ENH: Add support of shallow and deep copy to scalar volume display node

This is a followup to Slicer@f88c110.
tkatsoulas · Mar 20, 2023 · 76aaf3e · 76aaf3e
1 parent e468829
commit 76aaf3e
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Showing 4 changed files with 144 additions and 12 deletions.
diff --git a/Applications/SlicerApp/Testing/Python/CMakeLists.txt b/Applications/SlicerApp/Testing/Python/CMakeLists.txt
@@ -436,6 +436,7 @@ if(Slicer_USE_QtTesting AND Slicer_USE_PYTHONQT)
   slicer_add_python_unittest(SCRIPT DICOMReaders.py)
   slicer_add_python_unittest(SCRIPT KneeAtlasTest.py)
   slicer_add_python_unittest(SCRIPT sceneImport2428.py)
+  slicer_add_python_unittest(SCRIPT SlicerDisplayNodeSequenceTest.py)
   slicer_add_python_unittest(SCRIPT SlicerMRBMultipleSaveRestoreLoopTest.py)
   slicer_add_python_unittest(SCRIPT SlicerMRBMultipleSaveRestoreTest.py)
   slicer_add_python_unittest(SCRIPT SlicerMRBSaveRestoreCheckPathsTest.py)
@@ -463,6 +464,7 @@ if(Slicer_USE_QtTesting AND Slicer_USE_PYTHONQT)
   set(KIT_PYTHON_SCRIPTS
     AtlasTests.py
     sceneImport2428.py
+    SlicerDisplayNodeSequenceTest.py
     SlicerMRBMultipleSaveRestoreLoopTest.py
     SlicerMRBMultipleSaveRestoreTest.py
     SlicerMRBSaveRestoreCheckPathsTest.py

diff --git a/Applications/SlicerApp/Testing/Python/SlicerDisplayNodeSequenceTest.py b/Applications/SlicerApp/Testing/Python/SlicerDisplayNodeSequenceTest.py
@@ -0,0 +1,131 @@
+import slicer
+from slicer.ScriptedLoadableModule import *
+
+
+#
+# SlicerDisplayNodeSequenceTest
+#
+class SlicerDisplayNodeSequenceTest(ScriptedLoadableModule):
+    """Uses ScriptedLoadableModule base class, available at:
+    https://githuindex_1_display_node.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py
+    """
+
+    def __init__(self, parent):
+        ScriptedLoadableModule.__init__(self, parent)
+        self.parent.title = "SlicerDisplayNodeSequenceTest"
+        self.parent.categories = ["Testing.TestCases"]
+        self.parent.dependencies = []
+        self.parent.contributors = ["James Butler (PerkinElmer)"]
+        self.parent.helpText = """
+      This test has been added to check that a vtkMRMLScalarVolumeDisplayNode is appropriately copied into a sequence node.
+      """
+        self.parent.acknowledgementText = """
+    This file was originally developed by James Butler, PerkinElmer.
+    """
+
+
+#
+# SlicerDisplayNodeSequenceTestWidget
+#
+class SlicerDisplayNodeSequenceTestWidget(ScriptedLoadableModuleWidget):
+    """
+    """
+
+    def setup(self):
+        ScriptedLoadableModuleWidget.setup(self)
+
+
+#
+# SlicerDisplayNodeSequenceTestLogic
+#
+class SlicerDisplayNodeSequenceTestLogic(ScriptedLoadableModuleLogic):
+    """
+    """
+
+
+class SlicerDisplayNodeSequenceTestTest(ScriptedLoadableModuleTest):
+    """
+    """
+
+    def setUp(self):
+        """ Do whatever is needed to reset the state - typically a scene clear will be enough.
+        """
+        slicer.mrmlScene.Clear(0)
+
+    def runTest(self):
+        """Run as few or as many tests as needed here.
+        """
+        self.setUp()
+        self.test_ScalarVolumeDisplayNodeSequence()
+        self.delayDisplay('Test completed.')
+
+    def test_ScalarVolumeDisplayNodeSequence(self):
+        # Load first volume and apply custom display
+        import SampleData
+        sampleDataLogic = SampleData.SampleDataLogic()
+        mrHead = sampleDataLogic.downloadMRHead()
+        mrHead.GetDisplayNode().ApplyThresholdOn()
+        mrHead.GetDisplayNode().SetAutoWindowLevel(False)
+        mrHead.GetDisplayNode().SetWindowLevelMinMax(10, 120)
+        min, max = mrHead.GetImageData().GetScalarRange()
+        mrHead.GetDisplayNode().SetThreshold(0, max)
+        window_preset = 99
+        level_preset = 49
+        mrHead.GetDisplayNode().AddWindowLevelPreset(window_preset, level_preset)
+
+        # Load second volume and apply custom display
+        mrHead2 = sampleDataLogic.downloadMRHead()
+        mrHead2.GetDisplayNode().SetAndObserveColorNodeID("vtkMRMLColorTableNodeRed")
+        mrHead2.GetDisplayNode().ApplyThresholdOn()
+        min, max = mrHead2.GetImageData().GetScalarRange()
+        mrHead2.GetDisplayNode().SetThreshold(79, max)
+        mrHead2.GetDisplayNode().ApplyThresholdOn()
+        mrHead2.GetDisplayNode().SetAutoWindowLevel(False)
+        mrHead2.GetDisplayNode().SetWindowLevelMinMax(20, 100)
+        window_preset = 99
+        level_preset = 49
+        mrHead2.GetDisplayNode().AddWindowLevelPreset(window_preset, level_preset)
+        mrHead2.GetDisplayNode().AddWindowLevelPreset(window_preset - 1, level_preset - 1)
+
+        # Create a vtkMRMLScalarVolumeNode sequence
+        sequence_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode", "MySequenceNode")
+        sequence_node.SetDataNodeAtValue(mrHead, "0")
+        sequence_node.SetDataNodeAtValue(mrHead2, "1")
+
+        # Create a vtkMRMLScalarVolumeDisplayNode sequence
+        sequence_display_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode", "MySequenceDisplayNode")
+        sequence_display_node.SetDataNodeAtValue(mrHead.GetDisplayNode(), "0")
+        sequence_display_node.SetDataNodeAtValue(mrHead2.GetDisplayNode(), "1")
+
+        # Synchronize the two sequences and display
+        browser_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceBrowserNode", "MyBrowserNode")
+        browser_node.AddSynchronizedSequenceNode(sequence_node)
+        browser_node.AddSynchronizedSequenceNode(sequence_display_node)
+        volume_proxy_node = browser_node.GetProxyNode(sequence_node)
+        display_proxy_node = browser_node.GetProxyNode(sequence_display_node)
+        volume_proxy_node.SetAndObserveDisplayNodeID(display_proxy_node.GetID())
+        slicer.modules.sequences.toolBar().setActiveBrowserNode(browser_node)
+        slicer.util.setSliceViewerLayers(background=volume_proxy_node)
+
+        # Confirm the display properties have copied over into the Display sequence data nodes
+        index_0_display_node = sequence_display_node.GetDataNodeAtValue("0")
+        self.assertTrue(index_0_display_node.GetColorNodeID() == mrHead.GetDisplayNode().GetColorNodeID())
+        self.assertTrue(index_0_display_node.GetWindowLevelMin() == mrHead.GetDisplayNode().GetWindowLevelMin())
+        self.assertTrue(index_0_display_node.GetWindowLevelMax() == mrHead.GetDisplayNode().GetWindowLevelMax())
+        self.assertTrue(index_0_display_node.GetLowerThreshold() == mrHead.GetDisplayNode().GetLowerThreshold())
+        self.assertTrue(index_0_display_node.GetUpperThreshold() == mrHead.GetDisplayNode().GetUpperThreshold())
+        self.assertTrue(index_0_display_node.GetNumberOfWindowLevelPresets() == mrHead.GetDisplayNode().GetNumberOfWindowLevelPresets())
+        for i in range(mrHead.GetDisplayNode().GetNumberOfWindowLevelPresets()):
+            self.assertTrue(index_0_display_node.GetWindowPreset(i) == mrHead.GetDisplayNode().GetWindowPreset(i))
+            self.assertTrue(index_0_display_node.GetLevelPreset(i) == mrHead.GetDisplayNode().GetLevelPreset(i))
+
+        index_1_display_node = sequence_display_node.GetDataNodeAtValue("1")
+        self.assertTrue(index_1_display_node.GetColorNodeID() == mrHead2.GetDisplayNode().GetColorNodeID())
+        self.assertTrue(index_1_display_node.GetWindowLevelMin() == mrHead2.GetDisplayNode().GetWindowLevelMin())
+        self.assertTrue(index_1_display_node.GetWindowLevelMax() == mrHead2.GetDisplayNode().GetWindowLevelMax())
+        self.assertTrue(index_1_display_node.GetLowerThreshold() == mrHead2.GetDisplayNode().GetLowerThreshold())
+        self.assertTrue(index_1_display_node.GetUpperThreshold() == mrHead2.GetDisplayNode().GetUpperThreshold())
+        self.assertTrue(index_1_display_node.GetNumberOfWindowLevelPresets() == mrHead2.GetDisplayNode().GetNumberOfWindowLevelPresets())
+        for i in range(mrHead2.GetDisplayNode().GetNumberOfWindowLevelPresets()):
+            self.assertTrue(index_1_display_node.GetWindowPreset(i) == mrHead2.GetDisplayNode().GetWindowPreset(i))
+            self.assertTrue(index_1_display_node.GetLevelPreset(i) == mrHead2.GetDisplayNode().GetLevelPreset(i))
diff --git a/Libs/MRML/Core/vtkMRMLScalarVolumeDisplayNode.cxx b/Libs/MRML/Core/vtkMRMLScalarVolumeDisplayNode.cxx
@@ -352,14 +352,15 @@ void vtkMRMLScalarVolumeDisplayNode::ReadXMLAttributes(const char** atts)
 }
 
 //----------------------------------------------------------------------------
-// Copy the node\"s attributes to this object.
-// Does NOT copy: ID, FilePrefix, Name, VolumeID
-void vtkMRMLScalarVolumeDisplayNode::Copy(vtkMRMLNode *anode)
+void vtkMRMLScalarVolumeDisplayNode::CopyContent(vtkMRMLNode* anode, bool deepCopy/*=true*/)
 {
-  int disabledModify = this->StartModify();
-
-  Superclass::Copy(anode);
-  vtkMRMLScalarVolumeDisplayNode *node = (vtkMRMLScalarVolumeDisplayNode *) anode;
+  MRMLNodeModifyBlocker blocker(this);
+  Superclass::CopyContent(anode, deepCopy);
+  vtkMRMLScalarVolumeDisplayNode *node = vtkMRMLScalarVolumeDisplayNode::SafeDownCast(anode);
+  if (!node)
+    {
+    return;
+    }
 
   this->SetAutoWindowLevel( node->GetAutoWindowLevel() );
   this->SetWindowLevel(node->GetWindow(), node->GetLevel());
@@ -372,8 +373,6 @@ void vtkMRMLScalarVolumeDisplayNode::Copy(vtkMRMLNode *anode)
     this->AddWindowLevelPreset(node->GetWindowPreset(p), node->GetLevelPreset(p));
     }
 
-  this->EndModify(disabledModify);
-
 }
 
 //----------------------------------------------------------------------------

diff --git a/Libs/MRML/Core/vtkMRMLScalarVolumeDisplayNode.h b/Libs/MRML/Core/vtkMRMLScalarVolumeDisplayNode.h
@@ -54,9 +54,9 @@ class VTK_MRML_EXPORT vtkMRMLScalarVolumeDisplayNode : public vtkMRMLVolumeDispl
   /// Write this node's information to a MRML file in XML format.
   void WriteXML(ostream& of, int indent) override;
 
-  ///
-  /// Copy the node's attributes to this object
-  void Copy(vtkMRMLNode *node) override;
+  /// Copy node content (excludes basic data, such as name and node references).
+  /// \sa vtkMRMLNode::CopyContent
+  vtkMRMLCopyContentMacro(vtkMRMLScalarVolumeDisplayNode);
 
   ///
   /// Get node XML tag name (like Volume, Model)