public void SourceRead_InvalidFloatInSequence_ToTable(InvalidDataHandling dataHandlingStrategy)
{
var source = new DicomDatasetCollectionSource();
source.InvalidDataHandlingStrategy = dataHandlingStrategy;
//when we have a dicom file with an invalid Float number
var ds = new DicomDataset();
ds.Add(DicomTag.PatientAge, "123Y");
var sequence = new DicomSequence(DicomTag.AcquisitionContextSequence,
new DicomDataset()
{
{ DicomTag.WedgeAngleFloat, "3.40282347e+038" }
});
ds.Add(sequence);
var worklist = new ExplicitListDicomDatasetWorklist(new[] { ds }, "fish.dcm");
source.PreInitialize(worklist, new ThrowImmediatelyDataLoadEventListener());
source.FilenameField = "RelFileName";
DataTable dt = null;
switch (dataHandlingStrategy)
{
case InvalidDataHandling.MarkCorrupt:
dt = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
//row was not processed (which leaves data table with 0 rows and hence component returns null)
Assert.IsNull(dt);
//corrupt message should appear in the worklist
Assert.AreEqual(1, worklist.CorruptMessages.Count);
return;
case InvalidDataHandling.ConvertToNullAndWarn:
dt = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
Assert.AreEqual("123Y", dt.Rows[0]["PatientAge"]);
Assert.AreEqual("fish.dcm", dt.Rows[0]["RelFileName"]);
Assert.AreEqual(DBNull.Value, dt.Rows[0]["AcquisitionContextSequence"]);
Assert.AreEqual(0, worklist.CorruptMessages.Count);
break;
case InvalidDataHandling.ThrowException:
Assert.Throws <OverflowException>(() => source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken()));
return;
default:
throw new ArgumentOutOfRangeException("dataHandlingStrategy");
}
}
public void SourceRead_ToTable_IgnoringSuperflousColumn_LoadMetadata()
{
var repo = new MemoryCatalogueRepository();
var lmd = new LoadMetadata(repo, "MyLoad");
var cata1 = new Catalogue(repo, "PatientCatalogue");
var ci1 = new CatalogueItem(repo, cata1, "PatientAge");
var ti1 = new TableInfo(repo, "PatientTableInfo");
var colInfo1 = new ColumnInfo(repo, "PatientAge", "varchar(100)", ti1);
ci1.ColumnInfo_ID = colInfo1.ID;
ci1.SaveToDatabase();
cata1.LoadMetadata_ID = lmd.ID;
cata1.SaveToDatabase();
var cata2 = new Catalogue(repo, "FileCatalogue");
var ci2 = new CatalogueItem(repo, cata2, "RelFileName");
var ti2 = new TableInfo(repo, "FileTableInfo");
var colInfo2 = new ColumnInfo(repo, "RelFileName", "varchar(100)", ti2);
ci2.ColumnInfo_ID = colInfo2.ID;
ci2.SaveToDatabase();
cata2.LoadMetadata_ID = lmd.ID;
cata2.SaveToDatabase();
var source = new DicomDatasetCollectionSource();
source.InvalidDataHandlingStrategy = InvalidDataHandling.ThrowException;
var ds = new DicomDataset();
ds.Add(DicomTag.PatientAge, "123Y");
var sequence = new DicomSequence(DicomTag.AcquisitionContextSequence,
new DicomDataset()
{
{ DicomTag.WedgeAngleFloat, "3.40282347e+038" }
});
ds.Add(sequence);
var worklist = new ExplicitListDicomDatasetWorklist(new[] { ds }, "fish.dcm");
source.PreInitialize(worklist, new ThrowImmediatelyDataLoadEventListener());
source.FilenameField = "RelFileName";
source.UseAllTableInfoInLoadAsFieldMap = lmd;
var dt = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
Assert.AreEqual("123Y", dt.Rows[0]["PatientAge"]);
Assert.AreEqual("fish.dcm", dt.Rows[0]["RelFileName"]);
Assert.AreEqual(2, dt.Columns.Count);
}
public void SourceRead_InvalidFloat_ToTable(InvalidDataHandling dataHandlingStrategy)
{
var source = new DicomDatasetCollectionSource();
source.InvalidDataHandlingStrategy = dataHandlingStrategy;
var ds = new DicomDataset();
ds.Add(DicomTag.PatientAge, "123Y");
ds.Add(DicomTag.WedgeAngleFloat, "3.40282347e+038");
var worklist = new ExplicitListDicomDatasetWorklist(new[] { ds }, "fish.dcm", new Dictionary <string, string> {
{ "MessageGuid", "123x321" }
});
source.PreInitialize(worklist, new ThrowImmediatelyDataLoadEventListener());
source.FilenameField = "RelFileName";
DataTable dt = null;
switch (dataHandlingStrategy)
{
case InvalidDataHandling.ThrowException:
Assert.Throws <OverflowException>(() => source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken()));
return;
case InvalidDataHandling.ConvertToNullAndWarn:
var tomem = new ToMemoryDataLoadEventListener(true);
dt = source.GetChunk(tomem, new GracefulCancellationToken());
Assert.AreEqual(DBNull.Value, dt.Rows[0]["WedgeAngleFloat"]);
//should be a warning about WedgeAngleFloat logged
var warning = tomem.EventsReceivedBySender.SelectMany(e => e.Value).Single(v => v.ProgressEventType == ProgressEventType.Warning);
Assert.IsTrue(warning.Message.Contains("WedgeAngleFloat"));
Assert.IsTrue(warning.Message.Contains("MessageGuid"));
Assert.IsTrue(warning.Message.Contains("123x321"));
Assert.IsTrue(warning.Message.Contains("fish.dcm"));
break;
default:
throw new ArgumentOutOfRangeException("dataHandlingStrategy");
}
Assert.AreEqual("123Y", dt.Rows[0]["PatientAge"]);
Assert.AreEqual("fish.dcm", dt.Rows[0]["RelFileName"]);
}
public void TestStringTooLong(DataTooWideHandling strategy)
{
var ds = new DicomDataset();
#pragma warning disable CS0618 // Obsolete
ds.AutoValidate = false;
#pragma warning restore CS0618
ds.AddOrUpdate(DicomTag.AccessionNumber, "1342340123129473279427572495349757459347839479375974");
ds.GetValues <string>(DicomTag.AccessionNumber);
var source = new DicomDatasetCollectionSource();
var worklist = new ExplicitListDicomDatasetWorklist(new[] { ds }, "fish.dcm", new Dictionary <string, string>());
source.DataTooLongHandlingStrategy = strategy;
source.FilenameField = "abc";
source.PreInitialize(worklist, new ThrowImmediatelyDataLoadEventListener());
var dt = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
switch (strategy)
{
case DataTooWideHandling.None:
Assert.AreEqual("1342340123129473279427572495349757459347839479375974", dt.Rows[0]["AccessionNumber"]);
Assert.AreEqual(0, worklist.CorruptMessages.Count);
break;
case DataTooWideHandling.TruncateAndWarn:
Assert.AreEqual("1342340123129473", dt.Rows[0]["AccessionNumber"]);
Assert.AreEqual(0, worklist.CorruptMessages.Count);
break;
case DataTooWideHandling.MarkCorrupt:
Assert.IsNull(dt); //since dt has no rows it just returns null
Assert.AreEqual(1, worklist.CorruptMessages.Count);
break;
case DataTooWideHandling.ConvertToNullAndWarn:
Assert.AreEqual(DBNull.Value, dt.Rows[0]["AccessionNumber"]);
Assert.AreEqual(0, worklist.CorruptMessages.Count);
break;
default:
throw new ArgumentOutOfRangeException("strategy");
}
}
public void SourceReadSimpleTagToTable()
{
var source = new DicomDatasetCollectionSource();
var ds = new DicomDataset();
ds.Add(DicomTag.PatientAge, "123Y");
var worklist = new ExplicitListDicomDatasetWorklist(new [] { ds }, "fish.dcm");
source.PreInitialize(worklist, new ThrowImmediatelyDataLoadEventListener());
source.FilenameField = "RelFileName";
var dt = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
Assert.AreEqual("123Y", dt.Rows[0]["PatientAge"]);
Assert.AreEqual("fish.dcm", dt.Rows[0]["RelFileName"]);
}
public void SourceRead_ToTable_IgnoringSuperflousColumn_TableInfo()
{
var repo = new MemoryCatalogueRepository();
var ti = new TableInfo(repo, "MyTable");
new ColumnInfo(repo, "PatientAge", "varchar(100)", ti);
new ColumnInfo(repo, "RelFileName", "varchar(100)", ti);
var source = new DicomDatasetCollectionSource();
source.InvalidDataHandlingStrategy = InvalidDataHandling.ThrowException;
var ds = new DicomDataset();
ds.Add(DicomTag.PatientAge, "123Y");
var sequence = new DicomSequence(DicomTag.AcquisitionContextSequence,
new DicomDataset()
{
{ DicomTag.WedgeAngleFloat, "3.40282347e+038" }
});
ds.Add(sequence);
var worklist = new ExplicitListDicomDatasetWorklist(new[] { ds }, "fish.dcm");
source.PreInitialize(worklist, new ThrowImmediatelyDataLoadEventListener());
source.FilenameField = "RelFileName";
source.FieldMapTableIfAny = ti;
var dt = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
Assert.AreEqual("123Y", dt.Rows[0]["PatientAge"]);
Assert.AreEqual("fish.dcm", dt.Rows[0]["RelFileName"]);
Assert.AreEqual(2, dt.Columns.Count);
}
public void SourceRead_InvalidFloatInSequence_WithElevation_ToTable(InvalidDataHandling dataHandlingStrategy)
{
//create the elevation configuration
var elevationRules = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, "ElevationConfig.xml"));
File.WriteAllText(elevationRules.FullName,
@"<!DOCTYPE TagElevationRequestCollection
[
<!ELEMENT TagElevationRequestCollection (TagElevationRequest*)>
<!ELEMENT TagElevationRequest (ColumnName,ElevationPathway,Conditional?)>
<!ELEMENT ColumnName (#PCDATA)>
<!ELEMENT ElevationPathway (#PCDATA)>
<!ELEMENT Conditional (ConditionalPathway,ConditionalRegex)>
<!ELEMENT ConditionalPathway (#PCDATA)>
<!ELEMENT ConditionalRegex (#PCDATA)>
]>
<TagElevationRequestCollection>
<TagElevationRequest>
<ColumnName>WedgeAngleFloat</ColumnName>
<ElevationPathway>AcquisitionContextSequence->WedgeAngleFloat</ElevationPathway>
</TagElevationRequest>
</TagElevationRequestCollection>");
//setup the source reader
var source = new DicomDatasetCollectionSource();
source.InvalidDataHandlingStrategy = dataHandlingStrategy;
source.TagElevationConfigurationFile = elevationRules;
//don't load the sequence, just the elevation
source.TagBlacklist = new Regex("AcquisitionContextSequence");
//The dataset we are trying to load
var ds = new DicomDataset();
ds.Add(DicomTag.PatientAge, "123Y");
var sequence = new DicomSequence(DicomTag.AcquisitionContextSequence,
new DicomDataset()
{
{ DicomTag.WedgeAngleFloat, "3.40282347e+038" } //dodgy float in sequence (the sequence we are trying to elevate)
});
ds.Add(sequence);
var worklist = new ExplicitListDicomDatasetWorklist(new[] { ds }, "fish.dcm", new Dictionary <string, string> {
{ "MessageGuid", "123x321" }
});
source.PreInitialize(worklist, new ThrowImmediatelyDataLoadEventListener());
source.FilenameField = "RelFileName";
DataTable dt = null;
switch (dataHandlingStrategy)
{
case InvalidDataHandling.ThrowException:
Assert.Throws <OverflowException>(() => source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken()));
return;
case InvalidDataHandling.ConvertToNullAndWarn:
var tomem = new ToMemoryDataLoadEventListener(true);
dt = source.GetChunk(tomem, new GracefulCancellationToken());
Assert.AreEqual(DBNull.Value, dt.Rows[0]["WedgeAngleFloat"]);
//should be a warning about WedgeAngleFloat logged
var warning = tomem.EventsReceivedBySender.SelectMany(e => e.Value).Single(v => v.ProgressEventType == ProgressEventType.Warning);
Assert.IsTrue(warning.Message.Contains("WedgeAngleFloat"));
Assert.IsTrue(warning.Message.Contains("MessageGuid"));
Assert.IsTrue(warning.Message.Contains("123x321"));
Assert.IsTrue(warning.Message.Contains("fish.dcm"));
break;
default:
throw new ArgumentOutOfRangeException("dataHandlingStrategy");
}
Assert.AreEqual("123Y", dt.Rows[0]["PatientAge"]);
Assert.AreEqual("fish.dcm", dt.Rows[0]["RelFileName"]);
}