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ENH: Apply treatment machine part color from JSON descriptor file
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Re SlicerRt#218
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@cpinter
cpinter committed Feb 11, 2023
1 parent ac9c57b commit 17d179c
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Showing 3 changed files with 120 additions and 137 deletions.
220 changes: 102 additions & 118 deletions RoomsEyeView/Logic/vtkSlicerRoomsEyeViewModuleLogic.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
#include <vtkTransform.h>
#include <vtkTransformFilter.h>
#include <vtkTransformPolyDataFilter.h>
#include <vtkVector.h>

// VTKSYS includes
#include <vtksys/SystemTools.hxx>
Expand Down Expand Up @@ -140,8 +141,7 @@ rapidjson::Value& vtkSlicerRoomsEyeViewModuleLogic::vtkInternal::GetTreatmentMac
rapidjson::Value& partsArray = partsIt->value;

// Traverse parts and try to find the element with the given part type
rapidjson::SizeType index = 0;
while (index < partsArray.Size())
for (rapidjson::SizeType index=0; index < partsArray.Size(); ++index)
{
rapidjson::Value& currentObject = partsArray[index];
if (currentObject.IsObject())
Expand All @@ -152,7 +152,6 @@ rapidjson::Value& vtkSlicerRoomsEyeViewModuleLogic::vtkInternal::GetTreatmentMac
return currentObject;
}
}
++index;
}

// Not found
Expand Down Expand Up @@ -488,7 +487,6 @@ void vtkSlicerRoomsEyeViewModuleLogic::LoadTreatmentMachine(vtkMRMLRoomsEyeViewN
std::string subjectHierarchyFolderName = machineType + std::string("_Components");
vtkIdType rootFolderItem = shNode->CreateFolderItem(shNode->GetSceneItemID(), subjectHierarchyFolderName);

//
// Load treatment machine models

// Collimator - mandatory
Expand Down Expand Up @@ -522,125 +520,93 @@ void vtkSlicerRoomsEyeViewModuleLogic::SetupTreatmentMachineModels(vtkMRMLRoomsE
return;
}

//TODO: Store treatment machine component color and other properties in JSON

// Display all pieces of the treatment room and sets each piece a color to provide realistic representation

// Collimator - mandatory
vtkMRMLModelNode* collimatorModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, Collimator);
if (!collimatorModel)
{
vtkErrorMacro("SetupTreatmentMachineModels: Unable to access collimator model");
return;
}
vtkMRMLLinearTransformNode* collimatorToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::Collimator, vtkSlicerIECTransformLogic::Gantry);
collimatorModel->SetAndObserveTransformNodeID(collimatorToGantryTransformNode->GetID());
collimatorModel->CreateDefaultDisplayNodes();
collimatorModel->GetDisplayNode()->SetColor(0.7, 0.7, 0.95);

// Gantry - mandatory
vtkMRMLModelNode* gantryModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, Gantry);
if (!gantryModel)
{
vtkErrorMacro("SetupTreatmentMachineModels: Unable to access gantry model");
return;
}
vtkMRMLLinearTransformNode* gantryToFixedReferenceTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::Gantry, vtkSlicerIECTransformLogic::FixedReference);
gantryModel->SetAndObserveTransformNodeID(gantryToFixedReferenceTransformNode->GetID());
gantryModel->CreateDefaultDisplayNodes();
gantryModel->GetDisplayNode()->SetColor(0.95, 0.95, 0.95);

// Patient support - mandatory
vtkMRMLModelNode* patientSupportModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, PatientSupport);
if (!patientSupportModel)
{
vtkErrorMacro("SetupTreatmentMachineModels: Unable to access patient support model");
return;
}
vtkMRMLLinearTransformNode* patientSupportToPatientSupportRotationTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::PatientSupport, vtkSlicerIECTransformLogic::PatientSupportRotation);
patientSupportModel->SetAndObserveTransformNodeID(patientSupportToPatientSupportRotationTransformNode->GetID());
patientSupportModel->CreateDefaultDisplayNodes();
patientSupportModel->GetDisplayNode()->SetColor(0.85, 0.85, 0.85);

// Table top - mandatory
vtkMRMLModelNode* tableTopModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, TableTop);
if (!tableTopModel)
{
vtkErrorMacro("SetupTreatmentMachineModels: Unable to access table top model");
return;
}
vtkMRMLLinearTransformNode* tableTopToTableTopEccentricRotationTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::TableTop, vtkSlicerIECTransformLogic::TableTopEccentricRotation);
tableTopModel->SetAndObserveTransformNodeID(tableTopToTableTopEccentricRotationTransformNode->GetID());
tableTopModel->CreateDefaultDisplayNodes();
tableTopModel->GetDisplayNode()->SetColor(0, 0, 0);

// Linac body - optional
vtkMRMLModelNode* linacBodyModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, Body);
if (linacBodyModel)
for (int partIdx=0; partIdx<LastPartType; ++partIdx)
{
vtkMRMLLinearTransformNode* fixedReferenceToRasTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::FixedReference, vtkSlicerIECTransformLogic::RAS);
linacBodyModel->SetAndObserveTransformNodeID(fixedReferenceToRasTransformNode->GetID());
linacBodyModel->CreateDefaultDisplayNodes();
linacBodyModel->GetDisplayNode()->SetColor(0.9, 0.9, 0.9);
}
std::string partType = this->GetTreatmentMachinePartTypeAsString((TreatmentMachinePartType)partIdx);
vtkMRMLModelNode* partModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, (TreatmentMachinePartType)partIdx);
if (!partModel)
{
switch (partIdx)
{
case Collimator: case Gantry: case PatientSupport: case TableTop:
vtkErrorMacro("SetupTreatmentMachineModels: Unable to access " << partType << " model");
}
continue;
}

// Imaging panel left - optional
vtkMRMLModelNode* leftImagingPanelModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, ImagingPanelLeft);
if (leftImagingPanelModel)
{
vtkMRMLLinearTransformNode* leftImagingPanelToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::LeftImagingPanel, vtkSlicerIECTransformLogic::Gantry);
leftImagingPanelModel->SetAndObserveTransformNodeID(leftImagingPanelToGantryTransformNode->GetID());
leftImagingPanelModel->CreateDefaultDisplayNodes();
leftImagingPanelModel->GetDisplayNode()->SetColor(0.95, 0.95, 0.95);
}
// Set color
vtkVector3d partColor(this->GetColorForPartType(partType));
partModel->CreateDefaultDisplayNodes();
partModel->GetDisplayNode()->SetColor((double)partColor[0] / 255.0, (double)partColor[1] / 255.0, (double)partColor[2] / 255.0);

// Imaging panel right - optional
vtkMRMLModelNode* rightImagingPanelModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, ImagingPanelRight);
if (rightImagingPanelModel)
{
vtkMRMLLinearTransformNode* rightImagingPanelToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::RightImagingPanel, vtkSlicerIECTransformLogic::Gantry);
rightImagingPanelModel->SetAndObserveTransformNodeID(rightImagingPanelToGantryTransformNode->GetID());
rightImagingPanelModel->CreateDefaultDisplayNodes();
rightImagingPanelModel->GetDisplayNode()->SetColor(0.95, 0.95, 0.95);
}

// Flat panel - optional
vtkMRMLModelNode* flatPanelModel = this->Internal->GetTreatmentMachinePartModelNode(parameterNode, FlatPanel);
if (flatPanelModel)
{
vtkMRMLLinearTransformNode* flatPanelToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::FlatPanel, vtkSlicerIECTransformLogic::Gantry);
flatPanelModel->SetAndObserveTransformNodeID(flatPanelToGantryTransformNode->GetID());
flatPanelModel->CreateDefaultDisplayNodes();
flatPanelModel->GetDisplayNode()->SetColor(0.95, 0.95, 0.95);
// Setup transforms and collision detection
if (partIdx == Collimator)
{
vtkMRMLLinearTransformNode* collimatorToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::Collimator, vtkSlicerIECTransformLogic::Gantry);
partModel->SetAndObserveTransformNodeID(collimatorToGantryTransformNode->GetID());
this->CollimatorTableTopCollisionDetection->SetInputData(0, partModel->GetPolyData());
// Patient model is set when calculating collisions, as it can be changed dynamically
this->CollimatorPatientCollisionDetection->SetInputData(0, partModel->GetPolyData());
}
else if (partIdx == Gantry)
{
vtkMRMLLinearTransformNode* gantryToFixedReferenceTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::Gantry, vtkSlicerIECTransformLogic::FixedReference);
partModel->SetAndObserveTransformNodeID(gantryToFixedReferenceTransformNode->GetID());
this->GantryTableTopCollisionDetection->SetInputData(0, partModel->GetPolyData());
this->GantryPatientSupportCollisionDetection->SetInputData(0, partModel->GetPolyData());
// Patient model is set when calculating collisions, as it can be changed dynamically
this->GantryPatientCollisionDetection->SetInputData(0, partModel->GetPolyData());
}
else if (partIdx == PatientSupport)
{
vtkMRMLLinearTransformNode* patientSupportToPatientSupportRotationTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::PatientSupport, vtkSlicerIECTransformLogic::PatientSupportRotation);
partModel->SetAndObserveTransformNodeID(patientSupportToPatientSupportRotationTransformNode->GetID());
this->GantryPatientSupportCollisionDetection->SetInputData(1, partModel->GetPolyData());
}
else if (partIdx == TableTop)
{
vtkMRMLLinearTransformNode* tableTopToTableTopEccentricRotationTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::TableTop, vtkSlicerIECTransformLogic::TableTopEccentricRotation);
partModel->SetAndObserveTransformNodeID(tableTopToTableTopEccentricRotationTransformNode->GetID());
this->GantryTableTopCollisionDetection->SetInputData(1, partModel->GetPolyData());
this->CollimatorTableTopCollisionDetection->SetInputData(1, partModel->GetPolyData());
}
else if (partIdx == Body)
{
vtkMRMLLinearTransformNode* fixedReferenceToRasTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::FixedReference, vtkSlicerIECTransformLogic::RAS);
partModel->SetAndObserveTransformNodeID(fixedReferenceToRasTransformNode->GetID());
}
else if (partIdx == ImagingPanelLeft)
{
vtkMRMLLinearTransformNode* leftImagingPanelToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::LeftImagingPanel, vtkSlicerIECTransformLogic::Gantry);
partModel->SetAndObserveTransformNodeID(leftImagingPanelToGantryTransformNode->GetID());
}
else if (partIdx == ImagingPanelRight)
{
vtkMRMLLinearTransformNode* rightImagingPanelToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::RightImagingPanel, vtkSlicerIECTransformLogic::Gantry);
partModel->SetAndObserveTransformNodeID(rightImagingPanelToGantryTransformNode->GetID());
}
else if (partIdx == FlatPanel)
{
vtkMRMLLinearTransformNode* flatPanelToGantryTransformNode =
this->IECLogic->GetTransformNodeBetween(vtkSlicerIECTransformLogic::FlatPanel, vtkSlicerIECTransformLogic::Gantry);
partModel->SetAndObserveTransformNodeID(flatPanelToGantryTransformNode->GetID());
}
//TODO: ApplicatorHolder, ElectronApplicator?
}

//
// Set up collision detection between components
this->GantryTableTopCollisionDetection->SetInputData(0, gantryModel->GetPolyData());
this->GantryTableTopCollisionDetection->SetInputData(1, tableTopModel->GetPolyData());

this->GantryPatientSupportCollisionDetection->SetInputData(0, gantryModel->GetPolyData());
this->GantryPatientSupportCollisionDetection->SetInputData(1, patientSupportModel->GetPolyData());

this->CollimatorTableTopCollisionDetection->SetInputData(0, collimatorModel->GetPolyData());
this->CollimatorTableTopCollisionDetection->SetInputData(1, tableTopModel->GetPolyData());

//TODO: Whole patient (segmentation, CT) will need to be transformed when the table top is transformed
//vtkMRMLLinearTransformNode* patientModelTransforms = vtkMRMLLinearTransformNode::SafeDownCast(
// this->GetMRMLScene()->GetFirstNodeByName("TableTopEccentricRotationToPatientSupportTransform"));
//patientModel->SetAndObserveTransformNodeID(patientModelTransforms->GetID());
//TODO: Instead of this make the tableTop the fixed part in RAS

// Patient model is set when calculating collisions, as it can be changed dynamically
this->GantryPatientCollisionDetection->SetInputData(0, gantryModel->GetPolyData());
this->CollimatorPatientCollisionDetection->SetInputData(0, collimatorModel->GetPolyData());
// Set identity transform for patient (parent transform is taken into account when getting poly data from segmentation)
vtkNew<vtkTransform> identityTransform;
identityTransform->Identity();
Expand All @@ -657,6 +623,9 @@ void vtkSlicerRoomsEyeViewModuleLogic::LoadBasicCollimatorMountedDevices()
return;
}
//TODO:
//
// Create a JSON file for this just as if it would be a treatment machine and use the same functions as for those.
//
/*
std::string moduleShareDirectory = this->GetModuleShareDirectory();
std::string additionalDevicesDirectory = moduleShareDirectory + "/" + "AdditionalTreatmentModels";
Expand Down Expand Up @@ -1468,7 +1437,7 @@ std::string vtkSlicerRoomsEyeViewModuleLogic::CheckForCollisions(vtkMRMLRoomsEye
const char* vtkSlicerRoomsEyeViewModuleLogic::GetTreatmentMachinePartTypeAsString(TreatmentMachinePartType type)
{
switch (type)
{
{
case Collimator: return "Collimator";
case Gantry: return "Gantry";
case PatientSupport: return "PatientSupport";
Expand All @@ -1482,7 +1451,7 @@ const char* vtkSlicerRoomsEyeViewModuleLogic::GetTreatmentMachinePartTypeAsStrin
default:
// invalid type
return "";
}
}
}

//---------------------------------------------------------------------------
Expand Down Expand Up @@ -1533,10 +1502,25 @@ bool vtkSlicerRoomsEyeViewModuleLogic::GetFileToPartTransformMatrixPartType(std:
}

//---------------------------------------------------------------------------
int* vtkSlicerRoomsEyeViewModuleLogic::GetColorForPartType(std::string partType)
vtkVector3d vtkSlicerRoomsEyeViewModuleLogic::GetColorForPartType(std::string partType)
{
//TODO:
return nullptr;
rapidjson::Value& partObject = this->Internal->GetTreatmentMachinePart(partType);
if (partObject.IsNull())
{
// The part may not have been included in the description
return vtkVector3d(255, 255, 255);
}

rapidjson::Value& colorArray = partObject["Color"];
if (!colorArray.IsArray() || colorArray.Size() != 3 || !colorArray[0].IsInt())
{
vtkErrorMacro("GetFilePathForPartType: Invalid treatment machine color for part " << partType);
return vtkVector3d(255, 255, 255);
}

return vtkVector3d( (unsigned char)colorArray[0].GetInt(),
(unsigned char)colorArray[1].GetInt(),
(unsigned char)colorArray[2].GetInt() );
}

//---------------------------------------------------------------------------
Expand Down
9 changes: 4 additions & 5 deletions RoomsEyeView/Logic/vtkSlicerRoomsEyeViewModuleLogic.h
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ Ontario with funds provided by the Ontario Ministry of Health and Long-Term Care
class vtkCollisionDetectionFilter;
class vtkMatrix4x4;
class vtkPolyData;
class vtkVector3d;

class vtkMRMLRoomsEyeViewNode;
class vtkMRMLModelNode;
Expand All @@ -45,11 +46,10 @@ class VTK_SLICER_ROOMSEYEVIEW_LOGIC_EXPORT vtkSlicerRoomsEyeViewModuleLogic :
{
public:
/// Treatment machine part types
/// \sa LastComputationResult, GetLastComputationResult(),
/// GetLastComputationResultAsString()
/// \sa GetTreatmentMachinePartTypeAsString()
enum TreatmentMachinePartType
{
Collimator,
Collimator = 0,
Gantry,
PatientSupport,
TableTop,
Expand Down Expand Up @@ -133,7 +133,7 @@ class VTK_SLICER_ROOMSEYEVIEW_LOGIC_EXPORT vtkSlicerRoomsEyeViewModuleLogic :
/// \return Success flag
bool GetFileToPartTransformMatrixPartType(std::string partType, vtkMatrix4x4* fileToPartTransformMatrix);
/// Get part name for part type in the currently loaded treatment machine description
int* GetColorForPartType(std::string partType);
vtkVector3d GetColorForPartType(std::string partType);
/// Get part name for part type in the currently loaded treatment machine description
bool GetEnabledStateForPartType(std::string partType);

Expand Down Expand Up @@ -188,4 +188,3 @@ class VTK_SLICER_ROOMSEYEVIEW_LOGIC_EXPORT vtkSlicerRoomsEyeViewModuleLogic :
};

#endif

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