def createArray(
array_name,
n_components=1,
n_tuples=0,
array_type="float",
init_to_zero=0,
verbose=1):
assert (type(array_type) in [type, str]), "array_type must be a type or a str. Aborting."
if (type(array_type) is type):
assert (array_type in [float, int]), "if a type, array_type must be equal to float or int. Aborting."
if (array_type == float):
return myVTK.createFloatArray(
name=array_name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type == int):
return myVTK.createIntArray(
name=array_name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (type(array_type) is str):
assert (array_type in ["double", "float", "int", "short"]), "if a str, array_type must be equal to double, float, int or short. Aborting."
if (array_type == "float") or (array_type == "double"):
return myVTK.createFloatArray(
name=array_name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type == "int"):
return myVTK.createIntArray(
name=array_name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type == "short"):
return myVTK.createShortArray(
name=array_name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
def computeSectorsForLV(farray_rr,
farray_cc,
farray_ll,
n_r=1,
n_c=1,
n_l=1,
iarray_part_id=None,
verbose=0):
myVTK.myPrint(verbose, "*** computeSectorsForLV ***")
n_cells = farray_rr.GetNumberOfTuples()
iarray_sector = myVTK.createIntArray("sector_id", 1, n_cells)
for k_cell in range(n_cells):
if (iarray_part_id
is not None) and (int(iarray_part_id.GetTuple1(k_cell)) > 0):
sector_id = -1
else:
rr = farray_rr.GetTuple1(k_cell)
cc = farray_cc.GetTuple1(k_cell)
ll = farray_ll.GetTuple1(k_cell)
k_r = int(rr * n_r / 1.000001)
k_c = int(cc * n_c / 1.000001)
k_l = int((1. - ll) * n_l / 1.000001)
sector_id = k_l * n_c * n_r + k_c * n_r + k_r
iarray_sector.SetTuple1(k_cell, sector_id)
return iarray_sector
def addPhysicalGroupToMesh(
mesh,
msh_filename,
verbose=0):
mypy.my_print(verbose, "*** addPhysicalGroupToMesh ***")
n_cells = mesh.GetNumberOfCells()
iarray_part_id = myVTK.createIntArray(
name="part_id",
n_tuples=n_cells,
n_components=1)
mesh.GetCellData().AddArray(iarray_part_id)
msh = open(msh_filename)
context = ""
for line in msh:
if line.startswith("$Elements"):
context = "reading element number"
continue
elif line.startswith("$EndElements"):
context = ""
continue
if (context == "reading elements"):
splitted_line = line.split()
iarray_part_id.SetTuple(int(splitted_line[0])-1, [int(splitted_line[3])-1])
elif (context == "reading element number"):
n_elements = int(line)
assert (n_elements == n_cells)
context = "reading elements"
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
def computeSectorsForLV(
farray_rr,
farray_cc,
farray_ll,
n_r=1,
n_c=1,
n_l=1,
iarray_part_id=None,
verbose=0):
myVTK.myPrint(verbose, "*** computeSectorsForLV ***")
n_cells = farray_rr.GetNumberOfTuples()
iarray_sector = myVTK.createIntArray("sector_id", 1, n_cells)
for k_cell in range(n_cells):
if (iarray_part_id is not None) and (int(iarray_part_id.GetTuple1(k_cell)) > 0):
sector_id = -1
else:
rr = farray_rr.GetTuple1(k_cell)
cc = farray_cc.GetTuple1(k_cell)
ll = farray_ll.GetTuple1(k_cell)
k_r = int(rr*n_r/1.000001)
k_c = int(cc*n_c/1.000001)
k_l = int((1.-ll)*n_l/1.000001)
sector_id = k_l * n_c * n_r + k_c * n_r + k_r
iarray_sector.SetTuple1(k_cell, sector_id)
return iarray_sector
def computeSectorsForBiV(iarray_regions,
farray_rr,
farray_cc,
farray_ll,
n_r=[1] * 3,
n_c=[1] * 3,
n_l=[1] * 3,
iarray_part_id=None,
verbose=0):
myVTK.myPrint(verbose, "*** computeSectorsForBiV ***")
n_cells = iarray_regions.GetNumberOfTuples()
assert (farray_rr.GetNumberOfTuples() == n_cells)
assert (farray_cc.GetNumberOfTuples() == n_cells)
assert (farray_ll.GetNumberOfTuples() == n_cells)
iarray_sector = myVTK.createIntArray("sector_id", 1, n_cells)
for k_cell in range(n_cells):
if (iarray_part_id
is not None) and (int(iarray_part_id.GetTuple1(k_cell)) > 0):
sector_id = -1
else:
region_id = int(iarray_regions.GetTuple1(k_cell))
rr = farray_rr.GetTuple1(k_cell)
cc = farray_cc.GetTuple1(k_cell)
ll = farray_ll.GetTuple1(k_cell)
k_r = int(rr * n_r[region_id] / 1.000001)
k_c = int(cc * n_c[region_id] / 1.000001)
k_l = int((1. - ll) * n_l[region_id] / 1.000001)
sector_id = k_l * n_c[region_id] * n_r[region_id] \
+ k_c * n_r[region_id] \
+ k_r
if (region_id >= 1):
sector_id += n_r[0] * n_c[0] * n_l[0]
if (region_id >= 2):
sector_id += n_r[1] * n_c[1] * n_l[1]
iarray_sector.SetTuple1(k_cell, sector_id)
return iarray_sector
def computeSectorsForBiV(
iarray_regions,
farray_rr,
farray_cc,
farray_ll,
n_r=[1]*3,
n_c=[1]*3,
n_l=[1]*3,
iarray_part_id=None,
verbose=0):
myVTK.myPrint(verbose, "*** computeSectorsForBiV ***")
n_cells = iarray_regions.GetNumberOfTuples()
assert (farray_rr.GetNumberOfTuples() == n_cells)
assert (farray_cc.GetNumberOfTuples() == n_cells)
assert (farray_ll.GetNumberOfTuples() == n_cells)
iarray_sector = myVTK.createIntArray("sector_id", 1, n_cells)
for k_cell in range(n_cells):
if (iarray_part_id is not None) and (int(iarray_part_id.GetTuple1(k_cell)) > 0):
sector_id = -1
else:
region_id = int(iarray_regions.GetTuple1(k_cell))
rr = farray_rr.GetTuple1(k_cell)
cc = farray_cc.GetTuple1(k_cell)
ll = farray_ll.GetTuple1(k_cell)
k_r = int( rr *n_r[region_id]/1.000001)
k_c = int( cc *n_c[region_id]/1.000001)
k_l = int((1.-ll)*n_l[region_id]/1.000001)
sector_id = k_l * n_c[region_id] * n_r[region_id] \
+ k_c * n_r[region_id] \
+ k_r
if (region_id >= 1):
sector_id += n_r[0] * n_c[0] * n_l[0]
if (region_id >= 2):
sector_id += n_r[1] * n_c[1] * n_l[1]
iarray_sector.SetTuple1(k_cell, sector_id)
return iarray_sector
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 readMatLabImage(
filename,
field_name,
field_type,
spacing=[1.,1.,1.],
verbose=1):
myVTK.myPrint(verbose, "*** readMatLabImage ***")
assert (os.path.isfile(filename)), "Wrong filename. Aborting."
data = scipy.io.loadmat(filename)[field_name]
n_pixels_x = len(data)
n_pixels_y = len(data[0])
n_pixels_z = len(data[0][0])
n_pixels = n_pixels_x * n_pixels_y * n_pixels_z
#points = vtk.vtkPoints()
#points.SetNumberOfPoints(n_pixels)
#cell_array = vtk.vtkCellArray()
#cell = vtk.vtkVertex()
if (field_type == "int"):
array_data = myVTK.createIntArray(field_name, 1, n_pixels)
elif (field_type == "double"):
array_data = myVTK.createFloatArray(field_name, 1, n_pixels)
k_pixel = 0
for k_z in xrange(n_pixels_z):
for k_y in xrange(n_pixels_y):
for k_x in xrange(n_pixels_x):
#points.InsertPoint(k_pixel, [(k_x+0.5)/n_pixels_x,\
#(k_y+0.5)/n_pixels_y,\
#(k_z+0.5)/n_pixels_z])
#cell.GetPointIds().SetId(0, k_pixel)
#cell_array.InsertNextCell(cell)
#array_data.InsertTuple(k_pixel, [data[n_pixels_y-1-k_y][n_pixels_x-1-k_x][k_z]])
#array_data.InsertTuple(k_pixel, [data[n_pixels_y-1-k_y][k_x][k_z]])
#array_data.InsertTuple(k_pixel, [data[k_y][n_pixels_x-1-k_x][k_z]])
array_data.InsertTuple(k_pixel, [data[k_y][k_x][k_z]])
#array_data.InsertTuple(k_pixel, [data[n_pixels_x-1-k_x][n_pixels_y-1-k_y][k_z]])
#array_data.InsertTuple(k_pixel, [data[n_pixels_x-1-k_x][k_y][k_z]])
#array_data.InsertTuple(k_pixel, [data[k_x][n_pixels_y-1-k_y][k_z]])
#array_data.InsertTuple(k_pixel, [data[k_x][k_y][k_z]])
k_pixel += 1
#ugrid = vtk.vtkUnstructuredGrid()
#ugrid.SetPoints(points)
#ugrid.SetCells(vtk.VTK_VERTEX, cell_array)
#ugrid.GetCellData().AddArray(array_data)
#writeXMLUGrid(ugrid, case + ".vtu")
image = vtk.vtkImageData()
image.SetExtent(0, n_pixels_x-1, 0, n_pixels_y-1, 0, n_pixels_z-1)
image.SetSpacing(spacing)
image.GetPointData().AddArray(array_data)
return image
def createArray(name,
n_components=1,
n_tuples=0,
array_type="float",
init_to_zero=0,
verbose=0):
assert (type(array_type)
in (type, str)), "array_type must be a type or a str. Aborting."
if (type(array_type) is type):
assert (array_type in (float, int)), "Wrong array type. Aborting."
if (array_type == float):
return myvtk.createFloatArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type == int):
return myvtk.createIntArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (type(array_type) is str):
assert (array_type
in ("double", "float", "long", "unsigned long", "int",
"unsigned int", "short", "unsigned short", "char",
"unsigned char", "int64", "uint64", "int32", "uint32",
"int16", "uint16", "int8",
"uint8")), "Wrong array type. Aborting."
if (array_type == "float"):
return myvtk.createFloatArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type == "double"):
return myvtk.createDoubleArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("long", "int64")):
return myvtk.createLongArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("unsigned long", "uint64")):
return myvtk.createUnsignedLongArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("int", "int32")):
return myvtk.createIntArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("unsigned int", "uint32")):
return myvtk.createUnsignedIntArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("short", "int16")):
return myvtk.createShortArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("unsigned short", "uint16")):
return myvtk.createUnsignedShortArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("char", "int8")):
return myvtk.createCharArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
elif (array_type in ("unsigned char", "uint8")):
return myvtk.createUnsignedCharArray(name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose - 1)
def readMatLabImage(
filename,
field_name,
field_type,
spacing=[1.,1.,1.],
verbose=0):
mypy.my_print(verbose, "*** readMatLabImage ***")
assert (os.path.isfile(filename)), "Wrong filename (\""+filename+"\"). Aborting."
import scipy
data = scipy.io.loadmat(filename)[field_name]
n_pixels_x = len(data)
n_pixels_y = len(data[0])
n_pixels_z = len(data[0][0])
n_pixels = n_pixels_x * n_pixels_y * n_pixels_z
#points = vtk.vtkPoints()
#points.SetNumberOfPoints(n_pixels)
#cell_array = vtk.vtkCellArray()
#cell = vtk.vtkVertex()
if (field_type == "int"):
array_data = myvtk.createIntArray(
name=field_name,
n_components=1,
n_tuples=n_pixels)
elif (field_type == "double"):
array_data = myvtk.createFloatArray(
name=field_name,
n_components=1,
n_tuples=n_pixels)
k_pixel = 0
for k_z in range(n_pixels_z):
for k_y in range(n_pixels_y):
for k_x in range(n_pixels_x):
#points.InsertPoint(k_pixel, [(k_x+0.5)/n_pixels_x,\
#(k_y+0.5)/n_pixels_y,\
#(k_z+0.5)/n_pixels_z])
#cell.GetPointIds().SetId(0, k_pixel)
#cell_array.InsertNextCell(cell)
#array_data.SetTuple1(k_pixel, data[n_pixels_y-1-k_y][n_pixels_x-1-k_x][k_z])
#array_data.SetTuple1(k_pixel, data[n_pixels_y-1-k_y][k_x][k_z])
#array_data.SetTuple1(k_pixel, data[k_y][n_pixels_x-1-k_x][k_z])
array_data.SetTuple1(k_pixel, data[k_y][k_x][k_z])
#array_data.SetTuple1(k_pixel, data[n_pixels_x-1-k_x][n_pixels_y-1-k_y][k_z])
#array_data.SetTuple1(k_pixel, data[n_pixels_x-1-k_x][k_y][k_z])
#array_data.SetTuple1(k_pixel, data[k_x][n_pixels_y-1-k_y][k_z])
#array_data.SetTuple1(k_pixel, data[k_x][k_y][k_z])
k_pixel += 1
#ugrid = vtk.vtkUnstructuredGrid()
#ugrid.SetPoints(points)
#ugrid.SetCells(vtk.VTK_VERTEX, cell_array)
#ugrid.GetCellData().AddArray(array_data)
#writeXMLUGrid(ugrid, case+".vtu")
image = vtk.vtkImageData()
image.SetExtent(0, n_pixels_x-1, 0, n_pixels_y-1, 0, n_pixels_z-1)
image.SetSpacing(spacing)
image.GetPointData().AddArray(array_data)
return image
def createArray(
name,
n_components=1,
n_tuples=0,
array_type="float",
init_to_zero=0,
verbose=0):
assert (type(array_type) in (type, str)), "array_type must be a type or a str. Aborting."
if (type(array_type) is type):
assert (array_type in (float, int)), "Wrong array type. Aborting."
if (array_type == float):
return myvtk.createFloatArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type == int):
return myvtk.createIntArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (type(array_type) is str):
assert (array_type in ("double", "float", "long", "unsigned long", "int", "unsigned int", "short", "unsigned short", "char", "unsigned char", "int64", "uint64", "int32", "uint32", "int16", "uint16", "int8", "uint8")), "Wrong array type. Aborting."
if (array_type in ("float", "double")):
return myvtk.createFloatArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("long", "int64")):
return myvtk.createLongArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("unsigned long", "uint64")):
return myvtk.createUnsignedLongArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("int", "int32")):
return myvtk.createIntArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("unsigned int", "uint32")):
return myvtk.createUnsignedIntArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("short", "int16")):
return myvtk.createShortArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("unsigned short", "uint16")):
return myvtk.createUnsignedShortArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("char", "int8")):
return myvtk.createCharArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
elif (array_type in ("unsigned char", "uint8")):
return myvtk.createUnsignedCharArray(
name=name,
n_components=n_components,
n_tuples=n_tuples,
init_to_zero=init_to_zero,
verbose=verbose-1)
