def testDimensions(self):
		reader = vtkbxd.vtkLIFReader()
		reader.SetFileName(os.path.join(DATA_PATH, "512x_128y_10z_22t_2ch.lif"))
		reader.OpenFile()
		reader.Update()
		data = reader.GetOutput()
		self.assert_(data.GetDimensions() == (512, 128, 10), "Dimensions do not match")
コード例 #2
0
 def testDimensions(self):
     reader = vtkbxd.vtkLIFReader()
     reader.SetFileName(os.path.join(DATA_PATH,
                                     "512x_128y_10z_22t_2ch.lif"))
     reader.OpenFile()
     reader.Update()
     data = reader.GetOutput()
     self.assert_(data.GetDimensions() == (512, 128, 10),
                  "Dimensions do not match")
	def testMIP(self):
		reader = vtkbxd.vtkLIFReader()
		reader.SetFileName(os.path.join(DATA_PATH, "512x_128y_10z_22t_2ch.lif"))
		reader.OpenFile()
		reader.Update()
		data = reader.GetOutput()
		mip = vtkbxd.vtkImageSimpleMIP()
		mip.SetInput(data)
		pngwriter  = vtk.vtkPNGWriter()
		pngwriter.SetInput(mip.GetOutput())
		mip.Update()
		pngwriter.SetFileName("lif.png")
		pngwriter.Write()
コード例 #4
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 def testMIP(self):
     reader = vtkbxd.vtkLIFReader()
     reader.SetFileName(os.path.join(DATA_PATH,
                                     "512x_128y_10z_22t_2ch.lif"))
     reader.OpenFile()
     reader.Update()
     data = reader.GetOutput()
     mip = vtkbxd.vtkImageSimpleMIP()
     mip.SetInput(data)
     pngwriter = vtk.vtkPNGWriter()
     pngwriter.SetInput(mip.GetOutput())
     mip.Update()
     pngwriter.SetFileName("lif.png")
     pngwriter.Write()
コード例 #5
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ファイル: LIFDataSource.py プロジェクト: scijava/bioimagexd
    def __init__(self, filename="", imageNum=-1, channelNum=-1, reader=None):
        """
		Constructor of LIF DataSource
		"""
        DataSource.__init__(self)
        self.filename = filename
        self.imageName = ""
        self.setPath(filename)
        # LIF file can contain multiple images with multiple channels.
        # Define which image and channel is associated to this DataSource
        self.imageNum = imageNum
        self.channelNum = channelNum
        self.bitDepth = 0

        self.spacing = None
        self.voxelSize = None
        self.ctf = None

        # Use vtkLIFReader
        self.reader = vtkbxd.vtkLIFReader()
        self.reader.AddObserver('ProgressEvent', lib.messenger.send)
        lib.messenger.connect(self.reader, 'ProgressEvent',
                              self.updateProgress)

        # Open file if defined
        if self.filename:
            self.reader.SetFileName(self.convertFileName(self.filename))
            if self.reader.OpenFile():
                if reader:
                    self.reader.CopyHeaderInfo(reader)
                if self.reader.ReadLIFHeader():
                    self.reader.SetCurrentImage(self.imageNum)
                    self.reader.SetCurrentChannel(self.channelNum)
                    self.imageName = self.reader.GetImageName(self.imageNum)
                    self.createTimeStamps()
                    self.originalDimensions = self.internalGetDimensions()[0:3]
                else:
                    Logging.error(
                        "Failed to read the header of the LIF file correctly",
                        "Error in LIFDataSource.py in __init__, failed to read the header of the LIF file: %s"
                        % (self.filename))
                    return
            else:
                Logging.error(
                    "Failed to open file",
                    "Error in LIFDataSource.py in __init__, failed to open file: %s"
                    % (self.filename))
                return