def get_voxel_time_series(self, x, y, z, var=0, mode=0):
"""
Retrieve for a given voxel (x,y,z) the entire timeline.
:param x: int coordinate
:param y: int coordinate
:param z: int coordinate
:return: A complex dictionary with information about current voxel.
The main part will be a vector with all the values over time from the x,y,z coordinates.
"""
if self.region_mapping_volume is None:
raise exceptions.TVBException("Invalid method called for TS without Volume Mapping!")
volume_rm = self.region_mapping_volume
x, y, z = preprocess_space_parameters(x, y, z, volume_rm.length_1d, volume_rm.length_2d, volume_rm.length_3d)
idx_slices = slice(x, x + 1), slice(y, y + 1), slice(z, z + 1)
idx = int(volume_rm.get_data('array_data', idx_slices))
time_length = self.read_data_shape()[0]
var, mode = int(var), int(mode)
voxel_slices = prepare_time_slice(time_length), slice(var, var + 1), slice(idx, idx + 1), slice(mode, mode + 1)
label = volume_rm.connectivity.region_labels[idx]
background, back_min, back_max = None, None, None
if idx < 0:
back_min, back_max = self.get_min_max_values()
background = numpy.ones((time_length, 1)) * self.out_of_range(back_min)
label = 'background'
result = postprocess_voxel_ts(self, voxel_slices, background, back_min, back_max, label)
return result
def read_data_shape(self):
"""
Expose shape read on field data.
"""
try:
return self.get_data_shape('data')
except exceptions.TVBException:
self.logger.exception("Could not read data shape for TS!")
raise exceptions.TVBException("Invalid empty TimeSeries!")
def get_volume_view(self,
from_idx,
to_idx,
x_plane,
y_plane,
z_plane,
var=0,
mode=0):
"""
Retrieve 3 slices through the Volume TS, at the given X, y and Z coordinates, and in time [from_idx .. to_idx].
:param from_idx: int This will be the limit on the first dimension (time)
:param to_idx: int Also limit on the first Dimension (time)
:param x_plane: int coordinate
:param y_plane: int coordinate
:param z_plane: int coordinate
:return: An array of 3 Matrices 2D, each containing the values to display in planes xy, yz and xy.
"""
if self.region_mapping_volume is None:
raise exceptions.TVBException(
"Invalid method called for TS without Volume Mapping!")
volume_rm = self.region_mapping_volume
# Work with space inside Volume:
x_plane, y_plane, z_plane = preprocess_space_parameters(
x_plane, y_plane, z_plane, volume_rm.length_1d,
volume_rm.length_2d, volume_rm.length_3d)
slice_x, slice_y, slice_z = self.region_mapping_volume.get_volume_slice(
x_plane, y_plane, z_plane)
# Read from the current TS:
from_idx, to_idx, current_time_length = preprocess_time_parameters(
from_idx, to_idx,
self.read_data_shape()[0])
no_of_regions = self.read_data_shape()[2]
time_slices = slice(from_idx, to_idx), slice(
var, var + 1), slice(no_of_regions), slice(mode, mode + 1)
min_signal = self.get_min_max_values()[0]
regions_ts = self.read_data_slice(time_slices)[:, 0, :, 0]
regions_ts = numpy.hstack(
(regions_ts, numpy.ones(
(current_time_length, 1)) * self.out_of_range(min_signal)))
# Index from TS with the space mapping:
result_x, result_y, result_z = [], [], []
for i in range(0, current_time_length):
result_x.append(regions_ts[i][slice_x].tolist())
result_y.append(regions_ts[i][slice_y].tolist())
result_z.append(regions_ts[i][slice_z].tolist())
return [result_x, result_y, result_z]