def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkMarchingSquares(), 'Processing.',
('vtkImageData',), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def marchingSquares(img, iso=0.0, mode='center'):
s = img.shape
alg = vtk.vtkMarchingSquares()
sp = VTKNumpytoSP(img)
alg.SetInputData(sp)
alg.SetValue(0, iso)
alg.Update()
pds = alg.GetOutput()
a = vtk.vtkPolyDataConnectivityFilter()
a.SetInputData(pds)
if mode == 'center':
a.SetExtractionModeToClosestPointRegion()
a.SetClosestPoint(float(s[0]) / 2, float(s[1]) / 2, 0.0)
elif mode == 'all':
a.SetExtractionModeToAllRegions()
a.Update()
pds = a.GetOutput()
if pds.GetPoints() is None:
return np.asarray([[0.0, 0.0], [0.0, 0.0], [0.0, 0.0]])
else:
pds = VTKPDPointstoNumpy(pds)
if len(pds) <= 1:
return np.asarray([[0.0, 0.0], [0.0, 0.0], [0.0, 0.0]])
return pds
def marchingSquares(img, iso=0.0, mode='center', asNumpy=True):
alg = vtk.vtkMarchingSquares()
if asNumpy:
sp = VTKNumpytoSP(img)
else:
sp = img
alg.SetInputData(sp)
alg.SetValue(0, iso)
alg.Update()
pds = alg.GetOutput()
a = vtk.vtkPolyDataConnectivityFilter()
a.SetInputData(pds)
if mode == 'center':
a.SetExtractionModeToClosestPointRegion()
a.SetClosestPoint(0.0, 0.0, 0.0)
elif mode == 'all':
a.SetExtractionModeToAllRegions()
a.Update()
pds = a.GetOutput()
return pds
def threshold(self, value=None, flip=False):
"""
Create a polygonal Mesh from a Picture by filling regions with pixels
luminosity above a specified value.
Parameters
----------
value : float, optional
The default is None, e.i. 1/3 of the scalar range.
flip: bool, optional
Flip polygon orientations
Returns
-------
Mesh
A polygonal mesh.
"""
mgf = vtk.vtkImageMagnitude()
mgf.SetInputData(self._data)
mgf.Update()
msq = vtk.vtkMarchingSquares()
msq.SetInputData(mgf.GetOutput())
if value is None:
r0, r1 = self._data.GetScalarRange()
value = r0 + (r1 - r0) / 3
msq.SetValue(0, value)
msq.Update()
if flip:
rs = vtk.vtkReverseSense()
rs.SetInputData(msq.GetOutput())
rs.ReverseCellsOn()
rs.ReverseNormalsOff()
rs.Update()
output = rs.GetOutput()
else:
output = msq.GetOutput()
ctr = vtk.vtkContourTriangulator()
ctr.SetInputData(output)
ctr.Update()
return vedo.Mesh(ctr.GetOutput(), c='k').bc('t').lighting('off')
def filter_marching_squares(vtkObject, isovalue=1e-5):
"""
Create vtkMarchingSquares filter on vtkObject.
:param vtkObject: input
:param isovalue: contour value
:param vtkObject: :py:class:`vtk.vtkObject`
:type isovalue: float
>>> image_data = create_image_data_from_array(surf)
>>> squares = filter_marching_cubes(image_data)
>>> show(squares)
"""
squares = vtk.vtkMarchingSquares()
pipe(vtkObject, squares)
squares.SetValue(0, isovalue)
#squares.ComputeScalarsOn()
#squares.ComputeNormalsOn()
return squares
def filter_marching_squares(vtkObject, isovalue=1e-5):
"""
Create vtkMarchingSquares filter on vtkObject.
:param vtkObject: input
:param isovalue: contour value
:param vtkObject: :py:class:`vtk.vtkObject`
:type isovalue: float
>>> image_data = create_image_data_from_array(surf)
>>> squares = filter_marching_cubes(image_data)
>>> show(squares)
"""
squares = vtk.vtkMarchingSquares()
pipe(vtkObject, squares)
squares.SetValue(0, isovalue)
#squares.ComputeScalarsOn()
#squares.ComputeNormalsOn()
return squares
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
v16 = vtk.vtkVolume16Reader()
v16.SetDataDimensions(64,64)
v16.GetOutput().SetOrigin(0.0,0.0,0.0)
v16.SetDataByteOrderToLittleEndian()
v16.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
v16.SetImageRange(1,93)
v16.SetDataSpacing(3.2,3.2,1.5)
v16.Update()
myLocator = vtk.vtkMergePoints()
isoXY = vtk.vtkMarchingSquares()
isoXY.SetInputConnection(v16.GetOutputPort())
isoXY.GenerateValues(2,600,1200)
isoXY.SetImageRange(0,32,32,63,45,45)
isoXY.SetLocator(myLocator)
isoXYMapper = vtk.vtkPolyDataMapper()
isoXYMapper.SetInputConnection(isoXY.GetOutputPort())
isoXYMapper.SetScalarRange(600,1200)
isoXYActor = vtk.vtkActor()
isoXYActor.SetMapper(isoXYMapper)
isoYZ = vtk.vtkMarchingSquares()
isoYZ.SetInputConnection(v16.GetOutputPort())
isoYZ.GenerateValues(2,600,1200)
isoYZ.SetImageRange(32,32,32,63,46,92)
isoYZMapper = vtk.vtkPolyDataMapper()
isoYZMapper.SetInputConnection(isoYZ.GetOutputPort())
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
v16 = vtk.vtkVolume16Reader()
v16.SetDataDimensions(64,64)
v16.GetOutput().SetOrigin(0.0,0.0,0.0)
v16.SetDataByteOrderToLittleEndian()
v16.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
v16.SetImageRange(1,93)
v16.SetDataSpacing(3.2,3.2,1.5)
v16.Update()
myLocator = vtk.vtkMergePoints()
isoXY = vtk.vtkMarchingSquares()
isoXY.SetInputConnection(v16.GetOutputPort())
isoXY.GenerateValues(2,600,1200)
isoXY.SetImageRange(0,32,32,63,45,45)
isoXY.SetLocator(myLocator)
isoXYMapper = vtk.vtkPolyDataMapper()
isoXYMapper.SetInputConnection(isoXY.GetOutputPort())
isoXYMapper.SetScalarRange(600,1200)
isoXYActor = vtk.vtkActor()
isoXYActor.SetMapper(isoXYMapper)
isoYZ = vtk.vtkMarchingSquares()
isoYZ.SetInputConnection(v16.GetOutputPort())
isoYZ.GenerateValues(2,600,1200)
isoYZ.SetImageRange(32,32,32,63,46,92)
isoYZMapper = vtk.vtkPolyDataMapper()
isoYZMapper.SetInputConnection(isoYZ.GetOutputPort())
def __get_contour_data_vtk(self, x_grid, y_grid, z_grid, isovalue=[0]):
"""
wrapper for vtk marching squares function. Extracting contour information into bokeh compatible data type.
Less comfortable (no text labels, no coloring) but faster then __get_contour_data_mpl
:param x_grid:
:param y_grid:
:param z_grid:
:param isovalue:
:return:
"""
nx, ny = x_grid.shape
xmin = self._plot.x_range.start
xmax = self._plot.x_range.end
ymin = self._plot.y_range.start
ymax = self._plot.y_range.end
hx = (xmax - xmin) / (nx - 1)
hy = (ymax - ymin) / (ny - 1)
image = vtk.vtkImageData()
image.SetDimensions(nx, ny, 1)
image.SetOrigin(xmin, ymin, 0)
image.SetSpacing(hx, hy, 0)
data = vtk.vtkDoubleArray()
data.SetNumberOfComponents(1)
data.SetNumberOfTuples(image.GetNumberOfPoints())
data.SetName("Values")
# we load the z_data into vtk datatypes
vtk_data_array = numpy_support.numpy_to_vtk(z_grid.ravel(),
deep=True,
array_type=vtk.VTK_DOUBLE)
image.AllocateScalars(vtk.VTK_DOUBLE, 1)
image.GetPointData().SetScalars(vtk_data_array)
# apply marchign squares
ms = vtk.vtkMarchingSquares()
ms.SetInputData(image)
for i in range(isovalue.__len__()): # set isovalues
ms.SetValue(i, isovalue[i])
ms.SetImageRange(0,
image.GetDimensions()[0], 0,
image.GetDimensions()[1], 0, 0)
ms.Update()
# read output
poly = ms.GetOutput()
points = poly.GetPoints()
lines = poly.GetLines()
pts = numpy_support.vtk_to_numpy(points.GetData()) # get points
line_idx = numpy_support.vtk_to_numpy(lines.GetData()) # get lines
# lines are encoded as [nVerticesLine1, firstId, secondId, ... , nVerticesLine2...]
# We always have 2 vertices per line. This justifies the stride 3 pattern below
even_idx = line_idx[1::3]
odd_idx = line_idx[2::3]
x0 = pts[odd_idx, 0]
y0 = pts[odd_idx, 1]
x1 = pts[even_idx, 0]
y1 = pts[even_idx, 1]
data_contour = {'x0': x0, 'x1': x1, 'y0': y0, 'y1': y1}
data_contour_label = {}
return data_contour, data_contour_label
def main():
inputFileName, isoValue = get_program_parameters()
reader = vtk.vtkPNGReader()
if not reader.CanReadFile(inputFileName):
print("Error: Could not read %s ." % (inputFileName))
reader.SetFileName(inputFileName)
reader.Update()
iso = vtk.vtkMarchingSquares()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0, isoValue)
# Test smoothing here
if 1:
# Remove duplicate points and join up lines to form polylines
pCleaner = vtk.vtkCleanPolyData()
pCleaner.SetInputConnection(iso.GetOutputPort())
pStripper = vtk.vtkStripper()
pStripper.SetInputConnection(pCleaner.GetOutputPort())
# Downsample and smooth the polyline
pSpline = vtk.vtkSplineFilter()
mSplineResamplingLength = 50.0
mReferenceLength = 40.0
pSpline.SetLength(mSplineResamplingLength / mReferenceLength)
pSpline.SetSubdivideToLength()
pSpline.SetInputConnection(pStripper.GetOutputPort())
pTriangle = vtk.vtkTriangleFilter()
pTriangle.SetInputConnection(pSpline.GetOutputPort())
pTriangle.Update()
pCleaned = pTriangle.GetOutput()
newMapper = vtk.vtkDataSetMapper()
newMapper.SetInputConnection(pTriangle.GetOutputPort())
newActor = vtk.vtkActor()
newActor.SetMapper(newMapper)
isoMapper = vtk.vtkDataSetMapper()
isoMapper.SetInputConnection(iso.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetColor(0.8900, 0.8100, 0.3400)
poly = vtk.vtkContourTriangulator()
poly.SetInputConnection(iso.GetOutputPort())
polyMapper = vtk.vtkDataSetMapper()
polyMapper.SetInputConnection(poly.GetOutputPort())
polyMapper.ScalarVisibilityOff()
polyActor = vtk.vtkActor()
polyActor.SetMapper(polyMapper)
polyActor.GetProperty().SetColor(1.0000, 0.3882, 0.2784)
# Standard rendering classes
renderer = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.AddRenderer(renderer)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
renderer.AddActor(polyActor) # Important
renderer.AddActor(isoActor)
renderer.AddActor(newActor)
# Standard testing code.
renderer.SetBackground(0.5, 0.5, 0.5)
renWin.SetSize(800, 800)
camera = renderer.GetActiveCamera()
renderer.ResetCamera()
camera.Azimuth(180)
renWin.Render()
iren.Initialize()
iren.Start()
for i in range(image.GetNumberOfPoints()):
x,y,z = image.GetPoint(i)
data.SetValue(i,x**2+y**2+z**2)
image.GetPointData().AddArray(data)
image.AllocateScalars(vtk.VTK_DOUBLE, 1)
for z_id in range(image.GetDimensions()[2]):
for y_id in range(image.GetDimensions()[1]):
for x_id in range(image.GetDimensions()[0]):
id = image.ComputePointId((x_id, y_id, z_id))
value = image.GetPointData().GetArray("Values").GetValue(id)
image.SetScalarComponentFromDouble(x_id, y_id, z_id, 0, value)
ms = vtk.vtkMarchingSquares()
ms.SetInputData(image)
ms.SetValue(0, .5)
ms.SetValue(1, 1.0)
ms.SetImageRange(0, image.GetDimensions()[0], 0, image.GetDimensions()[1], 0, 0)
ms.Update()
poly = ms.GetOutput()
from matplotlib import pyplot as plt
import numpy as np
xx = np.zeros(poly.GetNumberOfPoints())
yy = np.zeros(poly.GetNumberOfPoints())
for i in range(poly.GetNumberOfPoints()):
x,y,z = poly.GetPoint(i)