def addCartesianCoordinates(
ugrid,
verbose=1):
myVTK.myPrint(verbose, "*** addCartesianCoordinates ***")
points = ugrid.GetPoints()
(farray_xx,
farray_yy,
farray_zz) = computeCartesianCoordinates(
points=points,
verbose=verbose-1)
ugrid.GetPointData().AddArray(farray_xx)
ugrid.GetPointData().AddArray(farray_yy)
ugrid.GetPointData().AddArray(farray_zz)
cell_centers = myVTK.getCellCenters(
mesh=ugrid,
verbose=verbose-1)
(farray_xx,
farray_yy,
farray_zz) = computeCartesianCoordinates(
points=cell_centers,
verbose=verbose-1)
ugrid.GetCellData().AddArray(farray_xx)
ugrid.GetCellData().AddArray(farray_yy)
ugrid.GetCellData().AddArray(farray_zz)
def addPseudoProlateSpheroidalCoordinatesAndBasisToBiV(
ugrid,
pdata_endLV,
pdata_endRV,
pdata_epi,
verbose=1):
myVTK.myPrint(verbose, "*** addPseudoProlateSpheroidalCoordinatesAndBasisToBiV ***")
(farray_rr,
farray_cc,
farray_ll,
farray_eRR,
farray_eCC,
farray_eLL) = computePseudoProlateSpheroidalCoordinatesAndBasisForBiV(
points=ugrid.GetPoints(),
iarray_regions=ugrid.GetPointData().GetArray("region_id"),
farray_c=ugrid.GetPointData().GetArray("c"),
farray_l=ugrid.GetPointData().GetArray("l"),
farray_eL=ugrid.GetPointData().GetArray("eL"),
pdata_endLV=pdata_endLV,
pdata_endRV=pdata_endRV,
pdata_epi=pdata_epi,
iarray_part_id=ugrid.GetPointData().GetArray("part_id"),
verbose=verbose-1)
ugrid.GetPointData().AddArray(farray_rr)
ugrid.GetPointData().AddArray(farray_cc)
ugrid.GetPointData().AddArray(farray_ll)
ugrid.GetPointData().AddArray(farray_eRR)
ugrid.GetPointData().AddArray(farray_eCC)
ugrid.GetPointData().AddArray(farray_eLL)
cell_centers = myVTK.getCellCenters(
mesh=ugrid,
verbose=verbose-1)
(farray_rr,
farray_cc,
farray_ll,
farray_eRR,
farray_eCC,
farray_eLL) = computePseudoProlateSpheroidalCoordinatesAndBasisForBiV(
points=cell_centers,
iarray_regions=ugrid.GetCellData().GetArray("region_id"),
farray_c=ugrid.GetCellData().GetArray("c"),
farray_l=ugrid.GetCellData().GetArray("l"),
farray_eL=ugrid.GetCellData().GetArray("eL"),
pdata_endLV=pdata_endLV,
pdata_endRV=pdata_endRV,
pdata_epi=pdata_epi,
iarray_part_id=ugrid.GetCellData().GetArray("part_id"),
verbose=verbose-1)
ugrid.GetCellData().AddArray(farray_rr)
ugrid.GetCellData().AddArray(farray_cc)
ugrid.GetCellData().AddArray(farray_ll)
ugrid.GetCellData().AddArray(farray_eRR)
ugrid.GetCellData().AddArray(farray_eCC)
ugrid.GetCellData().AddArray(farray_eLL)
def addRegionsToBiV(ugrid_mesh, pdata_endLV, pdata_endRV, pdata_epi, verbose=0):
myVTK.myPrint(verbose, "*** addRegionsToBiV ***")
points = ugrid_mesh.GetPoints()
iarray_region = computeRegionsForBiV(
points=points, pdata_endLV=pdata_endLV, pdata_endRV=pdata_endRV, pdata_epi=pdata_epi, verbose=verbose - 1
)
ugrid_mesh.GetPointData().AddArray(iarray_region)
cell_centers = myVTK.getCellCenters(mesh=ugrid_mesh, verbose=verbose - 1)
iarray_region = computeRegionsForBiV(
points=cell_centers, pdata_endLV=pdata_endLV, pdata_endRV=pdata_endRV, pdata_epi=pdata_epi, verbose=verbose - 1
)
ugrid_mesh.GetCellData().AddArray(iarray_region)
def addPDataNormals(
pdata,
orient_outward=1,
verbose=0):
myVTK.myPrint(verbose, "*** addPDataNormals ***")
poly_data_normals = vtk.vtkPolyDataNormals()
poly_data_normals.ComputePointNormalsOff()
poly_data_normals.ComputeCellNormalsOn()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
poly_data_normals.SetInputData(pdata)
else:
poly_data_normals.SetInput(pdata)
poly_data_normals.Update()
pdata = poly_data_normals.GetOutput()
if (orient_outward):
cell_centers = myVTK.getCellCenters(
mesh=pdata,
verbose=verbose-1)
cell_center = numpy.empty(3)
mesh_center = numpy.array(pdata.GetCenter())
normals = pdata.GetCellData().GetNormals()
normal = numpy.empty(3)
cnt_pos = 0
cnt_neg = 0
for k_cell in xrange(pdata.GetNumberOfCells()):
cell_centers.GetPoint(k_cell, cell_center)
outward = cell_center-mesh_center
outward /= numpy.linalg.norm(outward)
normals.GetTuple(k_cell, normal)
proj = numpy.dot(outward, normal)
if (proj > 0): cnt_pos += 1
else: cnt_neg += 1
#print cnt_pos
#print cnt_neg
if (cnt_neg > cnt_pos):
poly_data_normals.FlipNormalsOn()
poly_data_normals.Update()
pdata = poly_data_normals.GetOutput()
return pdata
def addPseudoProlateSpheroidalCoordinatesAndBasisToBiV(ugrid,
pdata_endLV,
pdata_endRV,
pdata_epi,
verbose=0):
myVTK.myPrint(
verbose, "*** addPseudoProlateSpheroidalCoordinatesAndBasisToBiV ***")
(farray_rr, farray_cc, farray_ll, farray_eRR, farray_eCC,
farray_eLL) = computePseudoProlateSpheroidalCoordinatesAndBasisForBiV(
points=ugrid.GetPoints(),
iarray_regions=ugrid.GetPointData().GetArray("region_id"),
farray_c=ugrid.GetPointData().GetArray("c"),
farray_l=ugrid.GetPointData().GetArray("l"),
farray_eL=ugrid.GetPointData().GetArray("eL"),
pdata_endLV=pdata_endLV,
pdata_endRV=pdata_endRV,
pdata_epi=pdata_epi,
iarray_part_id=ugrid.GetPointData().GetArray("part_id"),
verbose=verbose - 1)
ugrid.GetPointData().AddArray(farray_rr)
ugrid.GetPointData().AddArray(farray_cc)
ugrid.GetPointData().AddArray(farray_ll)
ugrid.GetPointData().AddArray(farray_eRR)
ugrid.GetPointData().AddArray(farray_eCC)
ugrid.GetPointData().AddArray(farray_eLL)
cell_centers = myVTK.getCellCenters(mesh=ugrid, verbose=verbose - 1)
(farray_rr, farray_cc, farray_ll, farray_eRR, farray_eCC,
farray_eLL) = computePseudoProlateSpheroidalCoordinatesAndBasisForBiV(
points=cell_centers,
iarray_regions=ugrid.GetCellData().GetArray("region_id"),
farray_c=ugrid.GetCellData().GetArray("c"),
farray_l=ugrid.GetCellData().GetArray("l"),
farray_eL=ugrid.GetCellData().GetArray("eL"),
pdata_endLV=pdata_endLV,
pdata_endRV=pdata_endRV,
pdata_epi=pdata_epi,
iarray_part_id=ugrid.GetCellData().GetArray("part_id"),
verbose=verbose - 1)
ugrid.GetCellData().AddArray(farray_rr)
ugrid.GetCellData().AddArray(farray_cc)
ugrid.GetCellData().AddArray(farray_ll)
ugrid.GetCellData().AddArray(farray_eRR)
ugrid.GetCellData().AddArray(farray_eCC)
ugrid.GetCellData().AddArray(farray_eLL)
def addCylindricalCoordinatesAndBasis(
ugrid,
points_AB,
verbose=0):
myVTK.myPrint(verbose, "*** addCylindricalCoordinatesAndBasis ***")
points = ugrid.GetPoints()
(farray_r,
farray_c,
farray_l,
farray_eR,
farray_eC,
farray_eL) = computeCylindricalCoordinatesAndBasis(
points=points,
points_AB=points_AB,
verbose=verbose-1)
ugrid.GetPointData().AddArray(farray_r)
ugrid.GetPointData().AddArray(farray_c)
ugrid.GetPointData().AddArray(farray_l)
ugrid.GetPointData().AddArray(farray_eR)
ugrid.GetPointData().AddArray(farray_eC)
ugrid.GetPointData().AddArray(farray_eL)
cell_centers = myVTK.getCellCenters(
mesh=ugrid,
verbose=verbose-1)
(farray_r,
farray_c,
farray_l,
farray_eR,
farray_eC,
farray_eL) = computeCylindricalCoordinatesAndBasis(
points=cell_centers,
points_AB=points_AB,
verbose=verbose-1)
ugrid.GetCellData().AddArray(farray_r)
ugrid.GetCellData().AddArray(farray_c)
ugrid.GetCellData().AddArray(farray_l)
ugrid.GetCellData().AddArray(farray_eR)
ugrid.GetCellData().AddArray(farray_eC)
ugrid.GetCellData().AddArray(farray_eL)
def addCartesianCoordinates(ugrid, verbose=0):
myVTK.myPrint(verbose, "*** addCartesianCoordinates ***")
points = ugrid.GetPoints()
(farray_xx, farray_yy,
farray_zz) = computeCartesianCoordinates(points=points,
verbose=verbose - 1)
ugrid.GetPointData().AddArray(farray_xx)
ugrid.GetPointData().AddArray(farray_yy)
ugrid.GetPointData().AddArray(farray_zz)
cell_centers = myVTK.getCellCenters(mesh=ugrid, verbose=verbose - 1)
(farray_xx, farray_yy,
farray_zz) = computeCartesianCoordinates(points=cell_centers,
verbose=verbose - 1)
ugrid.GetCellData().AddArray(farray_xx)
ugrid.GetCellData().AddArray(farray_yy)
ugrid.GetCellData().AddArray(farray_zz)
def addRegionsToBiV(ugrid_mesh,
pdata_endLV,
pdata_endRV,
pdata_epi,
verbose=0):
myVTK.myPrint(verbose, "*** addRegionsToBiV ***")
points = ugrid_mesh.GetPoints()
iarray_region = computeRegionsForBiV(points=points,
pdata_endLV=pdata_endLV,
pdata_endRV=pdata_endRV,
pdata_epi=pdata_epi,
verbose=verbose - 1)
ugrid_mesh.GetPointData().AddArray(iarray_region)
cell_centers = myVTK.getCellCenters(mesh=ugrid_mesh, verbose=verbose - 1)
iarray_region = computeRegionsForBiV(points=cell_centers,
pdata_endLV=pdata_endLV,
pdata_endRV=pdata_endRV,
pdata_epi=pdata_epi,
verbose=verbose - 1)
ugrid_mesh.GetCellData().AddArray(iarray_region)
def mapDataSetToCellData(
mesh_from,
type_of_support,
mesh_to,
farray_names,
type_of_mapping="PointsWithinRadius",
radius_is_relative=True,
radius=0.5,
n_closest_points=3,
threshold_dist=None,
threshold_val_min=None,
threshold_val_max=None,
verbose=0):
myVTK.myPrint(verbose, "*** mapDataSetToCellData ***")
if (type_of_support == "point"):
datapoints = mesh_from.GetPoints()
dataset = mesh_from.GetPointData()
point_locator = myVTK.getPointLocator(
mesh_from,
verbose=verbose-1)
elif (type_of_support == "cell"):
datapoints = myVTK.getCellCenters(
mesh=mesh_from,
verbose=verbose-1)
dataset = mesh_from.GetCellData()
point_locator = myVTK.getPointLocator(
datapoints,
verbose=verbose-1)
else:
assert (0)
pdata_cell_centers_to = myVTK.getCellCenters(mesh_to)
n_cells = mesh_to.GetNumberOfCells()
farrays_avg = {}
farrays_std = {}
for farray_name in farray_names:
assert (dataset.HasArray(farray_name)), "mesh has no array named "+farray_name+". Aborting."
farray_type = dataset.GetArray(farray_name).GetDataTypeAsString()
farray_n_components = dataset.GetArray(farray_name).GetNumberOfComponents()
farrays_avg[farray_name] = myVTK.createArray(farray_name+"_avg",
farray_n_components,
n_cells,
farray_type)
farrays_std[farray_name] = myVTK.createArray(farray_name+"_std",
farray_n_components,
n_cells,
farray_type)
points_within_radius = vtk.vtkIdList()
for k_cell in xrange(n_cells):
if (type_of_mapping == "ClosestPoints"):
point_locator.FindClosestNPoints(
n_closest_points,
pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
elif (type_of_mapping == "PointsWithinRadius"):
if (radius_is_relative):
l = (mesh_to.GetCell(k_cell).GetLength2())**(0.5)
actual_radius = l*radius
else:
actual_radius = radius
point_locator.FindPointsWithinRadius(
actual_radius,
pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
else:
assert (0)
#points_within_radius = myVTK.findPointsInCell(mesh_from.GetPoints(), mesh_to.GetCell(k_cell))
for farray_name in farray_names:
if (points_within_radius.GetNumberOfIds()):
values = [numpy.array(dataset.GetArray(farray_name).GetTuple(points_within_radius.GetId(k_id))) for k_id in xrange(points_within_radius.GetNumberOfIds()) if (threshold_dist is None) or (numpy.linalg.norm(numpy.array(datapoints.GetPoint(points_within_radius.GetId(k_id)))-numpy.array(pdata_cell_centers_to.GetPoint(k_cell))) < threshold_dist)]
#print "values = "+str(values)
if (threshold_val_min != None):
values = [value for value in values if (numpy.linalg.norm(value) > threshold_val_min)]
if (threshold_val_max != None):
values = [value for value in values if (numpy.linalg.norm(value) < threshold_val_max)]
#print "values = "+str(values)
if (len(values)):
avg = numpy.mean(values, 0)
std = numpy.std(values, 0)
else:
avg = [0]*farray_n_components
std = [0]*farray_n_components
else:
avg = [0]*farray_n_components
std = [0]*farray_n_components
farrays_avg[farray_name].SetTuple(k_cell, avg)
farrays_std[farray_name].SetTuple(k_cell, std)
for farray_name in farray_names:
mesh_to.GetCellData().AddArray(farrays_avg[farray_name])
mesh_to.GetCellData().AddArray(farrays_std[farray_name])
def mapDataSetToCellData(mesh_from,
type_of_support,
mesh_to,
farray_names,
type_of_mapping="PointsWithinRadius",
radius_is_relative=True,
radius=0.5,
n_closest_points=3,
threshold_dist=None,
threshold_val_min=None,
threshold_val_max=None,
verbose=0):
myVTK.myPrint(verbose, "*** mapDataSetToCellData ***")
if (type_of_support == "point"):
datapoints = mesh_from.GetPoints()
dataset = mesh_from.GetPointData()
point_locator = myVTK.getPointLocator(mesh_from, verbose=verbose - 1)
elif (type_of_support == "cell"):
datapoints = myVTK.getCellCenters(mesh=mesh_from, verbose=verbose - 1)
dataset = mesh_from.GetCellData()
point_locator = myVTK.getPointLocator(datapoints, verbose=verbose - 1)
else:
assert (0)
pdata_cell_centers_to = myVTK.getCellCenters(mesh_to)
n_cells = mesh_to.GetNumberOfCells()
farrays_avg = {}
farrays_std = {}
for farray_name in farray_names:
assert (dataset.HasArray(farray_name)
), "mesh has no array named " + farray_name + ". Aborting."
farray_type = dataset.GetArray(farray_name).GetDataTypeAsString()
farray_n_components = dataset.GetArray(
farray_name).GetNumberOfComponents()
farrays_avg[farray_name] = myVTK.createArray(farray_name + "_avg",
farray_n_components,
n_cells, farray_type)
farrays_std[farray_name] = myVTK.createArray(farray_name + "_std",
farray_n_components,
n_cells, farray_type)
points_within_radius = vtk.vtkIdList()
for k_cell in xrange(n_cells):
if (type_of_mapping == "ClosestPoints"):
point_locator.FindClosestNPoints(
n_closest_points, pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
elif (type_of_mapping == "PointsWithinRadius"):
if (radius_is_relative):
l = (mesh_to.GetCell(k_cell).GetLength2())**(0.5)
actual_radius = l * radius
else:
actual_radius = radius
point_locator.FindPointsWithinRadius(
actual_radius, pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
else:
assert (0)
#points_within_radius = myVTK.findPointsInCell(mesh_from.GetPoints(), mesh_to.GetCell(k_cell))
for farray_name in farray_names:
if (points_within_radius.GetNumberOfIds()):
values = [
numpy.array(
dataset.GetArray(farray_name).GetTuple(
points_within_radius.GetId(k_id)))
for k_id in xrange(points_within_radius.GetNumberOfIds())
if (threshold_dist is None) or (numpy.linalg.norm(
numpy.array(
datapoints.GetPoint(
points_within_radius.GetId(k_id))) -
numpy.array(pdata_cell_centers_to.GetPoint(k_cell))) <
threshold_dist)
]
#print "values = "+str(values)
if (threshold_val_min != None):
values = [
value for value in values
if (numpy.linalg.norm(value) > threshold_val_min)
]
if (threshold_val_max != None):
values = [
value for value in values
if (numpy.linalg.norm(value) < threshold_val_max)
]
#print "values = "+str(values)
if (len(values)):
avg = numpy.mean(values, 0)
std = numpy.std(values, 0)
else:
avg = [0] * farray_n_components
std = [0] * farray_n_components
else:
avg = [0] * farray_n_components
std = [0] * farray_n_components
farrays_avg[farray_name].SetTuple(k_cell, avg)
farrays_std[farray_name].SetTuple(k_cell, std)
for farray_name in farray_names:
mesh_to.GetCellData().AddArray(farrays_avg[farray_name])
mesh_to.GetCellData().AddArray(farrays_std[farray_name])
def addMappingToPointData(mesh_from,
type_of_support,
mesh_to,
farray_names,
radius=1.,
threshold_min=None,
threshold_max=None,
verbose=0):
mypy.my_print(verbose, "*** addMappingToPointData ***")
if (type_of_support == "point"):
dataset = mesh_from.GetPointData()
point_locator = myvtk.getPointLocator(mesh_from)
elif (type_of_support == "cell"):
dataset = mesh_from.GetPointData()
pdata_cell_centers_fr = myvtk.getCellCenters(mesh=mesh_from,
verbose=verbose - 1)
point_locator = myvtk.getPointLocator(pdata_cell_centers_fr)
n_points = mesh_to.GetNumberOfPoints()
farrays_avg = {}
farrays_std = {}
farrays_rat = {}
for farray_name in farray_names:
assert (dataset.HasArray(farray_name)
), "mesh has no array named " + farray_name + ". Aborting."
farray_type = dataset.GetArray(farray_name).GetDataTypeAsString()
farray_n_components = dataset.GetArray(
farray_name).GetNumberOfComponents()
farrays_avg[farray_name] = createArray(farray_name + "_avg",
farray_n_components, n_points,
farray_type)
farrays_std[farray_name] = createArray(farray_name + "_std",
farray_n_components, n_points,
farray_type)
farrays_rat[farray_name] = createArray(farray_name + "_rat",
farray_n_components, n_points,
farray_type)
points_within_radius = vtk.vtkIdList()
for k_point in xrange(n_points):
#point_locator.FindClosestNPoints(
#3,
#mesh_to.GetPoints().GetPoint(k_point),
#points_within_radius)
point_locator.FindPointsWithinRadius(
radius,
mesh_to.GetPoints().GetPoint(k_point), points_within_radius)
for farray_name in farray_names:
if (points_within_radius.GetNumberOfIds() > 0):
values = [
numpy.array(
dataset.GetArray(farray_name).GetTuple(
points_within_radius.GetId(k_id)))
for k_id in xrange(points_within_radius.GetNumberOfIds())
]
#print "values = "+str(values)
if (threshold_min != None):
values = [
value for value in values
if (numpy.linalg.norm(value) > threshold_min)
]
if (threshold_max != None):
values = [
value for value in values
if (numpy.linalg.norm(value) < threshold_max)
]
#print "values = "+str(values)
if (len(values) > 0):
avg = numpy.mean(values, 0)
std = numpy.std(values, 0)
rat = std / avg
else:
avg = [0] * n_components
std = [0] * n_components
rat = [0] * n_components
else:
avg = [0] * n_components
std = [0] * n_components
rat = [0] * n_components
farrays_avg[farray_name].SetTuple(k_point, avg)
farrays_std[farray_name].SetTuple(k_point, std)
farrays_rat[farray_name].SetTuple(k_point, rat)
for farray_name in farray_names:
mesh_to.GetPointData().AddArray(farrays_avg[farray_name])
mesh_to.GetPointData().AddArray(farrays_std[farray_name])
mesh_to.GetPointData().AddArray(farrays_rat[farray_name])
