ENH: Update Pre-Processing UI to improve BVR workflow

* 'Volume Node' and 'Output Directory' at top of UI were swapped
* 'Trial Name' moved to the config generation section as the
  '<blank>'.cfg field
* The segmentation generation section was redesigned to better convey
  the two separate generation methods
* The 'Adavnced Options' sections was renamed to 'Default
  Subdirectories', moved below the 'Segmentation Generation' section,
  and is now rendered as collapsed by default
* The 'VRG Resolution' fields from 'Advanced Options' was moved to the
  config generation section
* In the 'Generate Config' section, added file and path selectors to
  specify the camera calibration files, radiograph root directories, and
  volume files to be written to the generated config file. Also added
  'Voxel Size' fields that are automatically populated based on the
  selected input volume node.
* Elements in the .ui files were edited to be properly indexed and named

Co-authored-by: Amy M Morton <[email protected]>

AutoscoperM/AutoscoperM.py

@@ -211,11 +211,15 @@ def setup(self):
         self.ui.ankleSampleButton.connect("clicked(bool)", lambda: self.onSampleDataButtonClicked("2023-08-01-Ankle"))
 
         # Pre-processing Library Buttons
+        self.ui.volumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onCurrentNodeChanged)
         self.ui.tiffGenButton.connect("clicked(bool)", self.onGeneratePartialVolumes)
         self.ui.configGenButton.connect("clicked(bool)", self.onGenerateConfig)
         self.ui.segmentationButton.connect("clicked(bool)", self.onSegmentation)
-
+        self.ui.importModelsButton.connect("clicked(bool)", self.onImportModels)
         self.ui.loadPVButton.connect("clicked(bool)", self.onLoadPV)
+        self.ui.populateTrialNameListButton.connect("clicked(bool)", self.onPopulateTrialNameList)
+        self.ui.populatePartialVolumeListButton.connect("clicked(bool)", self.onPopulatePartialVolumeList)
+        self.ui.populateCameraCalListButton.connect("clicked(bool)", self.onPopulateCameraCalList)
 
         # Default output directory
         self.ui.mainOutputSelector.setCurrentPath(
@@ -225,6 +229,9 @@ def setup(self):
         # Make sure parameter node is initialized (needed for module reload)
         self.initializeParameterNode()
 
+        # Trigger any required UI updates based on the volume node selected by default
+        self.onCurrentNodeChanged()
+
     def cleanup(self):
         """
         Called when the application closes and the module widget is destroyed.
@@ -410,6 +417,18 @@ def onSampleDataButtonClicked(self, dataType):
         for cam in range(numCams):
             self.logic.AutoscoperSocket.loadFilters(cam, filterSettings)
 
+    def onCurrentNodeChanged(self):
+        """
+        Updates and UI components that correspond to the selected input volume node
+        """
+        volumeNode = self.ui.volumeSelector.currentNode()
+        if volumeNode:
+            with slicer.util.tryWithErrorDisplay("Failed to grab volume node information", waitCursor=True):
+                vSizeX, vSizeY, vSizeZ = self.logic.GetVolumeSpacing(volumeNode)
+            self.ui.voxelSizeX.value = vSizeX
+            self.ui.voxelSizeY.value = vSizeY
+            self.ui.voxelSizeZ.value = vSizeZ
+
     def onGeneratePartialVolumes(self):
         """
         This function creates partial volumes for each segment in the segmentation node for the selected volume node.
@@ -503,13 +522,19 @@ def onGenerateConfig(self):
                 self.ui.optOffPitch.value,
                 self.ui.optOffRoll.value,
             ]
+
             volumeFlip = [
                 int(self.ui.flipX.isChecked()),
                 int(self.ui.flipY.isChecked()),
                 int(self.ui.flipZ.isChecked()),
             ]
 
-            voxel_spacing = self.logic.GetVolumeSpacing(volumeNode)
+            voxel_spacing = [
+                self.ui.voxelSizeX.value,
+                self.ui.voxelSizeY.value,
+                self.ui.voxelSizeZ.value,
+            ]
+
             # generate the config file
             configFilePath = IO.generateConfigFile(
                 mainOutputDir,
@@ -524,9 +549,44 @@ def onGenerateConfig(self):
             self.ui.configSelector.setCurrentPath(configFilePath)
         slicer.util.messageBox("Success!")
 
+    def onImportModels(self):
+        """
+        Imports Models from a directory- converts to Segmentation Nodes
+        """
+        with slicer.util.tryWithErrorDisplay("Failed to compute results", waitCursor=True):
+            self.ui.progressBar.setValue(0)
+            self.ui.progressBar.setMaximum(100)
+
+            volumeNode = self.ui.volumeSelector.currentNode()
+
+            if not self.logic.validateInputs(voluemNode=volumeNode):
+                raise ValueError("Invalid inputs")
+                return
+
+            if self.ui.segGen_fileRadioButton.isChecked():
+                segmentationFileDir = self.ui.segGen_lineEdit.currentPath
+                if not self.logic.validatePaths(segmentationFileDir=segmentationFileDir):
+                    raise ValueError("Invalid paths")
+                    return
+                segmentationFiles = glob.glob(os.path.join(segmentationFileDir, "*.*"))
+                segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
+                segmentationNode.CreateDefaultDisplayNodes()
+                for idx, file in enumerate(segmentationFiles):
+                    returnedNode = IO.loadSegmentation(segmentationNode, file)
+                    if returnedNode:
+                        # get the segment from the returned node and add it to the segmentation node
+                        segment = returnedNode.GetSegmentation().GetNthSegment(0)
+                        segmentationNode.GetSegmentation().AddSegment(segment)
+                        slicer.mrmlScene.RemoveNode(returnedNode)
+                    self.ui.progressBar.setValue((idx + 1) / len(segmentationFiles) * 100)
+            else:  # Should never happen but just in case
+                raise Exception("Please select the 'Segmentation From Model' option in order to import models")
+                return
+        slicer.util.messageBox("Success!")
+
     def onSegmentation(self):
         """
-        Either launches the automatic segmentation process or loads in a set of segmentations from a directory
+        Launches the automatic segmentation process
         """
         with slicer.util.tryWithErrorDisplay("Failed to compute results", waitCursor=True):
             self.ui.progressBar.setValue(0)
@@ -561,24 +621,8 @@ def onSegmentation(self):
                         segmentationSequenceNode.SetDataNodeAtValue(segmentationNode, str(i))
                         slicer.mrmlScene.RemoveNode(segmentationNode)
                         currentVolumeNode = self.logic.getNextItemInSequence(volumeNode)
-            elif self.ui.segGen_fileRadioButton.isChecked():
-                segmentationFileDir = self.ui.segGen_lineEdit.currentPath
-                if not self.logic.validatePaths(segmentationFileDir=segmentationFileDir):
-                    raise ValueError("Invalid paths")
-                    return
-                segmentationFiles = glob.glob(os.path.join(segmentationFileDir, "*.*"))
-                segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
-                segmentationNode.CreateDefaultDisplayNodes()
-                for idx, file in enumerate(segmentationFiles):
-                    returnedNode = IO.loadSegmentation(segmentationNode, file)
-                    if returnedNode:
-                        # get the segment from the returned node and add it to the segmentation node
-                        segment = returnedNode.GetSegmentation().GetNthSegment(0)
-                        segmentationNode.GetSegmentation().AddSegment(segment)
-                        slicer.mrmlScene.RemoveNode(returnedNode)
-                    self.ui.progressBar.setValue((idx + 1) / len(segmentationFiles) * 100)
             else:  # Should never happen but just in case
-                raise Exception("No segmentation method selected")
+                raise Exception("Please select the 'Automatic Segmentation' option in order to generate segmentations")
                 return
         slicer.util.messageBox("Success!")
 
@@ -649,6 +693,64 @@ def onLoadPV(self):
 
         slicer.util.messageBox("Success!")
 
+    def onPopulateTrialNameList(self):
+        """
+        Populates trial name UI list using files from the selected radiograph directory
+        """
+        with slicer.util.tryWithErrorDisplay("Failed to compute results.", waitCursor=True):
+            self.populateListFromOutputSubDir(self.ui.trialList, self.ui.vrgSubDir.text, itemType="dir")
+
+    def onPopulatePartialVolumeList(self):
+        """
+        Populates partial volumes UI list using files from the selected PV directory
+        """
+        with slicer.util.tryWithErrorDisplay("Failed to compute results.", waitCursor=True):
+            self.populateListFromOutputSubDir(self.ui.partialVolumeList, self.ui.tiffSubDir.text)
+
+    def onPopulateCameraCalList(self):
+        """
+        Populates camera calibration UI list using files from the selected camera directory
+        """
+        with slicer.util.tryWithErrorDisplay("Failed to compute results.", waitCursor=True):
+            self.populateListFromOutputSubDir(self.ui.camCalList, self.ui.cameraSubDir.text)
+
+    def populateListFromOutputSubDir(self, listWidget, fileSubDir, itemType="file"):
+        """
+        Populates input UI list with files/directories that exist in the given input directory
+        """
+        listWidget.clear()
+
+        mainOutputDir = self.ui.mainOutputSelector.currentPath
+        if not self.logic.validateInputs(
+            listWidget=listWidget,
+            mainOutputDir=mainOutputDir,
+            fileSubDir=fileSubDir,
+        ):
+            raise ValueError("Invalid inputs")
+            return
+
+        fileDir = os.path.join(mainOutputDir, fileSubDir)
+        if not self.logic.validatePaths(fileDir=fileDir):
+            raise ValueError(f"Invalid input: subdirectory '{fileDir}' does not exist.")
+            return
+
+        if itemType == "file":
+            listFiles = [f.name for f in os.scandir(fileDir) if os.path.isfile(f)]
+        elif itemType == "dir":
+            listFiles = [f.name for f in os.scandir(fileDir) if os.path.isdir(f)]
+        else:
+            raise ValueError(
+                "Invalid input: can either search for type 'file' or 'dir' "
+                f"in specified path, but given itemType='{itemType}'"
+            )
+            return
+
+        for file in sorted(listFiles):
+            fileItem = qt.QListWidgetItem(file)
+            fileItem.setFlags(fileItem.flags() & ~qt.Qt.ItemIsSelectable)  # Remove the selectable flag
+            fileItem.setCheckState(qt.Qt.Unchecked)
+            listWidget.addItem(fileItem)
+
 
 #
 # AutoscoperMLogic