public void TestPatientAgeTag()
{
string filename = Path.Combine(TestContext.CurrentContext.TestDirectory, "test.dcm");
var dataset = new DicomDataset();
dataset.Add(DicomTag.SOPInstanceUID, "123.123.123");
dataset.Add(DicomTag.SOPClassUID, "123.123.123");
dataset.Add(new DicomAgeString(DicomTag.PatientAge, "009Y"));
var cSharpValue = DicomTypeTranslaterReader.GetCSharpValue(dataset, DicomTag.PatientAge);
Assert.AreEqual("009Y", cSharpValue);
var file = new DicomFile(dataset);
file.Save(filename);
var source = new DicomFileCollectionSource();
source.FilenameField = "Path";
source.PreInitialize(new ExplicitListDicomFileWorklist(new[] { filename }), new ThrowImmediatelyDataLoadEventListener());
var chunk = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
Assert.AreEqual("009Y", chunk.Rows[0]["PatientAge"]);
}
public void AssembleDataTableFromFileArchive()
{
var zip = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData.zip");
var dir = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData");
if (File.Exists(zip))
{
File.Delete(zip);
}
ZipFile.CreateFromDirectory(dir, zip);
var fileCount = Directory.GetFiles(dir, "*.dcm").Count();
var source = new DicomFileCollectionSource();
source.FilenameField = "RelativeFileArchiveURI";
source.PreInitialize(new FlatFileToLoadDicomFileWorklist(new FlatFileToLoad(new FileInfo(zip))), new ThrowImmediatelyDataLoadEventListener());
var toMemory = new ToMemoryDataLoadEventListener(true);
var result = source.GetChunk(toMemory, new GracefulCancellationToken());
//processed every file once
Assert.AreEqual(fileCount, toMemory.LastProgressRecieivedByTaskName.Single().Value.Progress.Value);
Assert.Greater(result.Columns.Count, 0);
}
public void AssembleDataTableFromFolder()
{
var file1 = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData/FileWithLotsOfTags.dcm"));
var file2 = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData/IM-0001-0013.dcm"));
var controlFile = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, "list.txt"));
File.WriteAllText(controlFile.FullName, file1.FullName + Environment.NewLine + file2.FullName);
var source = new DicomFileCollectionSource {
FilenameField = "RelativeFileArchiveURI"
};
source.PreInitialize(new FlatFileToLoadDicomFileWorklist(new FlatFileToLoad(controlFile)), new ThrowImmediatelyDataLoadEventListener());
var toMemory = new ToMemoryDataLoadEventListener(true);
var result = source.GetChunk(toMemory, new GracefulCancellationToken());
Assert.AreEqual(1, result.Rows.Count);
result = source.GetChunk(toMemory, new GracefulCancellationToken());
Assert.AreEqual(1, result.Rows.Count);
Assert.AreEqual(null, source.GetChunk(toMemory, new GracefulCancellationToken()));
}
public void Test_Linux_Root()
{
var source = new DicomFileCollectionSource {
ArchiveRoot = "/"
};
Assert.AreEqual("/", source.ArchiveRoot);
}
[TestCase(@"./bob/", @"./bob/fish.dcm", @"./fish.dcm")] //if the "root" is relative then we can still express this relative to it
public void Test_ApplyArchiveRootToMakeRelativePath(string root, string inputPath, string expectedRelativePath)
{
var source = new DicomFileCollectionSource {
ArchiveRoot = root
};
var result = source.ApplyArchiveRootToMakeRelativePath(inputPath);
Assert.AreEqual(expectedRelativePath, result);
}
public void TestRelativeUri_RelativeInput(string root)
{
var source = new DicomFileCollectionSource();
source.ArchiveRoot = root;
var result = source.ApplyArchiveRootToMakeRelativePath(@"\fish\1.dcm");
Assert.AreEqual(@"\fish\1.dcm", result);
result = source.ApplyArchiveRootToMakeRelativePath(@"fish\1.dcm");
Assert.AreEqual(@"fish\1.dcm", result);
}
public void AssembleDataTableFromFile()
{
var source = new DicomFileCollectionSource();
source.FilenameField = "RelativeFileArchiveURI";
var f = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\IM-0001-0013.dcm");
source.PreInitialize(new FlatFileToLoadDicomFileWorklist(new FlatFileToLoad(new FileInfo(f))), new ThrowImmediatelyDataLoadEventListener());
var result = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
Assert.AreEqual("IM00010013", result.TableName);
Assert.Greater(result.Columns.Count, 0);
Assert.IsNull(source.GetChunk(new ThrowImmediatelyDataLoadJob(), new GracefulCancellationToken()));
}
public void Test_SingleFile(bool expressRelative)
{
var db = GetCleanedServer(DatabaseType.MicrosoftSQLServer);
var source = new DicomFileCollectionSource {
FilenameField = "RelativeFileArchiveURI"
};
if (expressRelative)
{
source.ArchiveRoot = TestContext.CurrentContext.TestDirectory;
}
var f = new FlatFileToLoad(new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData/IM-0001-0013.dcm")));
source.PreInitialize(new FlatFileToLoadDicomFileWorklist(f), new ThrowImmediatelyDataLoadEventListener());
var tbl = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
var destination = new DataTableUploadDestination();
destination.PreInitialize(db, new ThrowImmediatelyDataLoadEventListener());
destination.AllowResizingColumnsAtUploadTime = true;
destination.ProcessPipelineData(tbl, new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
destination.Dispose(new ThrowImmediatelyDataLoadEventListener(), null);
var finalTable = db.ExpectTable(destination.TargetTableName);
using (var dt = finalTable.GetDataTable())
{
//should be 1 row in the final table
Assert.AreEqual(1, dt.Rows.Count);
//the path referenced should be the file read in relative/absolute format
Assert.AreEqual(expressRelative ? "./TestData/IM-0001-0013.dcm":
f.File.FullName.Replace('\\', '/')
, dt.Rows[0]["RelativeFileArchiveURI"]);
}
Assert.IsTrue(finalTable.Exists());
finalTable.Drop();
}
public void PipelineTest()
{
var source = new DicomFileCollectionSource();
source.FilenameField = "RelativeFileArchiveURI";
var f = new FlatFileToLoad(new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\IM-0001-0013.dcm")));
source.PreInitialize(new FlatFileToLoadDicomFileWorklist(f), new ThrowImmediatelyDataLoadEventListener());
var tbl = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
var destination = new DataTableUploadDestination();
destination.PreInitialize(DiscoveredDatabaseICanCreateRandomTablesIn, new ThrowImmediatelyDataLoadEventListener());
destination.AllowResizingColumnsAtUploadTime = true;
destination.ProcessPipelineData(tbl, new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
destination.Dispose(new ThrowImmediatelyDataLoadEventListener(), null);
var finalTable = DiscoveredDatabaseICanCreateRandomTablesIn.ExpectTable(destination.TargetTableName);
Assert.IsTrue(finalTable.Exists());
finalTable.Drop();
}
public void Test_ElevationXmlLoading()
{
#region xml values
const string validXml1 =
@"<TagElevationRequestCollection>
<TagElevationRequest>
<ColumnName>CodeValueCol</ColumnName>
<ElevationPathway>ProcedureCodeSequence->CodeValue</ElevationPathway>
</TagElevationRequest>
</TagElevationRequestCollection>";
const string validXml2 =
@"<TagElevationRequestCollection>
<TagElevationRequest>
<ColumnName>CodeValueCol2</ColumnName>
<ElevationPathway>ProcedureCodeSequence->CodeValue</ElevationPathway>
</TagElevationRequest>
</TagElevationRequestCollection>";
/// <summary>
/// Invalid because the pathway should be sequence->non sequence
/// </summary>
const string invalidXml =
@"<TagElevationRequestCollection>
<TagElevationRequest>
<ColumnName>CodeValueCol</ColumnName>
<ElevationPathway>CodeValue->CodeValue</ElevationPathway>
</TagElevationRequest>
</TagElevationRequestCollection>";
#endregion
var source = new DicomFileCollectionSource();
var file = Path.Combine(TestContext.CurrentContext.WorkDirectory, "me.xml");
//no elevation to start with
Assert.IsNull(source.LoadElevationRequestsFile());
//illegal file
File.WriteAllText(file, "<lolz>");
source.TagElevationConfigurationFile = new FileInfo(file);
var ex = Assert.Throws <XmlException>(() => source.LoadElevationRequestsFile());
StringAssert.Contains("Unexpected end of file", ex.Message);
File.WriteAllText(file, invalidXml);
var ex2 = Assert.Throws <TagNavigationException>(() => source.LoadElevationRequestsFile());
StringAssert.Contains("Navigation Token CodeValue was not the final token in the pathway", ex2.Message);
File.WriteAllText(file, validXml1);
Assert.AreEqual("CodeValueCol", source.LoadElevationRequestsFile().Requests.Single().ColumnName);
//Setting the xml property will override the file xml
source.TagElevationConfigurationXml = new DicomSource.TagElevationXml()
{
xml = "<lolz>"
};
var ex3 = Assert.Throws <XmlException>(() => source.LoadElevationRequestsFile());
StringAssert.Contains("Unexpected end of file", ex3.Message);
source.TagElevationConfigurationXml = new DicomSource.TagElevationXml()
{
xml = invalidXml
};
var ex4 = Assert.Throws <TagNavigationException>(() => source.LoadElevationRequestsFile());
StringAssert.Contains("Navigation Token CodeValue was not the final token in the pathway", ex4.Message);
source.TagElevationConfigurationXml = new DicomSource.TagElevationXml()
{
xml = validXml2
};
Assert.AreEqual("CodeValueCol2", source.LoadElevationRequestsFile().Requests.Single().ColumnName);
//now we go back to the file one (by setting the xml one to null)
source.TagElevationConfigurationXml = null;
Assert.AreEqual("CodeValueCol", source.LoadElevationRequestsFile().Requests.Single().ColumnName);
source.TagElevationConfigurationXml = new DicomSource.TagElevationXml()
{
xml = ""
};
Assert.AreEqual("CodeValueCol", source.LoadElevationRequestsFile().Requests.Single().ColumnName);
source.TagElevationConfigurationXml = new DicomSource.TagElevationXml()
{
xml = " \r\n "
};
Assert.AreEqual("CodeValueCol", source.LoadElevationRequestsFile().Requests.Single().ColumnName);
}
public void Test_ZipFile(bool expressRelative)
{
//get a clean database to upload to
var db = GetCleanedServer(DatabaseType.MicrosoftSQLServer);
//create a folder in which to generate some dicoms
var dirToLoad = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_ZipFile)));
if (dirToLoad.Exists)
{
dirToLoad.Delete(true);
}
dirToLoad.Create();
//generate some random dicoms
var r = new Random(999);
DicomDataGenerator generator = new DicomDataGenerator(r, dirToLoad, "CT")
{
MaximumImages = 5
};
var people = new PersonCollection();
people.GeneratePeople(1, r);
generator.GenerateTestDataFile(people, new FileInfo("./inventory.csv"), 1);
//This generates
// Test_ZipFile
// 2015
// 3
// 18
// 751140 2.25.166922918107154891877498685128076062226.dcm
// 751140 2.25.179610809676265137473873365625829826423.dcm
// 751140 2.25.201969634959506849065133495434871450465.dcm
// 751140 2.25.237492679533001779093365416814254319890.dcm
// 751140 2.25.316241631782653383510844072713132248731.dcm
var yearDir = dirToLoad.GetDirectories().Single();
StringAssert.IsMatch("\\d{4}", yearDir.Name);
//zip them up
FileInfo zip = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_ZipFile) + ".zip")); Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_ZipFile) + ".zip");
if (zip.Exists)
{
zip.Delete();
}
ZipFile.CreateFromDirectory(dirToLoad.FullName, zip.FullName);
//tell the source to load the zip
var f = new FlatFileToLoad(zip);
var source = new DicomFileCollectionSource {
FilenameField = "RelativeFileArchiveURI"
};
if (expressRelative)
{
source.ArchiveRoot = TestContext.CurrentContext.TestDirectory;
}
source.PreInitialize(new FlatFileToLoadDicomFileWorklist(f), new ThrowImmediatelyDataLoadEventListener());
var tbl = source.GetChunk(new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
var destination = new DataTableUploadDestination();
destination.PreInitialize(db, new ThrowImmediatelyDataLoadEventListener());
destination.AllowResizingColumnsAtUploadTime = true;
destination.ProcessPipelineData(tbl, new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
destination.Dispose(new ThrowImmediatelyDataLoadEventListener(), null);
var finalTable = db.ExpectTable(destination.TargetTableName);
using (var dt = finalTable.GetDataTable())
{
//should be 5 rows in the final table (5 images)
Assert.AreEqual(5, dt.Rows.Count);
string pathInDbToDicomFile = (string)dt.Rows[0]["RelativeFileArchiveURI"];
//We expect either something like:
// E:/RdmpDicom/Rdmp.Dicom.Tests/bin/Debug/netcoreapp2.2/Test_ZipFile.zip!2015/3/18/2.25.160787663560951826149226183314694084702.dcm
// ./Test_ZipFile.zip!2015/3/18/2.25.105592977437473375573190160334447272386.dcm
//the path referenced should be the file read in relative/absolute format
StringAssert.IsMatch(
expressRelative ? $@"./{zip.Name}![\d./]*.dcm":
$@"{Regex.Escape(zip.FullName.Replace('\\','/'))}![\d./]*.dcm",
pathInDbToDicomFile);
StringAssert.Contains(yearDir.Name, pathInDbToDicomFile, "Expected zip file to have subdirectories and for them to be loaded correctly");
//confirm we can read that out again
using (var pool = new ZipPool())
{
var path = new AmbiguousFilePath(TestContext.CurrentContext.TestDirectory, pathInDbToDicomFile);
Assert.IsNotNull(path.GetDataset(pool));
}
}
Assert.IsTrue(finalTable.Exists());
finalTable.Drop();
}
public void Test_ZipFileNotation(bool expressRelative)
{
//get a clean database to upload to
var db = GetCleanedServer(DatabaseType.MicrosoftSQLServer);
//create a folder in which to generate some dicoms
var dirToLoad = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_ZipFileNotation)));
if (dirToLoad.Exists)
{
dirToLoad.Delete(true);
}
dirToLoad.Create();
//generate some random dicoms
var r = new Random(999);
DicomDataGenerator generator = new DicomDataGenerator(r, dirToLoad, "CT")
{
MaximumImages = 5
};
var people = new PersonCollection();
people.GeneratePeople(1, r);
generator.GenerateTestDataFile(people, new FileInfo("./inventory.csv"), 1);
//This generates
// Test_ZipFile
// 2015
// 3
// 18
// 751140 2.25.166922918107154891877498685128076062226.dcm
// 751140 2.25.179610809676265137473873365625829826423.dcm
// 751140 2.25.201969634959506849065133495434871450465.dcm
// 751140 2.25.237492679533001779093365416814254319890.dcm
// 751140 2.25.316241631782653383510844072713132248731.dcm
var yearDir = dirToLoad.GetDirectories().Single();
StringAssert.IsMatch("\\d{4}", yearDir.Name);
//should be 5 images in the zip file
var dicomFiles = yearDir.GetFiles("*.dcm", SearchOption.AllDirectories);
Assert.AreEqual(5, dicomFiles.Length);
//e.g. \2015\3\18\2.25.223398837779449245317520567111874824918.dcm
//e.g. \2015\3\18\2.25.179610809676265137473873365625829826423.dcm
var relativePathWithinZip1 = dicomFiles[0].FullName.Substring(dirToLoad.FullName.Length);
var relativePathWithinZip2 = dicomFiles[1].FullName.Substring(dirToLoad.FullName.Length);
//zip them up
FileInfo zip = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_ZipFile) + ".zip")); Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_ZipFile) + ".zip");
if (zip.Exists)
{
zip.Delete();
}
ZipFile.CreateFromDirectory(dirToLoad.FullName, zip.FullName);
//e.g. E:\RdmpDicom\Rdmp.Dicom.Tests\bin\Debug\netcoreapp2.2\Test_ZipFile.zip!\2015\3\18\2.25.223398837779449245317520567111874824918.dcm
string pathToLoad1 = zip.FullName + "!" + relativePathWithinZip1;
string pathToLoad2 = zip.FullName + "!" + relativePathWithinZip2;
var loadMeTextFile = new FileInfo(Path.Combine(dirToLoad.FullName, "LoadMe.txt"));
//tell the source to load the zip
File.WriteAllText(loadMeTextFile.FullName, string.Join(Environment.NewLine, pathToLoad1, pathToLoad2));
var f = new FlatFileToLoad(loadMeTextFile);
//Setup source
var source = new DicomFileCollectionSource {
FilenameField = "RelativeFileArchiveURI"
};
if (expressRelative)
{
source.ArchiveRoot = TestContext.CurrentContext.TestDirectory;
}
var worklist = new FlatFileToLoadDicomFileWorklist(f);
//Setup destination
var destination = new DataTableUploadDestination {
AllowResizingColumnsAtUploadTime = true
};
//setup pipeline
var contextFactory = new DataFlowPipelineContextFactory <DataTable>();
var context = contextFactory.Create(PipelineUsage.FixedDestination | PipelineUsage.FixedDestination);
//run pipeline
var pipe = new DataFlowPipelineEngine <DataTable>(context, source, destination, new ThrowImmediatelyDataLoadEventListener());
pipe.Initialize(db, worklist);
pipe.ExecutePipeline(new GracefulCancellationToken());
var finalTable = db.ExpectTable(destination.TargetTableName);
using (var dt = finalTable.GetDataTable())
{
//should be 2 rows (since we told it to only load 2 files out of the zip)
Assert.AreEqual(2, dt.Rows.Count);
string pathInDbToDicomFile = (string)dt.Rows[0]["RelativeFileArchiveURI"];
//We expect either something like:
// E:/RdmpDicom/Rdmp.Dicom.Tests/bin/Debug/netcoreapp2.2/Test_ZipFile.zip!2015/3/18/2.25.160787663560951826149226183314694084702.dcm
// ./Test_ZipFile.zip!2015/3/18/2.25.105592977437473375573190160334447272386.dcm
//the path referenced should be the file read in relative/absolute format
StringAssert.IsMatch(
expressRelative ? $@"./{zip.Name}![\d./]*.dcm":
$@"{Regex.Escape(zip.FullName.Replace('\\','/'))}![\d./]*.dcm",
pathInDbToDicomFile);
StringAssert.Contains(yearDir.Name, pathInDbToDicomFile, "Expected zip file to have subdirectories and for them to be loaded correctly");
//confirm we can read that out again
using (var pool = new ZipPool())
{
var path = new AmbiguousFilePath(TestContext.CurrentContext.TestDirectory, pathInDbToDicomFile);
Assert.IsNotNull(path.GetDataset(pool));
}
}
Assert.IsTrue(finalTable.Exists());
finalTable.Drop();
}
