public void ReadJPEG()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleJPEG);
var elemCount = dcm.AllElements.Count;
Assert.AreEqual(elemCount, 80);
}
public void WriteLittleEndian()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
//Writing a file out
DICOMFileWriter.WriteLittleEndian("myPath.dcm", dcm);
}
public void ReadBigEndian()
{
var dcm = DICOMFileReader.Read(Resources.explicitBigEndian);
var elemCount = dcm.AllElements.Count;
Assert.AreEqual(elemCount, 44);
}
public void ReadImplicitLittleEndian()
{
var dcm = DICOMFileReader.Read(Resources.implicitLittleEndian);
var elemCount = dcm.AllElements.Count;
Assert.AreEqual(elemCount, 47);
}
public void ReadMultipleFL()
{
var dcm = DICOMFileReader.Read(Resources.MultpleFL);
var vmGreaterThan1 = dcm.FindAll("300A030A");
var el = vmGreaterThan1[0] as AbstractElement <float>;
Assert.IsTrue(el.Data_.Count > 1);
}
public void RemoveElementTest()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
//Remove elements by tag
dcm.Remove("00020000");
dcm.Remove(TagHelper.SEGMENT_NUMBER);
}
/// <summary>
/// Checks to see if the patient age is less than 89 years old
/// </summary>
/// <param name="file">Path to DICOM file containing patient information</param>
/// <returns>boolean indication test</returns>
public static bool YoungerThan89(string file)
{
//Check patient age - if 89 or older set anonymization options to
//Not conserve patient age
DICOMObject ageTest = DICOMFileReader.Read(file);
Date dob = ageTest.FindFirst(TagHelper.PATIENT_BIRTH_DATE.CompleteID) as Date;
int age = CalculateAge(dob);
return(age < 89);
}
public void ReplaceElementTest()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
var directChildren = dcm.Elements;
var allDescendants = dcm.AllElements;
//Finds the first instance of the Group Length element (0002,0000)
var firstInstance = dcm.FindFirst("00020000");
//Finds all instances of the Group Length element (0002,0000)
var allInstances = dcm.FindAll("00020000");
//Finds all Code Value (0008,0100) elements that are children of Procedure Code Sequence Elements (0008,1032)
var specificTree = dcm.FindAll(new Tag[] { TagHelper.ProcedureCodeSequence, TagHelper.CodeValue });
/// <summary>
/// Checks to see if the patient age is less than 89 years old
/// </summary>
/// <param name="file">Path to DICOM file containing patient information</param>
/// <returns>boolean indication test</returns>
public static bool YoungerThan89(string file)
{
//Check patient age - if 89 or older set anonymization options to
//Not conserve patient age
var ageTest = DICOMFileReader.Read(file);
var dob = ageTest.FindFirst(TagHelper.PatientBirthDate.CompleteID) as Date;
if (dob != null)
{
var age = CalculateAge(dob);
return(age < 89);
}
return(true);
}
public void ToXML()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
var xml = dcm.ToXML();
var dcm2 = DICOMObject.FromXML(xml);
Assert.AreEqual(dcm.Elements.Count, dcm2.Elements.Count);
Assert.AreEqual(dcm.AllElements.Count, dcm2.AllElements.Count);
for (int i = 0; i < dcm.Elements.Count; i++)
{
var el1 = dcm.Elements[i];
var el2 = dcm2.Elements[i];
CollectionAssert.AreEquivalent(el1.DData_, el2.DData_);
}
}
public void WorkingWithMultiValuesTest()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
//Study time is a dateTime value
var studyTime = dcm.FindFirst(TagHelper.STUDY_TIME) as Time;
var time = studyTime.Data; // data of type T (in this case system.datetime)
//Patient position holds double values
var positionEl = dcm.FindFirst(TagHelper.IMAGE_POSITION_PATIENT);
var position = positionEl as DecimalString;
//Patient position contains an array of double values {X,Y,Z}
var xyz = position.Data_; //Data as List<T> (in this case List<double>)
var x = xyz[0];
var y = xyz[1];
var z = xyz[2];
}
public void PatientIdReplaceTest()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
var sel = dcm.GetSelector();
sel.PatientID = DICOMForge.PatientID;
sel.PatientID.Data = "12345";
sel.PatientName.LastName = "Flinstone";
sel.PatientName.FirstName = "Fred";
var anon = new PatientIdAnonymizer("Homer", "Simpson", "678910");
anon.Anonymize(dcm);
Assert.AreEqual(sel.PatientID.Data, "678910");
Assert.AreEqual(sel.PatientName.LastName, "Simpson");
Assert.AreEqual(sel.PatientName.FirstName, "Homer");
}
public void WorkingWithSingleValuesTest()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
//The patient's name IDICOMElement
var pName = dcm.FindFirst(TagHelper.PATIENT_NAME);
//The patient's name strong typed for better data access
var strongName = dcm.FindFirst(TagHelper.PATIENT_NAME) as PersonName;
var firstName = strongName.FirstName;
var lastName = strongName.LastName;
//You can manipulate this way also
strongName.FirstName = "Fred";
strongName.LastName = "Flinstone";
//Generic casting
var genericName = dcm.FindFirst(TagHelper.PATIENT_NAME) as AbstractElement <string>;
var genValue = genericName.Data; // returns Flinstone^Fred
}
public static (string Value, PreambleStatus Status) Read(string filePath, string group, string element)
{
TransferSyntax syntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN;
PreambleStatus preambleStatus;
DICOMObject dicomObject = null;
using (var dicomBinaryReader = new DICOMBinaryReader(filePath))
{
preambleStatus = Read(dicomBinaryReader);
if (preambleStatus == PreambleStatus.Ok || preambleStatus == PreambleStatus.MismatchPreamble128)
{
List <IDICOMElement> metaElements = DICOMFileReader.ReadFileMetadata(dicomBinaryReader, ref syntax);
List <IDICOMElement> elements = metaElements.Concat(DICOMElementReader.ReadAllElements(dicomBinaryReader, syntax)).ToList();
dicomObject = new DICOMObject(elements);
}
}
IDICOMElement value = dicomObject?.Elements.FirstOrDefault(d => d.Tag.Group == group && d.Tag.Element == element);
return(value?.DData.ToString(), preambleStatus);
}
public void ReplaceElementTest()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
var directChildren = dcm.Elements;
var allDescendants = dcm.AllElements;
//Finds the first instance of the Group Length element (0002,0000)
var firstInstance = dcm.FindFirst("00020000");
//Finds all instances of the Group Length element (0002,0000)
var allInstances = dcm.FindAll("00020000");
//Finds all Code Value (0008,0100) elements that are children of Procedure Code Sequence Elements (0008,1032)
var specificTree = dcm.FindAll(new Tag[] { TagHelper.PROCEDURE_CODE_SEQUENCE, TagHelper.CODE_VALUE });
//Finds all elements that are of VR type PersonName
var allPersonsNameElements = dcm.FindAll(Enums.VR.PersonName);
//Whatever the referring physicians real name was, it is now Fred Flinstone
var refName = new PersonName {
FirstName = "Fred",
LastName = "Flinstone",
Tag = TagHelper.REFERRING_PHYSICIAN_NAME
};
dcm.Replace(refName);
//Even if it doesn't exist yet, add it
dcm.ReplaceOrAdd(refName);
Assert.AreEqual(refName.Data, new PersonName
{
FirstName = "Fred",
LastName = "Flinstone"
}
.Data);
}
public void WriteBigEndian()
{
var dcm = DICOMFileReader.Read(Resources.explicitLittleEndian);
var els = dcm.Elements.Count;
byte[] bytes;
using (var ms = new MemoryStream())
{
using (var dw = new DICOMBinaryWriter(ms))
{
var settings = new DICOMWriteSettings()
{
TransferSyntax = Enums.TransferSyntax.EXPLICIT_VR_BIG_ENDIAN, DoWriteIndefiniteSequences = false
};
DICOMObjectWriter.Write(dw, settings, dcm);
}
bytes = ms.ToArray();
}
var dcm2 = DICOMFileReader.Read(bytes);
Assert.AreEqual(dcm2.Elements.Count, els);
}
public static DoseMatrix Load(string dcmFile)
{
return(new DoseMatrix(DICOMFileReader.Read(dcmFile)));
}
public void Read()
{
var dcm = DICOMFileReader.Read(@"C:\Users\Rex\Desktop\BASSIN - 8577\IM-0001-0001.dcm");
var elemCount = dcm.AllElements.Count;
}
/// <summary>
/// Reads a DICOM file from a path
/// </summary>
/// <param name="filePath">the path to the file</param>
/// <returns></returns>
public static DICOMObject Read(string filePath)
{
return(DICOMFileReader.Read(filePath));
}
/// <summary>
/// Reads a DICOM file from a byte array
/// </summary>
/// <param name="file">the bytes of the DICOM file</param>
/// <returns></returns>
public static DICOMObject Read(byte[] file)
{
return(DICOMFileReader.Read(file));
}
public static RTDose Load(string dcmFile)
{
return(new RTDose(DICOMFileReader.Read(dcmFile)));
}
/// <summary>
/// Reads a DICOM file from a path
/// </summary>
/// <param name="filePath">the path to the file</param>
/// <param name="trySyntax">the transfer syntax to use in case there is no metadata explicitly included</param>
/// <returns>the DICOM Object</returns>
/// <example>
///<code>
///var dcm = DICOMObject.Read("mydcm.dcm");
///</code>
///</example>
public static async Task <DICOMObject> ReadAsync(string filePath,
TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
return(await DICOMFileReader.ReadAsync(filePath, trySyntax));
}
public static Image <Gray, double> Read(string fileName)
{
var dicomData = DICOMFileReader.Read(fileName);
return(Read(dicomData));
}
public static Image <Gray, double> Read(byte[] data)
{
var dicomData = DICOMFileReader.Read(data);
return(Read(dicomData));
}
/// <summary>
/// Reads a DICOM file from a path
/// </summary>
/// <param name="filePath">the path to the file</param>
/// <param name="trySyntax">the transfer syntax to use in case there is no metadata explicitly included</param>
/// <returns>the DICOM Object</returns>
/// <example>
///<code>
///var dcm = DICOMObject.Read("mydcm.dcm");
///</code>
///</example>
public static DICOMObject Read(string filePath,
TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
return(DICOMFileReader.Read(filePath, trySyntax));
}
public MainViewModel(ScriptContext context)
{
sc = context;
DoAnonymizeStudyIDs = true;
DoAnonymizeUIDs = true;
DateSettings = ESAPIAnon.Settings.DateSettings.NULL_AGE;
DoRemovePrivateTags = true;
DoPlans = DoStructures = DoDoses = DoImages = true;
DoResendToDaemon = false;
FirstName = "";
LastName = "";
Id = "";
AnonymizeCommand = new RelayCommand(() =>
{
//Get current patient id
var id = GetPatientId();
//Get current directory // Make patient folder if not exists
var path = Helpers.AssemblyDirectory;
var dir = Path.Combine(path, id);
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
//Read settings file
var ip = "100.75.16.108";
var scpAE = "Db Daemon";
var scpPort = 104;
UpdateStatus("Getting DICOM Files from the Daemon...");
CMove.GenerateDicomFiles(sc.Patient.Id, ip, scpPort.ToString(), scpAE, dir);
UpdateStatus("Anonymizing...");
var files = Directory.GetFiles(dir);
var dcms = files.ToList().Select(f => DICOMFileReader.Read(f)).ToList();
var settings = AnonymizeSettings.Generate(this);
var que = AnonymizationQue.Build(settings, dcms);
dcms.ForEach(d => que.Anonymize(d));
//Let user choose output
FolderBrowserDialog fbd = new FolderBrowserDialog();
fbd.Description = "Select DICOM File destination folder";
fbd.RootFolder = Environment.SpecialFolder.Desktop;
DialogResult result = fbd.ShowDialog();
if (result == DialogResult.OK)
{
var output = fbd.SelectedPath;
int i = 0;
foreach (var dcm in dcms)
{
var fileOut = Path.Combine(output, string.Format("{0}.dcm", i));
i++;
DICOMFileWriter.WriteLittleEndian(fileOut, dcm);
}
//Clean up directory
Directory.Delete(dir, true);
UpdateStatus("Complete!");
}
else
{
System.Windows.MessageBox.Show("You must select a file location!");
}
});
}
/// <summary>
/// Reads a DICOM file from a byte array
/// </summary>
/// <param name="file">the bytes of the DICOM file</param>
/// <param name="trySyntax">the transfer syntax to use in case there is no metadata explicitly included</param>
/// <returns></returns>
public static DICOMObject Read(byte[] file, TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
return(DICOMFileReader.Read(file, trySyntax));
}
public void ReadMetaXLittleEndian()
{
var dcm = DICOMFileReader.ReadFileMetadata(Properties.Resources.explicitLittleEndian);
Assert.AreEqual(dcm.Elements.Count, 7);
}
