def setUp(self):
"""Set up the testing environment"""
self.module = Module.Module()
self.dataunit = lib.DataUnit.CombinedDataUnit()
self.ch1rdr = vtk.vtkLSMReader()
self.ch2rdr = vtk.vtkLSMReader()
self.ch1rdr.SetFileName("/Users/kallepahajoki/BioImageXD/Data/sample1_series12.lsm")
self.ch2rdr.SetFileName("/Users/kallepahajoki/BioImageXD/Data/sample1_single.lsm")
def __init__(self, fileName=None, channel=0, ImageType=None):
from vtk import vtkLSMReader, vtkImageCast
import itk
itk.pipeline.__init__(self)
# if ImageType is None, give it a default value
# this is useful to avoid loading Base while loading this module
if ImageType == None:
ImageType = itk.Image.UC3
# remove useless SetInput() method created by the constructor of the pipeline class
# del self.SetInput
# set up the pipeline
self.connect(vtkLSMReader())
self.connect(vtkImageCast())
PType = itk.template(ImageType)[1][0]
if PType == itk.UC:
self[-1].SetOutputScalarTypeToUnsignedChar()
elif PType == itk.US:
self[-1].SetOutputScalarTypeToUnsignedShort()
self.connect(itk.VTKImageToImageFilter[ImageType].New())
self.connect(itk.ChangeInformationImageFilter[ImageType].New(
ChangeSpacing=True))
# and configure the pipeline
if fileName:
self.SetFileName(fileName)
self.SetChannel(channel)
def getChannel(datafile, chn):
datafile = os.path.join(DATA_PATH, datafile)
chrdr = vtk.vtkLSMReader()
chrdr.SetFileName(datafile)
chrdr.SetUpdateChannel(chn)
chrdr.Update()
ch = chrdr.GetOutput()
return ch
def getChannel(datafile, chn): datafile = os.path.join(DATA_PATH, datafile) chrdr = vtk.vtkLSMReader() chrdr.SetFileName(datafile) chrdr.SetUpdateChannel(chn) chrdr.Update() ch = chrdr.GetOutput() return ch
def __init__(self, fileName=None, channel=0, ImageType=None ):
from vtk import vtkLSMReader, vtkImageCast
import itk
itk.pipeline.__init__(self)
# if ImageType is None, give it a default value
# this is useful to avoid loading Base while loading this module
if ImageType == None:
ImageType = itk.Image.UC3
# remove useless SetInput() method created by the constructor of the pipeline class
# del self.SetInput
# set up the pipeline
self.connect( vtkLSMReader() )
self.connect( vtkImageCast() )
PType = itk.template(ImageType)[1][0]
if PType == itk.UC:
self.filters[-1].SetOutputScalarTypeToUnsignedChar()
elif PType == itk.US:
self.filters[-1].SetOutputScalarTypeToUnsignedShort()
self.connect( itk.VTKImageToImageFilter[ImageType].New() )
self.connect( itk.ChangeInformationImageFilter[ImageType].New( ChangeSpacing=True ) )
# and configure the pipeline
if fileName:
self.SetFileName( fileName )
self.SetChannel( channel )
import sys
sys.path.insert(0,"H:\\vtkBXD\\bin")
sys.path.insert(0,"..\\vtkBXD\\Wrapping\\Python")
#import vtkbxd
#D="/Users/dan/Documents/volumerender/colocsample/colocsample1b.lsm"
D="H:\\Data\\LSM\\Selli_noise2.lsm"
#D="H:\\Data\\LSM\\sample1_series12.lsm"
t=time.time()
def elapsed():
global t
return "(%.2fs elapsed)"%(time.time()-t)
r1=vtk.vtkLSMReader()
r1.SetFileName(D)
r1.SetUpdateChannel(0)
d1=r1.GetOutput()
r2=vtk.vtkLSMReader()
r2.SetFileName(D)
r2.SetUpdateChannel(1)
d2=r2.GetOutput()
print "Reading data"
ctf1=vtk.vtkColorTransferFunction()
ctf1.AddRGBPoint(0,0,0,0)
ctf1.AddRGBPoint(255.0,0,1.0,0)
#! /usr/bin/env python
import vtk
r = vtk.vtkLSMReader()
r.SetFileName("/media/sda12/Data/sample2.lsm")
r.Update()
print r.GetOutput()
#! /usr/bin/env python
import vtk
import sys
sys.path.insert(0,"../lib")
sys.path.insert(0,"..")
import ImageOperations
reader=vtk.vtkLSMReader()
reader.SetFileName("/home/kalpaha/BioImageXD/Data/sample2.lsm")
reader.SetUpdateChannel(0)
reader.SetUpdateTimePoint(5)
reader.Update()
ch1=reader.GetOutput()
reader2=vtk.vtkLSMReader()
reader2.SetFileName("/home/kalpaha/BioImageXD/Data/sample2.lsm")
reader2.SetUpdateChannel(1)
reader2.SetUpdateTimePoint(5)
reader2.Update()
ch2=reader2.GetOutput()
#w1=vtk.vtkXMLImageDataWriter()
#w1.SetFileName("Ch1.vti")
#w1.SetInput(ch1)
#w1.Write()
#w2=vtk.vtkXMLImageDataWriter()
#w2.SetFileName("Ch2.vti")
#w2.SetInput(ch2)
#w2.Write()
sys.path.insert(0, "..\\vtkBXD\\Wrapping\\Python")
#import vtkbxd
#D="/Users/dan/Documents/volumerender/colocsample/colocsample1b.lsm"
D = "H:\\Data\\LSM\\Selli_noise2.lsm"
#D="H:\\Data\\LSM\\sample1_series12.lsm"
t = time.time()
def elapsed():
global t
return "(%.2fs elapsed)" % (time.time() - t)
r1 = vtk.vtkLSMReader()
r1.SetFileName(D)
r1.SetUpdateChannel(0)
d1 = r1.GetOutput()
r2 = vtk.vtkLSMReader()
r2.SetFileName(D)
r2.SetUpdateChannel(1)
d2 = r2.GetOutput()
print "Reading data"
ctf1 = vtk.vtkColorTransferFunction()
ctf1.AddRGBPoint(0, 0, 0, 0)
ctf1.AddRGBPoint(255.0, 0, 1.0, 0)
#! /usr/bin/env python
import vtk
import sys
sys.path.insert(0, "../lib")
sys.path.insert(0, "..")
import ImageOperations
reader = vtk.vtkLSMReader()
reader.SetFileName("/home/kalpaha/BioImageXD/Data/sample2.lsm")
reader.SetUpdateChannel(0)
reader.SetUpdateTimePoint(5)
reader.Update()
ch1 = reader.GetOutput()
reader2 = vtk.vtkLSMReader()
reader2.SetFileName("/home/kalpaha/BioImageXD/Data/sample2.lsm")
reader2.SetUpdateChannel(1)
reader2.SetUpdateTimePoint(5)
reader2.Update()
ch2 = reader2.GetOutput()
#w1=vtk.vtkXMLImageDataWriter()
#w1.SetFileName("Ch1.vti")
#w1.SetInput(ch1)
#w1.Write()
#w2=vtk.vtkXMLImageDataWriter()
#w2.SetFileName("Ch2.vti")
#w2.SetInput(ch2)
#w2.Write()
coloc = vtk.vtkImageAutoThresholdColocalization()
coloc.AddInput(ch1)
