Merge pull request #102 from friskluft/POL2510_gldzm

GLDZM feature group

CMakeLists.txt

@@ -106,6 +106,7 @@ set(SOURCE
 	src/nyx/features/glcm.cpp
 	src/nyx/features/glcm_nontriv.cpp
 	src/nyx/features/gldm.cpp
+	src/nyx/features/gldzm.cpp
 	src/nyx/features/glrlm.cpp
 	src/nyx/features/glszm.cpp
 	src/nyx/features/hexagonality_polygonality.cpp

src/nyx/environment.h

@@ -29,7 +29,7 @@
 #define ONLINESTATSTHRESH "--onlineStatsThresh" // Environment :: onlineStatsThreshold	-- Example: --onlineStatsThresh=150
 #define XYRESOLUTION "--pixelsPerCentimeter"	// pixels per centimeter
 #define PXLDIST "--pixelDistance"				// used in neighbor features
-#define COARSEGRAYDEPTH "--coarseGrayDepth"		// Default - 8
+#define COARSEGRAYDEPTH "--coarseGrayDepth"		// Environment :: raw_coarse_grayscale_depth
 #define RAMLIMIT "--ramLimit"					// Optional. Limit for treating ROIs as non-trivial and for setting the batch size of trivial ROIs. Default - amount of available system RAM
 #define TEMPDIR "--tempDir"						// Optional. Used in processing non-trivial features. Default - system temp directory
 #define IBSICOMPLIANCE "--ibsi" // skip binning for grey level and grey tone features

src/nyx/feature_mgr.cpp

@@ -77,7 +77,7 @@ bool FeatureManager::check_11_correspondence()
 			else	// error - no providers
 			{
 				success = false;
-				std::cout << "Error: feature " << theFeatureSet.findFeatureNameByCode((AvailableFeatures)i_fcode) << " (code " << i_fcode << ") is not provided by any feature method \n";
+				std::cout << "Error: feature " << theFeatureSet.findFeatureNameByCode((AvailableFeatures)i_fcode) << " (code " << i_fcode << ") is not provided by any feature method. Check constructor of class FeatureManager\n";
 			}
 	}
 
@@ -199,15 +199,15 @@ void FeatureManager::build_user_requested_set()
 		FeatureMethod* fm = get_feature_method_by_code (fc);
 
 		if (fm == nullptr)
-			throw (std::runtime_error("Feature " + std::to_string(fc) + " is not provided by any feature method"));
+			throw (std::runtime_error("Feature " + std::to_string(fc) + " is not provided by any feature method. Check constructor of class FeatureManager"));
 
 		// first, save feature methods of fm's dependencies
 		for (auto depend_fc : fm->dependencies)
 		{
 			FeatureMethod* depend_fm = get_feature_method_by_code (depend_fc);
 
 			if (depend_fm == nullptr)
-				throw (std::runtime_error("Feature " + std::to_string(depend_fc) + " is not provided by any feature method"));
+				throw (std::runtime_error("Feature " + std::to_string(depend_fc) + " is not provided by any feature method. Check constructor of class FeatureManager"));
 
 			// save this fm if it's not yet saved
 			if (std::find(user_requested_features.begin(), user_requested_features.end(), depend_fm) == user_requested_features.end())

src/nyx/feature_mgr_init.cpp

@@ -14,6 +14,7 @@
 #include "features/geodetic_len_thickness.h"
 #include "features/glcm.h"
 #include "features/glrlm.h"
+#include "features/gldzm.h"
 #include "features/glszm.h"
 #include "features/gldm.h"
 #include "features/hexagonality_polygonality.h"
@@ -48,7 +49,8 @@ FeatureManager::FeatureManager()
 	register_feature (new FractalDimensionFeature());
 	register_feature (new GLCMFeature());	
 	register_feature (new GLRLMFeature());	
-	register_feature (new GLSZMFeature());	
+	register_feature (new GLDZMFeature());
+	register_feature (new GLSZMFeature());
 	register_feature (new GLDMFeature());
 	register_feature (new NGTDMFeature());
 	register_feature (new ImageMomentsFeature());

src/nyx/features/gldm.cpp

@@ -48,8 +48,8 @@ void GLDMFeature::calculate(LR& r)
 	bool disableGrayBinning = Environment::ibsi_compliance || nGrays >= piRange;
 
 	// Gather zones
-	for (int row = 0; row < D.height(); row++)
-		for (int col = 0; col < D.width(); col++)
+	for (int row = 0; row < D.get_height(); row++)
+		for (int col = 0; col < D.get_width(); col++)
 		{
 			// Find a non-blank pixel
 			PixIntens pi = Nyxus::to_grayscale (D.yx(row, col), r.aux_min, piRange, nGrays, disableGrayBinning);