private AcrNemaFile LoadFile(string filePath)
{
AcrNemaFile file = null;
try
{
if (DicomFile.IsDicomFile(filePath))
{
file = new DicomFile(filePath, false);
}
else if (AcrNemaFile.IsAcrNemaFile(filePath))
{
file = new AcrNemaFile(filePath, false);
}
else
{
Debug.LogError("Selected file is neither a DICOM nor an ACR-NEMA file.");
}
}
catch (Exception dicomFileException)
{
Debug.LogError($"Problems processing the DICOM file {filePath} :\n {dicomFileException}");
return(null);
}
return(file);
}
private static void ExtractDataandSave(string folderName, AcrNemaFile file)
{
var b = new XmlFile(file, true);
b.SaveTo(folderName + "//XML_WithoutPD.xml");
if (!file.HasPixelData)
{
return;
}
var pixelData = file.PixelData;
int count = 0;
foreach (var item in pixelData.ToBytesArray())
{
count++;
try
{
var ms = new MemoryStream(item);
Image img = Image.FromStream(ms);
img.Save(folderName + "//Image" + count + ".jpg");
img.Dispose();
}
catch
{
count--;
}
}
}
private static void PerformExtraction(string filePath)
{
AcrNemaFile file;
if (DicomFile.IsDicomFile(filePath))
{
file = new DicomFile(filePath, false);
}
else if (AcrNemaFile.IsAcrNemaFile(filePath))
{
file = new AcrNemaFile(filePath, false);
}
else
{
return;
}
string filename = new FileInfo(filePath).Name;
string fileFolder = Directory.GetParent(filePath) + "\\" + filename + "_dicom";
if (!Directory.Exists(fileFolder))
{
Directory.CreateDirectory(fileFolder);
}
ExtractDataandSave(fileFolder, file);
}
private DICOMSliceFile ReadDICOMFile(string filePath)
{
AcrNemaFile file = LoadFile(filePath);
if (file != null && file.HasPixelData)
{
DICOMSliceFile slice = new DICOMSliceFile();
slice.file = file;
// Read location
Tag locTag = new Tag("(0020,1041)");
if (file.DataSet.Contains(locTag))
{
DataElement elemLoc = file.DataSet[locTag];
slice.location = (float)Convert.ToDouble(elemLoc.Value[0]);
}
else
{
Debug.LogError($"Missing location tag in file: {filePath}.\n The file will not be imported");
return(null);
}
// Read intercept
Tag interceptTag = new Tag("(0028,1052)");
if (file.DataSet.Contains(interceptTag))
{
DataElement elemIntercept = file.DataSet[interceptTag];
slice.intercept = (float)Convert.ToDouble(elemIntercept.Value[0]);
}
else
{
Debug.LogWarning($"The file {filePath} is missing the intercept element. As a result, the default transfer function might not look good.");
}
// Read slope
Tag slopeTag = new Tag("(0028,1053)");
if (file.DataSet.Contains(slopeTag))
{
DataElement elemSlope = file.DataSet[slopeTag];
slice.slope = (float)Convert.ToDouble(elemSlope.Value[0]);
}
else
{
Debug.LogWarning($"The file {filePath} is missing the intercept element. As a result, the default transfer function might not look good.");
}
// Read pixel spacing
Tag pixelSpacingTag = new Tag("(0028,0030)");
if (file.DataSet.Contains(pixelSpacingTag))
{
DataElement elemPixelSpacing = file.DataSet[pixelSpacingTag];
slice.pixelSpacing = (float)Convert.ToDouble(elemPixelSpacing.Value[0]);
}
return(slice);
}
return(null);
}
private static bool IsDicomFile(string filePath)
{
if (DicomFile.IsDicomFile(filePath))
{
return(true);
}
if (AcrNemaFile.IsAcrNemaFile(filePath))
{
return(true);
}
return(false);
}
private DICOMSliceFile ReadDICOMFile(string filePath)
{
AcrNemaFile file = LoadFile(filePath);
if (file != null && file.HasPixelData)
{
DICOMSliceFile slice = new DICOMSliceFile();
slice.file = file;
slice.filePath = filePath;
Tag locTag = new Tag("(0020,1041)");
Tag posTag = new Tag("(0020,0032)");
Tag interceptTag = new Tag("(0028,1052)");
Tag slopeTag = new Tag("(0028,1053)");
Tag pixelSpacingTag = new Tag("(0028,0030)");
Tag seriesUIDTag = new Tag("(0020,000E)");
// Read location (optional)
if (file.DataSet.Contains(locTag))
{
DataElement elemLoc = file.DataSet[locTag];
slice.location = (float)Convert.ToDouble(elemLoc.Value[0]);
}
// If no location tag, read position tag (will need to calculate location afterwards)
else if (file.DataSet.Contains(posTag))
{
DataElement elemLoc = file.DataSet[posTag];
Vector3 pos = Vector3.zero;
pos.x = (float)Convert.ToDouble(elemLoc.Value[0]);
pos.y = (float)Convert.ToDouble(elemLoc.Value[1]);
pos.z = (float)Convert.ToDouble(elemLoc.Value[2]);
slice.position = pos;
slice.missingLocation = true;
}
else
{
Debug.LogError($"Missing location/position tag in file: {filePath}.\n The file will not be imported correctly.");
// Fallback: use counter as location
slice.location = (float)iFallbackLoc++;
}
// Read intercept
if (file.DataSet.Contains(interceptTag))
{
DataElement elemIntercept = file.DataSet[interceptTag];
slice.intercept = (float)Convert.ToDouble(elemIntercept.Value[0]);
}
else
{
Debug.LogWarning($"The file {filePath} is missing the intercept element. As a result, the default transfer function might not look good.");
}
// Read slope
if (file.DataSet.Contains(slopeTag))
{
DataElement elemSlope = file.DataSet[slopeTag];
slice.slope = (float)Convert.ToDouble(elemSlope.Value[0]);
}
else
{
Debug.LogWarning($"The file {filePath} is missing the intercept element. As a result, the default transfer function might not look good.");
}
// Read pixel spacing
if (file.DataSet.Contains(pixelSpacingTag))
{
DataElement elemPixelSpacing = file.DataSet[pixelSpacingTag];
slice.pixelSpacing = (float)Convert.ToDouble(elemPixelSpacing.Value[0]);
}
// Read series UID
if (file.DataSet.Contains(seriesUIDTag))
{
DataElement elemSeriesUID = file.DataSet[seriesUIDTag];
slice.seriesUID = Convert.ToString(elemSeriesUID.Value[0]);
}
return(slice);
}
return(null);
}
public override VolumeDataset Import()
{
DataElementDictionary dataElementDictionary = new DataElementDictionary();
UidDictionary uidDictionary = new UidDictionary();
try
{
dataElementDictionary.LoadFrom(Path.Combine(Application.streamingAssetsPath, "dicom-elements-2007.dic"), DictionaryFileFormat.BinaryFile);
uidDictionary.LoadFrom(Path.Combine(Application.streamingAssetsPath, "dicom-uids-2007.dic"), DictionaryFileFormat.BinaryFile);
}
catch (Exception dictionaryException)
{
Debug.LogError("Problems processing dictionaries:\n" + dictionaryException);
return(null);
}
IEnumerable <string> fileCandidates = Directory.EnumerateFiles(diroctoryPath, "*.*", recursive ? SearchOption.AllDirectories : SearchOption.TopDirectoryOnly)
.Where(p => p.EndsWith(".dcm") || p.EndsWith(".dicom") || p.EndsWith(".dicm"));
List <DICOMSliceFile> files = new List <DICOMSliceFile>();
foreach (string filePath in fileCandidates)
{
AcrNemaFile file = LoadFile(filePath);
if (file != null && file.HasPixelData)
{
DICOMSliceFile slice = new DICOMSliceFile();
slice.file = file;
// Read location
Tag locTag = new Tag("(0020,1041)");
if (file.DataSet.Contains(locTag))
{
DataElement elemLoc = file.DataSet[locTag];
slice.location = (float)Convert.ToDouble(elemLoc.Value[0]);
}
else
{
Debug.LogError($"Missing location tag in file: {filePath}.\n The file will not be imported");
continue;
}
// Read intercept
Tag interceptTag = new Tag("(0028,1052)");
if (file.DataSet.Contains(interceptTag))
{
DataElement elemIntercept = file.DataSet[interceptTag];
slice.intercept = (float)Convert.ToDouble(elemIntercept.Value[0]);
}
else
{
Debug.LogWarning($"The file {filePath} is missing the intercept element. As a result, the default transfer function might not look good.");
}
// Read slope
Tag slopeTag = new Tag("(0028,1053)");
if (file.DataSet.Contains(slopeTag))
{
DataElement elemSlope = file.DataSet[slopeTag];
slice.slope = (float)Convert.ToDouble(elemSlope.Value[0]);
}
else
{
Debug.LogWarning($"The file {filePath} is missing the intercept element. As a result, the default transfer function might not look good.");
}
files.Add(slice);
}
}
files.Sort((DICOMSliceFile a, DICOMSliceFile b) => { return(a.location.CompareTo(b.location)); });
Debug.Log($"Imported {files.Count} datasets");
if (files.Count <= 1)
{
Debug.LogError("Insufficient number of slices.");
return(null);
}
float minLoc = (float)files[0].location;
float maxLoc = (float)files[files.Count - 1].location;
float locRange = maxLoc - minLoc;
VolumeDataset dataset = new VolumeDataset();
dataset.dimX = files[0].file.PixelData.Columns;
dataset.dimY = files[0].file.PixelData.Rows;
dataset.dimZ = files.Count;
int dimension = dataset.dimX * dataset.dimY * dataset.dimZ;
dataset.data = new int[dimension];
for (int iSlice = 0; iSlice < files.Count; iSlice++)
{
DICOMSliceFile slice = files[iSlice];
PixelData pixelData = slice.file.PixelData;
int[] pixelArr = ToPixelArray(pixelData);
if (pixelArr == null) // This should not happen
{
pixelArr = new int[pixelData.Rows * pixelData.Columns];
}
for (int iRow = 0; iRow < pixelData.Rows; iRow++)
{
for (int iCol = 0; iCol < pixelData.Columns; iCol++)
{
int pixelIndex = (iRow * pixelData.Columns) + iCol;
int dataIndex = (iSlice * pixelData.Columns * pixelData.Rows) + (iRow * pixelData.Columns) + iCol;
int pixelValue = pixelArr[pixelIndex];
float hounsfieldValue = pixelValue * slice.slope + slice.intercept;
dataset.data[dataIndex] = (int)Mathf.Clamp(hounsfieldValue, -1024.0f, 3071.0f);
}
}
}
return(dataset);
}
public override VolumeDataset Import()
{
DataElementDictionary dataElementDictionary = new DataElementDictionary();
UidDictionary uidDictionary = new UidDictionary();
try
{
dataElementDictionary.LoadFrom(Path.Combine(Application.streamingAssetsPath, "dicom-elements-2007.dic"), DictionaryFileFormat.BinaryFile);
uidDictionary.LoadFrom(Path.Combine(Application.streamingAssetsPath, "dicom-uids-2007.dic"), DictionaryFileFormat.BinaryFile);
}
catch (Exception dictionaryException)
{
Debug.LogError("Problems processing dictionaries:\n" + dictionaryException);
return(null);
}
List <DICOMSliceFile> files = new List <DICOMSliceFile>();
foreach (string filePath in Directory.EnumerateFiles(diroctoryPath, "*.*", recursive ? SearchOption.AllDirectories : SearchOption.TopDirectoryOnly))
{
AcrNemaFile file = LoadFile(filePath);
if (file != null && file.HasPixelData)
{
DICOMSliceFile slice = new DICOMSliceFile();
slice.file = file;
DataElement sliceLocElem = file.DataSet[new Tag("(0020,1041)")];
slice.location = Convert.ToDouble(sliceLocElem.Value[0]);
files.Add(slice);
}
}
files.Sort((DICOMSliceFile a, DICOMSliceFile b) => { return(a.location.CompareTo(b.location)); });
Debug.Log($"Imported {files.Count} datasets");
if (files.Count <= 1)
{
Debug.LogError("Insufficient number of slices.");
return(null);
}
float minLoc = (float)files[0].location;
float maxLoc = (float)files[files.Count - 1].location;
float locRange = maxLoc - minLoc;
VolumeDataset dataset = new VolumeDataset();
dataset.dimX = files[0].file.PixelData.Columns;
dataset.dimY = files[0].file.PixelData.Rows;
dataset.dimZ = files.Count;
int dimension = dataset.dimX * dataset.dimY * dataset.dimZ;
dataset.data = new int[dimension];
for (int iSlice = 0; iSlice < files.Count; iSlice++)
{
DICOMSliceFile slice = files[iSlice];
PixelData pixelData = slice.file.PixelData;
int[] pixelArr = ToPixelArray(pixelData);
if (pixelArr == null) // This should not happen
{
pixelArr = new int[pixelData.Rows * pixelData.Columns];
}
for (int iRow = 0; iRow < pixelData.Rows; iRow++)
{
for (int iCol = 0; iCol < pixelData.Columns; iCol++)
{
int pixelIndex = (iRow * pixelData.Columns) + iCol;
int dataIndex = (iSlice * pixelData.Columns * pixelData.Rows) + (iRow * pixelData.Columns) + iCol;
dataset.data[dataIndex] = pixelArr[pixelIndex];
}
}
}
/*foreach (openDicom.DataStructure.DataSet.DataElement element in file.DataSet)
* {
* Debug.Log(file.DataSet.StreamPosition);
* Debug.Log(element.Tag.ToString() + " - " + element.VR.Tag.GetDictionaryEntry().Description);
* }*/
/*
* dataset.dimX = file.DataSet.GetEnumerator;
* dataset.dimY = dimY;
* dataset.dimZ = dimZ;
*
* int uDimension = dimX * dimY * dimZ;
* dataset.data = new int[uDimension];*/
return(dataset);
}