Merge branch 'main' into POL5610_3d_glszm

.github/workflows/build_cuda11_wheels.yml

@@ -12,7 +12,7 @@ jobs:
       matrix:
         os: [windows-2019, ubuntu-20.04]
         cibw_archs: ["auto64"]
-        cibw_build: ["cp38-*", "cp39-*", "cp310-*", "cp311-*",  "cp312-*"]
+        cibw_build: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/build_cuda12_wheels.yml

@@ -12,7 +12,7 @@ jobs:
       matrix:
         os: [windows-2019, ubuntu-20.04]
         cibw_archs: ["auto64"]
-        cibw_build: ["cp38-*", "cp39-*", "cp310-*", "cp311-*",  "cp312-*"]
+        cibw_build: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/build_wheels.yml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04, macos-13, windows-latest]
         cibw_archs: ["auto64"]
-        cibw_build: ["cp38-*", "cp39-*", "cp310-*", "cp311-*",  "cp312-*"]
+        cibw_build: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/publish_cuda11_pypi.yml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         os: [windows-2019, ubuntu-20.04]
         cibw_archs: ["auto64"]
-        cibw_build: ["cp38-*", "cp39-*", "cp310-*", "cp311-*",  "cp312-*"]
+        cibw_build: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/publish_cuda12_pypi.yml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         os: [windows-2019, ubuntu-20.04]
         cibw_archs: ["auto64"]
-        cibw_build: ["cp38-*", "cp39-*", "cp310-*", "cp311-*",  "cp312-*"]
+        cibw_build: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/publish_pypi.yml

@@ -16,7 +16,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04, macos-13, windows-latest]
         cibw_archs: ["auto64"]
-        cibw_build: ["cp38-*", "cp39-*", "cp310-*", "cp311-*",  "cp312-*"]
+        cibw_build: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3
@@ -86,7 +86,7 @@ jobs:
       matrix:
         os: [macos-13-xlarge]
         cibw_archs: ["arm64"]
-        cibw_build: ["cp39-*", "cp310-*", "cp311-*",  "cp312-*"]
+        cibw_build: ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 
     steps:
       - uses: actions/checkout@v3

CMakeLists.txt

@@ -168,6 +168,8 @@ set(SOURCE
 	src/nyx/features/3d_glcm.cpp
 	src/nyx/features/3d_glcm_nontriv.cpp
 	src/nyx/features/3d_glszm.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

ci-utils/install_prereq_linux.sh

@@ -69,7 +69,7 @@ cd ../../
 if [[ $BUILD_BOOST_DEP -eq 1 ]]; then
     for i in {1..5}
     do
-        curl -L https://boostorg.jfrog.io/artifactory/main/release/1.79.0/source/boost_1_79_0.tar.bz2 -o boost_1_79_0.tar.bz2 
+        curl -L https://archives.boost.io/release/1.79.0/source/boost_1_79_0.tar.bz2 -o boost_1_79_0.tar.bz2 
         if [ -f "boost_1_79_0.tar.bz2" ] ; then
             break
         fi

ci-utils/install_prereq_win.bat

@@ -42,7 +42,7 @@ popd
 
 if "%BUILD_Z5_DEP%" == "1" (
     for /l %%x in (1, 1, 5) do (
-        curl -L https://boostorg.jfrog.io/artifactory/main/release/1.79.0/source/boost_1_79_0.zip -o boost_1_79_0.zip
+        curl -L https://archives.boost.io/release/1.79.0/source/boost_1_79_0.zip -o boost_1_79_0.zip
         if  exist boost_1_79_0.zip (
             goto :continue_boost
         )

src/nyx/env_features.cpp

@@ -451,6 +451,76 @@ 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);
@@ -465,6 +535,51 @@ 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

@@ -32,6 +32,7 @@
 #include "features/3d_glcm.h"
 #include "features/3d_gldzm.h"
 #include "features/3d_glszm.h"
+#include "features/3d_glrlm.h"
 
 #include "features/focus_score.h"
 #include "features/power_spectrum.h"
@@ -76,6 +77,7 @@ FeatureManager::FeatureManager()
 	register_feature (new D3_GLCM_feature());
 	register_feature (new D3_GLDZM_feature());
 	register_feature (new D3_GLSZM_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
 {