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Segmentation: ORION3_Dendrites #11

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Segmentation: ORION3_Dendrites #11

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33 changes: 21 additions & 12 deletions lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@
*
* Refactor: ORION3_Dendrites
*/


#include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h"
#include "kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.h"

#include "kitchen-sink/01_Segmentation/dendrites_main/settingDefaultParameters.h"
#include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h"
#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.h"

/*
* Segmentation process which computes the distribution of the eigenvalues of
Expand All @@ -20,18 +20,27 @@ void orion_ORION3_Dendrites(orion_segmentation_param* param, ndarray3* vol) {
/* set the default parameters for the algorithm if none are set */
orion_settingDefaultParameters( param );

/*DEBUG*/orion_segmentation_param_dump( param );
/*[>DEBUG<]orion_segmentation_param_dump( param );*/

/*
* MAIN FUNCTION TO OBTAIN THE TRAINING SET OF BACKGROUND VOXELS
*
*/
/*
* STEP 1
* reading background samples using the Laplacian with the ISOTROPIC LOW
* PASS FILTER
/*********************************************************************/
/* MAIN FUNCTION TO OBTAIN THE TRAINING SET OF BACKGROUND VOXELS */
/* */
/* Run the code to compute the response to the discriminant function */
/*********************************************************************/

/* STEP 1
* ======
* reading background samples using the Laplacian with
* the **isotropic low pass filter**
*/
orion_readNegativeSamples(param, vol);

/* STEP 2
* ======
*
* Compute the feature vector
*/
vector_float* F = orion_getFeatures(param, vol);

WARN_UNIMPLEMENTED;
}
39 changes: 39 additions & 0 deletions lib/t/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
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Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
#include <stdlib.h>
#include <tap/basic.h>
#include <tap/float.h>

#include "kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.h"

#include "param/segmentation.h"
#include "io/format/mhd.h"

/*
% MATLAB

p.sigma = 2;
ORION3_Dendrites('test-data/DIADEM/NPF/NPF023', 'NPF023', p);

*/

int main(void) {
const float64 eps = 1;

plan(1);

/* read in the volume to process */
/*ndarray3* n = orion_read_mhd("test-data/DIADEM/NPF/NPF023/NPF023.mhd");*/
ndarray3* n = orion_read_mhd("test-data/ITK/HeadMRVolume/HeadMRVolume.mhd");

/* set up the parameters with sigma = 2 */
orion_segmentation_param* param = orion_segmentation_param_new();
array_add_float( param->scales, 2 );

orion_ORION3_Dendrites( param, n );


/* done */
orion_segmentation_param_free(param);
ndarray3_free(n);

return EXIT_SUCCESS;
}
1 change: 1 addition & 0 deletions make/test-rules.mk
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Expand Up @@ -2,6 +2,7 @@ ITK_MHD_TEST := $(BUILDTESTDIR)/integration/itk/mhd$(EXEEXT)
ITK_INTEGRATION_TESTS := \
$(BUILDTESTDIR)/integration/itk/itk$(EXEEXT) \
$(BUILDTESTDIR)/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeEigenvaluesGaussianFilter$(EXEEXT) \
$(BUILDTESTDIR)/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites$(EXEEXT) \
$(ITK_MHD_TEST)

$(ITK_INTEGRATION_TESTS): CPPFLAGS += $(ITK_CPPFLAGS)
Expand Down