private DicomRepopulatorProcessor GetProcessor(FileInfo inputCsv, FileInfo inputExtraMapping,
DirectoryInfo inputDicomDirectory, Action <DicomRepopulatorOptions> adjustOptions, string memberName,
out DicomRepopulatorOptions options,
out DirectoryInfo outputDirPath)
{
outputDirPath = new(Path.Combine(_outputFileBase, memberName));
//delete old content
if (Directory.Exists(outputDirPath.FullName))
{
Directory.Delete(outputDirPath.FullName, true);
}
Directory.CreateDirectory(outputDirPath.FullName);
options = new()
{
InputCsv = inputCsv?.FullName,
InputFolder = inputDicomDirectory?.FullName,
InputExtraMappings = inputExtraMapping?.FullName,
OutputFolder = outputDirPath.FullName,
NumThreads = 4
};
adjustOptions?.Invoke(options);
return(new());
}
}
public void SpacesInCsvHeaderTest()
{
string inputDirPath = Path.Combine(_inputFileBase, "SpacesInCsvHeaderTest");
const string testFileName = IM_0001_0013_NAME;
Directory.CreateDirectory(inputDirPath);
TestData.Create(new(Path.Combine(inputDirPath, testFileName)), TestData.IMG_013);
string outputDirPath = Path.Combine(_outputFileBase, "SpacesInCsvHeaderTest");
string expectedFile = Path.Combine(outputDirPath, testFileName);
var options = new DicomRepopulatorOptions
{
InputCsv = Path.Combine(TestContext.CurrentContext.TestDirectory, "SpacesInCsvHeaderTest.csv"),
InputFolder = inputDirPath,
OutputFolder = outputDirPath,
InputExtraMappings = CreateExtraMappingsFile("ID:PatientID").FullName,
NumThreads = 1
};
int result = new DicomRepopulatorProcessor().Process(options, CancellationToken.None);
Assert.AreEqual(0, result);
Assert.True(File.Exists(expectedFile), "Expected output file {0} to exist", expectedFile);
DicomFile file = DicomFile.Open(expectedFile);
Assert.AreEqual("NewPatientID1", file.Dataset.GetValue <string>(DicomTag.PatientID, 0));
}
public FilePathMatcher(CsvToDicomTagMapping map, DicomRepopulatorOptions options) : base(map, options)
{
if (map.FilenameColumn == null)
{
throw new ArgumentException("Map did not contain file name column");
}
Reader = new(map.CsvFile.OpenText(), new CsvConfiguration(System.Globalization.CultureInfo.CurrentCulture) with
{
TrimOptions = TrimOptions.Trim
});
public void MultipleSeriesTest(bool useSubfolder)
{
string inputDirPath = Path.Combine(_seriesFilesBase, "TestInput");
const string testFileName1 = IM_0001_0013_NAME;
const string testFileName2 = IM_0001_0019_NAME;
Directory.CreateDirectory(Path.Combine(inputDirPath, "Series1"));
Directory.CreateDirectory(Path.Combine(inputDirPath, "Series2"));
TestData.Create(new(Path.Combine(inputDirPath, "Series1", testFileName1)), TestData.IMG_013, true);
TestData.Create(new(Path.Combine(inputDirPath, "Series1", testFileName2)), TestData.IMG_013, false);
TestData.Create(new(Path.Combine(inputDirPath, "Series2", testFileName1)), TestData.IMG_019, true);
TestData.Create(new(Path.Combine(inputDirPath, "Series2", testFileName2)), TestData.IMG_019, false);
string outputDirPath = Path.Combine(_seriesFilesBase, "TestOutput");
string expectedFile1 = Path.Combine(outputDirPath, useSubfolder? "NewPatientID1/Series1" : "Series1", testFileName1);
string expectedFile2 = Path.Combine(outputDirPath, useSubfolder? "NewPatientID1/Series1" : "Series1", testFileName2);
string expectedFile3 = Path.Combine(outputDirPath, useSubfolder? "NewPatientID2/Series2" : "Series2", testFileName1);
string expectedFile4 = Path.Combine(outputDirPath, useSubfolder? "NewPatientID2/Series2" : "Series2", testFileName2);
var options = new DicomRepopulatorOptions
{
InputCsv = Path.Combine(TestContext.CurrentContext.TestDirectory, "TwoSeriesCsv.csv"),
InputFolder = inputDirPath,
OutputFolder = outputDirPath,
SubFolderColumn = useSubfolder ? "ID": null,
InputExtraMappings = CreateExtraMappingsFile("ID:PatientID").FullName,
NumThreads = 4
};
int result = new DicomRepopulatorProcessor().Process(options, CancellationToken.None);
Assert.AreEqual(0, result);
Assert.True(File.Exists(expectedFile1), "Expected output file {0} to exist", expectedFile1);
Assert.True(File.Exists(expectedFile2), "Expected output file {0} to exist", expectedFile2);
Assert.True(File.Exists(expectedFile3), "Expected output file {0} to exist", expectedFile3);
Assert.True(File.Exists(expectedFile4), "Expected output file {0} to exist", expectedFile4);
DicomFile file = DicomFile.Open(expectedFile1);
Assert.AreEqual("NewPatientID1", file.Dataset.GetValue <string>(DicomTag.PatientID, 0));
file = DicomFile.Open(expectedFile2);
Assert.AreEqual("NewPatientID1", file.Dataset.GetValue <string>(DicomTag.PatientID, 0));
file = DicomFile.Open(expectedFile3);
Assert.AreEqual("NewPatientID2", file.Dataset.GetValue <string>(DicomTag.PatientID, 0));
file = DicomFile.Open(expectedFile4);
Assert.AreEqual("NewPatientID2", file.Dataset.GetValue <string>(DicomTag.PatientID, 0));
}
public RepopulatorMatcher(CsvToDicomTagMapping map, DicomRepopulatorOptions options)
{
Options = options;
Map = map;
if (!Map.IsBuilt)
{
throw new ArgumentException("Map has not been built yet");
}
if (string.IsNullOrWhiteSpace(options.InputFolder))
{
throw new ArgumentException("InputFolder has not been set");
}
}
public IRepopulatorMatcher Create(CsvToDicomTagMapping map, DicomRepopulatorOptions options)
{
//We have a column that contains the exact location on disk of the image. This is the best because it lets us stream the CSV
if (map.FilenameColumn != null)
{
return(new FilePathMatcher(map, options));
}
//We have no file path column so must do matching based on 'key'. This will require loading entire CSV into memory which may break
//for very large datasets
if (map.TagColumns.Any(c =>
c.TagsToPopulate.Contains(DicomTag.SOPInstanceUID) ||
c.TagsToPopulate.Contains(DicomTag.SeriesInstanceUID) ||
c.TagsToPopulate.Contains(DicomTag.StudyInstanceUID)))
{
return(new TagMatcher(map, options));
}
return(null);
}
public RepopulatorUI()
{
InitializeComponent();
State = new();
try
{
if (File.Exists("RepopulatorUI.yaml"))
{
var des = new Deserializer();
State = des.Deserialize <DicomRepopulatorOptions>(File.ReadAllText(StateFile));
cbIncludeSubfolders.Checked = State.IncludeSubdirectories;
tbInputFolder.Text = State.InputFolder;
tbInputCsv.Text = State.InputCsv;
tbExtraMappings.Text = State.InputExtraMappings;
tbOutputFolder.Text = State.OutputFolder;
nThreads.Value = Math.Min(Math.Max(nThreads.Minimum, State.NumThreads), nThreads.Maximum);
nErrorThreshold.Value = Math.Min(Math.Max(nErrorThreshold.Minimum, State.ErrorThreshold), nErrorThreshold.Maximum);
tbFilePattern.Text = State.Pattern;
tbFilenameColumn.Text = State.FileNameColumn;
cbAnonymise.Checked = State.Anonymise;
cbDeleteAsYouGo.Checked = State.DeleteAsYouGo;
if (!string.IsNullOrWhiteSpace(State.CultureName))
{
tbCulture.Text = State.CultureName;
State.Culture = new(State.CultureName);
}
else
{
tbCulture.Text = State.Culture.DisplayName;
}
tbSubFolderColumn.Text = State.SubFolderColumn;
}
}
catch (Exception e)
{
MessageBox.Show(e.Message, "Error in RepopulatorUI.yaml", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
tt = new() { InitialDelay = 0, AutoPopDelay = 32767, ShowAlways = true };
tt.SetToolTip(btnInputFolder, HelpInputFolder);
tt.SetToolTip(lblInputFolder, HelpInputFolder);
tt.SetToolTip(btnInputCsv, HelpInputCsv);
tt.SetToolTip(lblInputCsv, HelpInputCsv);
tt.SetToolTip(btnExtraMappings, HelpExtraMappings);
tt.SetToolTip(lblExtraMappings, HelpExtraMappings);
tt.SetToolTip(cbIncludeSubfolders, HelpIncludeSubFolders);
tt.SetToolTip(lblFileNameColumn, HelpFileNameColumn);
tt.SetToolTip(lblFilePattern, HelpFilePattern);
tt.SetToolTip(btnOutputFolder, HelpOutputFolder);
tt.SetToolTip(lblOutputFolder, HelpOutputFolder);
tt.SetToolTip(btnCopyToClipboard, HelpCopyToClipboard);
tt.SetToolTip(lblErrorThreshold, HelpErrorThreshold);
tt.SetToolTip(lblDone, HelpDone);
tt.SetToolTip(lblErrors, HelpErrors);
tt.SetToolTip(lblCulture, HelpCulture);
tt.SetToolTip(lblSubFolder, HelpSubFolderColumn);
}