/// <summary>
/// Searches for the Series matching a given <see cref="Study"/>, in the local path specified by the user in the <see cref="Configuration"/>, and indexed by the DICOMDIR database.
/// Implements a local C-FIND at SERIES level command of the DICOM standard.
/// Implements
/// </summary>
/// <param name="configuration">Info on the path and hierarchy used to store the DICOM files.</param>
public static List <Series> CFINDLocalSeries(Configuration configuration, Study study)
{
string dicomDirPath = Path.Combine(configuration.fileDestination, "DICOMDIR");
// prepare to receive data
var localSeriesResponses = new List <Series>();
using (var fileStream = new FileStream(dicomDirPath, FileMode.OpenOrCreate, FileAccess.ReadWrite, FileShare.None))
{
var dicomDir = DicomDirectory.Open(fileStream);
if (dicomDir != null)
{
foreach (var patientRecord in dicomDir.RootDirectoryRecordCollection)
{
foreach (var studyRecord in patientRecord.LowerLevelDirectoryRecordCollection)
{
if (studyRecord.GetSingleValue <string>(DicomTag.StudyInstanceUID) ==
study.getStudyInstanceUID())
{
foreach (var seriesRecord in studyRecord.LowerLevelDirectoryRecordCollection)
{
seriesRecord.Add(DicomTag.StudyInstanceUID,
studyRecord.GetSingleValue <string>(DicomTag.StudyInstanceUID));
seriesRecord.Add(DicomTag.StudyDate,
studyRecord.GetSingleValue <string>(DicomTag.StudyDate));
Series mySeries = new Series(seriesRecord, configuration.seriesTemplate);
localSeriesResponses.Add(mySeries);
}
}
}
}
}
}
return(localSeriesResponses);
}
/// <summary>
/// Searches for Studies in the local path, specified by the user in the <see cref="Configuration"/>,
/// and indexed by the DICOMDIR database.
/// Implements a local C-FIND at STUDY level command of the DICOM standard
/// </summary>
/// <param name="configuration">Info on the path and hierarchy used to store the DICOM files.</param>
public static List <Study> CFINDLocalStudies(Configuration configuration)
{
string dicomDirPath = Path.Combine(configuration.fileDestination, "DICOMDIR");
// prepare to receive data
var localStudyResponses = new List <Study>();
using (var fileStream = new FileStream(dicomDirPath, FileMode.OpenOrCreate, FileAccess.ReadWrite, FileShare.None))
{
var dicomDir = DicomDirectory.Open(fileStream);
if (dicomDir != null)
{
foreach (var patientRecord in dicomDir.RootDirectoryRecordCollection)
{
foreach (var studyRecord in patientRecord.LowerLevelDirectoryRecordCollection)
{
studyRecord.Add(DicomTag.PatientName, patientRecord.GetSingleValue <string>(DicomTag.PatientName));
studyRecord.Add(DicomTag.PatientID, patientRecord.GetSingleValue <string>(DicomTag.PatientID));
Study myStudy = new Study(studyRecord, configuration.studyTemplate);
localStudyResponses.Add(myStudy);
}
}
}
}
return(localStudyResponses);
}
private static void ReadMedia(string fileName)
{
var dicomDirectory = DicomDirectory.Open(fileName);
foreach (var patientRecord in dicomDirectory.RootDirectoryRecordCollection)
{
Console.WriteLine(
"Patient: {0} ({1})",
patientRecord.GetSingleValue<string>(DicomTag.PatientName),
patientRecord.GetSingleValue<string>(DicomTag.PatientID));
foreach (var studyRecord in patientRecord.LowerLevelDirectoryRecordCollection)
{
Console.WriteLine("\tStudy: {0}", studyRecord.GetSingleValue<string>(DicomTag.StudyInstanceUID));
foreach (var seriesRecord in studyRecord.LowerLevelDirectoryRecordCollection)
{
Console.WriteLine("\t\tSeries: {0}", seriesRecord.GetSingleValue<string>(DicomTag.SeriesInstanceUID));
foreach (var imageRecord in seriesRecord.LowerLevelDirectoryRecordCollection)
{
Console.WriteLine(
"\t\t\tImage: {0} [{1}]",
imageRecord.GetSingleValue<string>(DicomTag.ReferencedSOPInstanceUIDInFile),
imageRecord.GetSingleValue<string>(DicomTag.ReferencedFileID));
}
}
}
}
}
public void Open_MediaStorageSOPInstanceUID_ShouldBeConsistent()
{
var dir = DicomDirectory.Open(TestData.Resolve("DICOMDIR"));
var expected = dir.FileMetaInfo.GetSingleValue <DicomUID>(DicomTag.MediaStorageSOPInstanceUID).UID;
var actual = dir.MediaStorageSOPInstanceUID.UID;
Assert.Equal(expected, actual);
}
public void Open_DicomDirFile_Succeeds()
{
var dir = DicomDirectory.Open(TestData.Resolve("DICOMDIR"));
var expected = DicomUID.MediaStorageDirectoryStorage.UID;
var actual = dir.FileMetaInfo.MediaStorageSOPClassUID.UID;
Assert.Equal(expected, actual);
}
static void Main(string[] args)
{
LogToDebugConsole("Performing Dicom directory dump:");
try
{
var dicomDirectory = DicomDirectory.Open(PathToDicomDirectoryFile);
LogToDebugConsole(dicomDirectory.WriteToString());
LogToDebugConsole("Dicom directory dump operation was successful");
}
catch (Exception ex)
{
LogToDebugConsole($"Error occured during Dicom directory dump. Error:{ex.Message}");
}
}
static void Main(string[] args)
{
LogToDebugConsole("Creating Dicom directory...");
try
{
//location where we will create the DICOMDIR file from the images
var pathToOutputDicomDirectoryFile = Path.Combine(PathToDicomImages, "DICOMDIR");
if (File.Exists(pathToOutputDicomDirectoryFile))
{
LogToDebugConsole($"Dicom directory file already exists at '{pathToOutputDicomDirectoryFile}'. Deleting...");
File.Delete(pathToOutputDicomDirectoryFile);
}
var directoryInfoForDicomImagesFolder = new DirectoryInfo(PathToDicomImages);
var dicomDir = new DicomDirectory();
foreach (var file in directoryInfoForDicomImagesFolder.GetFiles("*.*", SearchOption.AllDirectories))
{
var dicomFile = Dicom.DicomFile.Open(file.FullName);
dicomDir.AddFile(dicomFile, $@"000001\{file.Name}");
}
dicomDir.Save(pathToOutputDicomDirectoryFile);
LogToDebugConsole($"Dicom directory creation was successful. DICOMDIR file created at '{pathToOutputDicomDirectoryFile}'");
var dicomDirectory = DicomDirectory.Open(pathToOutputDicomDirectoryFile);
LogToDebugConsole("Outputing the newly created DICOM directory information to console");
LogToDebugConsole(dicomDirectory.WriteToString());
}
catch (Exception ex)
{
LogToDebugConsole($"Error occured during Dicom directory dump. Error:{ex.Message}");
}
}
static void Main(string[] args)
{
LogToDebugConsole("Performing Dicom directory dump:");
try
{
var dicomDirectory = DicomDirectory.Open(PathToDicomDirectoryFile);
var dicomDirectoryHelper = new OurDicomDirectoryHelper(LogToDebugConsole);
dicomDirectoryHelper.ShowDicomDirectoryMetaInformation(dicomDirectory);
foreach (var patientRecord in dicomDirectory.RootDirectoryRecordCollection)
{
dicomDirectoryHelper.Display(patientRecord);
foreach (var studyRecord in patientRecord.LowerLevelDirectoryRecordCollection)
{
dicomDirectoryHelper.Display(studyRecord);
foreach (var seriesRecord in studyRecord.LowerLevelDirectoryRecordCollection)
{
dicomDirectoryHelper.Display(seriesRecord);
foreach (var imageRecord in seriesRecord.LowerLevelDirectoryRecordCollection)
{
dicomDirectoryHelper.Display(imageRecord);
}
}
}
}
LogToDebugConsole("Dicom directory dump operation was successful");
}
catch (Exception ex)
{
LogToDebugConsole($"Error occured during Dicom directory dump. Error:{ex.Message}");
}
}
public static IEnumerable <Series> ExtractSeriesFromDicomDir(string path, bool generateMissingThumbnails)
{
var result = new List <DicomSeries>();
if (!DicomFile.HasValidHeader(path))
{
return(result);
}
try
{
var dicomDirectory = DicomDirectory.Open(path);
foreach (var patientRecord in dicomDirectory.RootDirectoryRecordCollection)
{
foreach (var studyRecord in patientRecord.LowerLevelDirectoryRecordCollection)
{
foreach (var seriesRecord in studyRecord.LowerLevelDirectoryRecordCollection)
{
var seriesRecordType = seriesRecord.GetSingleValueOrDefault(DicomTag.DirectoryRecordType, string.Empty);
if (seriesRecordType != "SERIES")
{
continue;
}
var series = new DicomSeries
{
SeriesInstanceUid = seriesRecord.GetSingleValueOrDefault(DicomTag.SeriesInstanceUID, ""),
Number = seriesRecord.GetSingleValueOrDefault(DicomTag.SeriesNumber, ""),
};
DicomSequence iconImageSequence;
if (seriesRecord.TryGetSequence(DicomTag.IconImageSequence, out iconImageSequence))
{
var iconImage = iconImageSequence.FirstOrDefault();
if (iconImage != null)
{
DicomImage image = new DicomImage(iconImage);
series.Thumbnail = image.RenderImage().AsWriteableBitmap();
}
}
foreach (var imageRecord in seriesRecord.LowerLevelDirectoryRecordCollection)
{
var imageRecordType = imageRecord.GetSingleValueOrDefault(DicomTag.DirectoryRecordType, string.Empty);
if (imageRecordType != "IMAGE")
{
continue;
}
var values = imageRecord.GetValues <string>(DicomTag.ReferencedFileID);
var relativePath = string.Join(@"\", values);
series.SopClassUid = imageRecord.GetSingleValueOrDefault(DicomTag.ReferencedSOPClassUIDInFile, "");
series.NumberOfImages += Math.Max(1, imageRecord.GetSingleValueOrDefault(DicomTag.NumberOfFrames, 1));
var absolutePath = Path.GetDirectoryName(path) + @"\\" + relativePath;
series.FileNames.Add(absolutePath);
}
if (generateMissingThumbnails && series.Thumbnail == null && series.FileNames.Count > 0)
{
GenerateThumbnail(series);
}
if (series.NumberOfImages > 0)
{
result.Add(series);
}
}
}
}
}
catch (Exception e)
{
logger.LogWarning(e, $"Could not read DICOMDIR file '{e.Message}' {e.StackTrace}");
}
return(result);
}
// Use this for initialization
void Start()
{
Unzip("Genomics", false);
Debug.Log("Loading DICOM DICT");
var dict = new DicomDictionary();
dict.Load(Application.dataPath + "/StreamingAssets/Dictionaries/DICOM Dictionary.xml", DicomDictionaryFormat.XML);
DicomDictionary.Default = dict;
annotationPath = Path.Combine(Application.persistentDataPath, "annotations.json");
if (File.Exists(annotationPath))
{
annotations = JsonUtility.FromJson <AnnotationCollection>(File.ReadAllText(annotationPath));
Debug.Log("Loaded " + annotations.annotations.Count + " annotations");
}
var meshMarkerPath = Path.Combine(Application.persistentDataPath, "MeshMarkers");
if (Directory.Exists(meshMarkerPath))
{
meshMarkers = Directory.GetFiles(meshMarkerPath, "*.*", SearchOption.AllDirectories);
}
var path = Unzip("DICOM");
Unzip("Volumes", false);
var offset = 0;
directoryMap = new Dictionary <GameObject, DicomDirectoryRecord>();
rootDirectoryMap = new Dictionary <DicomDirectoryRecord, string>();
openedItems = new Dictionary <GameObject, bool>();
var directories = Directory.GetDirectories(path);
if (directories.Length == 0)
{
status.text = "ERROR: No directories found!";
return;
}
status.text = "Loading...";
foreach (var directory in Directory.GetDirectories(path))
{
var directoryName = Path.GetFileName(directory);
Debug.Log("--DIRECTORY--" + directoryName);
var dd = DicomDirectory.Open(Path.Combine(directory, "DICOMDIR"));
rootDirectoryMap[dd.RootDirectoryRecord] = directory;
var tex = GetTexture2DForRecord(dd.RootDirectoryRecord);
var quad = Instantiate(quadPrefab, filebrowser);
quad.GetComponent <Renderer>().material.mainTexture = tex;
quad.transform.localPosition += new Vector3(offset, 0, 0);
quad.transform.Find("Canvas").Find("title").GetComponent <Text>().text = "Directory: " + directoryName;
quad.name = directory;
directoryMap[quad] = dd.RootDirectoryRecord;
openedItems[quad] = false;
quad.tag = "directory";
offset += 1;
}
recognizer = new GestureRecognizer();
recognizer.TappedEvent += Recognizer_TappedEvent;
recognizer.StartCapturingGestures();
status.text = "";
UpdateAnnotationsList();
testQuad.SetActive(false);
#if UNITY_EDITOR
testQuad.SetActive(true);
testQuad.transform.position = new Vector3(0, 0, 2);
var series = GetSeriesById("1.3.12.2.1107.5.1.4.50714.30000016083120205201500011155");
var seriesHandler = testQuad.GetComponent <OpenSeriesHandler>();
seriesHandler.record = series;
var modality = GetDicomTag(series, DicomTag.Modality);
var seriesDesc = GetDicomTag(series, DicomTag.SeriesDescription);
testQuad.name = "Series: " + modality + "\n" + seriesDesc;
Debug.Log(seriesDesc);
directoryMap[testQuad] = series;
rootDirectoryMap[series] = rootDirectoryMap[directoryMap.ElementAt(1).Value];
testQuad.GetComponent <TwoHandManipulatable>().enabled = true;
testQuad.transform.Find("3D_toggle").gameObject.SetActive(true);
testQuad.transform.Find("3D_toggle").GetComponent <InteractiveToggle>().SetSelection(true);
seriesHandler.ButtonPush("3D");
var slider = testQuad.transform.Find("zstack slider");
slider.gameObject.SetActive(true);
var sliderComponent = slider.GetComponent <SliderGestureControl>();
var n_images = series.LowerLevelDirectoryRecordCollection.Count();
sliderComponent.SetSpan(0, n_images);
sliderComponent.SetSliderValue(n_images / 2f);
testQuad.GetComponent <Renderer>().material.mainTexture = GetTexture2DForRecord(series);
var seriesId = series.Get <string>(DicomTag.SeriesInstanceUID, "no series id");
foreach (var a in annotations.annotations)
{
if (a.series == seriesId)
{
var annotation = Instantiate(annotationPrefab, testQuad.transform);
annotation.transform.localPosition = DeserializeVector(a.position, Vector3.zero);
annotation.transform.localRotation = Quaternion.Euler(DeserializeVector(a.rotation, Vector3.zero));
annotation.transform.localScale = DeserializeVector(a.scale, Vector3.one);
}
}
//WarmVolumeCache();
#endif
}
