From a237f3e7b52f296eac314f7fa2a9df5a4d4cd687 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 5 Nov 2015 16:56:53 -0600
Subject: [PATCH 01/55] wip: orion_multiscaleLaplacianFilter: implement
 multiscale processing

TODO: fix the FFT to treat data for ifftn as conjugate symmetric. This
will fix the code for finding the maximum response.
---
 .../multiscaleLaplacianFilter.c               | 92 ++++++++++++++++---
 .../multiscaleLaplacianFilter.h               |  6 +-
 .../multiscaleLaplacianFilter.c               |  4 +-
 3 files changed, 86 insertions(+), 16 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index 9657a0c..cf19d92 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -7,6 +7,7 @@
 
 #include "util/util.h"
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.h"
+#include "ndarray/ndarray3_fft.h"
 
 
 #define ORION_LAPLACIAN_HDAF_APPROX_DEGREE 60
@@ -52,23 +53,59 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 	int n = ORION_LAPLACIAN_HDAF_APPROX_DEGREE;
 
 	/* Fourier transform the input image */
-	ndarray3* v_fft = ndarray3_fftn(input_volume);
+	ndarray3_complex* v_fft = ndarray3_fftn_r2c(input_volume);
+	/*[>DEBUG<]ndarray3_complex_printf(v_fft, "v", "%8.3f", "%8.3f");*/
+	/*[>REMOVE DEBUG<]{
+		ndarray3* back =
+			ndarray3_ifftn_c2r( v_fft );
+
+		complex double ss = 0;
+		float64 sss = 0;
+		float64 inf_norm = -INFINITY;
+		for( int i = 0; i < ndarray3_complex_elems(v_fft); i++ ) {
+			sss += input_volume->p[i];
+			ss += v_fft->p[i];
+
+			float64 d = fabs(input_volume->p[i]
+				- back->p[i]);
+			if( d > inf_norm ) {
+				[> find max <]
+				inf_norm = d;
+			}
+		}
+		printf("sss %f; sum = %g + %gi\n", sss, creal(ss), cimag(ss));
+		complex_pixel_type zz000 = ndarray3_complex_get(v_fft, 0,0,0);
+		printf("zz(0,0,0) %f + %fi\n",  creal(zz000), cimag(zz000));
+		complex_pixel_type zz111 = ndarray3_complex_get(v_fft, 1,1,1);
+		printf("zz(1,1,1) %f + %fi\n",  creal(zz111), cimag(zz111));
+		printf("norm_∞: %f\n", inf_norm);
+
 
+		ndarray3_free(back);
 
+	}*/
 	output->laplacian
-		= ndarray3_new_with_size_from_ndarray3(input_volume);
+		= ndarray3_complex_new(
+			input_volume->sz[0],
+			input_volume->sz[1],
+			input_volume->sz[2] );
 	output->max_response_at_scale_idx
 		= ndarray3_new_with_size_from_ndarray3(input_volume);
 
 	int nx = v_fft->sz[0], ny = v_fft->sz[1], nz = v_fft->sz[2];
 
 	/* used to hold the Laplacian for a given scale */
-	ndarray3* cur_scale_laplacian =
-		ndarray3_new_with_size_from_ndarray3(input_volume);
+	ndarray3_complex* cur_scale_laplacian =
+		ndarray3_complex_new(
+			input_volume->sz[0],
+			input_volume->sz[1],
+			input_volume->sz[2]
+		);
 
 	size_t lap_scale_len = array_length_float(laplacian_scales);
 	bool recorded_maximum_scale = false;
 	for( int lap_idx = 0; lap_idx < lap_scale_len; lap_idx++ ) {
+		/* compute the Laplacian for each scale */
 		float laplacian_scale_factor = array_get_float( laplacian_scales, lap_idx );
 
 		float64 norm_const = _orion_ConstantToNormalizeFilter(laplacian_scale_factor);
@@ -77,16 +114,24 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 
 
 		NDARRAY3_LOOP_OVER_START( filt, i,j,k) {
-			/* normalise the generated Laplacian filter */
+			/* normalise the generated Laplacian filter
+			 *
+			 *     filt /= norm_const;
+			 */
 			ndarray3_set(filt, i,j,k,
 				ndarray3_get(filt, i,j,k)
 				/ norm_const
 			);
 
 			/* Apply the filter to the input volume using pointwise
-			 * multiplication in the Fourier domain. */
-			ndarray3_set(cur_scale_laplacian, i,j,k,
-				  ndarray3_get(v_fft, i,j,k)
+			 * multiplication in the Fourier domain.
+			 *
+			 *     cur_scale_laplacian = v_fft .* filt;
+			 *
+			 * NOTE: This is a complex multiplied by a scalar.
+			 */
+			ndarray3_complex_set(cur_scale_laplacian, i,j,k,
+				  ndarray3_complex_get(v_fft, i,j,k)
 				* ndarray3_get(filt,         i,j,k)
 			);
 		} NDARRAY3_LOOP_OVER_END;
@@ -94,12 +139,12 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 		/* Now apply the inverse Fourier transform to bring the
 		 * filtered volume back to the spatial domain */
 		ndarray3* cur_scale_filt_vol =
-			ndarray3_ifftn_symmetric( cur_scale_laplacian );
+			ndarray3_ifftn_c2r( cur_scale_laplacian );
 
 		/* check for maximum response across all scales */
 		if( !recorded_maximum_scale ) {
 			NDARRAY3_LOOP_OVER_START( cur_scale_laplacian, i,j,k) {
-				ndarray3_set( output->laplacian, i,j,k,
+				ndarray3_complex_set( output->laplacian, i,j,k,
 					ndarray3_get(cur_scale_laplacian, i,j,k)
 				    );
 				ndarray3_set( output->max_response_at_scale_idx, i,j,k,
@@ -110,13 +155,34 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 			recorded_maximum_scale = true;
 		} else {
 			if( p->multiscale ) {
-				WARN_UNIMPLEMENTED;
+				/* Multiscale approach */
+				NDARRAY3_LOOP_OVER_START( cur_scale_laplacian, i,j,k) {
+					complex_pixel_type* cur = &ndarray3_get(cur_scale_laplacian, i,j,k);
+					complex_pixel_type* lap = &ndarray3_get(output->laplacian, i,j,k);
+					if(   cabsf(*cur) >= cabsf(*lap) ) {
+						/* the current scale is recorded as the maximum at this point */
+						*lap = *cur;
+						ndarray3_set( output->scales, i,j,k,  lap_idx);
+					}
+				} NDARRAY3_LOOP_OVER_END;
 			} else {
-				WARN_UNIMPLEMENTED;
+				/* ISBI 2014 */
+				NDARRAY3_LOOP_OVER_START( cur_scale_laplacian, i,j,k) {
+					complex_pixel_type* cur = &ndarray3_get(cur_scale_laplacian, i,j,k);
+					complex_pixel_type* lap = &ndarray3_get(output->laplacian, i,j,k);
+					if( *cur > *lap ) {
+						*lap = *cur;
+					}
+				} NDARRAY3_LOOP_OVER_END;
 			}
 		}
+
+		ndarray3_free(cur_scale_filt_vol);
+		ndarray3_free(filt);
 	}
-	ndarray3_free(cur_scale_laplacian);
+
+	ndarray3_complex_free(cur_scale_laplacian);
+	ndarray3_complex_free(v_fft);
 
 	return output;
 }
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
index bab702b..dbf05d1 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
@@ -7,6 +7,7 @@
 
 /* local headers */
 #include "ndarray/ndarray3.h"
+#include "ndarray/ndarray3_complex.h"
 #include "container/array.h"
 #include "param/segmentation.h"
 
@@ -15,7 +16,7 @@ typedef struct {
 	/* each element contains the maximum response of the Laplacian over the
 	 * scales in `laplacian_scales`.
 	 */
-	ndarray3* laplacian;
+	ndarray3_complex* laplacian;
 
 	/* each element of scale_for_max_response contains the index of the
 	 * scale in `laplacian_scales` for which the response is maximised
@@ -33,6 +34,9 @@ extern orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 		array_float* laplacian_scales,
 		orion_segmentation_param* p );
 
+extern orion_multiscale_laplacian_output* orion_multiscale_laplacian_output_new();
+extern void orion_multiscale_laplacian_output_free(orion_multiscale_laplacian_output* r);
+
 #ifdef __cplusplus
 };
 #endif /* __cplusplus */
diff --git a/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index 79ec054..8ab6cbd 100644
--- a/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -37,8 +37,7 @@ int main(void) {
 		orion_segmentation_param_new();
 	orion_settingDefaultParameters(p);
 
-	ok(1, "stub for orion_multiscaleLaplacianFilter"); /* TODO stub: remove later */
-#if 0 /* stub */
+#if 1 /* stub */
 	orion_multiscale_laplacian_output* r =
 		orion_multiscaleLaplacianFilter( n, lap_scales, p );
 
@@ -46,6 +45,7 @@ int main(void) {
 	is_double(1199656.000000, ndarray3_sum_over_all_float64( r->laplacian ), eps, "sum of Laplacian response is as expected" );
 #endif
 
+	orion_multiscale_laplacian_output_free(r);
 	orion_segmentation_param_free(p);
 	array_free_float(lap_scales);
 	ndarray3_free(n);

From ac96bd841fe9fb83489df8c27017dc1de8f0caba Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 1 Jan 2016 23:08:52 -0600
Subject: [PATCH 02/55] add notes on the construction of the Laplacian in the
 Fourier domain

---
 .../multiscaleLaplacianFilter.c               | 44 ++++++++++---------
 .../multiscaleLaplacianFilter.h               |  6 ++-
 2 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index cf19d92..ca953e9 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -85,16 +85,15 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 
 	}*/
 	output->laplacian
-		= ndarray3_complex_new(
-			input_volume->sz[0],
-			input_volume->sz[1],
-			input_volume->sz[2] );
+		= ndarray3_new_with_size_from_ndarray3(input_volume);
 	output->max_response_at_scale_idx
 		= ndarray3_new_with_size_from_ndarray3(input_volume);
 
 	int nx = v_fft->sz[0], ny = v_fft->sz[1], nz = v_fft->sz[2];
 
-	/* used to hold the Laplacian for a given scale */
+	/* used to hold the Laplacian response in the Fourier domain for a
+	 * given scale
+	 */
 	ndarray3_complex* cur_scale_laplacian =
 		ndarray3_complex_new(
 			input_volume->sz[0],
@@ -137,15 +136,20 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 		} NDARRAY3_LOOP_OVER_END;
 
 		/* Now apply the inverse Fourier transform to bring the
-		 * filtered volume back to the spatial domain */
+		 * filtered volume back to the spatial domain.
+		 *
+		 * Again, note that the response is real because the input data
+		 * is real and we treat the data in `cur_scale_laplacian` after
+		 * applying the filter as conjugate symmetric.
+		 * */
 		ndarray3* cur_scale_filt_vol =
 			ndarray3_ifftn_c2r( cur_scale_laplacian );
 
 		/* check for maximum response across all scales */
 		if( !recorded_maximum_scale ) {
-			NDARRAY3_LOOP_OVER_START( cur_scale_laplacian, i,j,k) {
-				ndarray3_complex_set( output->laplacian, i,j,k,
-					ndarray3_get(cur_scale_laplacian, i,j,k)
+			NDARRAY3_LOOP_OVER_START( cur_scale_filt_vol, i,j,k) {
+				ndarray3_set( output->laplacian, i,j,k,
+					ndarray3_get(cur_scale_filt_vol, i,j,k)
 				    );
 				ndarray3_set( output->max_response_at_scale_idx, i,j,k,
 					lap_idx
@@ -156,22 +160,22 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 		} else {
 			if( p->multiscale ) {
 				/* Multiscale approach */
-				NDARRAY3_LOOP_OVER_START( cur_scale_laplacian, i,j,k) {
-					complex_pixel_type* cur = &ndarray3_get(cur_scale_laplacian, i,j,k);
-					complex_pixel_type* lap = &ndarray3_get(output->laplacian, i,j,k);
-					if(   cabsf(*cur) >= cabsf(*lap) ) {
+				NDARRAY3_LOOP_OVER_START( cur_scale_filt_vol, i,j,k) {
+					pixel_type cur = ndarray3_get(cur_scale_filt_vol, i,j,k);
+					pixel_type lap = ndarray3_get(output->laplacian, i,j,k);
+					if(   fabs(cur) >= fabs(lap) ) {
 						/* the current scale is recorded as the maximum at this point */
-						*lap = *cur;
-						ndarray3_set( output->scales, i,j,k,  lap_idx);
+						ndarray3_set(output->laplacian, i,j,k, lap);
+						ndarray3_set(output->max_response_at_scale_idx, i,j,k,  lap_idx);
 					}
 				} NDARRAY3_LOOP_OVER_END;
 			} else {
 				/* ISBI 2014 */
-				NDARRAY3_LOOP_OVER_START( cur_scale_laplacian, i,j,k) {
-					complex_pixel_type* cur = &ndarray3_get(cur_scale_laplacian, i,j,k);
-					complex_pixel_type* lap = &ndarray3_get(output->laplacian, i,j,k);
-					if( *cur > *lap ) {
-						*lap = *cur;
+				NDARRAY3_LOOP_OVER_START( cur_scale_filt_vol, i,j,k) {
+					pixel_type cur = ndarray3_get(cur_scale_filt_vol, i,j,k);
+					pixel_type lap = ndarray3_get(output->laplacian, i,j,k);
+					if( cur > lap ) {
+						ndarray3_set(output->laplacian, i,j,k, cur);
 					}
 				} NDARRAY3_LOOP_OVER_END;
 			}
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
index dbf05d1..873486e 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
@@ -15,8 +15,12 @@
 typedef struct {
 	/* each element contains the maximum response of the Laplacian over the
 	 * scales in `laplacian_scales`.
+	 *
+	 * The elements of this are not complex because we are operating on
+	 * only real-data and this means that the Fourier domain values are
+	 * conjugate symmetric.
 	 */
-	ndarray3_complex* laplacian;
+	ndarray3* laplacian;
 
 	/* each element of scale_for_max_response contains the index of the
 	 * scale in `laplacian_scales` for which the response is maximised

From 04664d4c99c5aa6343435a98c7770126dcf0048e Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 21 Jan 2016 12:41:08 -0600
Subject: [PATCH 03/55] WIP: stub out multiscale Laplacian filter

---
 .../DetectTrainingSet/multiscaleLaplacianFilter.c           | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index 8ab6cbd..42fdebd 100644
--- a/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/t/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -37,15 +37,17 @@ int main(void) {
 		orion_segmentation_param_new();
 	orion_settingDefaultParameters(p);
 
-#if 1 /* stub */
+#if 0 /* stub */
 	orion_multiscale_laplacian_output* r =
 		orion_multiscaleLaplacianFilter( n, lap_scales, p );
 
 	/* value take from MATLAB code above */
 	is_double(1199656.000000, ndarray3_sum_over_all_float64( r->laplacian ), eps, "sum of Laplacian response is as expected" );
-#endif
 
 	orion_multiscale_laplacian_output_free(r);
+#else
+	ok(1, "stubbed out");
+#endif
 	orion_segmentation_param_free(p);
 	array_free_float(lap_scales);
 	ndarray3_free(n);

From 9b5c7fa798b3c20e2af2bb175539c015bb55555f Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 18 Mar 2016 11:36:29 -0500
Subject: [PATCH 04/55] Rename volume parameter for orion_readNegativeSamples

---
 .../dendrites_main/DetectTrainingSet/readNegativeSamples.c      | 2 +-
 .../dendrites_main/DetectTrainingSet/readNegativeSamples.h      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
index 5861a7f..78da3b4 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
@@ -6,7 +6,7 @@
  */
 void orion_readNegativeSamples(
 		orion_segmentation_param* param,
-		ndarray3* input_volume ) {
+		ndarray3* vol ) {
 	WARN_UNIMPLEMENTED;
 
 	LOG_INFO("%s", "Detecting training set of background samples...");
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h
index 1a5b8fc..15f4fa0 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h
@@ -24,7 +24,7 @@ extern "C" {
 /* Function prototypes */
 extern void orion_readNegativeSamples(
 		orion_segmentation_param* param,
-		ndarray3* input_volume );
+		ndarray3* vol );
 
 #ifdef __cplusplus
 };

From cd7ace1edd041e983be1fa20dec954122ce3dfb9 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sun, 27 Mar 2016 23:10:40 -0500
Subject: [PATCH 05/55] Finalise the multiscale Laplacian filter

---
 .../multiscaleLaplacianFilter.c               | 41 ++++---------------
 1 file changed, 8 insertions(+), 33 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index ca953e9..22142e1 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -6,6 +6,7 @@
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h"
 
 #include "util/util.h"
+#include "simple-log/simplelog.h"
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.h"
 #include "ndarray/ndarray3_fft.h"
 
@@ -54,36 +55,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 
 	/* Fourier transform the input image */
 	ndarray3_complex* v_fft = ndarray3_fftn_r2c(input_volume);
-	/*[>DEBUG<]ndarray3_complex_printf(v_fft, "v", "%8.3f", "%8.3f");*/
-	/*[>REMOVE DEBUG<]{
-		ndarray3* back =
-			ndarray3_ifftn_c2r( v_fft );
-
-		complex double ss = 0;
-		float64 sss = 0;
-		float64 inf_norm = -INFINITY;
-		for( int i = 0; i < ndarray3_complex_elems(v_fft); i++ ) {
-			sss += input_volume->p[i];
-			ss += v_fft->p[i];
-
-			float64 d = fabs(input_volume->p[i]
-				- back->p[i]);
-			if( d > inf_norm ) {
-				[> find max <]
-				inf_norm = d;
-			}
-		}
-		printf("sss %f; sum = %g + %gi\n", sss, creal(ss), cimag(ss));
-		complex_pixel_type zz000 = ndarray3_complex_get(v_fft, 0,0,0);
-		printf("zz(0,0,0) %f + %fi\n",  creal(zz000), cimag(zz000));
-		complex_pixel_type zz111 = ndarray3_complex_get(v_fft, 1,1,1);
-		printf("zz(1,1,1) %f + %fi\n",  creal(zz111), cimag(zz111));
-		printf("norm_∞: %f\n", inf_norm);
-
 
-		ndarray3_free(back);
-
-	}*/
 	output->laplacian
 		= ndarray3_new_with_size_from_ndarray3(input_volume);
 	output->max_response_at_scale_idx
@@ -106,12 +78,12 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 	for( int lap_idx = 0; lap_idx < lap_scale_len; lap_idx++ ) {
 		/* compute the Laplacian for each scale */
 		float laplacian_scale_factor = array_get_float( laplacian_scales, lap_idx );
+		LOG_INFO("Computing Laplacian using scale: %f", laplacian_scale_factor);
 
 		float64 norm_const = _orion_ConstantToNormalizeFilter(laplacian_scale_factor);
 		ndarray3* filt = orion_Makefilter( nx,ny,nz,
 			n, laplacian_scale_factor, orion_Makefilter_FLAG_A);
 
-
 		NDARRAY3_LOOP_OVER_START( filt, i,j,k) {
 			/* normalise the generated Laplacian filter
 			 *
@@ -130,8 +102,8 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 			 * NOTE: This is a complex multiplied by a scalar.
 			 */
 			ndarray3_complex_set(cur_scale_laplacian, i,j,k,
-				  ndarray3_complex_get(v_fft, i,j,k)
-				* ndarray3_get(filt,         i,j,k)
+				  ndarray3_complex_get(v_fft,     i,j,k)
+				* ndarray3_get(filt,              i,j,k)
 			);
 		} NDARRAY3_LOOP_OVER_END;
 
@@ -162,7 +134,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 				/* Multiscale approach */
 				NDARRAY3_LOOP_OVER_START( cur_scale_filt_vol, i,j,k) {
 					pixel_type cur = ndarray3_get(cur_scale_filt_vol, i,j,k);
-					pixel_type lap = ndarray3_get(output->laplacian, i,j,k);
+					pixel_type lap = ndarray3_get(output->laplacian,  i,j,k);
 					if(   fabs(cur) >= fabs(lap) ) {
 						/* the current scale is recorded as the maximum at this point */
 						ndarray3_set(output->laplacian, i,j,k, lap);
@@ -171,6 +143,9 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 				} NDARRAY3_LOOP_OVER_END;
 			} else {
 				/* ISBI 2014 */
+				/* Check if the values themselves are larger
+				 * than the current maximum
+				 */
 				NDARRAY3_LOOP_OVER_START( cur_scale_filt_vol, i,j,k) {
 					pixel_type cur = ndarray3_get(cur_scale_filt_vol, i,j,k);
 					pixel_type lap = ndarray3_get(output->laplacian, i,j,k);

From 8d5c47283e6d56f26eefc4aec8f381c788d8a45a Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sun, 27 Mar 2016 23:45:04 -0500
Subject: [PATCH 06/55] Implement readNegativeSamples

---
 .../DetectTrainingSet/readNegativeSamples.c   | 23 ++++++++++++++++---
 .../DetectTrainingSet/readNegativeSamples.h   | 10 ++++----
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
index 78da3b4..8ba209e 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
@@ -4,11 +4,10 @@
  *
  * Refactor: readNegativeSamples
  */
-void orion_readNegativeSamples(
+orion_multiscale_laplacian_output*
+orion_readNegativeSamples(
 		orion_segmentation_param* param,
 		ndarray3* vol ) {
-	WARN_UNIMPLEMENTED;
-
 	LOG_INFO("%s", "Detecting training set of background samples...");
 
 	/*
@@ -17,4 +16,22 @@ void orion_readNegativeSamples(
 	 */
 	/*Lap = 0.5913./p.sigma;*/
 	/*Lap = 0.66./p.sigma;*/
+	/*%n=60;Lap = sqrt(2.0*n+1)./(sqrt(2)*(3.6853*p.sigma - 2.1676)*pi);*/
+	size_t n_scales = array_length_float( param->scales );
+	array_float* Lap =  array_new_float( n_scales );
+	for( size_t Lap_idx = 0; Lap_idx < n_scales; Lap_idx++ ) {
+		array_set_float( Lap, Lap_idx,
+			0.66 / array_get_float( param->scales, Lap_idx ) );
+	}
+
+	orion_multiscale_laplacian_output* lap_out = orion_multiscaleLaplacianFilter( vol, Lap, param );
+
+
+	/* Only the positive values are background voxels */
+	NDARRAY3_LOOP_OVER_START( lap_out->laplacian, i,j,k) {
+		ndarray3_set( lap_out->laplacian, i,j,k,
+			ndarray3_get( lap_out->laplacian, i,j,k) > 0 );
+	} NDARRAY3_LOOP_OVER_END;
+
+	return lap_out;
 }
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h
index 15f4fa0..d2b5048 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h
@@ -11,18 +11,16 @@
 #include "ndarray/ndarray3.h"
 #include "simple-log/simplelog.h"
 
-/* structs, enums */
-typedef struct {
-	bool multiscale;
-	vector_float spacing;
-} orion_readNegativeSamples_param;
+#include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h"
 
 #ifdef __cplusplus
 extern "C" {
 #endif /* __cplusplus */
 
 /* Function prototypes */
-extern void orion_readNegativeSamples(
+extern
+orion_multiscale_laplacian_output*
+orion_readNegativeSamples(
 		orion_segmentation_param* param,
 		ndarray3* vol );
 

From 9a7402765ce40362f0fef7473b704bfd806099b3 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 28 Mar 2016 12:05:16 -0500
Subject: [PATCH 07/55] Add comment about getFeatures function

---
 .../dendrites_main/ExtractFeatures/getFeatures.c               | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c
index cc4fab3..6b15699 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c
@@ -1,4 +1,5 @@
-/* TODO
+/*
+ * Get the Eigenvalues of the Hessian matrix as features.
  *
  * Refactor: getFeatures
  */

From 7df94714d3b37076465a83911e7e4131ee7c3367 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 28 Mar 2016 15:23:44 -0500
Subject: [PATCH 08/55] Remove TODO

---
 .../ExtractFeatures/computeEigenvaluesGaussianFilter.c         | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeEigenvaluesGaussianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeEigenvaluesGaussianFilter.c
index 954a1ec..0f609ac 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeEigenvaluesGaussianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeEigenvaluesGaussianFilter.c
@@ -28,8 +28,7 @@ array_orion_eig_feat_result* orion_computeEigenvaluesGaussianFilter(
 		die("Please refactor and remove use of apply_log as it is orthogonal to the eigenvalue filtering ( apply_log == %c )", apply_log);
 	}
 
-	/* TODO loop over all scales */
-
+	/* loop over all scales */
 	size_t n_scales = array_length_float(scales);
 	array_orion_eig_feat_result* all_results = array_new_orion_eig_feat_result(n_scales);
 	for( size_t scale_idx = 0; scale_idx < n_scales; scale_idx++ ) {

From 55f3491c06d454b0cabd891631ee9025c80abe10 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 11:53:03 -0500
Subject: [PATCH 09/55] Add notes about the contents of the Laplacian response

---
 .../DetectTrainingSet/multiscaleLaplacianFilter.c           | 2 +-
 .../DetectTrainingSet/multiscaleLaplacianFilter.h           | 3 +++
 .../dendrites_main/DetectTrainingSet/readNegativeSamples.c  | 6 +++++-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index 22142e1..6ee840d 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -75,7 +75,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 
 	size_t lap_scale_len = array_length_float(laplacian_scales);
 	bool recorded_maximum_scale = false;
-	for( int lap_idx = 0; lap_idx < lap_scale_len; lap_idx++ ) {
+	for( size_t lap_idx = 0; lap_idx < lap_scale_len; lap_idx++ ) {
 		/* compute the Laplacian for each scale */
 		float laplacian_scale_factor = array_get_float( laplacian_scales, lap_idx );
 		LOG_INFO("Computing Laplacian using scale: %f", laplacian_scale_factor);
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
index 873486e..3154f6e 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
@@ -24,6 +24,9 @@ typedef struct {
 
 	/* each element of scale_for_max_response contains the index of the
 	 * scale in `laplacian_scales` for which the response is maximised
+	 *
+	 * NOTE: Elements of this are of type `size_t`, but are stored in a
+	 * `pixel_type` for convenience.
 	 */
 	ndarray3* max_response_at_scale_idx;
 } orion_multiscale_laplacian_output;
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
index 8ba209e..d73024b 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
@@ -27,7 +27,11 @@ orion_readNegativeSamples(
 	orion_multiscale_laplacian_output* lap_out = orion_multiscaleLaplacianFilter( vol, Lap, param );
 
 
-	/* Only the positive values are background voxels */
+	/* Only the positive values are background voxels.
+	 *
+	 * We set the `laplacian` member to 1.0 or 0.0 depending on if it is in
+	 * the background.
+	 */
 	NDARRAY3_LOOP_OVER_START( lap_out->laplacian, i,j,k) {
 		ndarray3_set( lap_out->laplacian, i,j,k,
 			ndarray3_get( lap_out->laplacian, i,j,k) > 0 );

From 73dc304bd4bf8b055a5e339db10a3d29bea3f8a1 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 11:57:31 -0500
Subject: [PATCH 10/55] Compute features with scales adjusted by the volume
 spacing

---
 .../ExtractFeatures/computeFeatures.c         | 56 ++++++++++++++++++-
 .../ExtractFeatures/computeFeatures.h         | 10 +++-
 2 files changed, 60 insertions(+), 6 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c
index 9664709..7f21747 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c
@@ -1,9 +1,59 @@
-/* TODO
+/* Retrieve the feature vectors for the training instances.
  *
  * Refactor: computeFeatures
  */
 #include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.h"
 
-vector_float* orion_computeFeatures( orion_segmentation_param* param, ndarray3* vol ) {
-	WARN_UNIMPLEMENTED;
+#include "container/vector.h"
+#include "container/array.h"
+#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeEigenvaluesGaussianFilter.h"
+#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.h"
+
+orion_features* orion_computeFeatures(
+		orion_segmentation_param* param,
+		ndarray3* vol,
+		orion_multiscale_laplacian_output* laplacian_result) {
+	/*
+	 * The features are the eigenvalues of the Hessian Matrix
+	 * Set the parameters Low-pass filter that we want to use.
+	 */
+	bool filter_isotropic = false;
+	array_float* adjusted_scales;
+	orion_features* feat;
+
+	pixel_type spacing_0dim = vol->has_spacing ? vol->spacing[0] : 1.0;
+	/* only use the first scale if not multiscale */
+	size_t number_of_scales = param->multiscale
+		? array_length_float( param->scales )
+		: 1;
+
+	/* adjust the scales by the spacing of the first dimension */
+	adjusted_scales = array_new_float( number_of_scales );
+	for( size_t s_idx = 0 ; s_idx < number_of_scales; s_idx++ ) {
+		array_set_float( adjusted_scales, s_idx,
+			spacing_0dim * array_get_float( param->scales, s_idx )
+		);
+	}
+
+	array_orion_eig_feat_result* result;
+	/* compute the eigenvalues for the given scales */
+	if( filter_isotropic ) {
+		/* compute the eigenvalues using the Isotropic Low pass filter */
+		TODO(Dead code);
+		/* TODO Remove this
+		 * orion_compute_SecondOrderDerivatives(vol, sigma, 60);
+		 */
+	} else {
+		/* compute the eigenvalues using the Gaussian filter */
+		result = orion_computeEigenvaluesGaussianFilter(
+				vol,
+				EIG_FEAT_METHOD_SORT_FRANGI,
+				param->apply_log,
+				adjusted_scales );
+	}
+
+	/* Turn the result into feature vectors */
+	feat = orion_readEigenvaluesGaussianFilter( result, laplacian_result );
+
+	return feat;
 }
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.h
index a439f8e..446664a 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.h
@@ -7,16 +7,20 @@
 
 /* local headers */
 #include "ndarray/ndarray3.h"
-#include "container/vector.h"
 #include "param/segmentation.h"
-
+#include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h"
+#include "segmentation/orion_features.h"
 
 #ifdef __cplusplus
 extern "C" {
 #endif /* __cplusplus */
 
 /* Function prototypes */
-extern vector_float* orion_computeFeatures( orion_segmentation_param* param, ndarray3* vol );
+extern
+orion_features* orion_computeFeatures(
+		orion_segmentation_param* param,
+		ndarray3* vol,
+		orion_multiscale_laplacian_output* laplacian_result);
 
 #ifdef __cplusplus
 };

From b58fe55916dd6cbb668545204dfd7ac135e5672e Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 11:58:23 -0500
Subject: [PATCH 11/55] Helper function to compute features

---
 .../dendrites_main/ExtractFeatures/getFeatures.c          | 8 +++++---
 .../dendrites_main/ExtractFeatures/getFeatures.h          | 8 +++++++-
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c
index 6b15699..f3cbe6d 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.c
@@ -6,11 +6,13 @@
 #include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.h"
 
 #include "simple-log/simplelog.h"
-#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.h"
 
-vector_float* orion_getFeatures( orion_segmentation_param* param, ndarray3* vol ) {
+orion_features* orion_getFeatures(
+		orion_segmentation_param* param,
+		ndarray3* vol,
+		orion_multiscale_laplacian_output* laplacian_result ) {
 	LOG_INFO("Computing Eigenvalues of Hessian Matrix...");
-	vector_float* feat = orion_computeFeatures(param, vol);
+	orion_features* feat = orion_computeFeatures(param, vol, laplacian_result );
 	LOG_INFO("Done computing eigenvalues.");
 	return feat;
 }
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.h
index a4d1343..8670461 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.h
@@ -9,13 +9,19 @@
 #include "ndarray/ndarray3.h"
 #include "container/vector.h"
 #include "param/segmentation.h"
+#include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h"
+#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.h"
 
 #ifdef __cplusplus
 extern "C" {
 #endif /* __cplusplus */
 
 /* Function prototypes */
-extern vector_float* orion_getFeatures( orion_segmentation_param* param, ndarray3* vol );
+extern
+orion_features* orion_getFeatures(
+		orion_segmentation_param* param,
+		ndarray3* vol,
+		orion_multiscale_laplacian_output* laplacian_result );
 
 #ifdef __cplusplus
 };

From e2575b8b5534073ddde96d77863ee8e09b31c3ec Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 11:59:40 -0500
Subject: [PATCH 12/55] Translate the Gaussian response into feature vectors

---
 .../readEigenvaluesGaussianFilter.c           | 59 +++++++++++++++++++
 .../readEigenvaluesGaussianFilter.h           | 27 +++++++++
 lib/segmentation/orion_features.c             | 18 ++++++
 lib/segmentation/orion_features.h             | 39 ++++++++++++
 4 files changed, 143 insertions(+)
 create mode 100644 lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.h
 create mode 100644 lib/segmentation/orion_features.c
 create mode 100644 lib/segmentation/orion_features.h

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.c
index 14a3b04..3f5eca1 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.c
@@ -1,4 +1,63 @@
+#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.h"
+
+#include <math.h>
+
 /* TODO
+ *
+ * Returns a feature vector for every training instance.
+ *
+ * Uses the multiscale Laplacian response to choose the appropriate scale.
+ *
+ * Filters out NaN values in the feature vector.
  *
  * Refactor: readEigenvaluesGaussianFilter
  */
+orion_features* orion_readEigenvaluesGaussianFilter(
+		array_orion_eig_feat_result* eigen,
+		orion_multiscale_laplacian_output* laplacian_result ) {
+
+	orion_features* feat;
+
+	/* only keep the 2nd and 3rd eigenvalues */
+	orion_eig_feat_result* result_first_scale
+		= array_get_orion_eig_feat_result( eigen, 0 );
+
+	ndarray3* result_first_scale_first_eig
+		= array_get_ndarray3( result_first_scale->eig_feat, 0 );
+
+	size_t feat_instances = ndarray3_elems(result_first_scale_first_eig);
+
+	feat = orion_features_new( feat_instances );
+
+	/* Use the scale index in `laplacian_result` to create a length 2
+	 * feature vector for every training pixel.
+	 *
+	 * The features are the 2nd and 3rd eigenvalues at the maximal
+	 * Laplacian response scale.
+	 */
+	for( int n_idx = 0; n_idx < feat_instances; n_idx++ ) {
+		size_t scale_idx = (size_t)( laplacian_result->max_response_at_scale_idx->p[n_idx] );
+
+		orion_eig_feat_result* scale_result
+			= array_get_orion_eig_feat_result( eigen, scale_idx );
+
+		/* get the 2nd eigenvalue (at index 1) */
+		pixel_type eig_2nd = array_get_ndarray3( scale_result->eig_feat, 1 )->p[n_idx];
+
+		/* get the 3rd eigenvalue (at index 2) */
+		pixel_type eig_3rd = array_get_ndarray3( scale_result->eig_feat, 2 )->p[n_idx];
+
+		/* If NaN, then replace with zero.
+		 *
+		 * This is to prevent NaN propagation in other calculations.
+		 */
+		if( isnan(eig_2nd) ) { eig_2nd = 0; }
+		if( isnan(eig_3rd) ) { eig_3rd = 0; }
+
+		/* store in feature vector */
+		vector_set_float( feat->features[0], n_idx, eig_2nd );
+		vector_set_float( feat->features[1], n_idx, eig_3rd );
+	}
+
+	return feat;
+}
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.h
new file mode 100644
index 0000000..ba21d6b
--- /dev/null
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/readEigenvaluesGaussianFilter.h
@@ -0,0 +1,27 @@
+#ifndef ORION_READ_EIGEN_GAUSS_H
+#define ORION_READ_EIGEN_GAUSS_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+
+/* local headers */
+#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/array_eig_feat_result.h"
+#include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h"
+#include "segmentation/orion_features.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+extern
+orion_features* orion_readEigenvaluesGaussianFilter(
+		array_orion_eig_feat_result* eigen,
+		orion_multiscale_laplacian_output* laplacian_result );
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* ORION_READ_EIGEN_GAUSS_H */
diff --git a/lib/segmentation/orion_features.c b/lib/segmentation/orion_features.c
new file mode 100644
index 0000000..21d498e
--- /dev/null
+++ b/lib/segmentation/orion_features.c
@@ -0,0 +1,18 @@
+#include "segmentation/orion_features.h"
+
+orion_features* orion_features_new( size_t instances ) {
+	orion_features* f;
+	NEW( f, orion_features );
+	f->number_of_features = ORION_NUMBER_OF_SEGMENTATION_FEATURES;
+	f->number_of_instances = instances;
+	for( size_t f_idx = 0; f_idx < f->number_of_features; f_idx++ ) {
+		f->features[f_idx] = vector_new_float( instances );
+	}
+}
+
+void orion_features_free( orion_features* f ) {
+	for( size_t f_idx = 0; f_idx < f->number_of_features; f_idx++ ) {
+		vector_free_float( f->features[f_idx] );
+		f->features[f_idx] = NULL;
+	}
+}
diff --git a/lib/segmentation/orion_features.h b/lib/segmentation/orion_features.h
new file mode 100644
index 0000000..6948d8f
--- /dev/null
+++ b/lib/segmentation/orion_features.h
@@ -0,0 +1,39 @@
+#ifndef ORION_FEATURES_H
+#define ORION_FEATURES_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+
+/* local headers */
+#include "container/vector.h"
+
+/* structs, enums */
+#define ORION_NUMBER_OF_SEGMENTATION_FEATURES 2
+
+typedef struct {
+	/*
+	 * There are two features
+	 *
+	 * features[0]: The 2nd eigenvalue of the Gaussian filter.
+	 *
+	 * features[1]: The 3rd eigenvalue of the Gaussian filter.
+	 */
+	size_t number_of_features;
+	vector_float* features[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
+	size_t number_of_instances;
+} orion_features;
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+extern orion_features* orion_features_new( size_t instances );
+extern void orion_features_free( orion_features* f );
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* ORION_FEATURES_H */

From 9c975c7f18dba7a6dac1ce31640ca7d7aa5dc16a Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 12:00:18 -0500
Subject: [PATCH 13/55] ndarray3 function to compute minimum and maximum values

---
 lib/ndarray/ndarray3.c | 16 ++++++++++++++++
 lib/ndarray/ndarray3.h |  2 ++
 2 files changed, 18 insertions(+)

diff --git a/lib/ndarray/ndarray3.c b/lib/ndarray/ndarray3.c
index 76be529..14e0c81 100644
--- a/lib/ndarray/ndarray3.c
+++ b/lib/ndarray/ndarray3.c
@@ -1,6 +1,7 @@
 #include "ndarray/ndarray3.h"
 
 #include <math.h>
+#include <float.h>
 
 #include "util/string.h"
 
@@ -168,3 +169,18 @@ float64 ndarray3_sum_over_all_float64( const ndarray3* n ) {
 	}
 	return sum;
 }
+
+void ndarray3_minmax( ndarray3* n, pixel_type* min, pixel_type* max ) {
+	size_t nelem = ndarray3_elems( n );
+	*min = FLT_MAX;
+	*max = -FLT_MAX;
+	for( size_t idx = 0; idx < nelem; idx++ ) {
+		if( n->p[idx] < *min ) {
+			*min = n->p[idx];
+		}
+
+		if( n->p[idx] > *max ) {
+			*max = n->p[idx];
+		}
+	}
+}
diff --git a/lib/ndarray/ndarray3.h b/lib/ndarray/ndarray3.h
index 81a90a6..6864242 100644
--- a/lib/ndarray/ndarray3.h
+++ b/lib/ndarray/ndarray3.h
@@ -67,6 +67,8 @@ extern void ndarray3_dump( ndarray3* n );
 extern void ndarray3_printf( ndarray3* n, const char* variable_name, const char* format );
 extern void ndarray3_printf_matlab( ndarray3* n, const char* variable_name, const char* format );
 
+/* TODO document */
+extern void ndarray3_minmax( ndarray3* n, pixel_type* min, pixel_type* max );
 
 /* testing functions */
 extern bool ndarray3_is_same_size( ndarray3* a, ndarray3* b );

From 9a4f5e93424e7c5be3213fedcbc632efb4878e14 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:37:28 -0500
Subject: [PATCH 14/55] build: fix for linking of binary with ITK dep

---
 Makefile                |  1 +
 make/liborion-config.mk |  2 ++
 make/liborion.mk        |  4 ----
 make/util-rules.mk      | 14 ++++++++------
 4 files changed, 11 insertions(+), 10 deletions(-)
 create mode 100644 make/liborion-config.mk

diff --git a/Makefile b/Makefile
index 36b4bfa..0499cd2 100644
--- a/Makefile
+++ b/Makefile
@@ -29,6 +29,7 @@ include make/vaa3d-plugin-config.mk
 include make/test-config.mk
 include make/liborion3mat-config.mk
 include make/misc-config.mk
+include make/liborion-config.mk
 
 ## Generate the targets
 LIB_OBJ:= $(call OBJ_PATHSUBST.c,$(LIB_SRC.c))
diff --git a/make/liborion-config.mk b/make/liborion-config.mk
new file mode 100644
index 0000000..98f5e1e
--- /dev/null
+++ b/make/liborion-config.mk
@@ -0,0 +1,2 @@
+ITK_INTEGRATION_OBJ := $(EIGEN_FRANGI_LIB_OBJ) $(EIGEN_SATO_LIB_OBJ) \
+	$(ITK_INTEGRATION_LIB_OBJ)
diff --git a/make/liborion.mk b/make/liborion.mk
index 90c0af7..c6c51f5 100644
--- a/make/liborion.mk
+++ b/make/liborion.mk
@@ -1,7 +1,3 @@
-ITK_INTEGRATION_OBJ := $(EIGEN_FRANGI_LIB_OBJ) $(EIGEN_SATO_LIB_OBJ) \
-	$(ITK_INTEGRATION_LIB_OBJ)
-
 $(LIBORION.A): $(LIB_OBJ) $(ITK_INTEGRATION_OBJ)
 	mkdir -p `dirname $@`
 	$(AR) $(ARFLAGS) $@ $^
-
diff --git a/make/util-rules.mk b/make/util-rules.mk
index 87acdcb..cf93349 100644
--- a/make/util-rules.mk
+++ b/make/util-rules.mk
@@ -3,9 +3,11 @@ $(BINDIR)/subsample-volume/SubsampleVolume$(EXEEXT): $(SRCDIR)/subsample-volume/
 	$(CMAKE.generate) -B$(BINDIR)/subsample-volume -H$(SRCDIR)/subsample-volume
 	$(MAKE) -C$(BINDIR)/subsample-volume
 
-$(BINDIR)/segmentation/orion-segmentation$(EXEEXT): $(SRCDIR)/segmentation/orion-segmentation.c \
-		$(BUILDDIR)/simple-log/simplelog.o \
-		$(BUILDDIR)/util/util.o $(BUILDDIR)/util/string.o \
-		$(BUILDDIR)/param/segmentation.o $(BUILDDIR)/param/io.o \
-		$(BUILDDIR)/param/param.o \
-		$(BUILDDIR)/container/array.o
+BIN_ORION_SEGMENTATION := $(BINDIR)/segmentation/orion-segmentation$(EXEEXT)
+$(BIN_ORION_SEGMENTATION): CPPFLAGS += $(ITK_CPPFLAGS)
+$(BIN_ORION_SEGMENTATION): LDFLAGS  += $(ITK_LDFLAGS)
+$(BIN_ORION_SEGMENTATION): LDLIBS   += $(ITK_LDLIBS)
+$(BIN_ORION_SEGMENTATION): LDLIBS   += -lstdc++ # needs to add C++ library to link
+$(BIN_ORION_SEGMENTATION): \
+	$(SRCDIR)/segmentation/orion-segmentation.c \
+	$(LIBORION.A)

From 4bd97ae255095d2886611defabb117fb5cefaab1 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:38:08 -0500
Subject: [PATCH 15/55] Add function to reset array container size to zero

This allows for reusing a container.
---
 lib/container/array_impl.c | 5 +++++
 lib/container/array_impl.h | 2 ++
 2 files changed, 7 insertions(+)

diff --git a/lib/container/array_impl.c b/lib/container/array_impl.c
index 75a4074..27d1c5a 100644
--- a/lib/container/array_impl.c
+++ b/lib/container/array_impl.c
@@ -67,3 +67,8 @@ void TYPED_NAME(array_resize) ( TYPED_NAME(array)* array, size_t new_capacity )
 	RESIZE_COUNT(array->data, TYPE, new_capacity);
 	array->capacity = new_capacity;
 }
+
+void TYPED_NAME(array_reset) ( TYPED_NAME(array)* array ) {
+	assert( array != NULL );
+	array->length = 0;
+}
diff --git a/lib/container/array_impl.h b/lib/container/array_impl.h
index 796c149..167a2ca 100644
--- a/lib/container/array_impl.h
+++ b/lib/container/array_impl.h
@@ -33,6 +33,8 @@ extern void TYPED_NAME(array_add) ( TYPED_NAME(array)* array, TYPE data );
 
 /* ==== memory management ==== */
 extern void TYPED_NAME(array_resize) ( TYPED_NAME(array)* array, size_t new_capacity );
+/* Resets the length of the array to zero. Does not free elements! */
+extern void TYPED_NAME(array_reset) ( TYPED_NAME(array)* array );
 
 #ifdef __cplusplus
 };

From fce3af840fa6a713a02eb5be6312c3797ed5a87b Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:38:49 -0500
Subject: [PATCH 16/55] Export the filepath function for concatenating paths

---
 lib/io/path/path.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/io/path/path.h b/lib/io/path/path.h
index 4cdae3e..0ff0bff 100644
--- a/lib/io/path/path.h
+++ b/lib/io/path/path.h
@@ -39,6 +39,7 @@ extern char* orion_filepath_to_string(orion_filepath* fp);
 extern orion_filepath* orion_filepath_base( orion_filepath* fp );
 extern orion_filepath* orion_filepath_dir( orion_filepath* fp );
 
+extern orion_filepath* orion_filepath_cat( orion_filepath* fp1, orion_filepath* fp2 );
 extern orion_filepath* orion_filepath_sibling( orion_filepath* base, orion_filepath* relative);
 
 #ifdef __cplusplus

From 846be226a5af78ce27237d705840e9e55869c4f8 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:39:51 -0500
Subject: [PATCH 17/55] Add struct member for classifying background voxels by
 Laplacian response

---
 .../DetectTrainingSet/multiscaleLaplacianFilter.c |  4 ++++
 .../DetectTrainingSet/multiscaleLaplacianFilter.h |  7 +++++++
 .../DetectTrainingSet/readNegativeSamples.c       | 15 ++++++++++-----
 3 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index 6ee840d..46227fc 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -27,6 +27,9 @@ void orion_multiscale_laplacian_output_free(orion_multiscale_laplacian_output* r
 	if( r->max_response_at_scale_idx )
 		ndarray3_free( r->max_response_at_scale_idx );
 
+	if( r->is_background )
+		ndarray3_free( r->is_background );
+
 	free(r);
 }
 
@@ -35,6 +38,7 @@ orion_multiscale_laplacian_output* orion_multiscale_laplacian_output_new() {
 	NEW(r, orion_multiscale_laplacian_output);
 	r->laplacian = NULL;
 	r->max_response_at_scale_idx = NULL;
+	r->is_background = NULL;
 	return r;
 }
 
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
index 3154f6e..ab3d501 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h
@@ -29,6 +29,13 @@ typedef struct {
 	 * `pixel_type` for convenience.
 	 */
 	ndarray3* max_response_at_scale_idx;
+
+	/* Each element indicates if the Laplacian response at that voxel
+	 * should be classified as in in the background.
+	 *
+	 * Element is either 0.0 or 1.0.
+	 */
+	ndarray3* is_background;
 } orion_multiscale_laplacian_output;
 
 #ifdef __cplusplus
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
index d73024b..ec652bb 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
@@ -29,12 +29,17 @@ orion_readNegativeSamples(
 
 	/* Only the positive values are background voxels.
 	 *
-	 * We set the `laplacian` member to 1.0 or 0.0 depending on if it is in
-	 * the background.
+	 * We set the `is_background` member to 1.0 or 0.0 depending on if it is in
+	 * the background based on the response in `laplacian`.
+	 *
+	 * We are working in-place to save memory, so we transfer the contents
+	 * from `laplacian` to `is_background`.
 	 */
-	NDARRAY3_LOOP_OVER_START( lap_out->laplacian, i,j,k) {
-		ndarray3_set( lap_out->laplacian, i,j,k,
-			ndarray3_get( lap_out->laplacian, i,j,k) > 0 );
+	lap_out->is_background = lap_out->laplacian;
+	lap_out->laplacian = NULL;
+	NDARRAY3_LOOP_OVER_START( lap_out->is_background, i,j,k) {
+		ndarray3_set( lap_out->is_background, i,j,k,
+			ndarray3_get( lap_out->is_background, i,j,k) > 0 );
 	} NDARRAY3_LOOP_OVER_END;
 
 	return lap_out;

From 70b9321a31a0a2106126ba8941e24a6b3539ddae Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:41:39 -0500
Subject: [PATCH 18/55] Fix Laplacian adjusted scale creation

---
 .../dendrites_main/DetectTrainingSet/readNegativeSamples.c      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
index ec652bb..62c729d 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
@@ -20,7 +20,7 @@ orion_readNegativeSamples(
 	size_t n_scales = array_length_float( param->scales );
 	array_float* Lap =  array_new_float( n_scales );
 	for( size_t Lap_idx = 0; Lap_idx < n_scales; Lap_idx++ ) {
-		array_set_float( Lap, Lap_idx,
+		array_add_float( Lap,
 			0.66 / array_get_float( param->scales, Lap_idx ) );
 	}
 

From 90aa001c3177be70ea31d8b192e457ff7bf43cda Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:42:05 -0500
Subject: [PATCH 19/55] Add debug logging for multiscale Laplacian filter
 function

---
 .../DetectTrainingSet/multiscaleLaplacianFilter.c              | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index 46227fc..825ffd9 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -58,6 +58,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 	int n = ORION_LAPLACIAN_HDAF_APPROX_DEGREE;
 
 	/* Fourier transform the input image */
+	LOG_DEBUG("Computing Fourier transform of input volume");
 	ndarray3_complex* v_fft = ndarray3_fftn_r2c(input_volume);
 
 	output->laplacian
@@ -88,6 +89,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 		ndarray3* filt = orion_Makefilter( nx,ny,nz,
 			n, laplacian_scale_factor, orion_Makefilter_FLAG_A);
 
+		LOG_DEBUG("Applying Laplacian filter");
 		NDARRAY3_LOOP_OVER_START( filt, i,j,k) {
 			/* normalise the generated Laplacian filter
 			 *
@@ -118,6 +120,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 		 * is real and we treat the data in `cur_scale_laplacian` after
 		 * applying the filter as conjugate symmetric.
 		 * */
+		LOG_DEBUG("Inverse Fourier transform for scale %f", laplacian_scale_factor);
 		ndarray3* cur_scale_filt_vol =
 			ndarray3_ifftn_c2r( cur_scale_laplacian );
 

From ed05617464aa4849fcb5a4e0ab630b03cb8b0f18 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:43:40 -0500
Subject: [PATCH 20/55] Read ORION3 configuration format to set parameters for
 segmentation

---
 lib/param/io.c                        |  8 ++-
 lib/param/io.h                        |  2 +
 src/segmentation/orion-segmentation.c | 92 ++++++++++++++++++++++++++-
 3 files changed, 99 insertions(+), 3 deletions(-)

diff --git a/lib/param/io.c b/lib/param/io.c
index 8034180..62c835c 100644
--- a/lib/param/io.c
+++ b/lib/param/io.c
@@ -5,12 +5,14 @@ orion_io_param* orion_io_param_new() {
 	NEW( param, orion_io_param );
 	param->input_filename = NULL;
 	param->output_filename = NULL;
+	param->orion3_config_filename = NULL;
 	return param;
 }
 
 void orion_io_param_free(orion_io_param* param) {
-	free(param->input_filename);
-	free(param->output_filename);
+	if(param->input_filename) { free(param->input_filename); }
+	if(param->output_filename) { free(param->output_filename); }
+	if(param->orion3_config_filename) { free(param->orion3_config_filename); }
 	free(param);
 }
 
@@ -20,4 +22,6 @@ void orion_io_param_dump( orion_io_param* param ) {
 		fprintf(stderr, "\tinput: %s\n", param->input_filename);
 	if( param->output_filename )
 		fprintf(stderr, "\toutput: %s\n", param->output_filename);
+	if( param->orion3_config_filename )
+		fprintf(stderr, "\torion3_config: %s\n", param->orion3_config_filename);
 }
diff --git a/lib/param/io.h b/lib/param/io.h
index 6c63631..d4d4c46 100644
--- a/lib/param/io.h
+++ b/lib/param/io.h
@@ -7,6 +7,8 @@
 typedef struct {
 	char* input_filename;
 	char* output_filename;
+
+	char* orion3_config_filename;
 } orion_io_param;
 
 #ifdef __cplusplus
diff --git a/src/segmentation/orion-segmentation.c b/src/segmentation/orion-segmentation.c
index 81fd52d..91307f2 100644
--- a/src/segmentation/orion-segmentation.c
+++ b/src/segmentation/orion-segmentation.c
@@ -5,6 +5,15 @@
 #include "simple-log/simplelog.h"
 #include "param/param.h"
 #include "util/util.h"
+#include "util/util.h"
+#include "io/path/path.h"
+#include "io/format/mhd.h"
+
+#include "kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.h"
+
+#include "orion3-config-parser/parser.h"
+
+#define ORION_METAINFO_FILE_FMT_SUFFIX ".mhd"
 
 typedef struct {
 	orion_io_param* io;
@@ -21,6 +30,9 @@ void usage(char* program_name) {
     --input _path_   : _path_ is the filename for the input volume\n\
 \n\
     --output _path_  : _path_ is the filename for the output volume\n\
+\n\
+    --orion3-config _path_  : _path_ is the filename for the ORION3 configuration file\n\
+\n\
     --help           : show this information\n\
 ",
 		program_name
@@ -48,6 +60,11 @@ void parse_arguments( int argc, char * argv[], param_parse* param ) {
 				safe_malloc_and_strcpy(&(param->io->output_filename), argv[arg_idx+1]);
 			else
 				die("Missing argument to --output at %d", arg_idx + 1);
+		} else if(  strcmp( argv[arg_idx], "--orion3-config" ) == 0 ) {
+			if( arg_idx+1 < argc )
+				safe_malloc_and_strcpy(&(param->io->orion3_config_filename), argv[arg_idx+1]);
+			else
+				die("Missing argument to --orion3-config at %d", arg_idx + 1);
 		}
 	}
 
@@ -58,6 +75,67 @@ void parse_param_dump(param_parse* param) {
 	orion_segmentation_param_dump(param->segmentation);
 }
 
+void orion3_config_set_parameters(param_parse* param) {
+	orion3_param* config_param =
+		orion3_param_read_input_file( param->io->orion3_config_filename );
+
+	/* copy the scales from the configuration */
+	for( size_t scale_idx = 0; scale_idx < array_length_float(config_param->scales); scale_idx++ ) {
+		array_add_float( param->segmentation->scales,
+				array_get_float( config_param->scales, scale_idx ) );
+	}
+
+	/* copy the input volume from the configuration */
+	size_t n_volumes = array_length_str(config_param->volume_names);
+	if( n_volumes > 0 ) {
+		if( n_volumes == 1 ) {
+			/*
+			 * final path is:
+			 *
+			 * < path-to-volume-directory > / < volume-name > / < volume-name >.mhd
+			 */
+			orion_filepath* fp_base_dir = orion_filepath_new_from_string(config_param->path_to_volume_directory);
+
+			char* vol_name = array_get_str( config_param->volume_names, 0 );
+			size_t vol_name_len = strlen(vol_name);
+
+			char* vol_name_suffix;
+			NEW_COUNT(vol_name_suffix, char, vol_name_len + strlen(ORION_METAINFO_FILE_FMT_SUFFIX) + 1 );
+
+			strncpy(vol_name_suffix, vol_name, vol_name_len),
+
+			/* add MetaInfo suffix */
+			strncpy(vol_name_suffix + vol_name_len,
+					ORION_METAINFO_FILE_FMT_SUFFIX,
+					strlen(ORION_METAINFO_FILE_FMT_SUFFIX) + 1);
+
+			orion_filepath* fp_vol_dir = orion_filepath_new_from_string( vol_name );
+			orion_filepath* fp_vol_filename = orion_filepath_new_from_string( vol_name_suffix );
+
+			orion_filepath* fp_vol_dir_file = orion_filepath_cat( fp_vol_dir, fp_vol_filename );
+
+			orion_filepath* fp_vol_full_path = orion_filepath_cat( fp_base_dir, fp_vol_dir_file );
+
+			safe_malloc_and_strcpy(&(param->io->input_filename),
+				orion_filepath_to_string(fp_vol_full_path) );
+
+			free(vol_name_suffix);
+			orion_filepath_free(fp_vol_full_path);
+			orion_filepath_free(fp_vol_dir_file);
+			orion_filepath_free(fp_vol_filename);
+			orion_filepath_free(fp_base_dir);
+		} else {
+			die("Can not handle multiple volumes in configuration %s",
+					param->io->orion3_config_filename);
+		}
+	} else {
+		die("No volumes files given in configuration %s",
+				param->io->orion3_config_filename);
+	}
+
+	orion3_param_free( config_param );
+}
+
 int main( int argc, char * argv[] ) {
 	LOG_INFO("Starting %s", argv[0] );
 
@@ -68,8 +146,20 @@ int main( int argc, char * argv[] ) {
 
 	parse_arguments(argc, argv, param);
 
-	parse_param_dump(param);
+	/* read in parameters from configuration file */
+	if( param->io->orion3_config_filename ) {
+		orion3_config_set_parameters(param);
+	}
+
+	/*DEBUG*/parse_param_dump(param);
+
+	ndarray3* input_volume = orion_read_mhd( param->io->input_filename );
+
+	orion_ORION3_Dendrites( param->segmentation, input_volume );
 
+	ndarray3_free(input_volume);
+	orion_io_param_free(param->io);
+	orion_segmentation_param_free( param->segmentation );
 	LOG_INFO("Stopping %s", argv[0] );
 	return EXIT_SUCCESS;
 }

From f13e14530a48bf543c89f7f5dc96db076abd575a Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:44:14 -0500
Subject: [PATCH 21/55] Initialise multiscale segmentation to zero

---
 lib/param/segmentation.c | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/param/segmentation.c b/lib/param/segmentation.c
index 854029c..f71e031 100644
--- a/lib/param/segmentation.c
+++ b/lib/param/segmentation.c
@@ -6,6 +6,7 @@ orion_segmentation_param* orion_segmentation_param_new() {
 	orion_segmentation_param* param;
 	NEW( param, orion_segmentation_param );
 	param->scales = array_new_float( 10 );
+	param->multiscale = 0;
 
 	/* all attributes are unset at build */
 #define ATTR( NAME, TYPE ) \

From 2c5fdb98fd4eec7732356c8e173c5a9da781c75e Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:44:43 -0500
Subject: [PATCH 22/55] Show usage when tool is not given any arguments

---
 src/segmentation/orion-segmentation.c | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/segmentation/orion-segmentation.c b/src/segmentation/orion-segmentation.c
index 91307f2..4f4f241 100644
--- a/src/segmentation/orion-segmentation.c
+++ b/src/segmentation/orion-segmentation.c
@@ -41,7 +41,11 @@ void usage(char* program_name) {
 
 void parse_arguments( int argc, char * argv[], param_parse* param ) {
 	int arg_idx = 0;
-	for( arg_idx = 0; arg_idx < argc; arg_idx++ ) {
+	if( argc == 1 ) {
+		usage( argv[0] );
+		exit(EXIT_SUCCESS);
+	}
+	for( arg_idx = 1; arg_idx < argc; arg_idx++ ) {
 		if( strcmp( argv[arg_idx], "--help" ) == 0 ) {
 			usage( argv[0] );
 			exit(EXIT_SUCCESS);

From 7453e9d11672f949b4d4269799ab341bdfb341bc Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 31 Mar 2016 16:47:18 -0500
Subject: [PATCH 23/55] Add list of Debian packages required for building

---
 debian-packages | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 debian-packages

diff --git a/debian-packages b/debian-packages
new file mode 100644
index 0000000..3ab1309
--- /dev/null
+++ b/debian-packages
@@ -0,0 +1,2 @@
+cmake
+libinsighttoolkit4-dev

From 0079ec3201834eaa361509331031ee647bffef1f Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 1 Apr 2016 09:48:39 -0500
Subject: [PATCH 24/55] Use more general FFT that does not require even
 dimensions

---
 lib/ndarray/ndarray3_fft.c | 79 +++++++++++++++++++++++++++++++++++++-
 lib/ndarray/ndarray3_fft.h |  5 +++
 2 files changed, 82 insertions(+), 2 deletions(-)

diff --git a/lib/ndarray/ndarray3_fft.c b/lib/ndarray/ndarray3_fft.c
index 517e6c8..4b007a4 100644
--- a/lib/ndarray/ndarray3_fft.c
+++ b/lib/ndarray/ndarray3_fft.c
@@ -2,6 +2,7 @@
 
 #include <kiss_fft.h>
 #include <kiss_fftndr.h>
+#include <kiss_fftnd.h>
 
 ndarray3_complex* ndarray3_fftn_r2c( ndarray3* n ) {
 	ndarray3_complex* freq_data =
@@ -15,7 +16,7 @@ ndarray3_complex* ndarray3_fftn_r2c( ndarray3* n ) {
 	kiss_fftndr_cfg fft =
 		kiss_fftndr_alloc( dims, PIXEL_NDIMS, false , NULL, NULL);
 
-	kiss_fftndr(fft, (kiss_fft_scalar*)(n->p), freq_data->p );
+	kiss_fftndr(fft, (kiss_fft_scalar*)(n->p), (kiss_fft_cpx *)(freq_data->p) );
 
 	free(dims);
 	free(fft);
@@ -36,7 +37,7 @@ ndarray3* ndarray3_ifftn_c2r( ndarray3_complex* n ) {
 	kiss_fftndr_cfg ifft =
 		kiss_fftndr_alloc( dims, PIXEL_NDIMS, true , NULL, NULL);
 
-	kiss_fftndri(ifft, n->p, spatial_data->p );
+	kiss_fftndri(ifft, (kiss_fft_cpx *)(n->p), spatial_data->p );
 
 	size_t nelems = ndarray3_complex_elems( n );
 	for( int i = 0; i < nelems; i++ ) {
@@ -48,3 +49,77 @@ ndarray3* ndarray3_ifftn_c2r( ndarray3_complex* n ) {
 
 	return spatial_data;
 }
+
+ndarray3_complex* ndarray3_fftn_real( ndarray3* n ) {
+	ndarray3_complex* space_data =
+		ndarray3_complex_new(n->sz[0], n->sz[1], n->sz[2]);
+	NDARRAY3_LOOP_OVER_START( n, i,j,k ) {
+		ndarray3_complex_set( space_data, i,j,k, ndarray3_get(n, i,j,k) );
+	} NDARRAY3_LOOP_OVER_END;
+
+	ndarray3_complex* freq_data =
+		ndarray3_complex_new(n->sz[0], n->sz[1], n->sz[2]);
+
+	int* dims;
+	NEW_COUNT( dims, int, PIXEL_NDIMS );
+	dims[0] = n->sz[0];
+	dims[1] = n->sz[1];
+	dims[2] = n->sz[2];
+	kiss_fftnd_cfg fft =
+		kiss_fftnd_alloc( dims, PIXEL_NDIMS, false , NULL, NULL);
+	/*                                           ^
+	 *                                           |
+	 *                                           +---- forward FFT
+	 */
+
+	kiss_fftnd(fft, (kiss_fft_cpx *)(space_data->p), (kiss_fft_cpx *)(freq_data->p) );
+
+	ndarray3_complex_free(space_data);
+	free(dims);
+	free(fft);
+
+	return freq_data;
+}
+
+ndarray3* ndarray3_ifftn_real( ndarray3_complex* n ) {
+	ndarray3_complex* spatial_data_complex =
+		ndarray3_complex_new(n->sz[0], n->sz[1], n->sz[2]);
+
+	ndarray3* spatial_data =
+		ndarray3_new(n->sz[0], n->sz[1], n->sz[2]);
+
+	int* dims;
+	NEW_COUNT( dims, int, PIXEL_NDIMS );
+	dims[0] = n->sz[0];
+	dims[1] = n->sz[1];
+	dims[2] = n->sz[2];
+
+	kiss_fftnd_cfg ifft =
+		kiss_fftnd_alloc( dims, PIXEL_NDIMS, true , NULL, NULL);
+	/*                                           ^
+	 *                                           |
+	 *                                           +---- inverse FFT
+	 */
+
+	kiss_fftnd(ifft, (kiss_fft_cpx *)(n->p), (kiss_fft_cpx *)(spatial_data_complex->p) );
+
+	size_t nelems = ndarray3_complex_elems( n );
+	for( int i = 0; i < nelems; i++ ) {
+		spatial_data->p[i] /= nelems; /* scaling */
+	}
+
+	/* keep real part of `spatial_data_complex` */
+	NDARRAY3_LOOP_OVER_START( spatial_data_complex, i,j,k ) {
+		ndarray3_set( spatial_data, i,j,k,
+				crealf( ndarray3_complex_get( spatial_data_complex, i,j,k) )
+				);
+	} NDARRAY3_LOOP_OVER_END;
+
+	ndarray3_complex_free(spatial_data_complex);
+	free(dims);
+	free(ifft);
+
+	return spatial_data;
+}
+
+
diff --git a/lib/ndarray/ndarray3_fft.h b/lib/ndarray/ndarray3_fft.h
index dd81632..349390b 100644
--- a/lib/ndarray/ndarray3_fft.h
+++ b/lib/ndarray/ndarray3_fft.h
@@ -29,6 +29,8 @@ extern "C" {
  *
  * modulo numerical errors.
  *
+ * The data must have even dimensions.
+ *
  * See also:
  *    Kiss-FFT:
  *        kiss_fftndr, kiss_fftndri
@@ -39,6 +41,9 @@ extern "C" {
 extern ndarray3_complex* ndarray3_fftn_r2c( ndarray3* n );
 extern ndarray3* ndarray3_ifftn_c2r( ndarray3_complex* n );
 
+/* These functions allocate memory, but do not require even dimensions */
+extern ndarray3_complex* ndarray3_fftn_real( ndarray3* n );
+extern ndarray3* ndarray3_ifftn_real( ndarray3_complex* n );
 
 #ifdef __cplusplus
 };

From 85eea225e32f7c91a87a5a909f80366ffe9561bf Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 1 Apr 2016 09:56:04 -0500
Subject: [PATCH 25/55] Use more general n-d FFT functions when applying
 Laplacian filter

---
 .../DetectTrainingSet/multiscaleLaplacianFilter.c             | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index 825ffd9..b1eabf2 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -59,7 +59,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 
 	/* Fourier transform the input image */
 	LOG_DEBUG("Computing Fourier transform of input volume");
-	ndarray3_complex* v_fft = ndarray3_fftn_r2c(input_volume);
+	ndarray3_complex* v_fft = ndarray3_fftn_real(input_volume);
 
 	output->laplacian
 		= ndarray3_new_with_size_from_ndarray3(input_volume);
@@ -122,7 +122,7 @@ orion_multiscale_laplacian_output* orion_multiscaleLaplacianFilter(
 		 * */
 		LOG_DEBUG("Inverse Fourier transform for scale %f", laplacian_scale_factor);
 		ndarray3* cur_scale_filt_vol =
-			ndarray3_ifftn_c2r( cur_scale_laplacian );
+			ndarray3_ifftn_real( cur_scale_laplacian );
 
 		/* check for maximum response across all scales */
 		if( !recorded_maximum_scale ) {

From 5f672767c67500a8027d816fe784ed08ce910549 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 1 Apr 2016 09:56:53 -0500
Subject: [PATCH 26/55] Fix two memory bugs

- One function did not return the correct variable.
- Another called a function before the container length was set.
---
 .../dendrites_main/ExtractFeatures/computeFeatures.c            | 2 +-
 lib/segmentation/orion_features.c                               | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c
index 7f21747..87c5fac 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/computeFeatures.c
@@ -30,7 +30,7 @@ orion_features* orion_computeFeatures(
 	/* adjust the scales by the spacing of the first dimension */
 	adjusted_scales = array_new_float( number_of_scales );
 	for( size_t s_idx = 0 ; s_idx < number_of_scales; s_idx++ ) {
-		array_set_float( adjusted_scales, s_idx,
+		array_add_float( adjusted_scales,
 			spacing_0dim * array_get_float( param->scales, s_idx )
 		);
 	}
diff --git a/lib/segmentation/orion_features.c b/lib/segmentation/orion_features.c
index 21d498e..e6f52b3 100644
--- a/lib/segmentation/orion_features.c
+++ b/lib/segmentation/orion_features.c
@@ -8,6 +8,8 @@ orion_features* orion_features_new( size_t instances ) {
 	for( size_t f_idx = 0; f_idx < f->number_of_features; f_idx++ ) {
 		f->features[f_idx] = vector_new_float( instances );
 	}
+
+	return f;
 }
 
 void orion_features_free( orion_features* f ) {

From 4c3a94d14d8983d2647744c0082e5d58b8275d99 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 7 Apr 2016 15:26:31 -0500
Subject: [PATCH 27/55] Add PD KISS99 RNG code

Taken from <http://www.cse.yorku.ca/~oz/marsaglia-rng.html>.
---
 lib/numeric/kiss99_rng.c | 201 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 201 insertions(+)
 create mode 100644 lib/numeric/kiss99_rng.c

diff --git a/lib/numeric/kiss99_rng.c b/lib/numeric/kiss99_rng.c
new file mode 100644
index 0000000..d9d04e0
--- /dev/null
+++ b/lib/numeric/kiss99_rng.c
@@ -0,0 +1,201 @@
+#include <stdio.h>
+#define znew (z=36969*(z&65535)+(z>>16))
+#define wnew (w=18000*(w&65535)+(w>>16))
+#define MWC ((znew<<16)+wnew )
+#define SHR3 (jsr^=(jsr<<17), jsr^=(jsr>>13), jsr^=(jsr<<5))
+#define CONG (jcong=69069*jcong+1234567)
+#define FIB ((b=a+b),(a=b-a))
+#define KISS ((MWC^CONG)+SHR3)
+#define LFIB4 (c++,t[c]=t[c]+t[UC(c+58)]+t[UC(c+119)]+t[UC(c+178)])
+#define SWB (c++,bro=(x<y),t[c]=(x=t[UC(c+34)])-(y=t[UC(c+19)]+bro))
+#define UNI (KISS*2.328306e-10)
+#define VNI ((long) KISS)*4.656613e-10
+#define UC (unsigned char) /*a cast operation*/
+typedef unsigned long UL;
+/* Global static variables: */
+static UL z=362436069, w=521288629, jsr=123456789, jcong=380116160;
+static UL a=224466889, b=7584631, t[256];
+/* Use random seeds to reset z,w,jsr,jcong,a,b, and the table
+t[256]*/
+static UL x=0,y=0,bro; static unsigned char c=0;
+/* Example procedure to set the table, using KISS: */
+void settable(UL i1,UL i2,UL i3,UL i4,UL i5, UL i6)
+{ int i; z=i1;w=i2,jsr=i3; jcong=i4; a=i5; b=i6;
+for(i=0;i<256;i=i+1) t[i]=KISS;
+}
+/* This is a test main program. It should compile and print 7
+0's. */
+int main(void){
+int i; UL k;
+settable(12345,65435,34221,12345,9983651,95746118);
+for(i=1;i<1000001;i++){k=LFIB4;} printf("%u\n", k-1064612766U);
+for(i=1;i<1000001;i++){k=SWB ;} printf("%u\n", k- 627749721U);
+for(i=1;i<1000001;i++){k=KISS ;} printf("%u\n", k-1372460312U);
+for(i=1;i<1000001;i++){k=CONG ;} printf("%u\n", k-1529210297U);
+for(i=1;i<1000001;i++){k=SHR3 ;} printf("%u\n", k-2642725982U);
+for(i=1;i<1000001;i++){k=MWC ;} printf("%u\n", k- 904977562U);
+for(i=1;i<1000001;i++){k=FIB ;} printf("%u\n", k-3519793928U);
+}
+/*-----------------------------------------------------
+Write your own calling program and try one or more of
+the above, singly or in combination, when you run a
+simulation. You may want to change the simple 1-letter
+names, to avoid conflict with your own choices. */
+
+
+/* All that follows is comment, mostly from the initial
+   post. You may want to remove it */
+
+
+/* Any one of KISS, MWC, FIB, LFIB4, SWB, SHR3, or CONG
+   can be used in an expression to provide a random 32-bit
+   integer.
+
+
+   The KISS generator, (Keep It Simple Stupid), is
+   designed to combine the two multiply-with-carry
+   generators in MWC with the 3-shift register SHR3 and
+   the congruential generator CONG, using addition and
+   exclusive-or. Period about 2^123.
+   It is one of my favorite generators.
+
+
+   The MWC generator concatenates two 16-bit multiply-
+   with-carry generators, x(n)=36969x(n-1)+carry,
+   y(n)=18000y(n-1)+carry mod 2^16, has period about
+   2^60 and seems to pass all tests of randomness. A
+   favorite stand-alone generator---faster than KISS,
+   which contains it.
+
+
+   FIB is the classical Fibonacci sequence
+   x(n)=x(n-1)+x(n-2),but taken modulo 2^32.
+   Its period is 3*2^31 if one of its two seeds is odd
+   and not 1 mod 8. It has little worth as a RNG by
+   itself, but provides a simple and fast component for
+   use in combination generators.
+
+
+   SHR3 is a 3-shift-register generator with period
+   2^32-1. It uses y(n)=y(n-1)(I+L^17)(I+R^13)(I+L^5),
+   with the y's viewed as binary vectors, L the 32x32
+   binary matrix that shifts a vector left 1, and R its
+   transpose. SHR3 seems to pass all except those
+   related to the binary rank test, since 32 successive
+   values, as binary vectors, must be linearly
+   independent, while 32 successive truly random 32-bit
+   integers, viewed as binary vectors, will be linearly
+   independent only about 29% of the time.
+
+
+   CONG is a congruential generator with the widely used 69069
+   multiplier: x(n)=69069x(n-1)+1234567. It has period
+   2^32. The leading half of its 32 bits seem to pass
+   tests, but bits in the last half are too regular.
+
+
+   LFIB4 is an extension of what I have previously
+   defined as a lagged Fibonacci generator:
+   x(n)=x(n-r) op x(n-s), with the x's in a finite
+   set over which there is a binary operation op, such
+   as +,- on integers mod 2^32, * on odd such integers,
+   exclusive-or(xor) on binary vectors. Except for
+   those using multiplication, lagged Fibonacci
+   generators fail various tests of randomness, unless
+   the lags are very long. (See SWB below).
+   To see if more than two lags would serve to overcome
+   the problems of 2-lag generators using +,- or xor, I
+   have developed the 4-lag generator LFIB4 using
+   addition: x(n)=x(n-256)+x(n-179)+x(n-119)+x(n-55)
+   mod 2^32. Its period is 2^31*(2^256-1), about 2^287,
+   and it seems to pass all tests---in particular,
+   those of the kind for which 2-lag generators using
+   +,-,xor seem to fail. For even more confidence in
+   its suitability, LFIB4 can be combined with KISS,
+   with a resulting period of about 2^410: just use
+   (KISS+LFIB4) in any C expression.
+
+
+   SWB is a subtract-with-borrow generator that I
+   developed to give a simple method for producing
+   extremely long periods:
+   x(n)=x(n-222)-x(n-237)- borrow mod 2^32.
+   The 'borrow' is 0, or set to 1 if computing x(n-1)
+   caused overflow in 32-bit integer arithmetic. This
+   generator has a very long period, 2^7098(2^480-1),
+   about 2^7578. It seems to pass all tests of
+   randomness, except for the Birthday Spacings test,
+   which it fails badly, as do all lagged Fibonacci
+   generators using +,- or xor. I would suggest
+   combining SWB with KISS, MWC, SHR3, or CONG.
+   KISS+SWB has period >2^7700 and is highly
+   recommended.
+   Subtract-with-borrow has the same local behaviour
+   as lagged Fibonacci using +,-,xor---the borrow
+   merely provides a much longer period.
+   SWB fails the birthday spacings test, as do all
+   lagged Fibonacci and other generators that merely
+   combine two previous values by means of =,- or xor.
+   Those failures are for a particular case: m=512
+   birthdays in a year of n=2^24 days. There are
+   choices of m and n for which lags >1000 will also
+   fail the test. A reasonable precaution is to always
+   combine a 2-lag Fibonacci or SWB generator with
+   another kind of generator, unless the generator uses
+   *, for which a very satisfactory sequence of odd
+   32-bit integers results.
+
+
+   The classical Fibonacci sequence mod 2^32 from FIB
+   fails several tests. It is not suitable for use by
+   itself, but is quite suitable for combining with
+   other generators.
+
+
+   The last half of the bits of CONG are too regular,
+   and it fails tests for which those bits play a
+   significant role. CONG+FIB will also have too much
+   regularity in trailing bits, as each does. But keep
+   in mind that it is a rare application for which
+   the trailing bits play a significant role. CONG
+   is one of the most widely used generators of the
+   last 30 years, as it was the system generator for
+   VAX and was incorporated in several popular
+   software packages, all seemingly without complaint.
+
+
+   Finally, because many simulations call for uniform
+   random variables in 0<x<1 or -1<x<1, I use #define
+   statements that permit inclusion of such variates
+   directly in expressions: using UNI will provide a
+   uniform random real (float) in (0,1), while VNI will
+   provide one in (-1,1).
+
+
+   All of these: MWC, SHR3, CONG, KISS, LFIB4, SWB, FIB
+   UNI and VNI, permit direct insertion of the desired
+   random quantity into an expression, avoiding the
+   time and space costs of a function call. I call
+   these in-line-define functions. To use them, static
+   variables z,w,jsr,jcong,a and b should be assigned
+   seed values other than their initial values. If
+   LFIB4 or SWB are used, the static table t[256] must
+   be initialized.
+
+
+   A note on timing: It is difficult to provide exact
+   time costs for inclusion of one of these in-line-
+   define functions in an expression. Times may differ
+   widely for different compilers, as the C operations
+   may be deeply nested and tricky. I suggest these
+   rough comparisons, based on averaging ten runs of a
+   routine that is essentially a long loop:
+   for(i=1;i<10000000;i++) L=KISS; then with KISS
+   replaced with SHR3, CONG,... or KISS+SWB, etc. The
+   times on my home PC, a Pentium 300MHz, in nanoseconds:
+   FIB 49;LFIB4 77;SWB 80;CONG 80;SHR3 84;MWC 93;KISS 157;
+   VNI 417;UNI 450;
+*/
+
+
+

From 2291b9fe2aa77f743f368723e19f8187df8855d8 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Thu, 7 Apr 2016 16:19:41 -0500
Subject: [PATCH 28/55] Refactor the KISS99 RNG code

Wrap all the seed values inside a struct
---
 lib/numeric/kiss99_rng.c | 98 +++++++++++++++++++++++++++-------------
 1 file changed, 66 insertions(+), 32 deletions(-)

diff --git a/lib/numeric/kiss99_rng.c b/lib/numeric/kiss99_rng.c
index d9d04e0..96f3a86 100644
--- a/lib/numeric/kiss99_rng.c
+++ b/lib/numeric/kiss99_rng.c
@@ -1,40 +1,74 @@
 #include <stdio.h>
-#define znew (z=36969*(z&65535)+(z>>16))
-#define wnew (w=18000*(w&65535)+(w>>16))
-#define MWC ((znew<<16)+wnew )
-#define SHR3 (jsr^=(jsr<<17), jsr^=(jsr>>13), jsr^=(jsr<<5))
-#define CONG (jcong=69069*jcong+1234567)
-#define FIB ((b=a+b),(a=b-a))
-#define KISS ((MWC^CONG)+SHR3)
-#define LFIB4 (c++,t[c]=t[c]+t[UC(c+58)]+t[UC(c+119)]+t[UC(c+178)])
-#define SWB (c++,bro=(x<y),t[c]=(x=t[UC(c+34)])-(y=t[UC(c+19)]+bro))
-#define UNI (KISS*2.328306e-10)
-#define VNI ((long) KISS)*4.656613e-10
-#define UC (unsigned char) /*a cast operation*/
-typedef unsigned long UL;
+#include <stdint.h>
+
+/*
+ * George Marsaglia's KISS99 PRNG.
+ *
+ * Taken from Usenet posting from 1999-01-21 <http://www.cse.yorku.ca/~oz/marsaglia-rng.html>..
+ *
+ * Modified to keep state in struct.
+ */
+
+#define kiss99_rng_znew(state) (state->z=36969*(state->z&65535)+(state->z>>16))
+#define kiss99_rng_wnew(state) (state->w=18000*(state->w&65535)+(state->w>>16))
+#define kiss99_rng_MWC(state) ((kiss99_rng_znew(state)<<16)+kiss99_rng_wnew(state) )
+#define kiss99_rng_SHR3(state) (state->jsr^=(state->jsr<<17), state->jsr^=(state->jsr>>13), state->jsr^=(state->jsr<<5))
+#define kiss99_rng_CONG(state) (state->jcong=69069*state->jcong+1234567)
+#define kiss99_rng_FIB(state) ((state->b=state->a+state->b),(state->a=state->b-state->a))
+#define kiss99_rng_KISS(state) ((kiss99_rng_MWC(state)^kiss99_rng_CONG(state))+kiss99_rng_SHR3(state))
+#define kiss99_rng_LFIB4(state) (state->c++,state->t[state->c]=state->t[state->c]+state->t[kiss99_rng_UC(state->c+58)]+state->t[kiss99_rng_UC(state->c+119)]+state->t[kiss99_rng_UC(state->c+178)])
+#define kiss99_rng_SWB(state) (state->c++,state->bro=(state->x<state->y),state->t[state->c]=(state->x=state->t[kiss99_rng_UC(state->c+34)])-(state->y=state->t[kiss99_rng_UC(state->c+19)]+state->bro))
+#define kiss99_rng_UNI(state) (kiss99_rng_KISS(state)*2.328306e-10)
+#define kiss99_rng_VNI(state) ((long) kiss99_rng_KISS(state))*4.656613e-10
+#define kiss99_rng_UC (unsigned char) /*a cast operation*/
 /* Global static variables: */
-static UL z=362436069, w=521288629, jsr=123456789, jcong=380116160;
-static UL a=224466889, b=7584631, t[256];
+typedef struct {
+	/* seed values */
+	uint32_t z/*=362436069*/;
+	uint32_t w/*=521288629*/;
+	uint32_t jsr/*=123456789*/;
+	uint32_t jcong/*=380116160*/;
+	uint32_t a/*=224466889*/;
+	uint32_t b/*=7584631*/;
+	/* state table */
+	uint32_t t[256];
+
+	/* non-seed state: init to 0 */
+	uint32_t x/*=0*/;
+	uint32_t y/*=0*/;
+
+	/* temporary storage */
+	uint32_t bro;
+
+	/* counter: init to zero */
+	unsigned char c/*=0*/;
+} kiss99_rng_state;
+
 /* Use random seeds to reset z,w,jsr,jcong,a,b, and the table
-t[256]*/
-static UL x=0,y=0,bro; static unsigned char c=0;
+*/
 /* Example procedure to set the table, using KISS: */
-void settable(UL i1,UL i2,UL i3,UL i4,UL i5, UL i6)
-{ int i; z=i1;w=i2,jsr=i3; jcong=i4; a=i5; b=i6;
-for(i=0;i<256;i=i+1) t[i]=KISS;
+void kiss99_rng_set_table(kiss99_rng_state* state, uint32_t i1,uint32_t i2,uint32_t i3,uint32_t i4,uint32_t i5,uint32_t i6) {
+	int i;
+
+	/* init state */
+	state->x = 0; state->y = 0; state->c = 0;
+
+	state->z=i1;state->w=i2,state->jsr=i3; state->jcong=i4; state->a=i5; state->b=i6;
+	for(i=0;i<256;i=i+1) state->t[i]=kiss99_rng_KISS(state);
 }
-/* This is a test main program. It should compile and print 7
-0's. */
-int main(void){
-int i; UL k;
-settable(12345,65435,34221,12345,9983651,95746118);
-for(i=1;i<1000001;i++){k=LFIB4;} printf("%u\n", k-1064612766U);
-for(i=1;i<1000001;i++){k=SWB ;} printf("%u\n", k- 627749721U);
-for(i=1;i<1000001;i++){k=KISS ;} printf("%u\n", k-1372460312U);
-for(i=1;i<1000001;i++){k=CONG ;} printf("%u\n", k-1529210297U);
-for(i=1;i<1000001;i++){k=SHR3 ;} printf("%u\n", k-2642725982U);
-for(i=1;i<1000001;i++){k=MWC ;} printf("%u\n", k- 904977562U);
-for(i=1;i<1000001;i++){k=FIB ;} printf("%u\n", k-3519793928U);
+/* This is a test main program. It should compile and print 7 0's. */
+int main(void) {
+	int i; uint32_t k;
+	kiss99_rng_state s;
+	kiss99_rng_state* state = &s;
+	kiss99_rng_set_table(state, 12345,65435,34221,12345,9983651,95746118);
+	for(i=1;i<1000001;i++){k=kiss99_rng_LFIB4(state);} printf("%u\n", k-1064612766U);
+	for(i=1;i<1000001;i++){k=kiss99_rng_SWB(state) ;} printf("%u\n", k- 627749721U);
+	for(i=1;i<1000001;i++){k=kiss99_rng_KISS(state) ;} printf("%u\n", k-1372460312U);
+	for(i=1;i<1000001;i++){k=kiss99_rng_CONG(state) ;} printf("%u\n", k-1529210297U);
+	for(i=1;i<1000001;i++){k=kiss99_rng_SHR3(state) ;} printf("%u\n", k-2642725982U);
+	for(i=1;i<1000001;i++){k=kiss99_rng_MWC(state) ;} printf("%u\n", k- 904977562U);
+	for(i=1;i<1000001;i++){k=kiss99_rng_FIB(state) ;} printf("%u\n", k-3519793928U);
 }
 /*-----------------------------------------------------
 Write your own calling program and try one or more of

From 1d8a42052fd698fa9bcb85580852e1b5f73f337d Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sun, 10 Apr 2016 22:20:26 -0500
Subject: [PATCH 29/55] Organise the KISS99 RNG headers and tests

---
 lib/numeric/kiss99_rng.c   | 60 ++++++-----------------------------
 lib/numeric/kiss99_rng.h   | 64 ++++++++++++++++++++++++++++++++++++++
 lib/t/numeric/kiss99_rng.c | 24 ++++++++++++++
 3 files changed, 97 insertions(+), 51 deletions(-)
 create mode 100644 lib/numeric/kiss99_rng.h
 create mode 100644 lib/t/numeric/kiss99_rng.c

diff --git a/lib/numeric/kiss99_rng.c b/lib/numeric/kiss99_rng.c
index 96f3a86..873d766 100644
--- a/lib/numeric/kiss99_rng.c
+++ b/lib/numeric/kiss99_rng.c
@@ -1,49 +1,13 @@
-#include <stdio.h>
-#include <stdint.h>
+#include "numeric/kiss99_rng.h"
 
 /*
  * George Marsaglia's KISS99 PRNG.
  *
- * Taken from Usenet posting from 1999-01-21 <http://www.cse.yorku.ca/~oz/marsaglia-rng.html>..
+ * Taken from Usenet posting from 1999-01-21 <http://www.cse.yorku.ca/~oz/marsaglia-rng.html>.
  *
  * Modified to keep state in struct.
  */
 
-#define kiss99_rng_znew(state) (state->z=36969*(state->z&65535)+(state->z>>16))
-#define kiss99_rng_wnew(state) (state->w=18000*(state->w&65535)+(state->w>>16))
-#define kiss99_rng_MWC(state) ((kiss99_rng_znew(state)<<16)+kiss99_rng_wnew(state) )
-#define kiss99_rng_SHR3(state) (state->jsr^=(state->jsr<<17), state->jsr^=(state->jsr>>13), state->jsr^=(state->jsr<<5))
-#define kiss99_rng_CONG(state) (state->jcong=69069*state->jcong+1234567)
-#define kiss99_rng_FIB(state) ((state->b=state->a+state->b),(state->a=state->b-state->a))
-#define kiss99_rng_KISS(state) ((kiss99_rng_MWC(state)^kiss99_rng_CONG(state))+kiss99_rng_SHR3(state))
-#define kiss99_rng_LFIB4(state) (state->c++,state->t[state->c]=state->t[state->c]+state->t[kiss99_rng_UC(state->c+58)]+state->t[kiss99_rng_UC(state->c+119)]+state->t[kiss99_rng_UC(state->c+178)])
-#define kiss99_rng_SWB(state) (state->c++,state->bro=(state->x<state->y),state->t[state->c]=(state->x=state->t[kiss99_rng_UC(state->c+34)])-(state->y=state->t[kiss99_rng_UC(state->c+19)]+state->bro))
-#define kiss99_rng_UNI(state) (kiss99_rng_KISS(state)*2.328306e-10)
-#define kiss99_rng_VNI(state) ((long) kiss99_rng_KISS(state))*4.656613e-10
-#define kiss99_rng_UC (unsigned char) /*a cast operation*/
-/* Global static variables: */
-typedef struct {
-	/* seed values */
-	uint32_t z/*=362436069*/;
-	uint32_t w/*=521288629*/;
-	uint32_t jsr/*=123456789*/;
-	uint32_t jcong/*=380116160*/;
-	uint32_t a/*=224466889*/;
-	uint32_t b/*=7584631*/;
-	/* state table */
-	uint32_t t[256];
-
-	/* non-seed state: init to 0 */
-	uint32_t x/*=0*/;
-	uint32_t y/*=0*/;
-
-	/* temporary storage */
-	uint32_t bro;
-
-	/* counter: init to zero */
-	unsigned char c/*=0*/;
-} kiss99_rng_state;
-
 /* Use random seeds to reset z,w,jsr,jcong,a,b, and the table
 */
 /* Example procedure to set the table, using KISS: */
@@ -56,20 +20,14 @@ void kiss99_rng_set_table(kiss99_rng_state* state, uint32_t i1,uint32_t i2,uint3
 	state->z=i1;state->w=i2,state->jsr=i3; state->jcong=i4; state->a=i5; state->b=i6;
 	for(i=0;i<256;i=i+1) state->t[i]=kiss99_rng_KISS(state);
 }
-/* This is a test main program. It should compile and print 7 0's. */
-int main(void) {
-	int i; uint32_t k;
-	kiss99_rng_state s;
-	kiss99_rng_state* state = &s;
-	kiss99_rng_set_table(state, 12345,65435,34221,12345,9983651,95746118);
-	for(i=1;i<1000001;i++){k=kiss99_rng_LFIB4(state);} printf("%u\n", k-1064612766U);
-	for(i=1;i<1000001;i++){k=kiss99_rng_SWB(state) ;} printf("%u\n", k- 627749721U);
-	for(i=1;i<1000001;i++){k=kiss99_rng_KISS(state) ;} printf("%u\n", k-1372460312U);
-	for(i=1;i<1000001;i++){k=kiss99_rng_CONG(state) ;} printf("%u\n", k-1529210297U);
-	for(i=1;i<1000001;i++){k=kiss99_rng_SHR3(state) ;} printf("%u\n", k-2642725982U);
-	for(i=1;i<1000001;i++){k=kiss99_rng_MWC(state) ;} printf("%u\n", k- 904977562U);
-	for(i=1;i<1000001;i++){k=kiss99_rng_FIB(state) ;} printf("%u\n", k-3519793928U);
+
+kiss99_rng_state* kiss99_rng_state_new() {
+	kiss99_rng_state* state;
+	NEW(state, kiss99_rng_state );
+
+	return state;
 }
+
 /*-----------------------------------------------------
 Write your own calling program and try one or more of
 the above, singly or in combination, when you run a
diff --git a/lib/numeric/kiss99_rng.h b/lib/numeric/kiss99_rng.h
new file mode 100644
index 0000000..be700f1
--- /dev/null
+++ b/lib/numeric/kiss99_rng.h
@@ -0,0 +1,64 @@
+#ifndef NUMERIC_KISS99_RNG
+#define NUMERIC_KISS99_RNG 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+#include <stdint.h>
+
+/* local headers */
+#include "util/util.h"
+
+/* structs, enums */
+#define KISS99_RNG_RANDOM_MAX UINT32_MAX
+
+typedef struct {
+	/* seed values */
+	uint32_t z/*=362436069*/;
+	uint32_t w/*=521288629*/;
+	uint32_t jsr/*=123456789*/;
+	uint32_t jcong/*=380116160*/;
+	uint32_t a/*=224466889*/;
+	uint32_t b/*=7584631*/;
+	/* state table */
+	uint32_t t[256];
+
+	/* non-seed state: init to 0 */
+	uint32_t x/*=0*/;
+	uint32_t y/*=0*/;
+
+	/* temporary storage */
+	uint32_t bro;
+
+	/* counter: init to zero */
+	unsigned char c/*=0*/;
+} kiss99_rng_state;
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Macros */
+#define kiss99_rng_znew(state) (state->z=36969*(state->z&65535)+(state->z>>16))
+#define kiss99_rng_wnew(state) (state->w=18000*(state->w&65535)+(state->w>>16))
+#define kiss99_rng_MWC(state) ((kiss99_rng_znew(state)<<16)+kiss99_rng_wnew(state) )
+#define kiss99_rng_SHR3(state) (state->jsr^=(state->jsr<<17), state->jsr^=(state->jsr>>13), state->jsr^=(state->jsr<<5))
+#define kiss99_rng_CONG(state) (state->jcong=69069*state->jcong+1234567)
+#define kiss99_rng_FIB(state) ((state->b=state->a+state->b),(state->a=state->b-state->a))
+#define kiss99_rng_KISS(state) ((kiss99_rng_MWC(state)^kiss99_rng_CONG(state))+kiss99_rng_SHR3(state))
+#define kiss99_rng_LFIB4(state) (state->c++,state->t[state->c]=state->t[state->c]+state->t[kiss99_rng_UC(state->c+58)]+state->t[kiss99_rng_UC(state->c+119)]+state->t[kiss99_rng_UC(state->c+178)])
+#define kiss99_rng_SWB(state) (state->c++,state->bro=(state->x<state->y),state->t[state->c]=(state->x=state->t[kiss99_rng_UC(state->c+34)])-(state->y=state->t[kiss99_rng_UC(state->c+19)]+state->bro))
+#define kiss99_rng_UNI(state) (kiss99_rng_KISS(state)*2.328306e-10)
+#define kiss99_rng_VNI(state) ((int32_t) kiss99_rng_KISS(state))*4.656613e-10
+#define kiss99_rng_UC (unsigned char) /*a cast operation*/
+
+/* Function prototypes */
+extern void kiss99_rng_set_table(kiss99_rng_state* state, uint32_t i1,uint32_t i2,uint32_t i3,uint32_t i4,uint32_t i5,uint32_t i6);
+extern kiss99_rng_state* kiss99_rng_state_new();
+
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* NUMERIC_KISS99_RNG */
diff --git a/lib/t/numeric/kiss99_rng.c b/lib/t/numeric/kiss99_rng.c
new file mode 100644
index 0000000..801260e
--- /dev/null
+++ b/lib/t/numeric/kiss99_rng.c
@@ -0,0 +1,24 @@
+#include <tap/basic.h>
+#include <stdint.h>
+
+#include "numeric/kiss99_rng.h"
+
+/* This is a test main program. It should compile and print 7 0's. */
+int main(int argc, char** argv) {
+	int i; uint32_t k;
+
+	kiss99_rng_state* state = kiss99_rng_state_new();
+	kiss99_rng_set_table(state, 12345,65435,34221,12345,9983651,95746118);
+
+	plan(7);
+
+	for(i=1;i<1000001;i++){k=kiss99_rng_LFIB4(state);} is_int(0, k-1064612766U, "LFIB4");
+	for(i=1;i<1000001;i++){k=kiss99_rng_SWB(state) ;} is_int(0, k- 627749721U, "SWB");
+	for(i=1;i<1000001;i++){k=kiss99_rng_KISS(state) ;} is_int(0, k-1372460312U, "KISS");
+	for(i=1;i<1000001;i++){k=kiss99_rng_CONG(state) ;} is_int(0, k-1529210297U, "CONG");
+	for(i=1;i<1000001;i++){k=kiss99_rng_SHR3(state) ;} is_int(0, k-2642725982U, "SHR3");
+	for(i=1;i<1000001;i++){k=kiss99_rng_MWC(state) ;} is_int(0, k- 904977562U, "MWC");
+	for(i=1;i<1000001;i++){k=kiss99_rng_FIB(state) ;} is_int(0, k-3519793928U, "FIB");
+
+	return EXIT_SUCCESS;
+}

From 811515f9a69f9d19f5de6dd9b0f077f8a4c36f1d Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 11 Apr 2016 13:14:40 -0500
Subject: [PATCH 30/55] Remove unused variable

---
 lib/io/path/path.c | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/io/path/path.c b/lib/io/path/path.c
index 366d254..a82ea8a 100644
--- a/lib/io/path/path.c
+++ b/lib/io/path/path.c
@@ -21,7 +21,6 @@ orion_filepath* orion_filepath_new_from_string(const char* fp_string) {
 	char* fp_string_norm;
 	size_t fp_string_norm_len;
 	safe_malloc_and_strcpy(&fp_string_norm, fp_string);
-	size_t fp_string_len = strlen( fp_string );
 
 	orion_filepath* fp = _orion_filepath_init();
 

From 953ecddf349aca02cfcdc5a88d0018bc642bf417 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 11 Apr 2016 13:15:37 -0500
Subject: [PATCH 31/55] Add structure member to segmentation parameters for RNG
 state

---
 .../01_Segmentation/dendrites_main/ORION3_Dendrites.c         | 2 ++
 lib/param/segmentation.h                                      | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
index 6e2f813..9a32faa 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
@@ -20,6 +20,8 @@ void orion_ORION3_Dendrites(orion_segmentation_param* param, ndarray3* vol) {
 	/* set the default parameters for the algorithm if none are set */
 	orion_settingDefaultParameters( param );
 
+	TODO(intialise param->rng_state);
+
 	/*DEBUG*/orion_segmentation_param_dump( param );
 
 	/*
diff --git a/lib/param/segmentation.h b/lib/param/segmentation.h
index b65b89f..fc8f5c3 100644
--- a/lib/param/segmentation.h
+++ b/lib/param/segmentation.h
@@ -6,13 +6,15 @@
 
 #include "container/array.h"
 #include "util/float.h"
-
+#include "numeric/random.h"
 
 typedef struct {
 	array_float* scales;     /* sigma */
 	bool multiscale;
 	size_t number_of_stacks; /* length of volume_names */
 
+	orion_rand_state_t* rng_state;
+
 #define ATTR( NAME, TYPE ) \
 	bool has_ ## NAME; \
 	TYPE NAME;

From f077520c525a8f3c3b82c41cdbaa3bdd04da4a8f Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sat, 16 Apr 2016 11:23:02 -0500
Subject: [PATCH 32/55] Add function to free RNG state

---
 lib/numeric/kiss99_rng.c | 4 ++++
 lib/numeric/kiss99_rng.h | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/numeric/kiss99_rng.c b/lib/numeric/kiss99_rng.c
index 873d766..3c42942 100644
--- a/lib/numeric/kiss99_rng.c
+++ b/lib/numeric/kiss99_rng.c
@@ -28,6 +28,10 @@ kiss99_rng_state* kiss99_rng_state_new() {
 	return state;
 }
 
+void kiss99_rng_state_free(kiss99_rng_state* state) {
+	free(state);
+}
+
 /*-----------------------------------------------------
 Write your own calling program and try one or more of
 the above, singly or in combination, when you run a
diff --git a/lib/numeric/kiss99_rng.h b/lib/numeric/kiss99_rng.h
index be700f1..052606b 100644
--- a/lib/numeric/kiss99_rng.h
+++ b/lib/numeric/kiss99_rng.h
@@ -55,7 +55,7 @@ extern "C" {
 /* Function prototypes */
 extern void kiss99_rng_set_table(kiss99_rng_state* state, uint32_t i1,uint32_t i2,uint32_t i3,uint32_t i4,uint32_t i5,uint32_t i6);
 extern kiss99_rng_state* kiss99_rng_state_new();
-
+extern void kiss99_rng_state_free(kiss99_rng_state* state);
 
 #ifdef __cplusplus
 };

From 0ca88ca39dba0a053bb9201bf2ae2a93edea41c0 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sat, 16 Apr 2016 12:07:57 -0500
Subject: [PATCH 33/55] initialise the RNG when starting the segmentation

---
 .../dendrites_main/ORION3_Dendrites.c         |  9 +++-
 lib/numeric/random.c                          | 54 +++++++++++++++++++
 lib/numeric/random.h                          | 29 ++++++++++
 3 files changed, 91 insertions(+), 1 deletion(-)
 create mode 100644 lib/numeric/random.c
 create mode 100644 lib/numeric/random.h

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
index 9a32faa..c12b6dc 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
@@ -5,9 +5,14 @@
 
 
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h"
+#include "kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/getFeatures.h"
+#include "kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.h"
 
 #include "kitchen-sink/01_Segmentation/dendrites_main/settingDefaultParameters.h"
 
+#include "segmentation/orion_discriminant.h"
+#include "numeric/random.h"
+
 /*
  * Segmentation process which computes the distribution of the eigenvalues of
  * the Hessian matrix and assigns a cost function to eliminate background
@@ -20,7 +25,9 @@ void orion_ORION3_Dendrites(orion_segmentation_param* param, ndarray3* vol) {
 	/* set the default parameters for the algorithm if none are set */
 	orion_settingDefaultParameters( param );
 
-	TODO(intialise param->rng_state);
+	/* intialise PRNG */
+	param->rng_state = kiss99_rng_state_new();
+	kiss99_rng_init(param->rng_state);
 
 	/*DEBUG*/orion_segmentation_param_dump( param );
 
diff --git a/lib/numeric/random.c b/lib/numeric/random.c
new file mode 100644
index 0000000..41ccb21
--- /dev/null
+++ b/lib/numeric/random.c
@@ -0,0 +1,54 @@
+#include "config/config.h"
+
+#include "numeric/random.h"
+
+#if OS_UNIX
+  #include <sys/types.h>
+  #include <sys/stat.h>
+  #include <fcntl.h>
+  #include <unistd.h>
+#endif
+
+float64 orion_rand_uniform_dist(orion_rand_state_t* state) {
+	return ( (float64) kiss99_rng_KISS( state ) ) / KISS99_RNG_RANDOM_MAX;
+}
+
+uint32_t _orion_rand_seeds() {
+	uint32_t r;
+
+#if OS_UNIX
+	/* read from /dev/urandom */
+	int fn;
+	fn = open("/dev/urandom", O_RDONLY);
+	if (fn == - 1)
+		exit( -1 );
+	/* Failed ! */
+	if ( read(fn, &r, 4) != 4)
+		exit( - 1) ;
+	/* Failed ! */
+	close(fn);
+#elif defined(_CRT_RAND_S)
+	rand_s( &r );
+#else
+	die("%s", "Random seeding not implemented on this platform");
+#endif
+
+	return r;
+}
+
+/* Based on the report "Good Practice in (Pseudo)Random Number Generation for
+ * Bioinformatics Applications" by David Jones.
+ * <http://www0.cs.ucl.ac.uk/staff/d.jones/GoodPracticeRNG.pdf>
+ */
+/* Initialise KISS generator using /dev/urandom */
+void kiss99_rng_init(kiss99_rng_state* state) {
+	state->x = _orion_rand_seeds();
+	while (!( state->y = _orion_rand_seeds())); /* y must not be zero !  */
+	state->z = _orion_rand_seeds() ;
+	/* We don’t really need to set c as well but
+	   let's anyway
+	   ... */
+	/* NOTE: offset c by 1 to avoid z=c=0 */
+	state->c = _orion_rand_seeds() % 698769068 + 1; /* Should be less than 698769069 */
+}
+
diff --git a/lib/numeric/random.h b/lib/numeric/random.h
new file mode 100644
index 0000000..bac597f
--- /dev/null
+++ b/lib/numeric/random.h
@@ -0,0 +1,29 @@
+#ifndef ORION_NUMERIC_RANDOM_H
+#define ORION_NUMERIC_RANDOM_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+#include <stdint.h>
+
+/* local headers */
+#include "util/util.h"
+#include "numeric/kiss99_rng.h"
+
+/* structs, enums */
+typedef kiss99_rng_state orion_rand_state_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+extern
+float64 orion_rand_uniform_dist(orion_rand_state_t* state);
+extern void kiss99_rng_init(kiss99_rng_state* state);
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* ORION_NUMERIC_RANDOM_H */

From 39c203d7eb9ed344e6fcfb632f12441bb4ae2412 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sat, 16 Apr 2016 12:10:07 -0500
Subject: [PATCH 34/55] Project specific Vim settings with autocmd

---
 session.vim | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/session.vim b/session.vim
index 2b0b805..d4a5cf8 100644
--- a/session.vim
+++ b/session.vim
@@ -1,4 +1,3 @@
-set path+=lib
 let g:syntastic_c_include_dirs = [
 			\ 'lib',
 			\ 'external/c-tap-harness/c-tap-harness/tests',
@@ -38,4 +37,18 @@ function! ORION_GotoCorresponding()
 	endif
 endfunction
 
-nmap ,gg :call ORION_GotoCorresponding()<Return>
+augroup ORION_project
+	au!
+	exe "autocmd BufRead ". expand("<sfile>:p:h")."/* call ORION_project_settings()"
+augroup END
+
+function! ORION_project_settings()
+setl path+=lib
+
+compiler gcc
+let &l:makeprg='export CFLAGS="$CFLAGS -fPIC -Wall"; make PROD=1 BUILD_DEBUG=1 BUILD_ENABLE_ASAN=0 -j4'
+
+nmap <buffer> <F5> :make<Return>
+nmap <buffer> ,gg :call ORION_GotoCorresponding()<Return>
+
+endfunction

From 821a7d9b37372838625d00605fa9a85565ed52d8 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sat, 16 Apr 2016 12:13:54 -0500
Subject: [PATCH 35/55] Add algorithm for sampling without replacement

---
 lib/numeric/sample.c | 63 ++++++++++++++++++++++++++++++++++++++++++++
 lib/numeric/sample.h | 28 ++++++++++++++++++++
 2 files changed, 91 insertions(+)
 create mode 100644 lib/numeric/sample.c
 create mode 100644 lib/numeric/sample.h

diff --git a/lib/numeric/sample.c b/lib/numeric/sample.c
new file mode 100644
index 0000000..2de7c8f
--- /dev/null
+++ b/lib/numeric/sample.c
@@ -0,0 +1,63 @@
+#include "numeric/sample.h"
+
+#include <assert.h>
+
+/* Returns an array_int of length `sample_size`
+ * where each element is
+ *
+ * - in the range 0 to `population_size` - 1 and
+ * - sampled randomly without replacement.
+ *
+ * See Algorithm 3.4.2S of Knuth's book Seminumeric Algorithms: "Selection
+ * Sampling Technique".
+ */
+array_int* array_random_sample_int(
+		orion_rand_state_t* rng_state,
+		uint32_t sample_size,
+		uint32_t population_size) {
+	/* we can not sample more things than actually exist */
+	assert( sample_size <= population_size );
+
+	array_int* samples = array_new_int( sample_size );
+
+	/* To select $ n $ records at random from a set of $ N $, where
+	 * $ 0 < n ≤ N $ .  */
+	uint32_t n = sample_size;
+	uint32_t N = population_size;
+
+	/* S1. [Initialise.]
+	 *********************
+	 * - m: number of records selected so far
+	 * - t: total number of input records we have dealt with */
+	uint32_t m = 0;
+	uint32_t t = 0;
+
+	while( m < n ) {
+		/* S2. [Generate $ U $.]
+		 *************************
+		 * Generate a random number $ U $, from a uniform distribution
+		 * $ uniform(0, 1) $.  */
+		float32 U = orion_rand_uniform_dist(rng_state);
+		/* S3. [Test.]
+		 ***************
+		 * If $ (N - t) U ≥ n - m $, go to step S5. */
+		if( (N - t) * U >= n - m ) {
+			/* S5. [Skip.]
+			 ***************
+			 * Skip the next record (do not include it in the
+			 * sample), increase t by 1, and go to step S2.  */
+			t++;
+			continue;
+		} else {
+			/* S4. [Select.]
+			 *****************
+			 * Select the next record for the sample, and increase
+			 * m and t by 1.  If m < n, go to step S2; otherwise
+			 * the sample is complete and the algorithm terminates.  */
+			array_add_int( samples, t ); /* set m-th element to t */
+			m++;
+			t++;
+		}
+
+	}
+}
diff --git a/lib/numeric/sample.h b/lib/numeric/sample.h
new file mode 100644
index 0000000..51ee399
--- /dev/null
+++ b/lib/numeric/sample.h
@@ -0,0 +1,28 @@
+#ifndef NUMERIC_SAMPLE_H
+#define NUMERIC_SAMPLE_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+#include <stdint.h>
+
+/* local headers */
+#include "container/array.h"
+#include "numeric/random.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+extern
+array_int* array_random_sample_int(
+		orion_rand_state_t* rng_state,
+		uint32_t sample_size,
+		uint32_t population_size);
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* NUMERIC_SAMPLE_H */

From 11469a860948cc99ed90600806fc80c92576c8d7 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sat, 16 Apr 2016 12:14:29 -0500
Subject: [PATCH 36/55] Add test for uniform RNG (mean and variance)

---
 lib/t/numeric/random.c | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 lib/t/numeric/random.c

diff --git a/lib/t/numeric/random.c b/lib/t/numeric/random.c
new file mode 100644
index 0000000..5c39dbf
--- /dev/null
+++ b/lib/t/numeric/random.c
@@ -0,0 +1,42 @@
+#include <tap/basic.h>
+#include <tap/float.h>
+
+#include <math.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "numeric/random.h"
+#include "util/util.h"
+
+int main(int argc, char** argv) {
+	plan(2);
+
+
+	kiss99_rng_state* state = kiss99_rng_state_new();
+	kiss99_rng_init( state );
+
+	const size_t number_of_samples = 1E7;
+	/* theoretical mean and variance of
+	 * uniform distribution U(0,1) */
+	const float64 uniform_dist_mean = 0.5;
+	const float64 uniform_dist_var = 1.0/12.0;
+
+	float64 sum = 0.0;
+	float64 sum_of_sq = 0.0;
+	for( int i = 0; i < number_of_samples; i++ ) {
+		float64 sample = orion_rand_uniform_dist( state );
+
+		sum += sample;
+		sum_of_sq += SQUARED( sample - uniform_dist_mean );
+	}
+
+	float64 mean = sum / number_of_samples;
+	float64 var = sum_of_sq / number_of_samples;
+
+	/* 2 tests */
+	is_double( uniform_dist_mean, mean, 1E-3, "Mean of U(0,1) = 1/2" );
+	is_double( uniform_dist_var, var, 1E-3, "Variance of U(0,1) = 1/12" );
+
+	return EXIT_SUCCESS;
+}

From 3f4f73150b217bcef0e82eca9b61f82e046b059f Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Sun, 17 Apr 2016 14:53:15 -0500
Subject: [PATCH 37/55] Return the sample array

---
 lib/numeric/sample.c | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/numeric/sample.c b/lib/numeric/sample.c
index 2de7c8f..ee2e6ad 100644
--- a/lib/numeric/sample.c
+++ b/lib/numeric/sample.c
@@ -60,4 +60,6 @@ array_int* array_random_sample_int(
 		}
 
 	}
+
+	return samples;
 }

From e4087babb8e5e1251047f70db8de01efea7de8d7 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 25 Apr 2016 13:42:40 -0500
Subject: [PATCH 38/55] Update the discriminant function code

---
 .../compute2D_DiscrimantFunction.c            | 152 ++++++++++++++++++
 .../compute2D_DiscrimantFunction.h            |  33 ++++
 .../removeIsolatedResponses.c                 | 110 +++++++++++++
 .../removeIsolatedResponses.h                 |  34 ++++
 .../dendrites_main/ORION3_Dendrites.c         |  47 +++++-
 lib/segmentation/orion_discriminant.h         |  42 +++++
 6 files changed, 417 insertions(+), 1 deletion(-)
 create mode 100644 lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.h
 create mode 100644 lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h
 create mode 100644 lib/segmentation/orion_discriminant.h

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
index b516beb..d7855a6 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
@@ -1,4 +1,156 @@
+#include "kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.h"
+
+#include "kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h"
+
 /* TODO
  *
  * Refactor: compute2D_DiscrimantFunction
  */
+
+#define MAX_NUMBER_OF_HISTOGRAM_SAMPLES 1E6
+
+#include "numeric/sample.h"
+#include <math.h>
+#include <float.h>
+#include <assert.h>
+
+/* Private prototypes */
+void orion_hist3(
+		orion_segmentation_param* param,
+		orion_features* features,
+		array_int* indices,
+		orion_discriminant_function* discrim
+		);
+
+void orion_normaliseHistogram(
+		orion_segmentation_param* param,
+		orion_discriminant_function* discrim
+		);
+
+void orion_compute2D_DiscrimantFunction(
+		orion_segmentation_param* param,
+		orion_features* features,
+		array_int* instance_indices,
+		orion_discriminant_function* discrim
+		) {
+
+	size_t n_samples = array_length_int( instance_indices );
+	array_int* sample_instance_indices;
+	array_int* non_isolated_instance_indices;
+
+	if( n_samples > MAX_NUMBER_OF_HISTOGRAM_SAMPLES ) {
+		/* only process at most MAX_NUMBER_OF_HISTOGRAM_SAMPLES features */
+		sample_instance_indices =
+			array_random_sample_int(param->rng_state, n_samples, MAX_NUMBER_OF_HISTOGRAM_SAMPLES);
+		n_samples = MAX_NUMBER_OF_HISTOGRAM_SAMPLES;
+	} else {
+		/* we take it all */
+		sample_instance_indices =
+			array_new_int(n_samples);
+		for( size_t sample_idx = 0; sample_idx < n_samples; sample_idx++ ) {
+			array_add_int( sample_instance_indices, sample_idx );
+		}
+	}
+
+	/* remove noisy points and select instances outside a threshold */
+	orion_removeIsolatedResponses(
+		param,
+		features,
+		discrim,
+		sample_instance_indices,
+		&non_isolated_instance_indices );
+
+	n_samples = array_length_int( non_isolated_instance_indices );
+
+	/* set the binning parameters */
+	for( size_t feat_idx = 0; feat_idx < features->number_of_features; feat_idx++ ) {
+		discrim->min_value[feat_idx] =  FLT_MAX;
+		discrim->max_value[feat_idx] = -FLT_MAX;
+	}
+	for( size_t sample_idx = 0; sample_idx < n_samples; sample_idx++ ) {
+		size_t actual_sample_idx =
+			array_get_int(non_isolated_instance_indices, sample_idx);
+		for( size_t feat_idx = 0; feat_idx < features->number_of_features; feat_idx++ ) {
+			pixel_type cur_feature = vector_get_float(
+					features->features[feat_idx],
+					actual_sample_idx);
+			if( cur_feature < discrim->min_value[feat_idx] ) {
+				discrim->min_value[feat_idx] = cur_feature;
+			}
+			if( cur_feature > discrim->max_value[feat_idx] ) {
+				discrim->max_value[feat_idx] = cur_feature;
+			}
+		}
+	}
+	for( size_t feat_idx = 0; feat_idx < features->number_of_features; feat_idx++ ) {
+		discrim->step_size[feat_idx] =
+			( discrim->max_value[feat_idx] - discrim->min_value[feat_idx] )
+			/ ( param->bins );
+		/*[>DEBUG<]LOG_DEBUG( "feat: %d ; min: %f ; max: %f ; bins: %u ; step_size: %e",
+				feat_idx,
+				discrim->min_value[feat_idx],
+				discrim->max_value[feat_idx],
+				param->bins,
+				discrim->step_size[feat_idx]
+				);*/
+	}
+
+	/* compute the 2D histogram for edges */
+	orion_hist3(param, features, non_isolated_instance_indices, discrim);
+
+	/* normalise the histogram in order to compute the cost function */
+	orion_normaliseHistogram(param, discrim);
+
+	array_free_int( non_isolated_instance_indices );
+	array_free_int( sample_instance_indices );
+}
+
+/* Creates a 2D histogram
+ *
+ * TODO
+ *
+ * See also: MATLAB's hist3 function
+ */
+void orion_hist3(
+		orion_segmentation_param* param,
+		orion_features* features,
+		array_int* indices,
+		orion_discriminant_function* discrim
+		) {
+	/* we only support 2 features because this is a 2D histogram */
+	assert( 2 == features->number_of_features );
+	size_t indices_sz = array_length_int(indices);
+	size_t* feat_bin_idx;
+	NEW_COUNT( feat_bin_idx, size_t, features->number_of_features );
+
+	/* NOTE: histogram is allocated here: if the size of the bins change
+	 * for each dimension, then this will need to change */
+	discrim->histogram = ndarray3_new( param->bins, param->bins, 1);
+	NDARRAY3_LOOP_OVER_START( discrim->histogram, i,j,k ) {
+		ndarray3_set( discrim->histogram, i,j,k, 0.0 );
+	} NDARRAY3_LOOP_OVER_END;
+
+	for( int indices_idx = 0; indices_idx < indices_sz; indices_idx++ ) {
+		size_t feat_instance_idx = array_get_int( indices, indices_idx );
+		for( size_t feat_idx = 0; feat_idx < features->number_of_features; feat_idx++ ) {
+			pixel_type cur_feature = vector_get_float(
+					features->features[feat_idx],
+					feat_instance_idx);
+			feat_bin_idx[feat_idx] = floorf(
+					( cur_feature - discrim->min_value[feat_idx] )
+					/ ( discrim->step_size[feat_idx] )
+					);
+		}
+		/* increment by 1 */
+		ndarray3_set( discrim->histogram, feat_bin_idx[0], feat_bin_idx[1], 0,
+				1.0 + ndarray3_get(discrim->histogram, feat_bin_idx[0], feat_bin_idx[1], 0)
+				);
+	}
+}
+
+void orion_normaliseHistogram(
+		orion_segmentation_param* param,
+		orion_discriminant_function* discrim
+		) {
+	WARN_UNIMPLEMENTED;
+}
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.h
new file mode 100644
index 0000000..e23373d
--- /dev/null
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.h
@@ -0,0 +1,33 @@
+#ifndef ORION_COMPUTE2D_DISCRIM_H
+#define ORION_COMPUTE2D_DISCRIM_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+
+/* local headers */
+#include "segmentation/orion_discriminant.h"
+#include "container/array.h"
+#include "segmentation/orion_features.h"
+#include "param/segmentation.h"
+
+/* structs, enums */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+extern
+void orion_compute2D_DiscrimantFunction(
+		orion_segmentation_param* param,
+		orion_features* features,
+		array_int* instance_indices,
+		orion_discriminant_function* discrim
+		);
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* ORION_COMPUTE2D_DISCRIM_H */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c
index 8f7706c..5edf1dc 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c
@@ -1,4 +1,114 @@
+#include "kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h"
 /* TODO
  *
  * Refactor: removeIsolatedResponses
  */
+
+#include "numeric/sample.h"
+#include <float.h>
+#include "simple-log/simplelog.h"
+
+/* orion_removeIsolatedResponses
+ *
+ * Identify the indices of features that are non-isolated so that only features
+ * that are representative of a cluster are examined as part of the histogram.
+ */
+void orion_removeIsolatedResponses(
+		orion_segmentation_param* param,
+		orion_features*  features,
+		orion_discriminant_function* discrim,
+		array_int* sample_instance_indices,
+		array_int** non_isolated_instance_indices
+		) {
+
+	pixel_type* min_bound;
+	pixel_type* max_bound;
+
+	NEW_COUNT( min_bound, pixel_type, features->number_of_features );
+	NEW_COUNT( max_bound, pixel_type, features->number_of_features );
+
+	size_t sample_instance_indices_size = array_length_int( sample_instance_indices );
+
+	uint32_t iterations = 200;
+	size_t samples_in_each_round = 200;
+	if( samples_in_each_round > sample_instance_indices_size ) {
+		samples_in_each_round = sample_instance_indices_size;
+	}
+
+	*non_isolated_instance_indices = array_new_int( sample_instance_indices_size );
+
+
+	for( int feat_idx = 0; feat_idx < features->number_of_features; feat_idx++ ) {
+		/* init bounds to zero */
+		min_bound[feat_idx] = 0;
+		max_bound[feat_idx] = 0;
+
+		/* sample each feature independently */
+		for( uint32_t sample_round = 0; sample_round < iterations ; sample_round++ ) {
+			array_int* sample = array_random_sample_int(
+					param->rng_state,
+					samples_in_each_round,
+					sample_instance_indices_size );
+
+			pixel_type min_for_round = FLT_MAX, max_for_round = -FLT_MAX;
+			for( int sample_idx = 0; sample_idx < samples_in_each_round; sample_idx++ ) {
+				size_t sample_instance_idx = array_get_int( sample, sample_idx );
+				size_t instance_idx = array_get_int( sample_instance_indices, sample_instance_idx );
+
+				pixel_type cur_feature = vector_get_float(
+							features->features[feat_idx],
+							instance_idx
+						);
+
+				if( min_for_round > cur_feature ) { min_for_round = cur_feature; }
+				if( max_for_round < cur_feature ) { max_for_round = cur_feature; }
+			}
+
+			/* divide by iterations because we want the average of all the
+			 * rounds */
+			min_bound[feat_idx] += min_for_round / iterations;
+			max_bound[feat_idx] += max_for_round / iterations;
+
+			array_free_int( sample );
+			/*[>DEBUG<]LOG_DEBUG( "feat: %d ; min: %e ; max: %e",
+					feat_idx,
+					min_bound[feat_idx],
+					max_bound[feat_idx]);*/
+		}
+
+		pixel_type interval_size = max_bound[feat_idx] - min_bound[feat_idx];
+		pixel_type mean = (max_bound[feat_idx] - min_bound[feat_idx]) / 2.0;
+
+		/* re-assign to min and max bounds by creating region that is
+		 * three times the interval size */
+		min_bound[feat_idx] = mean - 2 * interval_size;
+		max_bound[feat_idx] = mean + 2 * interval_size;
+		/*[>DEBUG<]LOG_DEBUG( "feat: %d ; min: %e ; max: %e",
+				feat_idx,
+				min_bound[feat_idx],
+				max_bound[feat_idx]);*/
+	}
+
+	/* only keep values that are within both bounds */
+	for( int i = 0; i < sample_instance_indices_size; i++ ) {
+		size_t current_sample_idx = array_get_int( sample_instance_indices, i );
+		/* check if the feature is in the bounds for all features */
+		bool in_bounds = true;
+		for( int feat_idx = 0; in_bounds && feat_idx < features->number_of_features; feat_idx++ ) {
+			pixel_type cur_feature = vector_get_float(
+						features->features[feat_idx],
+						current_sample_idx
+					);
+			/*[>DEBUG<]LOG_DEBUG("cur feature: %f", cur_feature);*/
+			in_bounds &= cur_feature >= min_bound[feat_idx]
+				&&   cur_feature <= max_bound[feat_idx];
+		}
+		if( in_bounds ) {
+			array_add_int( *non_isolated_instance_indices, current_sample_idx );
+		}
+	}
+
+
+	free( min_bound );
+	free( max_bound );
+}
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h
new file mode 100644
index 0000000..57be871
--- /dev/null
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h
@@ -0,0 +1,34 @@
+#ifndef ORION_REMOVE_ISOLATED_REZ_H
+#define ORION_REMOVE_ISOLATED_REZ_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+
+/* local headers */
+#include "segmentation/orion_discriminant.h"
+#include "container/array.h"
+#include "segmentation/orion_features.h"
+#include "param/segmentation.h"
+
+/* structs, enums */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+extern
+void orion_removeIsolatedResponses(
+		orion_segmentation_param* param,
+		orion_features*  features,
+		orion_discriminant_function* discrim,
+		array_int* sample_instance_indices,
+		array_int** non_isolated_instance_indices
+		);
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* ORION_REMOVE_ISOLATED_REZ_H */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
index c12b6dc..4f8098e 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ORION3_Dendrites.c
@@ -40,7 +40,52 @@ void orion_ORION3_Dendrites(orion_segmentation_param* param, ndarray3* vol) {
 	 * reading background samples using the Laplacian with the ISOTROPIC LOW
 	 * PASS FILTER
 	 */
-	orion_readNegativeSamples(param, vol);
+	orion_multiscale_laplacian_output*
+		lap_output = orion_readNegativeSamples(param, vol);
+
+	/*
+	 * STEP 2
+	 *
+	 * Compute the feature vector
+	 */
+	orion_features* features = orion_getFeatures( param, vol, lap_output );
+
+	/* STEP 3
+	 *
+	 * Compute the discriminant functions and their response
+	 */
+	pixel_type min_scale, max_scale;
+	ndarray3_minmax(lap_output->max_response_at_scale_idx,
+			&min_scale, &max_scale );
+	/* Compute the discriminant function for each scale. */
+	orion_discriminant_function* discrim;
+	/* used to store the indices of the training instances */
+	array_int* scale_instances = array_new_int(10);
+	for( int scale_idx = min_scale; scale_idx <= max_scale; scale_idx++ ) {
+		/* Training instances for current scale:
+		 * Find all background features for this scale.
+		 */
+		array_reset_int(scale_instances); /* start the count over again */
+		for( size_t f_idx = 0; f_idx < features->number_of_instances; f_idx++ ) {
+			bool feat_is_background = (bool)(lap_output->is_background->p[f_idx]);
+			size_t feat_scale = (size_t)(lap_output->max_response_at_scale_idx->p[f_idx]);
+
+			if( feat_is_background && feat_scale == scale_idx ) {
+				array_add_int( scale_instances, f_idx );
+			}
+		}
+		LOG_DEBUG("There are %d training samples for the scale %f [index: %d]",
+				array_length_int(scale_instances),
+				array_get_float( param->scales, scale_idx ),
+				scale_idx );
+
+		orion_compute2D_DiscrimantFunction(param, features, scale_instances, discrim);
+	}
+	array_free_int(scale_instances);
 
 	WARN_UNIMPLEMENTED;
+
+	orion_multiscale_laplacian_output_free( lap_output );
+	orion_features_free(features);
+	kiss99_rng_state_free( param->rng_state );
 }
diff --git a/lib/segmentation/orion_discriminant.h b/lib/segmentation/orion_discriminant.h
new file mode 100644
index 0000000..22c7240
--- /dev/null
+++ b/lib/segmentation/orion_discriminant.h
@@ -0,0 +1,42 @@
+#ifndef ORION_DISCRIMINANT_H
+#define ORION_DISCRIMINANT_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+
+/* local headers */
+#include "segmentation/orion_features.h"
+#include "container/vector.h"
+#include "ndarray/ndarray3.h"
+
+/* structs, enums */
+/*TODO(Define struct members)*/
+typedef struct {
+
+	ndarray3* histogram; /* dimensions: [m, n, 1] */
+
+
+	/* store the minimum and maximum value for each feature */
+	pixel_type min_value[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
+	pixel_type max_value[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
+	/* for calculating the step size */
+	pixel_type step_size[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
+
+	/* location of bin edges for lookup */
+	vector_float* edges[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
+} orion_discriminant_function;
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+
+
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* ORION_DISCRIMINANT_H */

From f15e9829bffb3036506054d6c9fa6bbf59a7e74f Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 25 Apr 2016 14:05:31 -0500
Subject: [PATCH 39/55] Use die() instead of exit() for failures in
 _orion_rand_seeds

---
 lib/numeric/random.c | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/numeric/random.c b/lib/numeric/random.c
index 41ccb21..624892a 100644
--- a/lib/numeric/random.c
+++ b/lib/numeric/random.c
@@ -19,13 +19,14 @@ uint32_t _orion_rand_seeds() {
 #if OS_UNIX
 	/* read from /dev/urandom */
 	int fn;
-	fn = open("/dev/urandom", O_RDONLY);
+	char random_device[] = "/dev/urandom";
+	fn = open(random_device, O_RDONLY);
 	if (fn == - 1)
-		exit( -1 );
-	/* Failed ! */
+		/* Failed ! */
+		die("Could not open %s for seeding RNG", random_device);
 	if ( read(fn, &r, 4) != 4)
-		exit( - 1) ;
-	/* Failed ! */
+		/* Failed ! */
+		die("Could not read %s for seeding RNG", random_device);
 	close(fn);
 #elif defined(_CRT_RAND_S)
 	rand_s( &r );

From 7ee10ec025ace4900b36747407223e9a0f3ce64d Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 25 Apr 2016 15:16:51 -0500
Subject: [PATCH 40/55] Add platform-specific defines

---
 lib/config/platform.h     | 41 +++++++++++++++++++++++++++++++++++++++
 src/config/configurator.c |  8 +++-----
 2 files changed, 44 insertions(+), 5 deletions(-)
 create mode 100644 lib/config/platform.h

diff --git a/lib/config/platform.h b/lib/config/platform.h
new file mode 100644
index 0000000..5ac9700
--- /dev/null
+++ b/lib/config/platform.h
@@ -0,0 +1,41 @@
+#ifndef CONFIG_PLATFORM_H
+#define CONFIG_PLATFORM_H 1
+
+/* define OS_* macros */
+#if defined(_WIN32)
+  #define OS_WINDOWS 1
+#else
+  #define OS_UNIX 1
+#endif
+
+
+/* Platform specific settings */
+
+/* On Windows */
+#if OS_WINDOWS
+  #if _MSC_VER && !__INTEL_COMPILER
+    /* Microsoft compiler */
+
+    /* needed for the secure rand_s function */
+    #define _CRT_RAND_S 1
+    #include <stdlib.h>
+
+  #endif
+
+  /* the extension used for executables */
+  #ifndef PLATFORM_EXE_EXT
+    #define PLATFORM_EXE_EXT ".exe"
+  #endif /* PLATFORM_EXE_EXT */
+
+#endif /* OS_WINDOWS */
+
+#if OS_UNIX
+
+  /* the extension used for executables */
+  #ifndef PLATFORM_EXE_EXT
+    #define PLATFORM_EXE_EXT ""
+  #endif /* PLATFORM_EXE_EXT */
+
+#endif /* OS_UNIX */
+
+#endif /* CONFIG_PLATFORM_H */
diff --git a/src/config/configurator.c b/src/config/configurator.c
index 0eceada..036d9aa 100644
--- a/src/config/configurator.c
+++ b/src/config/configurator.c
@@ -1,3 +1,5 @@
+#include "config/platform.h"
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <stdbool.h>
@@ -9,11 +11,6 @@
 
 #define COMMAND_LINE_BUFFER_LENGTH 16384 /* pow(2,14) */
 
-/* the extension used for executables */
-#ifndef PLATFORM_EXE_EXT
-#define PLATFORM_EXE_EXT ""
-#endif /* PLATFORM_EXE_EXT */
-
 #define DEFAULT_CC "cc"
 #define DEFAULT_CFLAGS "-g3 -ggdb -Wall -Wundef -Wmissing-prototypes -Wmissing-declarations -Wstrict-prototypes -Wold-style-definition"
 
@@ -24,6 +21,7 @@
 #define CONFIG_HEADER_START \
 	"#ifndef CONFIG_H\n" \
 	"#define CONFIG_H 1\n\n" \
+	"#include \"config/platform.h\"\n\n" \
 
 #define CONFIG_HEADER_END \
 	"\n\n" \

From fb29a59110bcd425822bd232abc0136c5c32ebab Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 25 Apr 2016 15:17:41 -0500
Subject: [PATCH 41/55] Configuration generator output needs warning about
 editing

---
 src/config/configurator.c | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/config/configurator.c b/src/config/configurator.c
index 036d9aa..3a79e85 100644
--- a/src/config/configurator.c
+++ b/src/config/configurator.c
@@ -142,6 +142,10 @@ int main( int argc, char** argv ) {
 
 	FILE* config_h_fh = stdout;
 		/*= fopen(CONFIG_HEADER_FILENAME, "w");*/
+
+	/* warning to people that might want to edit the file */
+	fprintf(config_h_fh, "/* Generated by %s. DO NOT EDIT! */\n\n", argv[0]);
+
 	fprintf(config_h_fh, CONFIG_HEADER_START);
 	for(int test_idx = 0 ; test_idx < n_of_tests; test_idx++ ) {
 		config_test* cur_test = &config_test_gen[test_idx];

From 9405b057fa66fdb99a42beacca9935edc6f6160e Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 25 Apr 2016 15:18:24 -0500
Subject: [PATCH 42/55] Add NOECHO setting to decrease build output

This helps avoid having to see the long series of compiler flags.
---
 make/00-implicit-rules.mk | 15 ++++++++++-----
 make/helper.mk            |  3 +++
 make/liborion.mk          |  5 +++--
 3 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/make/00-implicit-rules.mk b/make/00-implicit-rules.mk
index ed8f4b6..18c54da 100644
--- a/make/00-implicit-rules.mk
+++ b/make/00-implicit-rules.mk
@@ -2,12 +2,14 @@
 $(BUILDDIR)/%.o : $(LIBDIR)/%.c
 	@$(MKDIR_DEPEND.c)
 	@$(MKDIR_BUILD)
-	$(COMPILE.c) -o $@ $<
+	@echo "  [ CC SRC $@ ]"
+	$(NOECHO)$(COMPILE.c) -o $@ $<
 
 $(BUILDTESTDIR)/%$(EXEEXT): $(TESTDIR)/%.c
 	@$(MKDIR_DEPEND.c)
 	@$(MKDIR_BUILDTESTDIR)
-	$(LINK.c) $^ $(LOADLIBES) $(LDLIBS) -o $@
+	@echo "  [ LINK TEST $@ ]"
+	$(NOECHO)$(LINK.c) $^ $(LOADLIBES) $(LDLIBS) -o $@
 ifdef BUILD_GCOV
 	# move the .gcno file to the directory with the executable
 	mv `basename $@ $(EXEEXT)`.gcno `dirname $@`
@@ -15,12 +17,14 @@ endif
 
 $(BUILDTESTDIR)/%$(EXEEXT): $(TESTDIR)/%.cxx
 	mkdir -p `dirname $@`
-	$(LINK.cc) $^ $(LOADLIBES) $(LDLIBS) -o $@
+	@echo "  [ LINK TEST $@ ]"
+	$(NOECHO)$(LINK.cc) $^ $(LOADLIBES) $(LDLIBS) -o $@
 
 $(BINDIR)/%$(EXEEXT): $(SRCDIR)/%.c
 	@$(MKDIR_DEPEND.c)
 	@$(MKDIR_BIN)
-	$(LINK.c) $^ $(LOADLIBES) $(LDLIBS) -o $@
+	@echo "  [ LINK BINARY $@ ]"
+	$(NOECHO)$(LINK.c) $^ $(LOADLIBES) $(LDLIBS) -o $@
 ifdef BUILD_GCOV
 	# move the .gcno file to the directory with the executable
 	mv `basename $@ $(EXEEXT)`.gcno `dirname $@`
@@ -29,4 +33,5 @@ endif
 $(BINDIR)/%.o : $(SRCDIR)/%.c
 	@$(MKDIR_DEPEND.c)
 	@$(MKDIR_BIN)
-	$(COMPILE.c) -o $@ $<
+	@echo "  [ CC SRC $@ ]"
+	$(NOECHO)$(COMPILE.c) -o $@ $<
diff --git a/make/helper.mk b/make/helper.mk
index 5abd4b3..184092e 100644
--- a/make/helper.mk
+++ b/make/helper.mk
@@ -1,3 +1,6 @@
+# set to empty in order to print commands
+NOECHO := @
+
 MAKEFLAGS += --warn-undefined-variables
 SHELL := bash
 .SHELLFLAGS := -eu -o pipefail -c
diff --git a/make/liborion.mk b/make/liborion.mk
index c6c51f5..ef64337 100644
--- a/make/liborion.mk
+++ b/make/liborion.mk
@@ -1,3 +1,4 @@
 $(LIBORION.A): $(LIB_OBJ) $(ITK_INTEGRATION_OBJ)
-	mkdir -p `dirname $@`
-	$(AR) $(ARFLAGS) $@ $^
+	@mkdir -p `dirname $@`
+	@echo "  [ AR $@ ]"
+	$(NOECHO)$(AR) $(ARFLAGS) $@ $^

From 8ccb0e4ff8a61bfb55afcd85d4106ff784478c5c Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 25 Apr 2016 15:54:45 -0500
Subject: [PATCH 43/55] Add a macro to increment ndarray3 elements

---
 lib/ndarray/ndarray3.h         |  1 +
 lib/ndarray/ndarray3_generic.h | 24 ++++++++++++++++++++++++
 2 files changed, 25 insertions(+)

diff --git a/lib/ndarray/ndarray3.h b/lib/ndarray/ndarray3.h
index 6864242..f165e3d 100644
--- a/lib/ndarray/ndarray3.h
+++ b/lib/ndarray/ndarray3.h
@@ -78,6 +78,7 @@ extern float64 ndarray3_sum_over_all_float64( const ndarray3* n );
 
 #define ndarray3_set              ndarray3_generic_set
 #define ndarray3_get              ndarray3_generic_get
+#define ndarray3_increment        ndarray3_generic_increment
 #define ndarray3_elems            ndarray3_generic_elems
 #define NDARRAY3_LOOP_OVER_START  NDARRAY3_GENERIC_LOOP_OVER_START
 #define NDARRAY3_LOOP_OVER_END    NDARRAY3_GENERIC_LOOP_OVER_END
diff --git a/lib/ndarray/ndarray3_generic.h b/lib/ndarray/ndarray3_generic.h
index 4f24a28..4bb8e58 100644
--- a/lib/ndarray/ndarray3_generic.h
+++ b/lib/ndarray/ndarray3_generic.h
@@ -74,6 +74,30 @@
 
 
 
+/** TODO document
+ *
+ *  ndarray3_increment( ndarray3* n, size_t i, size_t j, size_t k              )
+ */
+#define _real_ndarray3_generic_increment(_n, _n_i, _n_j, _n_k) \
+	do { \
+		++( *_ndarray3_generic_index( (_n), (_n_i), (_n_j), (_n_k) ) ); \
+	} while(0)
+#ifdef NDARRAY3_ASSERT_BOUNDS_ACCESS
+  #define ndarray3_generic_increment(_n, _n_i, _n_j, _n_k) \
+	do { \
+		if( likely(_ndarray3_generic_assert_bounds(_n, _n_i, _n_j, _n_k)) ) { \
+			_real_ndarray3_generic_increment(_n, _n_i, _n_j, _n_k); \
+		} else { \
+			die("ndarray3 (%p) access [%d,%d,%d]", _n, _n_i,_n_j,_n_k); \
+		} \
+	} while(0)
+#else
+  #define ndarray3_generic_increment(_n, _n_i, _n_j, _n_k) \
+	_real_ndarray3_generic_increment(_n, _n_i, _n_j, _n_k)
+#endif /* NDARRAY3_ASSERT_BOUNDS_ACCESS */
+
+
+
 /** TODO document
  *  NDARRAY3_GENERIC_LOOP_OVER_START( ndarray3* n, size_t i, size_t j, size_t k ) {
  *      / * code body * /

From b10251d77c0b60a469842ed9681a282e57d5de09 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Tue, 26 Apr 2016 17:15:08 -0500
Subject: [PATCH 44/55] Add functions to init and manipulate the 2D histogram

---
 .../compute2D_DiscrimantFunction.c             |  9 ++-------
 lib/segmentation/orion_discriminant.c          | 11 +++++++++++
 lib/segmentation/orion_discriminant.h          | 18 ++++++++++++++----
 3 files changed, 27 insertions(+), 11 deletions(-)
 create mode 100644 lib/segmentation/orion_discriminant.c

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
index d7855a6..0004eb0 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
@@ -125,10 +125,7 @@ void orion_hist3(
 
 	/* NOTE: histogram is allocated here: if the size of the bins change
 	 * for each dimension, then this will need to change */
-	discrim->histogram = ndarray3_new( param->bins, param->bins, 1);
-	NDARRAY3_LOOP_OVER_START( discrim->histogram, i,j,k ) {
-		ndarray3_set( discrim->histogram, i,j,k, 0.0 );
-	} NDARRAY3_LOOP_OVER_END;
+	orion_histogram_init( discrim, (param->bins + 1), (param->bins + 1) );
 
 	for( int indices_idx = 0; indices_idx < indices_sz; indices_idx++ ) {
 		size_t feat_instance_idx = array_get_int( indices, indices_idx );
@@ -142,9 +139,7 @@ void orion_hist3(
 					);
 		}
 		/* increment by 1 */
-		ndarray3_set( discrim->histogram, feat_bin_idx[0], feat_bin_idx[1], 0,
-				1.0 + ndarray3_get(discrim->histogram, feat_bin_idx[0], feat_bin_idx[1], 0)
-				);
+		orion_histogram_increment( discrim, feat_bin_idx[0], feat_bin_idx[1] );
 	}
 }
 
diff --git a/lib/segmentation/orion_discriminant.c b/lib/segmentation/orion_discriminant.c
new file mode 100644
index 0000000..8546881
--- /dev/null
+++ b/lib/segmentation/orion_discriminant.c
@@ -0,0 +1,11 @@
+#include "segmentation/orion_discriminant.h"
+
+void orion_histogram_init(orion_discriminant_function* discrim, size_t m, size_t n) {
+	discrim->m = m;
+	discrim->n = n;
+
+	NEW_COUNT(discrim->histogram, size_t, discrim->m * discrim->n);
+	for( int hist_idx = 0; hist_idx < orion_histogram_elems(discrim); hist_idx++ ) {
+		discrim->histogram[hist_idx] = 0;
+	}
+}
diff --git a/lib/segmentation/orion_discriminant.h b/lib/segmentation/orion_discriminant.h
index 22c7240..540f37b 100644
--- a/lib/segmentation/orion_discriminant.h
+++ b/lib/segmentation/orion_discriminant.h
@@ -12,9 +12,20 @@
 
 /* structs, enums */
 /*TODO(Define struct members)*/
-typedef struct {
 
-	ndarray3* histogram; /* dimensions: [m, n, 1] */
+/* TODO document */
+#define orion_histogram_elems( discrim ) ( discrim->m * discrim->n )
+
+#define _orion_histogram_index(discrim, bin_m, bin_n) (bin_m * discrim->m + bin_n)
+
+/* TODO document */
+#define orion_histogram_increment(discrim, bin_m, bin_n) \
+	( ++( discrim->histogram[ _orion_histogram_index(discrim, bin_m, bin_n)  ] ) )
+
+typedef struct {
+	size_t m; /* number of bins in the first dimension */
+	size_t n; /* number of bins in the second dimension */
+	size_t* histogram; /* dimensions: [m, n] */
 
 
 	/* store the minimum and maximum value for each feature */
@@ -32,8 +43,7 @@ extern "C" {
 #endif /* __cplusplus */
 
 /* Function prototypes */
-
-
+extern void orion_histogram_init(orion_discriminant_function* discrim, size_t m, size_t n);
 
 #ifdef __cplusplus
 };

From 79c0e10af9681ae2b087357a6073b4bda31bd2f3 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Tue, 26 Apr 2016 18:10:44 -0500
Subject: [PATCH 45/55] Improve indexing of histogram

---
 lib/segmentation/orion_discriminant.c |  6 +++---
 lib/segmentation/orion_discriminant.h | 14 +++++++-------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/lib/segmentation/orion_discriminant.c b/lib/segmentation/orion_discriminant.c
index 8546881..09a1bdf 100644
--- a/lib/segmentation/orion_discriminant.c
+++ b/lib/segmentation/orion_discriminant.c
@@ -1,10 +1,10 @@
 #include "segmentation/orion_discriminant.h"
 
 void orion_histogram_init(orion_discriminant_function* discrim, size_t m, size_t n) {
-	discrim->m = m;
-	discrim->n = n;
+	discrim->bin_sz[0] = m;
+	discrim->bin_sz[1] = n;
 
-	NEW_COUNT(discrim->histogram, size_t, discrim->m * discrim->n);
+	NEW_COUNT(discrim->histogram, size_t, discrim->bin_sz[0] * discrim->bin_sz[1]);
 	for( int hist_idx = 0; hist_idx < orion_histogram_elems(discrim); hist_idx++ ) {
 		discrim->histogram[hist_idx] = 0;
 	}
diff --git a/lib/segmentation/orion_discriminant.h b/lib/segmentation/orion_discriminant.h
index 540f37b..422a018 100644
--- a/lib/segmentation/orion_discriminant.h
+++ b/lib/segmentation/orion_discriminant.h
@@ -14,18 +14,18 @@
 /*TODO(Define struct members)*/
 
 /* TODO document */
-#define orion_histogram_elems( discrim ) ( discrim->m * discrim->n )
+#define orion_histogram_elems( discrim ) ( discrim->bin_sz[0] * discrim->bin_sz[1] )
 
-#define _orion_histogram_index(discrim, bin_m, bin_n) (bin_m * discrim->m + bin_n)
+#define _orion_histogram_index(discrim, bin_row, bin_col) (bin_row * discrim->bin_sz[1] + bin_col)
 
 /* TODO document */
-#define orion_histogram_increment(discrim, bin_m, bin_n) \
-	( ++( discrim->histogram[ _orion_histogram_index(discrim, bin_m, bin_n)  ] ) )
+#define orion_histogram_increment(discrim, bin_row, bin_col) \
+	( ++( discrim->histogram[ _orion_histogram_index(discrim, bin_row, bin_col)  ] ) )
 
 typedef struct {
-	size_t m; /* number of bins in the first dimension */
-	size_t n; /* number of bins in the second dimension */
-	size_t* histogram; /* dimensions: [m, n] */
+	/* number of bins in each dimension */
+	size_t bin_sz[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
+	size_t* histogram; /* dimensions: [bin_sz[0], bin_sz[1]] */
 
 
 	/* store the minimum and maximum value for each feature */

From 8a9b234801d62cee39a7ea934cfb2e3bdc424f7c Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Mon, 23 May 2016 19:20:13 -0500
Subject: [PATCH 46/55] VTK build configuration

---
 .gitignore                          |   1 +
 make/dep.mk                         |   1 +
 make/vtk-config.mk                  |  21 ++++++
 make/vtk/CMakeLists.txt             |  40 +++++++++++
 make/vtk/ImageMapper.cxx            | 102 ++++++++++++++++++++++++++++
 tool/script/extract-linker-flags.pl |   2 +-
 6 files changed, 166 insertions(+), 1 deletion(-)
 create mode 100644 make/vtk-config.mk
 create mode 100644 make/vtk/CMakeLists.txt
 create mode 100644 make/vtk/ImageMapper.cxx

diff --git a/.gitignore b/.gitignore
index 0cec9cb..292b45c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@ ITKIOFactoryRegistration
 cmake_install.cmake
 
 /make/itk/itk-config.mk.gen
+/make/vtk/vtk-config.mk.gen
 
 /ComputeFrangi/Makefile
 /ComputeFrangi/ComputeEigenValue_Sorted_Frangi
diff --git a/make/dep.mk b/make/dep.mk
index 118e036..8acec66 100644
--- a/make/dep.mk
+++ b/make/dep.mk
@@ -3,3 +3,4 @@ include make/kiss-fft-config.mk
 include make/vaa3d-config.mk
 include make/matlab-runtime-config.mk
 include make/itk-config.mk
+include make/vtk-config.mk
diff --git a/make/vtk-config.mk b/make/vtk-config.mk
new file mode 100644
index 0000000..d44eee3
--- /dev/null
+++ b/make/vtk-config.mk
@@ -0,0 +1,21 @@
+VTK_CONFIG_MK := make/vtk/vtk-config.mk.gen
+include $(VTK_CONFIG_MK)
+
+BIN_VTK_IMAGE_MAPPER := $(BINDIR)/vtk-image-mapper/ImageMapper$(EXEEXT)
+TEST_VTK_BUILD: $(BIN_VTK_IMAGE_MAPPER)
+
+$(BIN_VTK_IMAGE_MAPPER): CPPFLAGS += $(VTK_CPPFLAGS)
+$(BIN_VTK_IMAGE_MAPPER): LDFLAGS  += $(VTK_LDFLAGS)
+$(BIN_VTK_IMAGE_MAPPER): LDLIBS   += $(VTK_LDLIBS)
+$(BIN_VTK_IMAGE_MAPPER): make/vtk/ImageMapper.cxx
+	mkdir -p `dirname $@`
+	@echo "  [ LINK TEST $@ ]"
+	$(NOECHO)$(LINK.cc) $^ $(LOADLIBES) $(LDLIBS) -o $@
+
+$(VTK_CONFIG_MK):  make/vtk/CMakeLists.txt \
+		| $(BUILDDIR)
+	@$(MKDIR_BUILD)
+	$(CMAKE.generate) -B$(BUILDDIR)/.make/vtk -Hmake/vtk
+	echo "VTK_LDLIBS += `./tool/script/extract-linker-flags.pl < $(BUILDDIR)/.make/vtk/CMakeFiles/ImageMapper.dir/link.txt`" >> $@
+
+VTK_LDFLAGS += -msse2 -rdynamic
diff --git a/make/vtk/CMakeLists.txt b/make/vtk/CMakeLists.txt
new file mode 100644
index 0000000..a01a106
--- /dev/null
+++ b/make/vtk/CMakeLists.txt
@@ -0,0 +1,40 @@
+cmake_minimum_required(VERSION 2.8)
+
+PROJECT(ImageMapper)
+
+find_package(VTK REQUIRED)
+include(${VTK_USE_FILE})
+
+add_executable(ImageMapper MACOSX_BUNDLE ImageMapper)
+
+if(VTK_LIBRARIES)
+  target_link_libraries(ImageMapper ${VTK_LIBRARIES})
+else()
+  target_link_libraries(ImageMapper vtkHybrid vtkWidgets)
+endif()
+
+message( ${VTK_LIBRARIES} )
+
+
+foreach (incdir ${VTK_INCLUDE_DIRS})
+	set(VTK_CPPFLAGS "${VTK_CPPFLAGS} -I${incdir}")
+endforeach()
+
+foreach (libdir ${VTK_LIBRARY_DIRS})
+	set(VTK_LDFLAGS "${VTK_LDFLAGS} -L${libdir}")
+endforeach()
+
+foreach (lib ${VTK_LIBRARIES})
+	# this variable does not give the actual linker flags
+	#set(VTK_LDLIBS "${VTK_LDLIBS} -l${lib}")
+endforeach()
+
+set(VTK_CONFIG_MK_GEN "vtk-config.mk.gen" )
+file(WRITE ${VTK_CONFIG_MK_GEN} "VTK_CPPFLAGS := ${VTK_CPPFLAGS}\n")
+file(APPEND ${VTK_CONFIG_MK_GEN} "VTK_LDFLAGS := ${VTK_LDFLAGS}\n")
+file(APPEND ${VTK_CONFIG_MK_GEN} "VTK_LDLIBS := ${VTK_LDLIBS}\n")
+
+#get_cmake_property(_variableNames VARIABLES)
+#foreach (_variableName ${_variableNames})
+    #message(STATUS "${_variableName}=${${_variableName}}")
+#endforeach()
diff --git a/make/vtk/ImageMapper.cxx b/make/vtk/ImageMapper.cxx
new file mode 100644
index 0000000..121ffd5
--- /dev/null
+++ b/make/vtk/ImageMapper.cxx
@@ -0,0 +1,102 @@
+/* Need to initialise because we are building without CMake:
+ * <http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Factories_now_require_defines>
+ */
+#include <vtkAutoInit.h>
+VTK_MODULE_INIT(vtkRenderingOpenGL);
+VTK_MODULE_INIT(vtkInteractionStyle);
+VTK_MODULE_INIT(vtkRenderingFreeType);
+VTK_MODULE_INIT(vtkRenderingFreeTypeOpenGL);
+VTK_MODULE_INIT(vtkRenderingVolumeOpenGL);
+
+#include <vtkVersion.h>
+#include <vtkImageData.h>
+#include <vtkSmartPointer.h>
+#include <vtkRenderWindow.h>
+#include <vtkRenderWindowInteractor.h>
+#include <vtkInteractorStyleImage.h>
+#include <vtkRenderer.h>
+#include <vtkImageMapper.h>
+#include <vtkActor2D.h>
+#include <vtkImageSlice.h>
+
+static void CreateColorImage(vtkImageData*);
+
+int main(int, char *[])
+{
+	vtkSmartPointer<vtkImageData> colorImage = vtkSmartPointer<vtkImageData>::New();
+	CreateColorImage(colorImage);
+
+		vtkSmartPointer<vtkImageMapper> imageMapper = vtkSmartPointer<vtkImageMapper>::New();
+#if VTK_MAJOR_VERSION <= 5
+	imageMapper->SetInputConnection(colorImage->GetProducerPort());
+#else
+	imageMapper->SetInputData(colorImage);
+#endif
+	imageMapper->SetColorWindow(255);
+	imageMapper->SetColorLevel(127.5);
+
+		vtkSmartPointer<vtkActor2D> imageActor = vtkSmartPointer<vtkActor2D>::New();
+	imageActor->SetMapper(imageMapper);
+	imageActor->SetPosition(20, 20);
+
+		// Setup renderers
+		vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
+
+		// Setup render window
+		vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New();
+
+		renderWindow->AddRenderer(renderer);
+
+		// Setup render window interactor
+		vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor = vtkSmartPointer<vtkRenderWindowInteractor>::New();
+
+		vtkSmartPointer<vtkInteractorStyleImage> style = vtkSmartPointer<vtkInteractorStyleImage>::New();
+
+		renderWindowInteractor->SetInteractorStyle(style);
+
+		// Render and start interaction
+		renderWindowInteractor->SetRenderWindow(renderWindow);
+
+		//renderer->AddViewProp(imageActor);
+		renderer->AddActor2D(imageActor);
+
+		renderWindow->Render();
+	renderWindowInteractor->Start();
+
+		return EXIT_SUCCESS;
+}
+
+void CreateColorImage(vtkImageData* image)
+{
+	unsigned int dim = 20;
+
+		image->SetDimensions(dim, dim, 1);
+#if VTK_MAJOR_VERSION <= 5
+	image->SetNumberOfScalarComponents(3);
+	image->SetScalarTypeToUnsignedChar();
+	image->AllocateScalars();
+#else
+	image->AllocateScalars(VTK_UNSIGNED_CHAR,3);
+#endif
+	for(unsigned int x = 0; x < dim; x++)
+	{
+		for(unsigned int y = 0; y < dim; y++)
+		{
+			unsigned char* pixel = static_cast<unsigned char*>(image->GetScalarPointer(x,y,0));
+			if(x < dim/2)
+			{
+				pixel[0] = 255;
+				pixel[1] = 0;
+			}
+			else
+			{
+				pixel[0] = 0;
+				pixel[1] = 255;
+			}
+
+				pixel[2] = 0;
+		}
+	}
+
+		image->Modified();
+}
diff --git a/tool/script/extract-linker-flags.pl b/tool/script/extract-linker-flags.pl
index 968780f..22a561e 100755
--- a/tool/script/extract-linker-flags.pl
+++ b/tool/script/extract-linker-flags.pl
@@ -6,5 +6,5 @@
 use Text::ParseWords;
 
 my @words = shellwords(<>);
-my @ldlibs = grep { /(^-l)|\.a$/ } @words;
+my @ldlibs = grep { /(^-l)|\.a$|\.so/ } @words;
 print "@ldlibs";

From 52ee36d5c07fec47595f33048d0cfef7f350af5b Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 10 Jun 2016 15:44:40 -0500
Subject: [PATCH 47/55] Move the generated ITK/VTK make configuration into the
 BUILDDIR

This ensures that the configuration does not stay with the source code.
---
 .gitignore              | 3 ---
 make/itk-config.mk      | 2 +-
 make/itk/CMakeLists.txt | 2 +-
 make/vtk-config.mk      | 2 +-
 make/vtk/CMakeLists.txt | 2 +-
 5 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index 292b45c..824f05c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,9 +8,6 @@ CMakeFiles
 ITKIOFactoryRegistration
 cmake_install.cmake
 
-/make/itk/itk-config.mk.gen
-/make/vtk/vtk-config.mk.gen
-
 /ComputeFrangi/Makefile
 /ComputeFrangi/ComputeEigenValue_Sorted_Frangi
 
diff --git a/make/itk-config.mk b/make/itk-config.mk
index d263bc3..c4a5f6d 100644
--- a/make/itk-config.mk
+++ b/make/itk-config.mk
@@ -1,4 +1,4 @@
-ITK_CONFIG_MK := make/itk/itk-config.mk.gen
+ITK_CONFIG_MK := $(BUILDDIR)/.make/itk/itk-config.mk.gen
 include $(ITK_CONFIG_MK)
 
 $(ITK_CONFIG_MK):  make/itk/CMakeLists.txt \
diff --git a/make/itk/CMakeLists.txt b/make/itk/CMakeLists.txt
index 89c4d8b..e4052cb 100644
--- a/make/itk/CMakeLists.txt
+++ b/make/itk/CMakeLists.txt
@@ -26,7 +26,7 @@ foreach (lib ${ITK_LIBRARIES})
 	#set(ITK_LDLIBS "${ITK_LDLIBS} -l${lib}-4.8")
 endforeach()
 
-set(ITK_CONFIG_MK_GEN "itk-config.mk.gen" )
+set(ITK_CONFIG_MK_GEN "${CMAKE_BINARY_DIR}/itk-config.mk.gen" )
 file(WRITE ${ITK_CONFIG_MK_GEN} "ITK_CPPFLAGS := ${ITK_CPPFLAGS}\n")
 file(APPEND ${ITK_CONFIG_MK_GEN} "ITK_LDFLAGS := ${ITK_LDFLAGS}\n")
 file(APPEND ${ITK_CONFIG_MK_GEN} "ITK_LDLIBS := ${ITK_LDLIBS}\n")
diff --git a/make/vtk-config.mk b/make/vtk-config.mk
index d44eee3..c8165e5 100644
--- a/make/vtk-config.mk
+++ b/make/vtk-config.mk
@@ -1,4 +1,4 @@
-VTK_CONFIG_MK := make/vtk/vtk-config.mk.gen
+VTK_CONFIG_MK := $(BUILDDIR)/.make/vtk/vtk-config.mk.gen
 include $(VTK_CONFIG_MK)
 
 BIN_VTK_IMAGE_MAPPER := $(BINDIR)/vtk-image-mapper/ImageMapper$(EXEEXT)
diff --git a/make/vtk/CMakeLists.txt b/make/vtk/CMakeLists.txt
index a01a106..8b3695c 100644
--- a/make/vtk/CMakeLists.txt
+++ b/make/vtk/CMakeLists.txt
@@ -29,7 +29,7 @@ foreach (lib ${VTK_LIBRARIES})
 	#set(VTK_LDLIBS "${VTK_LDLIBS} -l${lib}")
 endforeach()
 
-set(VTK_CONFIG_MK_GEN "vtk-config.mk.gen" )
+set(VTK_CONFIG_MK_GEN "${CMAKE_BINARY_DIR}/vtk-config.mk.gen" )
 file(WRITE ${VTK_CONFIG_MK_GEN} "VTK_CPPFLAGS := ${VTK_CPPFLAGS}\n")
 file(APPEND ${VTK_CONFIG_MK_GEN} "VTK_LDFLAGS := ${VTK_LDFLAGS}\n")
 file(APPEND ${VTK_CONFIG_MK_GEN} "VTK_LDLIBS := ${VTK_LDLIBS}\n")

From 3e17468913f046c93f7e10d6f502fc9818c12b99 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 10 Jun 2016 15:54:10 -0500
Subject: [PATCH 48/55] Travis-CI: Add libvtk5-dev to the list of packages

---
 .travis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index ca7de46..8625d05 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,5 +1,9 @@
 language: c
 sudo: false
+addons:
+  apt:
+    packages:
+      - libvtk5-dev
 env:
   - PROD=1 TEST_VERBOSE=1
   - PROD=1 TEST_VERBOSE=1 COVERAGE=1

From 2dff9bbdcdacff9e695e30f786f73bb1d8c43c53 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 10 Jun 2016 23:03:12 -0500
Subject: [PATCH 49/55] Travis-CI: build in trusty environment

---
 .travis.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 8625d05..149aa11 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,5 +1,7 @@
 language: c
-sudo: false
+os: linux
+dist: trusty
+sudo: required
 addons:
   apt:
     packages:

From de503eabf907efdcb6a86c098d8652ad010f8d67 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 10 Jun 2016 23:10:39 -0500
Subject: [PATCH 50/55] Travis-CI: install ITK/VTK version from trusty packages

---
 .travis.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 149aa11..e4ad336 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,7 +5,8 @@ sudo: required
 addons:
   apt:
     packages:
-      - libvtk5-dev
+      - libvtk6-dev
+      - libinsighttoolkit4-dev
 env:
   - PROD=1 TEST_VERBOSE=1
   - PROD=1 TEST_VERBOSE=1 COVERAGE=1
@@ -13,10 +14,6 @@ compiler:
   - gcc
   - clang
 before_install:
-  - mkdir build
-  - git clone https://github.com/CBL-ORION/ITK-builds.git external/ITK
-  # path for CMake to search for built ITK
-  - export ITK_DIR="`( cd external/ITK/usr/local/lib/cmake/ITK-4.9 && pwd )`"
   - if [ "$COVERAGE" = 1 ]; then pip install --user cpp-coveralls;  fi
 script:
   # version of gcc on Travis-CI does not support ASAN flag

From f9c5cf68bd3e2d9ff5691a861ae78f709f865fde Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 10 Jun 2016 23:53:50 -0500
Subject: [PATCH 51/55] build: Add support for VTK C++ compilation

---
 Makefile                        | 13 ++++++++++++-
 make/00-implicit-rules.mk       |  8 +++++++-
 make/autodep.mk                 | 19 +++++++++++++------
 make/filter-vesselness-rules.mk |  4 ++--
 make/itk-config.mk              |  2 +-
 make/misc-config.mk             |  1 +
 make/misc-rules.mk              |  8 +++++++-
 make/util-rules.mk              |  6 +++---
 make/vtk-config.mk              |  2 +-
 9 files changed, 47 insertions(+), 16 deletions(-)

diff --git a/Makefile b/Makefile
index 0499cd2..a82317d 100644
--- a/Makefile
+++ b/Makefile
@@ -7,6 +7,14 @@ BIN_SRC_CONFIG.c   := $(SRCDIR)/config/configurator.c
 BIN_SRC.cc  := $(SRCDIR)/compute-filter/ComputeFilter.cxx $(SRCDIR)/subsample-volume/SubsampleVolume.cxx
 #LIB_SRC.c  := $(LIBDIR)/ndarray/ndarray3.c  # $(LIBDIR)/filter/hdaf/Makefilter.c
 LIB_SRC.c  := $(shell find $(LIBDIR) -path lib/t -prune -o  -type f -name '*.c' \! -name '*_impl.c' -print)
+LIB_SRC.cc  := $(shell find $(LIBDIR) \
+	-path lib/t -prune -o \
+	-path lib/vaa3d-plugin -prune -o \
+	-path lib/config -prune -o \
+	-path lib/filter/vesselness -prune -o \
+	-path lib/integration -prune -o \
+	-type f -name '*.cxx' -print)
+$(echo $(LIB_SRC.cc))
 TEST.c := $(shell find $(TESTDIR) -path lib/t/liborion3mat -prune -o -type f -name "*.c" -print)
 ifdef FEAT_LIBORION3MAT
 TEST.c  += $(TESTDIR)/liborion3mat/test.c
@@ -16,11 +24,13 @@ include make/autodep.mk
 
 ## Target files
 OBJ_PATHSUBST.c  = $(patsubst $(LIBDIR)/%.c,$(BUILDDIR)/%.o,$(1))
+OBJ_PATHSUBST.cc  = $(patsubst $(LIBDIR)/%.cxx,$(BUILDDIR)/%.o,$(1))
 TEST_PATHSUBST.c = $(patsubst $(TESTDIR)/%.c,$(BUILDTESTDIR)/%$(EXEEXT),$(1))
 BIN_PATHSUBST.c  = $(patsubst $(SRCDIR)/%.c,$(BINDIR)/%$(EXEEXT),$(1))
 BIN_PATHSUBST.cc  = $(patsubst $(SRCDIR)/%.cxx,$(BINDIR)/%$(EXEEXT),$(1))
 
-MKDIR_BUILD = mkdir -p `dirname $(call OBJ_PATHSUBST.c,$<)`
+MKDIR_BUILD.c = mkdir -p `dirname $(call OBJ_PATHSUBST.c,$<)`
+MKDIR_BUILD.cc = mkdir -p `dirname $(call OBJ_PATHSUBST.cc,$<)`
 MKDIR_BIN   = mkdir -p `dirname $(call BIN_PATHSUBST.c,$<)`
 MKDIR_BUILDTESTDIR = mkdir -p `dirname $(call TEST_PATHSUBST.c,$<)`
 
@@ -33,6 +43,7 @@ include make/liborion-config.mk
 
 ## Generate the targets
 LIB_OBJ:= $(call OBJ_PATHSUBST.c,$(LIB_SRC.c))
+LIB_OBJ+= $(call OBJ_PATHSUBST.cc,$(LIB_SRC.cc))
 
 TEST_OBJ:= $(call TEST_PATHSUBST.c,$(TEST.c))
 
diff --git a/make/00-implicit-rules.mk b/make/00-implicit-rules.mk
index 18c54da..ce550c9 100644
--- a/make/00-implicit-rules.mk
+++ b/make/00-implicit-rules.mk
@@ -1,10 +1,16 @@
 ### Implict rules
 $(BUILDDIR)/%.o : $(LIBDIR)/%.c
 	@$(MKDIR_DEPEND.c)
-	@$(MKDIR_BUILD)
+	@$(MKDIR_BUILD.c)
 	@echo "  [ CC SRC $@ ]"
 	$(NOECHO)$(COMPILE.c) -o $@ $<
 
+$(BUILDDIR)/%.o : $(LIBDIR)/%.cxx
+	@$(MKDIR_DEPEND.cc)
+	@$(MKDIR_BUILD.cc)
+	@echo "  [ CXX SRC $@ ]"
+	$(NOECHO)$(COMPILE.cc) -o $@ $<
+
 $(BUILDTESTDIR)/%$(EXEEXT): $(TESTDIR)/%.c
 	@$(MKDIR_DEPEND.c)
 	@$(MKDIR_BUILDTESTDIR)
diff --git a/make/autodep.mk b/make/autodep.mk
index a6513d1..eac55aa 100644
--- a/make/autodep.mk
+++ b/make/autodep.mk
@@ -1,8 +1,15 @@
 ## Dependency generation
-MAKEDEPEND.c = gcc -MM $(CPPFLAGS) -o $(df).d $<
-df = $(<:%.c=$(DEPDIR)/%)
-MKDIR_DEPEND.c = mkdir -p `dirname $(df).d`; $(MAKEDEPEND.c); \
-	    $(CP) $(df).d $(df).P; \
+MAKEDEPEND.c = gcc -MM $(CPPFLAGS) -o $(df.c).d $<
+MAKEDEPEND.cc = gcc -MM $(CXXFLAGS) $(CPPFLAGS) -o $(df.cc).d $<
+df.c = $(<:%.c=$(DEPDIR)/%)
+df.cc = $(<:%.cxx=$(DEPDIR)/%)
+MKDIR_DEPEND.c = mkdir -p `dirname $(df.c).d`; $(MAKEDEPEND.c); \
+	    $(CP) $(df.c).d $(df.c).P; \
 	    sed -e 's/$(HASHMARK).*//' -e 's/^[^:]*: *//' -e 's/ *\\$$//' \
-	        -e '/^$$/ d' -e 's/$$/ :/' < $(df).d >> $(df).P; \
-	    $(RM) $(df).d
+	        -e '/^$$/ d' -e 's/$$/ :/' < $(df.c).d >> $(df.c).P; \
+	    $(RM) $(df.c).d
+MKDIR_DEPEND.cc = mkdir -p `dirname $(df.cc).d`; $(MAKEDEPEND.cc); \
+	    $(CP) $(df.cc).d $(df.cc).P; \
+	    sed -e 's/$(HASHMARK).*//' -e 's/^[^:]*: *//' -e 's/ *\\$$//' \
+	        -e '/^$$/ d' -e 's/$$/ :/' < $(df.cc).d >> $(df.cc).P; \
+	    $(RM) $(df.cc).d
diff --git a/make/filter-vesselness-rules.mk b/make/filter-vesselness-rules.mk
index 24dcd04..274909a 100644
--- a/make/filter-vesselness-rules.mk
+++ b/make/filter-vesselness-rules.mk
@@ -3,11 +3,11 @@ $(EIGEN_FRANGI_LIB_OBJ): $(FILTER_FRANGI_OBJ)
 $(EIGEN_SATO_LIB_OBJ):   $(FILTER_SATO_OBJ)
 
 $(FILTER_FRANGI_OBJ): $(LIBDIR)/filter/vesselness/frangi/EigenFrangi.cxx
-	@$(MKDIR_BUILD)
+	@$(MKDIR_BUILD.cc)
 	$(CMAKE.generate) -B$(BUILDDIR)/filter/vesselness -H$(LIBDIR)/filter/vesselness
 	$(MAKE) -C$(BUILDDIR)/filter/vesselness
 $(FILTER_SATO_OBJ): $(LIBDIR)/filter/vesselness/sato/EigenSato.cxx
-	@$(MKDIR_BUILD)
+	@$(MKDIR_BUILD.cc)
 	$(CMAKE.generate) -B$(BUILDDIR)/filter/vesselness -H$(LIBDIR)/filter/vesselness
 	$(MAKE) -C$(BUILDDIR)/filter/vesselness
 
diff --git a/make/itk-config.mk b/make/itk-config.mk
index c4a5f6d..dbd7143 100644
--- a/make/itk-config.mk
+++ b/make/itk-config.mk
@@ -3,7 +3,7 @@ include $(ITK_CONFIG_MK)
 
 $(ITK_CONFIG_MK):  make/itk/CMakeLists.txt \
 		| $(BUILDDIR)
-	@$(MKDIR_BUILD)
+	@$(MKDIR_BUILD.c)
 	$(CMAKE.generate) -B$(BUILDDIR)/.make/itk -Hmake/itk
 	echo "ITK_LDLIBS += `./tool/script/extract-linker-flags.pl < $(BUILDDIR)/.make/itk/CMakeFiles/Pi.dir/link.txt`" >> $@
 
diff --git a/make/misc-config.mk b/make/misc-config.mk
index 564166e..a516171 100644
--- a/make/misc-config.mk
+++ b/make/misc-config.mk
@@ -1 +1,2 @@
 ITK_INTEGRATION_LIB_OBJ := $(BUILDDIR)/integration/itk/CMakeFiles/IntegrationITK.dir/itk.cxx.o
+VTK_VIS_LIB_OBJ := $(BUILDDIR)/vis/vis.o
diff --git a/make/misc-rules.mk b/make/misc-rules.mk
index 1511dd7..82842e4 100644
--- a/make/misc-rules.mk
+++ b/make/misc-rules.mk
@@ -11,6 +11,12 @@ $(BUILDDIR)/integration/itk/libIntegrationITK.a: \
 		$(FILTER_OBJ) \
 		$(BUILDDIR)/ndarray/array_ndarray3.o \
 		$(BUILDDIR)/ndarray/ndarray3.o
-	@$(MKDIR_BUILD)
+	@$(MKDIR_BUILD.cc)
 	$(CMAKE.generate) -B$(BUILDDIR)/integration/itk -H$(LIBDIR)/integration/itk
 	$(MAKE) -C$(BUILDDIR)/integration/itk
+
+$(VTK_VIS_LIB_OBJ): CPPFLAGS += $(VTK_CPPFLAGS)
+$(VTK_VIS_LIB_OBJ): CXXFLAGS += -std=c++11
+$(VTK_VIS_LIB_OBJ): LDFLAGS += $(VTK_LDFLAGS)
+$(VTK_VIS_LIB_OBJ): LDLIBS += $(VTK_LDLIBS)
+$(VTK_VIS_LIB_OBJ): $(LIBDIR)/vis/vis.cxx
diff --git a/make/util-rules.mk b/make/util-rules.mk
index cf93349..e9c2ae6 100644
--- a/make/util-rules.mk
+++ b/make/util-rules.mk
@@ -4,9 +4,9 @@ $(BINDIR)/subsample-volume/SubsampleVolume$(EXEEXT): $(SRCDIR)/subsample-volume/
 	$(MAKE) -C$(BINDIR)/subsample-volume
 
 BIN_ORION_SEGMENTATION := $(BINDIR)/segmentation/orion-segmentation$(EXEEXT)
-$(BIN_ORION_SEGMENTATION): CPPFLAGS += $(ITK_CPPFLAGS)
-$(BIN_ORION_SEGMENTATION): LDFLAGS  += $(ITK_LDFLAGS)
-$(BIN_ORION_SEGMENTATION): LDLIBS   += $(ITK_LDLIBS)
+$(BIN_ORION_SEGMENTATION): CPPFLAGS += $(ITK_CPPFLAGS) $(VTK_CPPFLAGS)
+$(BIN_ORION_SEGMENTATION): LDFLAGS  += $(ITK_LDFLAGS)  $(VTK_LDFLAGS)
+$(BIN_ORION_SEGMENTATION): LDLIBS   += $(ITK_LDLIBS)   $(VTK_LDLIBS)
 $(BIN_ORION_SEGMENTATION): LDLIBS   += -lstdc++ # needs to add C++ library to link
 $(BIN_ORION_SEGMENTATION): \
 	$(SRCDIR)/segmentation/orion-segmentation.c \
diff --git a/make/vtk-config.mk b/make/vtk-config.mk
index c8165e5..e5e1d7c 100644
--- a/make/vtk-config.mk
+++ b/make/vtk-config.mk
@@ -14,7 +14,7 @@ $(BIN_VTK_IMAGE_MAPPER): make/vtk/ImageMapper.cxx
 
 $(VTK_CONFIG_MK):  make/vtk/CMakeLists.txt \
 		| $(BUILDDIR)
-	@$(MKDIR_BUILD)
+	@$(MKDIR_BUILD.c)
 	$(CMAKE.generate) -B$(BUILDDIR)/.make/vtk -Hmake/vtk
 	echo "VTK_LDLIBS += `./tool/script/extract-linker-flags.pl < $(BUILDDIR)/.make/vtk/CMakeFiles/ImageMapper.dir/link.txt`" >> $@
 

From 9642be5d064c2030ecc3b5d1255278857be38dc5 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Wed, 29 Jun 2016 08:13:58 -0500
Subject: [PATCH 52/55] Identify TODO items

---
 .../How_sigma_relates_to_radii/testSigma.c           |  4 +++-
 .../DetectTrainingSet/IsotropicFilter/Makefilter.c   |  7 ++++---
 .../DetectTrainingSet/IsotropicFilter/compute_LP.c   |  2 +-
 .../IsotropicFilter/compute_Laplacian.c              |  2 +-
 .../DetectTrainingSet/IsotropicFilter/hdaf.c         |  5 ++---
 .../DetectTrainingSet/multiscaleLaplacianFilter.c    | 10 ++++------
 .../DetectTrainingSet/readNegativeSamples.c          |  6 +++---
 .../compute2D_DiscrimantFunction.c                   | 12 ++++++------
 .../getResponseToDiscriminantFunction.c              |  2 +-
 .../DiscriminantFunction/removeIsolatedResponses.c   |  6 ++----
 .../dendrites_main/ExtractFeatures/sortEigenvalues.c |  2 ++
 .../dendrites_main/Util/getInfoVolume.c              |  2 +-
 .../dendrites_main/Util/remove_small_conComp3D.c     |  2 +-
 13 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/How_sigma_relates_to_radii/testSigma.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/How_sigma_relates_to_radii/testSigma.c
index 7dea82b..8c3b102 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/How_sigma_relates_to_radii/testSigma.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/How_sigma_relates_to_radii/testSigma.c
@@ -1,4 +1,6 @@
-/* dead code
+/* TODO turn into test
  *
  * Refactor testSigma
+ *
+ * external/orion3mat/01_Segmentation/dendrites_main/DetectTrainingSet/How_sigma_relates_to_radii/testSigma.m
  */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.c
index f3827ac..55377f9 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.c
@@ -1,6 +1,3 @@
-/*
- * Refactor: Makefilter
- */
 
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.h"
 
@@ -11,6 +8,10 @@
 
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/hdaf.h"
 
+/* MATLAB version: Makefilter */
+
+/* TODO document
+ */
 ndarray3* orion_Makefilter(
 		size_t nx, size_t ny, size_t nz,
 		int hdaf_approx_degree,
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_LP.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_LP.c
index f50cf65..8984ce5 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_LP.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_LP.c
@@ -1,4 +1,4 @@
-/* TODO
+/* TODO: part of testing
  *
  * Refactor: compute_LP
  */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_Laplacian.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_Laplacian.c
index 3331b73..7c8b105 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_Laplacian.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_Laplacian.c
@@ -1,4 +1,4 @@
-/* TODO
+/* dead code
  *
  * Refactor: compute_Laplacian
  */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/hdaf.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/hdaf.c
index 6ce8d66..56729ac 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/hdaf.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/hdaf.c
@@ -1,12 +1,11 @@
-/*
- * Refactor: hdaf
- */
 #include "hdaf.h"
 
 #include <math.h>
 
 #include "numeric/func.h"
 
+/* MATLAB version: hdaf */
+
 /*
  * orion_hdaf( hdaf_approx_degree, scaling_constant, x)
  *
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
index b1eabf2..df091a9 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.c
@@ -1,8 +1,3 @@
-/* TODO
- *
- * Refactor: multiscaleLaplacianFilter
- */
-
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/multiscaleLaplacianFilter.h"
 
 #include "util/util.h"
@@ -42,7 +37,10 @@ orion_multiscale_laplacian_output* orion_multiscale_laplacian_output_new() {
 	return r;
 }
 
-/*
+/* MATLAB version: multiscaleLaplacianFilter */
+
+/* TODO document better
+ *
  * function that allows to get the maximum reponse of the Laplacian
  *
  * laplacian_scales: scales to use for calculating the Laplacian. These are
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
index 62c729d..9734a7c 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
@@ -1,8 +1,8 @@
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.h"
 
-/* TODO
- *
- * Refactor: readNegativeSamples
+/* MATLAB version: Refactor: readNegativeSamples */
+
+/* TODO document
  */
 orion_multiscale_laplacian_output*
 orion_readNegativeSamples(
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
index 0004eb0..4710572 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
@@ -2,14 +2,11 @@
 
 #include "kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h"
 
-/* TODO
- *
- * Refactor: compute2D_DiscrimantFunction
- */
-
 #define MAX_NUMBER_OF_HISTOGRAM_SAMPLES 1E6
 
 #include "numeric/sample.h"
+#include "vis/vis.hxx"
+
 #include <math.h>
 #include <float.h>
 #include <assert.h>
@@ -27,6 +24,9 @@ void orion_normaliseHistogram(
 		orion_discriminant_function* discrim
 		);
 
+/* MATLAB version: compute2D_DiscrimantFunction */
+
+/* TODO document */
 void orion_compute2D_DiscrimantFunction(
 		orion_segmentation_param* param,
 		orion_features* features,
@@ -107,7 +107,7 @@ void orion_compute2D_DiscrimantFunction(
 
 /* Creates a 2D histogram
  *
- * TODO
+ * TODO document
  *
  * See also: MATLAB's hist3 function
  */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/getResponseToDiscriminantFunction.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/getResponseToDiscriminantFunction.c
index 96a54bc..8a78647 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/getResponseToDiscriminantFunction.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/getResponseToDiscriminantFunction.c
@@ -1,4 +1,4 @@
-/* TODO
+/* TODO compare with the MATLAB code
  *
  * Refactor: getResponseToDiscriminantFunction
  */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c
index 5edf1dc..7c62149 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.c
@@ -1,13 +1,11 @@
 #include "kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/removeIsolatedResponses.h"
-/* TODO
- *
- * Refactor: removeIsolatedResponses
- */
 
 #include "numeric/sample.h"
 #include <float.h>
 #include "simple-log/simplelog.h"
 
+/* MATLAB version: removeIsolatedResponses */
+
 /* orion_removeIsolatedResponses
  *
  * Identify the indices of features that are non-isolated so that only features
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/sortEigenvalues.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/sortEigenvalues.c
index 53a2d98..2229c95 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/sortEigenvalues.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/ExtractFeatures/sortEigenvalues.c
@@ -1,4 +1,6 @@
 /* TODO
+ *
+ * dead code via computeFeaturesIsotropicFilter
  *
  * Refactor: sortEigenvalues
  */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/getInfoVolume.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/getInfoVolume.c
index 663f2dc..7b6c127 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/getInfoVolume.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/getInfoVolume.c
@@ -1,4 +1,4 @@
-/* TODO
+/* TODO remove this. Already available in mhd reading code
  *
  * Refactor: getInfoVolume
  */
diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/remove_small_conComp3D.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/remove_small_conComp3D.c
index a2a5f88..aadcc3b 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/remove_small_conComp3D.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/Util/remove_small_conComp3D.c
@@ -1,4 +1,4 @@
-/* TODO
+/* TODO create test case for this <https://github.com/zmughal/orion-rework/issues/29>
  *
  * Refactor: remove_small_conComp3D
  */

From 82fea6ac04993fc4139afcb85d7d5c4df6c885bd Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Wed, 29 Jun 2016 08:14:19 -0500
Subject: [PATCH 53/55] VTK linking and histogram normalisation work

---
 .../compute2D_DiscrimantFunction.c            | 18 ++++-
 lib/segmentation/orion_discriminant.c         |  2 +
 lib/segmentation/orion_discriminant.h         |  4 ++
 lib/vis/vis.cxx                               | 70 +++++++++++++++++++
 lib/vis/vis.hxx                               | 47 +++++++++++++
 5 files changed, 139 insertions(+), 2 deletions(-)
 create mode 100644 lib/vis/vis.cxx
 create mode 100644 lib/vis/vis.hxx

diff --git a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
index 4710572..d5a5fc1 100644
--- a/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
+++ b/lib/kitchen-sink/01_Segmentation/dendrites_main/DiscriminantFunction/compute2D_DiscrimantFunction.c
@@ -97,6 +97,7 @@ void orion_compute2D_DiscrimantFunction(
 
 	/* compute the 2D histogram for edges */
 	orion_hist3(param, features, non_isolated_instance_indices, discrim);
+	orion_discriminant_function_display( discrim );
 
 	/* normalise the histogram in order to compute the cost function */
 	orion_normaliseHistogram(param, discrim);
@@ -125,7 +126,7 @@ void orion_hist3(
 
 	/* NOTE: histogram is allocated here: if the size of the bins change
 	 * for each dimension, then this will need to change */
-	orion_histogram_init( discrim, (param->bins + 1), (param->bins + 1) );
+	orion_histogram_init( discrim, param->bins, param->bins );
 
 	for( int indices_idx = 0; indices_idx < indices_sz; indices_idx++ ) {
 		size_t feat_instance_idx = array_get_int( indices, indices_idx );
@@ -137,6 +138,10 @@ void orion_hist3(
 					( cur_feature - discrim->min_value[feat_idx] )
 					/ ( discrim->step_size[feat_idx] )
 					);
+			if( feat_bin_idx[feat_idx] >= discrim->bin_sz[feat_idx] ) {
+				/* max value goes in the last bin */
+				feat_bin_idx[feat_idx] = discrim->bin_sz[feat_idx] - 1;
+			}
 		}
 		/* increment by 1 */
 		orion_histogram_increment( discrim, feat_bin_idx[0], feat_bin_idx[1] );
@@ -147,5 +152,14 @@ void orion_normaliseHistogram(
 		orion_segmentation_param* param,
 		orion_discriminant_function* discrim
 		) {
-	WARN_UNIMPLEMENTED;
+	/* parameter for the smoothing of the Histogram */
+	pixel_type sigma = 5;
+
+	/* Apply sigmoid function to normalize the volume. Just in case that we
+	 * are not using the multiscale approach */
+	for( int hist_idx = 0; hist_idx < orion_histogram_elems(discrim); hist_idx++) {
+		/* 1 / (1 + exp(-h)) */
+		discrim->norm_histogram[hist_idx] =
+			1.0 / ( 1.0 + expf( -(discrim->histogram[hist_idx]) ) );
+	}
 }
diff --git a/lib/segmentation/orion_discriminant.c b/lib/segmentation/orion_discriminant.c
index 09a1bdf..86c509d 100644
--- a/lib/segmentation/orion_discriminant.c
+++ b/lib/segmentation/orion_discriminant.c
@@ -5,7 +5,9 @@ void orion_histogram_init(orion_discriminant_function* discrim, size_t m, size_t
 	discrim->bin_sz[1] = n;
 
 	NEW_COUNT(discrim->histogram, size_t, discrim->bin_sz[0] * discrim->bin_sz[1]);
+	NEW_COUNT(discrim->norm_histogram, pixel_type, discrim->bin_sz[0] * discrim->bin_sz[1]);
 	for( int hist_idx = 0; hist_idx < orion_histogram_elems(discrim); hist_idx++ ) {
 		discrim->histogram[hist_idx] = 0;
+		discrim->norm_histogram[hist_idx] = 0.0;
 	}
 }
diff --git a/lib/segmentation/orion_discriminant.h b/lib/segmentation/orion_discriminant.h
index 422a018..ce48607 100644
--- a/lib/segmentation/orion_discriminant.h
+++ b/lib/segmentation/orion_discriminant.h
@@ -25,8 +25,12 @@
 typedef struct {
 	/* number of bins in each dimension */
 	size_t bin_sz[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
+	/* stores count */
 	size_t* histogram; /* dimensions: [bin_sz[0], bin_sz[1]] */
 
+	/* histogram after normalisation */
+	pixel_type* norm_histogram; /* dimensions: [bin_sz[0], bin_sz[1]] */
+
 
 	/* store the minimum and maximum value for each feature */
 	pixel_type min_value[ORION_NUMBER_OF_SEGMENTATION_FEATURES];
diff --git a/lib/vis/vis.cxx b/lib/vis/vis.cxx
new file mode 100644
index 0000000..6463143
--- /dev/null
+++ b/lib/vis/vis.cxx
@@ -0,0 +1,70 @@
+#include "vis.hxx"
+
+#include <cstdint>
+
+void _orion_discriminant_function_to_vtkImageData(
+	orion_discriminant_function* discrim,
+	vtkImageData* image ) {
+
+	image->SetDimensions(discrim->bin_sz[0], discrim->bin_sz[1], 1);
+
+	uint32_t image_scalar_dim = 1;
+#if VTK_MAJOR_VERSION <= 5
+	image->SetNumberOfScalarComponents(image_scalar_dim);
+	image->SetScalarTypeToInt();
+	image->AllocateScalars();
+#else
+	image->AllocateScalars(VTK_INT, image_scalar_dim);
+#endif
+	int* vtkImagePixel = static_cast<int*>( image->GetScalarPointer(0,0,0) );
+	size_t* orion_disc_bins = discrim->histogram;
+	size_t hist_nelems = orion_histogram_elems( discrim );
+	for(size_t idx = 0; idx < hist_nelems; idx++, orion_disc_bins++, vtkImagePixel += image_scalar_dim ) {
+		vtkImagePixel[0] = *orion_disc_bins;
+	}
+}
+
+
+void orion_discriminant_function_display( orion_discriminant_function* discrim ) {
+	vtkSmartPointer<vtkImageData> colorImage = vtkSmartPointer<vtkImageData>::New();
+	_orion_discriminant_function_to_vtkImageData(discrim, colorImage);
+
+	vtkSmartPointer<vtkImageMapper> imageMapper = vtkSmartPointer<vtkImageMapper>::New();
+#if VTK_MAJOR_VERSION <= 5
+	imageMapper->SetInputConnection(colorImage->GetProducerPort());
+#else
+	imageMapper->SetInputData(colorImage);
+#endif
+	imageMapper->SetColorWindow(255);
+	imageMapper->SetColorLevel(127.5);
+
+	vtkSmartPointer<vtkActor2D> imageActor = vtkSmartPointer<vtkActor2D>::New();
+	imageActor->SetMapper(imageMapper);
+	imageActor->SetPosition(20, 20);
+
+		// Setup renderers
+		vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
+
+		// Setup render window
+		vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New();
+
+		renderWindow->AddRenderer(renderer);
+
+		// Setup render window interactor
+		vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor = vtkSmartPointer<vtkRenderWindowInteractor>::New();
+
+		vtkSmartPointer<vtkInteractorStyleImage> style = vtkSmartPointer<vtkInteractorStyleImage>::New();
+
+		renderWindowInteractor->SetInteractorStyle(style);
+
+		// Render and start interaction
+		renderWindowInteractor->SetRenderWindow(renderWindow);
+
+		//renderer->AddViewProp(imageActor);
+		renderer->AddActor2D(imageActor);
+
+		renderWindow->Render();
+	renderWindowInteractor->Start();
+
+
+}
diff --git a/lib/vis/vis.hxx b/lib/vis/vis.hxx
new file mode 100644
index 0000000..e89d833
--- /dev/null
+++ b/lib/vis/vis.hxx
@@ -0,0 +1,47 @@
+#ifndef ORION_VIS_H
+#define ORION_VIS_H 1
+
+/* system headers */
+#include <stdlib.h>
+#include <stdbool.h>
+
+#ifdef __cplusplus
+  /* Need to initialise because we are building without CMake:
+   * <http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Factories_now_require_defines>
+   */
+  #include <vtkAutoInit.h>
+  VTK_MODULE_INIT(vtkRenderingOpenGL);
+  VTK_MODULE_INIT(vtkInteractionStyle);
+  VTK_MODULE_INIT(vtkRenderingFreeType);
+  /*VTK_MODULE_INIT(vtkRenderingFreeTypeOpenGL);*/
+  VTK_MODULE_INIT(vtkRenderingVolumeOpenGL);
+
+
+  #include <vtkVersion.h>
+  #include <vtkImageData.h>
+  #include <vtkSmartPointer.h>
+  #include <vtkRenderWindow.h>
+  #include <vtkRenderWindowInteractor.h>
+  #include <vtkInteractorStyleImage.h>
+  #include <vtkRenderer.h>
+  #include <vtkImageMapper.h>
+  #include <vtkActor2D.h>
+  #include <vtkImageSlice.h>
+#endif
+
+/* local headers */
+#include "segmentation/orion_discriminant.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* Function prototypes */
+extern
+void orion_discriminant_function_display( orion_discriminant_function* discrim );
+
+#ifdef __cplusplus
+};
+#endif /* __cplusplus */
+
+#endif /* ORION_VIS_H */

From 94de3fef2bd0224b3c4960965a9da32e0bf785c1 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 23 Dec 2016 00:18:56 -0600
Subject: [PATCH 54/55] Set up Doxygen

---
 .gitignore         |    1 +
 Makefile           |    7 +-
 make/Doxyfile      | 2489 ++++++++++++++++++++++++++++++++++++++++++++
 make/config-dir.mk |    1 +
 4 files changed, 2497 insertions(+), 1 deletion(-)
 create mode 100644 make/Doxyfile

diff --git a/.gitignore b/.gitignore
index 824f05c..45290a1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,6 +19,7 @@ ComputeFilter
 /.build
 /.deps
 /bin
+/doxygen-doc
 
 *~
 *.a
diff --git a/Makefile b/Makefile
index a82317d..9d1ac78 100644
--- a/Makefile
+++ b/Makefile
@@ -55,7 +55,7 @@ CONFIG_HEADER_FILE := $(LIBDIR)/config/config.h
 $(CONFIG_HEADER_FILE): $(BIN_BIN_CONFIG.c)
 	$(BIN_BIN_CONFIG.c) > $@
 
-.PHONY: tags
+.PHONY: tags $(DOXYGENDIR)
 
 ifdef PROD
   DEV_TARGETS :=
@@ -78,6 +78,7 @@ clean:
 	-find . -type f -name '*.o' -delete
 	-find . -type f \( -name '*.gcda' -o -name '*.gcno' -o -name '*.gcov' \) -delete
 	-rm -Rf $(OUTPUT_DIRS)
+	-rm -Rf $(DOXYGENDIR)
 	-rm -Rf $(ITK_CONFIG_MK)
 	-rm -Rf $(GCOVDIR) $(LCOVDIR)
 	-rm -Rf $(CONFIG_HEADER_FILE)
@@ -90,6 +91,10 @@ include make/00-implicit-rules.mk
 -include $(LIB_SRC.c:$(LIBDIR)/%.c=$(DEPDIR)/$(LIBDIR)/%.P)
 -include $(TEST.c:$(TESTDIR)/%.c=$(DEPDIR)/$(TESTDIR)/%.P)
 
+doc: $(DOXYGENDIR)
+
+$(DOXYGENDIR): make/Doxyfile
+	doxygen $<
 tags:
 	ctags --exclude=external -R .
 	# add the ORION 3 code to the tags so that it is easy to jump to the other codebase
diff --git a/make/Doxyfile b/make/Doxyfile
new file mode 100644
index 0000000..ad0ca80
--- /dev/null
+++ b/make/Doxyfile
@@ -0,0 +1,2489 @@
+# Doxyfile 1.8.12
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
+# for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME           = "My Project"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER         =
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          =
+
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
+
+PROJECT_LOGO           =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       =
+
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
+
+CREATE_SUBDIRS         = NO
+
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
+
+OUTPUT_LANGUAGE        = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+# The default value is: YES.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
+
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
+# description.
+# The default value is: NO.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+# The default value is: NO.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
+
+FULL_PATH_NAMES        = YES
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH    =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
+
+JAVADOC_AUTOBRIEF      = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
+
+TAB_SIZE               = 4
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
+
+ALIASES                =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
+
+TCL_SUBST              =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. For
+# instance to make doxygen treat .inc files as Fortran files (default is PHP),
+# and .f files as C (default is Fortran), use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
+
+EXTENSION_MAPPING      =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT       = YES
+
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 0.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 0
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING            = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT   = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  =
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
+
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cxx \
+                         *.cpp \
+                         *.c++ \
+                         *.java \
+                         *.ii \
+                         *.ixx \
+                         *.ipp \
+                         *.i++ \
+                         *.inl \
+                         *.idl \
+                         *.ddl \
+                         *.odl \
+                         *.h \
+                         *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.cs \
+                         *.d \
+                         *.php \
+                         *.php4 \
+                         *.php5 \
+                         *.phtml \
+                         *.inc \
+                         *.m \
+                         *.markdown \
+                         *.md \
+                         *.mm \
+                         *.dox \
+                         *.py \
+                         *.pyw \
+                         *.f90 \
+                         *.f95 \
+                         *.f03 \
+                         *.f08 \
+                         *.f \
+                         *.for \
+                         *.tcl \
+                         *.vhd \
+                         *.vhdl \
+                         *.ucf \
+                         *.qsf
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE              = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE                =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH           =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS       = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH             =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS       = YES
+
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse-libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS          =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX     = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP         = NO
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET        = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP      = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI           = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX          = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH         = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT    = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX            = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH    = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX         = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE             = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES         =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER           =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE        = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES     = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE      = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE        = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE    =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION          = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT             = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE       =
+
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS        = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES         = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS         = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH            =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH               =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: YES.
+
+HAVE_DOT               = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS        = 0
+
+# When you want a differently looking font in the dot files that doxygen
+# generates you can specify the font name using DOT_FONTNAME. You need to make
+# sure dot is able to find the font, which can be done by putting it in a
+# standard location or by setting the DOTFONTPATH environment variable or by
+# setting DOT_FONTPATH to the directory containing the font.
+# The default value is: Helvetica.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTNAME           = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
+# dot graphs.
+# Minimum value: 4, maximum value: 24, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTSIZE           = 10
+
+# By default doxygen will tell dot to use the default font as specified with
+# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
+# the path where dot can find it using this tag.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_FONTPATH           =
+
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
+# each documented class showing the direct and indirect inheritance relations.
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
+# graph for each documented class showing the direct and indirect implementation
+# dependencies (inheritance, containment, and class references variables) of the
+# class with other documented classes.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+COLLABORATION_GRAPH    = YES
+
+# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
+# groups, showing the direct groups dependencies.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GROUP_GRAPHS           = YES
+
+# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LOOK               = NO
+
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
+# class node. If there are many fields or methods and many nodes the graph may
+# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
+# number of items for each type to make the size more manageable. Set this to 0
+# for no limit. Note that the threshold may be exceeded by 50% before the limit
+# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
+# but if the number exceeds 15, the total amount of fields shown is limited to
+# 10.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+UML_LIMIT_NUM_FIELDS   = 10
+
+# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
+# collaboration graphs will show the relations between templates and their
+# instances.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
+# YES then doxygen will generate a graph for each documented file showing the
+# direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDE_GRAPH          = YES
+
+# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
+# set to YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other documented
+# files.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable call graphs for selected
+# functions only using the \callgraph command. Disabling a call graph can be
+# accomplished by means of the command \hidecallgraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALL_GRAPH             = NO
+
+# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
+# dependency graph for every global function or class method.
+#
+# Note that enabling this option will significantly increase the time of a run.
+# So in most cases it will be better to enable caller graphs for selected
+# functions only using the \callergraph command. Disabling a caller graph can be
+# accomplished by means of the command \hidecallergraph.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+CALLER_GRAPH           = NO
+
+# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
+# hierarchy of all classes instead of a textual one.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
+# dependencies a directory has on other directories in a graphical way. The
+# dependency relations are determined by the #include relations between the
+# files in the directories.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DIRECTORY_GRAPH        = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. For an explanation of the image formats see the section
+# output formats in the documentation of the dot tool (Graphviz (see:
+# http://www.graphviz.org/)).
+# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
+# to make the SVG files visible in IE 9+ (other browsers do not have this
+# requirement).
+# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
+# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
+# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo,
+# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
+# png:gdiplus:gdiplus.
+# The default value is: png.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_IMAGE_FORMAT       = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+#
+# Note that this requires a modern browser other than Internet Explorer. Tested
+# and working are Firefox, Chrome, Safari, and Opera.
+# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
+# the SVG files visible. Older versions of IE do not have SVG support.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+INTERACTIVE_SVG        = NO
+
+# The DOT_PATH tag can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_PATH               =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the \dotfile
+# command).
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOTFILE_DIRS           =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS           =
+
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS           =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+
+PLANTUML_JAR_PATH      =
+
+# When using plantuml, the specified paths are searched for files specified by
+# the !include statement in a plantuml block.
+
+PLANTUML_INCLUDE_PATH  =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
+# that will be shown in the graph. If the number of nodes in a graph becomes
+# larger than this value, doxygen will truncate the graph, which is visualized
+# by representing a node as a red box. Note that doxygen if the number of direct
+# children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
+# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+# Minimum value: 0, maximum value: 10000, default value: 50.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_GRAPH_MAX_NODES    = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
+# generated by dot. A depth value of 3 means that only nodes reachable from the
+# root by following a path via at most 3 edges will be shown. Nodes that lay
+# further from the root node will be omitted. Note that setting this option to 1
+# or 2 may greatly reduce the computation time needed for large code bases. Also
+# note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+# Minimum value: 0, maximum value: 1000, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not seem
+# to support this out of the box.
+#
+# Warning: Depending on the platform used, enabling this option may lead to
+# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
+# read).
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_TRANSPARENT        = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10) support
+# this, this feature is disabled by default.
+# The default value is: NO.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_MULTI_TARGETS      = NO
+
+# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
+# explaining the meaning of the various boxes and arrows in the dot generated
+# graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
+# files that are used to generate the various graphs.
+# The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_CLEANUP            = YES
diff --git a/make/config-dir.mk b/make/config-dir.mk
index 41b5776..fbfc3e9 100644
--- a/make/config-dir.mk
+++ b/make/config-dir.mk
@@ -10,6 +10,7 @@ TESTDIR  := lib/t
 # output of ${LIBDIR} and ${TESTDIR}
 BUILDDIR := .build
 BUILDTESTDIR := $(BUILDDIR)/t
+DOXYGENDIR := doxygen-doc
 
 # output used to build deps information for make(1)
 DEPDIR   := .deps

From 4c4d700b0ce86a4344793b4599354b74ae292404 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 23 Dec 2016 00:19:35 -0600
Subject: [PATCH 55/55] Change Doxygen settings for this project

---
 make/Doxyfile | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/make/Doxyfile b/make/Doxyfile
index ad0ca80..9f0c73d 100644
--- a/make/Doxyfile
+++ b/make/Doxyfile
@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "My Project"
+PROJECT_NAME           = "ORION"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -51,14 +51,14 @@ PROJECT_BRIEF          =
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           =
+PROJECT_LOGO           = logo/orion-logo.svg
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       =
+OUTPUT_DIRECTORY       = doxygen-doc
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -435,7 +435,7 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = NO
+EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -790,7 +790,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  =
+INPUT                  = lib src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -864,7 +864,7 @@ FILE_PATTERNS          = *.c \
 # be searched for input files as well.
 # The default value is: NO.
 
-RECURSIVE              = NO
+RECURSIVE              = YES
 
 # The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a
@@ -873,14 +873,14 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                =
+EXCLUDE                = external bin .build
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
 # from the input.
 # The default value is: NO.
 
-EXCLUDE_SYMLINKS       = NO
+EXCLUDE_SYMLINKS       = YES
 
 # If the value of the INPUT tag contains directories, you can use the
 # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
@@ -1666,7 +1666,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -2331,7 +2331,7 @@ INCLUDED_BY_GRAPH      = YES
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALL_GRAPH             = NO
+CALL_GRAPH             = YES
 
 # If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
 # dependency graph for every global function or class method.
@@ -2343,7 +2343,7 @@ CALL_GRAPH             = NO
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALLER_GRAPH           = NO
+CALLER_GRAPH           = YES
 
 # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
 # hierarchy of all classes instead of a textual one.