ENH: Adding a self-test for distance maps

This closes #6

Liver/Testing/Python/CMakeLists.txt

@@ -1,2 +1,8 @@
 
-#slicer_add_python_unittest(SCRIPT ${MODULE_NAME}ModuleTest.py)
+# Test markups pluggable architecture
+slicerMacroBuildScriptedModule(
+  NAME DistanceMapsSelfTest
+  SCRIPTS DistanceMapsSelfTest.py
+  RESOURCES ${MARKUPS_PYTHON_RESOURCES}
+  )
+slicer_add_python_unittest(SCRIPT DistanceMapsSelfTest.py)

Liver/Testing/Python/DistanceMapsSelfTest.py

@@ -0,0 +1,137 @@
+import os
+import time
+import unittest
+import vtk, qt, ctk, slicer
+from slicer.ScriptedLoadableModule import *
+import logging
+
+#
+# DistanceMapsSelfTest
+#
+class DistanceMapsSelfTest(ScriptedLoadableModule):
+  def __init__(self, parent):
+    ScriptedLoadableModule.__init__(self, parent)
+    self.parent.title = "DistanceMapsSelfTest"
+    self.parent.categories = ["Testing.TestCases"]
+    self.parent.dependencies = []
+    self.parent.contributors = ["Rafael Palomar (OUS)"]
+    self.parent.helpText = """
+    This is a self-test to test the computation of distance maps
+    from segmentations
+    """
+    self.parent.acknowledgementText = """
+    This file was originally developed by Rafael Palomar (OUS) and was funded by
+    the Research Council of Norway (grant nr. 311393).
+    """
+
+#
+# DistanceMapsSelfTestWidget
+#
+class DistanceMapsSelfTestWidget(ScriptedLoadableModuleWidget):
+
+  def setup(self):
+    ScriptedLoadableModuleWidget.setup(self)
+
+    # Instantiate and connect widgets ...
+
+    # Create and configure the input segmentation node selector
+    self._inputSegmentationNodeSelector = slicer.qMRMLNodeComboBox()
+    self._inputSegmentationNodeSelector.nodeTypes = ["vtkMRMLSegmentationNode"]
+    self._inputSegmentationNodeSelector.selectNodeUponCreation = False
+    self._inputSegmentationNodeSelector.addEnabled = False
+    self._inputSegmentationNodeSelector.removeEnabled = False
+    self._inputSegmentationNodeSelector.noneEnabled = True
+    self._inputSegmentationNodeSelector.noneDisplay = "Choose a segmentation node"
+    self._inputSegmentationNodeSelector.showHidden = False
+    self._inputSegmentationNodeSelector.setMRMLScene(slicer.mrmlScene)
+    self._inputSegmentationNodeSelector.setToolTip("Segmentation to perform planning on.")
+    self._inputSegmentationNodeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
+                                                self.updateParameterNodeFromGUI)
+
+    self.layout.addWidget(self._inputSegmentationNodeSelector)
+
+    # Create and configure the input segmentation node selector
+    self._outputLabelMapNodeSelector = slicer.qMRMLNodeComboBox()
+    self._outputLabelMapNodeSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
+    self._outputLabelMapNodeSelector.selectNodeUponCreation = True
+    self._outputLabelMapNodeSelector.addEnabled = True
+    self._outputLabelMapNodeSelector.removeEnabled = True
+    self._outputLabelMapNodeSelector.noneEnabled = False
+    self._outputLabelMapNodeSelector.noneDisplay = "vtkMRMLLabelMapVolumeNode"
+    self._outputLabelMapNodeSelector.showHidden = False
+    self._outputLabelMapNodeSelector.setMRMLScene(slicer.mrmlScene)
+    self._outputLabelMapNodeSelector.setToolTip("Segmentation to perform planning on.")
+    self._outputLabelMapNodeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
+                                                self.updateParameterNodeFromGUI)
+
+    self.layout.addWidget(self._outputLabelMapNodeSelector)
+
+    # Add vertical spacer
+    self.layout.addStretch(1)
+
+  def cleanup(self):
+    pass
+
+  def updateParameterNodeFromGUI(self):
+    pass
+
+class DistanceMapsSelfTestLogic(ScriptedLoadableModuleLogic):
+
+  def __init__(self):
+    ScriptedLoadableModuleLogic.__init__(self)
+
+  def setUp(self):
+    pass
+
+  def test_compute_segment_distance_maps(self, segmentationNode, volumeNode, segment):
+
+    labelNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
+    segments = vtk.vtkStringArray()
+    segments.InsertNextValue(segment)
+    segLogic = slicer.vtkSlicerSegmentationsModuleLogic
+    segLogic.ExportSegmentsToLabelmapNode(segmentationNode, segments, labelNode, volumeNode)
+    import sitkUtils
+    import SimpleITK as sitk
+    image = sitkUtils.PullVolumeFromSlicer(labelNode)
+    distance = sitk.SignedMaurerDistanceMap(image,False,False,True)
+    sitkUtils.PushVolumeToSlicer(distance)
+
+
+
+  def run(self, segmentationNode, volumeNode):
+
+    """
+    Run the tests
+    """
+    slicer.util.delayDisplay('Running integration tests for Pluggable Markups')
+
+    self.test_compute_segment_distance_maps(segmentationNode, volumeNode, 'Tumor1')
+
+    logging.info('Test process completed')
+
+
+class DistanceMapsSelfTestTest(ScriptedLoadableModuleTest):
+  """
+  This is the test case
+  """
+  def setUp(self):
+    slicer.mrmlScene.Clear()
+    # logic = DistanceMapsSelfTestLogic()
+    # logic.setUp()
+
+  def runTest(self):
+    self.setUp()
+    self.test_DistanceMapsSelfTest1()
+
+  def test_DistanceMapsSelfTest1(self):
+
+    self.delayDisplay("Starting the Distance Map Test")
+
+    import SampleData
+    inputVolume = SampleData.downloadSample('LiverVolume000')
+    inputSegmentation = SampleData.downloadSample('LiverSegmentation000')
+
+    logic = DistanceMapsSelfTestLogic()
+    logic.run(inputSegmentation, inputVolume)
+
+    self.delayDisplay('Test passed!')