static void Main(string[] args)
{
// connect to the grid
var engine = new VelocityEngine();
Action <bool> orThrow = result => OrThrow(result, engine);
//orThrow(engine.loginToGrid(USER, PASS, GRID_IP, GRID_PORT, GRID_DB));
orThrow(engine.loginToWorkstation(USER, PASS, WORKSTATION_PATH, true));
AppDomain.CurrentDomain.ProcessExit += (source, data) => { engine.logout(); };
orThrow(engine.loadPatientByPatientId(PATIENT_ID));
Console.WriteLine("Loaded patient: {0}", PATIENT_ID);
orThrow(engine.loadPrimaryVolumeByUID(PRIMARY_UID));
Console.WriteLine("Loaded primary volume: {0}", PRIMARY_UID);
orThrow(engine.loadSecondaryVolumeByUID(SECONDARY_UID));
Console.WriteLine("Loaded secondary volume: {0}", SECONDARY_UID);
// load registration
ValidOrThrow(engine.loadRegistrationByName(REG_NAME), engine);
Console.WriteLine("Loaded registration: {0}", REG_NAME);
var structure = engine.loadStructureByName(STRUCT_1, STRUCTSET_1UID);
ValidOrThrow(structure, engine);
Console.WriteLine("Loading existing structure: {0}", STRUCT_1);
var structNames = new StringList(new string[] { STRUCT_1 });
var structAlphaBetaRatio = new DoubleList(new double[] { 2, DEFAULT_ALPHABETA_TISSUE });
var structUIDs = new StringList(new string[] { structure.getInstanceUID() });
var vo = engine.getVolumeOperations();
OrThrow(vo.createBEDoseByStructureUIDs(25, structNames, structUIDs, structAlphaBetaRatio) != -1, vo);
Console.WriteLine("Biological Effective Dose created");
}
/**
* Convenience function to test loading a patient and listing the associated volume UIDS.
*/
static void loadAndListVolumes(VelocityEngine engine, string patientId)
{
if (!engine.loadPatientByPatientId(patientId).isValid())
{
Console.WriteLine("Could not load patient id {0}, error: {1}", patientId, engine.getErrorMessage());
}
else
{
var volumeIds = engine.getPatientVolumeUIDs(patientId);
Console.WriteLine("Patient id {0} has volume UIDs: {1}", patientId, String.Join(", ", volumeIds));
}
}
static void Main(string[] args)
{
// connect to the grid
var engine = new VelocityEngine();
Action <bool> orThrow = result => OrThrow(result, engine);
//orThrow(engine.loginToGrid(USER, PASS, GRID_IP, GRID_PORT, GRID_DB));
orThrow(engine.loginToWorkstation(USER, PASS, WORKSTATION_PATH, true));
AppDomain.CurrentDomain.ProcessExit += (source, data) => { engine.logout(); };
ValidOrThrow(engine.loadPatientByPatientId(PATIENT_ID), engine);
Console.WriteLine("Loaded patient: {0}", PATIENT_ID);
ValidOrThrow(engine.loadPrimaryVolumeByUID(PRIMARY_UID), engine);
Console.WriteLine("Loaded primary volume: {0}", PRIMARY_UID);
ValidOrThrow(engine.loadSecondaryVolumeByUID(SECONDARY_UID), engine);
Console.WriteLine("Loaded secondary volume: {0}", SECONDARY_UID);
// load registration
ValidOrThrow(engine.loadRegistrationByName(REG_NAME), engine);
Console.WriteLine("Loaded registration: {0}", REG_NAME);
var structure = engine.loadStructureByName(STRUCT_1, STRUCTSET_1UID);
ValidOrThrow(structure, engine);
Console.WriteLine("Loading existing structure: {0}", STRUCT_1);
var bedStructure = new BedStructureVariables();
bedStructure.structureId = structure.getVelocityId();
bedStructure.alphaBetaRatio = 2;
bedStructure.structureName = structure.getName();
var calculationData = new BedDoseCalculationData();
calculationData.bedVariablesByStructure = new BedStructureVariablesList(new BedStructureVariables[] { bedStructure });
calculationData.fractions = 25;
var backgroundData = new BedBackgroundData();
backgroundData.alphaBetaRatio = DEFAULT_ALPHABETA_TISSUE;
var vo = engine.getVolumeOperations();
OrThrow(vo.createBEDose(calculationData, backgroundData, false) != -1, vo);
Console.WriteLine("Biological Effective Dose created");
}
static void Main(string[] args)
{
// connect to the grid
var engine = new VelocityEngine();
Action <bool> orThrow = result => OrThrow(result, engine);
//orThrow(engine.loginToGrid(USER, PASS, GRID_IP, GRID_PORT, GRID_DB));
orThrow(engine.loginToWorkstation(USER, PASS, WORKSTATION_PATH, true));
AppDomain.CurrentDomain.ProcessExit += (source, data) => { engine.logout(); };
orThrow(engine.loadPatientByPatientId(PATIENT_ID));
Console.WriteLine("Loaded patient: {0}", PATIENT_ID);
orThrow(engine.loadPrimaryVolumeByUID(PRIMARY_UID));
Console.WriteLine("Loaded primary volume: {0}", PRIMARY_UID);
orThrow(engine.loadSecondaryVolumeByUID(SECONDARY_UID));
Console.WriteLine("Loaded secondary volume: {0}", SECONDARY_UID);
// create registration
var regOps = engine.getRegistrationOperations();
Console.WriteLine("Creating registration object: {0}", REG_NAME);
var registration = regOps.createNewRegistration(REG_NAME);
ValidOrThrow(registration, regOps);
ValidOrThrow(engine.loadRegistration(registration.getVelocityId()), engine);
// first move the head into the right general area
var manualSettings = new ManualRegistrationSettingsStructure();
manualSettings.registrationMatrix = new MatrixR44d(1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, -0.308194699, -0.38874362499, -0.583499961, 1.0);
orThrow(regOps.performManualAlignment(manualSettings));
Console.WriteLine("Running rigid registration ...");
var rigidSettings = new RigidRegistrationSettingsStructure();
rigidSettings.roiStart[0] = -0.102021;
rigidSettings.roiStart[1] = -0.1362766;
rigidSettings.roiStart[2] = -0.55900709;
rigidSettings.roiEnd[0] = 0.100532;
rigidSettings.roiEnd[1] = 0.19934;
rigidSettings.roiEnd[2] = -0.254681;
rigidSettings.primaryStartLevel = 15084.0;
rigidSettings.primaryEndLevel = 20035.0;
rigidSettings.secondaryStartLevel = 16361.0;
rigidSettings.secondaryEndLevel = 22731.0;
rigidSettings.preprocessingMethod = PreprocessingFilterMethod.NoFilter;
rigidSettings.performInitialAutoAlignment = true;
rigidSettings.disableRotationsX = false;
rigidSettings.disableRotationsY = false;
rigidSettings.disableRotationsZ = false;
rigidSettings.maximumNumberOfIterations = 45;
rigidSettings.minimumStepLength = 0.0001;
rigidSettings.maximumStepLength = 17.0;
rigidSettings.samplesDenominator = 10;
rigidSettings.numberOfHistogramBins = 25;
orThrow(regOps.performRigidRegistration(rigidSettings));
Console.WriteLine("done");
// perform a deformable registration in the same area
Console.WriteLine("Performing deformable registration...");
var bsplineSettings = new BSplineDeformableRegistrationSettingsStructure();
bsplineSettings.roiStart[0] = -0.102021;
bsplineSettings.roiStart[1] = -0.1362766;
bsplineSettings.roiStart[2] = -0.55900709;
bsplineSettings.roiEnd[0] = 0.100532;
bsplineSettings.roiEnd[1] = 0.19934;
bsplineSettings.roiEnd[2] = -0.254681;
bsplineSettings.primaryStartLevel = 15084.0;
bsplineSettings.primaryEndLevel = 20035.0;
bsplineSettings.secondaryStartLevel = 16361.0;
bsplineSettings.secondaryEndLevel = 22731.0;
bsplineSettings.preprocessingMethod = PreprocessingFilterMethod.NoFilter;
bsplineSettings.numberOfMultiResolutionLevels = 3; // # so each List setting should be length 3
bsplineSettings.applyBoundaryContinuityConstraints = new BoolList(new bool[] { false, false, false });
bsplineSettings.applyTopologicalRegularizer = new BoolList(new bool[] { false, false, false });
var r3dZeroes = new VectorR3d(0.0);
bsplineSettings.topologicalRegularizerDistanceLimitingCoefficient = new VectorR3dList(new VectorR3d[] { r3dZeroes, r3dZeroes, r3dZeroes });
bsplineSettings.numberOfHistogramBins = new IntList(new int[] { 50, 50, 50 });
bsplineSettings.maximumNumberOfIterations = new IntList(new int[] { 30, 30, 30 });
bsplineSettings.maximumNumberOfConsecutiveOptimizerAttempts = new IntList(new int[] { 10, 10, 10 });
bsplineSettings.metricValuePercentageDifference = new DoubleList(new double[] { 0.0, 0.0, 0.0 });
bsplineSettings.minimumStepLength = new DoubleList(new double[] { 0.000001, 0.000001, 0.000001 });
bsplineSettings.maximumStepLength = new DoubleList(new double[] { 100.0, 100.0, 100.0 });
bsplineSettings.samplesDenominator = new IntList(new int[] { 5, 5, 5 });
bsplineSettings.relaxationFactor = new DoubleList(new double[] { 0.9, 0.9, 0.9 });
bsplineSettings.gradientMagnitudeTolerance = new DoubleList(Enumerable.Repeat(0.000000000000000000005, 3).ToArray());
bsplineSettings.gridCellSize = new VectorR3dList(new VectorR3d[] { new VectorR3d(5.0), new VectorR3d(10.0), new VectorR3d(15.0) });
bsplineSettings.gridCellSizeType = new CharList(new char[] { 'n', 'n', 'n' });
orThrow(regOps.performBsplineRegistration(bsplineSettings));
Console.WriteLine("done");
// save the changes
ValidOrThrow(regOps.saveRegistration(), regOps);
}
static void Main(string[] args)
{
// connect to the grid
var engine = new VelocityEngine();
Action <bool> orThrow = result => OrThrow(result, engine);
//orThrow(engine.loginToGrid(USER, PASS, GRID_IP, GRID_PORT, GRID_DB));
orThrow(engine.loginToWorkstation(USER, PASS, WORKSTATION_PATH, true));
AppDomain.CurrentDomain.ProcessExit += (source, data) => { engine.logout(); };
ValidOrThrow(engine.loadPatientByPatientId(PATIENT_ID), engine);
Console.WriteLine("Loaded patient: {0}", PATIENT_ID);
ValidOrThrow(engine.loadPrimaryVolumeByUID(PRIMARY_UID), engine);
Console.WriteLine("Loaded primary volume: {0}", PRIMARY_UID);
ValidOrThrow(engine.loadSecondaryVolumeByUID(SECONDARY_UID), engine);
Console.WriteLine("Loaded secondary volume: {0}", SECONDARY_UID);
ValidOrThrow(engine.loadRegistrationByName(DEFORMABLE_NAME), engine);
Console.WriteLine("Loaded registration: {0}", DEFORMABLE_NAME);
var rops = engine.getRegistrationOperations();
var sops = engine.getStructureOperations();
var primaryVolume = engine.getPrimaryVolume();
var secondaryVolume = engine.getSecondaryVolume();
// find an external structure
StructureSet primarySet = primaryVolume.getStructureSets().Where(ss => ss.getName() == "Original SIM").First();
Structure structure = primarySet.getStructures().Where(s => s.getName() == "Mandible").First();
Console.WriteLine("Using structure '{0}' from structure set '{1}'", structure.getName(), primarySet.getName());
// create a new structure set on the secondary volume
string targetSetName = DateTime.UtcNow.ToString("s", System.Globalization.CultureInfo.InvariantCulture).Substring(0, 16);
var targetSet = sops.createStructureSet(targetSetName, false);
ValidOrThrow(targetSet, sops);
// copy the external to the new structure set
Console.WriteLine("Copying structure to secondary...");
var structureIds = new IntList(new int[] { structure.getVelocityId() });
var newStructures = sops.copyStructuresToSecondary(structureIds, targetSet.getVelocityId());
// IMPORTANT: call save after finishing a set of modifications to a structure set
targetSet = sops.saveStructureSet(targetSet.getVelocityId());
OrThrow(newStructures.Count == 1, sops);
var newStructure = newStructures.First().Value;
Action metrics = delegate() {
var c = sops.conformality(structure.getVelocityId(), newStructure.getVelocityId());
Console.WriteLine("Conformality: {0}", c);
if (c < 0.0)
{
Console.WriteLine("Error: {0}", sops.getErrorMessage());
}
var mets = sops.surfaceDistanceMetrics(structure.getVelocityId(), newStructure.getVelocityId());
if (!mets.isValid)
{
Console.WriteLine("Error: {0}", sops.getErrorMessage());
}
else
{
Console.WriteLine("Metrics: Hausdorff={0}, min={1}, median={2}, mean={3}, stddev={4}",
mets.hausdorffDistance, mets.min, mets.median, mets.mean, mets.standardDeviation);
}
};
// show metrics on registration used for copying
metrics();
// now on an alternative registration
ValidOrThrow(engine.loadRegistrationByName(RIGID_NAME), engine);
Console.WriteLine("Loaded registration: {0}", RIGID_NAME);
metrics();
}
static void Main(string[] args)
{
const string USER = "******";
const string PASS = "******";
const string WORKSTATION_PATH = @"C:\Velocity\Databases\WKS414";
const string GRID_IP = "127.0.0.1";
const int GRID_PORT = 57000;
const string GRID_DB = "vscDatabase";
const string PATIENT_ID = "hyperarc";
// connect to db
var engine = new VelocityEngine();
Action <bool> orThrow = result => OrThrow(result, engine);
//orThrow(engine.loginToGrid(USER, PASS, GRID_IP, GRID_PORT, GRID_DB));
orThrow(engine.loginToWorkstation(USER, PASS, WORKSTATION_PATH, true));
AppDomain.CurrentDomain.ProcessExit += (source, data) => { engine.logout(); };
var volOps = engine.getVolumeOperations();
var patient = engine.loadPatientByPatientId(PATIENT_ID);
ValidOrThrow(patient, engine);
Console.WriteLine("Loaded patient: {0}", PATIENT_ID);
//sort CTs ascending by AcquisitionDate
var cts = patient.getVolumes("CT").OrderBy(o => o.getAcquisitionDate());
var doses = patient.getVolumes("RTDOSE");
// find all CT-DS in the same frame of reference
//if multiple DS for same CT pick first one that has a plan
var ctDosePair = new Dictionary <Volume, Volume>();
Console.WriteLine("Finding CT-DS pairs to be resampled");
foreach (Volume ct in cts)
{
var plans = ct.getLinkedPlans().ToList();
foreach (Volume d in doses)
{
if (d.getName() == "auto resampled" || d.getName() == "SUM RTDOSE")
{
continue;
}
if (ct.getFrameOfReferenceUID() == d.getFrameOfReferenceUID())
{
ctDosePair[ct] = d;
bool hasPlan = plans.Exists(p => p.getInstanceUID() == d.getPlanUID());
if (hasPlan)
{
break;
}
}
}
}
//resample doses onto the most recent CT
Console.WriteLine("Resampling DS onto most recent CT");
var primaryCT = cts.Last(); // most recent by Acq Date
var resampledDoses = new IntList(); // holds the ids of all doses to be summed
var primaryDoseId = -1;
foreach (Volume ct in ctDosePair.Keys)
{
var dose = ctDosePair[ct];
if (ct.getVelocityId() != primaryCT.getVelocityId())
{
//need to load CT-DS to activate/create DICOM registration needed for chain
ValidOrThrow(engine.loadPrimaryVolume(ct.getVelocityId()), engine);
Console.WriteLine("Loaded CT {0} as primary", ct.getName());
ValidOrThrow(engine.loadSecondaryVolume(dose.getVelocityId()), engine);
Console.WriteLine("Loaded dose {0} as secondary", dose.getName());
var dicomReg = engine.loadRegistrationByName("DICOM");
ValidOrThrow(dicomReg, engine);
// make new reg for resampling between primary CT and secondary CT
var ct2ctReg = makeAutoReg(engine, primaryCT, ct, "resample_reg");
//now load primary CT and dose, load chain reg and resample onto primary CT
ValidOrThrow(engine.loadPrimaryVolume(primaryCT.getVelocityId()), engine);
Console.WriteLine("Loaded CT {0} as primary volume", primaryCT.getName());
ValidOrThrow(engine.loadSecondaryVolume(dose.getVelocityId()), engine);
Console.WriteLine("Loaded Dose id {0} as secondary volume", dose.getName());
//load registration resample_reg + DICOM
orThrow(engine.loadChainRegistration(ct2ctReg.getVelocityId(), dicomReg.getVelocityId()));
Console.WriteLine("Loaded registration resample_reg + DICOM");
Console.WriteLine("Creating resampled dose...");
var id = volOps.createResampledVolume(VolumeResampleOperation.VolumeResampleReplace, "auto resampled");
if (id == -1)
{
Console.WriteLine("Error creating resampled dose {0}", volOps.getErrorMessage());
continue;
}
Console.WriteLine("Resampled dose created with id {0}", (id));
resampledDoses.Add(id);
}
else
{
//this dose does not require resample, same FOR as primary CT
primaryDoseId = dose.getVelocityId();
resampledDoses.Add(primaryDoseId);
}
}
Console.WriteLine("Summing {0} dose volumes ...", resampledDoses.Count());
ValidOrThrow(engine.loadPrimaryVolume(primaryDoseId), engine);
//load primary dose as anchor
Console.WriteLine("Loaded DS id {0} as primary volume", primaryDoseId);
int sumId = volOps.createResampledVolumeAggregate(VolumeResampleOperation.VolumeResampleAdd, resampledDoses, (int)ResampleFlags.Flags.AllowNone); // sum
if (sumId == -1)
{
Console.WriteLine("Error creating sum dose {0}", volOps.getErrorMessage());
}
else
{
Console.WriteLine("Sum dose created with id {0}", sumId);
}
}