def getRAWReader(self, Series_Info, Channel):
"""
create a tiff reader that reads then given channel of the given series
"""
XYDim = Series_Info['Resolution_X'] - 1
NumSect = Series_Info['Number_Sections'] - 1
XSpace = Series_Info['Voxel_Width_X']
YSpace = Series_Info['Voxel_Height_Y']
ZSpace = Series_Info['Voxel_Depth_Z']
RAWReader = vtk.vtkImageReader2()
if self.progressCallback:
RAWReader.AddObserver("ProgressEvent", lib.messenger.send)
lib.messenger.connect(RAWReader, 'ProgressEvent', self.progressCallback)
arr = vtk.vtkStringArray()
for i in Channel:
arr.InsertNextValue(os.path.join(self.path, i))
RAWReader.SetFileNames(arr)
if Series_Info['Bit_Depth'] == 8:
RAWReader.SetDataScalarTypeToUnsignedChar()
elif Series_Info['Bit_Depth'] == 12:
RAWReader.SetDataScalarTypeToUnsignedShort()
RAWReader.FileLowerLeftOff()
spacingX,spacingY,spacingZ = 1.0,1.0,1.0
if XSpace != 0.0 and YSpace != 0.0:
spacingY = YSpace / XSpace
if XSpace != 0.0 and ZSpace != 0.0:
spacingZ = ZSpace / XSpace
RAWReader.SetDataExtent(0, XYDim, 0, XYDim, 0, NumSect)
RAWReader.SetDataSpacing(spacingX, spacingY, spacingZ)
RAWReader.Update()
return RAWReader
def getTimepoint(self, n, onlyDims = 0):
"""
Return the nth timepoint
"""
if not self.reader:
self.reader = vtk.vtkImageReader2()
self.reader.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(self.reader, 'ProgressEvent', self.updateProgress)
eval("self.reader.SetDataScalarTypeTo%s()" % self.datatype)
x, y, z = self.dimensions
if z == 0:
z += 1
self.reader.SetDataExtent(0, x - 1, 0, y - 1, 0, z - 1)
self.reader.SetFileDimensionality(3)
self.reader.SetDataSpacing(self.spacing)
eval("self.reader.SetDataByteOrderTo%s()" % self.endianness)
#if self.tps == 1:
# self.reader.SetFileName(self.imgfile)
#else:
# print "Switching to dataset ", self.filepattern % (n + 1)
# self.reader.SetFileName(self.filepattern % (n + 1))
self.reader.SetFileName(self.dataFileName)
skip = n
for i in self.dimensions:
skip *= i
skip *= self.bytesPerPixel
self.reader.SetHeaderSize(skip)
self.reader.Update()
print self.reader.GetOutput()
return self.reader.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageReader2(),
'Processing.', (),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def get_image_data():
reader = vtk.vtkImageReader2()
reader.SetDataScalarTypeToUnsignedShort()
reader.SetFileDimensionality(2)
reader.SetFilePrefix("data/slice")
reader.SetDataExtent(0, 255, 0, 255, 1, 94)
reader.SetDataSpacing(1, 1, 2)
reader.UpdateWholeExtent()
return reader.GetOutput()
def main(argv):
colors = vtk.vtkNamedColors()
# Parse input arguments
if len(argv) != 3:
print("Usage: %s Input1Filename Input2Filename e.g. Ox.jpg Gourds2.jpg" % (argv[0]))
return
# Read the images
readerFactory = vtk.vtkImageReader2Factory()
imgReader1 = vtk.vtkImageReader2()
imgReader1 = readerFactory.CreateImageReader2(argv[1])
imgReader1.SetFileName(argv[1])
imgReader2 = vtk.vtkImageReader2()
# imgReader2.TakeReference(readerFactory.CreateImageReader2(argv[2]))
imgReader2 = readerFactory.CreateImageReader2(argv[2])
imgReader2.SetFileName(argv[2])
# Combine the images (blend takes multiple connections on the 0th input port)
blend = vtk.vtkImageBlend()
blend.AddInputConnection(imgReader1.GetOutputPort())
blend.AddInputConnection(imgReader2.GetOutputPort())
blend.SetOpacity(0, 0.5)
blend.SetOpacity(1, 0.5)
# Display the result
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
imageViewer = vtk.vtkImageViewer2()
imageViewer.SetInputConnection(blend.GetOutputPort())
imageViewer.SetupInteractor(renderWindowInteractor)
imageViewer.GetRenderer().ResetCamera()
imageViewer.GetRenderer().SetBackground(colors.GetColor3d("Peru"))
imageViewer.GetRenderWindow().SetWindowName("CombineImages")
imageViewer.GetRenderer().Render()
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
return 0
def get_image_data():
""" Reads the image data using the class vtkImageReader2. Returns
the result of the GetOutput() function call."""
reader = vtk.vtkImageReader2()
reader.SetDataScalarTypeToUnsignedShort()
reader.SetFileDimensionality(2)
reader.SetFilePrefix("data/slice")
reader.SetDataExtent(0, 255, 0, 255, 1, 94)
reader.SetDataSpacing(1, 1, 2)
#reader.SetDataByteOrderToBigEndian()
reader.SetNumberOfScalarComponents( 1 )
reader.UpdateWholeExtent()
return reader.GetOutput()
import vtk from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() # --------------------------------------------------------- # renderer and interactor ren = vtk.vtkRenderer() renWin = vtk.vtkRenderWindow() renWin.AddRenderer(ren) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(renWin) # --------------------------------------------------------- # read the volume reader = vtk.vtkImageReader2() reader.SetDataExtent(0, 63, 0, 63, 0, 92) reader.SetFileNameSliceOffset(1) reader.SetDataScalarTypeToUnsignedShort() reader.SetDataByteOrderToLittleEndian() reader.SetFilePrefix(str(VTK_DATA_ROOT) + "/Data/headsq/quarter") reader.SetDataSpacing(3.2, 3.2, 1.5) # --------------------------------------------------------- # set up the volume rendering volumeMapper = vtk.vtkVolumeTextureMapper3D() volumeMapper.SetInputConnection(reader.GetOutputPort()) volumeMapper.CroppingOn() volumeMapper.SetCroppingRegionPlanes((0.0, 141.6, 0.0, 201.6, 0.0, 138.0)) volumeColor = vtk.vtkColorTransferFunction()
def onButtonUpdate(self, evt):
try:
first = int(self.m_spinCtrlFirstNum.GetValue())
last = int(self.m_spinCtrlLastNum.GetValue())
except:
first = last = 0
fspec = self.m_filePicker.GetPath()
if self.m_check3DImage.IsChecked():
l = 0
fileName = fspec
else:
p0 = fspec.find('#')
p1 = fspec.rfind('#')
if p0 != -1:
l = p1 - p0 + 1
filePrefix = fspec[0:p0]
filePattern = '%%s%%0%dd' % (l) + fspec[p1 + 1:]
# This is the slice that we'll try to read
middle = int((first + last) / 2.0)
z0 = z1 = (middle - first)
fileName = (filePrefix + filePattern) % ('', middle)
else:
l = 0
fileName = fspec
if self.bIsDICOM:
# TODO: we're sorting this data in more than one place it seems...
indices = np.argsort(
np.array([float(f) for f in self._slice_locations]))
# choose a card from the middle of the deck
fileName = self._file_list[indices[len(indices) / 2]]
xspacing = float(self.m_textCtrlXSpacing.GetValue())
yspacing = float(self.m_textCtrlYSpacing.GetValue())
zspacing = float(self.m_textCtrlZSpacing.GetValue())
xsize = int(self.m_textCtrlXSize.GetValue())
ysize = int(self.m_textCtrlYSize.GetValue())
zsize = int(self.m_textCtrlZSize.GetValue())
header_size = int(self.m_textCtrlHeaderSize.GetValue())
numC = int(self.m_textCtrlNumberChannels.GetValue())
# this isn't quite correct, but will do for now...
swap_bytes = (
self.m_choiceDataEndian.GetStringSelection() == 'big endian')
if self.m_checkRawImage.IsChecked():
reader = vtk.vtkImageReader2()
reader.FileLowerLeftOn()
reader.SetSwapBytes(swap_bytes)
reader.SetHeaderSize(header_size)
reader.SetDataSpacing(xspacing, yspacing, zspacing)
reader.SetNumberOfScalarComponents(numC)
dt = self.m_choiceDataType.GetStringSelection()
if dt == 'unsigned char':
reader.SetDataScalarTypeToUnsignedChar()
elif dt == 'unsigned short':
reader.SetDataScalarTypeToUnsignedShort()
elif dt == 'short':
reader.SetDataScalarTypeToShort()
elif dt == 'int':
reader.SetDataScalarTypeToInt()
elif dt == 'float':
reader.SetDataScalarTypeToFloat()
elif dt == 'double':
reader.SetDataScalarTypeToDouble()
else:
reader = self._reader
reader.SetFileName(fileName)
if self.m_check3DImage.IsChecked():
z0 = z1 = int(zsize / 2)
reader.SetFileDimensionality(3)
else:
reader.SetFileDimensionality(2)
z0 = z1 = 0
# if image is either a 3D image or using raw importer, we need to explicitly set
# data extent
if self.m_check3DImage.IsChecked() or self.m_checkRawImage.IsChecked():
reader.SetDataExtent(0, xsize - 1, 0, ysize - 1, z0, z1)
w, h = self.m_bitmapPreview.GetSize()
try:
# update reader rather than image (for VTK-6 compatibility)
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
reader.Update()
else:
reader.GetOutput().Update()
image = reader.GetOutput()
flip = self.m_checkBoxFlipImage.GetValue()
wxBitmap = MicroViewIO.VTKImageToBitmap(image, w, h, flip=flip)
except:
w, h = self.m_bitmapPreview.GetSize()
wxBitmap = wx.EmptyBitmap(w, h)
logging.error("ImageImportDialog")
# paste into GUI
self.m_bitmapPreview.SetBitmap(wxBitmap)
def loadNRRDImage(filename):
import imagingTools
inFile = open(filename, 'r')
tag = inFile.readline()
if tag[0:8] != 'NRRD0004':
print "bad format!"
sys.exit()
line = inFile.readline().split()
while line[0] != 'type:':
line = inFile.readline().split()
coding = line[1]
print "coding", coding
while line[0] != 'dimension:':
line = inFile.readline().split()
dimensionality = int(line[1])
print "dimensionality", dimensionality
while line[0] != 'space:':
line = inFile.readline().split()
space = line[1]
print "space", space
while line[0] != 'sizes:':
line = inFile.readline().split()
dimensions = (int(line[1]), int(line[2]), int(line[3]))
print "dimensions", dimensions
while line[0] != 'space':
line = inFile.readline().split()
directionX = line[2]
directionY = line[3]
directionZ = line[4]
directionX = directionX[1:(len(directionX)) - 1].rsplit(',', 3)
directionY = directionY[1:(len(directionY)) - 1].rsplit(',', 3)
directionZ = directionZ[1:(len(directionZ)) - 1].rsplit(',', 3)
spacing = [0, 0, 0]
ordering = []
for i in range(3):
if directionX[i] != '0':
spacing[0] = float(directionX[i])
ordering.append(0)
elif directionY[i] != '0':
spacing[1] = float(directionY[i])
ordering.append(1)
else:
spacing[2] = float(directionZ[i])
ordering.append(2)
for i in range(3):
if spacing[i] < 0:
spacing[i] = -spacing[i]
print "spacing", spacing
while line[0] != 'endian:':
line = inFile.readline().split()
byteorder = line[1]
print "byteorder", byteorder
while line[0] != 'space':
line = inFile.readline().split()
originStr = line[2]
originSpl = originStr[1:(len(originStr)) - 1].rsplit(',', 3)
origin = [float(originSpl[0]), float(originSpl[1]), float(originSpl[2])]
print "origin", origin
print "ordering", ordering
if (space == "left-posterior-superior") or (space == "LPS"):
origin[1] = -origin[1]
reader = vtk.vtkImageReader2()
reader.SetDataExtent(
(0, dimensions[0] - 1, 0, dimensions[1] - 1, 0, dimensions[2] - 1))
# reader.SetDataDimensions(dimensions)
reader.SetDataOrigin(origin)
reader.SetDataSpacing([spacing[0], spacing[1], spacing[2]])
reader.SetFileDimensionality(dimensionality)
filenameSp = filename.rsplit(
'.', 2) # pas d'espaces ni de point dans le num du fichier!
if filenameSp[1] == "nhdr":
reader.SetFileName(filenameSp[0] + '.raw')
else:
reader.SetFileName(filename)
if byteorder == 'little':
reader.SetDataByteOrderToLittleEndian()
else:
reader.SetDataByteOrderToBigEndian()
if coding == 'uchar':
reader.SetDataScalarTypeToUnsignedChar()
elif coding == 'char':
reader.SetDataScalarTypeToUnsignedChar()
elif coding == 'ushort':
reader.SetDataScalarTypeToUnsignedShort()
elif coding == 'short':
reader.SetDataScalarTypeToUnsignedShort()
elif coding == 'float':
reader.SetDataScalarTypeToFloat()
else:
reader.SetDataScalarTypeToDouble()
reader.Update()
im = reader.GetOutput()
# if (space == "left-posterior-superior") or (space == "LPS"):
# im = imagingTools.permute(im,0,2,1)
# im = imagingTools.flipImage(im,2)
# #im = imagingTools.flipImage(im,0)
# im = imagingTools.flipImage(im,1)
return im
#!/usr/bin/env python
# This example shows how to load a 3D image into VTK and then reformat
# that image into a different orientation for viewing. It uses
# vtkImageReslice for reformatting the image, and uses vtkImageActor
# and vtkInteractorStyleImage to display the image. This InteractorStyle
# forces the camera to stay perpendicular to the XY plane.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Start by loading some data.
reader = vtk.vtkImageReader2()
reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetDataSpacing(3.2, 3.2, 1.5)
reader.SetDataOrigin(0.0, 0.0, 0.0)
reader.SetDataScalarTypeToUnsignedShort()
reader.UpdateWholeExtent()
# Calculate the center of the volume
reader.Update()
(xMin, xMax, yMin, yMax, zMin,
zMax) = reader.GetExecutive().GetWholeExtent(reader.GetOutputInformation(0))
(xSpacing, ySpacing, zSpacing) = reader.GetOutput().GetSpacing()
(x0, y0, z0) = reader.GetOutput().GetOrigin()
center = [
x0 + xSpacing * 0.5 * (xMin + xMax), y0 + ySpacing * 0.5 * (yMin + yMax),
z0 + zSpacing * 0.5 * (zMin + zMax)
def newImage(self):
# If a new image is selected then we create an independent reader
# (to prevent overwriting previous volumes with updateImage).
# We do not create a new reader on each updateImage to improve performence
# (avoid reallocation of the image).
self.reader = vtk.vtkImageReader2()
def __init__(self):
self.reader = vtk.vtkImageReader2()
def load(self, properties):
try:
filePath = properties['fileName']
headerInfo = ImportSliceOmaticFileReader.readHeader(filePath)
scalarType = vtk.VTK_CHAR
numberOfComponents = 1
sliceSize = headerInfo['dims'][0] * headerInfo['dims'][
1] * vtk.vtkDataArray.GetDataTypeSize(
scalarType) * numberOfComponents
headerSize = headerInfo['headerSize']
totalFilesize = os.path.getsize(filePath)
voxelDataSize = totalFilesize - headerSize
maxNumberOfSlices = int(voxelDataSize / sliceSize)
if headerInfo['dims'][2] > maxNumberOfSlices:
logging.error(
f"Tag file is expected to contain {headerInfo['dims'][2]} slices but it has only {maxNumberOfSlices}"
)
return False
reader = vtk.vtkImageReader2()
reader.SetFileName(filePath)
reader.SetFileDimensionality(3)
reader.SetDataExtent(0, headerInfo['dims'][0] - 1, 0,
headerInfo['dims'][1] - 1, 0,
headerInfo['dims'][2] - 1)
# reader.SetDataByteOrderToLittleEndian()
reader.SetDataScalarType(scalarType)
reader.SetNumberOfScalarComponents(numberOfComponents)
reader.SetHeaderSize(headerSize)
reader.SetFileLowerLeft(True) # to match input from NRRD reader
reader.Update()
tempLabelmapNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode', "__temp_SliceOmatic__")
tempLabelmapNode.SetImageDataConnection(reader.GetOutputPort())
# We assume file is in LPS and invert first and second axes
# to get volume in RAS.
import numpy as np
axisX = headerInfo['axisX']
axisY = headerInfo['axisY']
axisZ = np.cross(axisX, axisY)
spacing = headerInfo['spacing']
origin = headerInfo['origin']
ijkToLps = np.eye(4)
for row in range(3):
ijkToLps[row, 0] = axisX[row] * spacing[0]
ijkToLps[row, 1] = axisY[row] * spacing[1]
ijkToLps[row, 2] = axisZ[row] * spacing[2]
ijkToLps[row, 3] = origin[row]
lpsToRas = np.diag([-1.0, -1.0, 1.0, 1.0])
ijkToRas = np.dot(lpsToRas, ijkToLps)
ijkToRasVtk = slicer.util.vtkMatrixFromArray(ijkToRas)
tempLabelmapNode.SetIJKToRASMatrix(ijkToRasVtk)
tempLabelmapNode.Modified()
# Get node base name from filename
if 'name' in properties.keys():
baseName = properties['name']
else:
baseName = os.path.splitext(os.path.basename(filePath))[0]
baseName = slicer.mrmlScene.GenerateUniqueName(baseName)
loadedSegmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode', baseName)
slicer.modules.segmentations.logic(
).ImportLabelmapToSegmentationNode(tempLabelmapNode,
loadedSegmentationNode)
slicer.mrmlScene.RemoveNode(tempLabelmapNode)
except Exception as e:
logging.error('Failed to load file: ' + str(e))
import traceback
traceback.print_exc()
return False
self.parent.loadedNodes = [loadedSegmentationNode.GetID()]
return True
def onButtonUpdate(self, evt):
try:
first = int(self.m_spinCtrlFirstNum.GetValue())
last = int(self.m_spinCtrlLastNum.GetValue())
except:
first = last = 0
fspec = self.m_filePicker.GetPath()
if self.m_check3DImage.IsChecked():
l = 0
fileName = fspec
else:
p0 = fspec.find('#')
p1 = fspec.rfind('#')
if p0 != -1:
l = p1 - p0 + 1
filePrefix = fspec[0:p0]
filePattern = '%%s%%0%dd' % (l) + fspec[p1 + 1:]
# This is the slice that we'll try to read
middle = int((first + last) / 2.0)
z0 = z1 = (middle - first)
fileName = (filePrefix + filePattern) % ('', middle)
else:
l = 0
fileName = fspec
if self.bIsDICOM:
# TODO: we're sorting this data in more than one place it seems...
indices = np.argsort(
np.array([float(f) for f in self._slice_locations]))
# choose a card from the middle of the deck
fileName = self._file_list[indices[len(indices) / 2]]
xspacing = float(self.m_textCtrlXSpacing.GetValue())
yspacing = float(self.m_textCtrlYSpacing.GetValue())
zspacing = float(self.m_textCtrlZSpacing.GetValue())
xsize = int(self.m_textCtrlXSize.GetValue())
ysize = int(self.m_textCtrlYSize.GetValue())
zsize = int(self.m_textCtrlZSize.GetValue())
header_size = int(self.m_textCtrlHeaderSize.GetValue())
numC = int(self.m_textCtrlNumberChannels.GetValue())
# this isn't quite correct, but will do for now...
swap_bytes = (
self.m_choiceDataEndian.GetStringSelection() == 'big endian')
if self.m_checkRawImage.IsChecked():
reader = vtk.vtkImageReader2()
reader.FileLowerLeftOn()
reader.SetSwapBytes(swap_bytes)
reader.SetHeaderSize(header_size)
reader.SetDataSpacing(xspacing, yspacing, zspacing)
reader.SetNumberOfScalarComponents(numC)
dt = self.m_choiceDataType.GetStringSelection()
if dt == 'unsigned char':
reader.SetDataScalarTypeToUnsignedChar()
elif dt == 'unsigned short':
reader.SetDataScalarTypeToUnsignedShort()
elif dt == 'short':
reader.SetDataScalarTypeToShort()
elif dt == 'int':
reader.SetDataScalarTypeToInt()
elif dt == 'float':
reader.SetDataScalarTypeToFloat()
elif dt == 'double':
reader.SetDataScalarTypeToDouble()
else:
reader = self._reader
reader.SetFileName(fileName)
if self.m_check3DImage.IsChecked():
z0 = z1 = int(zsize / 2)
reader.SetFileDimensionality(3)
else:
reader.SetFileDimensionality(2)
z0 = z1 = 0
# if image is either a 3D image or using raw importer, we need to explicitly set
# data extent
if self.m_check3DImage.IsChecked() or self.m_checkRawImage.IsChecked():
reader.SetDataExtent(0, xsize - 1, 0, ysize - 1, z0, z1)
w, h = self.m_bitmapPreview.GetSize()
try:
# update reader rather than image (for VTK-6 compatibility)
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
reader.Update()
else:
reader.GetOutput().Update()
image = reader.GetOutput()
flip = self.m_checkBoxFlipImage.GetValue()
wxBitmap = MicroViewIO.VTKImageToBitmap(image, w, h, flip=flip)
except:
w, h = self.m_bitmapPreview.GetSize()
wxBitmap = wx.EmptyBitmap(w, h)
logging.error("ImageImportDialog")
# paste into GUI
self.m_bitmapPreview.SetBitmap(wxBitmap)