################################
def get_pick_vertices_slice(self, slice_number=0):
"""
Read vertices slice, to be used by WebGL visualizer with pick.
"""
slice_number = int(slice_number)
slice_triangles = self.triangles[
slice_number * SPLIT_PICK_MAX_TRIANGLE:
min(self._number_of_triangles, (slice_number + 1) * SPLIT_PICK_MAX_TRIANGLE)
]
result_vertices = []
cache_vertices = self.vertices.load()
for triang in slice_triangles:
result_vertices.append(cache_vertices[triang[0]])
result_vertices.append(cache_vertices[triang[1]])
result_vertices.append(cache_vertices[triang[2]])
return numpy.array(result_vertices)
def get_pick_vertex_normals_slice(self, slice_number=0):
"""
Read vertex-normals slice, to be used by WebGL visualizer with pick.
"""
slice_number = int(slice_number)
slice_triangles = self.triangles[
slice_number * SPLIT_PICK_MAX_TRIANGLE:
min(self.number_of_triangles.load(), (slice_number + 1) * SPLIT_PICK_MAX_TRIANGLE)
]
result_normals = []
cache_vertex_normals = self.vertex_normals.load()
for triang in slice_triangles:
result_normals.append(cache_vertex_normals[triang[0]])
result_normals.append(cache_vertex_normals[triang[1]])
result_normals.append(cache_vertex_normals[triang[2]])
return numpy.array(result_normals)
def get_pick_triangles_slice(self, slice_number=0):
"""
Read triangles slice, to be used by WebGL visualizer with pick.
"""
slice_number = int(slice_number)
no_of_triangles = (min(self._number_of_triangles, (slice_number + 1) * SPLIT_PICK_MAX_TRIANGLE)
- slice_number * SPLIT_PICK_MAX_TRIANGLE)
triangles_array = numpy.arange(no_of_triangles * 3).reshape((no_of_triangles, 3))
return triangles_array