public void Test_Sequence()
{
var subDatasets = new List <DicomDataset>
{
new DicomDataset
{
new DicomShortString(DicomTag.CodeValue, "CPELVD")
}
};
var dicomDataset = new DicomDataset
{
{ DicomTag.ProcedureCodeSequence, subDatasets.ToArray() }
};
object result = DicomTypeTranslaterReader.GetCSharpValue(dicomDataset, DicomTag.ProcedureCodeSequence);
object flat = DicomTypeTranslater.Flatten(result);
Console.WriteLine(flat);
StringAssert.Contains("CPELVD", (string)flat);
StringAssert.Contains("(0008,0100)", (string)flat);
}
private void WriteValue(CsvWriter writer, DicomCFindResponse response, DicomTag tag)
{
var val = DicomTypeTranslaterReader.GetCSharpValue(response.Dataset, tag);
if (val == null)
{
writer.WriteField("");
}
else
{
writer.WriteField(DicomTypeTranslater.Flatten(val));
}
}
protected override void OnLoad(EventArgs e)
{
base.OnLoad(e);
olvFileTags.ClearObjects();
try
{
var dicom = DicomFile.Open(_fileInfo.FullName, FileReadOption.ReadAll);
try
{
using var renderedImage = new DicomImage(dicom.Dataset).RenderImage().AsSharpImage();
using MemoryStream ms = new();
renderedImage.Save(ms, renderedImage.GetConfiguration().ImageFormatsManager.FindEncoder(PngFormat.Instance));
ms.Seek(0, SeekOrigin.Begin);
DicomImage = new(ms);
pictureBox1.Image = DicomImage;
}
catch (Exception)
{
//no picture
splitContainer1.Panel1Collapsed = true;
}
foreach (DicomItem item in dicom.Dataset)
{
var value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(dicom.Dataset, item));
olvFileTags.AddObject(new TagValueNode(item.Tag, value));
}
}
catch (Exception exception)
{
MessageBox.Show(exception.ToString(), "File Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
private static void RunBatch(IPersonCollection identifiers, ProgramOptions opts, Random r, DataTable[] batches, IBulkCopy[] uploaders)
{
Stopwatch swGeneration = new Stopwatch();
Stopwatch swReading = new Stopwatch();
Stopwatch swUploading = new Stopwatch();
try
{
using (var dicomGenerator = GetDataGenerator(opts, identifiers, r, out _))
{
for (int i = 0; i < opts.NumberOfStudies; i++)
{
swGeneration.Start();
var p = identifiers.People[r.Next(identifiers.People.Length)];
var ds = dicomGenerator.GenerateStudyImages(p, out Study s);
swGeneration.Stop();
foreach (DicomDataset dataset in ds)
{
var rows = new DataRow[batches.Length];
for (int j = 0; j < batches.Length; j++)
{
rows[j] = batches[j].NewRow();
}
swReading.Start();
foreach (DicomItem item in dataset)
{
var column = DicomTypeTranslaterReader.GetColumnNameForTag(item.Tag, false);
var value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(dataset, item));
foreach (DataRow row in rows)
{
if (row.Table.Columns.Contains(column))
{
row[column] = value ?? DBNull.Value;
}
}
}
for (int j = 0; j < batches.Length; j++)
{
batches[j].Rows.Add(rows[j]);
}
swReading.Stop();
}
//every 100 and last batch
if (i % 100 == 0 || i == opts.NumberOfStudies - 1)
{
swUploading.Start();
for (var j = 0; j < uploaders.Length; j++)
{
uploaders[j].Upload(batches[j]);
batches[j].Rows.Clear();
}
swUploading.Stop();
Console.WriteLine($"{DateTime.Now} Done {i} studies");
}
}
}
}
finally
{
for (var i = 0; i < uploaders.Length; i++)
{
uploaders[i].Dispose();
batches[i].Dispose();
}
}
Console.WriteLine("Total time Generating Dicoms:" + swGeneration.Elapsed);
Console.WriteLine("Total time Reading Dicoms:" + swReading.Elapsed);
Console.WriteLine("Total time Uploading Records:" + swUploading.Elapsed);
}
/// <summary>
/// Iterates through each DicomItem in the DicomDataset and creates a corresponding column in the DataTable (if it is a novel tag) and then populates
/// the DataTable with the data for the image.
/// </summary>
/// <param name="filename"></param>
/// <param name="ds"></param>
/// <param name="dt"></param>
/// <param name="listener"></param>
/// <param name="otherValuesToStoreInRow"></param>
protected void ProcessDataset(string filename, DicomDataset ds, DataTable dt, IDataLoadEventListener listener, Dictionary <string, string> otherValuesToStoreInRow = null)
{
if (_elevationRequests == null)
{
_elevationRequests = LoadElevationRequestsFile();
}
filename = ApplyArchiveRootToMakeRelativePath(filename);
var rowValues = new Dictionary <string, object>();
foreach (DicomItem item in ds)
{
//get the tag name (human readable)
var entry = item.Tag.DictionaryEntry;
string header = entry.Keyword;
if (ShouldSkip(dt, item.Tag))
{
continue;
}
object value;
switch (InvalidDataHandlingStrategy)
{
case InvalidDataHandling.ThrowException:
//enforce types and leave any Exceptions uncaught
value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(ds, item));
break;
case InvalidDataHandling.MarkCorrupt:
try
{
//try to enforce types
value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(ds, item));
}
catch (Exception ex)
{
//something went wrong pulling out the value
//mark it as corrupt
MarkCorrupt(ds);
//but make sure to warn people listening
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Could not GetCSharpValue for DicomItem " + item.Tag + "(" + entry.Keyword + ") for " + GetProblemFileDescription(filename, otherValuesToStoreInRow), ex));
//do not add the row to the table
return;
}
break;
case InvalidDataHandling.ConvertToNullAndWarn:
//try to enforce types
try
{
value = DicomTypeTranslater.Flatten(DicomTypeTranslaterReader.GetCSharpValue(ds, item));
}
catch (Exception ex)
{
//but make sure to warn people listening
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Could not GetCSharpValue for DicomItem " + item.Tag + "(" + entry.Keyword + ") for " + GetProblemFileDescription(filename, otherValuesToStoreInRow), ex));
if (InvalidDataHandlingStrategy == InvalidDataHandling.MarkCorrupt)
{
MarkCorrupt(ds);
continue;
}
//It went wrong, we couldn't enforce the type so just use null instead
value = DBNull.Value;
}
break;
default:
throw new ArgumentOutOfRangeException();
}
if (value is string && DataTooLongHandlingStrategy != DataTooWideHandling.None)
{
if (!IsValidLength(listener, item.Tag, (string)value))
{
//the string is too long!
switch (DataTooLongHandlingStrategy)
{
case DataTooWideHandling.TruncateAndWarn:
lock (_oDictLock)
{
value = ((string)value).Substring(0, _maxTagLengths[item.Tag]);
}
break;
case DataTooWideHandling.MarkCorrupt:
MarkCorrupt(ds);
continue;
case DataTooWideHandling.ConvertToNullAndWarn:
value = DBNull.Value;
break;
default:
throw new ArgumentOutOfRangeException();
}
}
}
try
{
rowValues.Add(header, value);
}
catch (Exception e)
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Error getting Tag '" + header + "' item.ValueRepresentation is (" + item.ValueRepresentation + ") " + GetProblemFileDescription(filename, otherValuesToStoreInRow), e));
}
}
//now run elevation requests
if (_elevationRequests != null)
{
foreach (TagElevationRequest request in _elevationRequests.Requests)
{
try
{
object value;
switch (InvalidDataHandlingStrategy)
{
case InvalidDataHandling.ThrowException:
value = request.Elevator.GetValue(ds);
break;
case InvalidDataHandling.ConvertToNullAndWarn:
try
{
value = request.Elevator.GetValue(ds);
}
catch (Exception e)
{
if (e is TagNavigationException)
{
throw;
}
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Error getting Tag for ElevationRequest '" + request.ColumnName + "' for " + GetProblemFileDescription(filename, otherValuesToStoreInRow), e));
value = DBNull.Value;
}
break;
default:
throw new ArgumentOutOfRangeException();
}
rowValues.Add(request.ColumnName, value);
}
catch (TagNavigationException e)
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Rule for column " + request.ColumnName + " failed to resolve GetValue for " + GetProblemFileDescription(filename, otherValuesToStoreInRow), e));
}
}
}
//do not add rows if there is nothing to store
if (!rowValues.Any())
{
return;
}
lock (_oDataTableLock)
{
var row = dt.Rows.Add();
row[FilenameField] = filename;
if (otherValuesToStoreInRow != null)
{
foreach (KeyValuePair <string, string> kvp in otherValuesToStoreInRow)
{
if (!dt.Columns.Contains(kvp.Key))
{
dt.Columns.Add(kvp.Key);
}
row[kvp.Key] = kvp.Value;
}
}
foreach (KeyValuePair <string, object> keyValuePair in rowValues)
{
Add(dt, row, keyValuePair.Key, keyValuePair.Value);
}
}
}
public void ExampleUsage_Simple()
{
//create an Fo-Dicom dataset with a single string
var ds = new DicomDataset(new List <DicomItem>()
{
new DicomShortString(DicomTag.PatientName, "Frank"),
new DicomAgeString(DicomTag.PatientAge, "032Y"),
new DicomDate(DicomTag.PatientBirthDate, new DateTime(2001, 1, 1))
});
object name = DicomTypeTranslaterReader.GetCSharpValue(ds, DicomTag.PatientName);
Assert.AreEqual(typeof(string), name.GetType());
Assert.AreEqual("Frank", name);
object age = DicomTypeTranslaterReader.GetCSharpValue(ds, DicomTag.PatientAge);
Assert.AreEqual(typeof(string), age.GetType());
Assert.AreEqual("032Y", age);
object dob = DicomTypeTranslaterReader.GetCSharpValue(ds, DicomTag.PatientBirthDate);
Assert.AreEqual(typeof(DateTime), dob.GetType());
Assert.AreEqual(new DateTime(2001, 01, 01), dob);
//create an Fo-Dicom dataset with string multiplicity
ds = new DicomDataset(new List <DicomItem>()
{
new DicomShortString(DicomTag.PatientName, "Frank", "Anderson")
});
//Get the C# type
object name2 = DicomTypeTranslaterReader.GetCSharpValue(ds, DicomTag.PatientName);
Assert.AreEqual(typeof(string[]), name2.GetType());
Assert.AreEqual(new string[] { "Frank", "Anderson" }, name2);
name2 = DicomTypeTranslater.Flatten(name2);
Assert.AreEqual(typeof(string), name2.GetType());
Assert.AreEqual("Frank\\Anderson", name2);
//create an Fo-Dicom dataset with a sequence
ds = new DicomDataset(new List <DicomItem>()
{
new DicomUniqueIdentifier(DicomTag.SOPInstanceUID, "1.2.3"),
new DicomSequence(DicomTag.ActualHumanPerformersSequence, new []
{
new DicomDataset(new List <DicomItem>()
{
new DicomShortString(DicomTag.PatientName, "Rabbit")
}),
new DicomDataset(new List <DicomItem>()
{
new DicomShortString(DicomTag.PatientName, "Roger")
})
})
});
var seq = (Dictionary <DicomTag, object>[])DicomTypeTranslaterReader.GetCSharpValue(ds, DicomTag.ActualHumanPerformersSequence);
Assert.AreEqual("Rabbit", seq[0][DicomTag.PatientName]);
Assert.AreEqual("Roger", seq[1][DicomTag.PatientName]);
var flattened = (string)DicomTypeTranslater.Flatten(seq);
Assert.AreEqual(
@"[0] -
(0010,0010) - Rabbit
[1] -
(0010,0010) - Roger" .Replace("\r", ""), flattened.Replace("\r", ""));
}