initial

CMakeLists.txt

@@ -167,6 +167,8 @@ set(SOURCE
 	src/nyx/features/3d_gldzm.cpp
 	src/nyx/features/3d_glcm.cpp
 	src/nyx/features/3d_glcm_nontriv.cpp
+	src/nyx/features/3d_glrlm.cpp
+	src/nyx/features/3d_glrlm_nontriv.cpp
 	src/nyx/features/intensity.cpp
 	src/nyx/features/neighbors.cpp
 	src/nyx/features/ngldm.cpp

src/nyx/env_features.cpp

@@ -446,6 +446,76 @@ bool Environment::expand_3D_featuregroup (const std::string& s)
 		return true;
 	}
 
+	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLCM))
+	{
+		theFeatureSet.enableAll (false);
+
+		auto F =
+		{
+			Nyxus::Feature3D::GLCM_ACOR,	
+			Nyxus::Feature3D::GLCM_ASM,
+			Nyxus::Feature3D::GLCM_CLUPROM,
+			Nyxus::Feature3D::GLCM_CLUSHADE,
+			Nyxus::Feature3D::GLCM_CLUTEND,
+			Nyxus::Feature3D::GLCM_CONTRAST,	
+			Nyxus::Feature3D::GLCM_CORRELATION,
+			Nyxus::Feature3D::GLCM_DIFAVE,
+			Nyxus::Feature3D::GLCM_DIFENTRO,
+			Nyxus::Feature3D::GLCM_DIFVAR,
+			Nyxus::Feature3D::GLCM_DIS,
+			Nyxus::Feature3D::GLCM_ENERGY,
+			Nyxus::Feature3D::GLCM_ENTROPY,
+			Nyxus::Feature3D::GLCM_HOM1,
+			Nyxus::Feature3D::GLCM_HOM2,
+			Nyxus::Feature3D::GLCM_ID,
+			Nyxus::Feature3D::GLCM_IDN,
+			Nyxus::Feature3D::GLCM_IDM,
+			Nyxus::Feature3D::GLCM_IDMN,	
+			Nyxus::Feature3D::GLCM_INFOMEAS1,
+			Nyxus::Feature3D::GLCM_INFOMEAS2,
+			Nyxus::Feature3D::GLCM_IV,
+			Nyxus::Feature3D::GLCM_JAVE,
+			Nyxus::Feature3D::GLCM_JE,
+			Nyxus::Feature3D::GLCM_JMAX,
+			Nyxus::Feature3D::GLCM_JVAR,
+			Nyxus::Feature3D::GLCM_SUMAVERAGE,	
+			Nyxus::Feature3D::GLCM_SUMENTROPY,	
+			Nyxus::Feature3D::GLCM_SUMVARIANCE,
+			Nyxus::Feature3D::GLCM_VARIANCE,
+			Nyxus::Feature3D::GLCM_ASM_AVE,
+			Nyxus::Feature3D::GLCM_ACOR_AVE,
+			Nyxus::Feature3D::GLCM_CLUPROM_AVE,
+			Nyxus::Feature3D::GLCM_CLUSHADE_AVE,
+			Nyxus::Feature3D::GLCM_CLUTEND_AVE,
+			Nyxus::Feature3D::GLCM_CONTRAST_AVE,
+			Nyxus::Feature3D::GLCM_CORRELATION_AVE,
+			Nyxus::Feature3D::GLCM_DIFAVE_AVE,
+			Nyxus::Feature3D::GLCM_DIFENTRO_AVE,
+			Nyxus::Feature3D::GLCM_DIFVAR_AVE,
+			Nyxus::Feature3D::GLCM_DIS_AVE,
+			Nyxus::Feature3D::GLCM_ENERGY_AVE,
+			Nyxus::Feature3D::GLCM_ENTROPY_AVE,
+			Nyxus::Feature3D::GLCM_HOM1_AVE,
+			Nyxus::Feature3D::GLCM_ID_AVE,
+			Nyxus::Feature3D::GLCM_IDN_AVE,
+			Nyxus::Feature3D::GLCM_IDM_AVE,
+			Nyxus::Feature3D::GLCM_IDMN_AVE,
+			Nyxus::Feature3D::GLCM_IV_AVE,
+			Nyxus::Feature3D::GLCM_JAVE_AVE,
+			Nyxus::Feature3D::GLCM_JE_AVE,
+			Nyxus::Feature3D::GLCM_INFOMEAS1_AVE,
+			Nyxus::Feature3D::GLCM_INFOMEAS2_AVE,
+			Nyxus::Feature3D::GLCM_VARIANCE_AVE,
+			Nyxus::Feature3D::GLCM_JMAX_AVE,
+			Nyxus::Feature3D::GLCM_JVAR_AVE,
+			Nyxus::Feature3D::GLCM_SUMAVERAGE_AVE,
+			Nyxus::Feature3D::GLCM_SUMENTROPY_AVE,
+			Nyxus::Feature3D::GLCM_SUMVARIANCE_AVE
+		};
+
+		theFeatureSet.enableFeatures(F);
+		return true;
+	}
 	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLDZM))
 	{
 		theFeatureSet.enableAll(false);
@@ -476,6 +546,50 @@ bool Environment::expand_3D_featuregroup (const std::string& s)
 		return true;
 	}
 
+	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup3D::FG3_GLRLM))
+	{
+		theFeatureSet.enableAll(false);
+
+		auto F =
+		{
+			Nyxus::Feature3D::GLRLM_SRE,	
+			Nyxus::Feature3D::GLRLM_LRE, 
+			Nyxus::Feature3D::GLRLM_GLN, 
+			Nyxus::Feature3D::GLRLM_GLNN, 
+			Nyxus::Feature3D::GLRLM_RLN,
+			Nyxus::Feature3D::GLRLM_RLNN, 
+			Nyxus::Feature3D::GLRLM_RP,
+			Nyxus::Feature3D::GLRLM_GLV, 
+			Nyxus::Feature3D::GLRLM_RV, 
+			Nyxus::Feature3D::GLRLM_RE, 
+			Nyxus::Feature3D::GLRLM_LGLRE, 
+			Nyxus::Feature3D::GLRLM_HGLRE, 
+			Nyxus::Feature3D::GLRLM_SRLGLE, 
+			Nyxus::Feature3D::GLRLM_SRHGLE, 
+			Nyxus::Feature3D::GLRLM_LRLGLE, 
+			Nyxus::Feature3D::GLRLM_LRHGLE, 
+
+			Nyxus::Feature3D::GLRLM_SRE_AVE,
+			Nyxus::Feature3D::GLRLM_LRE_AVE,
+			Nyxus::Feature3D::GLRLM_GLN_AVE,
+			Nyxus::Feature3D::GLRLM_GLNN_AVE,
+			Nyxus::Feature3D::GLRLM_RLN_AVE,
+			Nyxus::Feature3D::GLRLM_RLNN_AVE,
+			Nyxus::Feature3D::GLRLM_RP_AVE,
+			Nyxus::Feature3D::GLRLM_GLV_AVE,
+			Nyxus::Feature3D::GLRLM_RV_AVE,
+			Nyxus::Feature3D::GLRLM_RE_AVE,
+			Nyxus::Feature3D::GLRLM_LGLRE_AVE,
+			Nyxus::Feature3D::GLRLM_HGLRE_AVE,
+			Nyxus::Feature3D::GLRLM_SRLGLE_AVE,
+			Nyxus::Feature3D::GLRLM_SRHGLE_AVE,
+			Nyxus::Feature3D::GLRLM_LRLGLE_AVE,
+			Nyxus::Feature3D::GLRLM_LRHGLE_AVE
+		};
+
+		theFeatureSet.enableFeatures(F);
+		return true;
+	}
 	return false;
 }
 

src/nyx/feature_mgr_init.cpp

@@ -31,6 +31,7 @@
 #include "features/3d_intensity.h"
 #include "features/3d_glcm.h"
 #include "features/3d_gldzm.h"
+#include "features/3d_glrlm.h"
 
 #include "features/focus_score.h"
 #include "features/power_spectrum.h"
@@ -74,6 +75,7 @@ FeatureManager::FeatureManager()
 	register_feature (new D3_PixelIntensityFeatures());
 	register_feature (new D3_GLCM_feature());
 	register_feature (new D3_GLDZM_feature());
+	register_feature (new D3_GLRLM_feature());
 
 	// image quality
 	register_feature (new FocusScoreFeature());

src/nyx/features/3d_gldzm.h

@@ -1,13 +1,11 @@
 #pragma once
 
-#pragma once
-
 #include "../feature_method.h"
 #include "texture_feature.h"
 
 /// @brief Grey Level Distance Zone (GLDZM) features
 /// 
-/// Grey Level Dsitance Zone (GLDZM) quantifies distances zones of same intensity to the ROI border
+/// GLDZM quantifies distance zones of same intensity to the ROI border
 
 class D3_GLDZM_feature : public FeatureMethod, public TextureFeature
 {

src/nyx/featureset.cpp

@@ -780,6 +780,39 @@ namespace Nyxus
 		{ "3GLDZM_ZDM", Feature3D::GLDZM_ZDM },
 		{ "3GLDZM_ZDV", Feature3D::GLDZM_ZDV },
 		{ "3GLDZM_ZDE", Feature3D::GLDZM_ZDE },
+
+		{ "3GLRLM_SRE",					Feature3D::GLRLM_SRE },
+		{ "3GLRLM_LRE",					Feature3D::GLRLM_LRE },
+		{ "3GLRLM_GLN",					Feature3D::GLRLM_GLN },
+		{ "3GLRLM_GLNN",				Feature3D::GLRLM_GLNN },
+		{ "3GLRLM_RLN",					Feature3D::GLRLM_RLN },
+		{ "3GLRLM_RLNN",				Feature3D::GLRLM_RLNN },
+		{ "3GLRLM_RP",					Feature3D::GLRLM_RP },
+		{ "3GLRLM_GLV",					Feature3D::GLRLM_GLV },
+		{ "3GLRLM_RV",					Feature3D::GLRLM_RV },
+		{ "3GLRLM_RE",					Feature3D::GLRLM_RE },
+		{ "3GLRLM_LGLRE",				Feature3D::GLRLM_LGLRE },
+		{ "3GLRLM_HGLRE",				Feature3D::GLRLM_HGLRE },
+		{ "3GLRLM_SRLGLE",			Feature3D::GLRLM_SRLGLE },
+		{ "3GLRLM_SRHGLE",			Feature3D::GLRLM_SRHGLE },
+		{ "3GLRLM_LRLGLE",			Feature3D::GLRLM_LRLGLE },
+		{ "3GLRLM_LRHGLE",			Feature3D::GLRLM_LRHGLE },
+		{ "3GLRLM_SRE_AVE",			Feature3D::GLRLM_SRE_AVE },
+		{ "3GLRLM_LRE_AVE",			Feature3D::GLRLM_LRE_AVE },
+		{ "3GLRLM_GLN_AVE",			Feature3D::GLRLM_GLN_AVE },
+		{ "3GLRLM_GLNN_AVE",		Feature3D::GLRLM_GLNN_AVE },
+		{ "3GLRLM_RLN_AVE",			Feature3D::GLRLM_RLN_AVE },
+		{ "3GLRLM_RLNN_AVE",		Feature3D::GLRLM_RLNN_AVE },
+		{ "3GLRLM_RP_AVE",			Feature3D::GLRLM_RP_AVE },
+		{ "3GLRLM_GLV_AVE",			Feature3D::GLRLM_GLV_AVE },
+		{ "3GLRLM_RV_AVE",			Feature3D::GLRLM_RV_AVE },
+		{ "3GLRLM_RE_AVE",			Feature3D::GLRLM_RE_AVE },
+		{ "3GLRLM_LGLRE_AVE",		Feature3D::GLRLM_LGLRE_AVE },
+		{ "3GLRLM_HGLRE_AVE",		Feature3D::GLRLM_HGLRE_AVE },
+		{ "3GLRLM_SRLGLE_AVE",	Feature3D::GLRLM_SRLGLE_AVE },
+		{ "3GLRLM_SRHGLE_AVE",	Feature3D::GLRLM_SRHGLE_AVE },
+		{ "3GLRLM_LRLGLE_AVE",	Feature3D::GLRLM_LRLGLE_AVE },
+		{ "3GLRLM_LRHGLE_AVE",	Feature3D::GLRLM_LRHGLE_AVE },
 	};
 
 	std::map <std::string, Fgroup3D> UserFacing3dFeaturegroupNames =
@@ -790,6 +823,7 @@ namespace Nyxus
 		{ "*3D_ALL_TEXTURE*", Fgroup3D::FG3_TEXTURE },
 		{ "*3D_GLCM*", Fgroup3D::FG3_GLCM },
 		{ "*3D_GLDZM*", Fgroup3D::FG3_GLDZM },
+		{ "*3D_GLRLM*", Fgroup3D::FG3_GLRLM },
 		{ "*3D_ALL_NEIGHBOR*", Fgroup3D::FG3_NEIG },
 		{ "*3D_MOMENTS*", Fgroup3D::FG3_MOMENTS },
 	};

src/nyx/featureset.h

@@ -739,6 +739,41 @@ namespace Nyxus
 		GLDZM_ZDV,		// Zone Distance Variance
 		GLDZM_ZDE,		// Zone Distance Entropy
 
+		// GLRLM:
+		GLRLM_SRE,	// Short Run Emphasis 
+		GLRLM_LRE,	// Long Run Emphasis 
+		GLRLM_GLN,	// Gray Level Non-Uniformity 
+		GLRLM_GLNN,	// Gray Level Non-Uniformity Normalized 
+		GLRLM_RLN,	// Run Length Non-Uniformity
+		GLRLM_RLNN,	// Run Length Non-Uniformity Normalized 
+		GLRLM_RP,	// Run Percentage
+		GLRLM_GLV,	// Gray Level Variance 
+		GLRLM_RV,	// Run Variance 
+		GLRLM_RE,	// Run Entropy 
+		GLRLM_LGLRE,	// Low Gray Level Run Emphasis 
+		GLRLM_HGLRE,	// High Gray Level Run Emphasis 
+		GLRLM_SRLGLE,	// Short Run Low Gray Level Emphasis 
+		GLRLM_SRHGLE,	// Short Run High Gray Level Emphasis 
+		GLRLM_LRLGLE,	// Long Run Low Gray Level Emphasis 
+		GLRLM_LRHGLE,	// Long Run High Gray Level Emphasis 
+		// -- averages --
+		GLRLM_SRE_AVE,
+		GLRLM_LRE_AVE,
+		GLRLM_GLN_AVE,
+		GLRLM_GLNN_AVE,
+		GLRLM_RLN_AVE,
+		GLRLM_RLNN_AVE,
+		GLRLM_RP_AVE,
+		GLRLM_GLV_AVE,
+		GLRLM_RV_AVE,
+		GLRLM_RE_AVE,
+		GLRLM_LGLRE_AVE,
+		GLRLM_HGLRE_AVE,
+		GLRLM_SRLGLE_AVE,
+		GLRLM_SRHGLE_AVE,
+		GLRLM_LRLGLE_AVE,
+		GLRLM_LRHGLE_AVE,
+
 		_COUNT_
 	};
 
@@ -785,6 +820,7 @@ namespace Nyxus
 		FG3_TEXTURE,			// 3D_GLCM + 3D_GLRLM + 3D_DLSZM + etc
 		FG3_GLCM,
 		FG3_GLDZM,
+		FG3_GLRLM,
 		FG3_NEIG,
 		FG3_MOMENTS,
 		_COUNT_

src/nyx/reduce_trivial_rois.cpp

@@ -44,6 +44,7 @@
 #include "features/3d_intensity.h"
 #include "features/3d_glcm.h"
 #include "features/3d_gldzm.h"
+#include "features/3d_glrlm.h"
 //--future-- #include "features/3d_surface.h"
 
 #include "features/focus_score.h"
@@ -384,7 +385,11 @@ namespace Nyxus
 			STOPWATCH("3D GLDZM/3DGLDZM/3DGLDZM/#FFFF00", "\t=");
 			runParallel (D3_GLDZM_feature::reduce, n_threads, work_per_thread, job_size, &L, &roiData);
 		}		
-
+		if (D3_GLRLM_feature::required(theFeatureSet))
+		{
+			STOPWATCH("3D GLRLM/3DGLRLM/3DGLRLM/#FFFF00", "\t=");
+			runParallel(D3_GLRLM_feature::reduce, n_threads, work_per_thread, job_size, &L, &roiData);
+		}
 
 		//==== morphology/surface
 		//--future--