Merge branch 'main' into image_quality_v5

CMakeLists.txt

@@ -176,11 +176,13 @@ set(SOURCE
 	src/nyx/features/saturation.cpp
 	src/nyx/features/sharpness.cpp
 	src/nyx/features/specfunc.cpp
+	src/nyx/features/texture_feature.cpp
 	src/nyx/features/zernike.cpp
 	src/nyx/features/zernike_nontriv.cpp
 	src/nyx/helpers/timing.cpp
 	src/nyx/cli_fpimage_options.cpp
 	src/nyx/cli_gabor_options.cpp
+	src/nyx/cli_glcm_options.cpp
 	src/nyx/cli_nested_roi_options.cpp
 	src/nyx/common_stats.cpp
 	src/nyx/dirs_and_files.cpp

src/nyx/cli_glcm_options.cpp

@@ -0,0 +1,52 @@
+#include "cli_glcm_options.h"
+#include "features/glcm.h"
+
+using namespace Nyxus;
+
+bool GLCMoptions::parse_input()
+{
+	if (!rawAngles.empty())
+	{
+		//==== Parse rotations
+		if (!rawAngles.empty())
+		{
+			std::string ermsg;
+			if (!Nyxus::parse_delimited_string_list_to_ints(rawAngles, glcmAngles, ermsg))
+			{
+				std::cerr << "Error parsing list of integers " << rawAngles << ": " << ermsg << "\n";
+				return false;
+			}
+
+			// The angle list parsed well, let's tell it to GLCMFeature 
+			GLCMFeature::angles = glcmAngles;
+		}
+	}
+
+	if (!rawOffs.empty())
+	{
+		// string -> real
+		int x;
+		bool ok = Nyxus::parse_as_int (rawOffs, x);
+		if (!ok || x <= 0)
+		{
+			ermsg = "Error in " + rawOffs + ": expecting a positive integer value";
+			return false;
+		}
+
+		// set feature class parameter
+		GLCMFeature::offset = x;
+	}
+
+	return true;
+}
+
+bool GLCMoptions::empty()
+{
+	return rawAngles.empty() && rawOffs.empty();
+}
+
+std::string GLCMoptions::get_last_er_msg()
+{
+	return ermsg;
+}
+

src/nyx/cli_glcm_options.h

@@ -0,0 +1,25 @@
+#pragma once
+
+#include <string>
+#include <vector>
+
+class GLCMoptions
+{
+public:
+	// Parses 'raw*', set 'defined_' and 'ermsg'
+	bool parse_input();
+
+	std::string get_last_er_msg();
+
+	bool empty();
+
+	// intentionally public to be accessed by Environment
+	std::string rawOffs = "",	// matches GLCMOFFSET
+		rawAngles = "";			// matches GLCMANGLES
+
+	std::vector<int> glcmAngles = { 0, 45, 90, 135 };
+
+private:
+	bool defined_ = false;
+	std::string ermsg = "";
+};

src/nyx/environment.cpp

@@ -126,7 +126,7 @@ void Environment::show_cmdline_help()
 		<< "\t\t" << OPT << PXLDIST << "=<number of pixels as neighbor features radius> \n"
 		<< "\t\t\tDefault: 5 \n"
 		<< "\t\t" << OPT << COARSEGRAYDEPTH << "=<custom number of grayscale levels> \n"
-		<< "\t\t\tDefault: 256 \n"
+		<< "\t\t\tDefault: 64 \n"
 		<< "\t\t" << OPT << GLCMANGLES << "=<one or more comma separated rotation angles from set {0, 45, 90, and 135}> \n"
 		<< "\t\t\tDefault: 0,45,90,135 \n"
 		<< "\t\t" << OPT << VERBOSITY << "=<levels of verbosity 0 (silence), 1 (minimum output), 2 (1 + timing), 3 (2 + roi metrics + more timing), 4 (3 + diagnostic information)> \n"
@@ -265,6 +265,9 @@ bool Environment::find_string_argument(std::vector<std::string>::iterator& i, co
 	std::string a = arg;
 	if (actualArgName == a)
 	{
+		if (arg_value.length())
+			std::cerr << "Warning: " << a << " already has value \'" << arg_value << "\'\n";
+
 		arg_value = *++i;
 		recognizedArgs.push_back({ a, arg_value });
 		return true;
@@ -276,6 +279,9 @@ bool Environment::find_string_argument(std::vector<std::string>::iterator& i, co
 		auto pos = actualArgName.find(a);
 		if (pos != std::string::npos)
 		{
+			if (arg_value.length())
+				std::cerr << "Warning: " << a << " already has value \'" << arg_value << "\'\n";
+
 			arg_value = actualArgName.substr(a.length());
 			recognizedArgs.push_back({ a, arg_value });
 			return true;
@@ -358,7 +364,8 @@ bool Environment::parse_cmdline(int argc, char** argv)
 			find_string_argument(i, LOADERTHREADS, loader_threads) ||
 			find_string_argument(i, PXLSCANTHREADS, pixel_scan_threads) ||
 			find_string_argument(i, REDUCETHREADS, reduce_threads) ||
-			find_string_argument(i, GLCMANGLES, rawGlcmAngles) ||
+			find_string_argument(i, GLCMANGLES, glcmOptions.rawAngles) ||
+			find_string_argument(i, GLCMOFFSET, glcmOptions.rawOffs) ||
 			find_string_argument(i, PXLDIST, pixel_distance) ||
 			find_string_argument(i, COARSEGRAYDEPTH, raw_coarse_grayscale_depth) ||
 			find_string_argument(i, VERBOSITY, rawVerbosity) ||
@@ -584,9 +591,9 @@ bool Environment::parse_cmdline(int argc, char** argv)
 	if (!raw_coarse_grayscale_depth.empty())
 	{
 		// string -> integer
-		if (sscanf(raw_coarse_grayscale_depth.c_str(), "%d", &coarse_grayscale_depth) != 1 || coarse_grayscale_depth <= 0)
+		if (sscanf(raw_coarse_grayscale_depth.c_str(), "%d", &coarse_grayscale_depth) != 1)
 		{
-			std::cerr << "Error: " << COARSEGRAYDEPTH << "=" << raw_coarse_grayscale_depth << ": expecting a positive integer constant\n";
+			std::cerr << "Error: " << COARSEGRAYDEPTH << "=" << raw_coarse_grayscale_depth << ": expecting an integer constant\n";
 			return false;
 		}
 	}
@@ -601,20 +608,6 @@ bool Environment::parse_cmdline(int argc, char** argv)
 		}
 	}
 
-	//==== Parse rotations
-	if (!rawGlcmAngles.empty())
-	{
-		std::string ermsg;
-		if (!Nyxus::parse_delimited_string_list_to_ints(rawGlcmAngles, glcmAngles, ermsg))
-		{
-			std::cerr << "Error parsing list of integers " << rawGlcmAngles << ": " << ermsg << "\n";
-			return false;
-		}
-
-		// The angle list parsed well, let's tell it to GLCMFeature 
-		GLCMFeature::angles = glcmAngles;
-	}
-
 	//==== Parse the RAM limit (in megabytes)
 	if (!rawRamLimit.empty())
 	{
@@ -678,6 +671,17 @@ bool Environment::parse_cmdline(int argc, char** argv)
 		}
 	}
 
+	//==== Parse GLCM options
+	if (!glcmOptions.empty())
+	{
+		std::string ermsg;
+		if (!this->parse_glcm_options_raw_inputs(ermsg))
+		{
+			std::cerr << ermsg << "\n";
+			return false;
+		}
+	}
+
 	//==== Parse floating point image options
 	if (!fpimageOptions.empty())
 	{
@@ -852,7 +856,7 @@ int Environment::get_floating_point_precision()
 	return floating_point_precision;
 }
 
-unsigned int Environment::get_coarse_gray_depth()
+int Environment::get_coarse_gray_depth()
 {
 	return coarse_grayscale_depth;
 }
@@ -912,6 +916,17 @@ bool Environment::parse_gabor_options_raw_inputs(std::string& error_message)
 	return true;
 }
 
+bool Environment::parse_glcm_options_raw_inputs (std::string& error_message)
+{
+
+	if (!glcmOptions.parse_input())
+	{
+		error_message = glcmOptions.get_last_er_msg();
+		return false;
+	}
+	return true;
+}
+
 bool Environment::parse_fpimage_options_raw_inputs(std::string& error_message)
 {
 	if (!fpimageOptions.parse_input())

src/nyx/environment.h

@@ -8,12 +8,11 @@
 #include "environment_basic.h"
 #include "cli_fpimage_options.h"
 #include "cli_gabor_options.h"
+#include "cli_glcm_options.h"
 #include "cli_nested_roi_options.h"
 #include "roi_blacklist.h"
 #include "save_option.h"
 
-
-
 #ifdef USE_GPU
 	#include <cuda_runtime.h>
 #endif
@@ -31,7 +30,6 @@
 #define LOADERTHREADS "--loaderThreads"			// Environment :: n_loader_threads
 #define PXLSCANTHREADS "--pxlscanThreads"		// Environment :: n_pixel_scan_threads
 #define REDUCETHREADS "--reduceThreads"			// Environment :: n_reduce_threads
-#define GLCMANGLES "--glcmAngles"					// Environment :: rotAngles
 #define VERBOSITY "--verbose"					// Environment :: verbosity_level	-- Example: --verbosity=3
 #define ONLINESTATSTHRESH "--onlineStatsThresh" // Environment :: onlineStatsThreshold	-- Example: --onlineStatsThresh=150
 #define XYRESOLUTION "--pixelsPerCentimeter"	// pixels per centimeter
@@ -54,14 +52,18 @@
 #endif
 
 // Gabor feature CLI arguments
-#define GABOR_FREQS "--gaborfreqs"		// Example: "2,4,8,72"
+#define GABOR_FREQS "--gaborfreqs"		// Example: "2,4,8,72". Frequencies should atch thetas: --gaborfreqs=1,2,3,4,5 --gabortheta=30,30,45,90,90
 #define GABOR_GAMMA "--gaborgamma"		// Example: "0.1"
 #define GABOR_SIG2LAM "--gaborsig2lam"	// Example: "0.8"
 #define GABOR_KERSIZE "--gaborkersize"	// Example: "20"
 #define GABOR_F0 "--gaborf0"			// Example: "0.1"
-#define GABOR_THETA "--gabortheta"		// Example: "60"
+#define GABOR_THETA "--gabortheta"		// Example: "60,45,90"
 #define GABOR_THRESHOLD "--gaborthold"	// Example: "0.025"
 
+// GLCM feature
+#define GLCMANGLES "--glcmAngles"				// Environment :: rotAngles
+#define GLCMOFFSET "--glcmOff"					// Environment :: raw_glcm_
+
 // Nested ROI functionality
 #define NESTEDROI_CHNL_SIGNATURE "--hsig"		// Channel signature Example: "_c" in "p0_y1_r1_c1.ome.tiff"
 #define NESTEDROI_PARENT_CHNL "--hpar"			// Channel number that should be used as a provider of parent segments. Example: --hpar=1
@@ -129,9 +131,6 @@ class Environment: public BasicEnvironment
 	std::string pixel_distance = "";
 	int n_pixel_distance = 5;
 
-	std::string rawGlcmAngles = "";
-	std::vector<int> glcmAngles = {0, 45, 90, 135};
-
 	std::string rawVerbosity = "";	// 'verbosity_level' is inherited from BasicEnvironment
 
 	std::string rawOnlineStatsThresh = "";
@@ -174,7 +173,7 @@ class Environment: public BasicEnvironment
 
 	int get_floating_point_precision();
 
-	unsigned int get_coarse_gray_depth();
+	int get_coarse_gray_depth();
 	void set_coarse_gray_depth(unsigned int new_depth);
 
 	// implementation of SKIPROI
@@ -187,6 +186,10 @@ class Environment: public BasicEnvironment
 	bool parse_gabor_options_raw_inputs (std::string& error_message);
 	GaborOptions gaborOptions;
 
+	// implementation of GLCM feature options
+	bool parse_glcm_options_raw_inputs (std::string& error_message);
+	GLCMoptions glcmOptions;
+
 	// implementation of nested ROI options
 	bool parse_nested_options_raw_inputs (std::string& error_message);
 	NestedRoiOptions nestedOptions;
@@ -221,7 +224,7 @@ class Environment: public BasicEnvironment
 
 	int floating_point_precision = 10;	
 
-	unsigned int coarse_grayscale_depth = 256;
+	int coarse_grayscale_depth = 64;
 	std::string raw_coarse_grayscale_depth = "";
 
 	// data members implementing RAMLIMIT

src/nyx/feature_mgr.h

@@ -18,6 +18,10 @@ class FeatureManager
 
 	void apply_user_selection();
 
+	// Initializes feature classes 
+	// (allocates lookup tables, precalculates filter banks, etc.)
+	bool init_feature_classes();
+
 	// After compiling, returns the number of user-requested features
 	int get_num_requested_features();
 

src/nyx/feature_mgr_init.cpp

@@ -69,4 +69,8 @@ FeatureManager::FeatureManager()
 	register_feature (new PowerSpectrumFeature());
 	register_feature (new SaturationFeature());
 	register_feature (new SharpnessFeature());
+}bool FeatureManager::init_feature_classes()
+{
+	return GaborFeature::init_class();
 }
+

src/nyx/features/aabb.h

@@ -47,6 +47,14 @@ class AABB
 	inline StatsInt get_ymin() const { return ymin; }
 	inline StatsInt get_ymax() const { return ymax; }
 
+	void init_from_widthheight (StatsInt w, StatsInt h)
+	{
+		xmin = 0;
+		xmax = w;
+		ymin = 0;
+		ymax = h;
+	}
+
 	static std::tuple<StatsInt, StatsInt, StatsInt, StatsInt> from_pixelcloud (const std::vector<Pixel2>& P)
 	{
 		AABB bb;

src/nyx/features/contour.cpp

@@ -314,7 +314,7 @@ void ContourFeature::buildRegularContour(LR& r)
 	);
 
 	//==== Remove padding and save the contour image as a vector of non-blank pixels
-	AABB & bb = r.aabb; // r.aux_image_matrix.original_aabb;
+	AABB & bb = r.aabb;
 	int base_x = bb.get_xmin(),
 		base_y = bb.get_ymin();
 	r.contour.clear();
@@ -610,7 +610,7 @@ void ContourFeature::buildRegularContour_nontriv(LR& r)
 		}
 
 	//==== Remove padding and save the contour image as a vector of contour-onlu pixels
-	AABB& bb = r.aabb; // r.aux_image_matrix.original_aabb;
+	AABB& bb = r.aabb;
 	int base_x = bb.get_xmin(),
 		base_y = bb.get_ymin();
 	r.contour.clear();