protected Study CreateTestStudy1()
{
var studyUid = "1.2.3";
var sops = base.SetupMRSeries(4, 5, studyUid);
var xml = new StudyXml(studyUid);
var seriesUids = new Dictionary<string, string>();
var seriesModalities = new Dictionary<string, string>();
var modalities = new[] { "MR", "MR", "SC", "KO" };
foreach (var sop in sops)
{
//Make the UIDs constant.
var seriesUid = sop[DicomTags.SeriesInstanceUid].ToString();
if (!seriesUids.ContainsKey(seriesUid))
{
seriesModalities[seriesUid] = modalities[seriesUids.Count];
seriesUids[seriesUid] = string.Format("1.2.3.{0}", seriesUids.Count + 1);
}
var modality = seriesModalities[seriesUid];
seriesUid = seriesUids[seriesUid];
sop[DicomTags.SeriesInstanceUid].SetString(0, seriesUid);
sop[DicomTags.Modality].SetString(0, modality);
var file = new DicomFile("", new DicomAttributeCollection(), sop);
xml.AddFile(file);
}
var study = new Study();
study.Update(xml);
return study;
}
public RemoveInstanceFromStudyXmlCommand(StudyStorageLocation location, StudyXml studyXml, DicomFile file)
:base("Remove Instance From Study Xml", true)
{
_studyLocation = location;
_file = file;
_studyXml = studyXml;
}
public void AssertTagValueChanged(uint tag, string valueToSet, string originalCharacterSet, string expectedNewCharacterSet)
{
DicomAttributeCollection dataset = new DicomAttributeCollection();
SetupDataSet(dataset, originalCharacterSet);
DicomFile file = new DicomFile("test", CreateMetaInfo(), dataset);
Assert.AreEqual(originalCharacterSet, file.DataSet[DicomTags.SpecificCharacterSet].ToString());
SetTagCommand cmd = new SetTagCommand(tag, valueToSet);
Assert.AreEqual(cmd.CanSaveInUnicode, UnicodeAllowed, "SetTagCommand.CanSaveInUnicode returns an incorrect value");
Assert.IsTrue(cmd.Apply(file), "SetTagCommand.Apply failed");
var filename = string.Format("Test-{0}.dcm", DicomTagDictionary.GetDicomTag(tag).Name);
Assert.IsTrue(file.Save(filename), "Unable to save dicom file");
file = new DicomFile(filename);
file.Load();
if (valueToSet == null)
Assert.AreEqual(string.Empty, file.DataSet[tag].ToString());
else
Assert.AreEqual(valueToSet, file.DataSet[tag].ToString());
Assert.IsTrue(file.DataSet[DicomTags.SpecificCharacterSet].ToString().Equals(expectedNewCharacterSet));
Delete(filename);
}
/// <summary>
/// Run the decompressor.
/// </summary>
/// <param name="file"></param>
public void Process(ClearCanvas.Dicom.DicomFile file)
{
var proposedTs = ClearCanvas.Dicom.TransferSyntax.GetTransferSyntax(OutputTransferSyntax);
var currentTs = file.TransferSyntax;
ClearCanvas.Dicom.TransferSyntax finalTs = currentTs;
if (proposedTs != TransferSyntax.ExplicitVrBigEndian &&
proposedTs != TransferSyntax.ImplicitVrLittleEndian &&
proposedTs != TransferSyntax.ExplicitVrLittleEndian)
{
log.Warn("Decompressor cannot supports target transfer syntax of EVBE, IVLE, EVLE only. Using IVLE ..");
finalTs = TransferSyntax.ImplicitVrLittleEndian;
}
else
{
finalTs = proposedTs;
}
log.Info(string.Format("Deompress: Proposed: {0}, current {1}, final {2}", proposedTs, currentTs, finalTs));
if (currentTs != finalTs)
{
file.ChangeTransferSyntax(finalTs);
}
}
public static void MultiFrameProcess(DbStudy study)
{
string dcmPath = ADCM.GetStoreString();
var seriesList = Directory.GetDirectories(Path.Combine(dcmPath, study.study_uid));
foreach (var sePath in seriesList)
{
var filesList = Directory.GetFiles(sePath, "*.dcm");
if (filesList.Length < 2)
continue;
for (int i = 0; i < filesList.Length; i++)
{
var dcm = new DicomFile(filesList[i]);
dcm.Load();
int frameCount = dcm.DataSet[DicomTags.NumberOfFrames].GetInt16(0, 0);
if (frameCount > 1)
{
string newSeriesUID = sePath + "." + i;
newSeriesUID = newSeriesUID.Substring(newSeriesUID.LastIndexOf(Path.DirectorySeparatorChar) + 1);
string newSeriesPath = Path.Combine(dcmPath, study.study_uid, newSeriesUID);
Directory.CreateDirectory(newSeriesPath);
string fileName = Path.GetFileName(filesList[i]);
string oldPath = filesList[i];
string newPath = Path.Combine(newSeriesPath, fileName);
File.Move(filesList[i], Path.Combine(newSeriesPath, fileName));
}
}
}
foreach (string sePath in seriesList)
{
var filesCount = Directory.GetFiles(sePath);
if (filesCount.Length < 1)
Directory.Delete(sePath);
}
}
protected override void Dispose(bool disposing)
{
if (disposing)
{
_frame = null;
_dicomFile = null;
if (_imageSop != null)
{
_imageSop.Dispose();
_imageSop = null;
}
if (_sopDataSource != null)
{
_sopDataSource.Dispose();
_sopDataSource = null;
}
if (_filename != null)
{
if (File.Exists(_filename))
File.Delete(_filename);
_filename = null;
}
}
base.Dispose(disposing);
}
private void buttonCompress_Click(object sender, EventArgs e)
{
TransferSyntax syntax = this.comboBoxCompressionType.SelectedItem as TransferSyntax;
if (syntax == null)
{
MessageBox.Show("Transfer syntax not selected");
return;
}
DicomFile dicomFile = new DicomFile(textBoxSourceFile.Text);
dicomFile.Load();
if (dicomFile.TransferSyntax.Encapsulated)
{
MessageBox.Show(String.Format("Message encoded as {0}, cannot compress.", dicomFile.TransferSyntax));
return;
}
dicomFile.Filename = textBoxDestinationFile.Text;
dicomFile.ChangeTransferSyntax(syntax);
dicomFile.Save();
}
/// <summary>
/// Updates the Patient's Name tag in the specified <see cref="DicomFile"/>
/// based on the specified <see cref="StudyStorageLocation"/>. Normalization
/// may occur.
/// </summary>
/// <param name="file"></param>
/// <returns></returns>
public UpdateItem Apply(DicomFile file)
{
Platform.CheckForNullReference(file, "file");
string orginalPatientsNameInFile = file.DataSet[DicomTags.PatientsName].ToString();
// Note: only apply the name rules if we can't update it to match the study
if (!UpdateNameBasedOnTheStudy(file))
UpdateNameBasedOnRules(file);
string newPatientName = file.DataSet[DicomTags.PatientsName].ToString();
UpdateItem change = null;
if (!newPatientName.Equals(orginalPatientsNameInFile, StringComparison.InvariantCultureIgnoreCase))
{
change = new UpdateItem(DicomTags.PatientsName, orginalPatientsNameInFile, newPatientName);
StringBuilder log = new StringBuilder();
log.AppendLine(String.Format("AUTO-CORRECTION: SOP {0}", file.MediaStorageSopInstanceUid));
log.AppendLine(String.Format("\tPatient's Name: {0} ==> {1}. ",
change.OriginalValue, change.NewValue));
Platform.Log(LogLevel.Info, log.ToString());
}
return change;
}
protected override void ProcessFile(Model.WorkQueueUid queueUid, DicomFile file, ClearCanvas.Dicom.Utilities.Xml.StudyXml stream, bool compare)
{
Platform.CheckFalse(compare, "compare");
SopInstanceProcessor processor = new SopInstanceProcessor(Context);
FileInfo fileInfo = new FileInfo(file.Filename);
long fileSize = fileInfo.Length;
processor.InstanceStats.FileSize = (ulong)fileSize;
string sopInstanceUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, "File:" + fileInfo.Name);
processor.InstanceStats.Description = sopInstanceUid;
if (Study != null)
{
StudyComparer comparer = new StudyComparer();
DifferenceCollection list = comparer.Compare(file, Study, ServerPartition.GetComparisonOptions());
if (list != null && list.Count > 0)
{
Platform.Log(LogLevel.Warn, "Dicom file contains information inconsistent with the study in the system");
}
}
string groupID = ServerHelper.GetUidGroup(file, StorageLocation.ServerPartition, WorkQueueItem.InsertTime);
processor.ProcessFile(groupID, file, stream, false, false, null, null);
Statistics.StudyInstanceUid = StorageLocation.StudyInstanceUid;
if (String.IsNullOrEmpty(processor.Modality) == false)
Statistics.Modality = processor.Modality;
// Update the statistics
Statistics.NumInstances++;
}
protected override InstancePreProcessingResult PreProcessFile(Model.WorkQueueUid uid, DicomFile file)
{
// Return a result indicating the file has been reconciled.
InstancePreProcessingResult result = new InstancePreProcessingResult {AutoReconciled = true};
return result;
}
/// <summary>
/// Processes the specified <see cref="DicomFile"/> object.
/// </summary>
/// <param name="file"></param>
/// <returns></returns>
/// <exception cref="TargetStudyInvalidStateException">Thrown when the target study is in invalid state and cannot be updated.</exception>
public InstancePreProcessingResult Process(DicomFile file)
{
Platform.CheckForNullReference(file, "file");
AutoReconcilerResult preProcessingResult = null;
// Update the file based on the reconciliation in the past
IList<StudyHistory> histories = FindReconcileHistories(StorageLocation, file);
if (histories != null && histories.Count > 0)
{
preProcessingResult = ApplyHistories(file, histories);
}
if (preProcessingResult!=null)
{
StringBuilder log = new StringBuilder();
log.AppendLine(String.Format("AUTO-RECONCILE: {0}. SOP {1}", preProcessingResult.Action, file.MediaStorageSopInstanceUid));
foreach (UpdateItem change in preProcessingResult.Changes)
{
if (change.NewValue != null && !change.NewValue.Equals(change.OriginalValue))
{
log.AppendLine(String.Format("\tSet {0}: {1} => {2}", change.Tag, change.OriginalValue, change.NewValue));
}
}
Platform.Log(LogLevel.Info, log.ToString());
}
return preProcessingResult;
}
/// <summary>
/// Load the first instance from the first series of the StudyXml file for a study.
/// </summary>
/// <param name="location">The storage location of the study.</param>
/// <returns></returns>
protected static DicomFile LoadInstance(StudyStorageLocation location)
{
string studyXml = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (!File.Exists(studyXml))
{
return null;
}
FileStream stream = FileStreamOpener.OpenForRead(studyXml, FileMode.Open);
var theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, stream);
stream.Close();
stream.Dispose();
var xml = new StudyXml();
xml.SetMemento(theDoc);
IEnumerator<SeriesXml> seriesEnumerator = xml.GetEnumerator();
if (seriesEnumerator.MoveNext())
{
SeriesXml seriesXml = seriesEnumerator.Current;
IEnumerator<InstanceXml> instanceEnumerator = seriesXml.GetEnumerator();
if (instanceEnumerator.MoveNext())
{
InstanceXml instance = instanceEnumerator.Current;
var file = new DicomFile("file.dcm",new DicomAttributeCollection(), instance.Collection)
{TransferSyntax = instance.TransferSyntax};
return file;
}
}
return null;
}
public override bool Apply(DicomFile file)
{
if (_uidMapper == null)
return true; // Nothing to do
string oldSeriesUid = file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, String.Empty);
string oldSopUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, String.Empty);
string newSeriesUid;
if (_uidMapper.ContainsSeries(oldSeriesUid))
newSeriesUid = _uidMapper.FindNewSeriesUid(oldSeriesUid);
else
{
newSeriesUid = DicomUid.GenerateUid().UID;
_uidMapper.AddSeries(_originalStudy.StudyInstanceUid, _targetStudy.StudyInstanceUid, oldSeriesUid, newSeriesUid);
}
string newSopInstanceUid;
if (_uidMapper.ContainsSop(oldSopUid))
newSopInstanceUid = _uidMapper.FindNewSopUid(oldSopUid);
else
{
newSopInstanceUid = DicomUid.GenerateUid().UID;
_uidMapper.AddSop(oldSopUid, newSopInstanceUid);
}
file.DataSet[DicomTags.SeriesInstanceUid].SetStringValue(newSeriesUid);
file.DataSet[DicomTags.SopInstanceUid].SetStringValue(newSopInstanceUid);
file.MediaStorageSopInstanceUid = newSopInstanceUid;
// add Source Image Sequence
AddSourceImageSequence(file, oldSopUid);
return true;
}
public InsertInstanceCommand(DicomFile file, StudyStorageLocation location)
: base("Insert Instance into Database")
{
Platform.CheckForNullReference(file, "Dicom File object");
Platform.CheckForNullReference(location, "Study Storage Location");
_file = file;
_storageLocation = location;
}
public UpdateInstanceCommand(ServerPartition partition,
StudyStorageLocation studyLocation,
DicomFile file)
: base("Update existing SOP Instance")
{
_partition = partition;
_studyLocation = studyLocation;
_file = file;
}
//public static void ConvertBmpToDicomAndAddToExistingFolder(string bmpFilePath, string dicomFolderPath, string newFileName = "")
//{
// if (string.IsNullOrEmpty(newFileName)) newFileName = Path.GetFileNameWithoutExtension(bmpFilePath);
// if (Directory.GetFiles(dicomFolderPath)
// .Any(f => Path.GetFileName(f).ToLower().Contains(newFileName ?? throw new ArgumentNullException(nameof(newFileName)))))
// newFileName = DateTime.Now.ToString("yyyyMMddHHmmssfff");
// var dicomFileHighestInstanceNo = GetDicomFileWithHighestInstanceNumber(dicomFolderPath);
// var headers = GetDicomTags(dicomFileHighestInstanceNo);
// var newFilePath = Path.Combine(dicomFolderPath, newFileName ?? throw new ArgumentNullException(nameof(newFileName)));
// ConvertBmpToDicom(bmpFilePath, newFilePath, dicomFileHighestInstanceNo);
// var newFileInstanceNumber = headers.InstanceNumber.Values == null || headers.InstanceNumber.Values.Length < 1 ? 1 : int.Parse(headers.InstanceNumber.Values[0]) + 1;
// headers.InstanceNumber.Values = new[] { newFileInstanceNumber.ToString() };
// UpdateDicomHeaders(newFilePath, headers, DicomNewObjectType.NewImage);
//}
public static string GetPatientIdFromDicomFile(string dicomFilePath)
{
var dcmFile = new ClearCanvas.Dicom.DicomFile(dicomFilePath);
dcmFile.Load(dicomFilePath);
var patientIdTag = dcmFile.DataSet[1048608].Values as string[];
return(patientIdTag?[0]);
}
/// <summary>
/// Updates the given Dicom headers without trying to be clever.
/// </summary>
/// <param name="filepath"></param>
/// <param name="tags"></param>
public static void ForceUpdateDicomHeaders(string filepath, DicomTagCollection tags)
{
var dcmFile = new ClearCanvas.Dicom.DicomFile(filepath);
dcmFile.Load(filepath);
tags.ToList().ForEach(tag => UpdateTag(dcmFile, tag));
dcmFile.Save();
}
/// <summary>
/// Converts a <see cref="DicomMessage"/> instance into a <see cref="DicomFile"/>.
/// </summary>
/// <remarks>This routine sets the Source AE title, </remarks>
/// <param name="message"></param>
/// <param name="filename"></param>
/// <param name="assocParms"></param>
/// <returns></returns>
protected static DicomFile ConvertToDicomFile(DicomMessage message, string filename, AssociationParameters assocParms)
{
// This routine sets some of the group 0x0002 elements.
DicomFile file = new DicomFile(message, filename);
file.SourceApplicationEntityTitle = assocParms.CallingAE;
file.TransferSyntax = message.TransferSyntax;
return file;
}
private static ISopDataSource CreateSopDataSource()
{
var uid = DicomUid.GenerateUid().UID;
var dcf = new DicomFile();
dcf.MediaStorageSopInstanceUid = uid;
dcf.MediaStorageSopClassUid = DicomUids.SecondaryCaptureImageStorage.UID;
dcf.DataSet[DicomTags.SopInstanceUid].SetStringValue(uid);
dcf.DataSet[DicomTags.SopClassUid].SetStringValue(DicomUids.SecondaryCaptureImageStorage.UID);
return new TestDataSource(dcf);
}
/// <summary>
/// Constructor.
/// </summary>
/// <param name="path">The path to save the file.</param>
/// <param name="file">The file to save.</param>
/// <param name="failOnExists">If the file already exists, the file will save.</param>
public SaveDicomFileCommand(string path, DicomFile file, bool failOnExists)
: base("Save DICOM Message", true)
{
Platform.CheckForNullReference(path, "File name");
Platform.CheckForNullReference(file, "Dicom File object");
_path = path;
_file = file;
_failOnExists = failOnExists;
}
public static CommandBase CreateSaveDicomFileCommand(string path, DicomFile dcf, bool failIfExists)
{
switch (_disposition)
{
case FileProcessingDisposition.Availability:
return new SaveDicomFileCommand(path, dcf, failIfExists);
case FileProcessingDisposition.Performance:
default:
return new FastSaveDicomFileCommand(path, dcf, failIfExists);
}
}
public InsertStudyXmlCommand(DicomFile file, StudyXml stream, StudyStorageLocation storageLocation)
: base("Insert into Study XML", true)
{
Platform.CheckForNullReference(file, "Dicom File object");
Platform.CheckForNullReference(stream, "StudyStream object");
Platform.CheckForNullReference(storageLocation, "Study Storage Location");
_file = file;
_stream = stream;
_studyStorageLocation = storageLocation;
}
public StreamingSopDataSource(DicomFile file, IDicomFileLoader loader)
: base(file)
{
if (!loader.CanLoadCompleteHeader)
throw new ArgumentException("Loader must be capable of retrieving the full image header.", "loader");
if (!loader.CanLoadFramePixelData)
throw new ArgumentException("Loader must be capable of loading frame pixel data.", "loader");
_loader = loader;
//Have to assume this to be the case.
_fullHeaderRetrieved = true;
}
/// <summary>
/// Update the tags for the given files. Files will be given a generated SeriesInstanceUid and ImageUid.
/// </summary>
/// <param name="filesPath">List of files to apply the tags to.</param>
/// <param name="tags">The tags which you'd like to apply to the above files.</param>
public static void GenerateSeriesHeaderForAllFiles(string[] filesPath, DicomTagCollection tags, int uidpostfix = 1)
{
tags.SeriesInstanceUid.Values = new[] { GenerateNewSeriesUid(uidpostfix.ToString()) };
tags.ImageUid.Values = new[] { GenerateNewImageUid() };
foreach (var filepath in filesPath)
{
var dcmFile = new ClearCanvas.Dicom.DicomFile(filepath);
dcmFile.Load(filepath);
dcmFile = UpdateTags(dcmFile, tags, TagType.Series);
dcmFile.Save(filepath);
}
}
public static void UpdateImagePositionFromReferenceSeries(string[] dicomFilesToUpdate, string[] orientationDicomFiles)
{
if (dicomFilesToUpdate == null || dicomFilesToUpdate.Length == 0)
{
throw new ArgumentNullException("Orientation Dicom files not available to read from");
}
if (orientationDicomFiles == null || orientationDicomFiles.Length == 0)
{
throw new ArgumentNullException("Dicom files to copy orientation data to not available");
}
if (dicomFilesToUpdate.Length != orientationDicomFiles.Length)
{
throw new Exception("Number of files in \"Orientation dicom\" folder and \"Dicom Files to Update\" do not match");
}
var orderedFilesToUpdate = dicomFilesToUpdate
.OrderBy((f) =>
{
var vals = GetDicomTags(f).InstanceNumber.Values;
return(vals != null && vals.Length > 0 ?
int.Parse(GetDicomTags(f).InstanceNumber.Values[0])
: 0);
}).ToArray();
var orderedOrientationFiles = orientationDicomFiles
.OrderBy((f) =>
{
var vals = GetDicomTags(f).InstanceNumber.Values;
return(vals != null && vals.Length > 0 ?
int.Parse(GetDicomTags(f).InstanceNumber.Values[0])
: 0);
}).ToArray();
for (var i = 0; i < orderedFilesToUpdate.Count(); i++)
{
var fileToUpdate = orderedFilesToUpdate[i];
var orientationFile = orderedOrientationFiles[i];
var imagePatientOrientation = GetDicomTags(orientationFile).ImagePositionPatient;
var imageOrientation = GetDicomTags(orientationFile).ImageOrientation;
var frameOfReferenceUid = GetDicomTags(orientationFile).FrameOfReferenceUid;
var sliceLocation = GetDicomTags(orientationFile).SliceLocation;
var dcmFile = new ClearCanvas.Dicom.DicomFile();
dcmFile.Load(fileToUpdate);
dcmFile = UpdateArrayTag(dcmFile, imagePatientOrientation, imagePatientOrientation.Values);
dcmFile = UpdateArrayTag(dcmFile, imageOrientation, imageOrientation.Values);
dcmFile = UpdateArrayTag(dcmFile, frameOfReferenceUid, frameOfReferenceUid.Values);
dcmFile = UpdateArrayTag(dcmFile, sliceLocation, sliceLocation.Values);
dcmFile.Save(fileToUpdate);
}
}
public ImageStreamingContext(HttpListenerContext context)
{
Request = context.Request;
Response = context.Response;
NameValueCollection query = Request.QueryString;
#region INIT STUFF FOR PERFORMANCE TESTING
#if DEBUG
if (query["testcompressed"] != null)
{
testCompressed= true;
}
else if (query["testuncompressed"] != null)
{
testUncompressed = true;
}
if (_testCompressedImage == null)
{
using (Stream stream = typeof(ImageStreamingContext).Assembly.GetManifestResourceStream("ClearCanvas.ImageServer.Services.Streaming.ImageStreaming.Test.TestSamples.compressed.dcm"))
{
DicomFile file = new DicomFile();
file.Load(stream);
_testCompressedImage = DicomPixelData.CreateFrom(file);
}
}
if (_testUncompressedImage == null)
{
using (Stream stream = typeof(ImageStreamingContext).Assembly.GetManifestResourceStream("ClearCanvas.ImageServer.Services.Streaming.ImageStreaming.Test.TestSamples.uncompressed.dcm"))
{
DicomFile file = new DicomFile();
file.Load(stream);
_testUncompressedImage = DicomPixelData.CreateFrom(file);
}
}
#endif
#endregion
_frameNumber = 0;
if (query["FrameNumber"] != null)
int.TryParse(query["FrameNumber"], out _frameNumber);
_nextSeriesUid = query["nextSeriesUid"];
_nextSopUid = query["nextObjectUid"];
}
private ImageSop CreateImageSop(string patientId, string studyUid, string seriesUid, string sopUid)
{
DicomAttributeCollection dataSet = new DicomAttributeCollection();
base.SetupMR(dataSet);
DicomFile file = new DicomFile(null, new DicomAttributeCollection(), dataSet);
TestDataSource dataSource = new TestDataSource(file);
file.DataSet[DicomTags.PatientId].SetStringValue(patientId);
file.DataSet[DicomTags.StudyInstanceUid].SetStringValue(studyUid);
file.DataSet[DicomTags.SeriesInstanceUid].SetStringValue(seriesUid);
file.DataSet[DicomTags.SopInstanceUid].SetStringValue(sopUid);
return new ImageSop(dataSource);
}
public void TestProcessMessage()
{
try
{
Assert.IsNotNull(SynchronizationContext.Current, "SynchronizationContext.Current");
DicomFile file = new DicomFile("TileEntityHandlerTest.dcm");
DicomAttributeCollection dataSet = file.DataSet;
SetupSecondaryCapture(dataSet);
file.Save();
ImageViewerComponent viewer = new ImageViewerComponent();
viewer.Start();
viewer.LoadImages(new[] { "TileEntityHandlerTest.dcm" });
ManualResetEvent signal = new ManualResetEvent(false);
viewer.EventBroker.LayoutManagerCompleted += (s, e) => signal.Set();
viewer.Layout();
Console.WriteLine("Waiting for layout to complete");
if (!signal.WaitOne(20000))
Assert.Fail("Abort: something is not working properly.");
Console.WriteLine("Layout completed");
Assert.IsNotNull(viewer.PhysicalWorkspace);
Assert.IsNotNull(viewer.PhysicalWorkspace.ImageBoxes[0]);
Assert.IsNotNull(viewer.PhysicalWorkspace.ImageBoxes[0].Tiles[0]);
Tile tile = viewer.PhysicalWorkspace.ImageBoxes[0].Tiles[0] as Tile;
Assert.IsNotNull(tile.PresentationImage);
MockApplicationContext context = new MockApplicationContext();
TileEntityHandler handler = new TileEntityHandler { ApplicationContext = context };
handler.SetModelObject(tile);
ChangeClientRectangle(context, handler, 0, 0, 512, 512, "Case: Size is even");
ChangeClientRectangle(context, handler, 0, 0, 311, 311, "Case: Size is odd");
ChangeClientRectangle(context, handler, 10, 10, 300, 301, "Case: Left,Top are positive");
ChangeClientRectangle(context, handler, -10, -10, 512, 512, "Case: Left,Top are negative");
}
finally
{
File.Delete("TileEntityHandlerTest.dcm");
}
}
public TestPresentationImage() : base(TestPattern.CreateRGBKCorners(new Size(_width, _height)))
{
DicomFile dcf = new DicomFile();
dcf.DataSet[DicomTags.StudyInstanceUid].SetStringValue("1");
dcf.DataSet[DicomTags.SeriesInstanceUid].SetStringValue("2");
dcf.DataSet[DicomTags.SopInstanceUid].SetStringValue("3");
dcf.DataSet[DicomTags.SopClassUid].SetStringValue(SopClass.SecondaryCaptureImageStorageUid);
dcf.DataSet[DicomTags.InstanceNumber].SetStringValue("1");
dcf.DataSet[DicomTags.NumberOfFrames].SetStringValue("1");
dcf.MetaInfo[DicomTags.TransferSyntaxUid].SetStringValue(TransferSyntax.ImplicitVrLittleEndianUid);
dcf.MetaInfo[DicomTags.MediaStorageSopClassUid].SetStringValue(SopClass.SecondaryCaptureImageStorageUid);
dcf.MetaInfo[DicomTags.MediaStorageSopInstanceUid].SetStringValue("3");
_imageSop = new ImageSop(new TestDataSource(dcf));
}
/// <summary>
/// Gets the tags for a dicom file.
/// </summary>
/// <param name="filePath">The dicom file.</param>
/// <returns></returns>
public static DicomTagCollection GetDicomTags(string filePath)
{
var dcmFile = new ClearCanvas.Dicom.DicomFile(filePath);
dcmFile.Load(filePath);
var tags = new DicomTagCollection();
var updatedTags = new DicomTagCollection();
foreach (var tag in tags.ToList())
{
updatedTags.SetTagValue(tag.GetTagValue(), dcmFile.DataSet[tag.GetTagValue()].Values);
}
return(updatedTags);
}
private void ButtonLoadFile_Click(object sender, EventArgs e)
{
openFileDialog.DefaultExt = "dcm";
openFileDialog.ShowDialog();
DicomFile dicomFile = new DicomFile(openFileDialog.FileName);
DicomReadOptions options = new DicomReadOptions();
dicomFile.Load(options);
_theStream.AddFile(dicomFile);
}
private static DicomFile UpdateTags(
ClearCanvas.Dicom.DicomFile dcmFile, DicomTagCollection newTags, TagType tagType, bool overwriteIfNotProvided = false)
{
if (newTags == null)
{
return(dcmFile);
}
newTags.ToList().ForEach(tag =>
{
if (tag.DicomTagType == tagType)
{
dcmFile = UpdateTag(dcmFile, tag, overwriteIfNotProvided);
}
});
return(dcmFile);
}
private void AddSourceImageSequence(DicomFile file, string oldSopUid)
{
DicomAttributeSQ sourceImageSq;
if (!file.DataSet.Contains(DicomTags.SourceImageSequence))
{
sourceImageSq = new DicomAttributeSQ(DicomTags.SourceImageSequence);
file.DataSet[DicomTags.SourceImageSequence] = sourceImageSq;
}
else
sourceImageSq = file.DataSet[DicomTags.SourceImageSequence] as DicomAttributeSQ;
DicomSequenceItem item = new DicomSequenceItem();
item[DicomTags.ReferencedSopClassUid].SetStringValue(file.SopClass.Uid);
item[DicomTags.ReferencedSopInstanceUid].SetStringValue(oldSopUid);
sourceImageSq.AddSequenceItem(item);
}
public MockDicomPresentationImage(string filename) : base(new GrayscaleImageGraphic(10, 10))
{
if (Path.IsPathRooted(filename))
_filename = filename;
else
_filename = Path.Combine(Environment.CurrentDirectory, filename);
_dicomFile = new DicomFile();
_dicomFile.DataSet[DicomTags.SopClassUid].SetStringValue(SopClass.SecondaryCaptureImageStorageUid);
_dicomFile.DataSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
_dicomFile.MetaInfo[DicomTags.MediaStorageSopClassUid].SetStringValue(_dicomFile.DataSet[DicomTags.SopClassUid].ToString());
_dicomFile.MetaInfo[DicomTags.MediaStorageSopInstanceUid].SetStringValue(_dicomFile.DataSet[DicomTags.SopInstanceUid].ToString());
_dicomFile.Save(_filename);
_sopDataSource = new LocalSopDataSource(_dicomFile);
_imageSop = new ImageSop(_sopDataSource);
_frame = new MockFrame(_imageSop, 1);
}
public InsertStudyXmlCommand(DicomFile file, StudyXml studyXml, StudyLocation storageLocation, bool writeFile)
: base("Insert Study Xml", true)
{
_file = file;
_studyXml = studyXml;
_studyStorageLocation = storageLocation;
_writeFile = writeFile;
_settings = new StudyXmlOutputSettings
{
IncludePrivateValues = StudyXmlTagInclusion.IgnoreTag,
IncludeUnknownTags = StudyXmlTagInclusion.IgnoreTag,
IncludeLargeTags = StudyXmlTagInclusion.IncludeTagExclusion,
MaxTagLength = 2048,
IncludeSourceFileName = true
};
}
public InsertOrUpdateEntryCommand(String groupId,
StudyStorageLocation studyLocation,
DicomFile file, String duplicateStoragePath, String relativePath,
List<DicomAttributeComparisonResult> reasons)
: base("Insert Duplicate Queue Entry Command")
{
Platform.CheckForNullReference(groupId, "groupId");
Platform.CheckForNullReference(studyLocation, "studyLocation");
Platform.CheckForNullReference(file, "file");
_file = file;
_studyLocation = studyLocation;
_groupId = groupId;
_duplicateStoragePath = duplicateStoragePath;
_relativePath = relativePath;
_reasons = reasons;
}
public ImportSopResponse ImportSop(ImportSopRequest request)
{
try
{
var theFile = new DicomFile(string.Format("{0}{1}", request.SopInstanceUid, ServerPlatform.DicomFileExtension));
using (var stream = new LargeMemoryStream(request.SopInstance))
{
theFile.Load(stream);
}
var partition = ServerPartitionMonitor.Instance.GetPartition(request.CalledAETitle);
string aeTitle = theFile.SourceApplicationEntityTitle;
if (_importerContext == null)
_importerContext = new SopInstanceImporterContext(
String.Format("{0}_{1}", aeTitle, DateTime.Now.ToString("yyyyMMddhhmmss")),
partition.AeTitle, partition);
var utility = new SopInstanceImporter(_importerContext);
var importResult = utility.Import(theFile);
if (!importResult.Successful)
Platform.Log(LogLevel.Error, "Failure importing file file from Web Service: {0}, SOP Instance UID: {1}", importResult.ErrorMessage, request.SopInstanceUid);
else
Platform.Log(LogLevel.Info, "Processed import for SOP through Web Service: {0}.", request.SopInstanceUid);
var result = new ImportSopResponse
{
DicomStatusCode = importResult.DicomStatus.Code,
FailureMessage = importResult.ErrorMessage,
Successful = importResult.Successful
};
return result;
}
catch (Exception ex)
{
var message = string.Format("Failed to import files: {0}, SOP Instance UID: {1}", ex.Message, request.SopInstanceUid);
Platform.Log(LogLevel.Error, message);
throw new FaultException(message);
}
}
/// <summary>
/// This method will update a tag
/// </summary>
/// <param name="dcmFile"></param>
/// <param name="newTag"></param>
/// <param name="overwriteIfNotProvided"></param>
/// <returns></returns>
private static DicomFile UpdateTag(
ClearCanvas.Dicom.DicomFile dcmFile, IDicomTag newTag, bool overwriteIfNotProvided = false)
{
if (newTag?.Values == null && !overwriteIfNotProvided)
{
return(dcmFile);
}
var value = newTag?.Values != null && newTag.Values.Length > 0 ? newTag.Values[0] : "";
if (newTag?.GetValueType() == typeof(string[]))
{
var vals = new string[newTag.Values.Length];
newTag.Values.CopyTo(vals, 0);
dcmFile.DataSet[newTag.GetTagValue()].Values = vals;
}
else if (newTag?.GetValueType() == typeof(string))
{
dcmFile.DataSet[newTag.GetTagValue()].Values = value;
}
return(dcmFile);
}
public void HandleAllGetRequests(HttpListenerContext context)
{
var rc = new ResponseClass();
string studyuid = context.Request.QueryString["studyuid"];
string seriesuid = context.Request.QueryString["seriesuid"];
string check = context.Request.QueryString["check"];
if (!string.IsNullOrEmpty(check))
{
rc.Success = true;
rc.Message = "";
rc.Data = true;
string json = Newtonsoft.Json.JsonConvert.SerializeObject(rc);
this.SendTextResponse(context, json);
return;
}
var node = ADCM.GetSelectedNode();
try
{
LOG.Write("New request");
if (string.IsNullOrEmpty(studyuid) || string.IsNullOrEmpty(seriesuid))
{
throw new Exception("No studyuid or seriesuid provided");
}
bool downloaded = ADCM.DownloadOneSeries(studyuid, seriesuid);
if (!downloaded)
{
throw new Exception("Unable to download study");
}
string seriesPath = Path.Combine(node.LocalStorage, studyuid, seriesuid);
if (!Directory.Exists(seriesPath))
{
throw new Exception("Series path not found: " + seriesPath);
}
var dcmFiles = Directory.GetFiles(seriesPath, "*.dcm");
string filetouse = null;
decimal mid = dcmFiles.Length / 2;
int index = (int)Math.Ceiling(mid);
for (int i = index; i < dcmFiles.Length; i++)
{
var dcm = dcmFiles[i];
ClearCanvas.Dicom.DicomFile dcmFile = new ClearCanvas.Dicom.DicomFile(dcm);
dcmFile.Load();
ClearCanvas.ImageViewer.StudyManagement.LocalSopDataSource localds = new ClearCanvas.ImageViewer.StudyManagement.LocalSopDataSource(dcmFile);
if (!localds.IsImage)
{
continue;
}
else
{
filetouse = dcm;
break;
}
}
if (string.IsNullOrEmpty(filetouse))
{
for (int i = 0; i < dcmFiles.Length; i++)
{
var dcm = dcmFiles[i];
ClearCanvas.Dicom.DicomFile dcmFile = new ClearCanvas.Dicom.DicomFile(dcm);
dcmFile.Load();
ClearCanvas.ImageViewer.StudyManagement.LocalSopDataSource localds = new ClearCanvas.ImageViewer.StudyManagement.LocalSopDataSource(dcmFile);
if (!localds.IsImage)
{
continue;
}
else
{
filetouse = dcm;
break;
}
}
}
if (string.IsNullOrEmpty(filetouse))
{
throw new Exception("Unable to find image in downloaded DICOM files");
}
if (!File.Exists(filetouse))
{
throw new Exception("Unable to find DICOM file to use");
}
string base64String = Convert.ToBase64String(AIMG.GetImageBytesFromDcm(filetouse));
base64String = "data:image/jpeg;base64," + base64String;
rc.Success = true;
rc.Message = "";
rc.Data = base64String;
string json = Newtonsoft.Json.JsonConvert.SerializeObject(rc);
this.SendTextResponse(context, json);
}
catch (Exception ex)
{
LOG.Write("ERROR: " + ex.Message);
rc.Data = null;
rc.Success = false;
rc.Message = ex.Message;
string json = Newtonsoft.Json.JsonConvert.SerializeObject(rc);
this.SendTextResponse(context, json);
}
finally
{
string studypath = Path.Combine(node.LocalStorage, studyuid);
if (Directory.Exists(studypath))
{
Directory.Delete(studypath, true);
}
}
}
/// <summary>
/// Process the rule
/// </summary>
/// <param name="file"></param>
public void Process(ClearCanvas.Dicom.DicomFile file)
{
var proposedTs = ClearCanvas.Dicom.TransferSyntax.GetTransferSyntax(OutputTransferSyntax);
var currentTs = file.TransferSyntax;
var bitsStored = file.DataSet[DicomTags.BitsStored].GetInt16(0, 0);
var bitsAllocated = file.DataSet[DicomTags.BitsAllocated].GetInt16(0, 0);
var samplesPerPixel = file.DataSet[DicomTags.SamplesPerPixel].GetInt16(0, 0);
var photometricInterpretation = file.DataSet[DicomTags.PhotometricInterpretation].GetString(0, "");
log.Info(string.Format(
"compress: bits stored {0}, bits allocated {1}, samples per pixel {2}, photometric {3}",
bitsStored, bitsAllocated, samplesPerPixel, photometricInterpretation));
log.Info(string.Format("Compress: Proposed: {0}, current {1}", proposedTs, currentTs));
log.Info("Checking that proposed transfer syntax is consistent with the dataset");
ClearCanvas.Dicom.TransferSyntax finalTs = currentTs;
try
{
if (proposedTs == TransferSyntax.JpegBaselineProcess1)
{
ValidateJPEGBaselineProcess1(bitsAllocated, bitsStored, samplesPerPixel, photometricInterpretation);
}
else if (proposedTs == TransferSyntax.JpegExtendedProcess24)
{
ValidateJPEGExtendedProcess2And4(bitsAllocated, bitsStored, samplesPerPixel, photometricInterpretation);
}
else if (proposedTs == TransferSyntax.JpegLosslessNonHierarchicalFirstOrderPredictionProcess14SelectionValue1)
{
ValidateJpegLosslessNonHierarchicalFirstOrderPredictionProcess14SelectionValue1(bitsAllocated, bitsStored, samplesPerPixel, photometricInterpretation);
}
else if (proposedTs == TransferSyntax.Jpeg2000ImageCompression)
{
ValidateJpeg2000Lossy(bitsAllocated, bitsStored, samplesPerPixel, photometricInterpretation);
}
else if (proposedTs == TransferSyntax.Jpeg2000ImageCompressionLosslessOnly)
{
ValidateJpeg2000Lossless(bitsAllocated, bitsStored, samplesPerPixel, photometricInterpretation);
}
// Compression from non-compressed transfer syntaxes
if (currentTs == TransferSyntax.ImplicitVrLittleEndian ||
currentTs == TransferSyntax.ExplicitVrLittleEndian ||
currentTs == TransferSyntax.ExplicitVrBigEndian)
{
// This is fine ... we're compressing something that isn't compressed.
finalTs = proposedTs;
}
else
{
// Potentially a problem. We could be moving from a compressed syntax to
// another compress syntax. We know the target syntax is legal for this dataset
// but the toolkit pukes when moving encapsulated frames.
// TO DO: More work needed here.
finalTs = proposedTs;
}
log.Info(string.Format("Final ts {0}", finalTs));
}
catch (NotSupportedException nse)
{
log.Error("Compression would be illegal and will NOT be applied. " + nse.ToString());
}
if (currentTs != finalTs)
{
file.ChangeTransferSyntax(finalTs);
}
}
void IDicomServerHandler.OnReceiveRequestMessage(DicomServer server, ServerAssociationParameters association, byte presentationID, DicomMessage message)
{
if (message.CommandField == DicomCommandField.CEchoRequest)
{
server.SendCEchoResponse(presentationID, message.MessageId, DicomStatuses.Success);
return;
}
String studyInstanceUid = null;
String seriesInstanceUid = null;
DicomUid sopInstanceUid = null;
String patientName = null;
String accession = null;
String instanceNumber = null;
bool ok = message.DataSet[DicomTags.SopInstanceUid].TryGetUid(0, out sopInstanceUid);
if (ok)
{
ok = message.DataSet[DicomTags.SeriesInstanceUid].TryGetString(0, out seriesInstanceUid);
}
if (ok)
{
ok = message.DataSet[DicomTags.StudyInstanceUid].TryGetString(0, out studyInstanceUid);
}
if (ok)
{
ok = message.DataSet[DicomTags.PatientsName].TryGetString(0, out patientName);
}
if (ok)
{
ok = message.DataSet[DicomTags.AccessionNumber].TryGetString(0, out accession);
}
if (ok)
{
ok = message.DataSet[DicomTags.InstanceNumber].TryGetString(0, out instanceNumber);
}
if (!ok)
{
Platform.Log(LogLevel.Error, "Unable to retrieve UIDs from request message, sending failure status.");
server.SendCStoreResponse(presentationID, message.MessageId, sopInstanceUid.UID,
DicomStatuses.ProcessingFailure);
return;
}
TransferSyntax syntax = association.GetPresentationContext(presentationID).AcceptedTransferSyntax;
if (List)
{
Platform.Log(LogLevel.Info, message.Dump());
}
if (Bitbucket)
{
Platform.Log(LogLevel.Debug, "Received SOP Instance: {0} for patient {1} in syntax {2}", sopInstanceUid,
patientName, syntax.Name);
server.SendCStoreResponse(presentationID, message.MessageId,
sopInstanceUid.UID,
DicomStatuses.Success);
return;
}
if (!Directory.Exists(StorageLocation))
{
Directory.CreateDirectory(StorageLocation);
}
var path = new StringBuilder();
var series = seriesInstanceUid.Length > 8 ? seriesInstanceUid.Substring(seriesInstanceUid.Length - 8) : seriesInstanceUid;
path.AppendFormat("{0}{1}{2}{3}{4}", StorageLocation, Path.DirectorySeparatorChar,
accession, Path.DirectorySeparatorChar, series);
Directory.CreateDirectory(path.ToString());
path.AppendFormat("{0}{1}.dcm", Path.DirectorySeparatorChar, instanceNumber);
var dicomFile = new ClearCanvas.Dicom.DicomFile(message, path.ToString())
{
TransferSyntaxUid = syntax.UidString,
MediaStorageSopInstanceUid = sopInstanceUid.UID,
ImplementationClassUid = DicomImplementation.ClassUID.UID,
ImplementationVersionName = DicomImplementation.Version,
SourceApplicationEntityTitle = association.CallingAE,
MediaStorageSopClassUid = message.SopClass.Uid
};
dicomFile.Save(DicomWriteOptions.None);
Platform.Log(LogLevel.Debug, "Received SOP Instance: {0} for patient {1} in syntax {2}", sopInstanceUid,
patientName, syntax.Name);
server.SendCStoreResponse(presentationID, message.MessageId,
sopInstanceUid.UID,
DicomStatuses.Success);
}
private static DicomFile UpdateArrayTag(
ClearCanvas.Dicom.DicomFile dcmFile, IDicomTag newTag, IEnumerable value)
{
dcmFile.DataSet[newTag.GetTagValue()].Values = value;
return(dcmFile);
}
