Properly handle coordinate systems on import (#170)

* Reverse pixel array to correct coordinate space. NRRD: Convert to LPS space first.

* Convert from LPS to Unity coordinates

* Make sure we don't break old serialised objects

* Select slicing plane on add

* Make sure imported datasets will have the same rotation as before. Removed 90 degree rotation from outer object - do this in each importer instead.

Assets/Editor/SliceRenderingEditorWindow.cs

@@ -1,5 +1,6 @@
 using UnityEngine;
 using UnityEditor;
+using System.Linq;
 
 namespace UnityVolumeRendering
 {
@@ -62,6 +63,13 @@ private void OnGUI()
 
             if (spawnedPlanes.Length > 0)
                 selectedPlaneIndex = selectedPlaneIndex % spawnedPlanes.Length;
+
+            if (Selection.activeGameObject != null)
+            {
+                int index = System.Array.FindIndex(spawnedPlanes, plane => plane.gameObject == Selection.activeGameObject);
+                if (index != -1)
+                    selectedPlaneIndex = index;
+            }
 
             if (GUI.Toggle(new Rect(0.0f, 0.0f, 40.0f, 40.0f), inputMode == InputMode.Move, new GUIContent(moveIconTexture, "Move slice"), GUI.skin.button))
                 inputMode = InputMode.Move;
@@ -77,7 +85,7 @@ private void OnGUI()
                 SlicingPlane planeObj = spawnedPlanes[System.Math.Min(selectedPlaneIndex, spawnedPlanes.Length - 1)];
                 Vector3 planeScale = planeObj.transform.lossyScale;
 
-                float heightWidthRatio = planeScale.z / planeScale.x;
+                float heightWidthRatio = Mathf.Abs(planeScale.z / planeScale.x);
                 float bgWidth = Mathf.Min(this.position.width - 20.0f, (this.position.height - 50.0f) * 2.0f);
                 float bgHeight = Mathf.Min(bgWidth, this.position.height - 150.0f);
                 bgWidth = bgHeight / heightWidthRatio;
@@ -102,7 +110,7 @@ private void OnGUI()
                 {
                     Vector2 mouseOffset = relMousePosNormalised - prevMousePos;
                     if (Mathf.Abs(mouseOffset.y) > 0.00001f)
-                        planeObj.transform.Translate(Vector3.up * mouseOffset.y);
+                        planeObj.transform.Translate(planeObj.transform.up * mouseOffset.y, Space.World);
                 }
                 // Show value at mouse position.
                 else if (inputMode == InputMode.Inspect)
@@ -152,7 +160,7 @@ private void OnGUI()
 
                 if (GUI.Button(new Rect(0.0f, bgRect.y + bgRect.height + 40.0f, 70.0f, 20.0f), "<"))
                 {
-                    selectedPlaneIndex = (selectedPlaneIndex - 1) % spawnedPlanes.Length;
+                    selectedPlaneIndex = selectedPlaneIndex == 0 ? spawnedPlanes.Length - 1 : selectedPlaneIndex - 1;
                     Selection.activeGameObject = spawnedPlanes[selectedPlaneIndex].gameObject;
                 }
                 if (GUI.Button(new Rect(90.0f, bgRect.y + bgRect.height + 40.0f, 70.0f, 20.0f), ">"))
@@ -169,19 +177,22 @@ private void OnGUI()
                 if (GUI.Button(new Rect(200.0f, bgRect.y + bgRect.height + 0.0f, 120.0f, 20.0f), "Create XY plane"))
                 {
                     selectedPlaneIndex = spawnedPlanes.Length;
-                    volRend.CreateSlicingPlane();
+                    SlicingPlane plane = volRend.CreateSlicingPlane();
+                    UnityEditor.Selection.objects = new UnityEngine.Object[] { plane.gameObject };
                 }
                 else if (GUI.Button(new Rect(200.0f, bgRect.y + bgRect.height + 20.0f, 120.0f, 20.0f), "Create XZ plane"))
                 {
                     selectedPlaneIndex = spawnedPlanes.Length;
                     SlicingPlane plane = volRend.CreateSlicingPlane();
                     plane.transform.localRotation = Quaternion.Euler(90.0f, 0.0f, 0.0f);
+                    UnityEditor.Selection.objects = new UnityEngine.Object[] { plane.gameObject };
                 }
                 else if (GUI.Button(new Rect(200.0f, bgRect.y + bgRect.height + 40.0f, 120.0f, 20.0f), "Create ZY plane"))
                 {
                     selectedPlaneIndex = spawnedPlanes.Length;
                     SlicingPlane plane = volRend.CreateSlicingPlane();
                     plane.transform.localRotation = Quaternion.Euler(0.0f, 0.0f, 90.0f);
+                    UnityEditor.Selection.objects = new UnityEngine.Object[] { plane.gameObject };
                 }
             }
 
@@ -215,16 +226,16 @@ private Vector3 GetWorldPosition(Vector2 relativeMousePosition, SlicingPlane sli
         private Vector3 GetDataPosition(Vector2 relativeMousePosition, SlicingPlane slicingPlane)
         {
             Vector3 worldSpacePosition = GetWorldPosition(relativeMousePosition, slicingPlane);
-            Vector3 objSpacePoint = slicingPlane.targetObject.transform.InverseTransformPoint(worldSpacePosition);
+            Vector3 objSpacePoint = slicingPlane.targetObject.volumeContainerObject.transform.InverseTransformPoint(worldSpacePosition);
             Vector3 uvw = objSpacePoint + Vector3.one * 0.5f;
             VolumeDataset dataset = slicingPlane.targetObject.dataset;
-            return new Vector3(uvw.x * dataset.scaleX, uvw.y * dataset.scaleY,uvw.z * dataset.scaleZ);
+            return new Vector3(uvw.x * dataset.scale.x, uvw.y * dataset.scale.y, uvw.z * dataset.scale.z);
         }
 
         private float GetValueAtPosition(Vector2 relativeMousePosition, SlicingPlane slicingPlane)
         {
             Vector3 worldSpacePosition = GetWorldPosition(relativeMousePosition, slicingPlane);
-            Vector3 objSpacePoint = slicingPlane.targetObject.transform.InverseTransformPoint(worldSpacePosition);
+            Vector3 objSpacePoint = slicingPlane.targetObject.volumeContainerObject.transform.InverseTransformPoint(worldSpacePosition);
             VolumeDataset dataset = slicingPlane.targetObject.dataset;
             // Convert to texture coordinates.
             Vector3 uvw = objSpacePoint + Vector3.one * 0.5f;

Assets/Scripts/Importing/ImageFileImporter/Nifti.NET/NiftiImporter.cs

@@ -76,11 +76,10 @@ private void ImportInternal(VolumeDataset volumeDataset,Nifti.NET.Nifti niftiFil
             volumeDataset.dimZ = dimZ;
             volumeDataset.datasetName = "test";
             volumeDataset.filePath = filePath;
-            volumeDataset.scaleX = size.x;
-            volumeDataset.scaleY = size.y;
-            volumeDataset.scaleZ = size.z;
+            volumeDataset.scale = size;
 
             volumeDataset.FixDimensions();
+            volumeDataset.rotation = Quaternion.Euler(90.0f, 0.0f, 0.0f);
         }
     }
 }

Assets/Scripts/Importing/ImageFileImporter/SimpleITK/SimpleITKImageFileImporter.cs

@@ -49,6 +49,9 @@ private void ImportInternal(VolumeDataset volumeDataset, float[] pixelData,Vecto
 
             Image image = reader.Execute();
 
+            // Convert to LPS coordinate system (may be needed for NRRD and other datasets)
+            SimpleITK.DICOMOrient(image, "LPS");
+
             // Cast to 32-bit float
             image = SimpleITK.Cast(image, PixelIDValueEnum.sitkFloat32);
 
@@ -62,18 +65,23 @@ private void ImportInternal(VolumeDataset volumeDataset, float[] pixelData,Vecto
             pixelData = new float[numPixels];
             IntPtr imgBuffer = image.GetBufferAsFloat();
             Marshal.Copy(imgBuffer, pixelData, 0, numPixels);
-            spacing = image.GetSpacing();
 
+            spacing = image.GetSpacing();
 
             volumeDataset.data = pixelData;
             volumeDataset.dimX = (int)size[0];
             volumeDataset.dimY = (int)size[1];
             volumeDataset.dimZ = (int)size[2];
             volumeDataset.datasetName = "test";
             volumeDataset.filePath = filePath;
-            volumeDataset.scaleX = (float)(spacing[0] * size[0]);
-            volumeDataset.scaleY = (float)(spacing[1] * size[1]);
-            volumeDataset.scaleZ = (float)(spacing[2] * size[2]);
+            volumeDataset.scale = new Vector3(
+                (float)(spacing[0] * size[0]) / 1000.0f, // mm to m
+                (float)(spacing[1] * size[1]) / 1000.0f, // mm to m
+                (float)(spacing[2] * size[2]) / 1000.0f // mm to m
+            );
+
+            // Convert from LPS to Unity's coordinate system
+            ImporterUtilsInternal.ConvertLPSToUnityCoordinateSpace(volumeDataset);
 
             volumeDataset.FixDimensions();
         }

Assets/Scripts/Importing/ImageFileImporter/VASP/ParDatasetImporter.cs

@@ -142,6 +142,7 @@ private void ImportInternal(VolumeDataset dataFiller)
             {
                 dataFiller.data[i] = dataGrid[i];
             }
+            dataFiller.rotation = Quaternion.Euler(90.0f, 0.0f, 0.0f);
         }
 
         private string ParseLine()

Assets/Scripts/Importing/ImageSequenceImporter/ImageSequenceImporter/ImageSequenceImporter.cs

@@ -92,6 +92,7 @@ public VolumeDataset ImportSeries(IImageSequenceSeries series, ImageSequenceImpo
             VolumeDataset dataset = FillVolumeDataset(data, dimensions);
 
             dataset.FixDimensions();
+            dataset.rotation = Quaternion.Euler(90.0f, 0.0f, 0.0f);
 
             return dataset;
         }
@@ -211,9 +212,11 @@ private void FillVolumeInternal(VolumeDataset dataset,string name,int[] data, Ve
             dataset.dimX = dimensions.x;
             dataset.dimY = dimensions.y;
             dataset.dimZ = dimensions.z;
-            dataset.scaleX = 1f; // Scale arbitrarily normalised around the x-axis 
-            dataset.scaleY = (float)dimensions.y / (float)dimensions.x;
-            dataset.scaleZ = (float)dimensions.z / (float)dimensions.x;
+            dataset.scale = new Vector3(
+                1f, // Scale arbitrarily normalised around the x-axis 
+                (float)dimensions.y / (float)dimensions.x,
+                (float)dimensions.z / (float)dimensions.x
+            );
         }
 
 

Assets/Scripts/Importing/ImageSequenceImporter/OpenDICOM/DICOMImporter.cs

@@ -222,12 +222,15 @@ private void ImportSeriesInternal(List<DICOMSliceFile> files,VolumeDataset datas
 
             if (files[0].pixelSpacing > 0.0f)
             {
-                dataset.scaleX = files[0].pixelSpacing * dataset.dimX;
-                dataset.scaleY = files[0].pixelSpacing * dataset.dimY;
-                dataset.scaleZ = Mathf.Abs(files[files.Count - 1].location - files[0].location);
+                dataset.scale = new Vector3(
+                    files[0].pixelSpacing * dataset.dimX,
+                    files[0].pixelSpacing * dataset.dimY,
+                    Mathf.Abs(files[files.Count - 1].location - files[0].location)
+                );
             }
 
             dataset.FixDimensions();
+            dataset.rotation = Quaternion.Euler(90.0f, 0.0f, 0.0f);
         }
 
         private DICOMSliceFile ReadDICOMFile(string filePath)

Assets/Scripts/Importing/ImageSequenceImporter/SimpleITK/SimpleITKImageSequenceImporter.cs

@@ -134,7 +134,7 @@ public async Task<VolumeDataset> ImportSeriesAsync(IImageSequenceSeries series,
             return volumeDataset;
         }
 
-        private void ImportSeriesInternal(VectorString dicomNames, ImageSequenceSeries sequenceSeries, Image image, VectorUInt32 size, float[] pixelData,VolumeDataset volumeDataset)
+        private void ImportSeriesInternal(VectorString dicomNames, ImageSequenceSeries sequenceSeries, Image image, VectorUInt32 size, float[] pixelData, VolumeDataset volumeDataset)
         {
             ImageSeriesReader reader = new ImageSeriesReader();
 
@@ -162,6 +162,7 @@ private void ImportSeriesInternal(VectorString dicomNames, ImageSequenceSeries s
 
             for (int i = 0; i < pixelData.Length; i++)
                 pixelData[i] = Mathf.Clamp(pixelData[i], -1024, 3071);
+
             VectorDouble spacing = image.GetSpacing();
 
             volumeDataset.data = pixelData;
@@ -170,9 +171,14 @@ private void ImportSeriesInternal(VectorString dicomNames, ImageSequenceSeries s
             volumeDataset.dimZ = (int)size[2];
             volumeDataset.datasetName = "test";
             volumeDataset.filePath = dicomNames[0];
-            volumeDataset.scaleX = (float)(spacing[0] * size[0]);
-            volumeDataset.scaleY = (float)(spacing[1] * size[1]);
-            volumeDataset.scaleZ = (float)(spacing[2] * size[2]);
+            volumeDataset.scale = new Vector3(
+                (float)(spacing[0] * size[0]) / 1000.0f, // mm to m
+                (float)(spacing[1] * size[1]) / 1000.0f, // mm to m
+                (float)(spacing[2] * size[2]) / 1000.0f // mm to m
+            );
+
+            // Convert from LPS to Unity's coordinate system
+            ImporterUtilsInternal.ConvertLPSToUnityCoordinateSpace(volumeDataset);
 
             volumeDataset.FixDimensions();
         }

Assets/Scripts/Importing/ImporterUtilsInternal.cs

@@ -0,0 +1,20 @@
+using System.IO;
+using UnityEngine;
+using System;
+using UnityEditor;
+
+namespace UnityVolumeRendering
+{
+    public class ImporterUtilsInternal
+    {
+        public static void ConvertLPSToUnityCoordinateSpace(VolumeDataset volumeDataset)
+        {
+            volumeDataset.scale = new Vector3(
+                -volumeDataset.scale.x,
+                volumeDataset.scale.y,
+                volumeDataset.scale.z
+            );
+            volumeDataset.rotation = Quaternion.Euler(90.0f, 0.0f, 0.0f);
+        }
+    }
+}

Assets/Scripts/Importing/RawImporter/RawDatasetImporter.cs

@@ -95,8 +95,7 @@ await Task.Run(() => {
             }
             VolumeDataset dataset = new VolumeDataset();
 
-
-            await Task.Run(() => ImportInternal(dataset,reader,fs));
+            await Task.Run(() => ImportInternal(dataset, reader, fs));
 
             return dataset;
         }
@@ -126,6 +125,7 @@ private void ImportInternal(VolumeDataset dataset, BinaryReader reader, FileStre
             fs.Close();
 
             dataset.FixDimensions();
+            dataset.rotation = Quaternion.Euler(90.0f, 0.0f, 0.0f);
         }
         private int ReadDataValue(BinaryReader reader)
         {

Assets/Scripts/VolumeData/VolumeDataset.cs

@@ -5,14 +5,15 @@
 using Unity.Collections;
 using UnityEditor;
 using UnityEngine;
+using UnityEngine.Serialization;
 
 namespace UnityVolumeRendering
 {
     /// <summary>
     /// An imported dataset. Has a dimension and a 3D pixel array.
     /// </summary>
     [Serializable]
-    public class VolumeDataset : ScriptableObject
+    public class VolumeDataset : ScriptableObject, ISerializationCallbackReceiver
     {
         public string filePath;
 
@@ -24,11 +25,10 @@ public class VolumeDataset : ScriptableObject
         public int dimX, dimY, dimZ;
 
         [SerializeField]
-        public float scaleX = 1.0f;
-        [SerializeField]
-        public float scaleY = 1.0f;
+        public Vector3 scale = Vector3.one;
+
         [SerializeField]
-        public float scaleZ = 1.0f;
+        public Quaternion rotation;
 
         public float volumeScale;
 
@@ -44,6 +44,13 @@ public class VolumeDataset : ScriptableObject
         private SemaphoreSlim createDataTextureLock = new SemaphoreSlim(1, 1);
         private SemaphoreSlim createGradientTextureLock = new SemaphoreSlim(1, 1);
 
+        [SerializeField, System.Obsolete("Use scale instead")]
+        private float scaleX = 1.0f;
+        [SerializeField, System.Obsolete("Use scale instead")]
+        private float scaleY = 1.0f;
+        [SerializeField, System.Obsolete("Use scale instead")]
+        private float scaleZ = 1.0f;
+
         public Texture3D GetDataTexture()
         {
             if (dataTexture == null)
@@ -360,5 +367,18 @@ public float GetData(int x, int y, int z)
         {
             return data[x + y * dimX + z * (dimX * dimY)];
         }
+
+        public void OnBeforeSerialize()
+        {
+            scaleX = scale.x;
+            scaleY = scale.y;
+            scaleZ = scale.z;
+        }
+
+        public void OnAfterDeserialize()
+        {
+            scale = new Vector3(scaleX, scaleY, scaleZ);
+            Debug.Log(scale);
+        }
     }
 }

Assets/Scripts/VolumeObject/CrossSectionPlane.cs

@@ -45,7 +45,7 @@ public CrossSectionType GetCrossSectionType()
 
         public Matrix4x4 GetMatrix()
         {
-            return transform.worldToLocalMatrix * targetObject.transform.localToWorldMatrix;
+            return transform.worldToLocalMatrix * targetObject.volumeContainerObject.transform.localToWorldMatrix;
         }
     }
 }

Assets/Scripts/VolumeObject/CutoutBox.cs

@@ -61,7 +61,7 @@ public CrossSectionType GetCrossSectionType()
 
         public Matrix4x4 GetMatrix()
         {
-            return transform.worldToLocalMatrix * targetObject.transform.localToWorldMatrix;
+            return transform.worldToLocalMatrix * targetObject.volumeContainerObject.transform.localToWorldMatrix;
         }
     }
 }

Assets/Scripts/VolumeObject/CutoutSphere.cs

@@ -30,7 +30,7 @@ public CrossSectionType GetCrossSectionType()
 
     public Matrix4x4 GetMatrix()
     {
-        return transform.worldToLocalMatrix * targetObject.transform.localToWorldMatrix;
+        return transform.worldToLocalMatrix * targetObject.volumeContainerObject.transform.localToWorldMatrix;
     }
 
     private void OnEnable()