def computeRegionsForBiV(points,
pdata_endLV,
pdata_endRV,
pdata_epi,
verbose=0):
myVTK.myPrint(verbose, "*** computeRegionsForBiV ***")
myVTK.myPrint(verbose - 1, "Initializing cell locators...")
(cell_locator_endLV, closest_point_endLV, generic_cell, cellId_endLV,
subId, dist_endLV) = myVTK.getCellLocator(mesh=pdata_endLV,
verbose=verbose - 1)
(cell_locator_endRV, closest_point_endRV, generic_cell, cellId_endRV,
subId, dist_endRV) = myVTK.getCellLocator(mesh=pdata_endRV,
verbose=verbose - 1)
(cell_locator_epi, closest_point_epi, generic_cell, cellId_epi, subId,
dist_epi) = myVTK.getCellLocator(mesh=pdata_epi, verbose=verbose - 1)
n_points = points.GetNumberOfPoints()
iarray_region = myVTK.createIntArray("region_id", 1, n_points)
point = numpy.empty(3)
for k_point in range(n_points):
points.GetPoint(k_point, point)
cell_locator_endLV.FindClosestPoint(point, closest_point_endLV,
generic_cell, cellId_endLV, subId,
dist_endLV)
cell_locator_endRV.FindClosestPoint(point, closest_point_endRV,
generic_cell, cellId_endRV, subId,
dist_endRV)
cell_locator_epi.FindClosestPoint(point, closest_point_epi,
generic_cell, cellId_epi, subId,
dist_epi)
if (dist_endRV == max(dist_endLV, dist_endRV, dist_epi)):
iarray_region.SetTuple1(k_point, 0)
elif (dist_epi == max(dist_endLV, dist_endRV, dist_epi)):
iarray_region.SetTuple1(k_point, 1)
elif (dist_endLV == max(dist_endLV, dist_endRV, dist_epi)):
iarray_region.SetTuple1(k_point, 2)
return iarray_region
def maskImageWithMesh(
image,
mesh,
filter_with_field=None,
verbose=0):
myVTK.myPrint(verbose, "*** maskImageWithMesh ***")
n_points = image.GetNumberOfPoints()
farray_scalars_image = image.GetPointData().GetArray("scalars") # note that the field is defined at the points, not the cells
(cell_locator,
closest_point,
generic_cell,
k_cell,
subId,
dist) = myVTK.getCellLocator(
mesh=mesh,
verbose=verbose-1)
if (filter_with_field != None):
field = mesh.GetCellData().GetArray(filter_with_field[0])
field_values = filter_with_field[1]
points = vtk.vtkPoints()
farray_scalars = myVTK.createFloatArray(
name="scalars",
n_components=1)
point = numpy.empty(3)
for k_point in xrange(n_points):
image.GetPoint(k_point, point)
k_cell = cell_locator.FindCell(point)
if (k_cell == -1): continue
if (filter_with_field != None) and (field.GetTuple1(k_cell) not in field_values): continue
points.InsertNextPoint(point)
farray_scalars.InsertNextTuple(farray_scalars_image.GetTuple(k_point))
ugrid = vtk.vtkUnstructuredGrid()
ugrid.SetPoints(points)
ugrid.GetPointData().AddArray(farray_scalars)
myVTK.addVertices(
ugrid)
return ugrid
def getMaskedImageUsingMesh(
image,
mesh,
filter_with_field=None,
verbose=0):
mypy.my_print(verbose, "*** getMaskedImageUsingMesh ***")
n_points = image.GetNumberOfPoints()
farray_scalars_image = image.GetPointData().GetArray("scalars") # note that the field is defined at the points, not the cells
(cell_locator,
closest_point,
generic_cell,
k_cell,
subId,
dist) = myvtk.getCellLocator(
mesh=mesh,
verbose=verbose-1)
if (filter_with_field != None):
field = mesh.GetCellData().GetArray(filter_with_field[0])
field_values = filter_with_field[1]
points = vtk.vtkPoints()
farray_scalars = myvtk.createFloatArray(
name="scalars",
n_components=1)
point = numpy.empty(3)
for k_point in range(n_points):
image.GetPoint(k_point, point)
k_cell = cell_locator.FindCell(point)
if (k_cell == -1): continue
if (filter_with_field != None) and (field.GetTuple1(k_cell) not in field_values): continue
points.InsertNextPoint(point)
farray_scalars.InsertNextTuple(farray_scalars_image.GetTuple(k_point))
ugrid = vtk.vtkUnstructuredGrid()
ugrid.SetPoints(points)
ugrid.GetPointData().AddArray(farray_scalars)
myvtk.addVertices(
ugrid)
return ugrid
def computePseudoProlateSpheroidalCoordinatesAndBasisForBiV(
points,
iarray_regions,
farray_c,
farray_l,
farray_eL,
pdata_endLV,
pdata_endRV,
pdata_epi,
iarray_part_id=None,
verbose=1):
myVTK.myPrint(verbose, "*** computePseudoProlateSpheroidalCoordinatesAndBasisForBiV ***")
myVTK.myPrint(verbose, "Computing surface cell normals...")
pdata_endLV = myVTK.addPDataNormals(
pdata=pdata_endLV,
verbose=verbose-1)
pdata_endRV = myVTK.addPDataNormals(
pdata=pdata_endRV,
verbose=verbose-1)
pdata_epi = myVTK.addPDataNormals(
pdata=pdata_epi,
verbose=verbose)
myVTK.myPrint(verbose, "Initializing surface cell locators...")
(cell_locator_endLV,
closest_point_endLV,
generic_cell,
cellId_endLV,
subId,
dist_endLV) = myVTK.getCellLocator(
mesh=pdata_endLV,
verbose=verbose-1)
(cell_locator_endRV,
closest_point_endRV,
generic_cell,
cellId_endRV,
subId,
dist_endRV) = myVTK.getCellLocator(
mesh=pdata_endRV,
verbose=verbose-1)
(cell_locator_epi,
closest_point_epi,
generic_cell,
cellId_epi,
subId,
dist_epi) = myVTK.getCellLocator(
mesh=pdata_epi,
verbose=verbose-1)
myVTK.myPrint(verbose, "Computing local prolate spheroidal directions...")
n_points = points.GetNumberOfPoints()
farray_rr = myVTK.createFloatArray("rr", 1, n_points)
farray_cc = myVTK.createFloatArray("cc", 1, n_points)
farray_ll = myVTK.createFloatArray("ll", 1, n_points)
farray_eRR = myVTK.createFloatArray("eRR", 3, n_points)
farray_eCC = myVTK.createFloatArray("eCC", 3, n_points)
farray_eLL = myVTK.createFloatArray("eLL", 3, n_points)
c_lst_FWLV = numpy.array([farray_c.GetTuple(k_point)[0] for k_point in xrange(n_points) if (iarray_regions.GetTuple(k_point)[0] == 0)])
(c_avg_FWLV, c_std_FWLV) = myVTK.computeMeanStddevAngles(
angles=c_lst_FWLV,
angles_in_degrees=False,
angles_in_pm_pi=False)
myVTK.myPrint(verbose, "c_avg_FWLV = " + str(c_avg_FWLV))
c_lst_FWLV = (((c_lst_FWLV-c_avg_FWLV+math.pi)%(2*math.pi))-math.pi+c_avg_FWLV)
c_min_FWLV = min(c_lst_FWLV)
c_max_FWLV = max(c_lst_FWLV)
myVTK.myPrint(verbose, "c_min_FWLV = " + str(c_min_FWLV))
myVTK.myPrint(verbose, "c_max_FWLV = " + str(c_max_FWLV))
c_lst_S = numpy.array([farray_c.GetTuple(k_point)[0] for k_point in xrange(n_points) if (iarray_regions.GetTuple(k_point)[0] == 1)])
(c_avg_S, c_std_S) = myVTK.computeMeanStddevAngles(
angles=c_lst_S,
angles_in_degrees=False,
angles_in_pm_pi=False)
myVTK.myPrint(verbose, "c_avg_S = " + str(c_avg_S))
c_lst_S = (((c_lst_S-c_avg_S+math.pi)%(2*math.pi))-math.pi+c_avg_S)
c_min_S = min(c_lst_S)
c_max_S = max(c_lst_S)
myVTK.myPrint(verbose, "c_min_S = " + str(c_min_S))
myVTK.myPrint(verbose, "c_max_S = " + str(c_max_S))
c_lst_FWRV = numpy.array([farray_c.GetTuple(k_point)[0] for k_point in xrange(n_points) if (iarray_regions.GetTuple(k_point)[0] == 2)])
(c_avg_FWRV, c_std_FWRV) = myVTK.computeMeanStddevAngles(
angles=c_lst_FWRV,
angles_in_degrees=False,
angles_in_pm_pi=False)
myVTK.myPrint(verbose, "c_avg_FWRV = " + str(c_avg_FWRV))
c_lst_FWRV = (((c_lst_FWRV-c_avg_FWRV+math.pi)%(2*math.pi))-math.pi+c_avg_FWRV)
c_min_FWRV = min(c_lst_FWRV)
c_max_FWRV = max(c_lst_FWRV)
myVTK.myPrint(verbose, "c_min_FWRV = " + str(c_min_FWRV))
myVTK.myPrint(verbose, "c_max_FWRV = " + str(c_max_FWRV))
l_lst = [farray_l.GetTuple(k_point)[0] for k_point in xrange(n_points)]
l_min = min(l_lst)
l_max = max(l_lst)
for k_point in xrange(n_points):
if (iarray_part_id is not None) and (int(iarray_part_id.GetTuple(k_point)[0]) > 0):
rr = 0.
cc = 0.
ll = 0.
eRR = [1.,0.,0.]
eCC = [0.,1.,0.]
eLL = [0.,0.,1.]
else:
point = numpy.array(points.GetPoint(k_point))
region_id = iarray_regions.GetTuple(k_point)[0]
if (region_id == 0):
cell_locator_endLV.FindClosestPoint(
point,
closest_point_endLV,
generic_cell,
cellId_endLV,
subId,
dist_endLV)
cell_locator_epi.FindClosestPoint(
point,
closest_point_epi,
generic_cell,
cellId_epi,
subId,
dist_epi)
rr = dist_endLV/(dist_endLV+dist_epi)
c = farray_c.GetTuple(k_point)[0]
c = (((c-c_avg_FWLV+math.pi)%(2*math.pi))-math.pi+c_avg_FWLV)
cc = (c-c_min_FWLV) / (c_max_FWLV-c_min_FWLV)
l = farray_l.GetTuple(k_point)[0]
ll = (l-l_min) / (l_max-l_min)
normal_endLV = numpy.reshape(pdata_endLV.GetCellData().GetNormals().GetTuple(cellId_endLV), (3))
normal_epi = numpy.reshape(pdata_epi.GetCellData().GetNormals().GetTuple(cellId_epi), (3))
eRR = (1.-rr) * normal_endLV + rr * normal_epi
eRR /= numpy.linalg.norm(eRR)
eL = numpy.reshape(farray_eL.GetTuple(k_point), (3))
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
elif (region_id == 1):
cell_locator_endLV.FindClosestPoint(
point,
closest_point_endLV,
generic_cell,
cellId_endLV,
subId,
dist_endLV)
cell_locator_endRV.FindClosestPoint(
point,
closest_point_endRV,
generic_cell,
cellId_endRV,
subId,
dist_endRV)
rr = dist_endLV/(dist_endLV+dist_endRV)
c = farray_c.GetTuple(k_point)[0]
c = (((c-c_avg_S+math.pi)%(2*math.pi))-math.pi+c_avg_S)
cc = (c-c_min_S) / (c_max_S-c_min_S)
l = farray_l.GetTuple(k_point)[0]
ll = (l-l_min) / (l_max-l_min)
normal_endLV = numpy.reshape(pdata_endLV.GetCellData().GetNormals().GetTuple(cellId_endLV), (3))
normal_endRV = numpy.reshape(pdata_endRV.GetCellData().GetNormals().GetTuple(cellId_endRV), (3))
eRR = (1.-rr) * normal_endLV - rr * normal_endRV
eRR /= numpy.linalg.norm(eRR)
eL = numpy.reshape(farray_eL.GetTuple(k_point), (3))
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
if (region_id == 2):
cell_locator_endRV.FindClosestPoint(
point,
closest_point_endRV,
generic_cell,
cellId_endRV,
subId,
dist_endRV)
cell_locator_epi.FindClosestPoint(
point,
closest_point_epi,
generic_cell,
cellId_epi,
subId,
dist_epi)
rr = dist_endRV/(dist_endRV+dist_epi)
c = farray_c.GetTuple(k_point)[0]
c = (((c-c_avg_FWRV+math.pi)%(2*math.pi))-math.pi+c_avg_FWRV)
cc = (c-c_min_FWRV) / (c_max_FWRV-c_min_FWRV)
l = farray_l.GetTuple(k_point)[0]
ll = (l-l_min) / (l_max-l_min)
normal_endRV = numpy.reshape(pdata_endRV.GetCellData().GetNormals().GetTuple(cellId_endRV), (3))
normal_epi = numpy.reshape(pdata_epi.GetCellData().GetNormals().GetTuple(cellId_epi), (3))
eRR = (1.-rr) * normal_endRV + rr * normal_epi
eRR /= numpy.linalg.norm(eRR)
eL = numpy.reshape(farray_eL.GetTuple(k_point), (3))
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
farray_rr.InsertTuple(k_point, [rr])
farray_cc.InsertTuple(k_point, [cc])
farray_ll.InsertTuple(k_point, [ll])
farray_eRR.InsertTuple(k_point, eRR)
farray_eCC.InsertTuple(k_point, eCC)
farray_eLL.InsertTuple(k_point, eLL)
return (farray_rr,
farray_cc,
farray_ll,
farray_eRR,
farray_eCC,
farray_eLL)
def computePseudoProlateSpheroidalCoordinatesAndBasisForLV(
points,
farray_c,
farray_l,
farray_eL,
pdata_end,
pdata_epi,
iarray_part_id=None,
verbose=1):
myVTK.myPrint(verbose, "*** computePseudoProlateSpheroidalCoordinatesAndBasisForLV ***")
myVTK.myPrint(verbose, "Computing surface cell normals...")
pdata_end = myVTK.addPDataNormals(
pdata=pdata_end,
verbose=verbose-1)
pdata_epi = myVTK.addPDataNormals(
pdata=pdata_epi,
verbose=verbose)
myVTK.myPrint(verbose, "Initializing surface cell locators...")
(cell_locator_end,
closest_point_end,
generic_cell,
cellId_end,
subId,
dist_end) = myVTK.getCellLocator(
mesh=pdata_end,
verbose=verbose-1)
(cell_locator_epi,
closest_point_epi,
generic_cell,
cellId_epi,
subId,
dist_epi) = myVTK.getCellLocator(
mesh=pdata_epi,
verbose=verbose-1)
myVTK.myPrint(verbose, "Computing local prolate spheroidal directions...")
n_points = points.GetNumberOfPoints()
farray_rr = myVTK.createFloatArray("rr", 1, n_points)
farray_cc = myVTK.createFloatArray("cc", 1, n_points)
farray_ll = myVTK.createFloatArray("ll", 1, n_points)
farray_eRR = myVTK.createFloatArray("eRR", 3, n_points)
farray_eCC = myVTK.createFloatArray("eCC", 3, n_points)
farray_eLL = myVTK.createFloatArray("eLL", 3, n_points)
if (n_points == 0):
return (farray_rr,
farray_cc,
farray_ll,
farray_eRR,
farray_eCC,
farray_eLL)
c_lst = [farray_c.GetTuple(k_point)[0] for k_point in xrange(n_points)]
c_min = min(c_lst)
c_max = max(c_lst)
l_lst = [farray_l.GetTuple(k_point)[0] for k_point in xrange(n_points)]
l_min = min(l_lst)
l_max = max(l_lst)
for k_point in xrange(n_points):
if (iarray_part_id is not None) and (int(iarray_part_id.GetTuple(k_point)[0]) > 0):
rr = 0.
cc = 0.
ll = 0.
eRR = [1.,0.,0.]
eCC = [0.,1.,0.]
eLL = [0.,0.,1.]
else:
point = numpy.array(points.GetPoint(k_point))
cell_locator_end.FindClosestPoint(
point,
closest_point_end,
generic_cell,
cellId_end,
subId,
dist_end)
cell_locator_epi.FindClosestPoint(
point,
closest_point_epi,
generic_cell,
cellId_epi,
subId,
dist_epi)
rr = dist_end/(dist_end+dist_epi)
c = farray_c.GetTuple(k_point)[0]
cc = (c-c_min) / (c_max-c_min)
l = farray_l.GetTuple(k_point)[0]
ll = (l-l_min) / (l_max-l_min)
normal_end = numpy.reshape(pdata_end.GetCellData().GetNormals().GetTuple(cellId_end), (3))
normal_epi = numpy.reshape(pdata_epi.GetCellData().GetNormals().GetTuple(cellId_epi), (3))
eRR = (1.-rr) * normal_end + rr * normal_epi
eRR /= numpy.linalg.norm(eRR)
eL = numpy.reshape(farray_eL.GetTuple(k_point), (3))
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
farray_rr.InsertTuple(k_point, [rr])
farray_cc.InsertTuple(k_point, [cc])
farray_ll.InsertTuple(k_point, [ll])
farray_eRR.InsertTuple(k_point, eRR)
farray_eCC.InsertTuple(k_point, eCC)
farray_eLL.InsertTuple(k_point, eLL)
return (farray_rr,
farray_cc,
farray_ll,
farray_eRR,
farray_eCC,
farray_eLL)
def computePseudoProlateSpheroidalCoordinatesAndBasisForLV(
points,
farray_c,
farray_l,
farray_eL,
pdata_end,
pdata_epi,
iarray_part_id=None,
verbose=0):
myVTK.myPrint(
verbose,
"*** computePseudoProlateSpheroidalCoordinatesAndBasisForLV ***")
myVTK.myPrint(verbose - 1, "Computing surface cell normals...")
pdata_end = myVTK.addPDataNormals(pdata=pdata_end, verbose=verbose - 1)
pdata_epi = myVTK.addPDataNormals(pdata=pdata_epi, verbose=verbose - 1)
myVTK.myPrint(verbose - 1, "Initializing surface cell locators...")
(cell_locator_end, closest_point_end, generic_cell, cellId_end, subId,
dist_end) = myVTK.getCellLocator(mesh=pdata_end, verbose=verbose - 1)
(cell_locator_epi, closest_point_epi, generic_cell, cellId_epi, subId,
dist_epi) = myVTK.getCellLocator(mesh=pdata_epi, verbose=verbose - 1)
myVTK.myPrint(verbose - 1,
"Computing local prolate spheroidal directions...")
n_points = points.GetNumberOfPoints()
farray_rr = myVTK.createFloatArray("rr", 1, n_points)
farray_cc = myVTK.createFloatArray("cc", 1, n_points)
farray_ll = myVTK.createFloatArray("ll", 1, n_points)
farray_eRR = myVTK.createFloatArray("eRR", 3, n_points)
farray_eCC = myVTK.createFloatArray("eCC", 3, n_points)
farray_eLL = myVTK.createFloatArray("eLL", 3, n_points)
if (n_points == 0):
return (farray_rr, farray_cc, farray_ll, farray_eRR, farray_eCC,
farray_eLL)
c_lst = [farray_c.GetTuple1(k_point) for k_point in xrange(n_points)]
c_min = min(c_lst)
c_max = max(c_lst)
l_lst = [farray_l.GetTuple1(k_point) for k_point in xrange(n_points)]
l_min = min(l_lst)
l_max = max(l_lst)
pdata_end_normals = pdata_end.GetCellData().GetNormals()
pdata_epi_normals = pdata_epi.GetCellData().GetNormals()
pdata_end_normal = numpy.empty(3)
pdata_epi_normal = numpy.empty(3)
eL = numpy.empty(3)
point = numpy.empty(3)
for k_point in xrange(n_points):
if (iarray_part_id
is not None) and (int(iarray_part_id.GetTuple1(k_point)) > 0):
rr = 0.
cc = 0.
ll = 0.
eRR = numpy.array([1., 0., 0.])
eCC = numpy.array([0., 1., 0.])
eLL = numpy.array([0., 0., 1.])
else:
points.GetPoint(k_point, point)
cell_locator_end.FindClosestPoint(point, closest_point_end,
generic_cell, cellId_end, subId,
dist_end)
cell_locator_epi.FindClosestPoint(point, closest_point_epi,
generic_cell, cellId_epi, subId,
dist_epi)
rr = dist_end / (dist_end + dist_epi)
c = farray_c.GetTuple1(k_point)
cc = (c - c_min) / (c_max - c_min)
l = farray_l.GetTuple1(k_point)
ll = (l - l_min) / (l_max - l_min)
pdata_end_normals.GetTuple(cellId_end, pdata_end_normal)
pdata_epi_normals.GetTuple(cellId_epi, pdata_epi_normal)
eRR = (1. - rr) * pdata_end_normal + rr * pdata_epi_normal
eRR /= numpy.linalg.norm(eRR)
farray_eL.GetTuple(k_point, eL)
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
farray_rr.SetTuple1(k_point, rr)
farray_cc.SetTuple1(k_point, cc)
farray_ll.SetTuple1(k_point, ll)
farray_eRR.SetTuple(k_point, eRR)
farray_eCC.SetTuple(k_point, eCC)
farray_eLL.SetTuple(k_point, eLL)
return (farray_rr, farray_cc, farray_ll, farray_eRR, farray_eCC,
farray_eLL)
def computePseudoProlateSpheroidalCoordinatesAndBasisForBiV(
points,
iarray_regions,
farray_c,
farray_l,
farray_eL,
pdata_endLV,
pdata_endRV,
pdata_epi,
iarray_part_id=None,
verbose=0):
myVTK.myPrint(
verbose,
"*** computePseudoProlateSpheroidalCoordinatesAndBasisForBiV ***")
myVTK.myPrint(verbose - 1, "Computing surface cell normals...")
pdata_endLV = myVTK.addPDataNormals(pdata=pdata_endLV, verbose=verbose - 1)
pdata_endRV = myVTK.addPDataNormals(pdata=pdata_endRV, verbose=verbose - 1)
pdata_epi = myVTK.addPDataNormals(pdata=pdata_epi, verbose=verbose - 1)
myVTK.myPrint(verbose - 1, "Initializing surface cell locators...")
(cell_locator_endLV, closest_point_endLV, generic_cell, cellId_endLV,
subId, dist_endLV) = myVTK.getCellLocator(mesh=pdata_endLV,
verbose=verbose - 1)
(cell_locator_endRV, closest_point_endRV, generic_cell, cellId_endRV,
subId, dist_endRV) = myVTK.getCellLocator(mesh=pdata_endRV,
verbose=verbose - 1)
(cell_locator_epi, closest_point_epi, generic_cell, cellId_epi, subId,
dist_epi) = myVTK.getCellLocator(mesh=pdata_epi, verbose=verbose - 1)
myVTK.myPrint(verbose - 1,
"Computing local prolate spheroidal directions...")
n_points = points.GetNumberOfPoints()
farray_rr = myVTK.createFloatArray("rr", 1, n_points)
farray_cc = myVTK.createFloatArray("cc", 1, n_points)
farray_ll = myVTK.createFloatArray("ll", 1, n_points)
farray_eRR = myVTK.createFloatArray("eRR", 3, n_points)
farray_eCC = myVTK.createFloatArray("eCC", 3, n_points)
farray_eLL = myVTK.createFloatArray("eLL", 3, n_points)
c_lst_FWLV = numpy.array([
farray_c.GetTuple1(k_point) for k_point in xrange(n_points)
if (iarray_regions.GetTuple1(k_point) == 0)
])
(c_avg_FWLV,
c_std_FWLV) = myVTK.computeMeanStddevAngles(angles=c_lst_FWLV,
angles_in_degrees=False,
angles_in_pm_pi=False)
myVTK.myPrint(verbose - 1, "c_avg_FWLV = " + str(c_avg_FWLV))
c_lst_FWLV = (((c_lst_FWLV - c_avg_FWLV + math.pi) % (2 * math.pi)) -
math.pi + c_avg_FWLV)
c_min_FWLV = min(c_lst_FWLV)
c_max_FWLV = max(c_lst_FWLV)
myVTK.myPrint(verbose - 1, "c_min_FWLV = " + str(c_min_FWLV))
myVTK.myPrint(verbose - 1, "c_max_FWLV = " + str(c_max_FWLV))
c_lst_S = numpy.array([
farray_c.GetTuple1(k_point) for k_point in xrange(n_points)
if (iarray_regions.GetTuple1(k_point) == 1)
])
(c_avg_S, c_std_S) = myVTK.computeMeanStddevAngles(angles=c_lst_S,
angles_in_degrees=False,
angles_in_pm_pi=False)
myVTK.myPrint(verbose - 1, "c_avg_S = " + str(c_avg_S))
c_lst_S = (((c_lst_S - c_avg_S + math.pi) % (2 * math.pi)) - math.pi +
c_avg_S)
c_min_S = min(c_lst_S)
c_max_S = max(c_lst_S)
myVTK.myPrint(verbose - 1, "c_min_S = " + str(c_min_S))
myVTK.myPrint(verbose - 1, "c_max_S = " + str(c_max_S))
c_lst_FWRV = numpy.array([
farray_c.GetTuple1(k_point) for k_point in xrange(n_points)
if (iarray_regions.GetTuple1(k_point) == 2)
])
(c_avg_FWRV,
c_std_FWRV) = myVTK.computeMeanStddevAngles(angles=c_lst_FWRV,
angles_in_degrees=False,
angles_in_pm_pi=False)
myVTK.myPrint(verbose - 1, "c_avg_FWRV = " + str(c_avg_FWRV))
c_lst_FWRV = (((c_lst_FWRV - c_avg_FWRV + math.pi) % (2 * math.pi)) -
math.pi + c_avg_FWRV)
c_min_FWRV = min(c_lst_FWRV)
c_max_FWRV = max(c_lst_FWRV)
myVTK.myPrint(verbose - 1, "c_min_FWRV = " + str(c_min_FWRV))
myVTK.myPrint(verbose - 1, "c_max_FWRV = " + str(c_max_FWRV))
l_lst = [farray_l.GetTuple1(k_point) for k_point in xrange(n_points)]
l_min = min(l_lst)
l_max = max(l_lst)
point = numpy.empty(3)
for k_point in xrange(n_points):
if (iarray_part_id
is not None) and (int(iarray_part_id.GetTuple1(k_point)) > 0):
rr = 0.
cc = 0.
ll = 0.
eRR = [1., 0., 0.]
eCC = [0., 1., 0.]
eLL = [0., 0., 1.]
else:
points.GetPoint(k_point, point)
region_id = iarray_regions.GetTuple1(k_point)
if (region_id == 0):
cell_locator_endLV.FindClosestPoint(point, closest_point_endLV,
generic_cell, cellId_endLV,
subId, dist_endLV)
cell_locator_epi.FindClosestPoint(point, closest_point_epi,
generic_cell, cellId_epi,
subId, dist_epi)
rr = dist_endLV / (dist_endLV + dist_epi)
c = farray_c.GetTuple1(k_point)
c = (((c - c_avg_FWLV + math.pi) % (2 * math.pi)) - math.pi +
c_avg_FWLV)
cc = (c - c_min_FWLV) / (c_max_FWLV - c_min_FWLV)
l = farray_l.GetTuple1(k_point)
ll = (l - l_min) / (l_max - l_min)
normal_endLV = numpy.reshape(
pdata_endLV.GetCellData().GetNormals().GetTuple(
cellId_endLV), (3))
normal_epi = numpy.reshape(
pdata_epi.GetCellData().GetNormals().GetTuple(cellId_epi),
(3))
eRR = (1. - rr) * normal_endLV + rr * normal_epi
eRR /= numpy.linalg.norm(eRR)
eL = numpy.reshape(farray_eL.GetTuple(k_point), (3))
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
elif (region_id == 1):
cell_locator_endLV.FindClosestPoint(point, closest_point_endLV,
generic_cell, cellId_endLV,
subId, dist_endLV)
cell_locator_endRV.FindClosestPoint(point, closest_point_endRV,
generic_cell, cellId_endRV,
subId, dist_endRV)
rr = dist_endLV / (dist_endLV + dist_endRV)
c = farray_c.GetTuple1(k_point)
c = (((c - c_avg_S + math.pi) % (2 * math.pi)) - math.pi +
c_avg_S)
cc = (c - c_min_S) / (c_max_S - c_min_S)
l = farray_l.GetTuple1(k_point)
ll = (l - l_min) / (l_max - l_min)
normal_endLV = numpy.reshape(
pdata_endLV.GetCellData().GetNormals().GetTuple(
cellId_endLV), (3))
normal_endRV = numpy.reshape(
pdata_endRV.GetCellData().GetNormals().GetTuple(
cellId_endRV), (3))
eRR = (1. - rr) * normal_endLV - rr * normal_endRV
eRR /= numpy.linalg.norm(eRR)
eL = numpy.reshape(farray_eL.GetTuple(k_point), (3))
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
if (region_id == 2):
cell_locator_endRV.FindClosestPoint(point, closest_point_endRV,
generic_cell, cellId_endRV,
subId, dist_endRV)
cell_locator_epi.FindClosestPoint(point, closest_point_epi,
generic_cell, cellId_epi,
subId, dist_epi)
rr = dist_endRV / (dist_endRV + dist_epi)
c = farray_c.GetTuple1(k_point)
c = (((c - c_avg_FWRV + math.pi) % (2 * math.pi)) - math.pi +
c_avg_FWRV)
cc = (c - c_min_FWRV) / (c_max_FWRV - c_min_FWRV)
l = farray_l.GetTuple1(k_point)
ll = (l - l_min) / (l_max - l_min)
normal_endRV = numpy.reshape(
pdata_endRV.GetCellData().GetNormals().GetTuple(
cellId_endRV), (3))
normal_epi = numpy.reshape(
pdata_epi.GetCellData().GetNormals().GetTuple(cellId_epi),
(3))
eRR = (1. - rr) * normal_endRV + rr * normal_epi
eRR /= numpy.linalg.norm(eRR)
eL = numpy.reshape(farray_eL.GetTuple(k_point), (3))
eCC = numpy.cross(eL, eRR)
eCC /= numpy.linalg.norm(eCC)
eLL = numpy.cross(eRR, eCC)
farray_rr.SetTuple1(k_point, rr)
farray_cc.SetTuple1(k_point, cc)
farray_ll.SetTuple1(k_point, ll)
farray_eRR.SetTuple(k_point, eRR)
farray_eCC.SetTuple(k_point, eCC)
farray_eLL.SetTuple(k_point, eLL)
return (farray_rr, farray_cc, farray_ll, farray_eRR, farray_eCC,
farray_eLL)
def computeRegionsForBiV(points, pdata_endLV, pdata_endRV, pdata_epi, verbose=0):
myVTK.myPrint(verbose, "*** computeRegionsForBiV ***")
myVTK.myPrint(verbose, "Initializing cell locators...")
(cell_locator_endLV, closest_point_endLV, generic_cell, cellId_endLV, subId, dist_endLV) = myVTK.getCellLocator(
mesh=pdata_endLV, verbose=verbose - 1
)
(cell_locator_endRV, closest_point_endRV, generic_cell, cellId_endRV, subId, dist_endRV) = myVTK.getCellLocator(
mesh=pdata_endRV, verbose=verbose - 1
)
(cell_locator_epi, closest_point_epi, generic_cell, cellId_epi, subId, dist_epi) = myVTK.getCellLocator(
mesh=pdata_epi, verbose=verbose - 1
)
n_points = points.GetNumberOfPoints()
iarray_region = myVTK.createIntArray("region_id", 1, n_points)
for k_point in range(n_points):
point = numpy.array(points.GetPoint(k_point))
cell_locator_endLV.FindClosestPoint(point, closest_point_endLV, generic_cell, cellId_endLV, subId, dist_endLV)
cell_locator_endRV.FindClosestPoint(point, closest_point_endRV, generic_cell, cellId_endRV, subId, dist_endRV)
cell_locator_epi.FindClosestPoint(point, closest_point_epi, generic_cell, cellId_epi, subId, dist_epi)
if dist_endRV == max(dist_endLV, dist_endRV, dist_epi):
iarray_region.SetTuple(k_point, [0])
elif dist_epi == max(dist_endLV, dist_endRV, dist_epi):
iarray_region.SetTuple(k_point, [1])
elif dist_endLV == max(dist_endLV, dist_endRV, dist_epi):
iarray_region.SetTuple(k_point, [2])
return iarray_region