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 void ButtonLoadFile_Click(object sender, EventArgs e)
{
openFileDialog.DefaultExt = "dcm";
openFileDialog.ShowDialog();
DicomFile dicomFile = new DicomFile(openFileDialog.FileName);
dicomFile.Load(DicomReadOptions.Default);
_theStream.AddFile(dicomFile);
}
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));
}
}
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 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);
}
}
protected override void OnExecute(CommandProcessor theProcessor)
{
FileSize = 0;
var finfo = new FileInfo(_file.Filename);
if (finfo.Exists)
{
FileSize = finfo.Length;
}
// Setup the insert parameters
if (false == _stream.AddFile(_file, FileSize, _outputSettings))
{
Platform.Log(LogLevel.Error, "Unexpected error adding SOP to XML Study Descriptor for file {0}",
_file.Filename);
throw new ApplicationException("Unexpected error adding SOP to XML Study Descriptor for SOP: " +
_file.MediaStorageSopInstanceUid);
}
// Write it back out. We flush it out with every added image so that if a failure happens,
// we can recover properly.
string streamFile =
Path.Combine(_studyStorageLocation.GetStudyPath(), _studyStorageLocation.StudyInstanceUid + ".xml");
string gzStreamFile = streamFile + ".gz";
WriteStudyStream(streamFile, gzStreamFile, _stream);
}
protected override void OnExecute(CommandProcessor theProcessor)
{
long fileSize = 0;
if (File.Exists(_file.Filename))
{
var finfo = new FileInfo(_file.Filename);
fileSize = finfo.Length;
}
String seriesInstanceUid = _file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, string.Empty);
String sopInstanceUid = _file.DataSet[DicomTags.SopInstanceUid].GetString(0, string.Empty);
if (_studyXml.Contains(seriesInstanceUid, sopInstanceUid))
{
_duplicate = true;
}
// Setup the insert parameters
if (false == _studyXml.AddFile(_file, fileSize, _settings))
{
Platform.Log(LogLevel.Error, "Unexpected error adding SOP to XML Study Descriptor for file {0}",
_file.Filename);
throw new ApplicationException("Unexpected error adding SOP to XML Study Descriptor for SOP: " +
_file.MediaStorageSopInstanceUid);
}
if (_writeFile)
{
// Write it back out. We flush it out with every added image so that if a failure happens,
// we can recover properly.
bool fileCreated;
_studyStorageLocation.SaveStudyXml(_studyXml, out fileCreated);
}
}
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 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);
}
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 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);
}
protected override void OnExecute(CommandProcessor theProcessor)
{
if (!File.Exists(_path))
{
Platform.Log(LogLevel.Error, "Unexpected error finding file to add to XML {0}", _path);
throw new ApplicationException("Unexpected error finding file to add to XML {0}" + _path);
}
var finfo = new FileInfo(_path);
long fileSize = finfo.Length;
var dicomFile = new DicomFile(_path);
dicomFile.Load(DicomReadOptions.StorePixelDataReferences | DicomReadOptions.Default);
_sopInstanceUid = dicomFile.DataSet[DicomTags.SopInstanceUid];
_seriesInstanceUid = dicomFile.DataSet[DicomTags.SeriesInstanceUid];
// Setup the insert parameters
if (false == _stream.AddFile(dicomFile, fileSize))
{
Platform.Log(LogLevel.Error, "Unexpected error adding SOP to XML Study Descriptor for file {0}",
_path);
throw new ApplicationException("Unexpected error adding SOP to XML Study Descriptor for SOP: " +
dicomFile.MediaStorageSopInstanceUid);
}
}
protected override void OnExecute(CommandProcessor theProcessor)
{
// Setup the insert parameters
string seriesInstanceUid = _file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, string.Empty);
string sopinstanceUid = _file.MediaStorageSopInstanceUid;
FileSize = 0;
var finfo = new FileInfo(_file.Filename);
if (finfo.Exists)
{
FileSize = finfo.Length;
}
// Save the collection for undo purposes
SeriesXml seriesXml = _stream[seriesInstanceUid];
if (seriesXml != null)
{
InstanceXml instanceXml = seriesXml[sopinstanceUid];
if (instanceXml != null)
{
_saveCollection = instanceXml.Collection;
}
}
if (false == _stream.RemoveFile(_file))
{
Platform.Log(LogLevel.Warn, "SOP was unexpectedly not in XML Study Descriptor for file: {0}",
_file.Filename);
}
if (false == _stream.AddFile(_file, FileSize, _outputSettings))
{
Platform.Log(LogLevel.Error, "Unexpected error adding SOP to XML Study Descriptor for file {0}",
_file.Filename);
throw new ApplicationException("Unexpected error adding SOP to XML Study Descriptor for SOP: " +
_file.MediaStorageSopInstanceUid);
}
// Write it back out. We flush it out with every added image so that if a failure happens,
// we can recover properly.
WriteStudyStream(
Path.Combine(_studyStorageLocation.GetStudyPath(), _studyStorageLocation.StudyInstanceUid + ".xml"),
Path.Combine(_studyStorageLocation.GetStudyPath(), _studyStorageLocation.StudyInstanceUid + ".xml.gz"),
_stream);
}
protected override void OnUndo()
{
_studyXml.AddFile(_file);
string streamFile = _studyLocation.GetStudyXmlPath();
string gzStreamFile = streamFile + ".gz";
WriteStudyStream(streamFile, gzStreamFile, _studyXml);
}
internal void Update(DicomFile file)
{
Initialize(file);
LoadStudyXml(false);
_studyXml.AddFile(file);
//these have to be here, rather than in Initialize b/c they are
// computed from the series, which are parsed from the xml.
NumberOfStudyRelatedSeries = _studyXml.NumberOfStudyRelatedSeries;
NumberOfStudyRelatedInstances = _studyXml.NumberOfStudyRelatedInstances;
}
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 Create()
{
SelectFolderDialogCreationArgs args = new SelectFolderDialogCreationArgs();
args.Path = _lastFolder ?? Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
FileDialogResult result = base.Context.DesktopWindow.ShowSelectFolderDialogBox(args);
if (result.Action == DialogBoxAction.Ok)
{
_lastFolder = result.FileName;
StudyLoaderExtensionPoint xp = new StudyLoaderExtensionPoint();
IStudyLoader loader = (IStudyLoader)CollectionUtils.SelectFirst(xp.CreateExtensions(),
delegate(object extension) { return(((IStudyLoader)extension).Name == "DICOM_LOCAL"); });
var selected = base.Context.SelectedStudy;
loader.Start(new StudyLoaderArgs(selected.StudyInstanceUid, selected.Server, StudyLoaderOptions.Default));
StudyXml xml = new StudyXml();
Sop sop;
while (null != (sop = loader.LoadNextSop()))
{
xml.AddFile(((ILocalSopDataSource)sop.DataSource).File);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.IncludePrivateValues = StudyXmlTagInclusion.IgnoreTag;
settings.IncludeUnknownTags = StudyXmlTagInclusion.IgnoreTag;
settings.MaxTagLength = 100 * 1024;
settings.IncludeSourceFileName = true;
XmlDocument doc = xml.GetMemento(settings);
string fileName = System.IO.Path.Combine(result.FileName, "studyxml.xml");
XmlTextWriter writer = new XmlTextWriter(fileName, Encoding.UTF8);
writer.Formatting = Formatting.Indented;
writer.Indentation = 5;
doc.Save(writer);
}
}
public void Create()
{
SelectFolderDialogCreationArgs args = new SelectFolderDialogCreationArgs();
args.Path = _lastFolder ?? Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
FileDialogResult result = base.Context.DesktopWindow.ShowSelectFolderDialogBox(args);
if (result.Action == DialogBoxAction.Ok)
{
_lastFolder = result.FileName;
StudyLoaderExtensionPoint xp = new StudyLoaderExtensionPoint();
IStudyLoader loader = (IStudyLoader)CollectionUtils.SelectFirst(xp.CreateExtensions(),
delegate(object extension) { return ((IStudyLoader) extension).Name == "DICOM_LOCAL";});
var selected = base.Context.SelectedStudy;
loader.Start(new StudyLoaderArgs(selected.StudyInstanceUid, selected.Server, null));
StudyXml xml = new StudyXml();
Sop sop;
while (null != (sop = loader.LoadNextSop()))
{
xml.AddFile(((ILocalSopDataSource) sop.DataSource).File);
}
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.IncludePrivateValues = StudyXmlTagInclusion.IgnoreTag;
settings.IncludeUnknownTags = StudyXmlTagInclusion.IgnoreTag;
settings.MaxTagLength = 100 * 1024;
settings.IncludeSourceFileName = true;
XmlDocument doc = xml.GetMemento(settings);
string fileName = System.IO.Path.Combine(result.FileName, "studyxml.xml");
XmlTextWriter writer = new XmlTextWriter(fileName, Encoding.UTF8);
writer.Formatting = Formatting.Indented;
writer.Indentation = 5;
doc.Save(writer);
}
}
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));
}
public void CreationTest()
{
IList <DicomAttributeCollection> instanceList;
string studyInstanceUid = DicomUid.GenerateUid().UID;
instanceList = SetupMRSeries(4, 10, studyInstanceUid);
StudyXml studyXml = new StudyXml(studyInstanceUid);
string studyXmlFilename = Path.GetTempFileName();
foreach (DicomAttributeCollection instanceCollection in instanceList)
{
instanceCollection[DicomTags.PixelData] = null;
DicomFile theFile = new DicomFile("test", new DicomAttributeCollection(), instanceCollection);
SetupMetaInfo(theFile);
studyXml.AddFile(theFile);
WriteStudyStream(studyXmlFilename, studyXml);
}
StudyXml newXml = LoadStudyStream(studyXmlFilename);
if (!Compare(newXml, instanceList))
{
Assert.Fail("Comparison of StudyXML failed against base loaded from disk");
}
if (!Compare(studyXml, instanceList))
{
Assert.Fail("Comparison of StudyXML failed against base in memory");
}
}
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 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);
}
}
}
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 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);
}
}
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 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));
}
private void UpdateFilesystem()
{
Platform.Log(LogLevel.Info, "Updating filesystem...");
StudyXml studyXml = _oldStudyLocation.LoadStudyXml();
StudyXmlOutputSettings outputSettings = ImageServerCommonConfiguration.DefaultStudyXmlOutputSettings;
StudyXml newStudyXml = new StudyXml();
foreach (SeriesXml seriesXml in studyXml)
{
foreach (InstanceXml instanceXml in seriesXml)
{
string path = Path.Combine(_oldStudyPath, seriesXml.SeriesInstanceUid);
path = Path.Combine(path, instanceXml.SopInstanceUid);
path += ServerPlatform.DicomFileExtension;
if (!File.Exists(path))
{
Platform.Log(LogLevel.Info, "SOP {0} is referenced in study xml but does not exist. It will be removed");
continue; // file was removed but xml was not updated?
}
try
{
DicomFile file = new DicomFile(path);
file.Load();
InstanceInfo instance = new InstanceInfo
{
SeriesInstanceUid = file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, String.Empty),
SopInstanceUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, String.Empty)
};
UpdateDicomFile(file);
// Add into the temporary study xml
long fileSize = 0;
if (File.Exists(file.Filename))
{
FileInfo finfo = new FileInfo(file.Filename);
fileSize = finfo.Length;
}
newStudyXml.AddFile(file, fileSize, outputSettings);
_updatedSopList.Add(instance);
Platform.Log(ServerPlatform.InstanceLogLevel, "SOP {0} has been updated [{1} of {2}].", instance.SopInstanceUid, _updatedSopList.Count, _totalSopCount);
}
catch (Exception)
{
File.Delete(Path.Combine(_backupDir, instanceXml.SopInstanceUid) + ".bak"); //dont' need to restore this file
throw;
}
}
}
// Log any study-level warnings
if (_updatedSopList.Count != _totalSopCount)
{
Platform.Log(LogLevel.Warn, "Inconsistent data: expected {0} instances to be updated / Found {1}.", _totalSopCount, _updatedSopList.Count);
}
// update the header
Platform.Log(LogLevel.Info, "Generating new study header...");
string newStudyXmlPath = Path.Combine(NewStudyPath, _newStudyInstanceUid + ".xml");
string gzipStudyXmlPath = Path.Combine(NewStudyPath, _newStudyInstanceUid + ".xml.gz");
using (FileStream xmlStream = FileStreamOpener.OpenForSoleUpdate(newStudyXmlPath, FileMode.Create),
gzipStream = FileStreamOpener.OpenForSoleUpdate(gzipStudyXmlPath, FileMode.Create))
{
StudyXmlIo.WriteXmlAndGzip(newStudyXml.GetMemento(outputSettings), xmlStream, gzipStream);
xmlStream.Close();
gzipStream.Close();
}
}
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 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 CreationTest()
{
IList<DicomAttributeCollection> instanceList;
string studyInstanceUid = DicomUid.GenerateUid().UID;
instanceList = SetupMRSeries(4, 10, studyInstanceUid);
StudyXml studyXml = new StudyXml(studyInstanceUid);
string studyXmlFilename = Path.GetTempFileName();
foreach (DicomAttributeCollection instanceCollection in instanceList)
{
instanceCollection[DicomTags.PixelData] = null;
DicomFile theFile = new DicomFile("test", new DicomAttributeCollection(), instanceCollection);
SetupMetaInfo(theFile);
studyXml.AddFile(theFile);
WriteStudyStream(studyXmlFilename, studyXml);
}
StudyXml newXml = LoadStudyStream(studyXmlFilename);
if (!Compare(newXml, instanceList))
Assert.Fail("Comparison of StudyXML failed against base loaded from disk");
if (!Compare(studyXml, instanceList))
Assert.Fail("Comparison of StudyXML failed against base in memory");
}
private void RebuildStudyXml()
{
try
{
var studyXml = new StudyXml(Location.Study.StudyInstanceUid);
DicomFile lastLoadedFile = null;
FileProcessor.Process(Location.StudyFolder, "*.dcm", delegate(string file, out bool cancel)
{
cancel = _cancelRequested;
try
{
var dicomFile = new DicomFile(file);
dicomFile.Load(DicomReadOptions.Default |
DicomReadOptions.StorePixelDataReferences);
String sopInstanceUid = dicomFile.DataSet[DicomTags.SopInstanceUid].GetString(0, dicomFile.MediaStorageSopInstanceUid);
if (Path.GetFileNameWithoutExtension(file) == sopInstanceUid)
{
if (!studyXml.AddFile(dicomFile))
{
Platform.Log(LogLevel.Warn,
"Importing file that was in the wrong study folder: {0}",
file);
var context =
new ImportStudyContext(
dicomFile.SourceApplicationEntityTitle,
StudyStore.GetConfiguration(),EventSource.CurrentProcess);
var importer = new ImportFilesUtility(context);
var result = importer.Import(dicomFile,
BadFileBehaviourEnum.Delete,
FileImportBehaviourEnum.Move);
if (result.DicomStatus != DicomStatuses.Success)
{
Platform.Log(LogLevel.Error,
"Unable to import file: {0}",
result.ErrorMessage);
Failed = true;
FailureMessage = result.ErrorMessage;
}
}
else
lastLoadedFile = dicomFile;
}
else
{
Platform.Log(LogLevel.Info, "Ignoring duplicate file: {0}", file);
}
}
catch (Exception x)
{
Platform.Log(LogLevel.Error, x,
"Failed to load file for reprocessing: {0}", file);
Failed = true;
FailureMessage = x.Message;
}
}, false);
// This saves the study Xml to disk, and ensures the database is updated and the study is not marked as "deleted".
// If a cancel was requested, don't save the file, and it will remain "as is"
if (lastLoadedFile !=null && !_cancelRequested)
{
var p = new ProcessStudyUtility(Location) { IsReprocess = true };
p.ProcessFile(lastLoadedFile, studyXml, null);
}
}
catch (Exception x)
{
Platform.Log(LogLevel.Error, x, "Unexpected exception reindexing folder: {0}", Location.StudyFolder);
Failed = true;
FailureMessage = x.Message;
}
if (_cancelRequested)
Platform.Log(LogLevel.Info, "Cancel requested while rebuilding Study XML in folder: {0}", Location.StudyFolder);
else
Platform.Log(LogLevel.Info, "Rebuilt Study XML for study: {0}", Location.Study.StudyInstanceUid);
}
private void RebuildStudyXml()
{
try
{
var studyXml = new StudyXml(Location.Study.StudyInstanceUid);
DicomFile lastLoadedFile = null;
FileProcessor.Process(Location.StudyFolder, "*.dcm",
delegate(string file, out bool cancel)
{
cancel = _cancelRequested;
try
{
var dicomFile = new DicomFile(file);
dicomFile.Load(DicomReadOptions.Default | DicomReadOptions.StorePixelDataReferences);
String sopInstanceUid = dicomFile.DataSet[DicomTags.SopInstanceUid].GetString(0, dicomFile.MediaStorageSopInstanceUid);
if (Path.GetFileNameWithoutExtension(file) == sopInstanceUid)
{
if (!studyXml.AddFile(dicomFile))
{
Platform.Log(LogLevel.Warn, "Importing file that was in the wrong study folder: {0}", file);
var context = new ImportStudyContext(dicomFile.SourceApplicationEntityTitle, StudyStore.GetConfiguration(), EventSource.CurrentProcess);
var importer = new ImportFilesUtility(context);
var result = importer.Import(dicomFile, BadFileBehaviourEnum.Delete, FileImportBehaviourEnum.Move);
if (result.DicomStatus != DicomStatuses.Success)
{
Platform.Log(LogLevel.Error, "Unable to import file: {0}", result.ErrorMessage);
Failed = true;
FailureMessage = result.ErrorMessage;
}
}
else
{
lastLoadedFile = dicomFile;
}
}
else
{
Platform.Log(LogLevel.Info, "Ignoring duplicate file: {0}", file);
}
}
catch (Exception x)
{
Platform.Log(LogLevel.Error, x, "Failed to load file for reprocessing: {0}", file);
Failed = true;
FailureMessage = x.Message;
}
}, false);
// This saves the study Xml to disk, and ensures the database is updated and the study is not marked as "deleted".
// If a cancel was requested, don't save the file, and it will remain "as is"
if (lastLoadedFile != null && !_cancelRequested)
{
var p = new ProcessStudyUtility(Location)
{
IsReprocess = true
};
p.ProcessFile(lastLoadedFile, studyXml, null);
}
}
catch (Exception x)
{
Platform.Log(LogLevel.Error, x, "Unexpected exception reindexing folder: {0}", Location.StudyFolder);
Failed = true;
FailureMessage = x.Message;
}
if (_cancelRequested)
{
Platform.Log(LogLevel.Info, "Cancel requested while rebuilding Study XML in folder: {0}", Location.StudyFolder);
}
else
{
Platform.Log(LogLevel.Info, "Rebuilt Study XML for study: {0}", Location.Study.StudyInstanceUid);
}
}
/// <summary>
/// 刻录
/// </summary>
private void Writing()
{
List <IBurnMediaData> data = new List <IBurnMediaData>();
MediaFileSet mediaFileSet = new MediaFileSet();
mediaFileSet.Id = "Gold";
List <MediaFileSetStudy> fileSetStudies = new List <MediaFileSetStudy>();
string RootPath = "CD";
string studysPath = "IMAGES";
string studyitemPath = "Study{0}";
string seriesitemPath = "Series{0}";
string filename = "IM{0}";
string xmlSavePath = "studies";
string XmlName = "Study{0}.xml";
int study = -1;
int series = -1;
int Sopcount = -1;
string studyIndexName = "index.xml";
string xmlPath = Path.Combine(this.StagingFolderPath, xmlSavePath);
if (Directory.Exists(xmlPath))
{
Directory.Delete(xmlPath, true);
}
Directory.CreateDirectory(xmlPath);
if (MediaWriterSettings.Default.PortablePath == null || !Directory.Exists(MediaWriterSettings.Default.PortablePath))
{
this.Host.ShowMessageBox("指定光盘浏览器目录不存在", MessageBoxActions.Ok);
return;
}
FileDirectoryUtility.CopyFiles(MediaWriterSettings.Default.PortablePath, this.StagingFolderPath, true, true);
RootPath = Path.Combine(this.StagingFolderPath, studysPath);
DicomDirectory dicomDirectory = new DicomDirectory(VolumeName);
dicomDirectory.SourceApplicationEntityTitle = VolumeName;
dicomDirectory.FileSetId = "File Set Desc";
try
{
foreach (IStudyTreeItem item in Tree.Items)
{
StudyTreeItem treeitem = (StudyTreeItem)item;
if (!treeitem.Ischecked)
{
continue;
}
study++;
MediaFileSetStudy fileSet = new MediaFileSetStudy();
string tempstudypath = Path.Combine(RootPath, string.Format(studyitemPath, study));
StudyXml studyXml = new StudyXml();
foreach (ISeriesTreeItem seriss in treeitem.Tree.Items)
{
SeriesTreeItem seriesitem = (SeriesTreeItem)seriss;
if (!seriesitem.Ischecked)
{
continue;
}
series++;
string tempseriespath = Path.Combine(tempstudypath, string.Format(seriesitemPath, series));
if (Directory.Exists(tempseriespath))
{
Directory.Delete(tempseriespath, true);
}
Directory.CreateDirectory(tempseriespath);
foreach (var sop in seriesitem.Series.GetSopInstances())
{
if (LoadImageWorker.CancellationPending == true)
{
break;
}
if (File.Exists(sop.FilePath))
{
Sopcount++;
string temp = Path.Combine(tempseriespath, string.Format(filename, Sopcount));
File.Copy(sop.FilePath, temp);
int start = temp.IndexOf(studysPath);
string dirFilePath = temp.Substring(start);
dicomDirectory.AddFile(temp, dirFilePath);
string fileName = string.Format("..\\{0}", dirFilePath);
DicomFile file = new DicomFile(temp);
file.Load();
file.Filename = fileName;
studyXml.AddFile(file);
fileSet.UID = sop.StudyInstanceUid;
}
}
}
//保存studyXml
string xmlFileName = string.Format(XmlName, study);
string path = Path.Combine(xmlPath, xmlFileName);
StudyXmlOutputSettings settings = new StudyXmlOutputSettings();
settings.IncludeSourceFileName = true;
XmlDocument document = studyXml.GetMemento(settings);
// Create an XML declaration.
XmlDeclaration xmldecl;
xmldecl = document.CreateXmlDeclaration("1.0", null, null);
xmldecl.Encoding = "UTF-8";
document.Save(path);
fileSet.Value = Path.Combine(xmlSavePath, xmlFileName);;
fileSetStudies.Add(fileSet);
}
if (!Directory.Exists(RootPath))
{
throw new Exception(string.Format("复制检查图像到{0}目录出错", StagingFolderPath));
}
IBurnMediaData info = new BurnMediaData();
info.Type = MediaType.Dir;
info.Path = RootPath;
data.Add(info);
IBurnMediaData xml = new BurnMediaData();
xml.Path = xmlPath;
xml.Type = MediaType.Dir;
data.Add(xml);
string studyindexfilename = Path.Combine(this.StagingFolderPath, studyIndexName);
if (File.Exists(studyindexfilename))
{
File.Delete(studyindexfilename);
}
Stream stream = File.Open(studyindexfilename, FileMode.Create);
mediaFileSet.StudyIndex = fileSetStudies.ToArray();
XmlSerializer serializer = new XmlSerializer(typeof(MediaFileSet));
serializer.Serialize(stream, mediaFileSet);
IBurnMediaData studyindex = new BurnMediaData();
studyindex.Path = studyindexfilename;
studyindex.Type = MediaType.File;
data.Add(studyindex);
string dirfilename = Path.Combine(this.StagingFolderPath, "DICOMDIR");
dicomDirectory.Save(dirfilename);
info = new BurnMediaData();
info.Type = MediaType.File;
info.Path = dirfilename;
data.Add(info);
DoBurn(data);
}
catch (COMException ex)
{
this.Host.ShowMessageBox(ImapiReturnValues.GetName(ex.ErrorCode), MessageBoxActions.Ok);
}
catch (Exception e)
{
this.Host.ShowMessageBox(e.Message, MessageBoxActions.Ok);
}
finally
{
this.IsWriting = false;
}
}
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);
}
private void UpdateFilesystem()
{
Platform.Log(LogLevel.Info, "Updating filesystem...");
StudyXml studyXml = _oldStudyLocation.LoadStudyXml();
StudyXmlOutputSettings outputSettings = ImageServerCommonConfiguration.DefaultStudyXmlOutputSettings;
StudyXml newStudyXml = new StudyXml();
foreach (SeriesXml seriesXml in studyXml)
{
foreach (InstanceXml instanceXml in seriesXml)
{
string path = Path.Combine(_oldStudyPath, seriesXml.SeriesInstanceUid);
path = Path.Combine(path, instanceXml.SopInstanceUid);
path += ServerPlatform.DicomFileExtension;
if (!File.Exists(path))
{
Platform.Log(LogLevel.Info, "SOP {0} is referenced in study xml but does not exist. It will be removed");
continue; // file was removed but xml was not updated?
}
try
{
DicomFile file = new DicomFile(path);
file.Load();
InstanceInfo instance = new InstanceInfo
{
SeriesInstanceUid = file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, String.Empty),
SopInstanceUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, String.Empty)
};
UpdateDicomFile(file);
// Add into the temporary study xml
long fileSize = 0;
if (File.Exists(file.Filename))
{
FileInfo finfo = new FileInfo(file.Filename);
fileSize = finfo.Length;
}
newStudyXml.AddFile(file, fileSize, outputSettings);
_updatedSopList.Add(instance);
Platform.Log(ServerPlatform.InstanceLogLevel, "SOP {0} has been updated [{1} of {2}].", instance.SopInstanceUid, _updatedSopList.Count, _totalSopCount);
EventManager.FireEvent(this, new UpdateSopEventArgs { File = file, ServerPartitionEntry = _partition, WorkQueueUidEntry = null, WorkQueueEntry = _workQueue, FileLength = (ulong)fileSize });
}
catch (Exception)
{
File.Delete(Path.Combine(_backupDir, instanceXml.SopInstanceUid) + ".bak"); //dont' need to restore this file
throw;
}
}
}
// Log any study-level warnings
if (_updatedSopList.Count != _totalSopCount)
{
Platform.Log(LogLevel.Warn, "Inconsistent data: expected {0} instances to be updated / Found {1}.", _totalSopCount, _updatedSopList.Count);
}
// update the header
Platform.Log(LogLevel.Info, "Generating new study header...");
string newStudyXmlPath = Path.Combine(NewStudyPath, _newStudyInstanceUid + ".xml");
string gzipStudyXmlPath = Path.Combine(NewStudyPath, _newStudyInstanceUid + ".xml.gz");
using (FileStream xmlStream = FileStreamOpener.OpenForSoleUpdate(newStudyXmlPath, FileMode.Create),
gzipStream = FileStreamOpener.OpenForSoleUpdate(gzipStudyXmlPath, FileMode.Create))
{
StudyXmlIo.WriteXmlAndGzip(newStudyXml.GetMemento(outputSettings), xmlStream, gzipStream);
xmlStream.Close();
gzipStream.Close();
}
}
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);
}
