POL 4993 and 4995: fixes and optimization related to Hamdah's last wholeslide experience

src/nyx/env_features.cpp

@@ -1,3 +1,4 @@
+#include <algorithm>
 #include <exception>
 #include <fstream>
 #include <iomanip>
@@ -9,6 +10,17 @@
 #include <vector>
 #include "environment.h"
 #include "featureset.h"
+#include "features/basic_morphology.h"
+#include "features/chords.h"
+#include "features/convex_hull.h"
+#include "features/erosion.h"
+#include "features/caliper.h"
+#include "features/circle.h"
+#include "features/ellipse_fitting.h"
+#include "features/euler_number.h"
+#include "features/extrema.h"
+#include "features/fractal_dim.h"
+#include "features/geodetic_len_thickness.h"
 #include "features/gabor.h"
 #include "features/glcm.h"
 #include "features/gldm.h"
@@ -20,6 +32,7 @@
 #include "features/neighbors.h"
 #include "features/ngldm.h"
 #include "features/ngtdm.h"
+#include "features/roi_radius.h"
 #include "helpers/helpers.h"
 #include "helpers/system_resource.h"
 #include "helpers/timing.h"
@@ -166,8 +179,6 @@ bool Environment::spellcheck_raw_featurelist(const std::string& comma_separated_
 	return success;
 }
 
-
-
 // Returns:
 //		true if s is recognized as a group name
 //		false if not recognized (s may be an individual feature name)
@@ -177,6 +188,45 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
 	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_ALL))
 	{
 		Nyxus::theFeatureSet.enableAll();
+
+		// Handle whole-slide mode differently: disable features irrelevant to this mode (shape, neighbors, etc)
+		if (singleROI)
+		{
+			std::cout << box_text ("Activating whole slide (aka single-ROI) mode\n"
+				"ATTENTION: disabling inappplicable and time-sonsuming features:\n"
+				" - morphological features\n"
+				" - neighbor features\n"
+				" - GLDM, GLDZM, GLRLM, GLSZM, NGLDM, NGTDM");
+
+			theFeatureSet.disableFeatures(BasicMorphologyFeatures::featureset);
+			theFeatureSet.disableFeatures(EnclosingInscribingCircumscribingCircleFeature::featureset);
+			theFeatureSet.disableFeatures(ContourFeature::featureset);		// and its dependencies below (see file reduce_trivial_rois_manual.cpp)
+			theFeatureSet.disableFeatures(ConvexHullFeature::featureset);				// depends on ContourFeature
+			theFeatureSet.disableFeatures(FractalDimensionFeature::featureset);		// depends on ContourFeature
+			theFeatureSet.disableFeatures(GeodeticLengthThicknessFeature::featureset);	// depends on ContourFeature
+			theFeatureSet.disableFeatures(NeighborsFeature::featureset);				// depends on ContourFeature
+			theFeatureSet.disableFeatures(RoiRadiusFeature::featureset);				// depends on ContourFeature
+			theFeatureSet.disableFeatures(EllipseFittingFeature::featureset);
+			theFeatureSet.disableFeatures(EulerNumberFeature::featureset);
+			theFeatureSet.disableFeatures(ExtremaFeature::featureset);
+			theFeatureSet.disableFeatures(ErosionPixelsFeature::featureset);
+			theFeatureSet.disableFeatures(CaliperFeretFeature::featureset);
+			theFeatureSet.disableFeatures(CaliperMartinFeature::featureset);
+			theFeatureSet.disableFeatures(CaliperNassensteinFeature::featureset);
+			theFeatureSet.disableFeatures(ChordsFeature::featureset);
+
+			// enabling GaborFeature
+			// enabling ImageMomentsFeature
+			// enabling GLCMFeature
+
+			theFeatureSet.disableFeatures(GLDMFeature::featureset);		// costs about 4.72 %
+			theFeatureSet.disableFeatures(GLDZMFeature::featureset);	// costs about 38.14 %
+			theFeatureSet.disableFeatures(GLRLMFeature::featureset);	// costs about 17.29 %
+			theFeatureSet.disableFeatures(GLSZMFeature::featureset);	// costs about 15.94 %
+			theFeatureSet.disableFeatures(NGLDMfeature::featureset);	// costs about 3.57 %
+			theFeatureSet.disableFeatures(NGTDMFeature::featureset);	// costs about 5.13 %
+		}
+
 		return true; 
 	}
 	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_BUT_GABOR))
@@ -305,6 +355,7 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
 		return true;
 	}
 
+	// unrecognized feature group
 	return false;
 }
 
@@ -441,13 +492,13 @@ void Environment::expand_featuregroups()
 		if (dim() == 2)
 		{
 			if (expand_2D_featuregroup (s))
-				return;
+				continue;
 		}
 
 		if (dim() == 3)
 		{
 			if (expand_3D_featuregroup (s))
-				return;
+				continue;
 		}
 
 		// 's' is an individual feature name, not feature group name. Process it now

src/nyx/environment.cpp

@@ -9,13 +9,6 @@
 #include "environment.h"
 #include "featureset.h"
 #include "features/glcm.h"
-#include "features/gldm.h"
-#include "features/gldzm.h"
-#include "features/glrlm.h"
-#include "features/glszm.h"
-#include "features/image_moments.h"
-#include "features/ngldm.h"
-#include "features/ngtdm.h"
 #include "helpers/helpers.h"
 #include "helpers/system_resource.h"
 #include "helpers/timing.h"
@@ -484,6 +477,13 @@ bool Environment::parse_cmdline(int argc, char** argv)
 		return false;
 	}
 
+	//==== whole-slide mode
+	if (Nyxus::toupper(labels_dir) == Nyxus::toupper(intensity_dir))
+	{
+		singleROI = true;
+	}
+
+
 	if (rawOutpType == "")
 	{
 		std::cerr << "Error: Missing argument " << OUTPUTTYPE << "\n";
@@ -791,7 +791,7 @@ bool Environment::parse_cmdline(int argc, char** argv)
 		return false;
 	}
 
-	// --Feature names are ok, now expand feature group nicknames and set the enabled flag for each feature in 'theFeatureSet'
+	// --Feature names are ok, now expand feature group nicknames and enable each feature in 'theFeatureSet'
 	try
 	{
 		expand_featuregroups();
@@ -802,26 +802,6 @@ bool Environment::parse_cmdline(int argc, char** argv)
 		return false;
 	}
 
-	//==== Handle the whole-slide mode
-	if (Nyxus::toupper(labels_dir) == Nyxus::toupper(intensity_dir))
-	{
-		singleROI = true;
-		std::cout <<
-			"+-----------------------------------------------------------+\n"
-			"|                                                           |\n"
-			"|  Activating whole slide (aka single-ROI) mode             |\n"
-			"|  ATTENTION: disabling time-sonsuming erosions features    |\n"
-			"|                                                           |\n"
-			"+-----------------------------------------------------------+\n";
-
-		auto F = {
-			Feature2D::EROSIONS_2_VANISH,
-			Feature2D::EROSIONS_2_VANISH_COMPLEMENT,
-			Feature2D::GABOR
-		};
-		theFeatureSet.disableFeatures(F);
-	}
-
 	//==== Parse resolution
 	if (rawXYRes.length() > 0)
 	{

src/nyx/features/basic_morphology.cpp

@@ -7,44 +7,14 @@
 
 using namespace Nyxus;
 
-bool BasicMorphologyFeatures::required(const FeatureSet& fs) {
-	return fs.anyEnabled({
-		Feature2D::AREA_PIXELS_COUNT,
-		Feature2D::AREA_UM2,
-		Feature2D::ASPECT_RATIO,
-		Feature2D::BBOX_XMIN,
-		Feature2D::BBOX_YMIN,
-		Feature2D::BBOX_WIDTH,
-		Feature2D::BBOX_HEIGHT,
-		Feature2D::CENTROID_X,
-		Feature2D::CENTROID_Y,
-		Feature2D::COMPACTNESS,
-		Feature2D::DIAMETER_EQUAL_AREA,
-		Feature2D::EXTENT,
-		Feature2D::MASS_DISPLACEMENT,
-		Feature2D::WEIGHTED_CENTROID_X,
-		Feature2D::WEIGHTED_CENTROID_Y });
+bool BasicMorphologyFeatures::required(const FeatureSet& fs) 
+{
+	return fs.anyEnabled (BasicMorphologyFeatures::featureset);
 }
 
 BasicMorphologyFeatures::BasicMorphologyFeatures(): FeatureMethod("BasicMorphologyFeatures")
 {
-	provide_features({
-		Feature2D::AREA_PIXELS_COUNT,
-		Feature2D::AREA_UM2,
-		Feature2D::ASPECT_RATIO,
-		Feature2D::BBOX_XMIN,
-		Feature2D::BBOX_YMIN,
-		Feature2D::BBOX_WIDTH,
-		Feature2D::BBOX_HEIGHT,
-		Feature2D::CENTROID_X,
-		Feature2D::CENTROID_Y,
-		Feature2D::COMPACTNESS,
-		Feature2D::EXTENT,
-		Feature2D::MASS_DISPLACEMENT,
-		Feature2D::WEIGHTED_CENTROID_X,
-		Feature2D::WEIGHTED_CENTROID_Y,
-		Feature2D::DIAMETER_EQUAL_AREA
-		});
+	provide_features (BasicMorphologyFeatures::featureset);
 }
 
 void BasicMorphologyFeatures::calculate(LR& r)

src/nyx/features/basic_morphology.h

@@ -5,6 +5,27 @@
 class BasicMorphologyFeatures : public FeatureMethod
 {
 public:
+
+	const constexpr static std::initializer_list<Nyxus::Feature2D> featureset =
+	{
+		Nyxus::Feature2D::AREA_PIXELS_COUNT,
+		Nyxus::Feature2D::AREA_UM2,
+		Nyxus::Feature2D::ASPECT_RATIO,
+		Nyxus::Feature2D::BBOX_XMIN,
+		Nyxus::Feature2D::BBOX_YMIN,
+		Nyxus::Feature2D::BBOX_WIDTH,
+		Nyxus::Feature2D::BBOX_HEIGHT,
+		Nyxus::Feature2D::CENTROID_X,
+		Nyxus::Feature2D::CENTROID_Y,
+		Nyxus::Feature2D::COMPACTNESS,
+		Nyxus::Feature2D::DIAMETER_EQUAL_AREA,
+		Nyxus::Feature2D::EXTENT,
+		Nyxus::Feature2D::MASS_DISPLACEMENT,
+		Nyxus::Feature2D::WEIGHTED_CENTROID_X,
+		Nyxus::Feature2D::WEIGHTED_CENTROID_Y
+	};
+
+
 	BasicMorphologyFeatures();
 	void calculate (LR& r);
 	void osized_add_online_pixel(size_t x, size_t y, uint32_t intensity);

src/nyx/features/chords.h

@@ -16,21 +16,8 @@
 class ChordsFeature : public FeatureMethod
 {
 public:
-	ChordsFeature();
-
-	// Trivial
-	void calculate(LR& r);
-
-	// Non-trivial 
-	void osized_add_online_pixel (size_t x, size_t y, uint32_t intensity) {}
-	void osized_calculate (LR& r, ImageLoader& imloader);
-	void save_value (std::vector<std::vector<double>>& feature_vals);
-	static void process_1_batch (size_t start, size_t end, std::vector<int>* ptrLabels, std::unordered_map <int, LR>* ptrLabelData);
-
-	// Support of "manual" phase 2 
-	static bool required(const FeatureSet& fs)
+	const constexpr static std::initializer_list<Nyxus::Feature2D> featureset =
 	{
-		return fs.anyEnabled({
 				Nyxus::Feature2D::MAXCHORDS_MAX,
 				Nyxus::Feature2D::MAXCHORDS_MAX_ANG,
 				Nyxus::Feature2D::MAXCHORDS_MIN,
@@ -46,8 +33,26 @@ class ChordsFeature : public FeatureMethod
 				Nyxus::Feature2D::ALLCHORDS_MEDIAN,
 				Nyxus::Feature2D::ALLCHORDS_MEAN,
 				Nyxus::Feature2D::ALLCHORDS_MODE,
-				Nyxus::Feature2D::ALLCHORDS_STDDEV });
+				Nyxus::Feature2D::ALLCHORDS_STDDEV
+	};
+
+	ChordsFeature();
+
+	// Trivial
+	void calculate(LR& r);
+
+	// Non-trivial 
+	void osized_add_online_pixel (size_t x, size_t y, uint32_t intensity) {}
+	void osized_calculate (LR& r, ImageLoader& imloader);
+	void save_value (std::vector<std::vector<double>>& feature_vals);
+	static void process_1_batch (size_t start, size_t end, std::vector<int>* ptrLabels, std::unordered_map <int, LR>* ptrLabelData);
+
+	// Support of "manual" phase 2 
+	static bool required(const FeatureSet& fs)
+	{
+		return fs.anyEnabled (ChordsFeature::featureset);
 	}
+
 private:
 	const int n_angle_segments = 20;
 	const int n_side_segments = 100;

src/nyx/features/circle.cpp

@@ -5,7 +5,7 @@ using namespace Nyxus;
 
 EnclosingInscribingCircumscribingCircleFeature::EnclosingInscribingCircumscribingCircleFeature() : FeatureMethod("EnclosingInscribingCircumscribingCircleFeature")
 {
-    provide_features({ Feature2D::DIAMETER_MIN_ENCLOSING_CIRCLE, Feature2D::DIAMETER_INSCRIBING_CIRCLE, Feature2D::DIAMETER_CIRCUMSCRIBING_CIRCLE });
+    provide_features (EnclosingInscribingCircumscribingCircleFeature::featureset);
     add_dependencies({ Feature2D::PERIMETER, Feature2D::CENTROID_X, Feature2D::CENTROID_Y });    // Availability of feature 'PERIMETER' ensures availability of LR::contour
 }
 

src/nyx/features/circle.h

@@ -12,6 +12,13 @@
 class EnclosingInscribingCircumscribingCircleFeature: public FeatureMethod
 {
 public:
+	const constexpr static std::initializer_list<Nyxus::Feature2D> featureset =
+	{
+		Nyxus::Feature2D::DIAMETER_MIN_ENCLOSING_CIRCLE,
+		Nyxus::Feature2D::DIAMETER_INSCRIBING_CIRCLE,
+		Nyxus::Feature2D::DIAMETER_CIRCUMSCRIBING_CIRCLE
+	};
+
 	EnclosingInscribingCircumscribingCircleFeature();
 	void calculate(LR& r);
 	void osized_add_online_pixel(size_t x, size_t y, uint32_t intensity);