How to use slicer - 10 common examples

def setUp(self):
    """ Do whatever is needed to reset the state - typically a scene clear will be enough.
    """
    slicer.mrmlScene.Clear(0)
    #
    # first, get some data
    #
    import urllib
    downloads = (
        ('http://slicer.kitware.com/midas3/download?items=5768', 'tract1.vtk', slicer.util.loadFiberBundle),
        )

    for url,name,loader in downloads:
      filePath = slicer.app.temporaryPath + '/' + name
      if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
        print('Requesting download %s from %s...\n' % (name, url))
        urllib.urlretrieve(url, filePath)
      if loader:
        print('Loading %s...\n' % (name,))
        loader(filePath)
    self.delayDisplay('Finished with download and loading\n')

    # use the volumes module to replicate the bug report
    m = slicer.util.mainWindow()
    m.moduleSelector().selectModule('TractographyDisplay')
    self.delayDisplay("Entered Tractography module")

def setUp(self):
    """ Do whatever is needed to reset the state - typically a scene clear will be enough.
    """
    slicer.mrmlScene.Clear(0)
    #
    # first, get some data
    #
    import urllib
    downloads = (
        ('http://slicer.kitware.com/midas3/download?items=5768', 'tract1.vtk', slicer.util.loadFiberBundle),
        )

    for url,name,loader in downloads:
      filePath = slicer.app.temporaryPath + '/' + name
      if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
        print('Requesting download %s from %s...\n' % (name, url))
        urllib.urlretrieve(url, filePath)
      if loader:
        print('Loading %s...\n' % (name,))
        loader(filePath)

color_by_strategies = [
        ('Solid Color', displayNode.colorModeSolid),
        ('Of Tensor Property', displayNode.colorModeScalar),
#        (, displayNode.colorModeFunctionOfScalar),
#        ('Color Fibers By Mean Orientation', displayNode.colorModeUseCellScalars),
        ('Of Scalar Value', displayNode.colorModeScalarData),
        ('Color Fibers By Segment Orientation', displayNode.colorModePointFiberOrientation),
        ('Color Fibers By Mean Orientation', displayNode.colorModeMeanFiberOrientation),
    ]
    for widget_text, color_code in color_by_strategies:

        if not visibility.checked:
            visibility.click()

        solidColor = slicer.util.findChildren(tubeTab, text=widget_text)
        if len(solidColor) == 0:
            raise ValueError("Widget %s not found" % widget_text)
        else:
            solidColor = solidColor[0]
        solidColor.click()

        if displayNode and displayNode.GetColorMode() != color_code:
            self.delayDisplay('Setting Color Mode To %s Did not Work' % widget_text)
            raise Exception()
        else:
            self.delayDisplay("Setting Color Mode To %s Worked" % widget_text)

    visibility.click()

def test_TestTractographyDisplayColorBy(self, display_node='Tube'):
    self.delayDisplay("Starting the test")

    self.delayDisplay('Showing Advanced Display\n')
    advancedDisplay = slicer.util.findChildren(text='Advanced Display')[0]
    advancedDisplay.collapsed = False

    self.delayDisplay('Selecting tract1\n')
    tractNode = slicer.util.getNode('tract1')
    displayNode = getattr(tractNode, 'Get%sDisplayNode' % display_node)()
    tree = slicer.util.findChildren(name='TractographyDisplayTreeView')[0]
    model = tree.model()
    modelIndex = model.indexFromMRMLNode(tractNode)
    tree.setCurrentIndex(modelIndex)

    tubeTab = slicer.util.findChildren(advancedDisplay, name='%sTab' % display_node)[0]

    visibility = slicer.util.findChildren(tubeTab, text='Visibility')[0]

    color_by_strategies = [
        ('Solid Color', displayNode.colorModeSolid),

if len(freesurfer_found_segments) != len(self.freesurfer_wanted_segments):
        unpresent_segments = self.freesurfer_wanted_segments[:]
        for seg in freesurfer_found_segments:
          del unpresent_segments[unpresent_segments.index(seg)]
        unpresent_segments = map(lambda x: self.freesurfer_lut_dict[x.split('_')[-1]]['name'], unpresent_segments)
        logging.warning('Unable to find all segments, {} have not been found.'.format(unpresent_segments))
        logging.warning('LabelMap in path: {} has not been loaded into segmentationDict.'.format(path))
        return False

      for segmentId in to_remove_ids:
        segmentationNode.GetSegmentation().RemoveSegment(segmentId)

    elif self.color_table_id != 'None':
      segment_number = segmentationNode.GetSegmentation().GetNumberOfSegments()
      color_node = slicer.util.getNode(pattern=self.color_table_id)
      if (segment_number > 1):
        for segmentIndex in range(segment_number):
          segmentId = segmentationNode.GetSegmentation().GetNthSegmentID(segmentIndex)
          label_id = int(segmentId.split('_')[-1])

          color = [.0, .0, .0, .0]
          color_node.GetColor(label_id, color)
          segment_name = color_node.GetColorName(label_id)

          segment = segmentationNode.GetSegmentation().GetSegment(segmentId)
          segment.SetName(segment_name)
          segment.SetColor(color[:3])

      elif (segment_number==1):
        segmentId = segmentationNode.GetSegmentation().GetNthSegmentID(0)
        color = [.0, .0, .0, .0]

# Apply Button
    self.applyButton = qt.QPushButton("Apply")
    self.applyButton.toolTip = "Run the algorithm."
    self.applyButton.enabled = True
    self.layout.addWidget(self.applyButton)
    
    ### Output Area
    outputCollapsibleButton = ctk.ctkCollapsibleButton()
    outputCollapsibleButton.text = "Output"
    self.layout.addWidget(outputCollapsibleButton)

    # Layout within the dummy collapsible button
    outputFormLayout = qt.QFormLayout(outputCollapsibleButton)

    # Jacobian image (mrml output)
    self.outputJacobian = slicer.qMRMLNodeComboBox()
    self.outputJacobian.nodeTypes = ["vtkMRMLScalarVolumeNode"]
    self.outputJacobian.setMRMLScene( slicer.mrmlScene )
    self.outputJacobian.addEnabled = True
    self.outputJacobian.renameEnabled = True
    #self.outputJacobian.layout().addWidget(self.outputSelector)
    self.outputJacobian.setToolTip( "Output image of Jacobian matrix.vtkSlicerPlastimatchModuleLogicPython" )
    outputFormLayout.addRow("Jacobian image: ", self.outputJacobian)

    # output directory selector
#    self.outputDirectory = ctk.ctkDirectoryButton()
#    self.outputDirectory.directory = qt.QDir.homePath()
#    outputFormLayout.addRow("Output Directory: ", self.outputDirectory)
    
    # output statistics
    buttonLayout = qt.QHBoxLayout()
    self.minJacobian = qt.QLineEdit()

def runRegistration(self, start, end):
    assert start != -1 and end != -1
    seriesNumber = self.inputVolume.GetName().split(":")[0]
    self.outputTransform = self.createLinearTransformNode(seriesNumber + "-" + self.ZFRAME_TRANSFORM_NAME)

    params = {'inputVolume': self.inputVolume, 'startSlice': start, 'endSlice': end,
              'outputTransform': self.outputTransform}
    slicer.cli.run(slicer.modules.zframeregistration, None, params, wait_for_completion=True)