def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageWrapPad(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageWrapPad(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Make an image larger by repeating the data. Tile.
# Image pipeline
reader = vtk.vtkImageReader()
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetDataSpacing(3.2, 3.2, 1.5)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
pad = vtk.vtkImageWrapPad()
pad.SetInputConnection(reader.GetOutputPort())
pad.SetOutputWholeExtent(-100, 155, -100, 170, 0, 92)
pad.ReleaseDataFlagOff()
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(pad.GetOutputPort())
viewer.SetZSlice(22)
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
viewer.GetActor2D().SetDisplayPosition(150, 150)
viewer.Render()
# --- end of script --
#!/usr/bin/env python import vtk import sys from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() # Image pipeline size=400 image1 = vtk.vtkImageCanvasSource2D() image1.SetNumberOfScalarComponents(3) image1.SetScalarTypeToUnsignedChar() image1.SetExtent(0,size,0,size,0,0) image1.SetDrawColor(255,255,0) image1.FillBox(0,size,0,size) pad1 = vtk.vtkImageWrapPad() pad1.SetInputConnection(image1.GetOutputPort()) pad1.SetOutputWholeExtent(0,size,0,size,0,10) pad1.Update() image2 = vtk.vtkImageCanvasSource2D() image2.SetNumberOfScalarComponents(3) image2.SetScalarTypeToUnsignedChar() image2.SetExtent(0,size,0,size,0,0) image2.SetDrawColor(0,255,255) image2.FillBox(0,size,0,size) pad2 = vtk.vtkImageWrapPad() pad2.SetInputConnection(image2.GetOutputPort()) pad2.SetOutputWholeExtent(0,size,0,size,0,10) pad2.Update() checkers = vtk.vtkImageCheckerboard() checkers.SetInput1Data(pad1.GetOutput())
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Make an image larger by repeating the data. Tile.
# Image pipeline
reader = vtk.vtkImageReader()
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0,63,0,63,1,93)
reader.SetDataSpacing(3.2,3.2,1.5)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
pad = vtk.vtkImageWrapPad()
pad.SetInputConnection(reader.GetOutputPort())
pad.SetOutputWholeExtent(-100,155,-100,170,0,92)
pad.ReleaseDataFlagOff()
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(pad.GetOutputPort())
viewer.SetZSlice(22)
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
viewer.GetActor2D().SetDisplayPosition(150,150)
viewer.Render()
# --- end of script --
def read(self, variables, timestep):
#obtain temporal information
rawTimes = self._reader.GetOutputInformation(0).Get(vtk.vtkStreamingDemandDrivenPipeline.TIME_STEPS())
tunits = self._reader.GetTimeUnits()
converters = attrib_to_converters(tunits)
# pick particular timestep
if timestep is not None and rawTimes is not None:
utcconverter = attrib_to_converters("days since 1970-0-0")
abs_request_time = utcconverter[0](float(timestep)/(1000*60*60*24))
local_request_time = converters[5](abs_request_time)
# For now clamp to time range
if float(local_request_time) < rawTimes[0]:
local_request_time = rawTimes[0]
elif float(local_request_time) > rawTimes[-1]:
local_request_time = rawTimes[-1]
sddp = self._reader.GetExecutive()
sddp.SetUpdateTimeStep(0, local_request_time)
# enable only chosen array(s)
narrays = self._reader.GetNumberOfVariableArrays()
for x in range(0,narrays):
arrayname = self._reader.GetVariableArrayName(x)
if arrayname in variables:
#cherrypy.log("Enable " + arrayname)
self._reader.SetVariableArrayStatus(arrayname, 1)
else:
#cherrypy.log("Disable " + arrayname)
self._reader.SetVariableArrayStatus(arrayname, 0)
# wrap around to get the implicit cell
extent = self._reader.GetOutputInformation(0).Get(vtk.vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT())
pad = vtk.vtkImageWrapPad()
self._reader.Update()
data = self._reader.GetOutput()
da = data.GetPointData().GetArray(0).GetName();
data.GetPointData().SetActiveScalars(da)
pad.SetInputData(data)
pad.SetOutputWholeExtent(extent[0], extent[1]+1,
extent[2], extent[3],
extent[4], extent[5]);
# Convert to polydata
sf = vtk.vtkDataSetSurfaceFilter()
sf.SetInputConnection(pad.GetOutputPort())
# Error reading file?
if not sf.GetOutput():
raise IOError("Unable to load data file: " + self.filename)
# Convert to GeoJSON
gw = vtk.vtkGeoJSONWriter()
gw.SetInputConnection(sf.GetOutputPort())
gw.SetScalarFormat(2)
gw.WriteToOutputStringOn()
gw.Write()
gj = str(gw.RegisterAndGetOutputString()).replace('\n','')
return gj
def read(filename, vars, rqstTime):
''' Read a file or files from a directory given a wild-card expression
'''
# @todo Reading a single file of netcdf cf convention now
#cherrypy.log("vtkread " + filename + " " + vars + " " + str(time))
reader = vtk.vtkNetCDFCFReader() #get test data
reader.SphericalCoordinatesOff()
reader.SetOutputTypeToImage()
reader.ReplaceFillValueWithNanOn()
reader.SetFileName(filename)
reader.UpdateInformation()
#obtain temporal information
rawTimes = reader.GetOutputInformation(0).Get(vtk.vtkStreamingDemandDrivenPipeline.TIME_STEPS())
tunits = reader.GetTimeUnits()
converters = attrib_to_converters(tunits)
# pick particular timestep
if rqstTime is not None and rawTimes is not None:
utcconverter = attrib_to_converters("days since 1970-0-0")
abs_request_time = utcconverter[0](float(rqstTime)/(1000*60*60*24))
local_request_time = converters[5](abs_request_time)
# For now clamp to time range
if float(local_request_time) < rawTimes[0]:
local_request_time = rawTimes[0]
elif float(local_request_time) > rawTimes[-1]:
local_request_time = rawTimes[-1]
sddp = reader.GetExecutive()
sddp.SetUpdateTimeStep(0, local_request_time)
# enable only chosen array(s)
narrays = reader.GetNumberOfVariableArrays()
for x in range(0,narrays):
arrayname = reader.GetVariableArrayName(x)
if arrayname in vars:
#cherrypy.log("Enable " + arrayname)
reader.SetVariableArrayStatus(arrayname, 1)
else:
#cherrypy.log("Disable " + arrayname)
reader.SetVariableArrayStatus(arrayname, 0)
# wrap around to get the implicit cell
extent = reader.GetOutputInformation(0).Get(vtk.vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT())
pad = vtk.vtkImageWrapPad()
reader.Update()
data = reader.GetOutput()
da = data.GetPointData().GetArray(0).GetName();
data.GetPointData().SetActiveScalars(da)
pad.SetInputData(data)
pad.SetOutputWholeExtent(extent[0], extent[1]+1,
extent[2], extent[3],
extent[4], extent[5]);
# Convert to polydata
sf = vtk.vtkDataSetSurfaceFilter()
sf.SetInputConnection(pad.GetOutputPort())
# Error reading file?
if not sf.GetOutput():
raise IOError("Unable to load data file: " + filename)
# Convert to GeoJSON
gw = vtk.vtkGeoJSONWriter()
gw.SetInputConnection(sf.GetOutputPort())
gw.SetScalarFormat(2)
gw.WriteToOutputStringOn()
gw.Write()
gj = str(gw.RegisterAndGetOutputString()).replace('\n','')
return gj
def VTKConvolve(im,numret=0,k=5,clip=1,x=1,y=1,wrap=0,mirror=1,constant=None,
kernel=None):
if type(im) == np.ndarray: i = NumToVTKImage(im)
else: i = im
d = i.GetDimensions()
e = i.GetExtent()
dtest = np.sort(d)
if sum(dtest[:2]) == 2: onedim=1
else: onedim = 0
if (d[0] == 1): oned = 1
elif (d[1] == 1): oned = 2
else: oned = 0
if x and not y: oned = 2
if y and not x: oned = 1
if onedim: oned = 1
if constant is not None:
ip = vtk.vtkImageConstantPad()
if d[0] > 1: x0,x1=-k,d[0]+k-1
else: x0,x1=0,0
if d[1] > 1: y0,y1=-k,d[1]+k-1
else: y0,y1=0,0
ip.SetOutputWholeExtent(x0,x1,y0,y1,0,0)
ip.SetConstant(constant)
ip.SetInputData(i)
i = ip.GetOutput()
ip.Update()
elif mirror:
ip = vtk.vtkImageMirrorPad()
if d[0] > 1: x0,x1=-k,d[0]+k-1
else: x0,x1=0,0
if d[1] > 1: y0,y1=-k,d[1]+k-1
else: y0,y1=0,0
ip.SetOutputWholeExtent(x0,x1,y0,y1,0,0)
ip.SetInputData(i)
i = ip.GetOutput()
ip.Update()
elif wrap:
ip = vtk.vtkImageWrapPad()
if d[0] > 1: x0,x1=-k,d[0]+k-1
else: x0,x1=0,0
if d[1] > 1: y0,y1=-k,d[1]+k-1
else: y0,y1=0,0
ip.SetOutputWholeExtent(x0,x1,y0,y1,0,0)
ip.SetInputData(i)
i = ip.GetOutput()
ip.Update()
c = vtk.vtkImageConvolve()
if kernel is None:
if k == 3: k1 = np.asarray([0.25,0.5,0.25])
elif k == 5: k1 = np.asarray([0.0625,0.25,0.375,0.25,0.0625])
if onedim: ke = np.ones((k,k),np.float64) * k1
elif not oned: ke = k1[::,np.newaxis]*k1[np.newaxis,::]
elif oned == 1: ke = np.zeros((k,k),np.float64); ke[::,2] = k1
elif oned == 2: ke = np.zeros((k,k),np.float64); ke[2] = k1
ke = np.ravel(ke)
ke = ke / np.sum(ke)
if onedim: ke = len(k1)*ke
else:
k = kernel.shape[0]
ke = np.ravel(kernel)
if k == 3: c.SetKernel3x3(ke)
if k == 5: c.SetKernel5x5(ke)
if k == 7: c.SetKernel7x7(ke)
c.SetInputData(i)
o = c.GetOutput()
c.Update()
if clip:
ic = vtk.vtkImageClip()
notx = -(not x) * 0
noty = -(not y) * 0
ic.SetOutputWholeExtent(notx,d[0]-1+notx,noty,d[1]-1+noty,0,0)
ic.SetInputData(o)
ic.ClipDataOn()
o = ic.GetOutput()
ic.Update()
if numret: return VTKImageToNum(o)
else: return o
def VTKImageTransform(x,dx,dy,numret=False,reverse=False,origsize=None,
cubic=False,interp=True,scalex=1,scaley=1,constant=0,wrap=False,
mirror=False):
maxdx = max([int(max(abs(dx.ravel()))+1),(dx.shape[1]-x.shape[1])])
maxdy = max([int(max(abs(dy.ravel()))+1),(dx.shape[0]-x.shape[0])])
dx = dx.astype(np.float32)
dy = dy.astype(np.float32)
if scalex > 1:
xx = np.arange(x.shape[1])
dx = (xx[np.newaxis,::]+dx).astype(np.float32)
dy = VTKGrowN(dy,scalex,1,numret=True)
dx = VTKGrowN(dx,scalex,1,numret=True)
dx = (dx-np.arange(scalex*x.shape[1])[np.newaxis,::]).\
astype(np.float32)
if scaley > 1:
yy = np.arange(x.shape[0])
dy = (yy[::,np.newaxis]+dy).astype(np.float32)
dy = VTKGrowN(dy,1,scaley,numret=True)
dx = VTKGrowN(dx,1,scaley,numret=True)
dy = (dy-np.arange(scaley*x.shape[0])[::,np.newaxis]).\
astype(np.float32)
if type(x) == np.ndarray: i = NumToVTKImage(x)
else: i = x
if type(dx) == np.ndarray: tx = NumToVTKImage(dx)
else: tx = dx
if type(dy) == np.ndarray: ty = NumToVTKImage(dy)
else: ty = dy
dm = ty.GetDimensions()
dz = np.zeros(dy.shape,dy.dtype)
tz = NumToVTKImage(dz)
a = vtk.vtkImageAppendComponents()
a.AddInputData(tx)
a.AddInputData(ty)
a.AddInputData(tz)
a.Update()
t = a.GetOutput()
r = vtk.vtkGridTransform()
r.SetDisplacementGridData(t)
r.Update()
s = vtk.vtkImageReslice()
s.WrapOff()
s.MirrorOn()
if interp:
s.InterpolateOn()
if cubic: s.SetInterpolationModeToCubic()
else: s.SetInterpolationModeToLinear()
s.SetOutputDimensionality(2)
if reverse:
r.SetInterpolationModeToLinear()
r.SetInverseTolerance(0.001)
r.SetInverseIterations(1000)
r.DebugOff()
ir = r.GetInverse()
ir.SetInterpolationModeToLinear()
ir.SetInverseTolerance(0.001)
ir.SetInverseIterations(1000)
ir.GlobalWarningDisplayOff()
s.SetResliceTransform(ir)
s.AutoCropOutputOff()
if origsize: s.SetOutputExtent(0,origsize[1]-1,0,origsize[0]-1,0,0)
else: s.SetOutputExtent(0,scalex*dm[0]-1,0,scaley*dm[1]-1,0,0)
else:
r.SetInterpolationModeToCubic()
r.SetInverseTolerance(0.001)
r.SetInverseIterations(1000)
r.GlobalWarningDisplayOff()
s.SetOutputExtent(0,scalex*dm[0]-1,0,scaley*dm[1]-1,0,0)
s.AutoCropOutputOff()
s.SetResliceTransform(r)
if mirror: ip = vtk.vtkImageMirrorPad()
elif wrap: ip = vtk.vtkImageWrapPad()
else: ip = vtk.vtkImageConstantPad(); ip.SetConstant(constant)
ip.SetOutputWholeExtent(0-maxdx,dm[0]-1+maxdx,0-maxdy,dm[1]-1+maxdy,0,0)
ip.SetInputData(i)
ip.Update()
s.SetInputData(ip.GetOutput())
o=s.GetOutput()
s.Update()
if numret: ri = VTKImageToNum(o)
else: ri = o
return ri
def main():
colors = vtk.vtkNamedColors()
file_name, start_label, end_label = get_program_parameters()
if start_label > end_label:
end_label, start_label = start_label, end_label
# Generate cubes from labels
# 1) Read the meta file
# 2) Convert point data to cell data
# 3) Convert to geometry and display
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_name)
reader.Update()
# Pad the volume so that we can change the point data into cell
# data.
extent = reader.GetOutput().GetExtent()
pad = vtk.vtkImageWrapPad()
pad.SetInputConnection(reader.GetOutputPort())
pad.SetOutputWholeExtent(extent[0], extent[1] + 1, extent[2], extent[3] + 1, extent[4], extent[5] + 1)
pad.Update()
# Copy the scalar point data of the volume into the scalar cell data
pad.GetOutput().GetCellData().SetScalars(reader.GetOutput().GetPointData().GetScalars())
selector = vtk.vtkThreshold()
selector.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_CELLS,
vtk.vtkDataSetAttributes().SCALARS)
selector.SetInputConnection(pad.GetOutputPort())
selector.ThresholdBetween(start_label, end_label)
selector.Update()
# Shift the geometry by 1/2
transform = vtk.vtkTransform()
transform.Translate(-0.5, -0.5, -0.5)
transform_model = vtk.vtkTransformFilter()
transform_model.SetTransform(transform)
transform_model.SetInputConnection(selector.GetOutputPort())
geometry = vtk.vtkGeometryFilter()
geometry.SetInputConnection(transform_model.GetOutputPort())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(geometry.GetOutputPort())
mapper.SetScalarRange(start_label, end_label)
mapper.SetScalarModeToUseCellData()
mapper.SetColorModeToMapScalars()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
renderer = vtk.vtkRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window.SetSize(640, 480)
render_window.SetWindowName('GenerateCubesFromLabels')
render_window_interactor = vtk.vtkRenderWindowInteractor()
render_window_interactor.SetRenderWindow(render_window)
renderer.AddActor(actor)
renderer.SetBackground(colors.GetColor3d('DarkSlateBlue'))
render_window.Render()
camera = renderer.GetActiveCamera()
camera.SetPosition(42.301174, 939.893457, -124.005030)
camera.SetFocalPoint(224.697134, 221.301653, 146.823706)
camera.SetViewUp(0.262286, -0.281321, -0.923073)
camera.SetDistance(789.297581)
camera.SetClippingRange(168.744328, 1509.660206)
render_window_interactor.Start()
