All Slicer modules succesfully compiled into BBTK boxes :P

[creaCLI.git] / bbtk_Slicer_PKG / src / bbSlicerDemonRegistrationBRAINS.h

diff --git a/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.h b/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.h
new file mode 100644 (file)
index 0000000..8482ead
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.h
@@ -0,0 +1,136 @@
+#ifndef __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+#define __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT DemonRegistrationBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( DemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( movingVolume , std::string );
+BBTK_DECLARE_INPUT ( fixedVolume , std::string );
+BBTK_DECLARE_INPUT ( inputPixelType , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldVolume , std::string );
+BBTK_DECLARE_INPUT ( outputPixelType , std::string );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( registrationFilterType , std::string );
+BBTK_DECLARE_INPUT ( smoothDisplacementFieldSigma , double );
+BBTK_DECLARE_INPUT ( numberOfPyramidLevels , int );
+BBTK_DECLARE_INPUT ( minimumFixedPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( minimumMovingPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( arrayOfPyramidLevelIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( histogramMatch , bool );
+BBTK_DECLARE_INPUT ( numberOfHistogramBins , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( medianFilterSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( initializeWithDisplacementField , std::string );
+BBTK_DECLARE_INPUT ( initializeWithTransform , std::string );
+BBTK_DECLARE_INPUT ( maskProcessingMode , std::string );
+BBTK_DECLARE_INPUT ( fixedBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( movingBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( lowerThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( upperThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( backgroundFillValue , int );
+BBTK_DECLARE_INPUT ( seedForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( neighborhoodForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldPrefix , std::string );
+BBTK_DECLARE_INPUT ( outputCheckerboardVolume , std::string );
+BBTK_DECLARE_INPUT ( checkerboardPatternSubdivisions , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputNormalized , bool );
+BBTK_DECLARE_INPUT ( outputDebug , bool );
+BBTK_DECLARE_INPUT ( gradientType , int );
+BBTK_DECLARE_INPUT ( smoothingUp , double );
+BBTK_DECLARE_INPUT ( maxStepLength , double );
+BBTK_DECLARE_INPUT ( turnOffDiffeomorph , bool );
+BBTK_DECLARE_INPUT ( UseDebugImageViewer , bool );
+BBTK_DECLARE_INPUT ( PromptAfterImageSend , bool );
+BBTK_DECLARE_INPUT ( numberOfBCHApproximationTerms , int );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( DemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "DemonRegistrationBRAINS" ) ;
+    BBTK_AUTHOR ( "This tool was developed by Hans J. Johnson and Greg Harris." ) ;
+    BBTK_DESCRIPTION ( "This program finds a deformation field to warp a moving image onto a fixed image.  The images must be of the same signal kind, and contain an image of the same kind of object.  This program uses the Thirion Demons warp software in ITK, the Insight Toolkit.  Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp." ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(DemonRegistrationBRAINS , movingVolume , "movingVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , fixedVolume , "fixedVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , inputPixelType , "inputPixelType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDisplacementFieldVolume , "outputDisplacementFieldVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputPixelType , "outputPixelType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , registrationFilterType , "registrationFilterType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , smoothDisplacementFieldSigma , "smoothDisplacementFieldSigma" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfPyramidLevels , "numberOfPyramidLevels" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , minimumFixedPyramid , "minimumFixedPyramid" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , minimumMovingPyramid , "minimumMovingPyramid" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , arrayOfPyramidLevelIterations , "arrayOfPyramidLevelIterations" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , histogramMatch , "histogramMatch" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfHistogramBins , "numberOfHistogramBins" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , medianFilterSize , "medianFilterSize" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , initializeWithDisplacementField , "initializeWithDisplacementField" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , initializeWithTransform , "initializeWithTransform" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , maskProcessingMode , "maskProcessingMode" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , fixedBinaryVolume , "fixedBinaryVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , movingBinaryVolume , "movingBinaryVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , lowerThresholdForBOBF , "lowerThresholdForBOBF" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , upperThresholdForBOBF , "upperThresholdForBOBF" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , backgroundFillValue , "backgroundFillValue" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , seedForBOBF , "seedForBOBF" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , neighborhoodForBOBF , "neighborhoodForBOBF" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDisplacementFieldPrefix , "outputDisplacementFieldPrefix" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputCheckerboardVolume , "outputCheckerboardVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , checkerboardPatternSubdivisions , "checkerboardPatternSubdivisions" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputNormalized , "outputNormalized" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDebug , "outputDebug" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , gradientType , "gradientType" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , smoothingUp , "smoothingUp" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , maxStepLength , "maxStepLength" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , turnOffDiffeomorph , "turnOffDiffeomorph" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , UseDebugImageViewer , "UseDebugImageViewer" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , PromptAfterImageSend , "PromptAfterImageSend" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfBCHApproximationTerms , "numberOfBCHApproximationTerms" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( DemonRegistrationBRAINS ) ;
+}
+
+#endif // __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+
+