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Use SimpleITK for image sequence datasets (#226)
* Use SimpleITK's image sequence importer when available * SimpleITKDicomImporter * Use image file importer for tiff
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -7,7 +7,8 @@ public enum ImageFileFormat | |
| { | ||
| VASP, | ||
| NRRD, | ||
| NIFTI | ||
| NIFTI, | ||
| Unknown | ||
| } | ||
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| /// <summary> | ||
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186 changes: 186 additions & 0 deletions
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Assets/Scripts/Importing/ImageSequenceImporter/SimpleITK/SimpleITKDICOMImporter.cs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,186 @@ | ||
| #if UVR_USE_SIMPLEITK | ||
| using UnityEngine; | ||
| using System; | ||
| using itk.simple; | ||
| using System.Runtime.InteropServices; | ||
| using System.Collections.Generic; | ||
| using System.IO; | ||
| using System.Threading.Tasks; | ||
|
|
||
| namespace UnityVolumeRendering | ||
| { | ||
| /// <summary> | ||
| /// SimpleITK-based DICOM importer. | ||
| /// Has support for JPEG2000 and more. | ||
| /// </summary> | ||
| public class SimpleITKDICOMImporter : IImageSequenceImporter | ||
| { | ||
| public class ImageSequenceSlice : IImageSequenceFile | ||
| { | ||
| public string filePath; | ||
|
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| public string GetFilePath() | ||
| { | ||
| return filePath; | ||
| } | ||
| } | ||
|
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| public class ImageSequenceSeries : IImageSequenceSeries | ||
| { | ||
| public List<ImageSequenceSlice> files = new List<ImageSequenceSlice>(); | ||
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| public IEnumerable<IImageSequenceFile> GetFiles() | ||
| { | ||
| return files; | ||
| } | ||
| } | ||
|
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| public IEnumerable<IImageSequenceSeries> LoadSeries(IEnumerable<string> files, ImageSequenceImportSettings settings) | ||
| { | ||
| List<ImageSequenceSeries> seriesList= LoadSeriesInternal(files); | ||
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| return seriesList; | ||
| } | ||
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| public async Task<IEnumerable<IImageSequenceSeries>> LoadSeriesAsync(IEnumerable<string> files, ImageSequenceImportSettings settings) | ||
| { | ||
| List<ImageSequenceSeries> seriesList = null; | ||
| await Task.Run(() => seriesList=LoadSeriesInternal(files)); | ||
|
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| return seriesList; | ||
| } | ||
|
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| private List<ImageSequenceSeries> LoadSeriesInternal(IEnumerable<string> files) | ||
| { | ||
| HashSet<string> directories = new HashSet<string>(); | ||
|
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| foreach (string file in files) | ||
| { | ||
| string dir = Path.GetDirectoryName(file); | ||
| if (!directories.Contains(dir)) | ||
| directories.Add(dir); | ||
| } | ||
|
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| List<ImageSequenceSeries> seriesList = new List<ImageSequenceSeries>(); | ||
| Dictionary<string, VectorString> directorySeries = new Dictionary<string, VectorString>(); | ||
| foreach (string directory in directories) | ||
| { | ||
| VectorString seriesIDs = ImageSeriesReader.GetGDCMSeriesIDs(directory); | ||
| directorySeries.Add(directory, seriesIDs); | ||
|
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| } | ||
|
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| foreach (var dirSeries in directorySeries) | ||
| { | ||
| foreach (string seriesID in dirSeries.Value) | ||
| { | ||
| VectorString dicom_names = ImageSeriesReader.GetGDCMSeriesFileNames(dirSeries.Key, seriesID); | ||
| ImageSequenceSeries series = new ImageSequenceSeries(); | ||
| foreach (string file in dicom_names) | ||
| { | ||
| ImageSequenceSlice sliceFile = new ImageSequenceSlice(); | ||
| sliceFile.filePath = file; | ||
| series.files.Add(sliceFile); | ||
| } | ||
| seriesList.Add(series); | ||
| } | ||
| } | ||
| return seriesList; | ||
| } | ||
|
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| public VolumeDataset ImportSeries(IImageSequenceSeries series, ImageSequenceImportSettings settings) | ||
| { | ||
| Image image = null; | ||
| float[] pixelData = null; | ||
| VectorUInt32 size = null; | ||
| VectorString dicomNames = null; | ||
|
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| // Create dataset | ||
| VolumeDataset volumeDataset = ScriptableObject.CreateInstance<VolumeDataset>(); | ||
|
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| ImageSequenceSeries sequenceSeries = (ImageSequenceSeries)series; | ||
| if (sequenceSeries.files.Count == 0) | ||
| { | ||
| Debug.LogError("Empty series. No files to load."); | ||
| return null; | ||
| } | ||
|
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| ImportSeriesInternal(dicomNames, sequenceSeries, image, size, pixelData, volumeDataset); | ||
|
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| return volumeDataset; | ||
| } | ||
|
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| public async Task<VolumeDataset> ImportSeriesAsync(IImageSequenceSeries series, ImageSequenceImportSettings settings) | ||
| { | ||
| Image image = null; | ||
| float[] pixelData = null; | ||
| VectorUInt32 size = null; | ||
| VectorString dicomNames = null; | ||
|
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| // Create dataset | ||
| VolumeDataset volumeDataset = ScriptableObject.CreateInstance<VolumeDataset>(); | ||
|
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| ImageSequenceSeries sequenceSeries = (ImageSequenceSeries)series; | ||
| if (sequenceSeries.files.Count == 0) | ||
| { | ||
| Debug.LogError("Empty series. No files to load."); | ||
| settings.progressHandler.Fail(); | ||
| return null; | ||
| } | ||
|
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| await Task.Run(() => ImportSeriesInternal(dicomNames, sequenceSeries, image, size, pixelData, volumeDataset)); | ||
|
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| return volumeDataset; | ||
| } | ||
|
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| private void ImportSeriesInternal(VectorString dicomNames, ImageSequenceSeries sequenceSeries, Image image, VectorUInt32 size, float[] pixelData, VolumeDataset volumeDataset) | ||
| { | ||
| ImageSeriesReader reader = new ImageSeriesReader(); | ||
|
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| dicomNames = new VectorString(); | ||
|
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| foreach (var dicomFile in sequenceSeries.files) | ||
| dicomNames.Add(dicomFile.filePath); | ||
| reader.SetFileNames(dicomNames); | ||
|
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| image = reader.Execute(); | ||
|
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| // Cast to 32-bit float | ||
| image = SimpleITK.Cast(image, PixelIDValueEnum.sitkFloat32); | ||
|
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| size = image.GetSize(); | ||
|
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| int numPixels = 1; | ||
| for (int dim = 0; dim < image.GetDimension(); dim++) | ||
| numPixels *= (int)size[dim]; | ||
|
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| // Read pixel data | ||
| pixelData = new float[numPixels]; | ||
| IntPtr imgBuffer = image.GetBufferAsFloat(); | ||
| Marshal.Copy(imgBuffer, pixelData, 0, numPixels); | ||
|
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| for (int i = 0; i < pixelData.Length; i++) | ||
| pixelData[i] = Mathf.Clamp(pixelData[i], -1024, 3071); | ||
|
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| VectorDouble spacing = image.GetSpacing(); | ||
|
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| volumeDataset.data = pixelData; | ||
| volumeDataset.dimX = (int)size[0]; | ||
| volumeDataset.dimY = (int)size[1]; | ||
| volumeDataset.dimZ = (int)size[2]; | ||
| volumeDataset.datasetName = Path.GetFileName(dicomNames[0]); | ||
| volumeDataset.filePath = dicomNames[0]; | ||
| 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 | ||
| ); | ||
|
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| // Convert from LPS to Unity's coordinate system | ||
| ImporterUtilsInternal.ConvertLPSToUnityCoordinateSpace(volumeDataset); | ||
|
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| volumeDataset.FixDimensions(); | ||
| } | ||
| } | ||
| } | ||
| #endif |
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