Documentation/Nightly/Developers/SlicerExecutionModel/Programmatic Invocation

Goal

A large amount of functionality is available in command line modules for processing images and models. Some applications would like to use several modules together in a workflow or as a background processing task.

Implementation Example

This example shows calling the Model Maker (from the Editor). This example is in Tcl, but the same API can be used from C++ or Python. The idea is to query for the Model Maker module (and bail out if it is not loaded). Then to create a MRMLNode with the parameters you want for the model maker. These would be the same parameters you would set interactively. The model maker logic and gui classes are then told about the node and told to start processing. The processing then goes on in the background.

Note: check the command line module xml file for the to know the correct symbols and data types for parameters (see the <name> field for the correct parameter name string).

  #
  # create a model using the command line module
  # based on the current editor parameters
  #

  #
  # get the image data for the label layer
  #
  set sliceLogic [lindex [vtkSlicerSliceLogic ListInstances] 0]
  set layerLogic [$sliceLogic GetLabelLayer]
  set volumeNode [$layerLogic GetVolumeNode]
  if { $volumeNode == "" } {
    errorDialog "Cannot make model - no volume node for $layerLogic in $sliceLogic."
    return
  }

  #
  # find the Model Maker
  # - call Enter to be sure GUI has been built
  # - find the GUI - for non-tcl use, try vtkSlicerApplication::GetModuleGUIByName
  set modelMaker ""
  foreach gui [vtkCommandLineModuleGUI ListInstances] {
    if { [$gui GetGUIName] == "Model Maker" } {
      set modelMaker $gui
    }
  }

  if { $modelMaker == "" } {
    errorDialog "Cannot make model: no Model Maker Module found."
  }

  $modelMaker Enter

  #
  # set up the model maker node
  #
  set moduleNode [$::slicer3::MRMLScene CreateNodeByClass "vtkMRMLCommandLineModuleNode"]
  $::slicer3::MRMLScene AddNode $moduleNode
  $moduleNode SetModuleDescription "Model Maker"

  $moduleNode SetParameterAsString "Name" "Quick Model"
  $moduleNode SetParameterAsString "FilterType" "Sinc"
  $moduleNode SetParameterAsBool "GenerateAll" "0"
  $moduleNode SetParameterAsString "Labels" [EditorGetPaintLabel]
  $moduleNode SetParameterAsBool "JointSmooth" 1
  $moduleNode SetParameterAsBool "SplitNormals" 1
  $moduleNode SetParameterAsBool "PointNormals" 1
  $moduleNode SetParameterAsBool "SkipUnNamed" 1
  $moduleNode SetParameterAsInt "Start" -1
  $moduleNode SetParameterAsInt "End" -1
  if { [[$o(smooth) GetWidget] GetSelectedState] } {
    $moduleNode SetParameterAsDouble "Decimate" 0.25
    $moduleNode SetParameterAsDouble "Smooth" 10
  } else {
    $moduleNode SetParameterAsDouble "Decimate" 0
    $moduleNode SetParameterAsDouble "Smooth" 0
  }

  $moduleNode SetParameterAsString "InputVolume" [$volumeNode GetID]

  #
  # output 
  # - make a new hierarchy node if needed
  #
  set outHierarchy [[$::slicer3::MRMLScene GetNodesByClassByName "vtkMRMLModelHierarchyNode" "Editor Models"] GetItemAsObject 0]
  if { $outHierarchy == "" } {
    set outHierarchy [$::slicer3::MRMLScene CreateNodeByClass "vtkMRMLModelHierarchyNode"]
    $outHierarchy SetScene $::slicer3::MRMLScene
    $outHierarchy SetName "Editor Models"
    $::slicer3::MRMLScene AddNode $outHierarchy
  }

  $moduleNode SetParameterAsString "ModelSceneFile" [$outHierarchy GetID]



  # 
  # run the task (in the background)
  # - use the GUI to provide progress feedback
  # - use the GUI's Logic to invoke the task
  # - model will show up when the processing is finished
  #
  $modelMaker SetCommandLineModuleNode $moduleNode
  [$modelMaker GetLogic] SetCommandLineModuleNode $moduleNode
  [$modelMaker GetLogic] Apply $moduleNode

  $this statusText "Model Making Started..."

  #
  # clean up our references
  #
  $moduleNode Delete
  $outHierarchy Delete
  $modelMaker Enter

Module entry points

The Tcl example above assumes that the entry point of module description has been initialized with the correct target. For the shared object modules, description target specifies module entry point as a string. In case if such target has not been initialized properly (i.e., is set to "Unknown"), it has to be initialized manually. Otherwise, module execution will not happen (this can be concluded from the warning Module reports that it is a Shared Object Module but does not have a shared object module target, and the command line will begin with "Unknown" instead of "slicer:0x.....").

Here's how the module entry point can be properly initialized (refer to ProcessGUIEvents() in Modules/CommandLineModule/vtkCommandLineModuleGUI.cxx, Slicer3 trunk). NOTE: this has been tested for the C++ "Linear registration" module.

  ModuleDescription moduleDesc = moduleNode->GetModuleDescription();

  // Set up the temporary directory for the module (not sure why this is not done in Tcl example)
  moduleLogic->SetTemporaryDirectory(app->GetTemporaryDirectory());

  if(moduleDesc.GetTarget() == "Unknown"){

    // Entry point is unknown
    assert(moduleDesc.GetType() == "SharedObjectModule");
    typedef int (*ModuleEntryPoint)(int argc, char* argv[]);
    itksys::DynamicLoader::LibraryHandle lib =
      itksys::DynamicLoader::OpenLibrary(moduleDesc.GetLocation().c_str());

    if(lib){
      ModuleEntryPoint entryPoint =
        (ModuleEntryPoint) itksys::DynamicLoader::GetSymbolAddress(
          lib, "ModuleEntryPoint");
      if(entryPoint){
        char entryPointAsText[256];
        std::string entryPointAsString;
        sprintf(entryPointAsText, "%p", entryPoint);
        entryPointAsString = std::string("slicer:")+entryPointAsText;

        // Set target in the description
        moduleDesc.SetTarget(entryPointAsString);

        // Important: Update the description in the module node -- description is not a pointer!
        moduleNode->SetModuleDescription(moduleDesc);
      } else {
        std::cerr << "Failed to find entry point. Abort." << std::endl;
        abort();
      }
    } else {
      std::cerr << "Failed to locate module library. Abort." << std::endl;
      abort();
    }
  }

C++ example

Update the CMakeLists.txt to include

${CommandLineModule_SOURCE_DIR}
${CommandLineModule_BINARY_DIR}

The following code shows an example of executing Linear registration CLM from the C++ code. This was done in the context of ChangeTracker Slicer GUI module.

// Use LinearRegistration module to rigidly align input scans
void DoITKGlobalRegistration(vtkSlicerApplication *app){
  // Init some useful references
  vtkCommandLineModuleGUI *linearRegistrationGUI = NULL;
  vtkMRMLCommandLineModuleNode *linearRegistrationNode = NULL;
  vtkMRMLScene *scene = this->ChangeTrackerNode->GetScene();
  vtkMRMLChangeTrackerNode *ctNode = this->ChangeTrackerNode;
  vtkMRMLScalarVolumeNode *outputVolumeNode = NULL;
  vtkMRMLTransformNode *lrTransform = NULL;

  linearRegistrationGUI = static_cast<vtkCommandLineModuleGUI*>(app->GetModuleGUIByName("Linear registration"));
  if(!linearRegistrationGUI){
    std::cerr << "Cannot find LinearRegistration module. Aborting." << std::endl;
    abort();
  }

  linearRegistrationGUI->Enter();

  linearRegistrationNode = static_cast<vtkMRMLCommandLineModuleNode*>(scene->CreateNodeByClass("vtkMRMLCommandLineModuleNode"));
  if(!linearRegistrationNode){
    std::cerr << "Cannot create LinearRegistration node. Aborting." << std::endl;
    abort;
  }

  // Add node to the scene
  scene->AddNode(linearRegistrationNode);
  // This will actually search and find the initialized description for the node
  linearRegistrationNode->SetModuleDescription("Linear registration");

  // Create output volume node
  vtkMRMLScalarVolumeNode *scan1Node = static_cast<vtkMRMLScalarVolumeNode*>(scene->GetNodeByID(ctNode->GetScan1_Ref()));
  outputVolumeNode = this->CreateVolumeNode(scan1Node, "TG_scan2_Global");
  ctNode->SetScan2_GlobalRef(outputVolumeNode->GetID());

  linearRegistrationNode->SetParameterAsString("FixedImageFileName",
    ctNode->GetScan1_Ref());

  linearRegistrationNode->SetParameterAsString("MovingImageFileName",
    ctNode->GetScan2_Ref());

  linearRegistrationNode->SetParameterAsString("ResampledImageFileName",
    ctNode->GetScan2_GlobalRef());

  vtkCommandLineModuleLogic *moduleLogic = linearRegistrationGUI->GetLogic();

  linearRegistrationGUI->SetCommandLineModuleNode(linearRegistrationNode);
  linearRegistrationGUI->GetLogic()->SetCommandLineModuleNode(linearRegistrationNode);

  // Now check and initialize the module entry point, if necessary
  ModuleDescription moduleDesc =
    linearRegistrationNode->GetModuleDescription();
  moduleLogic->SetTemporaryDirectory(app->GetTemporaryDirectory());
  if(moduleDesc.GetTarget() == "Unknown"){
    // Entry point is unknown
    // "Linear registration" is shared object module, at least at this moment
    assert(moduleDesc.GetType() == "SharedObjectModule");
    typedef int (*ModuleEntryPoint)(int argc, char* argv[]);
    itksys::DynamicLoader::LibraryHandle lib =
      itksys::DynamicLoader::OpenLibrary(moduleDesc.GetLocation().c_str());
    if(lib){
      ModuleEntryPoint entryPoint =
        (ModuleEntryPoint) itksys::DynamicLoader::GetSymbolAddress(lib, "ModuleEntryPoint");

      if(entryPoint){
        char entryPointAsText[256];
        std::string entryPointAsString;

        sprintf(entryPointAsText, "%p", entryPoint);
        entryPointAsString = std::string("slicer:")+entryPointAsText;
        moduleDesc.SetTarget(entryPointAsString);
        linearRegistrationNode->SetModuleDescription(moduleDesc);
      } else {
        std::cerr << "Failed to find entry point for Linear registration. Abort." << std::endl;
        abort();
      }
    } else {
      std::cerr << "Failed to locate module library. Abort." << std::endl;
      abort();
    }
  }

  linearRegistrationGUI->GetLogic()->Apply(linearRegistrationNode);

  std::cout << "Linear registration module started..." << std::endl;

  linearRegistrationNode->Delete();

  // IMPORTANT: If you delete GUI object, as Tcl example above advices, Slicer will segfault at exit, 
  // since GUI objects of this kind are deleted in Slicer3.cxx, line 1986. I would say, don't do it.
  // linearRegistrationGUI->Delete();
}

Python Example

The following example calls the Substract Images command line module directly from Python (presented by Luca Antiga at the AHM 2009).

import Slicer
from Slicer import slicer
volume1 = slicer.MRMLScene.GetNodeByID(“vtkMRMLVolumeNode1”)
volume2 = slicer.MRMLScene.GetNodeByID(“vtkMRMLVolumeNode2”)
plugin = Slicer.Plugin(“Subtract Images”)
plugin.Execute(volume1.GetID(),volume2.GetID()

The next snippet calls the Grayscale Model Maker on a provided vtkMRMLScalarVolumeNode named outVolume and saves the generated gray scale model to a provided vtkMRMLModelNode named outGeometry.

import Slicer
from Slicer import slicer
# get or create the outVolume and outGeometry nodes
plugin = Slicer.Plugin("Grayscale Model Maker")
plugin.Execute(outVolume,outGeometry,threshold=10,smooth=15,decimate=0.25,splitnormals=True,pointnormals=True)

In both cases the called command line module will run hidden.