public void TestExclusionsImmediatelyAfterSerialization()
{
//NOTE: previously, this test failed because the excluded tags were not added to the
//xml collection until after it had been deserialized at least once from the xml.
foreach (string[] testSet in _overlappingTagTestSets)
{
List <DicomFile> images = SetupImages(testSet.Length);
SetTestAttribute(images, testSet);
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
{
xml.AddFile(file);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 1024;
XmlDocument doc = xml.GetMemento(settings);
List <InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
ValidateSimpleDataSets(testSet, dataSets, settings);
//do a little extra validation, what the hay.
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
ValidateSimpleDataSets(testSet, dataSets, settings);
}
}
public void TestMultipleSerializations()
{
List <DicomFile> images = SetupImages(4);
XmlDocument doc = null;
StudyXml xml;
int i;
for (i = 0; i < images.Count; ++i)
{
xml = new StudyXml();
if (doc != null)
{
xml.SetMemento(doc);
}
xml.AddFile(images[i]);
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
doc = xml.GetMemento(settings);
}
xml = new StudyXml();
xml.SetMemento(doc);
List <InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
i = 0;
foreach (DicomFile file in images)
{
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
}
public void TestExcludePrivateTags()
{
List <DicomFile> images = SetupImages(2);
StudyXml xml = new StudyXml();
DicomTag privateTag =
new DicomTag(0x00210010, "Private Tag", "Private Tag", DicomVr.LTvr, false, 1, uint.MaxValue, false);
foreach (DicomFile file in images)
{
file.DataSet[privateTag].SetStringValue("My Private Tag");
xml.AddFile(file);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
XmlDocument doc = xml.GetMemento(settings);
List <InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
{
Assert.IsFalse(dataSet.Contains(privateTag));
}
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
{
Assert.IsFalse(dataSet.Contains(privateTag));
}
}
/// <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 void TestSopClass()
{
List <DicomFile> images = SetupImages(4);
string seriesUid = images[0].DataSet[DicomTags.SeriesInstanceUid].ToString();
images[0].MediaStorageSopClassUid = SopClass.EnhancedCtImageStorageUid;
images[1].MediaStorageSopClassUid = SopClass.EnhancedMrImageStorageUid;
images[2].MediaStorageSopClassUid = SopClass.EnhancedSrStorageUid;
images[3].MediaStorageSopClassUid = SopClass.EnhancedXaImageStorageUid;
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
{
xml.AddFile(file);
}
XmlDocument doc = xml.GetMemento(new StudyXmlOutputSettings());
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedCtImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedMrImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedSrStorageUid);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedXaImageStorageUid);
xml = new StudyXml();
xml.SetMemento(doc);
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedCtImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedMrImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedSrStorageUid);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedXaImageStorageUid);
}
public void TestBaseInstanceExclusionAfterSerialization()
{
foreach (string[] testSet in _overlappingTagTestSets)
{
List <DicomFile> images = SetupImages(testSet.Length);
SetTestAttribute(images, testSet);
StudyXml xml = new StudyXml();
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
xml = new StudyXml();
xml.AddFile(images[0]);
xml.AddFile(images[1]);
XmlDocument doc = xml.GetMemento(settings);
settings.MaxTagLength = 1024;
xml.AddFile(images[2]); //re-add
doc = xml.GetMemento(settings);
xml = new StudyXml();
xml.SetMemento(doc);
doc = xml.GetMemento(settings);
xml.AddFile(images[2]); //re-add
doc = xml.GetMemento(settings);
xml = new StudyXml();
xml.SetMemento(doc);
xml.AddFile(images[1]); //re-add
doc = xml.GetMemento(settings);
}
}
/// <summary>
/// Gets the <see cref="StudyXml"/> if it exists in this storage location.
/// </summary>
/// <remarks>
/// </remarks>
/// <returns></returns>
public StudyXml LoadStudyXml()
{
// TODO: Use FileStreamOpener instead
// Can't do it until we break the dependency of ImageServer.Common on Model
if (_studyXml == null)
{
lock (SyncRoot)
{
try
{
Stream xmlStream = Open(GetStudyXmlPath());
if (xmlStream != null)
{
var theMemento = new StudyXmlMemento();
using (xmlStream)
{
StudyXmlIo.Read(theMemento, xmlStream);
xmlStream.Close();
}
_studyXml = new StudyXml();
_studyXml.SetMemento(theMemento);
}
}
catch (Exception)
{ }
}
}
return(_studyXml);
}
public void TestTransferSyntax()
{
List <DicomFile> images = SetupImages(4);
string seriesUid = images[0].DataSet[DicomTags.SeriesInstanceUid].ToString();
images[0].TransferSyntax = TransferSyntax.Jpeg2000ImageCompression;
images[1].TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
images[2].TransferSyntax = TransferSyntax.ExplicitVrBigEndian;
images[3].TransferSyntax = TransferSyntax.Jpeg2000ImageCompressionLosslessOnly;
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
{
xml.AddFile(file);
}
XmlDocument doc = xml.GetMemento(new StudyXmlOutputSettings());
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompression);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrLittleEndian);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrBigEndian);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompressionLosslessOnly);
xml = new StudyXml();
xml.SetMemento(doc);
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompression);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrLittleEndian);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrBigEndian);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompressionLosslessOnly);
}
public void TestSopClass()
{
List<DicomFile> images = SetupImages(4);
string seriesUid = images[0].DataSet[DicomTags.SeriesInstanceUid].ToString();
images[0].MediaStorageSopClassUid = SopClass.EnhancedCtImageStorageUid;
images[1].MediaStorageSopClassUid = SopClass.EnhancedMrImageStorageUid;
images[2].MediaStorageSopClassUid = SopClass.EnhancedSrStorageUid;
images[3].MediaStorageSopClassUid = SopClass.EnhancedXaImageStorageUid;
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
xml.AddFile(file);
XmlDocument doc = xml.GetMemento(new StudyXmlOutputSettings());
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedCtImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedMrImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedSrStorageUid);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedXaImageStorageUid);
xml = new StudyXml();
xml.SetMemento(doc);
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedCtImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedMrImageStorageUid);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedSrStorageUid);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].SopClass.Uid, SopClass.EnhancedXaImageStorageUid);
}
private void LoadStudyXml(bool throwIfNotExists)
{
if (_studyXml == null)
{
if (StudyXmlUri == null)
{
throw new DataStoreException("The study xml location must be set.");
}
XmlDocument doc = new XmlDocument();
_studyXml = new StudyXml(StudyInstanceUid);
if (File.Exists(StudyXmlUri.LocalDiskPath))
{
using (FileStream stream = GetFileStream(FileMode.Open, FileAccess.Read))
{
StudyXmlIo.Read(doc, stream);
_studyXml.SetMemento(doc);
}
}
else if (throwIfNotExists)
{
throw new FileNotFoundException("The study xml file could not be found", StudyXmlUri.LocalDiskPath);
}
}
}
/// <summary>
/// Apply the rules.
/// </summary>
/// <remarks>
/// When rules are applied, we are simply adding new <see cref="ServerDatabaseCommand"/> instances
/// for the rules to the currently executing <see cref="ServerCommandProcessor"/>. They will be
/// executed after all other rules have been executed.
/// </remarks>
protected override void OnExecute(CommandProcessor theProcessor)
{
string studyXmlFile = Path.Combine(_directory, String.Format("{0}.xml", _studyInstanceUid));
StudyXml theXml = new StudyXml(_studyInstanceUid);
if (File.Exists(studyXmlFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(studyXmlFile, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, fileStream);
theXml.SetMemento(theMemento);
fileStream.Close();
}
}
else
{
string errorMsg = String.Format("Unable to load study XML file of restored study: {0}", studyXmlFile);
Platform.Log(LogLevel.Error, errorMsg);
throw new ApplicationException(errorMsg);
}
DicomFile defaultFile = null;
bool rulesExecuted = false;
foreach (SeriesXml seriesXml in theXml)
{
foreach (InstanceXml instanceXml in seriesXml)
{
// Skip non-image objects
if (instanceXml.SopClass.Equals(SopClass.KeyObjectSelectionDocumentStorage)
|| instanceXml.SopClass.Equals(SopClass.GrayscaleSoftcopyPresentationStateStorageSopClass)
|| instanceXml.SopClass.Equals(SopClass.BlendingSoftcopyPresentationStateStorageSopClass)
|| instanceXml.SopClass.Equals(SopClass.ColorSoftcopyPresentationStateStorageSopClass))
{
// Save the first one encountered, just in case the whole study is non-image objects.
if (defaultFile == null)
defaultFile = new DicomFile("test", new DicomAttributeCollection(), instanceXml.Collection);
continue;
}
DicomFile file = new DicomFile("test", new DicomAttributeCollection(), instanceXml.Collection);
_context.Message = file;
_engine.Execute(_context);
rulesExecuted = true;
break;
}
if (rulesExecuted) break;
}
if (!rulesExecuted && defaultFile != null)
{
_context.Message = defaultFile;
_engine.Execute(_context);
}
}
/// <summary>
/// Get a list of paths to the first image in each series within the study being processed.
/// </summary>
/// <returns></returns>
private List <string> GetFirstInstanceInEachStudySeries()
{
var fileList = new List <string>();
if (_studyXml == null)
{
string studyXml = _location.GetStudyXmlPath();
if (!File.Exists(studyXml))
{
return(fileList);
}
_studyXml = new StudyXml();
using (FileStream stream = FileStreamOpener.OpenForRead(studyXml, FileMode.Open))
{
var theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, stream);
stream.Close();
_studyXml.SetMemento(theDoc);
}
}
// Note, we try and force ourselves to have an uncompressed
// image, if one exists. That way the rules will be reapplied on the object
// if necessary for compression.
foreach (SeriesXml seriesXml in _studyXml)
{
InstanceXml saveInstance = null;
foreach (InstanceXml instance in seriesXml)
{
if (instance.TransferSyntax.Encapsulated)
{
if (saveInstance == null)
{
saveInstance = instance;
}
}
else
{
saveInstance = instance;
break;
}
}
if (saveInstance != null)
{
string path = Path.Combine(_location.GetStudyPath(), seriesXml.SeriesInstanceUid);
path = Path.Combine(path, saveInstance.SopInstanceUid + ServerPlatform.DicomFileExtension);
fileList.Add(path);
}
}
return(fileList);
}
public void TestSameSequenceWithExclusionsMultipleSerializations()
{
List <DicomFile> images = SetupImagesWithVoiLutSequenceA(3);
StudyXml newStudyXml;
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 1024;
List <DicomFile> first2Images = new List <DicomFile>();
first2Images.AddRange(images.GetRange(0, 2));
List <InstanceXmlDicomAttributeCollection> dataSets1 = GetInstanceXmlDataSets(first2Images, out newStudyXml, settings);
for (int i = 0; i < first2Images.Count; ++i)
{
DicomAttributeSQ sequence = (DicomAttributeSQ)dataSets1[i][DicomTags.VoiLutSequence];
for (int j = 0; j < sequence.Count; ++j)
{
Assert.IsTrue(((InstanceXmlDicomSequenceItem)sequence[j]).ExcludedTags[0].TagValue == DicomTags.LutData);
}
}
Assert.AreEqual(dataSets1[0][DicomTags.VoiLutSequence], dataSets1[1][DicomTags.VoiLutSequence]);
newStudyXml.AddFile(images[2]);
XmlDocument document = newStudyXml.GetMemento(settings);
//SaveStudyXml(document, @"c:\stewart\studyxml3.xml");
newStudyXml = new StudyXml();
newStudyXml.SetMemento(document);
List <InstanceXmlDicomAttributeCollection> dataSets2 = GetInstanceXmlDataSets(newStudyXml);
for (int i = 0; i < first2Images.Count; ++i)
{
DicomAttributeSQ sequence = (DicomAttributeSQ)dataSets2[i][DicomTags.VoiLutSequence];
for (int j = 0; j < sequence.Count; ++j)
{
Assert.IsTrue(((InstanceXmlDicomSequenceItem)sequence[j]).ExcludedTags[0].TagValue == DicomTags.LutData);
}
}
Assert.AreEqual(dataSets1[0][DicomTags.VoiLutSequence], dataSets2[0][DicomTags.VoiLutSequence]);
Assert.AreEqual(dataSets1[1][DicomTags.VoiLutSequence], dataSets2[1][DicomTags.VoiLutSequence]);
Assert.AreEqual(dataSets2[0][DicomTags.VoiLutSequence], dataSets2[1][DicomTags.VoiLutSequence]);
Assert.AreEqual(dataSets2[0][DicomTags.VoiLutSequence], dataSets2[2][DicomTags.VoiLutSequence]);
}
/// <summary>
/// Load the StudyXml file.
/// </summary>
/// <param name="studyXmlFile"></param>
public void LoadStudyXml(string studyXmlFile)
{
using (Stream fileStream = FileStreamOpener.OpenForRead(studyXmlFile, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, fileStream);
_studyXml = new StudyXml(_storageLocation.StudyInstanceUid);
_studyXml.SetMemento(theMemento);
fileStream.Close();
}
}
private static StudyXml GetStudyXml(StudyStorageLocation storageLocation)
{
StudyXml studyXml = new StudyXml();
string studyXmlPath = Path.Combine(storageLocation.GetStudyPath(), storageLocation.StudyInstanceUid + ".xml");
using (Stream stream = FileStreamOpener.OpenForRead(studyXmlPath, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, stream);
studyXml.SetMemento(theMemento);
stream.Close();
}
return(studyXml);
}
/// <summary>
/// Load the StudyXml file.
/// </summary>
/// <param name="studyXmlFile"></param>
public void LoadStudyXml(string studyXmlFile)
{
using (Stream fileStream = FileStreamOpener.OpenForRead(studyXmlFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
_studyXml = new StudyXml(_storageLocation.StudyInstanceUid);
_studyXml.SetMemento(theDoc);
fileStream.Close();
}
}
public void TestExcludeBinaryTags()
{
List <DicomFile> images = SetupImages(3);
images[2].DataSet[DicomTags.SpectroscopyData].Values = new float[6];
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
{
file.DataSet[DicomTags.RedPaletteColorLookupTableData].Values = new byte[256];
file.DataSet[DicomTags.GreenPaletteColorLookupTableData].Values = new byte[256];
file.DataSet[DicomTags.BluePaletteColorLookupTableData].Values = new byte[256];
xml.AddFile(file);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 100;
XmlDocument doc = xml.GetMemento(settings);
//SaveStudyXml(doc, @"C:\stewart\testxml.xml");
List <InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
{
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.RedPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.GreenPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.BluePaletteColorLookupTableData));
}
//This attribute has a short value, so it should not be excluded.
Assert.IsFalse(dataSets[2].IsTagExcluded(DicomTags.SpectroscopyData));
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
{
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.RedPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.GreenPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.BluePaletteColorLookupTableData));
}
//This attribute has a short value, so it should not be excluded.
Assert.IsFalse(dataSets[2].IsTagExcluded(DicomTags.SpectroscopyData));
}
private void _buttonLoadGzipXml_Click(object sender, EventArgs e)
{
openFileDialog.DefaultExt = "gzip";
openFileDialog.ShowDialog();
Stream fileStream = openFileDialog.OpenFile();
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.ReadGzip(theDoc, fileStream);
fileStream.Close();
_theStream = new StudyXml();
_theStream.SetMemento(theDoc);
}
/// <summary>
/// Helper method to load a <see cref="StudyXml"/> instance for a given study location.
/// </summary>
/// <param name="location"></param>
/// <returns></returns>
public static StudyXml LoadStudyXml(StudyStorageLocation location)
{
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
StudyXml theXml = new StudyXml();
if (File.Exists(streamFile))
{
// allocate the random number generator here, in case we need it below
Random rand = new Random();
// Go into a retry loop, to handle if the study is being processed right now
for (int i = 0; ; i++)
{
try
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
return(theXml);
}
}
catch (IOException)
{
if (i < 5)
{
Thread.Sleep(rand.Next(5, 50)); // Sleep 5-50 milliseconds
continue;
}
throw;
}
}
}
return(theXml);
}
/// <summary>
/// Gets the study header (via <see cref="GetStudyHeader"/>), unzips the gzipped stream, and returns it as <see cref="StudyXml"/>.
/// </summary>
/// <param name="callingAETitle">AE title of the local application.</param>
/// <param name="parameters">Input parameters.</param>
/// <returns></returns>
public StudyXml GetStudyXml(string callingAETitle, HeaderStreamingParameters parameters)
{
XmlDocument doc;
using (var stream = GetStudyHeader(callingAETitle, parameters))
{
using (var gzStream = new GZipStream(stream, CompressionMode.Decompress))
{
doc = new XmlDocument();
doc.Load(gzStream);
gzStream.Close();
}
}
var studyXml = new StudyXml();
studyXml.SetMemento(doc);
return(studyXml);
}
/// <summary>
/// Gets the study header (via <see cref="GetStudyHeader"/>), unzips the gzipped stream, and returns it as <see cref="StudyXml"/>.
/// </summary>
/// <param name="callingAETitle">AE title of the local application.</param>
/// <param name="parameters">Input parameters.</param>
/// <returns></returns>
public StudyXml GetStudyXml(string callingAETitle, HeaderStreamingParameters parameters)
{
StudyXmlMemento theMemento;
using (var stream = GetStudyHeader(callingAETitle, parameters))
{
using (var gzStream = new GZipStream(stream, CompressionMode.Decompress))
{
theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, gzStream);
gzStream.Close();
}
}
var studyXml = new StudyXml();
studyXml.SetMemento(theMemento);
return(studyXml);
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
private StudyXml LoadStudyStream(string location)
{
StudyXml theXml = new StudyXml();
if (File.Exists(location))
{
using (Stream fileStream = new FileStream(location, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
return theXml;
}
private InstanceXml GetInstanceXml(StudyXmlOutputSettings outputSettings, out DicomFile real)
{
var xml = new StudyXml();
real = new DicomFile();
SetupMR(real.DataSet);
real.MediaStorageSopClassUid = real.DataSet[DicomTags.SopClassUid].ToString();
real.MetaInfo[DicomTags.SopClassUid].SetString(0, real.DataSet[DicomTags.SopClassUid].ToString());
var bytes = new Byte[2048];
real.DataSet[DicomTags.RedPaletteColorLookupTableData].Values = bytes;
var privateTag = new DicomTag(0x00111301, "Private Tag", "PrivateTag", DicomVr.CSvr, false, 1, 1, false);
real.DataSet[privateTag].SetString(0, "Private");
var sequences = (DicomSequenceItem[])real.DataSet[DicomTags.RequestAttributesSequence].Values;
var firstItem = sequences.First();
firstItem[DicomTags.RedPaletteColorLookupTableData].Values = bytes;
var attr = real.DataSet[DicomTags.ReferencedStudySequence];
var sequenceItem = new DicomSequenceItem();
attr.AddSequenceItem(sequenceItem);
sequenceItem[privateTag].SetString(0, "Private");
xml.AddFile(real);
var memento = xml.GetMemento(outputSettings ?? new StudyXmlOutputSettings
{
IncludeLargeTags = StudyXmlTagInclusion.IncludeTagExclusion,
IncludePrivateValues = StudyXmlTagInclusion.IgnoreTag,
MaxTagLength = 1024
});
xml = new StudyXml();
xml.SetMemento(memento);
return(xml.First().First());
}
private static List <InstanceXmlDicomAttributeCollection> GetInstanceXmlDataSets(IEnumerable <DicomFile> images, out StudyXml newStudyXml, StudyXmlOutputSettings settings)
{
StudyXml xml = new StudyXml();
foreach (DicomFile image in images)
{
xml.AddFile(image);
}
XmlDocument doc = xml.GetMemento(settings);
//SaveStudyXml(doc, @"c:\stewart\LastStudyXml.xml");
newStudyXml = new StudyXml();
newStudyXml.SetMemento(doc);
doc = newStudyXml.GetMemento(settings);
//SaveStudyXml(doc, @"c:\stewart\LastStudyXml2.xml");
return(GetInstanceXmlDataSets(newStudyXml));
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <returns>The <see cref="StudyXml"/> instance for the study</returns>
private StudyXml LoadStudyXml()
{
StudyXml theXml = new StudyXml();
String streamFile = Path.Combine(_rootPath, _studyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
return theXml;
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
private StudyXml LoadStudyStream(string location)
{
StudyXml theXml = new StudyXml();
if (File.Exists(location))
{
using (Stream fileStream = new FileStream(location, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
return(theXml);
}
public StudyXml LoadStudyXml(bool refresh)
{
lock (SyncRoot)
{
Stream xmlStream = Open(GetStudyXmlPath());
if (xmlStream != null)
{
var theMemento = new StudyXmlMemento();
using (xmlStream)
{
StudyXmlIo.Read(theMemento, xmlStream);
xmlStream.Close();
}
_studyXml = new StudyXml();
_studyXml.SetMemento(theMemento);
}
}
return(_studyXml);
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for the <see cref="StudyLocation"/>
/// </summary>
/// <returns>The <see cref="StudyXml"/> instance</returns>
public StudyXml LoadStudyXml()
{
var theXml = new StudyXml();
string streamFile = GetStudyXmlPath();
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
var theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
return(theXml);
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
protected virtual StudyXml LoadStudyXml(StudyStorageLocation location)
{
StudyXml theXml = new StudyXml();
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
return(theXml);
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <returns>The <see cref="StudyXml"/> instance for the study</returns>
private StudyXml LoadStudyXml()
{
var theXml = new StudyXml();
String streamFile = Path.Combine(_rootPath, _studyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, fileStream);
theXml.SetMemento(theMemento);
fileStream.Close();
}
}
return(theXml);
}
/// <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 theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, stream);
stream.Close();
stream.Dispose();
var xml = new StudyXml();
xml.SetMemento(theMemento);
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);
}
protected static StudyXml LoadStudyXml(StudyStorageLocation location)
{
// This method should be combined with StudyStorageLocation.LoadStudyXml()
StudyXml theXml = new StudyXml(location.StudyInstanceUid);
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, fileStream);
theXml.SetMemento(theMemento);
fileStream.Close();
}
}
return(theXml);
}
public void TestEqualAfterSerialization()
{
foreach (string[] testSet in _overlappingTagTestSets)
{
List <DicomFile> images = SetupImages(testSet.Length);
SetTestAttribute(images, testSet);
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
{
xml.AddFile(file);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 1024;
XmlDocument doc = xml.GetMemento(settings);
List <InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
int i = 0;
foreach (DicomFile file in images)
{
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
i = 0;
foreach (DicomFile file in images)
{
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
}
}
public void TestMultipleSerializations()
{
List<DicomFile> images = SetupImages(4);
XmlDocument doc = null;
StudyXml xml;
int i;
for(i = 0; i < images.Count; ++i)
{
xml = new StudyXml();
if (doc != null)
xml.SetMemento(doc);
xml.AddFile(images[i]);
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
doc = xml.GetMemento(settings);
}
xml = new StudyXml();
xml.SetMemento(doc);
List<InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
i = 0;
foreach (DicomFile file in images)
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
public void TestExcludeBinaryTags()
{
List<DicomFile> images = SetupImages(3);
images[2].DataSet[DicomTags.SpectroscopyData].Values = new float[6];
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
{
file.DataSet[DicomTags.RedPaletteColorLookupTableData].Values = new byte[256];
file.DataSet[DicomTags.GreenPaletteColorLookupTableData].Values = new byte[256];
file.DataSet[DicomTags.BluePaletteColorLookupTableData].Values = new byte[256];
xml.AddFile(file);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 100;
XmlDocument doc = xml.GetMemento(settings);
//SaveStudyXml(doc, @"C:\stewart\testxml.xml");
List<InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
{
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.RedPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.GreenPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.BluePaletteColorLookupTableData));
}
//This attribute has a short value, so it should not be excluded.
Assert.IsFalse(dataSets[2].IsTagExcluded(DicomTags.SpectroscopyData));
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
{
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.RedPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.GreenPaletteColorLookupTableData));
Assert.IsTrue(dataSet.IsTagExcluded(DicomTags.BluePaletteColorLookupTableData));
}
//This attribute has a short value, so it should not be excluded.
Assert.IsFalse(dataSets[2].IsTagExcluded(DicomTags.SpectroscopyData));
}
public void TestExcludePrivateTags()
{
List<DicomFile> images = SetupImages(2);
StudyXml xml = new StudyXml();
DicomTag privateTag =
new DicomTag(0x00210010, "Private Tag", "Private Tag", DicomVr.LTvr, false, 1, uint.MaxValue, false);
foreach (DicomFile file in images)
{
file.DataSet[privateTag].SetStringValue("My Private Tag");
xml.AddFile(file);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
XmlDocument doc = xml.GetMemento(settings);
List<InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
Assert.IsFalse(dataSet.Contains(privateTag));
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
foreach (InstanceXmlDicomAttributeCollection dataSet in dataSets)
Assert.IsFalse(dataSet.Contains(privateTag));
}
public void TestBaseInstanceTagsPastEnd()
{
//NOTE: previously, this test failed because, during xml serialization, only the
//instance's own attributes were iterated over; if there were tags in the base instance
//that went past the end of the individual instances, no 'EmptyAttributes' got added
//to the xml and there would be extra attributes in the instances on deserialization.
List<DicomFile> images = SetupImages(2);
DicomFile smallFile = new DicomFile(null);
images.Add(smallFile);
base.SetupMetaInfo(smallFile);
DicomAttributeCollection theSet = smallFile.DataSet;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("ORIGINAL\\PRIMARY\\OTHER\\M\\FFE");
theSet[DicomTags.InstanceCreationDate].SetStringValue("20070618");
theSet[DicomTags.InstanceCreationTime].SetStringValue("133600");
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.MrImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue("20070618");
theSet[DicomTags.StudyTime].SetStringValue("133600");
theSet[DicomTags.SeriesDate].SetStringValue("20070618");
theSet[DicomTags.SeriesTime].SetStringValue("133700");
theSet[DicomTags.AccessionNumber].SetStringValue("A1234");
theSet[DicomTags.Modality].SetStringValue("MR");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.ManufacturersModelName].SetNullValue();
theSet[DicomTags.InstitutionName].SetStringValue("Mount Sinai Hospital");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("HEART");
theSet[DicomTags.SeriesDescription].SetStringValue("Heart 2D EPI BH TRA");
theSet[DicomTags.StudyInstanceUid].SetStringValue(images[0].DataSet[DicomTags.StudyInstanceUid].ToString());
theSet[DicomTags.SeriesInstanceUid].SetStringValue(images[0].DataSet[DicomTags.SeriesInstanceUid].ToString());
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().ToString());
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
xml.AddFile(file);
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
XmlDocument doc = xml.GetMemento(settings);
List<InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
int i = 0;
foreach (DicomFile file in images)
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
i = 0;
foreach (DicomFile file in images)
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
public void TestTransferSyntax()
{
List<DicomFile> images = SetupImages(4);
string seriesUid = images[0].DataSet[DicomTags.SeriesInstanceUid].ToString();
images[0].TransferSyntax = TransferSyntax.Jpeg2000ImageCompression;
images[1].TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
images[2].TransferSyntax = TransferSyntax.ExplicitVrBigEndian;
images[3].TransferSyntax = TransferSyntax.Jpeg2000ImageCompressionLosslessOnly;
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
xml.AddFile(file);
XmlDocument doc = xml.GetMemento(new StudyXmlOutputSettings());
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompression);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrLittleEndian);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrBigEndian);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompressionLosslessOnly);
xml = new StudyXml();
xml.SetMemento(doc);
Assert.AreEqual(xml[seriesUid][images[0].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompression);
Assert.AreEqual(xml[seriesUid][images[1].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrLittleEndian);
Assert.AreEqual(xml[seriesUid][images[2].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.ExplicitVrBigEndian);
Assert.AreEqual(xml[seriesUid][images[3].DataSet[DicomTags.SopInstanceUid]].TransferSyntax, TransferSyntax.Jpeg2000ImageCompressionLosslessOnly);
}
public void TestBaseInstanceExclusionAfterSerialization()
{
foreach (string[] testSet in _overlappingTagTestSets)
{
List<DicomFile> images = SetupImages(testSet.Length);
SetTestAttribute(images, testSet);
StudyXml xml = new StudyXml();
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
xml = new StudyXml();
xml.AddFile(images[0]);
xml.AddFile(images[1]);
XmlDocument doc = xml.GetMemento(settings);
settings.MaxTagLength = 1024;
xml.AddFile(images[2]); //re-add
doc = xml.GetMemento(settings);
xml = new StudyXml();
xml.SetMemento(doc);
doc = xml.GetMemento(settings);
xml.AddFile(images[2]); //re-add
doc = xml.GetMemento(settings);
xml = new StudyXml();
xml.SetMemento(doc);
xml.AddFile(images[1]); //re-add
doc = xml.GetMemento(settings);
}
}
private InstanceXml GetInstanceXml(StudyXmlOutputSettings outputSettings, out DicomFile real)
{
var xml = new StudyXml();
real = new DicomFile();
SetupMR(real.DataSet);
real.MediaStorageSopClassUid = real.DataSet[DicomTags.SopClassUid].ToString();
real.MetaInfo[DicomTags.SopClassUid].SetString(0, real.DataSet[DicomTags.SopClassUid].ToString());
var bytes = new Byte[2048];
real.DataSet[DicomTags.RedPaletteColorLookupTableData].Values = bytes;
var privateTag = new DicomTag(0x00111301, "Private Tag", "PrivateTag", DicomVr.CSvr, false, 1, 1, false);
real.DataSet[privateTag].SetString(0, "Private");
var sequences = (DicomSequenceItem[])real.DataSet[DicomTags.RequestAttributesSequence].Values;
var firstItem = sequences.First();
firstItem[DicomTags.RedPaletteColorLookupTableData].Values = bytes;
var attr = real.DataSet[DicomTags.ReferencedStudySequence];
var sequenceItem = new DicomSequenceItem();
attr.AddSequenceItem(sequenceItem);
sequenceItem[privateTag].SetString(0, "Private");
xml.AddFile(real);
var memento = xml.GetMemento(outputSettings ?? new StudyXmlOutputSettings
{
IncludeLargeTags = StudyXmlTagInclusion.IncludeTagExclusion,
IncludePrivateValues = StudyXmlTagInclusion.IgnoreTag,
MaxTagLength = 1024
});
xml = new StudyXml();
xml.SetMemento(memento);
return xml.First().First();
}
public void TestBaseInstanceTagsPastEnd()
{
//NOTE: previously, this test failed because, during xml serialization, only the
//instance's own attributes were iterated over; if there were tags in the base instance
//that went past the end of the individual instances, no 'EmptyAttributes' got added
//to the xml and there would be extra attributes in the instances on deserialization.
List <DicomFile> images = SetupImages(2);
DicomFile smallFile = new DicomFile(null);
images.Add(smallFile);
base.SetupMetaInfo(smallFile);
DicomAttributeCollection theSet = smallFile.DataSet;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("ORIGINAL\\PRIMARY\\OTHER\\M\\FFE");
theSet[DicomTags.InstanceCreationDate].SetStringValue("20070618");
theSet[DicomTags.InstanceCreationTime].SetStringValue("133600");
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.MrImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue("20070618");
theSet[DicomTags.StudyTime].SetStringValue("133600");
theSet[DicomTags.SeriesDate].SetStringValue("20070618");
theSet[DicomTags.SeriesTime].SetStringValue("133700");
theSet[DicomTags.AccessionNumber].SetStringValue("A1234");
theSet[DicomTags.Modality].SetStringValue("MR");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.ManufacturersModelName].SetNullValue();
theSet[DicomTags.InstitutionName].SetStringValue("Mount Sinai Hospital");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("HEART");
theSet[DicomTags.SeriesDescription].SetStringValue("Heart 2D EPI BH TRA");
theSet[DicomTags.StudyInstanceUid].SetStringValue(images[0].DataSet[DicomTags.StudyInstanceUid].ToString());
theSet[DicomTags.SeriesInstanceUid].SetStringValue(images[0].DataSet[DicomTags.SeriesInstanceUid].ToString());
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().ToString());
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
{
xml.AddFile(file);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
XmlDocument doc = xml.GetMemento(settings);
List <InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
int i = 0;
foreach (DicomFile file in images)
{
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
i = 0;
foreach (DicomFile file in images)
{
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
protected virtual StudyXml LoadStudyXml(StudyStorageLocation location)
{
StudyXml theXml = new StudyXml();
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, fileStream);
theXml.SetMemento(theMemento);
fileStream.Close();
}
}
return theXml;
}
/// <summary>
/// Apply the rules.
/// </summary>
/// <remarks>
/// When rules are applied, we are simply adding new <see cref="ServerDatabaseCommand"/> instances
/// for the rules to the currently executing <see cref="ServerCommandProcessor"/>. They will be
/// executed after all other rules have been executed.
/// </remarks>
protected override void OnExecute(CommandProcessor theProcessor)
{
string studyXmlFile = Path.Combine(_directory, String.Format("{0}.xml", _studyInstanceUid));
StudyXml theXml = new StudyXml(_studyInstanceUid);
if (File.Exists(studyXmlFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(studyXmlFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
else
{
string errorMsg = String.Format("Unable to load study XML file of restored study: {0}", studyXmlFile);
Platform.Log(LogLevel.Error, errorMsg);
throw new ApplicationException(errorMsg);
}
DicomFile defaultFile = null;
bool rulesExecuted = false;
foreach (SeriesXml seriesXml in theXml)
{
foreach (InstanceXml instanceXml in seriesXml)
{
// Skip non-image objects
if (instanceXml.SopClass.Equals(SopClass.KeyObjectSelectionDocumentStorage) ||
instanceXml.SopClass.Equals(SopClass.GrayscaleSoftcopyPresentationStateStorageSopClass) ||
instanceXml.SopClass.Equals(SopClass.BlendingSoftcopyPresentationStateStorageSopClass) ||
instanceXml.SopClass.Equals(SopClass.ColorSoftcopyPresentationStateStorageSopClass))
{
// Save the first one encountered, just in case the whole study is non-image objects.
if (defaultFile == null)
{
defaultFile = new DicomFile("test", new DicomAttributeCollection(), instanceXml.Collection);
}
continue;
}
DicomFile file = new DicomFile("test", new DicomAttributeCollection(), instanceXml.Collection);
_context.Message = file;
_engine.Execute(_context);
rulesExecuted = true;
break;
}
if (rulesExecuted)
{
break;
}
}
if (!rulesExecuted && defaultFile != null)
{
_context.Message = defaultFile;
_engine.Execute(_context);
}
}
private void PopulateSeries(string studyInstanceUid)
{
LogTextPanel.Text = "";
StatisticsLog.Text = "";
HeaderStreamingServiceClient proxy = null;
try
{
proxy = new HeaderStreamingServiceClient();
HeaderStreamingParameters parms = new HeaderStreamingParameters();
parms.StudyInstanceUID = studyInstanceUid;
parms.ServerAETitle = ServerAE.Text;
parms.ReferenceID = Guid.NewGuid().ToString();
TimeSpanStatistics servicecall = new TimeSpanStatistics();
servicecall.Start();
Stream stream = proxy.GetStudyHeader(AETitle.Text, parms);
servicecall.End();
var decompression = new TimeSpanStatistics();
decompression.Start();
//GZipStream gzipStream = new GZipStream(stream, CompressionMode.Decompress);
var theMemento = new StudyXmlMemento();
StudyXmlIo.ReadGzip(theMemento, stream);
//doc.Load(gzipStream);
decompression.End();
var settings = new XmlWriterSettings();
//settings.Indent = true;
settings.NewLineOnAttributes = false;
settings.OmitXmlDeclaration = true;
settings.Encoding = Encoding.UTF8;
StringWriter sw = new StringWriter();
XmlWriter writer = XmlWriter.Create(sw, settings);
theMemento.Document.WriteTo(writer);
writer.Flush();
Log(sw.ToString());
TimeSpanStatistics loading = new TimeSpanStatistics();
loading.Start();
StudyXml xml = new StudyXml();
xml.SetMemento(theMemento);
loading.End();
int sopCounter = 0;
SeriesTree.Nodes.Clear();
foreach(SeriesXml series in xml)
{
TreeNode seriesNode = new TreeNode(series.SeriesInstanceUid);
SeriesTree.Nodes.Add(seriesNode);
foreach(InstanceXml instance in series)
{
TreeNode instanceNode = new TreeNode(instance.SopInstanceUid);
seriesNode.Nodes.Add(instanceNode);
sopCounter++;
}
}
StatisticsLog.Text="";
StatisticsLog.Text += String.Format("\r\nHeader Size (Decompressed): {0} KB", sw.ToString().Length / 1024);
StatisticsLog.Text += String.Format("\r\nWCF Service call : {0} ms", servicecall.Value.TotalMilliseconds);
StatisticsLog.Text += String.Format("\r\nDecompression : {0} ms", decompression.Value.TotalMilliseconds);
StatisticsLog.Text += String.Format("\r\nLoading StudyXml : {0} ms", loading.Value.TotalMilliseconds);
SeriesLabel.Text = String.Format("Series : {0} \tInstances: {1}", SeriesTree.Nodes.Count, sopCounter);
stream.Close();
}
catch(FaultException<StudyIsInUseFault> ex)
{
timer1.Stop();
MessageBox.Show(String.Format("StudyIsInUseFault received:{0}\n\nState={1}" ,
ex.Message, ex.Detail.StudyState));
}
catch (FaultException<StudyIsNearlineFault> ex)
{
timer1.Stop();
MessageBox.Show("StudyIsNearlineFault received:\n" + ex.Message);
}
catch (FaultException<StudyNotFoundFault> ex)
{
timer1.Stop();
MessageBox.Show("StudyNotFoundFault received:\n" + ex.Message);
}
catch (Exception ex)
{
timer1.Stop();
MessageBox.Show(ex.Message);
}
finally
{
if (proxy.State == CommunicationState.Opened)
proxy.Close();
}
}
/// <summary>
/// Get a list of paths to the first image in each series within the study being processed.
/// </summary>
/// <returns></returns>
private List<string> GetFirstInstanceInEachStudySeries()
{
var fileList = new List<string>();
if (_studyXml == null)
{
string studyXml = _location.GetStudyXmlPath();
if (!File.Exists(studyXml))
{
return fileList;
}
_studyXml = new StudyXml();
using (FileStream stream = FileStreamOpener.OpenForRead(studyXml, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, stream);
stream.Close();
_studyXml.SetMemento(theMemento);
}
}
// Note, we try and force ourselves to have an uncompressed
// image, if one exists. That way the rules will be reapplied on the object
// if necessary for compression.
foreach (SeriesXml seriesXml in _studyXml)
{
InstanceXml saveInstance = null;
foreach (InstanceXml instance in seriesXml)
{
if (instance.TransferSyntax.Encapsulated)
{
if (saveInstance == null)
saveInstance = instance;
}
else
{
saveInstance = instance;
break;
}
}
if (saveInstance != null)
{
string path = Path.Combine(_location.GetStudyPath(), seriesXml.SeriesInstanceUid);
path = Path.Combine(path, saveInstance.SopInstanceUid + ServerPlatform.DicomFileExtension);
fileList.Add(path);
}
}
return fileList;
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
protected virtual StudyXml LoadStudyXml(StudyStorageLocation location)
{
StudyXml theXml = new StudyXml();
StudyXmlLoadTime.Add(
delegate
{
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
}
);
return theXml;
}
public void TestSameSequenceWithExclusionsMultipleSerializations()
{
List<DicomFile> images = SetupImagesWithVoiLutSequenceA(3);
StudyXml newStudyXml;
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 1024;
List<DicomFile> first2Images = new List<DicomFile>();
first2Images.AddRange(images.GetRange(0, 2));
List<InstanceXmlDicomAttributeCollection> dataSets1 = GetInstanceXmlDataSets(first2Images, out newStudyXml, settings);
for (int i = 0; i < first2Images.Count; ++i)
{
DicomAttributeSQ sequence = (DicomAttributeSQ)dataSets1[i][DicomTags.VoiLutSequence];
for (int j = 0; j < sequence.Count; ++j)
Assert.IsTrue(((InstanceXmlDicomSequenceItem)sequence[j]).ExcludedTags[0].TagValue == DicomTags.LutData);
}
Assert.AreEqual(dataSets1[0][DicomTags.VoiLutSequence], dataSets1[1][DicomTags.VoiLutSequence]);
newStudyXml.AddFile(images[2]);
XmlDocument document = newStudyXml.GetMemento(settings);
//SaveStudyXml(document, @"c:\stewart\studyxml3.xml");
newStudyXml = new StudyXml();
newStudyXml.SetMemento(document);
List<InstanceXmlDicomAttributeCollection> dataSets2 = GetInstanceXmlDataSets(newStudyXml);
for (int i = 0; i < first2Images.Count; ++i)
{
DicomAttributeSQ sequence = (DicomAttributeSQ)dataSets2[i][DicomTags.VoiLutSequence];
for (int j = 0; j < sequence.Count; ++j)
Assert.IsTrue(((InstanceXmlDicomSequenceItem)sequence[j]).ExcludedTags[0].TagValue == DicomTags.LutData);
}
Assert.AreEqual(dataSets1[0][DicomTags.VoiLutSequence], dataSets2[0][DicomTags.VoiLutSequence]);
Assert.AreEqual(dataSets1[1][DicomTags.VoiLutSequence], dataSets2[1][DicomTags.VoiLutSequence]);
Assert.AreEqual(dataSets2[0][DicomTags.VoiLutSequence], dataSets2[1][DicomTags.VoiLutSequence]);
Assert.AreEqual(dataSets2[0][DicomTags.VoiLutSequence], dataSets2[2][DicomTags.VoiLutSequence]);
}
private void _buttonLoadGzipXml_Click(object sender, EventArgs e)
{
openFileDialog.DefaultExt = "gzip";
openFileDialog.ShowDialog();
Stream fileStream = openFileDialog.OpenFile();
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.ReadGzip(theDoc, fileStream);
fileStream.Close();
_theStream = new StudyXml();
_theStream.SetMemento(theDoc);
}
private static List<InstanceXmlDicomAttributeCollection> GetInstanceXmlDataSets(IEnumerable<DicomFile> images, out StudyXml newStudyXml, StudyXmlOutputSettings settings)
{
StudyXml xml = new StudyXml();
foreach (DicomFile image in images)
xml.AddFile(image);
XmlDocument doc = xml.GetMemento(settings);
//SaveStudyXml(doc, @"c:\stewart\LastStudyXml.xml");
newStudyXml = new StudyXml();
newStudyXml.SetMemento(doc);
doc = newStudyXml.GetMemento(settings);
//SaveStudyXml(doc, @"c:\stewart\LastStudyXml2.xml");
return GetInstanceXmlDataSets(newStudyXml);
}
public void TestEqualAfterSerialization()
{
foreach (string[] testSet in _overlappingTagTestSets)
{
List<DicomFile> images = SetupImages(testSet.Length);
SetTestAttribute(images, testSet);
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
xml.AddFile(file);
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 1024;
XmlDocument doc = xml.GetMemento(settings);
List<InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
int i = 0;
foreach (DicomFile file in images)
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
i = 0;
foreach (DicomFile file in images)
ValidateEqualExceptExclusions(file.DataSet, dataSets[i++], DicomTags.ImageComments, DicomTags.PixelData);
}
}
public void TestExclusionsImmediatelyAfterSerialization()
{
//NOTE: previously, this test failed because the excluded tags were not added to the
//xml collection until after it had been deserialized at least once from the xml.
foreach (string[] testSet in _overlappingTagTestSets)
{
List<DicomFile> images = SetupImages(testSet.Length);
SetTestAttribute(images, testSet);
StudyXml xml = new StudyXml();
foreach (DicomFile file in images)
xml.AddFile(file);
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.MaxTagLength = 1024;
XmlDocument doc = xml.GetMemento(settings);
List<InstanceXmlDicomAttributeCollection> dataSets = GetInstanceXmlDataSets(xml);
ValidateSimpleDataSets(testSet, dataSets, settings);
//do a little extra validation, what the hay.
xml = new StudyXml();
xml.SetMemento(doc);
dataSets = GetInstanceXmlDataSets(xml);
ValidateSimpleDataSets(testSet, dataSets, settings);
}
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for the <see cref="StudyLocation"/>
/// </summary>
/// <returns>The <see cref="StudyXml"/> instance</returns>
public StudyXml LoadStudyXml()
{
var theXml = new StudyXml();
string streamFile = GetStudyXmlPath();
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
var theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
return theXml;
}