Documentation/Nightly/Developers/SlicerExecutionModel/Programmatic Invocation - Revision history

Lasso: Updated example that calls CLI from C++

2019-08-06T15:03:48Z

Updated example that calls CLI from C++

Lasso: moved Slicer3:Execution Model Documentation:Programmatic Invocation to Documentation/Nightly/Developers/SlicerExecutionModel/Programmatic Invocation: Slicer3 documentation is not maintained anymore and it is not clear for readers if the conten

2015-06-16T21:34:08Z

moved Slicer3:Execution Model Documentation:Programmatic Invocation to Documentation/Nightly/Developers/SlicerExecutionModel/Programmatic Invocation: Slicer3 documentation is not maintained anymore and it is not clear for readers if the conten

Haehn: /* Python Example */

2011-02-02T01:41:54Z

Python Example

Fedorov at 16:21, 28 April 2010

2010-04-28T16:21:52Z

Fedorov: /* Implementation Example */

2010-04-28T16:18:59Z

Implementation Example

Pieper: /* Implementation Example */

2010-03-29T13:42:19Z

Implementation Example

Haehn at 20:40, 23 March 2009

2009-03-23T20:40:33Z

Fedorov: /* C++ example */

2008-11-17T18:32:54Z

C++ example

Fedorov: /* Module entry points */

2008-11-14T21:09:16Z

Module entry points

Fedorov: /* Module entry points */

2008-11-14T21:09:00Z

Module entry points

@@ Line 129: / Line 129: @@
 </pre>
-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.
+The following code shows an example of creating model node from scalar volume node in C++, using Grayscale Model Maker module.
 <pre>
-// Use LinearRegistration module to rigidly align input scans
+// All data processing should be implemented in my module logic class. However,
-void DoITKGlobalRegistration(vtkSlicerApplication *app){
+// module logic classes cannot directly access other module logic classes. Therefore,
-  // Init some useful references
+// when my module logic is created in my module class, logic of all other modules that
-  vtkCommandLineModuleGUI *linearRegistrationGUI = NULL;
+// my module uses are retrieved and set in my module logic.
-   vtkMRMLCommandLineModuleNode *linearRegistrationNode = NULL;
+//-----------------------------------------------------------------------------
-   vtkMRMLScene *scene = this->ChangeTrackerNode->GetScene();
+vtkMRMLAbstractLogic* qSlicerMyModule::createLogic()
-   vtkMRMLChangeTrackerNode *ctNode = this->ChangeTrackerNode;
-   vtkMRMLScalarVolumeNode *outputVolumeNode = NULL;
+   vtkSlicerMyModuleLogic* moduleLogic = vtkSlicerMyModuleLogic::New();
-   vtkMRMLTransformNode *lrTransform = NULL;
+   qSlicerAbstractCoreModule* gsModelMakerModule = qSlicerCoreApplication::application()->moduleManager()->module("GrayscaleModelMaker");
-  linearRegistrationGUI = static_cast<vtkCommandLineModuleGUI*>(app->GetModuleGUIByName("Linear registration"));
+// This method implements the processing that it is available from the GUI or other modules
-  if(!linearRegistrationGUI){
+//-----------------------------------------------------------------------------
-    std::cerr << "Cannot find LinearRegistration module. Aborting." << std::endl;
+vtkMRMLModelNode* vtkSlicerMyModuleLogic::CreateModelByThresholding(vtkMRMLScalarVolumeNode* volumeNode, double threshold)
-    abort();
+  vtkMRMLScene *scene = this->GetMRMLScene();
-   linearRegistrationGUI->Enter();
+   // create output node
-   linearRegistrationNode = static_cast<vtkMRMLCommandLineModuleNode*>(scene->CreateNodeByClass("vtkMRMLCommandLineModuleNode"));
+   // create CLI module node and set parameters
-   if(!linearRegistrationNode){
+  vtkMRMLCommandLineModuleNode* cliNode = this->GrayscaleModelMakerLogic->CreateNodeInScene();
-    std::cerr << "Cannot create LinearRegistration node. Aborting." << std::endl;
+  cliNode->SetParameterAsNode("InputVolume", volumeNode);
-    abort;
+   cliNode->SetParameterAsNode("OutputGeometry", outputNode);
+  cliNode->SetParameterAsFloat("Threshold", threshold);
-   // Add node to the scene
+   // run processing (wait until it is completed)
-   scene->AddNode(linearRegistrationNode);
+   this->GrayscaleModelMakerLogic->ApplyAndWait(cliNode);
-   // Create output volume node
+   // clean up temporary node
-   vtkMRMLScalarVolumeNode *scan1Node = static_cast<vtkMRMLScalarVolumeNode*>(scene->GetNodeByID(ctNode->GetScan1_Ref()));
+   scene->RemoveNode(cliNode);
-   linearRegistrationNode->SetParameterAsString("FixedImageFileName",
+   return outputNode;
-    ctNode->GetScan1_Ref());
-  linearRegistrationNode->Delete();
+// Call the logic method from my module widget
+//-----------------------------------------------------------------------------
 </pre>
 == Python Example ==

@@ Line 196: / Line 196: @@
 import Slicer
 from Slicer import slicer
-volume1 = slicer.MRMLScene.GetNodeByID(“vtkMRMLVolumeNode1”)
+volume1 = slicer.MRMLScene.GetNodeByID(“vtkMRMLScalarVolumeNode1”)
-volume2 = slicer.MRMLScene.GetNodeByID(“vtkMRMLVolumeNode2”)
+volume2 = slicer.MRMLScene.GetNodeByID(“vtkMRMLScalarVolumeNode2”)
 plugin = Slicer.Plugin(“Subtract Images”)
-plugin.Execute(volume1.GetID(),volume2.GetID()
+plugin.Execute(volume1,volume2)
 </pre>

@@ Line 118: / Line 118: @@
    [$modelMaker GetLogic] Apply $moduleNode
    ...
 </pre>
@@ Line 224: / Line 178: @@
    linearRegistrationGUI->SetCommandLineModuleNode(linearRegistrationNode);
    linearRegistrationGUI->GetLogic()->SetCommandLineModuleNode(linearRegistrationNode);
    linearRegistrationGUI->GetLogic()->Apply(linearRegistrationNode);
@@ Line 264: / Line 185: @@
    linearRegistrationNode->Delete();
+}
 </pre>

← Older revision		Revision as of 16:18, 28 April 2010
Line 107:		Line 107:


		+	</pre>
		+
		+	When you are calling a shared object module, you need to add another call to initialize the pointer to the module entry point:
		+
		+	<pre>
		+	...
		+	$modelMaker SetCommandLineModuleNode $moduleNode
		+	[$modelMaker GetLogic] SetCommandLineModuleNode $moduleNode
		+	[$modelMaker GetLogic] LazyEvaluateModuleTarget $moduleNode
		+	[$modelMaker GetLogic] Apply $moduleNode
		+	...
	</pre>		</pre>

← Older revision		Revision as of 13:42, 29 March 2010
Line 6:		Line 6:

	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.		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).''

	<pre>		<pre>

← Older revision	Revision as of 21:34, 16 June 2015
(No difference)

← Older revision		Revision as of 20:40, 23 March 2009
Line 257:		Line 257:
	}		}
	</pre>		</pre>
		+
		+
		+	== Python Example ==
		+
		+	The following example calls the Substract Images command line module directly from Python (presented by Luca Antiga at the AHM 2009).
		+
		+	<pre>
		+	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()
		+	</pre>
		+
		+	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.
		+
		+	<pre>
		+	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)
		+	</pre>
		+
		+	In both cases the called command line module will run hidden.

@@ Line 252: / Line 252: @@
    linearRegistrationNode->Delete();
-   // I am not sure next line is necessary, since we have not created the GUI.
+   // IMPORTANT: If you delete GUI object, as Tcl example above advices, Slicer will segfault at exit,
-   // GUI is however deleted in the Tcl example above -- let the Slicer experts decide, what is right.
+   // since GUI objects of this kind are deleted in Slicer3.cxx, line 1986. I would say, don't do it.
    // linearRegistrationGUI->Delete();
+}
 </pre>

@@ Line 109: / Line 109: @@
 == Module entry points ==
-The Tcl example above assumes that the entry point of [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classModuleDescription.html 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:x.....").
+The Tcl example above assumes that the entry point of [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classModuleDescription.html 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.