Merge pull request PolusAI#242 from friskluft/POL5510_fix_allmorphology

fixed all-morphology and other group nicknames
friskluft · Oct 31, 2024 · d2cce58 · d2cce58
2 parents b1789a3 + 22fee06
commit d2cce58
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Showing 4 changed files with 19 additions and 54 deletions.
diff --git a/README.md b/README.md
@@ -343,7 +343,7 @@ Apart from defining your feature set by explicitly specifying comma-separated fe
 | \*all_glszm\* | glszm_sae, glszm_lae, glszm_gln, glszm_glnn, glszm_szn, glszm_sznn, glszm_zp, glszm_glv, glszm_zv, glszm_ze, glszm_lglze, glszm_hglze, glszm_salgle, glszm_sahgle, glszm_lalgle, glszm_lahgle
 | \*all_gldm\* | gldm_sde, gldm_lde, gldm_gln, gldm_dn, gldm_dnn, gldm_glv, gldm_dv, gldm_de, gldm_lgle, gldm_hgle, gldm_sdlgle, gldm_sdhgle, gldm_ldlgle, gldm_ldhgle
 | \*all_ngtdm\* | ngtdm_coarseness, ngtdm_contrast, ngtdm_busyness, ngtdm_complexity, ngtdm_strength
-| \*all_easy\* | All the features except the most time-consuming GABOR, GLCM, and the group of 2D moment features
+| \*wholeslide\* | All the features except those irrelevant for the whole-slide use case (BasicMorphology, EnclosingInscribingCircumscribingCircle, ConvexHull, FractalDimension, GeodeticLengthThickness, Neighbor, RoiRadius, EllipseFitting, EulerNumber, Extrema, ErosionPixel, CaliperFeret, CaliperMartin, CaliperNassenstein, and Chords)
 | \*all\* | All the features 
 
 ## Command line usage

diff --git a/src/nyx/env_features.cpp b/src/nyx/env_features.cpp
@@ -245,16 +245,6 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
 		return true;
 	}
 
-	if ((Fgroup2D) fgcode == Fgroup2D::FG2_EASY)
-	{
-		theFeatureSet.enableAll();
-		theFeatureSet.disableFeatures(GaborFeature::featureset);
-		theFeatureSet.disableFeatures(GLCMFeature::featureset);
-		theFeatureSet.disableFeatures(Imoms2D_feature::featureset);
-		theFeatureSet.disableFeatures(Smoms2D_feature::featureset);
-		return true;
-	}
-
 	if ((Fgroup2D) fgcode == Fgroup2D::FG2_NEIG)
 	{
 		Nyxus::theFeatureSet.enableFeatures (NeighborsFeature::featureset, enable);
@@ -268,51 +258,28 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
 	}
 	if ((Fgroup2D) fgcode == Fgroup2D::FG2_MORPHOLOGY)
 	{
-		auto F = {
-			Feature2D::AREA_PIXELS_COUNT,
-			Feature2D::AREA_UM2,
-			Feature2D::CENTROID_X,
-			Feature2D::CENTROID_Y,
-			Feature2D::DIAMETER_EQUAL_AREA,
-			Feature2D::WEIGHTED_CENTROID_Y,
-			Feature2D::WEIGHTED_CENTROID_X,
-			Feature2D::COMPACTNESS,
-			Feature2D::BBOX_YMIN,
-			Feature2D::BBOX_XMIN,
-			Feature2D::BBOX_HEIGHT,
-			Feature2D::BBOX_WIDTH,
-			Feature2D::MAJOR_AXIS_LENGTH,
-			Feature2D::MINOR_AXIS_LENGTH,
-			Feature2D::ECCENTRICITY,
-			Feature2D::ORIENTATION,
-			Feature2D::ROUNDNESS,
-			Feature2D::EXTENT,
-			Feature2D::ASPECT_RATIO,
-			Feature2D::DIAMETER_EQUAL_PERIMETER,
-			Feature2D::CONVEX_HULL_AREA,
-			Feature2D::SOLIDITY,
-			Feature2D::PERIMETER,
-			Feature2D::EDGE_MEAN_INTENSITY,
-			Feature2D::EDGE_STDDEV_INTENSITY,
-			Feature2D::EDGE_MAX_INTENSITY,
-			Feature2D::EDGE_MIN_INTENSITY,
-			Feature2D::CIRCULARITY,
-			Feature2D::MASS_DISPLACEMENT };
-		Nyxus::theFeatureSet.enableFeatures (F, enable);
+		theFeatureSet.enableFeatures (BasicMorphologyFeatures::featureset, enable);
+		theFeatureSet.enableFeatures (EnclosingInscribingCircumscribingCircleFeature::featureset, enable);
+		theFeatureSet.enableFeatures (ContourFeature::featureset, enable);
+		theFeatureSet.enableFeatures (ConvexHullFeature::featureset, enable);	
+		theFeatureSet.enableFeatures (FractalDimensionFeature::featureset, enable);
+		theFeatureSet.enableFeatures (GeodeticLengthThicknessFeature::featureset, enable);	
+		theFeatureSet.enableFeatures (NeighborsFeature::featureset, enable);
+		theFeatureSet.enableFeatures (RoiRadiusFeature::featureset, enable);
+		theFeatureSet.enableFeatures (EllipseFittingFeature::featureset, enable);
+		theFeatureSet.enableFeatures (EulerNumberFeature::featureset, enable);
+		theFeatureSet.enableFeatures (ExtremaFeature::featureset, enable);
+		theFeatureSet.enableFeatures (ErosionPixelsFeature::featureset, enable);
+		theFeatureSet.enableFeatures (CaliperFeretFeature::featureset, enable);
+		theFeatureSet.enableFeatures (CaliperMartinFeature::featureset, enable);
+		theFeatureSet.enableFeatures (CaliperNassensteinFeature::featureset, enable);
+		theFeatureSet.enableFeatures (ChordsFeature::featureset, enable);
+
 		return true;
 	}
 	if ((Fgroup2D)fgcode == Fgroup2D::FG2_BASIC_MORPHOLOGY)
 	{
-		auto F = {
-			Feature2D::AREA_PIXELS_COUNT,
-			Feature2D::AREA_UM2,
-			Feature2D::CENTROID_X,
-			Feature2D::CENTROID_Y,
-			Feature2D::BBOX_YMIN,
-			Feature2D::BBOX_XMIN,
-			Feature2D::BBOX_HEIGHT,
-			Feature2D::BBOX_WIDTH };
-		Nyxus::theFeatureSet.enableFeatures (F, enable);
+		theFeatureSet.enableFeatures (BasicMorphologyFeatures::featureset, enable);
 		return true;
 	}
 	if ((Fgroup2D)fgcode == Fgroup2D::FG2_GLCM)

diff --git a/src/nyx/featureset.cpp b/src/nyx/featureset.cpp
@@ -611,7 +611,6 @@ namespace Nyxus
 		{ "*ALL_NGTDM*", Fgroup2D::FG2_NGTDM },
 		{ "*ALL_BUT_GABOR*", Fgroup2D::FG2_BUT_GABOR },
 		{ "*ALL_BUT_GLCM*", Fgroup2D::FG2_ALL_BUT_GLCM },
-		{ "*ALL_EASY*", Fgroup2D::FG2_EASY },
 		{ "*ALL_NEIGHBOR*", Fgroup2D::FG2_NEIG },
 		{ "*GEOMOMS*", Fgroup2D::FG2_GEOMOMENTS },
 		{ "*IGEOMOMS*", Fgroup2D::FG2_GEOMOMENTS_I },

diff --git a/src/nyx/featureset.h b/src/nyx/featureset.h
@@ -709,7 +709,6 @@ namespace Nyxus
 		FG2_NGTDM,
 		FG2_BUT_GABOR,
 		FG2_ALL_BUT_GLCM, 
-		FG2_EASY, 
 		FG2_NEIG,
 		FG2_GEOMOMENTS,		// shape and intensity geometric moments
 		FG2_GEOMOMENTS_I,	// intensity geometric moments