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layerView.py
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layerView.py
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'''
Created on Dec 6, 2015
@author: root
'''
from PyQt4 import QtGui
from PyQt4 import Qt
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
import vtk
import sys
import gzip
import cPickle as pickle
import numpy
from matplotlib.cbook import Null
class layerView(QtGui.QWidget):
'''
classdocs
'''
def __init__(self, fileName):
super(layerView, self).__init__()
self.initUI()
self.fname = fileName
def initUI(self):
self.frame = QtGui.QFrame()
self.widgetLayout = QtGui.QVBoxLayout()
self.setLayout(self.widgetLayout)
self.widgetLayout.addWidget(self.frame)
self.frameLayout = QtGui.QVBoxLayout()
self.frame.setLayout(self.frameLayout)
self.vtkWidget = QVTKRenderWindowInteractor(self.frame)
self.frameLayout.addWidget(self.vtkWidget)
self.sliceNumber = QtGui.QLineEdit("50")
self.sliceConfirm = QtGui.QPushButton("confirm")
self.sliceConfirm.clicked.connect(self.showLayer)
self.sliceButtonLayout = QtGui.QHBoxLayout()
self.sliceButtonLayout.addWidget(self.sliceNumber)
self.sliceButtonLayout.addWidget(self.sliceConfirm)
self.frameLayout.addLayout(self.sliceButtonLayout)
self.volume = vtk.vtkVolume()
self.ren = vtk.vtkRenderer()
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
self.show()
self.iren.Initialize()
self.setGeometry(300, 300, 300, 150)
self.setWindowTitle('Layer View')
self.show()
def showLayer(self):
if self.volume != Null:
self.ren.RemoveVolume(self.volume)
sliceNumber = self.sliceNumber.text()
sliceIntArray = sliceNumber.toUInt()
sliceInt = sliceIntArray[0]
print "cool, it is done"
fr=gzip.open(self.fname[:-3]+"voxr","rb")
dataRed=pickle.load(fr)
self.data_matrix_red=numpy.uint8(dataRed)
self.data_matrix_red=self.data_matrix_red[sliceInt-1:sliceInt+1,:,:]
with file('layerView.txt', 'w') as outfile:
for data_slice in self.data_matrix_red:
# The formatting string indicates that I'm writing out
# the values in left-justified columns 7 characters in width
# with 2 decimal places.
numpy.savetxt(outfile, data_slice,fmt='%-7.1f')
# Writing out a break to indicate different slices...
outfile.write('# New slice\n')
self.dataImporterR = vtk.vtkImageImport()
data_string = self.data_matrix_red.tostring()
self.dataImporterR.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterR.SetDataScalarTypeToUnsignedChar()
self.dataImporterR.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_red.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterR.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterR.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
fg=gzip.open(self.fname[:-3]+"voxg","rb")
dataGreen=pickle.load(fg)
self.data_matrix_green=numpy.uint8(dataGreen)
self.data_matrix_green = self.data_matrix_green[sliceInt-1:sliceInt+1,:,:]
self.dataImporterG = vtk.vtkImageImport()
data_string = self.data_matrix_green.tostring()
self.dataImporterG.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterG.SetDataScalarTypeToUnsignedChar()
self.dataImporterG.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_green.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterG.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterG.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
fb=gzip.open(self.fname[:-3]+"voxb","rb")
dataBlue=pickle.load(fb)
self.data_matrix_blue=numpy.uint8(dataBlue)
self.data_matrix_blue = self.data_matrix_blue[sliceInt-1:sliceInt+1,:,:]
self.dataImporterB = vtk.vtkImageImport()
data_string = self.data_matrix_blue.tostring()
self.dataImporterB.CopyImportVoidPointer(data_string, len(data_string))
self.dataImporterB.SetDataScalarTypeToUnsignedChar()
self.dataImporterB.SetNumberOfScalarComponents(1)
xdim,ydim,zdim=self.data_matrix_blue.shape
#self.dataImporter.SetDataExtent(0, zdim-1, 0, vtkPiecewiseFunctionb-1, 0, xdim-1)
self.dataImporterB.SetDataExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
#self.dataImporter.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.dataImporterB.SetWholeExtent(0, zdim-1, 0, ydim-1, 0, xdim-1)
self.append = vtk.vtkImageAppendComponents()
self.append.SetInputConnection(self.dataImporterR.GetOutputPort())
self.append.AddInputConnection(self.dataImporterG.GetOutputPort())
self.append.AddInputConnection(self.dataImporterB.GetOutputPort())
self.append.Update()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputConnection(self.append.GetOutputPort())
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.ShadeOff()
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.IndependentComponentsOn()
opacityTF1 = vtk.vtkPiecewiseFunction()
opacityTF1.AddPoint( 0.0, 0.0 )
opacityTF1.AddPoint( 1.0, 0.33)
opacityTF1.AddPoint( 128.0, 0.33)
opacityTF1.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(0,opacityTF1)
colourTF1 = vtk.vtkColorTransferFunction()
colourTF1.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF1.AddRGBPoint( 1.0, 0.0, 0.0, 0.1 )
colourTF1.AddRGBPoint( 128.0, 0.0, 0.0, 0.5 )
colourTF1.AddRGBPoint( 255.0, 0.0, 0.0, 1.0 )
volumeProperty.SetColor(0,colourTF1)
opacityTF2 = vtk.vtkPiecewiseFunction()
opacityTF2.AddPoint( 0.0, 0.0 )
opacityTF2.AddPoint( 1.0, 0.33 )
opacityTF2.AddPoint( 128.0, 0.33)
opacityTF2.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(1,opacityTF2)
colourTF2 = vtk.vtkColorTransferFunction()
colourTF2.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF2.AddRGBPoint( 1.0, 0.0, 0.1, 0.0 )
colourTF2.AddRGBPoint( 128.0, 0.0, 0.5, 0.0 )
colourTF2.AddRGBPoint( 255.0, 0.0, 1.0, 0.0 )
volumeProperty.SetColor(1,colourTF2)
opacityTF3 = vtk.vtkPiecewiseFunction()
opacityTF3.AddPoint( 0.0, 0.0 )
opacityTF3.AddPoint( 1.0, 0.33 )
opacityTF3.AddPoint( 128.0, 0.33)
opacityTF3.AddPoint( 255.0, 0.33 )
volumeProperty.SetScalarOpacity(2,opacityTF3)
colourTF3 = vtk.vtkColorTransferFunction()
colourTF3.AddRGBPoint( 0.0, 0.0, 0.0, 0.0 )
colourTF3.AddRGBPoint( 1.0, 0.1, 0.0, 0.0 )
colourTF3.AddRGBPoint( 128.0, 0.5, 0.0, 0.0 )
colourTF3.AddRGBPoint( 255.0, 1.0, 0.0, 0.0 )
volumeProperty.SetColor(2,colourTF3)
self.volume.SetMapper(volumeMapper)
self.volume.SetProperty(volumeProperty)
#self.ren.RemoveActor(self.actor)
self.ren.AddVolume(self.volume)
self.ren.SetBackground(0, 0, 0)
# A simple function to be called when the user decides to quit the application.
def exitCheck(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
# Tell the application to use the function as an exit check.
light = vtk.vtkLight()
#light.SetColor(1, 1, 1)
light.SwitchOff()
self.ren.AddLight(light)
renderWin = self.vtkWidget.GetRenderWindow()
renderWin.AddObserver("AbortCheckEvent", exitCheck)
self.iren.Initialize()
self.iren.Start()
if __name__ == "__main__":
#import sys;sys.argv = ['', 'Test.testName']
cube = numpy.ones((50,50,50))
#layerView = layerView(self.fname)