Added option for clamping Hounsfield scale values (now OFF by default) (mlavik1#262)

Author: mlavik1

Assets/Editor/ImportSettingsEditorWindow.cs

@@ -37,6 +37,12 @@ private void OnGUI()
             PlayerPrefs.SetInt("NormaliseScaleOnImport", normaliseScaleOnImport ? 1 : 0);
             EditorGUILayout.EndHorizontal();
 
+            EditorGUILayout.BeginHorizontal();
+            EditorGUILayout.LabelField("Clamp Hounsfield values to body tissues range?");
+            bool clampHounsfield = EditorGUILayout.Toggle("", PlayerPrefs.GetInt("ClampHounsfield") > 0);
+            PlayerPrefs.SetInt("ClampHounsfield", clampHounsfield ? 1 : 0);
+            EditorGUILayout.EndHorizontal();
+
             EditorGUILayout.Space();
             EditorGUILayout.Space();
 

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

@@ -147,7 +147,8 @@ public VolumeDataset ImportSeries(IImageSequenceSeries series, ImageSequenceImpo
             // Create dataset
             VolumeDataset dataset = ScriptableObject.CreateInstance<VolumeDataset>();
 
-            ImportSeriesInternal(files, dataset, settings.progressHandler);
+            bool clampHounsfield = PlayerPrefs.GetInt("ClampHounsfield") > 0;
+            ImportSeriesInternal(files, dataset, settings.progressHandler, clampHounsfield);
 
             return dataset;
         }
@@ -165,11 +166,12 @@ public async Task<VolumeDataset> ImportSeriesAsync(IImageSequenceSeries series,
             // Create dataset
             VolumeDataset dataset = ScriptableObject.CreateInstance<VolumeDataset>();
 
-            await Task.Run(() => ImportSeriesInternal(files,dataset, settings.progressHandler));
+            bool clampHounsfield = PlayerPrefs.GetInt("ClampHounsfield") > 0;
+            await Task.Run(() => ImportSeriesInternal(files,dataset, settings.progressHandler, clampHounsfield));
 
             return dataset;
         }
-        private void ImportSeriesInternal(List<DICOMSliceFile> files,VolumeDataset dataset, IProgressHandler progress)
+        private void ImportSeriesInternal(List<DICOMSliceFile> files,VolumeDataset dataset, IProgressHandler progress, bool clampHounsfield)
         {
             // Calculate slice location from "Image Position" (0020,0032)
             CalculateSliceLocations(files);
@@ -205,7 +207,10 @@ private void ImportSeriesInternal(List<DICOMSliceFile> files,VolumeDataset datas
                         int pixelValue = pixelArr[pixelIndex];
                         float hounsfieldValue = pixelValue * slice.slope + slice.intercept;
 
-                        dataset.data[dataIndex] = Mathf.Clamp(hounsfieldValue, -1024.0f, 3071.0f);
+                        if (clampHounsfield)
+                            hounsfieldValue = Mathf.Clamp(hounsfieldValue, -1024.0f, 3071.0f);
+
+                        dataset.data[dataIndex] = hounsfieldValue;
                     }
                 }
             }

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

@@ -105,7 +105,8 @@ public VolumeDataset ImportSeries(IImageSequenceSeries series, ImageSequenceImpo
                 return null;
             }
 
-            ImportSeriesInternal(dicomNames, sequenceSeries, image, size, pixelData, volumeDataset);
+            bool clampHounsfield = PlayerPrefs.GetInt("ClampHounsfield") > 0;
+            ImportSeriesInternal(dicomNames, sequenceSeries, image, size, pixelData, volumeDataset, clampHounsfield);
 
             return volumeDataset;
         }
@@ -128,12 +129,13 @@ public async Task<VolumeDataset> ImportSeriesAsync(IImageSequenceSeries series,
                 return null;
             }
 
-            await Task.Run(() => ImportSeriesInternal(dicomNames, sequenceSeries, image, size, pixelData, volumeDataset));
+            bool clampHounsfield = PlayerPrefs.GetInt("ClampHounsfield") > 0;
+            await Task.Run(() => ImportSeriesInternal(dicomNames, sequenceSeries, image, size, pixelData, volumeDataset, clampHounsfield));
 
             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, bool clampHounsfield)
         {
             ImageSeriesReader reader = new ImageSeriesReader();
 
@@ -163,7 +165,12 @@ private void ImportSeriesInternal(VectorString dicomNames, ImageSequenceSeries s
             Marshal.Copy(imgBuffer, pixelData, 0, numPixels);
 
             for (int i = 0; i < pixelData.Length; i++)
-                pixelData[i] = Mathf.Clamp(pixelData[i], -1024, 3071);
+            {
+                if (clampHounsfield)
+                    pixelData[i] = Mathf.Clamp(pixelData[i], -1024.0f, 3071.0f);
+                else
+                    pixelData[i] = pixelData[i];
+            }
 
             VectorDouble spacing = image.GetSpacing();