def SplitDisconectedParts(polydata):
"""
"""
conn = vtkPolyDataConnectivityFilter()
conn.SetInputData(polydata)
conn.SetExtractionModeToAllRegions()
conn.Update()
nregions = conn.GetNumberOfExtractedRegions()
conn.SetExtractionModeToSpecifiedRegions()
conn.Update()
polydata_collection = []
# Update progress value in GUI
progress = nregions -1
if progress:
UpdateProgress = vu.ShowProgress(progress)
for region in range(nregions):
conn.InitializeSpecifiedRegionList()
conn.AddSpecifiedRegion(region)
conn.Update()
p = vtkPolyData()
p.DeepCopy(conn.GetOutput())
polydata_collection.append(p)
if progress:
UpdateProgress(region, _("Splitting disconnected regions..."))
return polydata_collection
def SelectLargestPart(polydata):
"""
"""
UpdateProgress = vu.ShowProgress(1)
conn = vtkPolyDataConnectivityFilter()
conn.SetInputData(polydata)
conn.SetExtractionModeToLargestRegion()
conn.AddObserver("ProgressEvent", lambda obj, evt:
UpdateProgress(conn, "Getting largest part..."))
conn.Update()
result = vtkPolyData()
result.DeepCopy(conn.GetOutput())
return result
def PeelDown(self, currentPeel):
for i in range(0, self.numberOfPeels):
currentPeel = self.SliceDown(currentPeel)
currentPeel = self.MapImageOnCurrentPeel(currentPeel)
newPeel = vtkPolyData()
newPeel.DeepCopy(currentPeel)
self.peel.append(newPeel)
# GetCurrentPeelActor()
# newPeelActor = vtkActor()
# newPeelActor = currentPeelActor
# peelActors.push_back(newPeelActor)
self.currentPeelNo += 1
def SliceDown(self, currentPeel):
# Warp using the normals
warp = vtkWarpVector()
warp.SetInputData(fixMesh(downsample(currentPeel))) # fixMesh here updates normals needed for warping
warp.SetInputArrayToProcess(0, 0, 0, vtkDataObject().FIELD_ASSOCIATION_POINTS,
vtkDataSetAttributes().NORMALS)
warp.SetScaleFactor(-1)
warp.Update()
out = vtkPolyData()
out = upsample(warp.GetPolyDataOutput())
out = smooth(out)
out = fixMesh(out)
out = cleanMesh(out)
currentPeel = out
return currentPeel
def writepolydata(filename, points, normals, cells):
polydata = vtkPolyData()
vtkpoints = vtkPoints()
vtkpoints.SetData(numpy_to_vtk(points))
polydata.SetPoints(vtkpoints)
polydata.GetPointData().SetNormals(numpy_to_vtk(normals))
triangles = vtkCellArray()
for i, j, k in cells:
triangles.InsertNextCell(3)
triangles.InsertCellPoint(i)
triangles.InsertCellPoint(j)
triangles.InsertCellPoint(k)
polydata.SetPolys(triangles)
wr = vtkPolyDataWriter()
wr.SetFileName(filename)
wr.SetInputData(polydata)
wr.Write()
def write_poly_data(cls, var, filename: str, attr_names: str) -> None:
vol = vtkPolyData()
verts = vtkPoints()
# noinspection PyArgumentList
lines = vtkCellArray()
# Retained, but not used. 'Fungus' is current, not 'Afumigatus'
# if isinstance(var, AfumigatusCellTreeList):
# adjacency = var.adjacency
#
# for i, j in adjacency.keys():
# if i != j:
# line = vtkLine()
# line.GetPointIds().SetId(0, i)
# line.GetPointIds().SetId(1, j)
# lines.InsertNextCell(line)
#
# el
if not isinstance(var, CellList):
raise NotImplementedError(
f'Only supported CellTree or CellList for POLY_DATA. \
Got {type(var)}'
)
for index in var.alive():
cell = var[index]
# noinspection PyArgumentList
verts.InsertNextPoint(cell['point'][2], cell['point'][1], cell['point'][0])
alive_cells = np.take(var.cell_data, var.alive())
for attr_name in attr_names:
cell_attr = alive_cells[attr_name]
scalars = numpy_to_vtk(num_array=cell_attr)
scalars.SetName(attr_name)
vol.GetPointData().AddArray(scalars)
vol.SetPoints(verts)
vol.SetLines(lines)
writer = vtkPolyDataWriter()
writer.SetFileName(filename)
writer.SetInputData(vol)
writer.Write()
def JoinSeedsParts(polydata, point_id_list):
"""
The function require vtkPolyData and point id
from vtkPolyData.
"""
conn = vtkPolyDataConnectivityFilter()
conn.SetInputData(polydata)
conn.SetExtractionModeToPointSeededRegions()
UpdateProgress = vu.ShowProgress(1 + len(point_id_list))
pos = 1
for seed in point_id_list:
conn.AddSeed(seed)
UpdateProgress(pos, _("Analysing selected regions..."))
pos += 1
conn.AddObserver("ProgressEvent", lambda obj, evt:
UpdateProgress(conn, "Getting selected parts"))
conn.Update()
result = vtkPolyData()
result.DeepCopy(conn.GetOutput())
return result
def compute_tubes(trk, direction):
"""Compute and assign colors to a vtkTube for visualization of a single tract
:param trk: nx3 array of doubles (x, y, z) point coordinates composing the tract
:type trk: numpy.ndarray
:param direction: nx3 array of int (x, y, z) RGB colors in the range 0 - 255
:type direction: numpy.ndarray
:return: a vtkTubeFilter instance
:rtype: vtkTubeFilter
"""
numb_points = trk.shape[0]
points = vtkPoints()
lines = vtkCellArray()
colors = vtkUnsignedCharArray()
colors.SetNumberOfComponents(4)
k = 0
lines.InsertNextCell(numb_points)
for j in range(numb_points):
points.InsertNextPoint(trk[j, :])
colors.InsertNextTuple(direction[j, :])
lines.InsertCellPoint(k)
k += 1
trk_data = vtkPolyData()
trk_data.SetPoints(points)
trk_data.SetLines(lines)
trk_data.GetPointData().SetScalars(colors)
# make it a tube
trk_tube = vtkTubeFilter()
trk_tube.SetRadius(0.5)
trk_tube.SetNumberOfSides(4)
trk_tube.SetInputData(trk_data)
trk_tube.Update()
return trk_tube
def convert_cells_to_vtk(cells: CellList) -> vtkPolyData:
cell_data: CellData = cells.cell_data
live_cells = cells.alive()
cell_data = cell_data[live_cells]
fields = dict(cell_data.dtype.fields) # type: ignore
fields.pop('point')
points = vtkPoints()
poly = vtkPolyData()
poly.SetPoints(points)
if not len(cell_data):
return poly
# vtk uses coordinate ordering x, y, z while we use z, y, x.
points.SetData(numpy_to_vtk(np.flip(cell_data['point'], axis=1)))
point_data = poly.GetPointData()
for field, (dtype, *_) in fields.items():
data = cell_data[field]
# numpy_to_vtk doesn't handle bool for some reason
if dtype == np.dtype('bool'):
data = data.astype(np.dtype('uint8'))
# noinspection PyBroadException
try:
scalar = numpy_to_vtk(data)
except Exception:
print(f'Unhandled data type in field {field}')
continue
scalar.SetName(field)
point_data.AddArray(scalar)
return poly
def RequestData(self, request, inInfoVec, outInfoVec):
from vtkmodules.vtkCommonCore import vtkFloatArray, vtkPoints
from vtkmodules.vtkCommonDataModel import (
vtkCellArray, vtkCompositeDataSet, vtkPartitionedDataSet,
vtkPartitionedDataSetCollection, vtkPolyData)
output = vtkPartitionedDataSetCollection.GetData(outInfoVec)
partitioned_datasets = []
partitioned_dataset_names = []
# Parse line file
if not self._filename:
print_error("SAVGReader requires a FileName")
return 0
# Stores lines of text from the file associated with each group of
# geometries encountered.
geometries = {"lines": [], "points": [], "poly": []}
# Read the file and build up data structure to hold the primitives
with open(self._filename, "r") as file:
current = None
for line in file:
parts = line.split("#")
line = parts[0].strip().lower()
if len(line) < 1:
continue
if not_supported(line):
continue
if line.startswith("lin"):
geometries["lines"].append({"rgba": None, "values": []})
current = geometries["lines"][-1]
line_parts = line.split(" ")
if len(line_parts) == 5:
current["rgba"] = [float(n) for n in line_parts[1:]]
elif line.startswith("point"):
geometries["points"].append({
"rgba": None,
"values": [],
})
current = geometries["points"][-1]
line_parts = line.split(" ")
if len(line_parts) == 5:
current["rgba"] = [float(n) for n in line_parts[1:]]
elif line.startswith("poly"):
geometries["poly"].append({
"rgba": None,
"npts": None,
"values": [],
})
current = geometries["poly"][-1]
line_parts = line.split(" ")
if len(line_parts) == 2:
current["npts"] = int(line_parts[1])
elif len(line_parts) == 6:
current["rgba"] = [float(n) for n in line_parts[1:5]]
current["npts"] = int(line_parts[5])
elif line.startswith("end"):
current = None
else:
if current is not None:
if "npts" in current and current["npts"] is not None:
# polygon, known num pts per poly
if len(current["values"]) == current["npts"]:
# Reached the number of points for the current one,
# start a new one.
geometries["poly"].append({
"npts":
current["npts"],
"rgba":
current["rgba"],
"values": []
})
current = geometries["poly"][-1]
pt, pt_col, pt_n = get_coords_from_line(line)
if pt:
current["values"].append({
"pos": pt,
})
color = pt_col or current["rgba"]
if color:
current["values"][-1]["col"] = color
if pt_n:
current["values"][-1]["norm"] = pt_n
# Build lines polydata if there were any lines
if geometries["lines"]:
line_points = vtkPoints()
line_cells = vtkCellArray()
line_point_colors = vtkFloatArray()
line_point_colors.SetNumberOfComponents(4)
line_point_colors.SetName("rgba_colors")
line_point_normals = vtkFloatArray()
line_point_normals.SetNumberOfComponents(3)
line_point_normals.SetName("vertex_normals")
pt_count = 0
for batch in geometries["lines"]:
num_in_batch = len(batch["values"])
first_in_batch = True
for coord in batch["values"]:
if "pos" in coord:
line_points.InsertNextPoint(coord["pos"])
if "norm" in coord:
line_point_normals.InsertNextTuple(coord["norm"])
if "col" in coord:
line_point_colors.InsertNextTuple(coord["col"])
if first_in_batch:
line_cells.InsertNextCell(num_in_batch)
first_in_batch = False
line_cells.InsertCellPoint(pt_count)
pt_count += 1
output_lines = vtkPolyData()
output_lines.SetPoints(line_points)
output_lines.SetLines(line_cells)
if line_point_colors.GetNumberOfTuples() > 0:
output_lines.GetPointData().AddArray(line_point_colors)
if line_point_normals.GetNumberOfTuples() > 0:
output_lines.GetPointData().AddArray(line_point_normals)
ds = vtkPartitionedDataSet()
ds.SetNumberOfPartitions(1)
ds.SetPartition(0, output_lines)
partitioned_datasets.append(ds)
partitioned_dataset_names.append("Lines")
# Build the points polydata if we found points
if geometries["points"]:
p_points = vtkPoints()
p_cells = vtkCellArray()
p_point_colors = vtkFloatArray()
p_point_colors.SetNumberOfComponents(4)
p_point_colors.SetName("rgba_colors")
p_point_normals = vtkFloatArray()
p_point_normals.SetNumberOfComponents(3)
p_point_normals.SetName("vertex_normals")
p_count = 0
for batch in geometries["points"]:
num_in_batch = len(batch["values"])
first_in_batch = True
for coord in batch["values"]:
if "pos" in coord:
p_points.InsertNextPoint(coord["pos"])
if "norm" in coord:
p_point_normals.InsertNextTuple(coord["norm"])
if "col" in coord:
p_point_colors.InsertNextTuple(coord["col"])
if first_in_batch:
p_cells.InsertNextCell(num_in_batch)
first_in_batch = False
p_cells.InsertCellPoint(p_count)
p_count += 1
output_points = vtkPolyData()
output_points.SetPoints(p_points)
output_points.SetVerts(p_cells)
if p_point_colors.GetNumberOfTuples() > 0:
output_points.GetPointData().AddArray(p_point_colors)
if p_point_normals.GetNumberOfTuples() > 0:
output_points.GetPointData().AddArray(p_point_normals)
ds = vtkPartitionedDataSet()
ds.SetNumberOfPartitions(1)
ds.SetPartition(0, output_points)
partitioned_datasets.append(ds)
partitioned_dataset_names.append("Points")
# Build the polygons if there were any
if geometries["poly"]:
poly_points = vtkPoints()
poly_cells = vtkCellArray()
poly_point_colors = vtkFloatArray()
poly_point_colors.SetNumberOfComponents(4)
poly_point_colors.SetName("rgba_colors")
poly_point_normals = vtkFloatArray()
poly_point_normals.SetNumberOfComponents(3)
poly_point_normals.SetName("vertex_normals")
pt_count = 0
for batch in geometries["poly"]:
num_in_batch = len(batch["values"])
if num_in_batch < 1:
continue
first_in_batch = True
for coord in batch["values"]:
if "pos" in coord:
poly_points.InsertNextPoint(coord["pos"])
if "norm" in coord:
poly_point_normals.InsertNextTuple(coord["norm"])
if "col" in coord:
poly_point_colors.InsertNextTuple(coord["col"])
if first_in_batch:
np_in_cell = num_in_batch
poly_cells.InsertNextCell(np_in_cell)
first_in_batch = False
poly_cells.InsertCellPoint(pt_count)
pt_count += 1
output_polys = vtkPolyData()
output_polys.SetPoints(poly_points)
output_polys.SetPolys(poly_cells)
if poly_point_colors.GetNumberOfTuples() > 0:
output_polys.GetPointData().AddArray(poly_point_colors)
if poly_point_normals.GetNumberOfTuples() > 0:
output_polys.GetPointData().AddArray(poly_point_normals)
ds = vtkPartitionedDataSet()
ds.SetNumberOfPartitions(1)
ds.SetPartition(0, output_polys)
partitioned_datasets.append(ds)
partitioned_dataset_names.append("Polygons")
# Add any partioned datasets we created
output.SetNumberOfPartitionedDataSets(len(partitioned_datasets))
for idx, pds in enumerate(partitioned_datasets):
output.SetPartitionedDataSet(idx, pds)
output.GetMetaData(idx).Set(vtkCompositeDataSet.NAME(),
partitioned_dataset_names[idx])
return 1
def _do_surface_creation(self, mask, mask_sFormMatrix=None):
if mask_sFormMatrix is None:
mask_sFormMatrix = vtkMatrix4x4()
value = np.mean(mask.GetScalarRange())
# Use the mask to create isosurface
mc = vtkContourFilter()
mc.SetInputData(mask)
mc.SetValue(0, value)
mc.ComputeNormalsOn()
mc.Update()
# Mask isosurface
refSurface = mc.GetOutput()
# Create a uniformly meshed surface
tmpPeel = downsample(refSurface)
# Standard space coordinates
# Apply coordinate transform to the meshed mask
mask_ijk2xyz = vtkTransform()
mask_ijk2xyz.SetMatrix(mask_sFormMatrix)
mask_ijk2xyz_filter = vtkTransformPolyDataFilter()
mask_ijk2xyz_filter.SetInputData(tmpPeel)
mask_ijk2xyz_filter.SetTransform(mask_ijk2xyz)
mask_ijk2xyz_filter.Update()
# Smooth the mesh
tmpPeel = smooth(mask_ijk2xyz_filter.GetOutput())
# Configure calculation of normals
tmpPeel = fixMesh(tmpPeel)
# Remove duplicate points etc
# tmpPeel = cleanMesh(tmpPeel)
# Generate triangles
tmpPeel = upsample(tmpPeel)
tmpPeel = smooth(tmpPeel)
tmpPeel = fixMesh(tmpPeel)
tmpPeel = cleanMesh(tmpPeel)
refImageSpace2_xyz_transform = vtkTransform()
refImageSpace2_xyz_transform.SetMatrix(vtk_utils.numpy_to_vtkMatrix4x4(np.linalg.inv(self.affine)))
self.refImageSpace2_xyz = vtkTransformPolyDataFilter()
self.refImageSpace2_xyz.SetTransform(refImageSpace2_xyz_transform)
xyz2_refImageSpace_transform = vtkTransform()
xyz2_refImageSpace_transform.SetMatrix(vtk_utils.numpy_to_vtkMatrix4x4(self.affine))
self.xyz2_refImageSpace = vtkTransformPolyDataFilter()
self.xyz2_refImageSpace.SetTransform(xyz2_refImageSpace_transform)
currentPeel = tmpPeel
self.currentPeelNo = 0
currentPeel= self.MapImageOnCurrentPeel(currentPeel)
newPeel = vtkPolyData()
newPeel.DeepCopy(currentPeel)
newPeel.DeepCopy(currentPeel)
self.peel_normals = vtkFloatArray()
self.peel_centers = vtkFloatArray()
self.peel.append(newPeel)
self.currentPeelActor = vtkActor()
if not np.all(np.equal(self.affine, np.eye(4))):
affine_vtk = self.CreateTransformedVTKAffine()
self.currentPeelActor.SetUserMatrix(affine_vtk)
self.GetCurrentPeelActor(currentPeel)
self.peelActors.append(self.currentPeelActor)
# locator will later find the triangle on the peel surface where the coil's normal intersect
self.locator = vtkCellLocator()
self.PeelDown(currentPeel)
def ribbon(molecule):
"""Create an actor for ribbon molecular representation.
Parameters
----------
molecule : Molecule
The molecule to be rendered.
Returns
-------
molecule_actor : vtkActor
Actor created to render the rubbon representation of the molecule to be
visualized.
References
----------
Richardson, J.S. The anatomy and taxonomy of protein structure
`Advances in Protein Chemistry, 1981, 34, 167-339.
<https://doi.org/10.1016/S0065-3233(08)60520-3>`_
"""
coords = get_all_atomic_positions(molecule)
all_atomic_numbers = get_all_atomic_numbers(molecule)
num_total_atoms = molecule.total_num_atoms
secondary_structures = np.ones(num_total_atoms)
for i in range(num_total_atoms):
secondary_structures[i] = ord('c')
resi = molecule.residue_seq[i]
for j, _ in enumerate(molecule.sheet):
sheet = molecule.sheet[j]
if molecule.chain[i] != sheet[0] or resi < sheet[1] or \
resi > sheet[3]:
continue
secondary_structures[i] = ord('s')
for j, _ in enumerate(molecule.helix):
helix = molecule.helix[j]
if molecule.chain[i] != helix[0] or resi < helix[1] or \
resi > helix[3]:
continue
secondary_structures[i] = ord('h')
output = cdmvtk.vtkPolyData()
# for atomic numbers
atomic_num_arr = numpy_to_vtk(num_array=all_atomic_numbers,
deep=True,
array_type=ccvtk.VTK_ID_TYPE)
# setting the array name to atom_type as vtkProteinRibbonFilter requires
# the array to be named atom_type
atomic_num_arr.SetName("atom_type")
output.GetPointData().AddArray(atomic_num_arr)
# for atom names
atom_names = ccvtk.vtkStringArray()
# setting the array name to atom_types as vtkProteinRibbonFilter requires
# the array to be named atom_types
atom_names.SetName("atom_types")
atom_names.SetNumberOfTuples(num_total_atoms)
for i in range(num_total_atoms):
atom_names.SetValue(i, molecule.atom_names[i])
output.GetPointData().AddArray(atom_names)
# for residue sequences
residue_seq = numpy_to_vtk(num_array=molecule.residue_seq,
deep=True,
array_type=ccvtk.VTK_ID_TYPE)
residue_seq.SetName("residue")
output.GetPointData().AddArray(residue_seq)
# for chain
chain = numpy_to_vtk(num_array=molecule.chain,
deep=True,
array_type=ccvtk.VTK_UNSIGNED_CHAR)
chain.SetName("chain")
output.GetPointData().AddArray(chain)
# for secondary structures
s_s = numpy_to_vtk(num_array=secondary_structures,
deep=True,
array_type=ccvtk.VTK_UNSIGNED_CHAR)
s_s.SetName("secondary_structures")
output.GetPointData().AddArray(s_s)
# for secondary structures begin
newarr = np.ones(num_total_atoms)
s_sb = numpy_to_vtk(num_array=newarr,
deep=True,
array_type=ccvtk.VTK_UNSIGNED_CHAR)
s_sb.SetName("secondary_structures_begin")
output.GetPointData().AddArray(s_sb)
# for secondary structures end
newarr = np.ones(num_total_atoms)
s_se = numpy_to_vtk(num_array=newarr,
deep=True,
array_type=ccvtk.VTK_UNSIGNED_CHAR)
s_se.SetName("secondary_structures_end")
output.GetPointData().AddArray(s_se)
# for is_hetatm
is_hetatm = numpy_to_vtk(num_array=molecule.is_hetatm,
deep=True,
array_type=ccvtk.VTK_UNSIGNED_CHAR)
is_hetatm.SetName("ishetatm")
output.GetPointData().AddArray(is_hetatm)
# for model
model = numpy_to_vtk(num_array=molecule.model,
deep=True,
array_type=ccvtk.VTK_UNSIGNED_INT)
model.SetName("model")
output.GetPointData().AddArray(model)
table = PeriodicTable()
# for colors and radii of hetero-atoms
radii = np.ones((num_total_atoms, 3))
rgb = np.ones((num_total_atoms, 3))
for i in range(num_total_atoms):
radii[i] = np.repeat(table.atomic_radius(all_atomic_numbers[i], 'VDW'),
3)
rgb[i] = table.atom_color(all_atomic_numbers[i])
Rgb = numpy_to_vtk(num_array=rgb,
deep=True,
array_type=ccvtk.VTK_UNSIGNED_CHAR)
Rgb.SetName("rgb_colors")
output.GetPointData().SetScalars(Rgb)
Radii = numpy_to_vtk(num_array=radii,
deep=True,
array_type=ccvtk.VTK_FLOAT)
Radii.SetName("radius")
output.GetPointData().SetVectors(Radii)
# setting the coordinates
points = numpy_to_vtk_points(coords)
output.SetPoints(points)
ribbonFilter = dcvtk.vtkProteinRibbonFilter()
ribbonFilter.SetInputData(output)
ribbonFilter.SetCoilWidth(0.2)
ribbonFilter.SetDrawSmallMoleculesAsSpheres(0)
mapper = rcvtk.vtkPolyDataMapper()
mapper.SetInputConnection(ribbonFilter.GetOutputPort())
molecule_actor = rcvtk.vtkActor()
molecule_actor.SetMapper(mapper)
return molecule_actor