def read_vrml(rw, input_filename):
importer = vtk.vtkVRMLImporter()
importer.SetFileName(input_filename)
importer.Read()
importer.SetRenderWindow(rw)
importer.Update()
rw.Render()
ren = importer.GetRenderer()
actors = ren.GetActors()
actors.InitTraversal()
actors_list = [actors.GetNextActor()
for _x in range(ren.GetNumberOfPropsRendered())]
return actors_list, ren
def getPolyData(self):
# VRML importer
importer = vtk.vtkVRMLImporter()
# WRL file to upload
importer.SetFileName(self.filepath)
# Read data
importer.Read()
self.polydata = vtk.vtkPolyData()
append = vtk.vtkAppendPolyData()
renActors = importer.GetRenderer().GetActors()
renActors.InitTraversal()
actor = renActors.GetNextActor()
i = 0
while (actor != None):
actor.GetProperty().SetAmbientColor(i, 1 - i, 0.0)
actor.GetProperty().SetAmbient(1)
append.AddInputData(actor.GetMapper().GetInput())
actor = renActors.GetNextActor()
i += 0.05
append.Update()
self.polydata.DeepCopy(append.GetOutput())
return self.polydata
def main():
filename = get_program_parameters()
colors = vtk.vtkNamedColors()
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window_interactor = vtk.vtkRenderWindowInteractor()
render_window_interactor.SetRenderWindow(render_window)
# VRML Import
importer = vtk.vtkVRMLImporter()
importer.SetFileName(filename)
importer.SetRenderWindow(render_window)
importer.Update()
actors = vtk.vtkActorCollection()
actors = renderer.GetActors()
print("There are", actors.GetNumberOfItems(), "actors")
renderer.SetBackground(colors.GetColor3d("Burlywood"))
render_window.SetSize(512, 512)
render_window.Render()
render_window_interactor.Start()
def main():
filename, actorname = get_program_parameters()
print("Showing", actorname, "from", filename)
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window_interactor = vtk.vtkRenderWindowInteractor()
render_window_interactor.SetRenderWindow(render_window)
# VRML Import
importer = vtk.vtkVRMLImporter()
importer.SetFileName(filename)
importer.Read()
importer.SetRenderWindow(render_window)
importer.Update()
# ----------------------------------------------------------
def_actor = importer.GetVRMLDEFObject(actorname)
if def_actor is None:
print("Cannot locate actor", actorname, "in", filename)
# importer.Print()
actor = vtk.vtkActor(actorname)
color = {0.89, 0.81, 0.34}
actor.GetProperty().SetColor(color)
actor.GetProperty().SetRepresentationToWireframe()
transform = vtk.vtkTransform()
transform.Translate(actor.GetCenter()[0],
actor.GetCenter()[1],
actor.GetCenter()[2])
# axes
axes = vtk.vtkAxesActor()
l = [0.0, 0.0, 0.0]
l[0] = (actor.GetBounds()[1] - actor.GetBounds()[0]) * 1.5
l[1] = (actor.GetBounds()[3] - actor.GetBounds()[2]) * 1.5
l[2] = (actor.GetBounds()[5] - actor.GetBounds()[4]) * 1.5
axes.SetTotalLength(l)
axes.SetUserTransform(transform)
renderer.AddActor(axes)
named_colors = vtk.vtkNamedColors()
renderer.SetBackground(named_colors.GetColor3d("Azure"))
render_window.Render()
render_window_interactor.Start()
def showVRML(self, fileName):
vtk = self.vtk
importer = vtk.vtkVRMLImporter()
importer.SetFileName(fileName)
importer.Read()
ren = importer.GetRenderer()
ren.SetBackground(0.1, 0.2, 0.4)
ren.ResetCamera()
w = self.winManager.newWindow(fileName)
importer.SetRenderWindow(w.vtkWidget.GetRenderWindow())
w.vtkWidget.GetRenderWindow().AddRenderer(ren)
w.show()
w.vtkWidget.Initialize()
w.vtkWidget.Start()
return w
def readVRML(self, filename=None):
if filename is not None:
self.filename = filename
r = vtk.vtkVRMLImporter()
r.SetFileName( self.filename )
r.Update()
actors = r.GetRenderer().GetActors()
actors.InitTraversal()
self.polydata = actors.GetNextActor().GetMapper().GetInput()
if self.polydata.GetPoints()==None:
raise IOError, 'file not loaded'
else:
self._loadPoints()
self._loadTriangles()
def multi_read_surface(file_name):
clean_name, file_extension = os.path.splitext(file_name)
if file_extension == ".obj":
obj_in = vtk.vtkOBJReader()
obj_in.SetFileName(file_name)
obj_in.Update()
pd = obj_in.GetOutput()
return pd
elif file_extension == ".wrl":
vrmlin = vtk.vtkVRMLImporter()
vrmlin.SetFileName(file_name)
vrmlin.Update()
pd = vrmlin.GetRenderer().GetActors().GetLastActor().GetMapper(
).GetInput()
return pd
elif file_extension == ".vtk":
pd_in = vtk.vtkPolyDataReader()
pd_in.SetFileName(file_name)
pd_in.Update()
pd = pd_in.GetOutput()
return pd
elif file_extension == ".vtp":
pd_in = vtk.vtkXMLPolyDataReader()
pd_in.SetFileName(file_name)
pd_in.Update()
pd = pd_in.GetOutput()
return pd
elif file_extension == ".stl":
pd_in = vtk.vtkSTLReader()
pd_in.SetFileName(file_name)
pd_in.Update()
pd = pd_in.GetOutput()
return pd
elif file_extension == ".ply":
pd_in = vtk.vtkPLYReader()
pd_in.SetFileName(file_name)
pd_in.Update()
pd = pd_in.GetOutput()
return pd
else:
print("Can not read files with extenstion", file_extension)
return None
def load_object_3d(self, path, viewer_3d):
generic_reader = vtkDataReader()
generic_reader.SetFileName(path)
if generic_reader.OpenVTKFile() and generic_reader.ReadHeader():
if generic_reader.IsFileStructuredPoints():
raise Exception("Cannot read VTK structured points")
elif generic_reader.IsFilePolyData():
reader = vtkPolyDataReader()
reader.SetFileName(path)
object_3d = Object3D(reader.GetOutput(), path)
elif generic_reader.IsFileStructuredGrid():
reader = vtkStructuredGridReader()
reader.SetFileName(path)
object_3d = Object3D(reader.GetOutput(), path)
elif generic_reader.IsFileUnstructuredGrid():
reader = vtkUnstructuredGridReader()
reader.SetFileName(path)
object_3d = Object3D(reader.GetOutput(), path)
elif generic_reader.IsFileRectilinearGrid():
reader = vtkRectilinearGridReader()
reader.SetFileName(path)
object_3d = Object3D(reader.GetOutput(), path)
else:
raise Exception("Cannot read VTK file containing type %i" %
generic_reader.GetFileType())
viewer_3d.objects_3d.append(object_3d)
else:
importer = vtkVRMLImporter()
importer.SetFileName(path)
importer.Update()
actors = importer.GetRenderer().GetActors()
number_of_actors = actors.GetNumberOfItems()
actors.InitTraversal()
for i in range(number_of_actors):
actor = actors.GetNextItem()
object_3d = Object3D(path + ", %i" % i)
object_3d.actor.SetProperty(actor.GetProperty())
object_3d.actor.SetMapper(actor.GetMapper())
viewer_3d.objects_3d.append(object_3d)
def load_WRL(filename):
"""Loads VRML 2.0 mesh files.
Parameters
----------
filename: str
name of the meh file on disk
Returns
-------
vertices: ndarray
numpy array of the coordinates of the mesh's nodes
faces: ndarray
numpy array of the faces' nodes connectivities
"""
from vtk import vtkVRMLImporter
import re
_check_file(filename)
# Checking version
with open(filename, 'r') as f:
line = f.readline()
ver = re.search(r'#VRML\s+V(\d.\d)', line).group(1)
if not ver == '2.0':
raise NotImplementedError(
'VRML loader only supports VRML 2.0 format (version %s given)'
% ver)
importer = vtkVRMLImporter()
importer.SetFileName(filename)
importer.Update()
actors = importer.GetRenderer().GetActors()
actors.InitTraversal()
dataset = actors.GetNextActor().GetMapper().GetInput()
return _dump_vtk(dataset)
def vrml_read(filename):
'''
读取并显示vrml格式的文件
filename:文件的路径
'''
colors = vtk.vtkNamedColors()
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
importer = vtk.vtkVRMLImporter()
importer.SetFileName(filename)
importer.SetRenderWindow(renderWindow)
importer.Update()
actors = renderer.GetActors()
print("There are %d actors" % actors.GetNumberOfItems())
renderer.SetBackground(colors.GetColor3d("Burlwood"))
renderWindow.SetSize(512, 512)
renderWindow.Render()
renderWindowInteractor.Start()
def __init__ (self, renwin, file_name):
"""Initializes the class given a vtkRenderWindow and a
file_name."""
debug ("In VRMLImporter::__init__ ()")
self.file_name = file_name
self.renwin = renwin
orig_actors = self._get_actors (self.renwin)
self.vrml_imp = vtk.vtkVRMLImporter ()
self.vrml_imp.SetFileName (file_name)
self.vrml_imp.SetRenderWindow (self.renwin)
try:
self.vrml_imp.ComputeNormalsOn ()
except AttributeError:
pass
self.vrml_imp.Read ()
self.renwin.Render ()
final_actors = self._get_actors (self.renwin)
self.actors = []
for act in final_actors:
if act not in orig_actors:
self.actors.append (act)
def load(inputobj, c=None, alpha=1, threshold=False, spacing=(), unpack=True):
"""
Load ``Actor`` and ``Volume`` from file.
The output will depend on the file extension. See examples below.
:param c: color in RGB format, hex, symbol or name
:param alpha: transparency/opacity of the polygonal data.
For volumetric data `(tiff, slc, vti etc..)`:
:param list c: can be a list of any length of colors. This list represents the color
transfer function values equally spaced along the range of the volumetric scalar.
:param list alpha: can be a list of any length of tranparencies. This list represents the
transparency transfer function values equally spaced along the range of the volumetric scalar.
:param float threshold: value to draw the isosurface, False by default to return a ``Volume``.
If set to True will return an ``Actor`` with automatic choice of the isosurfacing threshold.
:param list spacing: specify the voxel spacing in the three dimensions
:param bool unpack: only for multiblock data, if True returns a flat list of objects.
:Examples:
.. code-block:: python
from vtkplotter import datadir, load, show
# Return an Actor
g = load(datadir+'250.vtk')
show(g)
# Return a list of 2 Actors
g = load([datadir+'250.vtk', datadir+'270.vtk'])
show(g)
# Return a list of actors by reading all files in a directory
# (if directory contains DICOM files then a Volume is returned)
g = load(datadir+'timecourse1d/')
show(g)
# Return a Volume. Color/Opacity transfer functions can be specified too.
g = load(datadir+'embryo.slc')
g.c(['y','lb','w']).alpha((0.0, 0.4, 0.9, 1))
show(g)
# Return an Actor from a SLC volume with automatic thresholding
g = load(datadir+'embryo.slc', threshold=True)
show(g)
"""
acts = []
if utils.isSequence(inputobj):
flist = inputobj
else:
import glob
flist = sorted(glob.glob(inputobj))
for fod in flist:
if os.path.isfile(fod): ### it's a file
if fod.endswith("wrl"):
importer = vtk.vtkVRMLImporter()
importer.SetFileName(fod)
importer.Read()
importer.Update()
actors = importer.GetRenderer().GetActors(
) #vtkActorCollection
actors.InitTraversal()
for i in range(actors.GetNumberOfItems()):
act = actors.GetNextActor()
acts.append(act)
else:
a = _load_file(fod, c, alpha, threshold, spacing, unpack)
acts.append(a)
elif os.path.isdir(fod): ### it's a directory or DICOM
flist = os.listdir(fod)
if '.dcm' in flist[0]: ### it's DICOM
reader = vtk.vtkDICOMImageReader()
reader.SetDirectoryName(fod)
reader.Update()
image = reader.GetOutput()
if len(spacing) == 3:
image.SetSpacing(spacing[0], spacing[1], spacing[2])
if threshold is False:
if c is None and alpha == 1:
c = ['b', 'lb', 'lg', 'y',
'r'] # good for blackboard background
alpha = (0.0, 0.0, 0.2, 0.4, 0.8, 1)
#c = ['lb','db','dg','dr'] # good for white backgr
#alpha = (0.0, 0.0, 0.2, 0.6, 0.8, 1)
actor = Volume(image, c, alpha)
else:
actor = isosurface(image, threshold=threshold)
actor.color(c).alpha(alpha)
acts.append(actor)
else: ### it's a normal directory
utils.humansort(flist)
for ifile in flist:
a = _load_file(fod + '/' + ifile, c, alpha, threshold,
spacing, unpack)
acts.append(a)
else:
colors.printc("~times Error in load(): cannot find", fod, c=1)
if len(acts) == 1:
if not acts[0]:
colors.printc("~times Error in load(): cannot load", inputobj, c=1)
return acts[0]
elif len(acts) == 0:
colors.printc("~times Error in load(): cannot load", inputobj, c=1)
return None
else:
return acts
def wrl_importer(filepath, asset=None, texture_resolver=None, **kwargs):
"""Allows importing VRML 2.0 meshes.
Uses VTK and assumes that the first actor in the scene is the one
that we want.
Parameters
----------
asset : `object`, optional
An optional asset that may help with loading. This is unused for this
implementation.
texture_resolver : `callable`, optional
A callable that recieves the mesh filepath and returns a single
path to the texture to load.
\**kwargs : `dict`, optional
Any other keyword arguments.
Returns
-------
shape : :map:`PointCloud` or subclass
The correct shape for the given inputs.
"""
import vtk
from vtk.util.numpy_support import vtk_to_numpy
vrml_importer = vtk.vtkVRMLImporter()
vrml_importer.SetFileName(str(filepath))
vrml_importer.Update()
# Get the first actor.
actors = vrml_importer.GetRenderer().GetActors()
actors.InitTraversal()
mapper = actors.GetNextActor().GetMapper()
mapper_dataset = mapper.GetInput()
if actors.GetNextActor():
# There was more than one actor!
warnings.warn('More than one actor was detected in the scene. Only '
'single scene actors are currently supported.')
# Get the Data
polydata = vtk.vtkPolyData.SafeDownCast(mapper_dataset)
# We must have point data!
points = vtk_to_numpy(polydata.GetPoints().GetData()).astype(np.float)
trilist = vtk_ensure_trilist(polydata)
texture = None
if texture_resolver is not None:
texture_path = texture_resolver(filepath)
if texture_path is not None and texture_path.exists():
texture = mio.import_image(texture_path)
# Three different outcomes - either we have a textured mesh, a coloured
# mesh or just a plain mesh. Let's try each in turn.
# Textured
tcoords = None
try:
tcoords = vtk_to_numpy(polydata.GetPointData().GetTCoords())
except Exception:
pass
if isinstance(tcoords, np.ndarray) and tcoords.size == 0:
tcoords = None
# Colour-per-vertex
try:
colour_per_vertex = vtk_to_numpy(mapper.GetLookupTable().GetTable()) / 255.
except Exception:
pass
if isinstance(colour_per_vertex, np.ndarray) and colour_per_vertex.size == 0:
colour_per_vertex = None
return _construct_shape_type(points, trilist, tcoords, texture,
colour_per_vertex)
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
importer = vtk.vtkVRMLImporter()
importer.SetRenderWindow(renWin)
importer.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/bot2.wrl")
importer.Read()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
importer.GetRenderer().SetBackground(0.1,0.2,0.4)
importer.GetRenderWindow().SetSize(300,300)
#
# the importer created the renderer
renCollection = renWin.GetRenderers()
renCollection.InitTraversal()
ren = renCollection.GetNextItem()
#
# change view up to +z
#
ren.GetActiveCamera().SetPosition(-3.25303,3.46205,3.15906)
ren.GetActiveCamera().SetFocalPoint(0,0,0)
ren.GetActiveCamera().SetViewUp(0.564063,0.825024,-0.0341876)
#
# let the renderer compute good position and focal point
#
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
importer = vtk.vtkVRMLImporter()
importer.SetRenderWindow(renWin)
importer.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/bot2.wrl")
importer.Read()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
importer.GetRenderer().SetBackground(0.1, 0.2, 0.4)
importer.GetRenderWindow().SetSize(300, 300)
#
# the importer created the renderer
renCollection = renWin.GetRenderers()
renCollection.InitTraversal()
ren = renCollection.GetNextItem()
#
# change view up to +z
#
ren.GetActiveCamera().SetPosition(-3.25303, 3.46205, 3.15906)
ren.GetActiveCamera().SetFocalPoint(0, 0, 0)
ren.GetActiveCamera().SetViewUp(0.564063, 0.825024, -0.0341876)
#
# let the renderer compute good position and focal point
def process_file_bu_3dfe(config, file_name, output_dir):
bu_3dfe_dir = config['preparedata']['raw_data_dir']
base_name = os.path.basename(file_name)
name_pd = bu_3dfe_dir + file_name + '_RAW.wrl'
name_bmp = bu_3dfe_dir + file_name + '_F3D.bmp'
name_lm = bu_3dfe_dir + file_name + '_RAW_84_LMS.txt'
name_path = os.path.dirname(file_name)
o_dir_image = output_dir + '/images/' + name_path + '/'
o_dir_lm = output_dir + '/2D LM/' + name_path + '/'
if not os.path.exists(o_dir_image):
os.makedirs(o_dir_image)
if not os.path.exists(o_dir_lm):
os.makedirs(o_dir_lm)
lock_file = o_dir_image + base_name + '.lock'
if not os.path.isfile(name_pd):
print(name_pd, ' could not read')
return False
if not os.path.isfile(name_bmp):
print(name_bmp, ' could not read')
return False
if not os.path.isfile(name_lm):
print(name_lm, ' could not read')
return False
if os.path.isfile(lock_file):
print(file_name, ' is locked - skipping')
return True
create_lock_file(lock_file)
print('Rendering ', file_name)
win_size = config['data_loader']['args']['image_size']
off_screen_rendering = config['preparedata']['off_screen_rendering']
n_views = config['data_loader']['args']['n_views']
slack = 5
# Load Landmarks
points = vtk.vtkPoints()
lms = vtk.vtkPolyData()
with open(name_lm) as f:
for line in f:
line = line.strip("/n")
x, y, z = np.double(line.split(" "))
points.InsertNextPoint(x, y, z)
lms.SetPoints(points)
del points
vrmlin = vtk.vtkVRMLImporter()
vrmlin.SetFileName(name_pd)
vrmlin.Update()
pd = vrmlin.GetRenderer().GetActors().GetLastActor().GetMapper().GetInput()
pd.GetPointData().SetScalars(None)
# Load texture
texture_image = vtk.vtkBMPReader()
texture_image.SetFileName(name_bmp)
texture_image.Update()
texture = vtk.vtkTexture()
texture.SetInterpolate(1)
texture.SetQualityTo32Bit()
texture.SetInputConnection(texture_image.GetOutputPort())
# Initialize Camera
ren = vtk.vtkRenderer()
ren.SetBackground(1, 1, 1)
ren.GetActiveCamera().SetPosition(0, 0, 1)
ren.GetActiveCamera().SetFocalPoint(0, 0, 0)
ren.GetActiveCamera().SetViewUp(0, 1, 0)
ren.GetActiveCamera().SetParallelProjection(1)
# Initialize RenderWindow
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(win_size, win_size)
ren_win.SetOffScreenRendering(off_screen_rendering)
# Initialize Transform
t = vtk.vtkTransform()
t.Identity()
t.Update()
# Transform (assuming only one mesh)
trans = vtk.vtkTransformPolyDataFilter()
trans.SetInputData(pd)
trans.SetTransform(t)
trans.Update()
trans_lm = vtk.vtkTransformPolyDataFilter()
trans_lm.SetInputData(lms)
trans_lm.SetTransform(t)
trans_lm.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(trans.GetOutput())
actor_text = vtk.vtkActor()
actor_text.SetMapper(mapper)
actor_text.SetTexture(texture)
actor_text.GetProperty().SetColor(1, 1, 1)
actor_text.GetProperty().SetAmbient(1.0)
actor_text.GetProperty().SetSpecular(0)
actor_text.GetProperty().SetDiffuse(0)
ren.AddActor(actor_text)
actor_geometry = vtk.vtkActor()
actor_geometry.SetMapper(mapper)
ren.AddActor(actor_geometry)
w2if = vtk.vtkWindowToImageFilter()
w2if.SetInput(ren_win)
writer_png = vtk.vtkPNGWriter()
writer_png.SetInputConnection(w2if.GetOutputPort())
scale = vtk.vtkImageShiftScale()
scale.SetOutputScalarTypeToUnsignedChar()
scale.SetInputConnection(w2if.GetOutputPort())
scale.SetShift(0)
scale.SetScale(-255)
writer_png_2 = vtk.vtkPNGWriter()
writer_png_2.SetInputConnection(scale.GetOutputPort())
for view in range(n_views):
name_rgb = o_dir_image + base_name + '_' + str(view) + '.png'
name_geometry = o_dir_image + base_name + '_' + str(
view) + '_geometry.png'
name_depth = o_dir_image + base_name + '_' + str(view) + '_zbuffer.png'
name_2dlm = o_dir_lm + base_name + '_' + str(view) + '.txt'
if not os.path.isfile(name_rgb):
# print('Rendering ', name_rgb)
rx, ry, rz, s, tx, ty = random_transform(config)
t.Identity()
t.RotateY(ry)
t.RotateX(rx)
t.RotateZ(rz)
t.Update()
trans.Update()
trans_lm.Update()
xmin = -150
xmax = 150
ymin = -150
ymax = 150
zmin = trans.GetOutput().GetBounds()[4]
zmax = trans.GetOutput().GetBounds()[5]
xlen = xmax - xmin
ylen = ymax - ymin
cx = 0
cy = 0
extend_factor = 1.0
side_length = max([xlen, ylen]) * extend_factor
zoom_fac = win_size / side_length
ren.GetActiveCamera().SetParallelScale(side_length / 2)
ren.GetActiveCamera().SetPosition(cx, cy, 500)
ren.GetActiveCamera().SetFocalPoint(cx, cy, 0)
ren.GetActiveCamera().SetClippingRange(500 - zmax - slack,
500 - zmin + slack)
# Save textured image
w2if.SetInputBufferTypeToRGB()
actor_geometry.SetVisibility(False)
actor_text.SetVisibility(True)
mapper.Modified()
ren.Modified() # force actors to have the correct visibility
ren_win.Render()
w2if.Modified(
) # Needed here else only first rendering is put to file
writer_png.SetFileName(name_rgb)
writer_png.Write()
actor_text.SetVisibility(False)
actor_geometry.SetVisibility(True)
mapper.Modified()
ren.Modified() # force actors to have the correct visibility
ren_win.Render()
w2if.Modified(
) # Needed here else only first rendering is put to file
writer_png.SetFileName(name_geometry)
writer_png.Write()
ren.Modified() # force actors to have the correct visibility
ren_win.Render()
w2if.SetInputBufferTypeToZBuffer()
w2if.Modified()
writer_png_2.SetFileName(name_depth)
writer_png_2.Write()
actor_geometry.SetVisibility(False)
actor_text.SetVisibility(True)
ren.Modified()
# Write transformed landmarks
f = open(name_2dlm, 'w')
t_lm = trans_lm.GetOutput()
for i in range(t_lm.GetNumberOfPoints()):
x_pos = t_lm.GetPoint(i)[0]
y_pos = t_lm.GetPoint(i)[1]
x_pos_screen = (x_pos - cx) * zoom_fac + win_size / 2
y_pos_screen = -(y_pos - cy) * zoom_fac + win_size / 2
line = str(x_pos_screen) + ' ' + str(y_pos_screen) + '\n'
f.write(line)
f.close()
del writer_png_2, writer_png, ren_win, actor_geometry, actor_text, mapper, w2if, t, trans, vrmlin, texture
del texture_image
del lms, trans_lm
delete_lock_file(lock_file)
def main():
filename = get_program_parameters()
colors = vtk.vtkNamedColors()
print("Reading " + filename)
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window_interactor = vtk.vtkRenderWindowInteractor()
render_window_interactor.SetRenderWindow(render_window)
# VRML Import
importer = vtk.vtkVRMLImporter()
importer.SetFileName(filename)
importer.SetRenderWindow(render_window)
importer.Update()
actors = vtk.vtkActorCollection()
actors = renderer.GetActors()
print("There are", actors.GetNumberOfItems(), "actors")
actors.InitTraversal()
for a in range(0, actors.GetNumberOfItems()):
actor = actors.GetNextActor()
# The importer shininess parameter is between 0 and 1. VTK specular power is usually 10 - 100.
# Also, the default for the specular factor for VRML is 1, while VTK's
# is 0
specular_power = actor.GetProperty().GetSpecularPower()
if specular_power <= 1.0:
actor.GetProperty().SetSpecularPower(specular_power * 128.0)
specular = actor.GetProperty().GetSpecular()
if specular == 0.0:
actor.GetProperty().SetSpecular(1.0)
# if 0
# The VRML default ambient intensity is .2
ambient_intensity = actor.GetProperty().GetAmbient()
if ambient_intensity == 0.0:
actor.GetProperty().SetAmbient(.2)
# endif
mapper = actor.GetMapper()
if (mapper):
data_set = mapper.GetInput()
if not data_set.GetPointData().GetNormals():
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(data_set)
normals.SplittingOff()
normals.Update()
mapper.SetInputData(normals.GetOutput())
# If there is a lookup table, convert it to point data
lut = mapper.GetLookupTable()
if lut and mapper.GetScalarVisibility():
pc = vtk.vtkUnsignedCharArray()
pc.SetNumberOfComponents(4)
pc.SetNumberOfTuples(lut.GetNumberOfColors())
for t in range(0, lut.GetNumberOfColors()):
lutc = lut.GetTableValue(t)
lutuc = ['', '', '', '']
lut.GetColorAsUnsignedChars(lutc, lutuc)
pc.SetTypedTuple(t, lutuc)
mapper.SetLookupTable(None)
mapper.GetInput().GetPointData().SetScalars(pc)
renderer.ResetCamera()
renderer.GetActiveCamera().Azimuth(30)
renderer.GetActiveCamera().Elevation(30)
renderer.GetActiveCamera().Dolly(1.4)
renderer.ResetCameraClippingRange()
renderer.SetBackground(colors.GetColor3d("PaleGreen"))
render_window.SetSize(640, 480)
render_window.Render()
render_window_interactor.Start()
def main(input_filename,
areas_filename,
scale,
is_imx,
exportPath=None,
exportType=False,
reduction=70,
radius=RADIUS,
combine=False):
# TODO: The following doesn't hide the RenderWindow :/
# factGraphics = vtk.vtkGraphicsFactory()
# factGraphics.SetUseMesaClasses(1)
# factImage = vtk.vtkImagingFactory()
# factImage.SetUseMesaClasses(1)
if exportPath is None:
pos = areas_filename.rfind("/")
filename = os.path.splitext(input_filename)[0]
posFilename = filename.rfind("/")
exportPath = areas_filename[:pos] + "/Meshes" + filename[posFilename:]
else:
filename = os.path.splitext(input_filename)[0]
pos = filename.rfind("/")
if pos == -1:
exportPath += "/"
exportPath += filename[pos:]
print(exportPath)
if is_imx:
vrml_filename = os.path.splitext(input_filename)[0] + ".vrml"
names_filename = os.path.splitext(input_filename)[0] + ".names"
args = [
"{}".format(input_filename), "{}".format(vrml_filename),
"{}".format(names_filename)
]
p = Process(target=parse_imx.main, args=[args])
p.start()
p.join()
names_list = []
with open(names_filename) as f:
for line in f:
line = re.sub(r'\n', '', line)
names_list.append(line)
else:
vrml_filename = input_filename
names_list = None
rw = vtk.vtkRenderWindow()
rwi = vtk.vtkRenderWindowInteractor()
rwi.SetRenderWindow(rw)
# rw.OffScreenRenderingOn()
importer = vtk.vtkVRMLImporter()
importer.SetFileName(vrml_filename)
# importer = vtk.vtk3DSImporter()
# importer.SetFileName("cube.3ds")
importer.Read()
importer.SetRenderWindow(rw)
importer.Update()
rw.Render()
ren = importer.GetRenderer()
actors = ren.GetActors()
actors.InitTraversal()
rwExport = vtk.vtkRenderWindow()
# rwExport.OffScreenRenderingOn()
renExport = vtk.vtkRenderer()
rwExport.AddRenderer(renExport)
rwExport.Render()
if is_imx:
csv = "Object,Pre_Area,Post_Area,Post/Pre,X,Y,Z,Name\n"
else:
csv = "Object,Pre_Area,Post_Area,Post/Pre,X,Y,Z\n"
print(
"-------- Repairing original mesh and Calculating areas (This process might take a long time, please wait) -----------"
)
for i in range(ren.GetNumberOfPropsRendered()):
sys.stdout.write("%d _" % i)
actor = actors.GetNextActor()
polydata = actor.GetMapper().GetInput()
polydataCopy = vtk.vtkPolyData()
polydataCopy.DeepCopy(polydata)
area_pre = compute_area(actor)
centroid = actor.GetCenter()
rescaled = False
try:
rw.Render()
(center, rotation) = axisAligment(actor)
rw.Render()
open_actor(actor, i, scale, radius)
except ValueError as e:
# [KNOWN BUG] The sizes are corrected, but not the position
scale = scale * 2
open_actor(actor, i, scale, radius)
rescaled = True
area_post = compute_area(actor) / scale**2
if is_imx:
data = []
data.extend([i, area_pre, area_post, area_post / area_pre])
data.extend(centroid)
data.append(names_list[i])
csv += "%d,%f,%f,%f,%f,%f,%f,%s\n" % tuple(data)
else:
data = []
data.extend([i, area_pre, area_post, area_post / area_pre])
data.extend(centroid)
csv += "%d,%f,%f,%f,%f,%f,%f\n" % tuple(data)
if exportType != "None":
initActorForExport(actor, rwExport, scale, reduction)
toOriginalPos(actor, center, rotation)
if names_list is not None:
name = names_list[i]
else:
name = i
if exportType == "Stl":
save_stl(actor.GetMapper().GetInput(), exportPath,
str(name) + "_R")
save_stl(polydataCopy, exportPath, str(name) + "_O")
renExport.RemoveActor(actor)
elif exportType == "Vrml":
save_vrml(str(name) + "_R", exportPath, rwExport)
renExport.RemoveActor(actor)
actorOld = vtk.vtkActor()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polydataCopy)
actorOld.SetMapper(mapper)
renExport.AddActor(actorOld)
save_vrml(str(name) + "_O", exportPath, rwExport)
renExport.RemoveActor(actorOld)
elif exportType == "Obj":
save_obj(rwExport, exportPath, str(name) + "_R")
renExport.RemoveActor(actor)
actorOld = vtk.vtkActor()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polydataCopy)
actorOld.SetMapper(mapper)
renExport.AddActor(actorOld)
save_obj(rwExport, exportPath, str(name) + "_O")
renExport.RemoveActor(actorOld)
ren.RemoveActor(actor)
if rescaled:
scale /= 2
with open(areas_filename, 'w') as f:
f.write(csv)
if is_imx:
os.remove(vrml_filename)
os.remove(names_filename)
rw.Finalize()
print("")
def _load_file(filename, c, alpha, threshold, spacing, unpack):
fl = filename.lower()
################################################################# other formats:
if fl.endswith(".xml") or fl.endswith(".xml.gz") or fl.endswith(".xdmf"):
# Fenics tetrahedral file
actor = loadDolfin(filename)
elif fl.endswith(".neutral") or fl.endswith(".neu"): # neutral tetrahedral file
actor = loadNeutral(filename)
elif fl.endswith(".gmsh"): # gmesh file
actor = loadGmesh(filename)
elif fl.endswith(".pcd"): # PCL point-cloud format
actor = loadPCD(filename)
actor.GetProperty().SetPointSize(2)
elif fl.endswith(".off"):
actor = loadOFF(filename)
elif fl.endswith(".3ds"): # 3ds format
actor = load3DS(filename)
elif fl.endswith(".wrl"):
importer = vtk.vtkVRMLImporter()
importer.SetFileName(filename)
importer.Read()
importer.Update()
actors = importer.GetRenderer().GetActors() #vtkActorCollection
actors.InitTraversal()
wacts = []
for i in range(actors.GetNumberOfItems()):
act = actors.GetNextActor()
wacts.append(act)
actor = Assembly(wacts)
################################################################# volumetric:
elif fl.endswith(".tif") or fl.endswith(".slc") or fl.endswith(".vti") \
or fl.endswith(".mhd") or fl.endswith(".nrrd") or fl.endswith(".nii") \
or fl.endswith(".dem"):
img = loadImageData(filename, spacing)
if threshold is False:
if c is None and alpha == 1:
c = ['b','lb','lg','y','r'] # good for blackboard background
alpha = (0.0, 0.0, 0.2, 0.4, 0.8, 1)
actor = Volume(img, c, alpha)
else:
actor = Volume(img).isosurface(threshold=threshold)
actor.color(c).alpha(alpha)
################################################################# 2D images:
elif fl.endswith(".png") or fl.endswith(".jpg") or fl.endswith(".bmp") or fl.endswith(".jpeg"):
if ".png" in fl:
picr = vtk.vtkPNGReader()
elif ".jpg" in fl or ".jpeg" in fl:
picr = vtk.vtkJPEGReader()
elif ".bmp" in fl:
picr = vtk.vtkBMPReader()
picr.SetFileName(filename)
picr.Update()
actor = Picture() # object derived from vtk.vtkImageActor()
actor.SetInputData(picr.GetOutput())
if alpha is None:
alpha = 1
actor.SetOpacity(alpha)
################################################################# multiblock:
elif fl.endswith(".vtm") or fl.endswith(".vtmb"):
read = vtk.vtkXMLMultiBlockDataReader()
read.SetFileName(filename)
read.Update()
mb = read.GetOutput()
if unpack:
acts = []
for i in range(mb.GetNumberOfBlocks()):
b = mb.GetBlock(i)
if isinstance(b, (vtk.vtkPolyData,
vtk.vtkImageData,
vtk.vtkUnstructuredGrid,
vtk.vtkStructuredGrid,
vtk.vtkRectilinearGrid)):
acts.append(b)
return acts
else:
return mb
################################################################# numpy:
elif fl.endswith(".npy"):
acts = loadNumpy(filename)
if unpack == False:
return Assembly(acts)
return acts
elif fl.endswith(".geojson") or fl.endswith(".geojson.gz"):
return loadGeoJSON(fl)
################################################################# polygonal mesh:
else:
if fl.endswith(".vtk"): # read all legacy vtk types
#output can be:
# PolyData, StructuredGrid, StructuredPoints, UnstructuredGrid, RectilinearGrid
reader = vtk.vtkDataSetReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.ReadAllTensorsOn()
reader.ReadAllFieldsOn()
reader.ReadAllNormalsOn()
reader.ReadAllColorScalarsOn()
elif fl.endswith(".ply"):
reader = vtk.vtkPLYReader()
elif fl.endswith(".obj"):
reader = vtk.vtkOBJReader()
elif fl.endswith(".stl"):
reader = vtk.vtkSTLReader()
elif fl.endswith(".byu") or fl.endswith(".g"):
reader = vtk.vtkBYUReader()
elif fl.endswith(".foam"): # OpenFoam
reader = vtk.vtkOpenFOAMReader()
elif fl.endswith(".pvd"):
reader = vtk.vtkXMLGenericDataObjectReader()
elif fl.endswith(".vtp"):
reader = vtk.vtkXMLPolyDataReader()
elif fl.endswith(".vts"):
reader = vtk.vtkXMLStructuredGridReader()
elif fl.endswith(".vtu"):
reader = vtk.vtkXMLUnstructuredGridReader()
elif fl.endswith(".vtr"):
reader = vtk.vtkXMLRectilinearGridReader()
elif fl.endswith(".pvtk"):
reader = vtk.vtkPDataSetReader()
elif fl.endswith(".pvtr"):
reader = vtk.vtkXMLPRectilinearGridReader()
elif fl.endswith("pvtu"):
reader = vtk.vtkXMLPUnstructuredGridReader()
elif fl.endswith(".txt") or fl.endswith(".xyz"):
reader = vtk.vtkParticleReader() # (format is x, y, z, scalar)
elif fl.endswith(".facet"):
reader = vtk.vtkFacetReader()
else:
return None
reader.SetFileName(filename)
reader.Update()
routput = reader.GetOutput()
if not routput:
colors.printc("~noentry Unable to load", filename, c=1)
return None
actor = Actor(routput, c, alpha)
if fl.endswith(".txt") or fl.endswith(".xyz"):
actor.GetProperty().SetPointSize(4)
actor.filename = filename
return actor
def wrl_importer(filepath, asset=None, texture_resolver=None, **kwargs):
"""Allows importing VRML 2.0 meshes.
Uses VTK and assumes that the first actor in the scene is the one
that we want.
Parameters
----------
asset : `object`, optional
An optional asset that may help with loading. This is unused for this
implementation.
texture_resolver : `callable`, optional
A callable that recieves the mesh filepath and returns a single
path to the texture to load.
\**kwargs : `dict`, optional
Any other keyword arguments.
Returns
-------
shape : :map:`PointCloud` or subclass
The correct shape for the given inputs.
"""
import vtk
from vtk.util.numpy_support import vtk_to_numpy
vrml_importer = vtk.vtkVRMLImporter()
vrml_importer.SetFileName(str(filepath))
vrml_importer.Update()
# Get the first actor.
actors = vrml_importer.GetRenderer().GetActors()
actors.InitTraversal()
mapper = actors.GetNextActor().GetMapper()
mapper_dataset = mapper.GetInput()
if actors.GetNextActor():
# There was more than one actor!
warnings.warn('More than one actor was detected in the scene. Only '
'single scene actors are currently supported.')
# Get the Data
polydata = vtk.vtkPolyData.SafeDownCast(mapper_dataset)
# We must have point data!
points = vtk_to_numpy(polydata.GetPoints().GetData()).astype(np.float)
trilist = vtk_ensure_trilist(polydata)
texture = None
if texture_resolver is not None:
texture_path = texture_resolver(filepath)
if texture_path is not None and texture_path.exists():
texture = mio.import_image(texture_path)
# Three different outcomes - either we have a textured mesh, a coloured
# mesh or just a plain mesh. Let's try each in turn.
# Textured
tcoords = None
try:
tcoords = vtk_to_numpy(polydata.GetPointData().GetTCoords())
except Exception:
pass
if isinstance(tcoords, np.ndarray) and tcoords.size == 0:
tcoords = None
# Colour-per-vertex
try:
colour_per_vertex = vtk_to_numpy(
mapper.GetLookupTable().GetTable()) / 255.
except Exception:
pass
if isinstance(colour_per_vertex,
np.ndarray) and colour_per_vertex.size == 0:
colour_per_vertex = None
return _construct_shape_type(points, trilist, tcoords, texture,
colour_per_vertex)
