SimpleITK importers: Respect spacing. Added more comments.

Assets/Editor/SimpleITK/SimpleITKManager.cs

@@ -9,6 +9,12 @@ using System.IO.Compression;
 
 namespace UnityVolumeRendering
 {
+    /// <summary>
+    /// Manager for the SimpleITK integration.
+    /// Since SimpleITK is a native library that requires binaries to be built for your target platform,
+    ///  SimpleITK will be disabled by default and can be enabled through this class.
+    /// The binaries will be downloaded automatically.
+    /// </summary>
     public class SimpleITKManager
     {
         private static string SimpleITKDefinition = "UVR_USE_SIMPLEITK";
@@ -24,8 +30,14 @@ namespace UnityVolumeRendering
 
         public static void EnableSITK(bool enable)
         {
-            List<BuildTargetGroup> buildTargetGroups = new List<BuildTargetGroup> (){ BuildTargetGroup.Standalone };
+            if (!HasDownloadedBinaries())
+            {
+                EditorUtility.DisplayDialog("Missing SimpleITK binaries", "You need to download the SimpleITK binaries before you can enable SimpleITK.", "Ok");
+                return;
+            }
 
+            // Enable the UVR_USE_SIMPLEITK preprocessor definition for standalone target
+            List<BuildTargetGroup> buildTargetGroups = new List<BuildTargetGroup> (){ BuildTargetGroup.Standalone };
             foreach (BuildTargetGroup group in buildTargetGroups)
             {
                 List<string> defines = PlayerSettings.GetScriptingDefineSymbolsForGroup(group).Split(';').ToList();

Assets/Scripts/Importing/DatasetImporterUtility.cs

@@ -18,7 +18,6 @@ namespace UnityVolumeRendering
 
     public class DatasetImporterUtility
     {
-
         public static DatasetType GetDatasetType(string filePath)
         {
             DatasetType datasetType;

Assets/Scripts/Importing/ImageFileImporter/Interface/IImageFileImporter.cs

@@ -9,6 +9,10 @@ namespace UnityVolumeRendering
         NIFTI
     }
 
+    /// <summary>
+    /// Interface for single file dataset importers (NRRD, NIFTI, etc.).
+    /// These datasets contain only one single file.
+    /// </summary>
     public interface IImageFileImporter
     {
         VolumeDataset Import(String filePath);

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

@@ -8,9 +8,11 @@ using System.IO;
 
 namespace UnityVolumeRendering
 {
+    /// <summary>
+    /// SimpleITK-based DICOM importer.
+    /// </summary>
     public class SimpleITKImageFileImporter : IImageFileImporter
     {
-
         public VolumeDataset Import(string filePath)
         {
             ImageFileReader reader = new ImageFileReader();
@@ -23,7 +25,6 @@ namespace UnityVolumeRendering
             image = SimpleITK.Cast(image, PixelIDValueEnum.sitkFloat32);
 
             VectorUInt32 size = image.GetSize();
-            Debug.Log("Image size: " + size[0] + " " + size[1] + " " + size[2]);
 
             int numPixels = 1;
             for (int dim = 0; dim < image.GetDimension(); dim++)
@@ -34,6 +35,8 @@ namespace UnityVolumeRendering
             IntPtr imgBuffer = image.GetBufferAsFloat();
             Marshal.Copy(imgBuffer, pixelData, 0, numPixels);
 
+            VectorDouble spacing = image.GetSpacing();
+
             // Create dataset
             VolumeDataset volumeDataset = new VolumeDataset();
             volumeDataset.data = pixelData;
@@ -42,6 +45,11 @@ namespace UnityVolumeRendering
             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.FixDimensions();
 
             return volumeDataset;
         }

Assets/Scripts/Importing/ImageSequenceImporter/Interface/IImageSequenceImporter.cs

@@ -18,9 +18,27 @@ namespace UnityVolumeRendering
         IEnumerable<IImageSequenceFile> GetFiles();
     }
 
+    /// <summary>
+    /// Importer for image sequence datasets, such as DICOM and image sequences.
+    /// These datasets usually contain one file per slice.
+    /// </summary>
     public interface IImageSequenceImporter
     {
+        /// <summary>
+        /// Read a list of files, and return all image sequence series.
+        /// Normally a directory will only contain a single series,
+        ///  but if a folder contains multiple series/studies than this function will return all of them.
+        /// Each series should be imported separately, resulting in one dataset per series. (mostly relevant for DICOM)
+        /// </summary>
+        /// <param name="files">Files to load. Typically all the files stored in a specific (DICOM) directory.</param>
+        /// <returns>List of image sequence series.</returns>
         IEnumerable<IImageSequenceSeries> LoadSeries(IEnumerable<string> files);
+        
+        /// <summary>
+        /// Import a single image sequence series.
+        /// </summary>
+        /// <param name="series">The series to import</param>
+        /// <returns>Imported 3D volume dataset.</returns>
         VolumeDataset ImportSeries(IImageSequenceSeries series);
     }
 }

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

@@ -14,8 +14,7 @@ namespace UnityVolumeRendering
 {
     /// <summary>
     /// DICOM importer.
-    /// Reads a 3D DICOM dataset from a folder.
-    /// The folder needs to contain several .dcm/.dicom files, where each file is a slice of the same dataset.
+    /// Reads a 3D DICOM dataset from a list of DICOM files.
     /// </summary>
     public class DICOMImporter : IImageSequenceImporter
     {

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

@@ -95,7 +95,6 @@ namespace UnityVolumeRendering
             image = SimpleITK.Cast(image, PixelIDValueEnum.sitkFloat32);
 
             VectorUInt32 size = image.GetSize();
-            Debug.Log("Image size: " + size[0] + " " + size[1] + " " + size[2]);
 
             int numPixels = 1;
             for (int dim = 0; dim < image.GetDimension(); dim++)
@@ -109,6 +108,8 @@ namespace UnityVolumeRendering
             for (int i = 0; i < pixelData.Length; i++)
                 pixelData[i] = Mathf.Clamp(pixelData[i], -1024, 3071);
 
+            VectorDouble spacing = image.GetSpacing();
+
             // Create dataset
             VolumeDataset volumeDataset = new VolumeDataset();
             volumeDataset.data = pixelData;
@@ -117,6 +118,11 @@ namespace UnityVolumeRendering
             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.FixDimensions();
 
             return volumeDataset;
         }

Assets/Scripts/Importing/ImporterFactory.cs

@@ -3,8 +3,19 @@ using UnityEngine;
 
 namespace UnityVolumeRendering
 {
+    /// <summary>
+    /// Factory for creating importers, for each format.
+    /// Use this if you only want to import a dataset, without deciding which importer to use.
+    /// Some dataset formats can be imported using several different importers, in which case this factory will return the best alternative.
+    /// </summary>
     public class ImporterFactory
     {
+        /// <summary>
+        /// Create an importer for an image sequence dataset (multiple files) of the specified format.
+        /// Use this for DICOM and image sequences.
+        /// </summary>
+        /// <param name="format">Format of the dataset.</param>
+        /// <returns></returns>
         public static IImageSequenceImporter CreateImageSequenceImporter(ImageSequenceFormat format)
         {
             Type importerType = GetImageSequenceImporterType(format);
@@ -19,6 +30,12 @@ namespace UnityVolumeRendering
             }
         }
 
+        /// <summary>
+        /// Create an importer for an image file dataset (single file) of the specified format.
+        /// Use this for NRRD, NIFTI and VASP/PARCHG.
+        /// </summary>
+        /// <param name="format">Format of the dataset.</param>
+        /// <returns></returns>
         public static IImageFileImporter CreateImageFileImporter(ImageFileFormat format)
         {
             Type importerType = GetImageFileImporterType(format);