Merge pull request #30 from JEHoctor/dev/issue-4

Dev/issue 4

Q3DC/CMakeLists.txt

@@ -9,6 +9,7 @@ set(MODULE_PYTHON_SCRIPTS
 set(MODULE_PYTHON_RESOURCES
   Resources/Icons/${MODULE_NAME}.png
   Resources/UI/${MODULE_NAME}.ui
+  Resources/Data/base_fiducial_legend.csv
   )
 
 #-----------------------------------------------------------------------------

Q3DC/Q3DC.py

@@ -1,6 +1,9 @@
 import vtk, qt, ctk, slicer
 from slicer.ScriptedLoadableModule import *
+from slicer.util import NodeModify
 import csv, os
+from collections import defaultdict
+from pathlib import Path
 import json
 import time
 import math
@@ -90,6 +93,27 @@ def setup(self):
         self.ui.inputLandmarksSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onLandmarksChanged)
         self.ui.landmarkComboBox.connect('currentIndexChanged(QString)', self.UpdateInterface)
         self.ui.surfaceDeplacementCheckBox.connect('stateChanged(int)', self.onSurfaceDeplacementStateChanged)
+
+        # --------------- anatomical legend --------------
+        self.suggested_landmarks = self.logic.load_suggested_landmarks()
+        self.anatomical_legend_space = self.ui.landmarkModifLayout
+        self.anatomical_radio_buttons_layout = qt.QHBoxLayout()
+        self.anatomical_legend_space.addLayout(self.anatomical_radio_buttons_layout)
+        self.init_anatomical_radio_buttons()
+
+        self.anatomical_legend = None
+        self.init_anatomical_legend()
+        self.anatomical_legend_view = slicer.qMRMLTableView()
+        self.anatomical_legend_view.setMRMLTableNode(self.anatomical_legend)
+        self.anatomical_legend_space.addWidget(self.anatomical_legend_view)
+        self.anatomical_legend_view.show()
+        self.anatomical_legend_view.setSelectionBehavior(
+            qt.QAbstractItemView.SelectRows
+        )
+        self.anatomical_legend_view.connect('selectionChanged()', self.on_legend_row_selected)
+
+        self.anatomical_radio_buttons[0].toggle()
+
         #        ----------------- Compute Mid Point -------------
         self.ui.landmarkComboBox1.connect('currentIndexChanged(int)', self.UpdateInterface)
         self.ui.landmarkComboBox2.connect('currentIndexChanged(int)', self.UpdateInterface)
@@ -313,6 +337,94 @@ def UpdateInterface(self):
                                                     self.ui.fidListComboBoxlineLB.currentNode())
         self.logic.UpdateThreeDView(self.ui.landmarkComboBox.currentText)
 
+    def init_anatomical_legend(self):
+        if self.anatomical_legend is None:
+            for table_node in slicer.mrmlScene.GetNodesByClass('vtkMRMLTableNode'):
+                if table_node.GetAttribute('Q3DC.is_anatomical_legend') == 'True':
+                    self.anatomical_legend = table_node
+            if self.anatomical_legend is None:
+                self.anatomical_legend = slicer.vtkMRMLTableNode()
+                self.anatomical_legend.SetSaveWithScene(False)
+                self.anatomical_legend.SetLocked(True)
+                slicer.mrmlScene.AddNode(self.anatomical_legend)
+                self.anatomical_legend.SetAttribute('Q3DC.is_anatomical_legend', 'True')
+
+        al = self.anatomical_legend
+        with NodeModify(al):
+            al.RemoveAllColumns()
+            al.AddColumn().SetName('Landmark')
+            al.AddColumn().SetName('Description')
+            al.SetUseColumnNameAsColumnHeader(True)
+
+    def init_anatomical_radio_buttons(self):
+        self.anatomical_radio_buttons = \
+            [qt.QRadioButton(region) for region in self.suggested_landmarks.keys()]
+        for i in range(self.anatomical_radio_buttons_layout.count()-1, -1, -1):
+            self.anatomical_radio_buttons_layout.itemAt[i].widget().setParent(None)
+        for radio_button in self.anatomical_radio_buttons:
+            self.anatomical_radio_buttons_layout.addWidget(radio_button)
+            radio_button.toggled.connect(
+                lambda state, _radio_button=radio_button:
+                    self.on_anatomical_radio_button_toggled(state, _radio_button)
+            )
+
+    def on_anatomical_radio_button_toggled(self, state, radio_button):
+        if state:
+            self.init_anatomical_legend()
+            region = radio_button.text
+
+            al = self.anatomical_legend
+            with NodeModify(al):
+                for landmark, description in self.suggested_landmarks[region]:
+                    new_row_index = al.AddEmptyRow()
+                    al.SetCellText(new_row_index, 0, landmark)
+                    al.SetCellText(new_row_index, 1, description)
+            self.anatomical_legend_view.resizeColumnsToContents()
+
+    def on_legend_row_selected(self):
+        # Calculate the index of the selected point.
+        fidList = self.logic.selectedFidList
+        if not fidList:
+            return
+        selectedFidReflID = self.logic.findIDFromLabel(
+            fidList,
+            self.ui.landmarkComboBox.currentText
+        )
+        if selectedFidReflID is None:
+            # code would run correctly if we continued but wouldn't do anything
+            return
+        fid_index = fidList.GetNthControlPointIndexByID(selectedFidReflID)
+        old_name = fidList.GetNthControlPointLabel(fid_index)
+
+        # Look in the legend for the info from the selected row.
+        selected_indices = self.anatomical_legend_view.selectedIndexes()
+        if len(selected_indices) != 2:
+            return
+        name_index, description_index = selected_indices
+        row_index = name_index.row()
+        name = self.anatomical_legend.GetCellText(row_index, 0)
+        description = self.anatomical_legend.GetCellText(row_index, 1)
+
+        # Refuse to create multiple fiducials with the same name.
+        for i in range(fidList.GetNumberOfControlPoints()):
+            if name == fidList.GetNthControlPointLabel(i):
+                return
+
+        # Set the name and description of the selected point.
+        fidList.SetNthControlPointLabel(fid_index, name)
+        fidList.SetNthControlPointDescription(fid_index, description)
+
+        # Update the landmark combo boxes to reflect the name change.
+        self.logic.updateLandmarkComboBox(fidList, self.ui.landmarkComboBox, False)
+        self.ui.landmarkComboBox.setCurrentText(name)
+        for box in (self.ui.landmarkComboBox1, self.ui.landmarkComboBox2):
+            new_selection = box.currentText
+            if new_selection == old_name:
+                new_selection = name
+            self.logic.updateLandmarkComboBox(fidList, box)
+            box.setCurrentText(new_selection)
+        self.UpdateInterface()
+
     def onModelChanged(self):
         print("-------Model Changed--------")
         if self.logic.selectedModel:
@@ -541,6 +653,20 @@ def __init__(self, interface):
         self.decimalPoint = chr(system.decimalPoint())
         self.comboboxdict = dict()
 
+    @staticmethod
+    def load_suggested_landmarks():
+        suggested_landmarks = defaultdict(list)
+        suggestions_path = \
+            Path(__file__).parent / 'Resources' / 'Data' / 'base_fiducial_legend.csv'
+        with suggestions_path.open(newline='') as suggestions_file:
+            reader = csv.DictReader(suggestions_file)
+            for row in reader:
+                region = row['Region'].title()
+                landmark = row['Landmark']
+                name = row['Name']
+                suggested_landmarks[region].append((landmark, name))
+        return suggested_landmarks
+
     def initComboboxdict(self):
         self.comboboxdict[self.interface.landmarkComboBoxA] = None
         self.comboboxdict[self.interface.landmarkComboBoxB] = None
@@ -1100,14 +1226,12 @@ def deleteLandmark(self, fidList, label):
             if value is fidList:
                 key.removeItem(key.findText(label))
 
-    def findIDFromLabel(self, fidList, landmarkLabel):
+    @staticmethod
+    def findIDFromLabel(fidList, landmarkLabel):
         # find the ID of the markupsNode from the label of a landmark!
-        landmarkDescription = self.decodeJSON(fidList.GetAttribute("landmarkDescription"))
-        if not landmarkDescription:
-            return None
-        for ID, value in landmarkDescription.items():
-            if value["landmarkLabel"] == landmarkLabel:
-                return ID
+        for i in range(fidList.GetNumberOfFiducials()):
+            if landmarkLabel == fidList.GetNthFiducialLabel(i):
+                return fidList.GetNthMarkupID(i)
         return None
 
     def getClosestPointIndex(self, fidNode, inputPolyData, landmarkID):
@@ -1768,10 +1892,9 @@ def displayROI(self, inputModelNode, scalarName):
         PolyData.Modified()
         displayNode = inputModelNode.GetModelDisplayNode()
         displayNode.SetScalarVisibility(False)
-        disabledModify = displayNode.StartModify()
-        displayNode.SetActiveScalarName(scalarName)
-        displayNode.SetScalarVisibility(True)
-        displayNode.EndModify(disabledModify)
+        with NodeModify(displayNode):
+            displayNode.SetActiveScalarName(scalarName)
+            displayNode.SetScalarVisibility(True)
 
     def findROI(self, fidList):
         hardenModel = slicer.app.mrmlScene().GetNodeByID(fidList.GetAttribute("hardenModelID"))

Q3DC/Resources/Data/base_fiducial_legend.csv

@@ -0,0 +1,72 @@
+Region,Landmark,Name
+CRANIAL BASE,Ba,Basion
+CRANIAL BASE,S,Sella
+CRANIAL BASE,N,Nasion
+NASOMAXILLARY COMPLEX,A,A-point
+NASOMAXILLARY COMPLEX,ANS,Anterior Nasal Spine
+NASOMAXILLARY COMPLEX,PNS,Posterior Nasal Spine
+NASOMAXILLARY COMPLEX,OrR,Right Orbitale
+NASOMAXILLARY COMPLEX,OrL,Left Orbitale
+NASOMAXILLARY COMPLEX,ZygR,Right Zygomatic
+NASOMAXILLARY COMPLEX,ZygL,Left Zygomatic
+NASOMAXILLARY COMPLEX,NCR,Right Nasal Cavity
+NASOMAXILLARY COMPLEX,NCL,Left Nasal Cavity
+NASOMAXILLARY COMPLEX,PFR,Right Palatine Foramen
+NASOMAXILLARY COMPLEX,PFL,Left Palatine Foramen
+NASOMAXILLARY COMPLEX,IFr,Incisal Foramen
+NASOMAXILLARY COMPLEX,UR6,Right Maxillary molar cusp tip
+NASOMAXILLARY COMPLEX,UL6,Left Maxillary molar cusp tip
+NASOMAXILLARY COMPLEX,UR’6,Right Maxillary molar root apex
+NASOMAXILLARY COMPLEX,UL’6,Left Maxillary molar root apex
+NASOMAXILLARY COMPLEX,UR6AB,Buccal Alveolar Bone Level at first molar
+NASOMAXILLARY COMPLEX,UL6AB,Buccal Alveolar Bone Level at first molar
+NASOMAXILLARY COMPLEX,UR5,Right Maxillary 2nd premolar cusp tip
+NASOMAXILLARY COMPLEX,UL5,Left Maxillary 2nd premolar cusp tip
+NASOMAXILLARY COMPLEX,UR’5,Right Maxillary 2nd premolar root apex
+NASOMAXILLARY COMPLEX,UL’5,Left Maxillary 2nd premolar root apex
+NASOMAXILLARY COMPLEX,UR4,Right Maxillary 1st premolar cusp tip
+NASOMAXILLARY COMPLEX,UL4,Left Maxillary 1st premolar cusp tip
+NASOMAXILLARY COMPLEX,UR’4,Right Maxillary 1st premolar root apex
+NASOMAXILLARY COMPLEX,UL’4,Left Maxillary 1st premolar root apex
+NASOMAXILLARY COMPLEX,UR3,Right Maxillary 1st premolar cusp tip
+NASOMAXILLARY COMPLEX,UL3,Left Maxillary 1st premolar cusp tip
+NASOMAXILLARY COMPLEX,UR’3,Right Maxillary 1st premolar root apex
+NASOMAXILLARY COMPLEX,UL’3,Left Maxillary 1st premolar root apex
+NASOMAXILLARY COMPLEX,U1,Maxillary incisor incisal edge
+NASOMAXILLARY COMPLEX,U’1,Maxillary incisor root apex
+MANDIBLE,B,B-point
+MANDIBLE,Pog,Pogonion
+MANDIBLE,Me,Menton
+MANDIBLE,Gn,Gnathion
+MANDIBLE,RGo,Right Gonion
+MANDIBLE,LGo,Left  Gonion
+MANDIBLE,RSGo,Right Superior Gonion
+MANDIBLE,RIGo,Right Inferior Gonion
+MANDIBLE,LSGo,Left Superior Gonion
+MANDIBLE,LIGo,Left Inferior Gonion
+MANDIBLE,RCo,Right Condylion
+MANDIBLE,LCo,Left Condylion
+MANDIBLE,RLCP,Right Lateral Condylar pole
+MANDIBLE,RMCP,Right Medial Condylar pole
+MANDIBLE,LLCP,Left Lateral Condylar pole
+MANDIBLE,LMCP,Left Medial Condylar pole
+MANDIBLE,LR6,Right Mandibular molar cusp tip
+MANDIBLE,LL6,Left Maxillary molar cusp tip
+MANDIBLE,LR’6,Right Maxillary molar root apex
+MANDIBLE,LL’6,Left Maxillary molar root apex
+MANDIBLE,LR6AB,Buccal Alveolar Bone Level at first molar
+MANDIBLE,LL6AB,Buccal Alveolar Bone Level at first molar
+MANDIBLE,LR5,Right Maxillary 2nd premolar cusp tip
+MANDIBLE,LL5,Left Maxillary 2nd premolar cusp tip
+MANDIBLE,LR’5,Right Maxillary 2nd premolar root apex
+MANDIBLE,LL’5,Left Maxillary 2nd premolar root apex
+MANDIBLE,LR4,Right Maxillary 1st premolar cusp tip
+MANDIBLE,LL4,Left Maxillary 1st premolar cusp tip
+MANDIBLE,LR’4,Right Maxillary 1st premolar root apex
+MANDIBLE,LL’4,Left Maxillary 1st premolar root apex
+MANDIBLE,LR3,Right Maxillary 1st premolar cusp tip
+MANDIBLE,LL3,Left Maxillary 1st premolar cusp tip
+MANDIBLE,LR’3,Right Maxillary 1st premolar root apex
+MANDIBLE,LL’3,Left Maxillary 1st premolar root apex
+MANDIBLE,L1,Maxillary incisor incisal edge
+MANDIBLE,L’1,Maxillary incisor root apex

Q3DC/Resources/UI/Q3DC.ui

@@ -56,7 +56,7 @@
      <property name="contentsFrameShape">
       <enum>QFrame::StyledPanel</enum>
      </property>
-     <layout class="QVBoxLayout" name="verticalLayout_2">
+     <layout class="QVBoxLayout" name="landmarkModifLayout">
       <item>
        <layout class="QHBoxLayout" name="inputModelLayout">
         <item>
@@ -189,6 +189,13 @@
         </item>
        </layout>
       </item>
+      <item>
+       <widget class="QLabel" name="landmarkLegendLabel">
+        <property name="text">
+         <string>Landmark Legend</string>
+        </property>
+       </widget>
+      </item>
      </layout>
     </widget>
    </item>