/// <summary>
/// Saves given instances to temp files and performs requested operation on each of the saved file.
/// NOTE: The temp file must me manually deleted during post save operation or it will stay in the temp folder.
/// <exception cref="AimManagerException">AimManagerException</exception> can be thrown if save of an annotation fails.
/// </summary>
/// <param name="aimAnnotationReferences">List of annotation containers to save</param>
/// <param name="postSaveProcessor">Operation to perform on each saved temp file</param>
public void WriteDicomAnnotationsToTempFiles(List <IAimObjectReference> aimAnnotationReferences, Action <string> postSaveProcessor)
{
if (aimAnnotationReferences == null)
{
return;
}
var aim3Annotations = aimAnnotationReferences.Where(aimObject => aimObject != null && aimObject.AimVersion == AimVersion.AimVersion3).ToList();
if (aim3Annotations.Any())
{
using (var aim3NativeHelper = new Aim3.Aim3NativeDcmHelper())
{
foreach (var aim3Annotation in aim3Annotations)
{
var tempFileName = aim3NativeHelper.WriteAnnotationToTempFile(aim3Annotation);
if (tempFileName != null && postSaveProcessor != null)
{
postSaveProcessor(tempFileName);
}
else if (tempFileName != null)
{
// TODO - delete temp file?
}
}
}
}
var aim4Annotations = aimAnnotationReferences.Where(aimObject => aimObject != null && aimObject.AimVersion == AimVersion.AimVersion4).ToList();
if (aim4Annotations.Any())
{
using (var aim4NativeHelper = new Aim4.Aim4NativeDcmHelper())
{
foreach (var aim4Annotation in aim4Annotations)
{
var tempFileName = aim4NativeHelper.WriteAnnotationToTempFile(aim4Annotation);
if (tempFileName != null && postSaveProcessor != null)
{
postSaveProcessor(tempFileName);
}
else if (tempFileName != null)
{
// TODO - delete temp file?
}
}
}
}
if (aim3Annotations.Count + aim4Annotations.Count != aimAnnotationReferences.Count)
{
Platform.Log(LogLevel.Error, "AimManager.WriteDicomAnnotationsToTempFiles: not all annotations can be saved to DICOM files.");
throw new NotImplementedException("Cannot save some of the annotations to DICOM files. Unknown version of AIM was encountered?");
}
}
// Loads annotations from local storage
private List <IAimDocumentInstance> LoadLocalAimDocumentsForStudy(string studyInstanceUid)
{
var seriesIdentifier = new SeriesIdentifier {
StudyInstanceUid = studyInstanceUid, Modality = AimManager.AimModality
};
var seriesEntryRequest = new GetSeriesEntriesRequest {
Criteria = new SeriesEntry {
Series = seriesIdentifier
}
};
IList <SeriesEntry> entries = null;
Platform.GetService <IStudyStoreQuery>(s => entries = s.GetSeriesEntries(seriesEntryRequest).SeriesEntries);
var instanceToAimFileInfoMap = new Dictionary <string, AimFileInfo>();
// Get all unique AE Titles for the study. Can study have more than one?
// We only need to query each AETitle once, or there will be duplicates/errors.
var studyAes = (from seriesEntry in entries where seriesEntry != null select seriesEntry.Series.RetrieveAE).GroupBy(ae => ae.AETitle).Select(ae1 => ae1.First()).OfType <IDicomServiceNode>().ToList();
if (!studyAes.Any())
{
Platform.Log(LogLevel.Debug, "Study ({0}} has no SR (AIM Annotations) objects", studyInstanceUid);
return(null);
}
foreach (var studyAe in studyAes)
{
IStudyLoader studyLoader;
try
{
studyLoader = studyAe.GetService <IStudyLoader>();
}
catch (Exception ex)
{
throw new AimManagerException("Cannot get study loader", ex);
}
int numberOfSops = studyLoader.Start(new StudyLoaderArgs(studyInstanceUid, null, new StudyLoaderOptions(true)));
for (int i = 0; i < numberOfSops; i++)
{
using (var sop = studyLoader.LoadNextSop())
{
if (sop != null && sop.Modality == AimManager.AimModality)
{
var localSopDataSource = sop.DataSource as ILocalSopDataSource;
if (localSopDataSource != null)
{
var filePathName = localSopDataSource.Filename;
switch (AimManager.GetAimVersionFromSop(sop))
{
case AimVersion.AimVersion3:
instanceToAimFileInfoMap.Add(filePathName,
new AimFileInfo(AimVersion.AimVersion3, sop.StudyInstanceUid, sop.SeriesInstanceUid, sop.SopInstanceUid));
break;
case AimVersion.AimVersion4:
instanceToAimFileInfoMap.Add(filePathName,
new AimFileInfo(AimVersion.AimVersion4, sop.StudyInstanceUid, sop.SeriesInstanceUid, sop.SopInstanceUid));
break;
}
}
}
}
}
}
if (instanceToAimFileInfoMap.Any())
{
var aimDocumentInstances = new List <IAimDocumentInstance>();
var aim4Instances = instanceToAimFileInfoMap.Where(instance => instance.Value.AimVersion == AimVersion.AimVersion4).ToList();
if (aim4Instances.Any())
{
using (var dcmHelper = new Aim4.Aim4NativeDcmHelper())
{
foreach (var instanceInfo in aim4Instances)
{
var aimDocumentInstance = ReadAimDocumentFromDicomFile(dcmHelper,
instanceInfo.Key, instanceInfo.Value.StudyInstanceUid,
instanceInfo.Value.SeriesInstanceUid, instanceInfo.Value.SopInstanceUid);
if (aimDocumentInstance != null)
{
aimDocumentInstances.Add(aimDocumentInstance);
}
}
}
}
return(aimDocumentInstances.Any() ? aimDocumentInstances : null);
}
return(null);
}
public static List <string> ConvertAnnotationsFromXmlToDicomFiles(AimVersion aimVersion, List <string> xmlAnnotationsFilePathNames, IBackgroundTaskContext context, out List <string> invalidFiles)
{
Platform.CheckForNullReference(xmlAnnotationsFilePathNames, "xmlAnnotationsFilePathNames");
var convertedAnnotations = new List <string>();
invalidFiles = new List <string>();
switch (aimVersion)
{
case AimVersion.AimVersion3:
{
int cnt = 0;
using (var aim3NativeXmlHelper = new Aim3.Aim3NativeXmlHelper())
{
using (var aim3NativeDcmHelper = new Aim3.Aim3NativeDcmHelper())
{
foreach (string aimFile in xmlAnnotationsFilePathNames.Where(pathName => pathName != null))
{
// Read XML file
ReportTaskProgress(context, cnt, xmlAnnotationsFilePathNames.Count, String.Format("Reading file {0}", Path.GetFileName(aimFile)));
var annotations = aim3NativeXmlHelper.ReadAnnotationsFromFile(aimFile);
if (annotations.IsNullOrEmpty())
{
Platform.Log(LogLevel.Info, "No annotation is read from file {0}", Path.GetFileName(aimFile));
invalidFiles.Add(Path.GetFileName(aimFile));
}
else
{
// Write to temp file
ReportTaskProgress(context, cnt, xmlAnnotationsFilePathNames.Count,
String.Format("Read {0} annotations from file {1}", annotations.Count, Path.GetFileName(aimFile)));
int dcmFileCnt = 0;
foreach (var annotation in annotations)
{
ReportTaskProgress(context, cnt, xmlAnnotationsFilePathNames.Count,
String.Format("Writing converted annotation to temporary file [{0} of {1}]", ++dcmFileCnt, annotations.Count));
var tempFileName = aim3NativeDcmHelper.WriteAnnotationToTempFile(annotation);
convertedAnnotations.Add(tempFileName);
ReportTaskProgress(context, cnt, xmlAnnotationsFilePathNames.Count,
String.Format("Wrote converted annotation to file {0} [{1} of {2}]", tempFileName, dcmFileCnt, annotations.Count));
}
}
if (context != null && context.CancelRequested)
{
break;
}
cnt++;
}
}
}
}
break;
case AimVersion.AimVersion4:
{
int cnt = 0;
using (var aim4NativeXmlHelper = new Aim4.Aim4NativeXmlHelper())
{
using (var aim4NativeDcmHelper = new Aim4.Aim4NativeDcmHelper())
{
foreach (string aimFile in xmlAnnotationsFilePathNames.Where(pathName => pathName != null))
{
// Read XML file
ReportTaskProgress(context, cnt, xmlAnnotationsFilePathNames.Count, String.Format("Reading file {0}", Path.GetFileName(aimFile)));
var annotation = aim4NativeXmlHelper.ReadAnnotationFromFile(aimFile);
if (annotation == null)
{
Platform.Log(LogLevel.Info, "No annotation is read from file {0}", Path.GetFileName(aimFile));
invalidFiles.Add(Path.GetFileName(aimFile));
}
else
{
// Write to temp file
ReportTaskProgress(context, cnt, xmlAnnotationsFilePathNames.Count,
String.Format("Read annotation collection from file {0}", Path.GetFileName(aimFile)));
var tempFileName = aim4NativeDcmHelper.WriteAnnotationToTempFile(annotation);
convertedAnnotations.Add(tempFileName);
ReportTaskProgress(context, cnt, xmlAnnotationsFilePathNames.Count,
String.Format("Wrote converted annotation collection to file {0}", tempFileName));
}
if (context != null && context.CancelRequested)
{
break;
}
cnt++;
}
}
}
}
break;
default:
Debug.Assert(false, "AimManager.ConvertAnnotationsFromXmlToDicomFiles: Unexpected AIM version");
break;
}
return(convertedAnnotations);
}
// Loads annotations from local storage
private List<IAimDocumentInstance> LoadLocalAimDocumentsForStudy(string studyInstanceUid)
{
var seriesIdentifier = new SeriesIdentifier { StudyInstanceUid = studyInstanceUid, Modality = AimManager.AimModality };
var seriesEntryRequest = new GetSeriesEntriesRequest { Criteria = new SeriesEntry { Series = seriesIdentifier } };
IList<SeriesEntry> entries = null;
Platform.GetService<IStudyStoreQuery>(s => entries = s.GetSeriesEntries(seriesEntryRequest).SeriesEntries);
var instanceToAimFileInfoMap = new Dictionary<string, AimFileInfo>();
// Get all unique AE Titles for the study. Can study have more than one?
// We only need to query each AETitle once, or there will be duplicates/errors.
var studyAes = (from seriesEntry in entries where seriesEntry != null select seriesEntry.Series.RetrieveAE).GroupBy(ae => ae.AETitle).Select(ae1 => ae1.First()).OfType<IDicomServiceNode>().ToList();
if (!studyAes.Any())
{
Platform.Log(LogLevel.Debug, "Study ({0}} has no SR (AIM Annotations) objects", studyInstanceUid);
return null;
}
foreach (var studyAe in studyAes)
{
IStudyLoader studyLoader;
try
{
studyLoader = studyAe.GetService<IStudyLoader>();
}
catch (Exception ex)
{
throw new AimManagerException("Cannot get study loader", ex);
}
int numberOfSops = studyLoader.Start(new StudyLoaderArgs(studyInstanceUid, null, new StudyLoaderOptions(true)));
for (int i = 0; i < numberOfSops; i++)
{
using (var sop = studyLoader.LoadNextSop())
{
if (sop != null && sop.Modality == AimManager.AimModality)
{
var localSopDataSource = sop.DataSource as ILocalSopDataSource;
if (localSopDataSource != null)
{
var filePathName = localSopDataSource.Filename;
switch (AimManager.GetAimVersionFromSop(sop))
{
case AimVersion.AimVersion3:
instanceToAimFileInfoMap.Add(filePathName,
new AimFileInfo(AimVersion.AimVersion3, sop.StudyInstanceUid, sop.SeriesInstanceUid, sop.SopInstanceUid));
break;
case AimVersion.AimVersion4:
instanceToAimFileInfoMap.Add(filePathName,
new AimFileInfo(AimVersion.AimVersion4, sop.StudyInstanceUid, sop.SeriesInstanceUid, sop.SopInstanceUid));
break;
}
}
}
}
}
}
if (instanceToAimFileInfoMap.Any())
{
var aimDocumentInstances = new List<IAimDocumentInstance>();
var aim4Instances = instanceToAimFileInfoMap.Where(instance => instance.Value.AimVersion == AimVersion.AimVersion4).ToList();
if (aim4Instances.Any())
{
using (var dcmHelper = new Aim4.Aim4NativeDcmHelper())
{
foreach (var instanceInfo in aim4Instances)
{
var aimDocumentInstance = ReadAimDocumentFromDicomFile(dcmHelper,
instanceInfo.Key, instanceInfo.Value.StudyInstanceUid,
instanceInfo.Value.SeriesInstanceUid, instanceInfo.Value.SopInstanceUid);
if (aimDocumentInstance != null)
aimDocumentInstances.Add(aimDocumentInstance);
}
}
}
return aimDocumentInstances.Any() ? aimDocumentInstances : null;
}
return null;
}
