[5.6] BUG: Fix loading of sequence nodes

Modules/Loadable/Sequences/MRML/vtkMRMLSequenceBrowserNode.cxx

@@ -100,9 +100,17 @@ void vtkMRMLSequenceBrowserNode::SynchronizationProperties::FromString( std::str
         {
         this->SaveChanges=(!attValue.compare("true"));
         }
-      if (!attName.compare("saveChanges"))
+      if (!attName.compare("missingItemMode"))
         {
-        this->MissingItemMode = vtkMRMLSequenceBrowserNode::GetMissingItemModeFromString(attValue);
+        MissingItemModeType missingItemMode = vtkMRMLSequenceBrowserNode::GetMissingItemModeFromString(attValue);
+        if (this->MissingItemMode != MissingItemInvalid)
+          {
+          this->MissingItemMode = missingItemMode;
+          }
+        else
+          {
+          vtkGenericWarningMacro("Ignore unknown missingItemMode value: '" << attValue << "'");
+          }
         }
       }
     }
@@ -1528,7 +1536,7 @@ vtkMRMLSequenceBrowserNode::MissingItemModeType vtkMRMLSequenceBrowserNode::GetM
 {
   for (int i = 0; i<vtkMRMLSequenceBrowserNode::NumberOfMissingItemModes; i++)
     {
-    if (missingItemModeString == GetRecordingSamplingModeAsString(i))
+    if (missingItemModeString == GetMissingItemModeAsString(i))
       {
       // found it
       return MissingItemModeType(i);

Modules/Loadable/Sequences/Testing/CMakeLists.txt

@@ -1 +1,4 @@
 add_subdirectory(Cxx)
+if(Slicer_USE_PYTHONQT)
+  add_subdirectory(Python)
+endif()

Modules/Loadable/Sequences/Testing/Python/CMakeLists.txt

@@ -0,0 +1,7 @@
+if(Slicer_USE_QtTesting AND Slicer_USE_PYTHONQT)
+  slicerMacroBuildScriptedModule(
+    NAME SequencesSelfTest
+    SCRIPTS SequencesSelfTest.py
+    )
+  slicer_add_python_unittest(SCRIPT SequencesSelfTest.py)
+endif()

Modules/Loadable/Sequences/Testing/Python/SequencesSelfTest.py

@@ -0,0 +1,147 @@
+import os
+import shutil
+
+import slicer
+from slicer.ScriptedLoadableModule import *
+
+
+#
+# SequencesSelfTest
+#
+
+
+class SequencesSelfTest(ScriptedLoadableModule):
+    def __init__(self, parent):
+        ScriptedLoadableModule.__init__(self, parent)
+        self.parent.title = "SequencesSelfTest"
+        self.parent.categories = ["Testing.TestCases"]
+        self.parent.dependencies = ["Sequences"]
+        self.parent.contributors = ["Andras Lasso (PerkLab, Queen's)"]
+        self.parent.helpText = """This is a self test for Sequences related node and widgets."""
+        parent.acknowledgementText = """This file was originally developed by Andras Lasso, PerkLab, Queen's University
+            and was funded in part by NIH 1R01HL153166-01 (Computer Modeling of the Tricuspid Valve in Hypoplastic Left Heart Syndrome)"""
+
+
+#
+# SequencesSelfTestWidget
+#
+
+
+class SequencesSelfTestWidget(ScriptedLoadableModuleWidget):
+    def setup(self):
+        ScriptedLoadableModuleWidget.setup(self)
+
+
+#
+# SequencesSelfTestLogic
+#
+
+
+class SequencesSelfTestLogic(ScriptedLoadableModuleLogic):
+    """This class should implement all the actual
+    computation done by your module.  The interface
+    should be such that other python code can import
+    this class and make use of the functionality without
+    requiring an instance of the Widget
+    """
+
+    def __init__(self):
+        pass
+
+
+class SequencesSelfTestTest(ScriptedLoadableModuleTest):
+    """This is the test case for your scripted module."""
+
+    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_SequencesSelfTest_FullTest1()
+
+    # ------------------------------------------------------------------------------
+    def test_SequencesSelfTest_FullTest1(self):
+        # Check for Sequences module
+        self.assertTrue(slicer.modules.sequences)
+
+        self.section_SetupPathsAndNames()
+        self.section_ReplaySavedSequence()
+        self.delayDisplay("Test passed")
+
+    # ------------------------------------------------------------------------------
+    def section_SetupPathsAndNames(self):
+        # Set constants
+        self.sequencesSelfTestDir = slicer.app.temporaryPath + "/SequencesSelfTest"
+        print("Test directory: " + self.sequencesSelfTestDir)
+        if not os.access(self.sequencesSelfTestDir, os.F_OK):
+            os.mkdir(self.sequencesSelfTestDir)
+        self.assertTrue(os.access(self.sequencesSelfTestDir, os.F_OK))
+
+    # ------------------------------------------------------------------------------
+    def section_ReplaySavedSequence(self):
+
+        def clearSavedSceneFolder(savedSceneDir):
+            # Clear the output savedScene folder
+            for sceneFiles in ["SequencesSelfTest.mrml", "Data/CTPCardioSeq.seq.nrrd", "Data/CTPCardioSeq.nrrd", "Data"]:
+                try:
+                    os.remove(os.path.join(savedSceneDir, sceneFiles))
+                except OSError:
+                    pass
+            shutil.rmtree(savedSceneDir, True)
+
+        def checkSequenceItems(browserNode, sequenceNode):
+            volumeNode = browserNode.GetProxyNode(sequenceNode)
+
+            # Check voxel values of item number 5
+            browserNode.SetSelectedItemNumber(5)
+            voxelArray = slicer.util.arrayFromVolume(volumeNode)
+            self.assertAlmostEqual(voxelArray.mean(), -886.678, delta=0.1)
+
+            # Check voxel values of item number 15
+            browserNode.SetSelectedItemNumber(15)
+            voxelArray = slicer.util.arrayFromVolume(volumeNode)
+            self.assertAlmostEqual(voxelArray.mean(), -898.4033, delta=0.1)
+
+        self.delayDisplay("Load sequence data")
+
+        # Get a sequence node
+        import SampleData
+        sequenceNode = SampleData.SampleDataLogic().downloadSample("CTPCardioSeq")
+
+        # Find corresponding sequence browser node
+        browserNode = slicer.modules.sequences.logic().GetFirstBrowserNodeForSequenceNode(sequenceNode)
+
+        # Check sequence information
+        self.assertEqual(browserNode.GetNumberOfItems(), 26)
+        self.assertEqual(browserNode.GetMasterSequenceNode().GetIndexName(), "frame")
+        volumeNode = browserNode.GetProxyNode(sequenceNode)
+        self.assertIsNotNone(volumeNode)
+
+        self.delayDisplay("Test browsing of sequence")
+        checkSequenceItems(browserNode, sequenceNode)
+
+        # Test saving and loading of sequence
+        savedSceneDir = os.path.join(self.sequencesSelfTestDir, "savedscene")
+        clearSavedSceneFolder(savedSceneDir)
+
+        if not os.access(savedSceneDir, os.F_OK):
+            os.mkdir(savedSceneDir)
+        self.assertTrue(os.access(savedSceneDir, os.F_OK))
+
+        self.delayDisplay("Test saving of sequence")
+        self.assertTrue(slicer.app.applicationLogic().SaveSceneToSlicerDataBundleDirectory(savedSceneDir, None))
+
+        self.delayDisplay("Test loading of sequence")
+        slicer.mrmlScene.Clear(0)
+        slicer.util.loadScene(os.path.join(savedSceneDir, "savedscene.mrml"))
+        # Remove temporary folder to not pollute the file system
+        clearSavedSceneFolder(savedSceneDir)
+
+        self.delayDisplay("Test browsing of loaded sequence")
+        browserNode = slicer.util.getFirstNodeByClassByName("vtkMRMLSequenceBrowserNode", "CTPCardioSeq browser")
+        self.assertIsNotNone(browserNode)
+        sequenceNode = slicer.util.getFirstNodeByClassByName("vtkMRMLSequenceNode", "CTPCardioSeq")
+        self.assertIsNotNone(sequenceNode)
+        checkSequenceItems(browserNode, sequenceNode)