/// <summary>
/// Gets an array <see cref="IDicomCodecFactory"/> instances.
/// </summary>
/// <returns></returns>
public static IDicomCodecFactory[] GetCodecFactories()
{
DicomCodecFactoryExtensionPoint ep = new DicomCodecFactoryExtensionPoint();
object[] extensions = ep.CreateExtensions();
IDicomCodecFactory[] codecFactories = new IDicomCodecFactory[extensions.Length];
extensions.CopyTo(codecFactories, 0);
return(codecFactories);
}
private bool ProcessWorkQueueUid(Model.WorkQueue item, WorkQueueUid sop, StudyXml studyXml, IDicomCodecFactory theCodecFactory)
{
Platform.CheckForNullReference(item, "item");
Platform.CheckForNullReference(sop, "sop");
Platform.CheckForNullReference(studyXml, "studyXml");
if (!studyXml.Contains(sop.SeriesInstanceUid, sop.SopInstanceUid))
{
// Uid was inserted but not in the study xml.
// Auto-recovery might have detect problem with that file and remove it from the study.
// Assume the study xml has been corrected and ignore the uid.
Platform.Log(LogLevel.Warn, "Skipping SOP {0} in series {1}. It is no longer part of the study.", sop.SopInstanceUid, sop.SeriesInstanceUid);
// Delete it out of the queue
DeleteWorkQueueUid(sop);
return true;
}
string basePath = Path.Combine(StorageLocation.GetStudyPath(), sop.SeriesInstanceUid);
basePath = Path.Combine(basePath, sop.SopInstanceUid);
string path;
if (sop.Extension != null)
path = basePath + "." + sop.Extension;
else
path = basePath + ServerPlatform.DicomFileExtension;
try
{
ProcessFile(item, sop, path, studyXml, theCodecFactory);
// WorkQueueUid has been deleted out by the processor
return true;
}
catch (Exception e)
{
if (e.InnerException != null && e.InnerException is DicomCodecUnsupportedSopException)
{
Platform.Log(LogLevel.Warn, e, "Instance not supported for compressor: {0}. Deleting WorkQueue entry for SOP {1}", e.Message, sop.SopInstanceUid);
item.FailureDescription = e.InnerException != null ? e.InnerException.Message : e.Message;
// Delete it out of the queue
DeleteWorkQueueUid(sop);
return false;
}
Platform.Log(LogLevel.Error, e, "Unexpected exception when compressing file: {0} SOP Instance: {1}", path, sop.SopInstanceUid);
item.FailureDescription = e.InnerException != null ? e.InnerException.Message : e.Message;
sop.FailureCount++;
UpdateWorkQueueUid(sop);
return false;
}
}
/// <summary>
/// Set an <see cref="IDicomCodecFactory"/> for a transfer syntax, overriding the current value.
/// </summary>
/// <param name="syntax">The transfer syntax of the codec.</param>
/// <param name="factory">The factory for the codec.</param>
public static void SetCodec(TransferSyntax syntax, IDicomCodecFactory factory)
{
if (factory != null)
{
_dictionary[syntax] = factory;
}
else
{
_dictionary.Remove(syntax);
}
}
public DicomCompressCommand(DicomMessageBase file, XmlDocument parms, bool failOnCodecException)
: base("DICOM Compress Command", true)
{
_file = file;
_failOnCodecException = failOnCodecException;
XmlElement element = parms.DocumentElement;
string syntax = element.Attributes["syntax"].Value;
_syntax = TransferSyntax.GetTransferSyntax(syntax);
if (_syntax == null)
{
string failureDescription =
String.Format("Invalid transfer syntax in compression command: {0}", element.Attributes["syntax"].Value);
Platform.Log(LogLevel.Error, "Error with input syntax: {0}", failureDescription);
throw new DicomCodecException(failureDescription);
}
IDicomCodecFactory[] codecs = DicomCodecRegistry.GetCodecFactories();
IDicomCodecFactory theCodecFactory = null;
foreach (IDicomCodecFactory codec in codecs)
{
if (codec.CodecTransferSyntax.Equals(_syntax))
{
theCodecFactory = codec;
break;
}
}
if (theCodecFactory == null)
{
string failureDescription = String.Format("Unable to find codec for compression: {0}", _syntax.Name);
Platform.Log(LogLevel.Error, "Error with compression input parameters: {0}", failureDescription);
throw new DicomCodecException(failureDescription);
}
_codec = theCodecFactory.GetDicomCodec();
_parms = theCodecFactory.GetCodecParameters(parms);
}
/// <summary>
/// Process all of the SOP Instances associated with a <see cref="WorkQueue"/> item.
/// </summary>
/// <param name="item">The <see cref="WorkQueue"/> item.</param>
/// <returns>A value indicating whether the uid list has been successfully processed</returns>
/// <param name="theCodecFactory">The factor for doing the compression</param>
protected bool ProcessUidList(Model.WorkQueue item, IDicomCodecFactory theCodecFactory)
{
StudyXml studyXml = LoadStudyXml(StorageLocation);
int successfulProcessCount = 0;
int totalCount = WorkQueueUidList.Count;
foreach (WorkQueueUid sop in WorkQueueUidList)
{
if (sop.Failed)
{
continue;
}
if (CancelPending)
{
Platform.Log(LogLevel.Info,
"Received cancel request while compressing study {0}. {1} instances successfully processed.",
StorageLocation.StudyInstanceUid, successfulProcessCount);
return(successfulProcessCount > 0);
}
if (ProcessWorkQueueUid(item, sop, studyXml, theCodecFactory))
{
successfulProcessCount++;
}
}
if (successfulProcessCount > 0)
{
Platform.Log(LogLevel.Info, "Completed compression of study {0}. {1} instances successfully processed.",
StorageLocation.StudyInstanceUid, successfulProcessCount);
}
return(successfulProcessCount > 0 && totalCount == successfulProcessCount);
}
/// <summary>
/// Gets an array <see cref="IDicomCodecFactory"/> instances.
/// </summary>
/// <returns></returns>
public static IDicomCodecFactory[] GetCodecFactories()
{
DicomCodecFactoryExtensionPoint ep = new DicomCodecFactoryExtensionPoint();
object[] extensions = ep.CreateExtensions();
IDicomCodecFactory[] codecFactories = new IDicomCodecFactory[extensions.Length];
extensions.CopyTo(codecFactories, 0);
return codecFactories;
}
protected void ProcessFile(Model.WorkQueue item, WorkQueueUid sop, string path, StudyXml studyXml, IDicomCodecFactory theCodecFactory)
{
DicomFile file;
_instanceStats = new CompressInstanceStatistics();
_instanceStats.ProcessTime.Start();
// Use the command processor for rollback capabilities.
using (ServerCommandProcessor processor = new ServerCommandProcessor("Processing WorkQueue Compress DICOM File"))
{
string modality = String.Empty;
try
{
file = new DicomFile(path);
_instanceStats.FileLoadTime.Start();
file.Load(DicomReadOptions.StorePixelDataReferences | DicomReadOptions.Default);
_instanceStats.FileLoadTime.End();
modality = file.DataSet[DicomTags.Modality].GetString(0, String.Empty);
FileInfo fileInfo = new FileInfo(path);
_instanceStats.FileSize = (ulong)fileInfo.Length;
// Get the Patients Name for processing purposes.
String patientsName = file.DataSet[DicomTags.PatientsName].GetString(0, "");
if (file.TransferSyntax.Equals(theCodecFactory.CodecTransferSyntax))
{
// Delete the WorkQueueUid item
processor.AddCommand(new DeleteWorkQueueUidCommand(sop));
// Do the actual processing
if (!processor.Execute())
{
Platform.Log(LogLevel.Warn, "Failure deleteing WorkQueueUid: {0} for SOP: {1}", processor.Description, file.MediaStorageSopInstanceUid);
Platform.Log(LogLevel.Warn, "Compression file that failed: {0}", file.Filename);
}
else
{
Platform.Log(LogLevel.Warn, "Skip compressing SOP {0}. Its current transfer syntax is {1}",
file.MediaStorageSopInstanceUid, file.TransferSyntax.Name);
}
}
else
{
IDicomCodec codec = theCodecFactory.GetDicomCodec();
// Create a context for applying actions from the rules engine
var context = new ServerActionContext(file, StorageLocation.FilesystemKey, ServerPartition, item.StudyStorageKey);
context.CommandProcessor = processor;
var parms = theCodecFactory.GetCodecParameters(item.Data);
var compressCommand =
new DicomCompressCommand(context.Message, theCodecFactory.CodecTransferSyntax, codec, parms);
processor.AddCommand(compressCommand);
var save = new SaveDicomFileCommand(file.Filename, file, false);
processor.AddCommand(save);
// Update the StudyStream object, must be done after compression
// and after the compressed image has been successfully saved
var insertStudyXmlCommand = new UpdateStudyXmlCommand(file, studyXml, StorageLocation);
processor.AddCommand(insertStudyXmlCommand);
// Delete the WorkQueueUid item
processor.AddCommand(new DeleteWorkQueueUidCommand(sop));
// Do the actual processing
if (!processor.Execute())
{
_instanceStats.CompressTime.Add(compressCommand.CompressTime);
Platform.Log(LogLevel.Error, "Failure compressing command {0} for SOP: {1}", processor.Description, file.MediaStorageSopInstanceUid);
Platform.Log(LogLevel.Error, "Compression file that failed: {0}", file.Filename);
throw new ApplicationException("Unexpected failure (" + processor.FailureReason + ") executing command for SOP: " + file.MediaStorageSopInstanceUid,processor.FailureException);
}
_instanceStats.CompressTime.Add(compressCommand.CompressTime);
Platform.Log(ServerPlatform.InstanceLogLevel, "Compress SOP: {0} for Patient {1}", file.MediaStorageSopInstanceUid,
patientsName);
}
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception when {0}. Rolling back operation.",
processor.Description);
processor.Rollback();
throw;
}
finally
{
_instanceStats.ProcessTime.End();
_studyStats.AddSubStats(_instanceStats);
_studyStats.StudyInstanceUid = StorageLocation.StudyInstanceUid;
if (String.IsNullOrEmpty(modality) == false)
_studyStats.Modality = modality;
// Update the statistics
_studyStats.NumInstances++;
}
}
}
/// <summary>
/// Process all of the SOP Instances associated with a <see cref="WorkQueue"/> item.
/// </summary>
/// <param name="item">The <see cref="WorkQueue"/> item.</param>
/// <returns>A value indicating whether the uid list has been successfully processed</returns>
/// <param name="theCodecFactory">The factor for doing the compression</param>
protected bool ProcessUidList(Model.WorkQueue item, IDicomCodecFactory theCodecFactory)
{
StudyXml studyXml = LoadStudyXml(StorageLocation);
int successfulProcessCount = 0;
int totalCount = WorkQueueUidList.Count;
foreach (WorkQueueUid sop in WorkQueueUidList)
{
if (sop.Failed)
continue;
if (CancelPending)
{
Platform.Log(LogLevel.Info,
"Received cancel request while compressing study {0}. {1} instances successfully processed.",
StorageLocation.StudyInstanceUid, successfulProcessCount);
return successfulProcessCount > 0;
}
if (ProcessWorkQueueUid(item, sop, studyXml, theCodecFactory))
successfulProcessCount++;
}
if (successfulProcessCount > 0)
Platform.Log(LogLevel.Info,"Completed compression of study {0}. {1} instances successfully processed.",
StorageLocation.StudyInstanceUid, successfulProcessCount);
return successfulProcessCount > 0 && totalCount == successfulProcessCount;
}
/// <summary>
/// Set an <see cref="IDicomCodecFactory"/> for a transfer syntax, overriding the current value.
/// </summary>
/// <param name="syntax">The transfer syntax of the codec.</param>
/// <param name="factory">The factory for the codec.</param>
public static void SetCodec(TransferSyntax syntax, IDicomCodecFactory factory)
{
Dictionary[syntax] = factory;
}
private bool ProcessWorkQueueUid(Model.WorkQueue item, WorkQueueUid sop, StudyXml studyXml, IDicomCodecFactory theCodecFactory)
{
Platform.CheckForNullReference(item, "item");
Platform.CheckForNullReference(sop, "sop");
Platform.CheckForNullReference(studyXml, "studyXml");
if (!studyXml.Contains(sop.SeriesInstanceUid, sop.SopInstanceUid))
{
// Uid was inserted but not in the study xml.
// Auto-recovery might have detect problem with that file and remove it from the study.
// Assume the study xml has been corrected and ignore the uid.
Platform.Log(LogLevel.Warn, "Skipping SOP {0} in series {1}. It is no longer part of the study.", sop.SopInstanceUid, sop.SeriesInstanceUid);
// Delete it out of the queue
DeleteWorkQueueUid(sop);
return(true);
}
string basePath = Path.Combine(StorageLocation.GetStudyPath(), sop.SeriesInstanceUid);
basePath = Path.Combine(basePath, sop.SopInstanceUid);
string path;
if (sop.Extension != null)
{
path = basePath + "." + sop.Extension;
}
else
{
path = basePath + ServerPlatform.DicomFileExtension;
}
try
{
ProcessFile(item, sop, path, studyXml, theCodecFactory);
// WorkQueueUid has been deleted out by the processor
return(true);
}
catch (Exception e)
{
if (e.InnerException != null && e.InnerException is DicomCodecUnsupportedSopException)
{
Platform.Log(LogLevel.Warn, e, "Instance not supported for compressor: {0}. Deleting WorkQueue entry for SOP {1}", e.Message, sop.SopInstanceUid);
item.FailureDescription = e.InnerException != null ? e.InnerException.Message : e.Message;
// Delete it out of the queue
DeleteWorkQueueUid(sop);
return(false);
}
Platform.Log(LogLevel.Error, e, "Unexpected exception when compressing file: {0} SOP Instance: {1}", path, sop.SopInstanceUid);
item.FailureDescription = e.InnerException != null ? e.InnerException.Message : e.Message;
sop.FailureCount++;
UpdateWorkQueueUid(sop);
return(false);
}
}
protected override void ProcessItem(Model.WorkQueue item)
{
LoadUids(item);
if (WorkQueueUidList.Count == 0)
{
// No UIDs associated with the WorkQueue item. Set the status back to idle
PostProcessing(item,
WorkQueueProcessorStatus.Idle,
WorkQueueProcessorDatabaseUpdate.ResetQueueState);
return;
}
XmlElement element = item.Data.DocumentElement;
string syntax = element.Attributes["syntax"].Value;
TransferSyntax compressSyntax = TransferSyntax.GetTransferSyntax(syntax);
if (compressSyntax == null)
{
item.FailureDescription =
String.Format("Invalid transfer syntax in compression WorkQueue item: {0}", element.Attributes["syntax"].Value);
Platform.Log(LogLevel.Error, "Error with work queue item {0}: {1}", item.GetKey(), item.FailureDescription);
base.PostProcessingFailure(item, WorkQueueProcessorFailureType.Fatal);
return;
}
if (Study == null)
{
item.FailureDescription =
String.Format("Compression item does not have a linked Study record");
Platform.Log(LogLevel.Error, "Error with work queue item {0}: {1}", item.GetKey(), item.FailureDescription);
base.PostProcessingFailure(item, WorkQueueProcessorFailureType.Fatal);
return;
}
Platform.Log(LogLevel.Info,
"Compressing study {0} for Patient {1} (PatientId:{2} A#:{3}) on partition {4} to {5}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description, compressSyntax.Name);
IDicomCodecFactory[] codecs = DicomCodecRegistry.GetCodecFactories();
IDicomCodecFactory theCodecFactory = null;
foreach (IDicomCodecFactory codec in codecs)
{
if (codec.CodecTransferSyntax.Equals(compressSyntax))
{
theCodecFactory = codec;
break;
}
}
if (theCodecFactory == null)
{
item.FailureDescription = String.Format("Unable to find codec for compression: {0}", compressSyntax.Name);
Platform.Log(LogLevel.Error, "Error with work queue item {0}: {1}", item.GetKey(), item.FailureDescription);
base.PostProcessingFailure(item, WorkQueueProcessorFailureType.Fatal);
return;
}
if (!ProcessUidList(item, theCodecFactory))
{
PostProcessingFailure(item, WorkQueueProcessorFailureType.NonFatal);
}
else
{
Platform.Log(LogLevel.Info,
"Completed Compressing study {0} for Patient {1} (PatientId:{2} A#:{3}) on partition {4} to {5}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description, compressSyntax.Name);
if (compressSyntax.LossyCompressed)
{
UpdateStudyStatus(StorageLocation, StudyStatusEnum.OnlineLossy, compressSyntax);
}
else
{
UpdateStudyStatus(StorageLocation, StudyStatusEnum.OnlineLossless, compressSyntax);
}
PostProcessing(item,
WorkQueueProcessorStatus.Pending,
WorkQueueProcessorDatabaseUpdate.None); // batch processed, not complete
}
}
protected void ProcessFile(Model.WorkQueue item, WorkQueueUid sop, string path, StudyXml studyXml, IDicomCodecFactory theCodecFactory)
{
DicomFile file = null;
_instanceStats = new CompressInstanceStatistics();
_instanceStats.ProcessTime.Start();
// Use the command processor for rollback capabilities.
using (ServerCommandProcessor processor = new ServerCommandProcessor("Processing WorkQueue Compress DICOM File"))
{
string modality = String.Empty;
try
{
file = new DicomFile(path);
_instanceStats.FileLoadTime.Start();
file.Load(DicomReadOptions.StorePixelDataReferences | DicomReadOptions.Default);
_instanceStats.FileLoadTime.End();
modality = file.DataSet[DicomTags.Modality].GetString(0, String.Empty);
FileInfo fileInfo = new FileInfo(path);
_instanceStats.FileSize = (ulong)fileInfo.Length;
// Get the Patients Name for processing purposes.
String patientsName = file.DataSet[DicomTags.PatientsName].GetString(0, "");
if (file.TransferSyntax.Equals(theCodecFactory.CodecTransferSyntax))
{
// Delete the WorkQueueUid item
processor.AddCommand(new DeleteWorkQueueUidCommand(sop));
// Do the actual processing
if (!processor.Execute())
{
Platform.Log(LogLevel.Warn, "Failure deleteing WorkQueueUid: {0} for SOP: {1}", processor.Description, file.MediaStorageSopInstanceUid);
Platform.Log(LogLevel.Warn, "Compression file that failed: {0}", file.Filename);
}
else
{
Platform.Log(LogLevel.Warn, "Skip compressing SOP {0}. Its current transfer syntax is {1}",
file.MediaStorageSopInstanceUid, file.TransferSyntax.Name);
}
}
else
{
IDicomCodec codec = theCodecFactory.GetDicomCodec();
// Create a context for applying actions from the rules engine
var context = new ServerActionContext(file, StorageLocation.FilesystemKey, ServerPartition, item.StudyStorageKey);
context.CommandProcessor = processor;
var parms = theCodecFactory.GetCodecParameters(item.Data);
var compressCommand =
new DicomCompressCommand(context.Message, theCodecFactory.CodecTransferSyntax, codec, parms);
processor.AddCommand(compressCommand);
var save = new SaveDicomFileCommand(file.Filename, file, false);
processor.AddCommand(save);
// Update the StudyStream object, must be done after compression
// and after the compressed image has been successfully saved
var insertStudyXmlCommand = new UpdateStudyXmlCommand(file, studyXml, StorageLocation);
processor.AddCommand(insertStudyXmlCommand);
// Delete the WorkQueueUid item
processor.AddCommand(new DeleteWorkQueueUidCommand(sop));
// Do the actual processing
if (!processor.Execute())
{
EventManager.FireEvent(this, new FailedUpdateSopEventArgs {
File = file, ServerPartitionEntry = context.ServerPartition, WorkQueueUidEntry = sop, WorkQueueEntry = WorkQueueItem, FileLength = (ulong)insertStudyXmlCommand.FileSize, FailureMessage = processor.FailureReason
});
_instanceStats.CompressTime.Add(compressCommand.CompressTime);
Platform.Log(LogLevel.Error, "Failure compressing command {0} for SOP: {1}", processor.Description, file.MediaStorageSopInstanceUid);
Platform.Log(LogLevel.Error, "Compression file that failed: {0}", file.Filename);
throw new ApplicationException("Unexpected failure (" + processor.FailureReason + ") executing command for SOP: " + file.MediaStorageSopInstanceUid, processor.FailureException);
}
_instanceStats.CompressTime.Add(compressCommand.CompressTime);
Platform.Log(ServerPlatform.InstanceLogLevel, "Compress SOP: {0} for Patient {1}", file.MediaStorageSopInstanceUid,
patientsName);
EventManager.FireEvent(this, new UpdateSopEventArgs {
File = file, ServerPartitionEntry = context.ServerPartition, WorkQueueUidEntry = sop, WorkQueueEntry = WorkQueueItem, FileLength = (ulong)insertStudyXmlCommand.FileSize
});
}
}
catch (Exception e)
{
EventManager.FireEvent(this, new FailedUpdateSopEventArgs {
File = file, ServerPartitionEntry = ServerPartition, WorkQueueUidEntry = sop, WorkQueueEntry = WorkQueueItem, FileLength = (ulong)new FileInfo(path).Length, FailureMessage = processor.FailureReason
});
Platform.Log(LogLevel.Error, e, "Unexpected exception when {0}. Rolling back operation.",
processor.Description);
processor.Rollback();
throw;
}
finally
{
_instanceStats.ProcessTime.End();
_studyStats.AddSubStats(_instanceStats);
_studyStats.StudyInstanceUid = StorageLocation.StudyInstanceUid;
if (String.IsNullOrEmpty(modality) == false)
{
_studyStats.Modality = modality;
}
// Update the statistics
_studyStats.NumInstances++;
}
}
}
/// <summary>
/// Set an <see cref="IDicomCodecFactory"/> for a transfer syntax, overriding the current value.
/// </summary>
/// <param name="syntax">The transfer syntax of the codec.</param>
/// <param name="factory">The factory for the codec.</param>
public static void SetCodec(TransferSyntax syntax, IDicomCodecFactory factory)
{
Dictionary[syntax] = factory;
}
/// <summary>
/// Set an <see cref="IDicomCodecFactory"/> for a transfer syntax, overriding the current value.
/// </summary>
/// <param name="syntax">The transfer syntax of the codec.</param>
/// <param name="factory">The factory for the codec.</param>
public static void SetCodec(TransferSyntax syntax, IDicomCodecFactory factory)
{
if (factory != null) _dictionary[syntax] = factory;
else _dictionary.Remove(syntax);
}
