public void InternalTransferSyntax_Setter_AppliesToAllSequenceDepths()
{
var ds = new DicomDataset {
{ DicomTag.PatientID, "1" }
};
var sps = new DicomDataset {
{ DicomTag.ScheduledStationName, "1" }
};
var spcs = new DicomDataset {
{ DicomTag.ContextIdentifier, "1" }
};
sps.Add(new DicomSequence(DicomTag.ScheduledProtocolCodeSequence, spcs));
ds.Add(new DicomSequence(DicomTag.ScheduledProcedureStepSequence, sps));
var newSyntax = DicomTransferSyntax.DeflatedExplicitVRLittleEndian;
ds.InternalTransferSyntax = newSyntax;
Assert.Equal(newSyntax, ds.InternalTransferSyntax);
Assert.Equal(
newSyntax,
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).First().InternalTransferSyntax);
Assert.Equal(
newSyntax,
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).First().GetSequence(
DicomTag.ScheduledProtocolCodeSequence).Items[0].InternalTransferSyntax);
}
public void Constructor_FromDataset_SequenceItemsNotLinked()
{
var ds = new DicomDataset {
{ DicomTag.PatientID, "1" }
};
var sps = new DicomDataset {
{ DicomTag.ScheduledStationName, "1" }
};
var spcs = new DicomDataset {
{ DicomTag.ContextIdentifier, "1" }
};
sps.Add(new DicomSequence(DicomTag.ScheduledProtocolCodeSequence, spcs));
ds.Add(new DicomSequence(DicomTag.ScheduledProcedureStepSequence, sps));
var ds2 = new DicomDataset(ds);
ds2.AddOrUpdate(DicomTag.PatientID, "2");
ds2.GetSequence(DicomTag.ScheduledProcedureStepSequence).Items[0].AddOrUpdate(DicomTag.ScheduledStationName, "2");
ds2.GetSequence(DicomTag.ScheduledProcedureStepSequence).Items[0].GetSequence(
DicomTag.ScheduledProtocolCodeSequence).Items[0].AddOrUpdate(DicomTag.ContextIdentifier, "2");
Assert.Equal("1", ds.GetSingleValue <string>(DicomTag.PatientID));
Assert.Equal(
"1",
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).First().GetString(DicomTag.ScheduledStationName));
Assert.Equal(
"1",
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).First().GetSequence(
DicomTag.ScheduledProtocolCodeSequence).First().GetString(DicomTag.ContextIdentifier));
}
public void Constructor_FromDataset_DataReproduced()
{
var ds = new DicomDataset {
{ DicomTag.PatientID, "1" }
};
var sps1 = new DicomDataset {
{ DicomTag.ScheduledStationName, "1" }
};
var sps2 = new DicomDataset {
{ DicomTag.ScheduledStationName, "2" }
};
var spcs1 = new DicomDataset {
{ DicomTag.ContextIdentifier, "1" }
};
var spcs2 = new DicomDataset {
{ DicomTag.ContextIdentifier, "2" }
};
var spcs3 = new DicomDataset {
{ DicomTag.ContextIdentifier, "3" }
};
sps1.Add(new DicomSequence(DicomTag.ScheduledProtocolCodeSequence, spcs1, spcs2));
sps2.Add(new DicomSequence(DicomTag.ScheduledProtocolCodeSequence, spcs3));
ds.Add(new DicomSequence(DicomTag.ScheduledProcedureStepSequence, sps1, sps2));
Assert.Equal("1", ds.GetString(DicomTag.PatientID));
Assert.Equal(
"1",
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).First().GetString(DicomTag.ScheduledStationName));
Assert.Equal(
"2",
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).Items[1].GetString(DicomTag.ScheduledStationName));
Assert.Equal(
"1",
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).First().GetSequence(
DicomTag.ScheduledProtocolCodeSequence).First().GetString(DicomTag.ContextIdentifier));
Assert.Equal(
"2",
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).First().GetSequence(
DicomTag.ScheduledProtocolCodeSequence).Items[1].GetString(DicomTag.ContextIdentifier));
Assert.Equal(
"3",
ds.GetSequence(DicomTag.ScheduledProcedureStepSequence).Items[1].GetSequence(
DicomTag.ScheduledProtocolCodeSequence).First().GetString(DicomTag.ContextIdentifier));
}
public static List <double[, ]> FindROI(Dicom.DicomDataset structFile, string containsName, bool closeContours, bool removeIslands) //Change from void after!!!
{
//First make an array that will hold potential indices. Make it size 10 for redundancy
int[] indices = new int[10];
//Now make a dictionary to hold all potential organ names, and their index in the structFile.
Dictionary <string, int> organList = new Dictionary <string, int>();
//Now loop through all organs to check for matches and add to dictionary organList.
var structureSet = structFile.GetSequence(DicomTag.StructureSetROISequence).Items;
for (int count = 0; count < structureSet.Count; count++)
{
string organName = structureSet[count].GetString(DicomTag.ROIName);
if (organName.ToLower().Contains(containsName))
{
organList.Add(organName, count);
}
}
//Now ask the user which one they want.
Console.WriteLine("Please Select the desired ROI: \n");
Dictionary <string, int> .KeyCollection keys = organList.Keys; //Get the keys from the dictionary
int i = 1;
foreach (string key in keys)//write all options to the console
{
Console.WriteLine(i + ": {0}", key);
i++;
}
Console.Write("\n Enter a number: ");
string input = Console.ReadLine();
int inputNum;
while ((!Int32.TryParse(input, out inputNum)) || (inputNum > (i - 1)))
{
Console.WriteLine("Error: enter only the corresponding integer for the desired ROI.");
Console.Write("Enter a number: ");
input = Console.ReadLine();
}
//subtract 1 from inputNum to get correct index.
inputNum--;
ROIName = organList.ElementAt(inputNum).Key;
//Now the dictionary value for the key organSelection gives the correct ROI.
int organIndex = organList[ROIName];
var rawContours = structFile.GetSequence(DicomTag.ROIContourSequence).Items[organIndex].GetSequence(DicomTag.ContourSequence).Items; //This is the list of all 2d Contours for the organ.
//make a jagged array to hold all contours
//double[][] tempContours = new double[rawContours.Count][];
double[,] finalContours;
//Make a list which will hold the different contours.
List <double[, ]> contours = new List <double[, ]>();
//each element is an array holding the contour data for each contour of the specified organ
for (i = 0; i < rawContours.Count; i++)
{
//initialize size of array, then load in contour data.
double[] tempContours = rawContours[i].Get <double[]>(DicomTag.ContourData);
//Now convert from 1 column to 3 for x,y,z:
int row = 0;
finalContours = new double[tempContours.Length / 3, 3];
for (int j = 0; j < tempContours.Length; j++)
{
int column = j % 3;
finalContours[row, column] = tempContours[j];
if (column == 2)
{
row++;
}
}
contours.Add(finalContours);
}
if (closeContours == true) //close contours if true
{
contours = ContourFixing.ClosedLooper(contours);
}
if (removeIslands == true) //remove islands if true
{
contours = ContourFixing.IslandRemover(contours);
}
Console.WriteLine("Successfully retrieved contours.");
//convert back to a double array.
return(contours);
}
