def createScanlines(self, scanlineVolume):
imgDim = self.inputVolume.GetImageData().GetDimensions()
drawFilter = vtk.vtkImageCanvasSource2D()
drawFilter.SetExtent(0,imgDim[0]-1,0,imgDim[1]-1,0,0)
drawFilter.SetScalarTypeToUnsignedChar()
drawFilter.SetDrawColor(0) # Color for background
drawFilter.FillBox(0,imgDim[0]-1,0,imgDim[1]-1) # Initialize background
drawFilter.SetDrawColor(1) # Color for scanlines
# Draw each scanline
for i in range(self.numberOfScanlines):
drawFilter.FillTube(int(self.scanlines[i].startPoint[0]),int(self.scanlines[i].startPoint[1]),int(self.scanlines[i].endPoint[0]),int(self.scanlines[i].endPoint[1]),0.5)
drawFilter.Update()
# Copy scanline slice to match the Z-dimension of input US volume
numOfSlices = imgDim[2]
imageAppendFilter = vtk.vtkImageAppend()
imageAppendFilter.SetAppendAxis(2)
for _ in range(numOfSlices):
imageAppendFilter.AddInputData(drawFilter.GetOutput())
imageAppendFilter.Update()
# Set scanline imagedata
scanlineVolume.SetIJKToRASMatrix(self.ijkToRas)
scanlineVolume.SetRASToIJKMatrix(self.rasToIjk)
scanlineVolume.SetAndObserveImageData(imageAppendFilter.GetOutput())
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageAppend(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def getMaskFromPoints(points, mx, my, mz, value=255):
"""
Create a mask where all given points are set to value (between 0-255)
"""
if value > 255:
value = 255
elif value < 0:
value = 0
size = mx * my
pointStructString = "%dB" % size
pointData = []
for y in range(0, my):
for x in range(0, mx):
pointData.append(value * points.get((x, y), 0))
packedPointString = struct.pack(pointStructString, *pointData)
importer = vtk.vtkImageImport()
importer.CopyImportVoidPointer(packedPointString, mx * my)
importer.SetDataScalarTypeToUnsignedChar()
importer.SetNumberOfScalarComponents(1)
importer.SetDataExtent(0, mx - 1, 0, my - 1, 0, 0)
importer.SetWholeExtent(0, mx - 1, 0, my - 1, 0, 0)
importer.Update()
append = vtk.vtkImageAppend()
append.SetAppendAxis(2)
for z in range(0, mz):
append.SetInput(z, importer.GetOutput())
append.Update()
image2 = append.GetOutput()
return image2
def Execute(self):
if self.Mesh == None:
self.PrintError("Error: no Mesh.")
acquiredMesh = self.Mesh
acquiredKSpace = None
if (self.KSpaceDimensionality == 3) or not self.SliceSelection:
origin = [
self.FOVCenter[0] - self.FOV[0] / 2.0,
self.FOVCenter[1] - self.FOV[1] / 2.0,
self.FOVCenter[2] - self.FOV[2] / 2.0,
]
spacing = [
self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2],
]
acquiredKSpace = self.AcquireKSpace(self.Mesh, origin, spacing)
elif self.KSpaceDimensionality == 2:
spacing = [
self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2],
]
kSpaceAppend = vtk.vtkImageAppend()
kSpaceAppend.SetAppendAxis(2)
sliceLocations = []
sliceLocation = self.FOVCenter[2] - self.FOV[2] / 2.0
while sliceLocation <= self.FOVCenter[2] + self.FOV[2] / 2.0:
sliceLocations.append(sliceLocation)
sliceLocation += self.SliceSpacing
bounds = self.Mesh.GetBounds()
for sliceLocation in sliceLocations:
self.PrintLog("Processing slice at " + str(sliceLocation))
origin = [self.FOVCenter[0] - self.FOV[0] / 2.0, self.FOVCenter[1] - self.FOV[1] / 2.0, sliceLocation]
sliceKSpace = self.AcquireKSpace(self.Mesh, origin, spacing)
kSpaceAppend.AddInput(sliceKSpace)
kSpaceAppend.Update()
acquiredKSpace = kSpaceAppend.GetOutput()
self.KSpace = self.ComputeKSpaceOperation(acquiredKSpace)
def BuildEditedImage(imagedata, points):
"""
Editing the original image in accordance with the edit
points in the editor, it is necessary to generate the
vtkPolyData via vtkContourFilter
"""
init_values = None
for point in points:
x, y, z = point
colour = points[point]
imagedata.SetScalarComponentFromDouble(x, y, z, 0, colour)
imagedata.Update()
if not(init_values):
xi = x
xf = x
yi = y
yf = y
zi = z
zf = z
init_values = 1
if (xi > x):
xi = x
elif(xf < x):
xf = x
if (yi > y):
yi = y
elif(yf < y):
yf = y
if (zi > z):
zi = z
elif(zf < z):
zf = z
clip = vtk.vtkImageClip()
clip.SetInput(imagedata)
clip.SetOutputWholeExtent(xi, xf, yi, yf, zi, zf)
clip.Update()
gauss = vtk.vtkImageGaussianSmooth()
gauss.SetInput(clip.GetOutput())
gauss.SetRadiusFactor(0.6)
gauss.Update()
app = vtk.vtkImageAppend()
app.PreserveExtentsOn()
app.SetAppendAxis(2)
app.SetInput(0, imagedata)
app.SetInput(1, gauss.GetOutput())
app.Update()
return app.GetOutput()
def CreateVolumeFromSlices(vtkImages, spacing):
"""
Creates a volume from a set of slices (2D vtkImage objects).
"""
vtkImageAppend = vtk.vtkImageAppend()
vtkImageAppend.SetAppendAxis(2)
for sliceIndex in range(0, len(vtkImages)):
vtkImageAppend.SetInput(sliceIndex, vtkImages[sliceIndex])
output = vtkImageAppend.GetOutput()
output.SetSpacing(spacing)
output.Update()
return output
def FixGantryTilt(imagedata, tilt):
"""
Fix gantry tilt given a vtkImageData and the tilt value. Return new
vtkImageData.
"""
# Retrieve data from original imagedata
extent = [int(value) for value in imagedata.GetExtent()]
origin = imagedata.GetOrigin()
spacing = [float(value) for value in imagedata.GetSpacing()]
n_slices = int(extent[5])
new_zspacing = math.cos(tilt*(math.acos(-1.0)/180.0)) * spacing[2] #zspacing
translate_coef = math.tan(tilt*math.pi/180.0)*new_zspacing*(n_slices-1)
# Class responsible for translating data
reslice = vtk.vtkImageReslice()
reslice.SetInput(imagedata)
reslice.SetInterpolationModeToLinear()
# Translation will create new pixels. Let's set new pixels' colour to black.
reslice.SetBackgroundLevel(imagedata.GetScalarRange()[0])
# Class responsible for append translated data
append = vtk.vtkImageAppend()
append.SetAppendAxis(2)
# Translate and append each slice
for i in xrange(n_slices+1):
slice_imagedata = vtk.vtkImageData()
value = math.tan(tilt*math.pi/180.0) * new_zspacing * i
new_origin1 = origin[1] + value - translate_coef
# Translate data
reslice.SetOutputOrigin(origin[0], new_origin1, origin[2])
reslice.SetOutputExtent(extent[0], extent[1], extent[2], extent[3], i,i)
reslice.Update()
# Append data
slice_imagedata.DeepCopy(reslice.GetOutput())
slice_imagedata.UpdateInformation()
append.AddInput(slice_imagedata)
append.Update()
# Final imagedata
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(append.GetOutput())
imagedata.SetSpacing(spacing[0], spacing[1], new_zspacing)
imagedata.SetExtent(extent)
imagedata.UpdateInformation()
return imagedata
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
NoConfigModuleMixin.__init__(self)
self._imageStack = None
self._transformStack = None
#
self._itkExporterStack = []
self._imageAppend = vtk.vtkImageAppend()
# stack of images should become volume
self._imageAppend.SetAppendAxis(2)
self._viewFrame = self._createViewFrame(
{'Module (self)' : self})
self.config_to_logic()
self.logic_to_config()
self.config_to_view()
def RollMap( self, baseImage ):
# baseImage.Update()
if self.world_cut == self.map_cut: return baseImage
baseExtent = baseImage.GetExtent()
baseSpacing = baseImage.GetSpacing()
x0 = baseExtent[0]
x1 = baseExtent[1]
newCut = self.NormalizeMapLon( self.world_cut )
delCut = newCut - self.map_cut
# print " %%%%%% Roll Map %%%%%%: world_cut=%.1f, map_cut=%.1f, newCut=%.1f " % ( float(self.world_cut), float(self.map_cut), float(newCut) )
imageLen = x1 - x0 + 1
sliceSize = imageLen * ( delCut / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent = list( baseExtent )
extent[0:2] = [ x0, x0 + sliceCoord - 1 ]
clip0 = vtk.vtkImageClip()
if vtk.VTK_MAJOR_VERSION <= 5: clip0.SetInput( baseImage )
else: clip0.SetInputData( baseImage )
clip0.SetOutputWholeExtent( extent[0], extent[1], extent[2], extent[3], extent[4], extent[5] )
extent[0:2] = [ x0 + sliceCoord, x1 ]
clip1 = vtk.vtkImageClip()
if vtk.VTK_MAJOR_VERSION <= 5: clip1.SetInput( baseImage )
else: clip1.SetInputData( baseImage )
clip1.SetOutputWholeExtent( extent[0], extent[1], extent[2], extent[3], extent[4], extent[5] )
append = vtk.vtkImageAppend()
append.SetAppendAxis( 0 )
append.SetInputConnection ( clip1.GetOutputPort() )
append.AddInputConnection ( clip0.GetOutputPort() )
imageInfo = vtk.vtkImageChangeInformation()
imageInfo.SetInputConnection( append.GetOutputPort() )
imageInfo.SetOutputOrigin( 0.0, 0.0, 0.0 )
imageInfo.SetOutputExtentStart( 0, 0, 0 )
imageInfo.SetOutputSpacing( baseSpacing[0], baseSpacing[1], baseSpacing[2] )
imageInfo.Update()
result = imageInfo.GetOutput()
return result
def RollMap( self, baseImage ):
if self.world_cut == self.map_cut: return baseImage
baseExtent = baseImage.GetExtent()
baseSpacing = baseImage.GetSpacing()
x0 = baseExtent[0]
x1 = baseExtent[1]
newCut = self.NormalizeMapLon( self.world_cut )
delCut = newCut - self.map_cut
# print " %%%%%% Roll Map %%%%%%: world_cut=%.1f, map_cut=%.1f, newCut=%.1f " % ( float(self.world_cut), float(self.map_cut), float(newCut) )
imageLen = x1 - x0 + 1
sliceSize = imageLen * ( delCut / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent = list( baseExtent )
extent[0:2] = [ x0, x0 + sliceCoord - 1 ]
clip0 = vtk.vtkImageClip()
if vtk.VTK_MAJOR_VERSION <= 5: clip0.SetInput(baseImage)
else: clip0.SetInputData(baseImage)
clip0.SetOutputWholeExtent( extent[0], extent[1], extent[2], extent[3], extent[4], extent[5] )
extent[0:2] = [ x0 + sliceCoord, x1 ]
clip1 = vtk.vtkImageClip()
if vtk.VTK_MAJOR_VERSION <= 5: clip1.SetInput(baseImage)
else: clip1.SetInputData(baseImage)
clip1.SetOutputWholeExtent( extent[0], extent[1], extent[2], extent[3], extent[4], extent[5] )
append = vtk.vtkImageAppend()
append.SetAppendAxis( 0 )
append.AddInputConnection( clip1.GetOutputPort() )
append.AddInputConnection( clip0.GetOutputPort() )
imageInfo = vtk.vtkImageChangeInformation()
imageInfo.SetInputConnection( append.GetOutputPort() )
imageInfo.SetOutputOrigin( 0.0, 0.0, 0.0 )
imageInfo.SetOutputExtentStart( 0, 0, 0 )
imageInfo.SetOutputSpacing( baseSpacing[0], baseSpacing[1], baseSpacing[2] )
imageInfo.Update()
result = imageInfo.GetOutput()
return result
def append(self, volumes, axis='z', preserveExtents=False):
"""
Take the components from multiple inputs and merges them into one output.
Except for the append axis, all inputs must have the same extent.
All inputs must have the same number of scalar components.
The output has the same origin and spacing as the first input.
The origin and spacing of all other inputs are ignored.
All inputs must have the same scalar type.
:param int,str axis: axis expanded to hold the multiple images.
:param bool preserveExtents: if True, the extent of the inputs is used to place
the image in the output. The whole extent of the output is the union of the input
whole extents. Any portion of the output not covered by the inputs is set to zero.
The origin and spacing is taken from the first input.
.. code-block:: python
from vedo import load, datadir
vol = load(datadir+'embryo.tif')
vol.append(vol, axis='x').show()
"""
ima = vtk.vtkImageAppend()
ima.SetInputData(self.imagedata())
if not utils.isSequence(volumes):
volumes = [volumes]
for volume in volumes:
if isinstance(volume, vtk.vtkImageData):
ima.AddInputData(volume)
else:
ima.AddInputData(volume.imagedata())
ima.SetPreserveExtents(preserveExtents)
if axis == "x":
axis = 0
elif axis == "y":
axis = 1
elif axis == "z":
axis = 2
ima.SetAppendAxis(axis)
ima.Update()
return self._update(ima.GetOutput())
def append(self, pictures, axis='z', preserveExtents=False):
"""
Append the input images to the current one along the specified axis.
Except for the append axis, all inputs must have the same extent.
All inputs must have the same number of scalar components.
The output has the same origin and spacing as the first input.
The origin and spacing of all other inputs are ignored.
All inputs must have the same scalar type.
:param int,str axis: axis expanded to hold the multiple images.
:param bool preserveExtents: if True, the extent of the inputs is used to place
the image in the output. The whole extent of the output is the union of the input
whole extents. Any portion of the output not covered by the inputs is set to zero.
The origin and spacing is taken from the first input.
.. code-block:: python
from vedo import Picture, dataurl
pic = Picture(dataurl+'dog.jpg').pad()
pic.append([pic,pic,pic], axis='y')
pic.append([pic,pic,pic,pic], axis='x')
pic.show(axes=1)
"""
ima = vtk.vtkImageAppend()
ima.SetInputData(self._data)
if not utils.isSequence(pictures):
pictures = [pictures]
for p in pictures:
if isinstance(p, vtk.vtkImageData):
ima.AddInputData(p)
else:
ima.AddInputData(p._data)
ima.SetPreserveExtents(preserveExtents)
if axis == "x":
axis = 0
elif axis == "y":
axis = 1
ima.SetAppendAxis(axis)
ima.Update()
return self._update(ima.GetOutput())
def RollMap( self, baseImage ):
baseImage.Update()
if self.world_cut == self.map_cut: return baseImage
baseExtent = baseImage.GetExtent()
baseSpacing = baseImage.GetSpacing()
x0 = baseExtent[0]
x1 = baseExtent[1]
newCut = NormalizeLon( self.world_cut )
delCut = NormalizeLon( self.map_cut - newCut )
imageLen = x1 - x0 + 1
sliceSize = imageLen * ( delCut / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent = list( baseExtent )
extent[0:2] = [ x0, x0 + sliceCoord - 1 ]
clip0 = vtk.vtkImageClip()
clip0.SetInput( baseImage )
clip0.SetOutputWholeExtent( extent[0], extent[1], extent[2], extent[3], extent[4], extent[5] )
extent[0:2] = [ x0 + sliceCoord, x1 ]
clip1 = vtk.vtkImageClip()
clip1.SetInput( baseImage )
clip1.SetOutputWholeExtent( extent[0], extent[1], extent[2], extent[3], extent[4], extent[5] )
append = vtk.vtkImageAppend()
append.SetAppendAxis( 0 )
append.AddInput( clip1.GetOutput() )
append.AddInput( clip0.GetOutput() )
imageInfo = vtk.vtkImageChangeInformation()
imageInfo.SetInputConnection( append.GetOutputPort() )
imageInfo.SetOutputOrigin( 0.0, 0.0, 0.0 )
imageInfo.SetOutputExtentStart( 0, 0, 0 )
imageInfo.SetOutputSpacing( baseSpacing[0], baseSpacing[1], baseSpacing[2] )
result = imageInfo.GetOutput()
result.Update()
return result
def reader_vti(filename):
logging.debug("In data.reader_vti()")
append = vtk.vtkImageAppend()
append.ReleaseDataFlagOn()
append.SetAppendAxis(2)
reader = vtk.vtkXMLImageDataReader()
reader.ReleaseDataFlagOn()
if os.path.exists(filename):
reader.SetFileName(filename)
# reader.GetOutput().Register(reader)
reader.Update()
return vtk.vtkImageData.SafeDownCast(reader.GetOutput())
else:
i = 0
paths = []
while True:
partName = filename.replace(".vti", "{0}.vti".format(i))
# print partName
if os.path.exists(partName):
paths.append(partName)
else:
break
i = i + 1
# paths.reverse()
for i, partName in enumerate(paths):
reader = vtk.vtkXMLImageDataReader()
reader.ReleaseDataFlagOn()
reader.SetFileName(partName)
# reader.GetOutput().Register(reader)
reader.Update()
append.SetInput(i, reader.GetOutput())
append.Update()
output = append.GetOutput()
for i in range(append.GetNumberOfInputs()):
append.GetInput(i).ReleaseData()
return output
def GetNodeBasisImages(self, node_id, antialias = False):
"""Returns a vtkImageData of all wavelet or scaling function
basis images for a given node."""
if self.data_loaded:
if self.WordleImages:
self.WordleView.SetRandomSeed(0);
# Scaling functions coeffs are defined wrt parent node scaling functions...
# Need to create separate images (Z) for each column of matrix result
# Bases is D x N matrix
image_cols = self.Bases[node_id]
self.WordleView.SetColorByArray(True)
imgAppend = vtk.vtkImageAppend()
imgAppend.SetAppendAxis(2) # Z
for ii in range(self.Bases[node_id].shape[1]):
coeffs = VN.numpy_to_vtk(self.Bases[node_id][:,ii]*100, deep=True)
coeffs.SetName('coefficient')
c_sign = VN.numpy_to_vtk(N.sign(self.Bases[node_id][:,ii]), deep=True)
c_sign.SetName('sign')
self.WordleTable.RemoveColumn(2)
self.WordleTable.RemoveColumn(1)
self.WordleTable.AddColumn(coeffs)
self.WordleTable.AddColumn(c_sign)
self.WordleView.RemoveAllRepresentations()
self.WordleView.AddRepresentationFromInput(self.WordleTable)
self.WordleTable.Modified()
img = vtk.vtkImageData()
img.DeepCopy(self.WordleView.GetImageData(antialias))
img.GetPointData().GetScalars().SetName('DiffIntensity')
imgAppend.AddInput(img)
imgAppend.Update()
return imgAppend.GetOutput()
else:
# Scaling functions coeffs are defined wrt parent node scaling functions...
# Display all detail coordinates for a given leaf node
# Need to create separate images (Z) for each column of matrix result
if self.isCompressed:
# V now already chopped to AmbientDimension
# Compute all detail images for that dimension
# print "DS Calculating center image"
# print node_id, self.Centers[node_id].shape, self.V.T.shape, self.cm.shape
image_cols = self.V*self.Bases[node_id]
imR = self.imR
imC = self.imC
else:
image_cols = self.Bases[node_id]
imR = self.imR
imC = self.imC
# To make it linear, it is the correct order (one image after another) to .ravel()
images_linear = N.asarray(image_cols.T).ravel()
intensity = VN.numpy_to_vtk(images_linear, deep=True)
intensity.SetName('DiffIntensity')
imageData = vtk.vtkImageData()
imageData.SetOrigin(0,0,0)
imageData.SetSpacing(1,1,1)
imageData.SetDimensions(imR, imC, image_cols.shape[1])
imageData.GetPointData().AddArray(intensity)
imageData.GetPointData().SetActiveScalars('DiffIntensity')
return imageData
else:
raise IOError, "Can't get image until data is loaded successfully"
def __init__(
self,
inputobj=None,
c='RdBu_r',
alpha=(0.0, 0.0, 0.2, 0.4, 0.8, 1.0),
alphaGradient=None,
alphaUnit=1,
mode=0,
shade=False,
spacing=None,
dims=None,
origin=None,
mapper='smart',
):
vtk.vtkVolume.__init__(self)
BaseGrid.__init__(self)
###################
if isinstance(inputobj, str):
if "https://" in inputobj:
from vedo.io import download
inputobj = download(inputobj, verbose=False) # fpath
elif os.path.isfile(inputobj):
pass
else:
inputobj = sorted(glob.glob(inputobj))
###################
if 'gpu' in mapper:
self._mapper = vtk.vtkGPUVolumeRayCastMapper()
elif 'opengl_gpu' in mapper:
self._mapper = vtk.vtkOpenGLGPUVolumeRayCastMapper()
elif 'smart' in mapper:
self._mapper = vtk.vtkSmartVolumeMapper()
elif 'fixed' in mapper:
self._mapper = vtk.vtkFixedPointVolumeRayCastMapper()
elif isinstance(mapper, vtk.vtkMapper):
self._mapper = mapper
else:
print("Error unknown mapper type", [mapper])
raise RuntimeError()
self.SetMapper(self._mapper)
###################
inputtype = str(type(inputobj))
#colors.printc('Volume inputtype', inputtype)
if inputobj is None:
img = vtk.vtkImageData()
elif utils.isSequence(inputobj):
if isinstance(inputobj[0], str): # scan sequence of BMP files
ima = vtk.vtkImageAppend()
ima.SetAppendAxis(2)
pb = utils.ProgressBar(0, len(inputobj))
for i in pb.range():
f = inputobj[i]
picr = vtk.vtkBMPReader()
picr.SetFileName(f)
picr.Update()
mgf = vtk.vtkImageMagnitude()
mgf.SetInputData(picr.GetOutput())
mgf.Update()
ima.AddInputData(mgf.GetOutput())
pb.print('loading...')
ima.Update()
img = ima.GetOutput()
else:
if "ndarray" not in inputtype:
inputobj = np.array(inputobj)
if len(inputobj.shape) == 1:
varr = numpy_to_vtk(inputobj,
deep=True,
array_type=vtk.VTK_FLOAT)
else:
if len(inputobj.shape) > 2:
inputobj = np.transpose(inputobj, axes=[2, 1, 0])
varr = numpy_to_vtk(inputobj.ravel(order='F'),
deep=True,
array_type=vtk.VTK_FLOAT)
varr.SetName('input_scalars')
img = vtk.vtkImageData()
if dims is not None:
img.SetDimensions(dims)
else:
if len(inputobj.shape) == 1:
colors.printc(
"Error: must set dimensions (dims keyword) in Volume.",
c='r')
raise RuntimeError()
img.SetDimensions(inputobj.shape)
img.GetPointData().SetScalars(varr)
#to convert rgb to numpy
# img_scalar = data.GetPointData().GetScalars()
# dims = data.GetDimensions()
# n_comp = img_scalar.GetNumberOfComponents()
# temp = numpy_support.vtk_to_numpy(img_scalar)
# numpy_data = temp.reshape(dims[1],dims[0],n_comp)
# numpy_data = numpy_data.transpose(0,1,2)
# numpy_data = np.flipud(numpy_data)
elif "ImageData" in inputtype:
img = inputobj
elif isinstance(inputobj, Volume):
img = inputobj.inputdata()
elif "UniformGrid" in inputtype:
img = inputobj
elif hasattr(
inputobj,
"GetOutput"): # passing vtk object, try extract imagdedata
if hasattr(inputobj, "Update"):
inputobj.Update()
img = inputobj.GetOutput()
elif isinstance(inputobj, str):
from vedo.io import loadImageData, download
if "https://" in inputobj:
inputobj = download(inputobj, verbose=False)
img = loadImageData(inputobj)
else:
colors.printc("Volume(): cannot understand input type:\n",
inputtype,
c='r')
return
if dims is not None:
img.SetDimensions(dims)
if origin is not None:
img.SetOrigin(origin) ### DIFFERENT from volume.origin()!
if spacing is not None:
img.SetSpacing(spacing)
self._data = img
self._mapper.SetInputData(img)
self.mode(mode).color(c).alpha(alpha).alphaGradient(alphaGradient)
self.GetProperty().SetShade(True)
self.GetProperty().SetInterpolationType(1)
self.GetProperty().SetScalarOpacityUnitDistance(alphaUnit)
# remember stuff:
self._mode = mode
self._color = c
self._alpha = alpha
self._alphaGrad = alphaGradient
self._alphaUnit = alphaUnit
def straightenVolume(self,
outputStraightenedVolume,
curveNode,
volumeNode,
sliceSizeMm,
outputSpacingMm,
rotationAngleDeg=0.0):
"""
Compute straightened volume (useful for example for visualization of curved vessels)
"""
originalCurvePoints = curveNode.GetCurvePointsWorld()
sampledPoints = vtk.vtkPoints()
if not slicer.vtkMRMLMarkupsCurveNode.ResamplePoints(
originalCurvePoints, sampledPoints, outputSpacingMm[2], False):
return False
sliceExtent = [
int(sliceSizeMm[0] / outputSpacingMm[0]),
int(sliceSizeMm[1] / outputSpacingMm[1])
]
inputSpacing = volumeNode.GetSpacing()
lines = vtk.vtkCellArray()
lines.InsertNextCell(sampledPoints.GetNumberOfPoints())
for pointIndex in range(sampledPoints.GetNumberOfPoints()):
lines.InsertCellPoint(pointIndex)
sampledCurvePoly = vtk.vtkPolyData()
sampledCurvePoly.SetPoints(sampledPoints)
sampledCurvePoly.SetLines(lines)
#print(sampledPoints.GetPoint(3))
# Get physical coordinates from voxel coordinates
volumeRasToIjkTransformMatrix = vtk.vtkMatrix4x4()
volumeNode.GetRASToIJKMatrix(volumeRasToIjkTransformMatrix)
transformWorldToVolumeRas = vtk.vtkMatrix4x4()
slicer.vtkMRMLTransformNode.GetMatrixTransformBetweenNodes(
None, volumeNode.GetParentTransformNode(),
transformWorldToVolumeRas)
transformWorldToIjk = vtk.vtkTransform()
transformWorldToIjk.Concatenate(transformWorldToVolumeRas)
transformWorldToIjk.Scale(inputSpacing)
transformWorldToIjk.Concatenate(volumeRasToIjkTransformMatrix)
transformPolydataWorldToIjk = vtk.vtkTransformPolyDataFilter()
transformPolydataWorldToIjk.SetInputData(sampledCurvePoly)
transformPolydataWorldToIjk.SetTransform(transformWorldToIjk)
reslicer = vtk.vtkSplineDrivenImageSlicer()
append = vtk.vtkImageAppend()
scaledImageData = vtk.vtkImageData()
scaledImageData.ShallowCopy(volumeNode.GetImageData())
scaledImageData.SetSpacing(inputSpacing)
reslicer.SetInputData(scaledImageData)
reslicer.SetPathConnection(transformPolydataWorldToIjk.GetOutputPort())
reslicer.SetSliceExtent(*sliceExtent)
reslicer.SetSliceSpacing(outputSpacingMm[0], outputSpacingMm[1])
reslicer.SetIncidence(vtk.vtkMath.RadiansFromDegrees(rotationAngleDeg))
nbPoints = sampledPoints.GetNumberOfPoints()
for ptId in reversed(range(nbPoints)):
reslicer.SetOffsetPoint(ptId)
reslicer.Update()
tempSlice = vtk.vtkImageData()
tempSlice.DeepCopy(reslicer.GetOutput(0))
append.AddInputData(tempSlice)
append.SetAppendAxis(2)
append.Update()
straightenedVolumeImageData = append.GetOutput()
straightenedVolumeImageData.SetOrigin(0, 0, 0)
straightenedVolumeImageData.SetSpacing(1.0, 1.0, 1.0)
dims = straightenedVolumeImageData.GetDimensions()
ijkToRas = vtk.vtkMatrix4x4()
ijkToRas.SetElement(0, 0, 0.0)
ijkToRas.SetElement(1, 0, 0.0)
ijkToRas.SetElement(2, 0, -outputSpacingMm[0])
ijkToRas.SetElement(0, 1, 0.0)
ijkToRas.SetElement(1, 1, outputSpacingMm[1])
ijkToRas.SetElement(2, 1, 0.0)
ijkToRas.SetElement(0, 2, outputSpacingMm[2])
ijkToRas.SetElement(1, 2, 0.0)
ijkToRas.SetElement(2, 2, 0.0)
outputStraightenedVolume.SetIJKToRASMatrix(ijkToRas)
outputStraightenedVolume.SetAndObserveImageData(
straightenedVolumeImageData)
outputStraightenedVolume.CreateDefaultDisplayNodes()
return True
def main():
fn = get_program_parameters()
# A script to test the stencil filter with a polydata stencil.
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetDataSpacing(0.8, 0.8, 1.5)
reader.SetDataOrigin(0.0, 0.0, 0.0)
reader.SetFileName(fn)
sphere = vtk.vtkSphereSource()
sphere.SetPhiResolution(12)
sphere.SetThetaResolution(12)
sphere.SetCenter(102, 102, 0)
sphere.SetRadius(60)
triangle = vtk.vtkTriangleFilter()
triangle.SetInputConnection(sphere.GetOutputPort())
stripper = vtk.vtkStripper()
stripper.SetInputConnection(triangle.GetOutputPort())
dataToStencil = vtk.vtkPolyDataToImageStencil()
dataToStencil.SetInputConnection(stripper.GetOutputPort())
dataToStencil.SetOutputSpacing(0.8, 0.8, 1.5)
dataToStencil.SetOutputOrigin(0.0, 0.0, 0.0)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(reader.GetOutputPort())
stencil.SetStencilConnection(dataToStencil.GetOutputPort())
stencil.ReverseStencilOn()
stencil.SetBackgroundValue(500)
# test again with a contour
reader2 = vtk.vtkPNGReader()
reader2.SetDataSpacing(0.8, 0.8, 1.5)
reader2.SetDataOrigin(0.0, 0.0, 0.0)
reader2.SetFileName(fn)
plane = vtk.vtkPlane()
plane.SetOrigin(0, 0, 0)
plane.SetNormal(0, 0, 1)
cutter = vtk.vtkCutter()
cutter.SetInputConnection(sphere.GetOutputPort())
cutter.SetCutFunction(plane)
stripper2 = vtk.vtkStripper()
stripper2.SetInputConnection(cutter.GetOutputPort())
dataToStencil2 = vtk.vtkPolyDataToImageStencil()
dataToStencil2.SetInputConnection(stripper2.GetOutputPort())
dataToStencil2.SetOutputSpacing(0.8, 0.8, 1.5)
dataToStencil2.SetOutputOrigin(0.0, 0.0, 0.0)
stencil2 = vtk.vtkImageStencil()
stencil2.SetInputConnection(reader2.GetOutputPort())
stencil2.SetStencilConnection(dataToStencil2.GetOutputPort())
stencil2.SetBackgroundValue(500)
imageAppend = vtk.vtkImageAppend()
imageAppend.SetInputConnection(stencil.GetOutputPort())
imageAppend.AddInputConnection(stencil2.GetOutputPort())
viewer = vtk.vtkImageViewer()
interator = vtk.vtkRenderWindowInteractor()
viewer.SetInputConnection(imageAppend.GetOutputPort())
viewer.SetupInteractor(interator)
viewer.SetZSlice(0)
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
viewer.GetRenderWindow().SetWindowName('PolyDataToImageDataStencil')
viewer.Render()
interator.Start()
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: no Mesh.')
## if (self.FOVNormal != [0.0, 0.0, 1.0]):
##
## translation = [-self.FOVCenter[0], -self.FOVCenter[1], -self.FOVCenter[2]]
##
## referenceNormal = [0.0, 0.0, 1.0]
## rotationAxis = [0.0, 0.0, 0.0]
## vtk.vtkMath.Normalize(self.FOVNormal)
## vtk.vtkMath.Cross(self.FOVNormal,referenceNormal,rotationAxis)
## angle = self.AngleBetweenNormals(referenceNormal,self.FOVNormal) / vtk.vtkMath.Pi() * 180.0
##
## transform = vtk.vtkTransform()
## transform.PostMultiply()
## transform.Translate(translation)
## transform.RotateWXYZ(angle,rotationAxis)
## transform.Translate(self.FOVCenter)
##
## transformFilter = vtk.vtkTransformFilter()
## transformFilter.SetInput(self.Mesh)
## transformFilter.SetTransform(transform)
## transformFilter.Update()
##
## acquiredMesh = transformFilter.GetOutput()
if (self.KSpaceDimensionality == 3) or not self.SliceModel:
origin = [self.FOVCenter[0] - self.FOV[0]/2.0,
self.FOVCenter[1] - self.FOV[1]/2.0,
self.FOVCenter[2] - self.FOV[2]/2.0]
spacing = [self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]]
self.KSpace = self.AcquireKSpace(self.Mesh,origin,spacing)
elif self.KSpaceDimensionality == 2:
kSpaceAppend = vtk.vtkImageAppend()
kSpaceAppend.SetAppendAxis(2)
sliceLocations = []
sliceLocation = self.FOVCenter[2] - self.FOV[2]/2.0
while (sliceLocation < self.FOVCenter[2] + self.FOV[2]/2.0):
sliceLocations.append(sliceLocation)
sliceLocation += self.SliceSpacing
spacing = [self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]]
bounds = self.Mesh.GetBounds()
for sliceLocation in sliceLocations:
self.PrintLog("Processing slice at" + float(sliceLocation))
origin = [self.FOVCenter[0] - self.FOV[0]/2.0,
self.FOVCenter[1] - self.FOV[1]/2.0,
sliceLocation]
clipper1 = vtk.vtkClipDataSet()
clipper1.SetInput(self.Mesh)
clipper1.InsideOutOff()
plane1 = vtk.vtkPlane()
plane1.SetNormal(0.0,0.0,1.0)
plane1.SetOrigin(0.0,0.0,sliceLocation - self.SliceThickness / 2.0)
clipper1.SetClipFunction(plane1)
clipper1.Update()
clipper2 = vtk.vtkClipDataSet()
clipper2.SetInput(clipper1.GetOutput())
clipper2.InsideOutOn()
plane2 = vtk.vtkPlane()
plane2.SetNormal(0.0,0.0,1.0)
plane2.SetOrigin(0.0,0.0,sliceLocation + self.SliceThickness / 2.0)
clipper2.SetClipFunction(plane2)
clipper2.Update()
clipper2Bounds = clipper2.GetOutput().GetBounds()
cleaner = vtk.vtkExtractUnstructuredGrid()
cleaner.SetInput(clipper2.GetOutput())
cleaner.ExtentClippingOn()
cleaner.SetExtent(clipper2Bounds[0],clipper2Bounds[1],
clipper2Bounds[2],clipper2Bounds[3],
sliceLocation-self.SliceThickness/2.0,sliceLocation+self.SliceThickness/2.0)
cleaner.Update()
tetraFilter = vtk.vtkDataSetTriangleFilter()
tetraFilter.SetInput(cleaner.GetOutput())
tetraFilter.Update()
sliceMesh = tetraFilter.GetOutput()
self.PrintLog("Number of integration elements:" + int(sliceMesh.GetNumberOfCells()))
sliceKSpace = self.AcquireKSpace(sliceMesh,origin,spacing)
kSpaceAppend.AddInput(sliceKSpace)
kSpaceAppend.Update()
self.KSpace = self.ComputeKSpaceOperation(kSpaceAppend.GetOutput())
def getBoundedMap(self, baseImage, dataLocation, map_cut_size,
map_border_size):
baseImage.Update()
baseExtent = baseImage.GetExtent()
baseSpacing = baseImage.GetSpacing()
x0 = baseExtent[0]
x1 = baseExtent[1]
y0 = baseExtent[2]
y1 = baseExtent[3]
imageLen = [x1 - x0 + 1, y1 - y0 + 1]
selectionDim = [map_cut_size[0] / 2, map_cut_size[1] / 2]
dataXLoc = dataLocation[0]
imageInfo = vtk.vtkImageChangeInformation()
dataYbounds = [
dataLocation[1] - selectionDim[1],
dataLocation[1] + selectionDim[1]
]
vertExtent = [y0, y1]
bounded_dims = None
if dataYbounds[0] > -90.0:
yOffset = dataYbounds[0] + 90.0
extOffset = int(round((yOffset / 180.0) * imageLen[1]))
vertExtent[0] = y0 + extOffset
self.y0 = dataYbounds[0]
if dataYbounds[1] < 90.0:
yOffset = 90.0 - dataYbounds[1]
extOffset = int(round((yOffset / 180.0) * imageLen[1]))
vertExtent[1] = y1 - extOffset
overlapsBorder = (
self.NormalizeMapLon(dataLocation[0] - selectionDim[0]) >
self.NormalizeMapLon(dataLocation[0] + selectionDim[0]))
if overlapsBorder:
cut0 = self.NormalizeMapLon(dataXLoc + selectionDim[0])
sliceSize = imageLen[0] * ((cut0 - self.map_cut) / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent = list(baseExtent)
extent[0:2] = [x0, x0 + sliceCoord - 1]
clip0 = vtk.vtkImageClip()
clip0.SetInput(baseImage)
clip0.SetOutputWholeExtent(extent[0], extent[1], vertExtent[0],
vertExtent[1], extent[4], extent[5])
size0 = extent[1] - extent[0] + 1
self.x0 = dataLocation[0] - selectionDim[0]
cut1 = self.NormalizeMapLon(self.x0)
sliceSize = imageLen[0] * ((cut1 - self.map_cut) / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent[0:2] = [x0 + sliceCoord, x1]
clip1 = vtk.vtkImageClip()
clip1.SetInput(baseImage)
clip1.SetOutputWholeExtent(extent[0], extent[1], vertExtent[0],
vertExtent[1], extent[4], extent[5])
size1 = extent[1] - extent[0] + 1
# print "Set Corner pos: %s, cuts: %s " % ( str(self.x0), str( (cut0, cut1) ) )
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInput(clip1.GetOutput())
append.AddInput(clip0.GetOutput())
bounded_dims = (size0 + size1, vertExtent[1] - vertExtent[0] + 1)
imageInfo.SetInputConnection(append.GetOutputPort())
else:
self.x0 = dataXLoc - selectionDim[0]
cut0 = self.NormalizeMapLon(self.x0)
sliceSize = imageLen[0] * ((cut0 - self.map_cut) / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent = list(baseExtent)
extent[0] = x0 + sliceCoord - 1
cut1 = self.NormalizeMapLon(dataXLoc + selectionDim[0])
sliceSize = imageLen[0] * ((cut1 - self.map_cut) / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent[1] = x0 + sliceCoord
clip = vtk.vtkImageClip()
clip.SetInput(baseImage)
clip.SetOutputWholeExtent(extent[0], extent[1], vertExtent[0],
vertExtent[1], extent[4], extent[5])
bounded_dims = (extent[1] - extent[0] + 1,
vertExtent[1] - vertExtent[0] + 1)
# print "Set Corner pos: %s, dataXLoc: %s " % ( str(self.x0), str( (dataXLoc, selectionDim[0]) ) )
imageInfo.SetInputConnection(clip.GetOutputPort())
imageInfo.SetOutputOrigin(0.0, 0.0, 0.0)
imageInfo.SetOutputExtentStart(0, 0, 0)
imageInfo.SetOutputSpacing(baseSpacing[0], baseSpacing[1],
baseSpacing[2])
result = imageInfo.GetOutput()
result.Update()
return result, bounded_dims
def getBoundedMap(self, baseImage, dataLocation, map_cut_size):
baseExtent = baseImage.GetExtent()
baseSpacing = baseImage.GetSpacing()
x0 = baseExtent[0]
x1 = baseExtent[1]
y0 = baseExtent[2]
y1 = baseExtent[3]
imageLen = [x1 - x0 + 1, y1 - y0 + 1]
selectionDim = [map_cut_size[0] / 2, map_cut_size[1] / 2]
dataXLoc = NormalizeLon(dataLocation[0])
imageInfo = vtk.vtkImageChangeInformation()
dataYbounds = [
dataLocation[1] - selectionDim[1],
dataLocation[1] + selectionDim[1]
]
vertExtent = [y0, y1]
bounded_dims = None
if dataYbounds[0] > -90.0:
yOffset = dataYbounds[0] + 90.0
extOffset = int(round((yOffset / 180.0) * imageLen[1]))
vertExtent[0] = y0 + extOffset
self.y0 = dataYbounds[0]
if dataYbounds[1] < 90.0:
yOffset = 90.0 - dataYbounds[1]
extOffset = int(round((yOffset / 180.0) * imageLen[1]))
vertExtent[1] = y1 - extOffset
if ((dataXLoc > selectionDim[0]) and (dataXLoc <
(360 - selectionDim[0]))):
cut0 = dataXLoc - selectionDim[0]
sliceSize = imageLen[0] * (cut0 / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent = list(baseExtent)
extent[0] = x0 + sliceCoord - 1
cut1 = dataXLoc + selectionDim[0]
sliceSize = imageLen[0] * (cut1 / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent[1] = x0 + sliceCoord
clip = vtk.vtkImageClip()
if vtk.VTK_MAJOR_VERSION <= 5: clip.SetInput(baseImage)
else: clip.SetInputData(baseImage)
clip.SetOutputWholeExtent(extent[0], extent[1], vertExtent[0],
vertExtent[1], extent[4], extent[5])
self.x0 = cut0
bounded_dims = (extent[1] - extent[0] + 1,
vertExtent[1] - vertExtent[0] + 1)
imageInfo.SetInputConnection(clip.GetOutputPort())
else:
cut0 = NormalizeLon(dataXLoc + selectionDim[0])
sliceSize = imageLen[0] * (cut0 / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent = list(baseExtent)
extent[0:2] = [x0, x0 + sliceCoord - 1]
clip0 = vtk.vtkImageClip()
if vtk.VTK_MAJOR_VERSION <= 5: clip0.SetInput(baseImage)
else: clip0.SetInputData(baseImage)
clip0.SetOutputWholeExtent(extent[0], extent[1], vertExtent[0],
vertExtent[1], extent[4], extent[5])
size0 = extent[1] - extent[0] + 1
cut1 = NormalizeLon(dataLocation[0] - selectionDim[0])
sliceSize = imageLen[0] * (cut1 / 360.0)
sliceCoord = int(round(x0 + sliceSize))
extent[0:2] = [x0 + sliceCoord, x1]
clip1 = vtk.vtkImageClip()
if vtk.VTK_MAJOR_VERSION <= 5: clip1.SetInput(baseImage)
else: clip1.SetInputData(baseImage)
clip1.SetOutputWholeExtent(extent[0], extent[1], vertExtent[0],
vertExtent[1], extent[4], extent[5])
size1 = extent[1] - extent[0] + 1
self.x0 = cut1
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInput(clip1.GetOutput())
append.AddInput(clip0.GetOutput())
bounded_dims = (size0 + size1, vertExtent[1] - vertExtent[0] + 1)
imageInfo.SetInputConnection(append.GetOutputPort())
imageInfo.SetOutputOrigin(0.0, 0.0, 0.0)
imageInfo.SetOutputExtentStart(0, 0, 0)
imageInfo.SetOutputSpacing(baseSpacing[0], baseSpacing[1],
baseSpacing[2])
imageInfo.Update()
result = imageInfo.GetOutput()
return result, bounded_dims
magnify2 = vtk.vtkImageMagnify()
magnify2.SetInputConnection(reader.GetOutputPort())
magnify2.SetMagnificationFactors(IMAGE_MAG_X, IMAGE_MAG_Y, IMAGE_MAG_Z)
magnify2.ReleaseDataFlagOn()
# a filter that does in place processing (magnify ReleaseDataFlagOn)
cursor = vtk.vtkImageCursor3D()
cursor.SetInputConnection(magnify1.GetOutputPort())
cursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X, CURSOR_Y * IMAGE_MAG_Y,
CURSOR_Z * IMAGE_MAG_Z)
cursor.SetCursorValue(255)
cursor.SetCursorRadius(50 * IMAGE_MAG_X)
# stream to increase coverage of in place filter.
# put the two together in one image
imageAppend = vtk.vtkImageAppend()
imageAppend.SetAppendAxis(0)
imageAppend.AddInputConnection(magnify2.GetOutputPort())
imageAppend.AddInputConnection(cursor.GetOutputPort())
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(imageAppend.GetOutputPort())
viewer.SetZSlice(CURSOR_Z * IMAGE_MAG_Z)
viewer.SetColorWindow(200)
viewer.SetColorLevel(80)
# viewer DebugOn
viewer.Render()
viewer.SetPosition(50, 50)
# make interface
viewer.Render()
def __init__(
self,
inputobj=None,
c=('b', 'lb', 'lg', 'y', 'r'),
alpha=(0.0, 0.0, 0.2, 0.4, 0.8, 1),
alphaGradient=None,
mode=0,
origin=None,
spacing=None,
shape=None,
mapperType='smart',
):
vtk.vtkVolume.__init__(self)
ActorBase.__init__(self)
inputtype = str(type(inputobj))
#colors.printc('Volume inputtype', inputtype)
if isinstance(inputobj, str):
import glob
inputobj = sorted(glob.glob(inputobj))
if inputobj is None:
img = vtk.vtkImageData()
elif utils.isSequence(inputobj):
if isinstance(inputobj[0], str): # scan sequence of BMP files
ima = vtk.vtkImageAppend()
ima.SetAppendAxis(2)
pb = utils.ProgressBar(0, len(inputobj))
for i in pb.range():
f = inputobj[i]
picr = vtk.vtkBMPReader()
picr.SetFileName(f)
picr.Update()
mgf = vtk.vtkImageMagnitude()
mgf.SetInputData(picr.GetOutput())
mgf.Update()
ima.AddInputData(mgf.GetOutput())
pb.print('loading..')
ima.Update()
img = ima.GetOutput()
else:
if "ndarray" not in inputtype:
inputobj = np.array(inputobj)
varr = numpy_to_vtk(inputobj.ravel(order='F'),
deep=True,
array_type=vtk.VTK_FLOAT)
varr.SetName('input_scalars')
img = vtk.vtkImageData()
if shape is not None:
img.SetDimensions(shape)
else:
img.SetDimensions(inputobj.shape)
img.GetPointData().SetScalars(varr)
#to convert rgb to numpy
# img_scalar = data.GetPointData().GetScalars()
# dims = data.GetDimensions()
# n_comp = img_scalar.GetNumberOfComponents()
# temp = numpy_support.vtk_to_numpy(img_scalar)
# numpy_data = temp.reshape(dims[1],dims[0],n_comp)
# numpy_data = numpy_data.transpose(0,1,2)
# numpy_data = np.flipud(numpy_data)
elif "ImageData" in inputtype:
img = inputobj
elif "UniformGrid" in inputtype:
img = inputobj
elif "UnstructuredGrid" in inputtype:
img = inputobj
mapperType = 'tetra'
elif hasattr(
inputobj,
"GetOutput"): # passing vtk object, try extract imagdedata
if hasattr(inputobj, "Update"):
inputobj.Update()
img = inputobj.GetOutput()
else:
colors.printc("Volume(): cannot understand input type:\n",
inputtype,
c=1)
return
if 'gpu' in mapperType:
self._mapper = vtk.vtkGPUVolumeRayCastMapper()
elif 'opengl_gpu' in mapperType:
self._mapper = vtk.vtkOpenGLGPUVolumeRayCastMapper()
elif 'smart' in mapperType:
self._mapper = vtk.vtkSmartVolumeMapper()
elif 'fixed' in mapperType:
self._mapper = vtk.vtkFixedPointVolumeRayCastMapper()
elif 'tetra' in mapperType:
self._mapper = vtk.vtkProjectedTetrahedraMapper()
elif 'unstr' in mapperType:
self._mapper = vtk.vtkUnstructuredGridVolumeRayCastMapper()
else:
print("Error unknown mapperType", mapperType)
raise RuntimeError()
if origin is not None:
img.SetOrigin(origin)
if spacing is not None:
img.SetSpacing(spacing)
if shape is not None:
img.SetDimensions(shape)
self._imagedata = img
self._mapper.SetInputData(img)
self.SetMapper(self._mapper)
self.mode(mode).color(c).alpha(alpha).alphaGradient(alphaGradient)
self.GetProperty().SetInterpolationType(1)
# remember stuff:
self._mode = mode
self._color = c
self._alpha = alpha
self._alphaGrad = alphaGradient
magnify2.SetInputConnection(reader.GetOutputPort())
magnify2.SetMagnificationFactors(IMAGE_MAG_X, IMAGE_MAG_Y, IMAGE_MAG_Z)
magnify2.ReleaseDataFlagOn()
# a filter that does in place processing (magnify ReleaseDataFlagOn)
cursor = vtk.vtkImageCursor3D()
cursor.SetInputConnection(magnify1.GetOutputPort())
cursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X,
CURSOR_Y * IMAGE_MAG_Y,
CURSOR_Z * IMAGE_MAG_Z)
cursor.SetCursorValue(255)
cursor.SetCursorRadius(50 * IMAGE_MAG_X)
# stream to increase coverage of in place filter.
# put the two together in one image
imageAppend = vtk.vtkImageAppend()
imageAppend.SetAppendAxis(0)
imageAppend.AddInputConnection(magnify2.GetOutputPort())
imageAppend.AddInputConnection(cursor.GetOutputPort())
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(imageAppend.GetOutputPort())
viewer.SetZSlice(CURSOR_Z * IMAGE_MAG_Z)
viewer.SetColorWindow(200)
viewer.SetColorLevel(80)
# viewer DebugOn
viewer.Render()
viewer.SetPosition(50, 50)
# make interface
viewer.Render()
def CreateImageData(self, filelist, zspacing, size, bits):
message = _("Generating multiplanar visualization...")
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
x,y = size
px, py = utils.predict_memory(len(filelist), x, y, bits)
utils.debug("Image Resized to >>> %f x %f" % (px, py))
if (x == px) and (y == py):
const.REDUCE_IMAGEDATA_QUALITY = 0
else:
const.REDUCE_IMAGEDATA_QUALITY = 1
if not(const.REDUCE_IMAGEDATA_QUALITY):
update_progress= vtk_utils.ShowProgress(1, dialog_type = "ProgressDialog")
array = vtk.vtkStringArray()
for x in range(len(filelist)):
if not self.running:
return False
array.InsertValue(x,filelist[x])
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileNames(array)
reader.AddObserver("ProgressEvent", lambda obj,evt:
update_progress(reader,message))
reader.Update()
if not self.running:
reader.AbortExecuteOn()
return False
# The zpacing is a DicomGroup property, so we need to set it
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(reader.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
else:
update_progress= vtk_utils.ShowProgress(2*len(filelist),
dialog_type = "ProgressDialog")
# Reformat each slice and future append them
appender = vtk.vtkImageAppend()
appender.SetAppendAxis(2) #Define Stack in Z
# Reformat each slice
for x in range(len(filelist)):
# TODO: We need to check this automatically according
# to each computer's architecture
# If the resolution of the matrix is too large
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileName(filelist[x])
reader.AddObserver("ProgressEvent", lambda obj,evt:
update_progress(reader,message))
reader.Update()
#Resample image in x,y dimension
slice_imagedata = ResampleImage2D(reader.GetOutput(), px, py, update_progress)
#Stack images in Z axes
appender.AddInput(slice_imagedata)
#appender.AddObserver("ProgressEvent", lambda obj,evt:update_progress(appender))
appender.Update()
# The zpacing is a DicomGroup property, so we need to set it
if not self.running:
return False
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(appender.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
imagedata.AddObserver("ProgressEvent", lambda obj,evt:
update_progress(imagedata,message))
imagedata.Update()
return imagedata
def CreateImageData(self, filelist, zspacing, size, bits):
message = _("Generating multiplanar visualization...")
if not const.VTK_WARNING:
log_path = os.path.join(const.LOG_FOLDER, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
x, y = size
px, py = utils.predict_memory(len(filelist), x, y, bits)
utils.debug("Image Resized to >>> %f x %f" % (px, py))
if (x == px) and (y == py):
const.REDUCE_IMAGEDATA_QUALITY = 0
else:
const.REDUCE_IMAGEDATA_QUALITY = 1
if not (const.REDUCE_IMAGEDATA_QUALITY):
update_progress = vtk_utils.ShowProgress(
1, dialog_type="ProgressDialog")
array = vtk.vtkStringArray()
for x in xrange(len(filelist)):
if not self.running:
return False
array.InsertValue(x, filelist[x])
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileNames(array)
reader.AddObserver(
"ProgressEvent",
lambda obj, evt: update_progress(reader, message))
reader.Update()
if not self.running:
reader.AbortExecuteOn()
return False
# The zpacing is a DicomGroup property, so we need to set it
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(reader.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
else:
update_progress = vtk_utils.ShowProgress(
2 * len(filelist), dialog_type="ProgressDialog")
# Reformat each slice and future append them
appender = vtk.vtkImageAppend()
appender.SetAppendAxis(2) #Define Stack in Z
# Reformat each slice
for x in xrange(len(filelist)):
# TODO: We need to check this automatically according
# to each computer's architecture
# If the resolution of the matrix is too large
if not self.running:
return False
reader = vtkgdcm.vtkGDCMImageReader()
reader.SetFileName(filelist[x])
reader.AddObserver(
"ProgressEvent",
lambda obj, evt: update_progress(reader, message))
reader.Update()
#Resample image in x,y dimension
slice_imagedata = ResampleImage2D(reader.GetOutput(), px, py,
update_progress)
#Stack images in Z axes
appender.AddInput(slice_imagedata)
#appender.AddObserver("ProgressEvent", lambda obj,evt:update_progress(appender))
appender.Update()
# The zpacing is a DicomGroup property, so we need to set it
if not self.running:
return False
imagedata = vtk.vtkImageData()
imagedata.DeepCopy(appender.GetOutput())
spacing = imagedata.GetSpacing()
imagedata.SetSpacing(spacing[0], spacing[1], zspacing)
imagedata.AddObserver(
"ProgressEvent",
lambda obj, evt: update_progress(imagedata, message))
imagedata.Update()
return imagedata
def GetProjectedImages(self, IDlist, wordle_on = True, antialias = False):
"""Given a list of IDs selected from a parallel coordinates plot, returns
a vtkImageData with all of the projected (reduced dimensionality by SVD) images
for those IDs. (e.g. typically 120 dim rather than original 768 dim for MNIST digits)"""
if self.data_loaded:
if self.WordleImages and wordle_on:
self.WordleView.SetRandomSeed(0);
# Need to create separate images (Z) for each column of matrix result
# Bases is D x N matrix
if self.isCompressed:
Xtmp = self.X[:,IDlist]*self.V
# numpy should automatically do tiling!!
X_orig = Xtmp + self.cm
else:
X_orig = self.X[:,IDlist]
self.WordleView.SetColorByArray(False)
self.WordleView.Update()
imgAppend = vtk.vtkImageAppend()
imgAppend.SetAppendAxis(2) # Z
for ii in range(X_orig.shape[1]):
coeffs = VN.numpy_to_vtk(X_orig[:,ii]*100, deep=True)
coeffs.SetName('coefficient')
c_sign = VN.numpy_to_vtk(N.sign(X_orig[:,ii]), deep=True)
c_sign.SetName('sign')
self.WordleTable.RemoveColumn(2)
self.WordleTable.RemoveColumn(1)
self.WordleTable.AddColumn(coeffs)
self.WordleTable.AddColumn(c_sign)
self.WordleView.RemoveAllRepresentations()
self.WordleView.AddRepresentationFromInput(self.WordleTable)
self.WordleTable.Modified()
img = vtk.vtkImageData()
img.DeepCopy(self.WordleView.GetImageData(antialias))
img.GetPointData().GetScalars().SetName('Intensity')
imgAppend.AddInput(img)
imgAppend.Update()
return imgAppend.GetOutput()
else:
if self.isCompressed:
# V now already chopped to AmbientDimension
Xtmp = (self.V*self.X[:,IDlist]).T
# numpy should automatically do tiling!!
X_orig = Xtmp + self.cm
imR = self.imR
imC = self.imC
else:
X_orig = self.X[:,IDlist]
imR = self.imR
imC = self.imC
# To make it linear, it is the correct order (one image after another) to .ravel()
X_linear = N.asarray(X_orig.T).ravel()
# Going ahead and using numpy_support here... Much faster!!!
Xvtk = VN.numpy_to_vtk(X_linear, deep=True) # even with the (necessary) deep copy
Xvtk.SetName('Intensity')
imageData = vtk.vtkImageData()
imageData.SetOrigin(0,0,0)
imageData.SetSpacing(1,1,1)
imageData.SetDimensions(imR, imC, X_orig.shape[1])
imageData.GetPointData().AddArray(Xvtk)
imageData.GetPointData().SetActiveScalars('Intensity')
return imageData
else:
raise IOError, "Can't get image until data is loaded successfully"
def getBoundedMap( self, baseImage, dataLocation, map_cut_size ):
baseImage.Update()
baseExtent = baseImage.GetExtent()
baseSpacing = baseImage.GetSpacing()
x0 = baseExtent[0]
x1 = baseExtent[1]
y0 = baseExtent[2]
y1 = baseExtent[3]
imageLen = [ x1 - x0 + 1, y1 - y0 + 1 ]
selectionDim = [ map_cut_size[0]/2, map_cut_size[1]/2 ]
dataXLoc = NormalizeLon( dataLocation[0] )
imageInfo = vtk.vtkImageChangeInformation()
dataYbounds = [ dataLocation[1]-selectionDim[1], dataLocation[1]+selectionDim[1] ]
vertExtent = [ y0, y1 ]
bounded_dims = None
if dataYbounds[0] > -90.0:
yOffset = dataYbounds[0] + 90.0
extOffset = int( round( ( yOffset / 180.0 ) * imageLen[1] ) )
vertExtent[0] = y0 + extOffset
self.y0 = dataYbounds[0]
if dataYbounds[1] < 90.0:
yOffset = 90.0 - dataYbounds[1]
extOffset = int( round( ( yOffset / 180.0 ) * imageLen[1] ) )
vertExtent[1] = y1 - extOffset
if (( dataXLoc > selectionDim[0] ) and ( dataXLoc < ( 360 - selectionDim[0]) )):
cut0 = dataXLoc - selectionDim[0]
sliceSize = imageLen[0] * ( cut0 / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent = list( baseExtent )
extent[0] = x0 + sliceCoord - 1
cut1 = dataXLoc + selectionDim[0]
sliceSize = imageLen[0] * ( cut1 / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent[1] = x0 + sliceCoord
clip = vtk.vtkImageClip()
clip.SetInput( baseImage )
clip.SetOutputWholeExtent( extent[0], extent[1], vertExtent[0], vertExtent[1], extent[4], extent[5] )
self.x0 = cut0
bounded_dims = ( extent[1] - extent[0] + 1, vertExtent[1] - vertExtent[0] + 1 )
imageInfo.SetInputConnection( clip.GetOutputPort() )
else:
cut0 = NormalizeLon( dataXLoc + selectionDim[0] )
sliceSize = imageLen[0] * ( cut0 / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent = list( baseExtent )
extent[0:2] = [ x0, x0 + sliceCoord - 1 ]
clip0 = vtk.vtkImageClip()
clip0.SetInput( baseImage )
clip0.SetOutputWholeExtent( extent[0], extent[1], vertExtent[0], vertExtent[1], extent[4], extent[5] )
size0 = extent[1] - extent[0] + 1
cut1 = NormalizeLon( dataLocation[0] - selectionDim[0] )
sliceSize = imageLen[0] * ( cut1 / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent[0:2] = [ x0 + sliceCoord, x1 ]
clip1 = vtk.vtkImageClip()
clip1.SetInput( baseImage )
clip1.SetOutputWholeExtent( extent[0], extent[1], vertExtent[0], vertExtent[1], extent[4], extent[5] )
size1 = extent[1] - extent[0] + 1
self.x0 = cut1
append = vtk.vtkImageAppend()
append.SetAppendAxis( 0 )
append.AddInput( clip1.GetOutput() )
append.AddInput( clip0.GetOutput() )
bounded_dims = ( size0 + size1, vertExtent[1] - vertExtent[0] + 1 )
imageInfo.SetInputConnection( append.GetOutputPort() )
imageInfo.SetOutputOrigin( 0.0, 0.0, 0.0 )
imageInfo.SetOutputExtentStart( 0, 0, 0 )
imageInfo.SetOutputSpacing( baseSpacing[0], baseSpacing[1], baseSpacing[2] )
result = imageInfo.GetOutput()
result.Update()
return result, bounded_dims
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: no Mesh.')
## if (self.FOVNormal != [0.0, 0.0, 1.0]):
##
## translation = [-self.FOVCenter[0], -self.FOVCenter[1], -self.FOVCenter[2]]
##
## referenceNormal = [0.0, 0.0, 1.0]
## rotationAxis = [0.0, 0.0, 0.0]
## vtk.vtkMath.Normalize(self.FOVNormal)
## vtk.vtkMath.Cross(self.FOVNormal,referenceNormal,rotationAxis)
## angle = self.AngleBetweenNormals(referenceNormal,self.FOVNormal) / vtk.vtkMath.Pi() * 180.0
##
## transform = vtk.vtkTransform()
## transform.PostMultiply()
## transform.Translate(translation)
## transform.RotateWXYZ(angle,rotationAxis)
## transform.Translate(self.FOVCenter)
##
## transformFilter = vtk.vtkTransformFilter()
## transformFilter.SetInput(self.Mesh)
## transformFilter.SetTransform(transform)
## transformFilter.Update()
##
## acquiredMesh = transformFilter.GetOutput()
if (self.KSpaceDimensionality == 3) or not self.SliceModel:
origin = [
self.FOVCenter[0] - self.FOV[0] / 2.0,
self.FOVCenter[1] - self.FOV[1] / 2.0,
self.FOVCenter[2] - self.FOV[2] / 2.0
]
spacing = [
self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]
]
self.KSpace = self.AcquireKSpace(self.Mesh, origin, spacing)
elif self.KSpaceDimensionality == 2:
kSpaceAppend = vtk.vtkImageAppend()
kSpaceAppend.SetAppendAxis(2)
sliceLocations = []
sliceLocation = self.FOVCenter[2] - self.FOV[2] / 2.0
while (sliceLocation < self.FOVCenter[2] + self.FOV[2] / 2.0):
sliceLocations.append(sliceLocation)
sliceLocation += self.SliceSpacing
spacing = [
self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]
]
bounds = self.Mesh.GetBounds()
for sliceLocation in sliceLocations:
self.PrintLog("Processing slice at" + float(sliceLocation))
origin = [
self.FOVCenter[0] - self.FOV[0] / 2.0,
self.FOVCenter[1] - self.FOV[1] / 2.0, sliceLocation
]
clipper1 = vtk.vtkClipDataSet()
clipper1.SetInput(self.Mesh)
clipper1.InsideOutOff()
plane1 = vtk.vtkPlane()
plane1.SetNormal(0.0, 0.0, 1.0)
plane1.SetOrigin(0.0, 0.0,
sliceLocation - self.SliceThickness / 2.0)
clipper1.SetClipFunction(plane1)
clipper1.Update()
clipper2 = vtk.vtkClipDataSet()
clipper2.SetInput(clipper1.GetOutput())
clipper2.InsideOutOn()
plane2 = vtk.vtkPlane()
plane2.SetNormal(0.0, 0.0, 1.0)
plane2.SetOrigin(0.0, 0.0,
sliceLocation + self.SliceThickness / 2.0)
clipper2.SetClipFunction(plane2)
clipper2.Update()
clipper2Bounds = clipper2.GetOutput().GetBounds()
cleaner = vtk.vtkExtractUnstructuredGrid()
cleaner.SetInput(clipper2.GetOutput())
cleaner.ExtentClippingOn()
cleaner.SetExtent(clipper2Bounds[0], clipper2Bounds[1],
clipper2Bounds[2], clipper2Bounds[3],
sliceLocation - self.SliceThickness / 2.0,
sliceLocation + self.SliceThickness / 2.0)
cleaner.Update()
tetraFilter = vtk.vtkDataSetTriangleFilter()
tetraFilter.SetInput(cleaner.GetOutput())
tetraFilter.Update()
sliceMesh = tetraFilter.GetOutput()
self.PrintLog("Number of integration elements:" +
int(sliceMesh.GetNumberOfCells()))
sliceKSpace = self.AcquireKSpace(sliceMesh, origin, spacing)
kSpaceAppend.AddInput(sliceKSpace)
kSpaceAppend.Update()
self.KSpace = self.ComputeKSpaceOperation(kSpaceAppend.GetOutput())
def getBoundedMap( self, baseImage, dataLocation ):
# print " @@@ MapManager: getBoundedMap "
baseExtent = baseImage.GetExtent()
baseSpacing = baseImage.GetSpacing()
x0 = baseExtent[0]
x1 = baseExtent[1]
y0 = baseExtent[2]
y1 = baseExtent[3]
imageLen = [ x1 - x0 + 1, y1 - y0 + 1 ]
selectionDim = [ self.map_cut_size[0]/2, self.map_cut_size[1]/2 ]
dataXLoc = dataLocation[0]
imageInfo = vtk.vtkImageChangeInformation()
dataYbounds = [ dataLocation[1]-selectionDim[1], dataLocation[1]+selectionDim[1] ]
vertExtent = [ y0, y1 ]
bounded_dims = None
if dataYbounds[0] > -90.0:
yOffset = dataYbounds[0] + 90.0
extOffset = int( round( ( yOffset / 180.0 ) * imageLen[1] ) )
vertExtent[0] = y0 + extOffset
self.y0 = dataYbounds[0]
if dataYbounds[1] < 90.0:
yOffset = 90.0 - dataYbounds[1]
extOffset = int( round( ( yOffset / 180.0 ) * imageLen[1] ) )
vertExtent[1] = y1 - extOffset
overlapsBorder = ( self.NormalizeMapLon(dataLocation[0]-selectionDim[0]) > self.NormalizeMapLon(dataLocation[0]+selectionDim[0]) )
if overlapsBorder:
cut0 = self.NormalizeMapLon( dataXLoc + selectionDim[0] )
sliceSize = imageLen[0] * ( ( cut0 - self.map_cut ) / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent = list( baseExtent )
extent[0:2] = [ x0, x0 + sliceCoord - 1 ]
clip0 = vtk.vtkImageClip()
clip0.ClipDataOn()
clip0.SetInput( baseImage )
clip0.SetOutputWholeExtent( extent[0], extent[1], vertExtent[0], vertExtent[1], extent[4], extent[5] )
size0 = extent[1] - extent[0] + 1
self.x0 = dataLocation[0] - selectionDim[0]
cut1 = self.NormalizeMapLon( self.x0 )
sliceSize = imageLen[0] * ( ( cut1 - self.map_cut )/ 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent[0:2] = [ x0 + sliceCoord, x1 ]
clip1 = vtk.vtkImageClip()
clip1.ClipDataOn()
if vtk.VTK_MAJOR_VERSION <= 5: clip1.SetInput( baseImage )
else: clip1.SetInputData( baseImage )
clip1.SetOutputWholeExtent( extent[0], extent[1], vertExtent[0], vertExtent[1], extent[4], extent[5] )
size1 = extent[1] - extent[0] + 1
# print "Set Corner pos: %s, cuts: %s " % ( str(self.x0), str( (cut0, cut1) ) )
append = vtk.vtkImageAppend()
append.SetAppendAxis( 0 )
append.AddInputConnection( clip1.GetOutputPort() )
append.AddInputConnection( clip0.GetOutputPort() )
bounded_dims = ( size0 + size1, vertExtent[1] - vertExtent[0] + 1 )
imageInfo.SetInputConnection( append.GetOutputPort() )
else:
self.x0 = dataXLoc - selectionDim[0]
cut0 = self.NormalizeMapLon( self.x0 )
sliceSize = imageLen[0] * ( ( cut0 - self.map_cut ) / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent = list( baseExtent )
extent[0] = x0 + sliceCoord - 1
cut1 = self.NormalizeMapLon( dataXLoc + selectionDim[0] )
sliceSize = imageLen[0] * ( ( cut1 - self.map_cut ) / 360.0 )
sliceCoord = int( round( x0 + sliceSize) )
extent[1] = x0 + sliceCoord
clip = vtk.vtkImageClip()
clip.ClipDataOn()
if vtk.VTK_MAJOR_VERSION <= 5: clip.SetInput( baseImage )
else: clip.SetInputData( baseImage )
clip.SetOutputWholeExtent( extent[0], extent[1], vertExtent[0], vertExtent[1], extent[4], extent[5] )
bounded_dims = ( extent[1] - extent[0] + 1, vertExtent[1] - vertExtent[0] + 1 )
# print "Set Corner pos: %s, dataXLoc: %s " % ( str(self.x0), str( (dataXLoc, selectionDim[0]) ) )
clip.Update()
imageInfo.SetInputConnection( clip.GetOutputPort() )
imageInfo.SetOutputOrigin( 0.0, 0.0, 0.0 )
imageInfo.SetOutputExtentStart( 0, 0, 0 )
imageInfo.SetOutputSpacing( baseSpacing[0], baseSpacing[1], baseSpacing[2] )
imageInfo.Update()
result = imageInfo.GetOutput()
return result, bounded_dims
def __init__(self, inputobj=None):
vtk.vtkImageSlice.__init__(self)
Base3DProp.__init__(self)
BaseVolume.__init__(self)
self._mapper = vtk.vtkImageResliceMapper()
self._mapper.SliceFacesCameraOn()
self._mapper.SliceAtFocalPointOn()
self._mapper.SetAutoAdjustImageQuality(False)
self._mapper.BorderOff()
self.lut = None
self.property = vtk.vtkImageProperty()
self.property.SetInterpolationTypeToLinear()
self.SetProperty(self.property)
###################
if isinstance(inputobj, str):
if "https://" in inputobj:
from vedo.io import download
inputobj = download(inputobj, verbose=False) # fpath
elif os.path.isfile(inputobj):
pass
else:
inputobj = sorted(glob.glob(inputobj))
###################
inputtype = str(type(inputobj))
if inputobj is None:
img = vtk.vtkImageData()
if isinstance(inputobj, Volume):
img = inputobj.imagedata()
self.lut = utils.ctf2lut(inputobj)
elif utils.isSequence(inputobj):
if isinstance(inputobj[0], str): # scan sequence of BMP files
ima = vtk.vtkImageAppend()
ima.SetAppendAxis(2)
pb = utils.ProgressBar(0, len(inputobj))
for i in pb.range():
f = inputobj[i]
picr = vtk.vtkBMPReader()
picr.SetFileName(f)
picr.Update()
mgf = vtk.vtkImageMagnitude()
mgf.SetInputData(picr.GetOutput())
mgf.Update()
ima.AddInputData(mgf.GetOutput())
pb.print('loading...')
ima.Update()
img = ima.GetOutput()
else:
if "ndarray" not in inputtype:
inputobj = np.array(inputobj)
if len(inputobj.shape) == 1:
varr = utils.numpy2vtk(inputobj, dtype=float)
else:
if len(inputobj.shape) > 2:
inputobj = np.transpose(inputobj, axes=[2, 1, 0])
varr = utils.numpy2vtk(inputobj.ravel(order='F'),
dtype=float)
varr.SetName('input_scalars')
img = vtk.vtkImageData()
img.SetDimensions(inputobj.shape)
img.GetPointData().AddArray(varr)
img.GetPointData().SetActiveScalars(varr.GetName())
elif "ImageData" in inputtype:
img = inputobj
elif isinstance(inputobj, Volume):
img = inputobj.inputdata()
elif "UniformGrid" in inputtype:
img = inputobj
elif hasattr(
inputobj,
"GetOutput"): # passing vtk object, try extract imagdedata
if hasattr(inputobj, "Update"):
inputobj.Update()
img = inputobj.GetOutput()
elif isinstance(inputobj, str):
from vedo.io import loadImageData, download
if "https://" in inputobj:
inputobj = download(inputobj, verbose=False)
img = loadImageData(inputobj)
else:
colors.printc("VolumeSlice: cannot understand input type:\n",
inputtype,
c='r')
return
self._data = img
self._mapper.SetInputData(img)
self.SetMapper(self._mapper)
