Merge pull request #237 from friskluft/POL5328_inten_geo_moments

POL5328 2D intensity geometric moments

CMakeLists.txt

@@ -161,8 +161,9 @@ set(SOURCE
 	src/nyx/features/hexagonality_polygonality.cpp
 	src/nyx/features/image_matrix.cpp
 	src/nyx/features/image_matrix_nontriv.cpp
-	src/nyx/features/image_moments.cpp
-	src/nyx/features/image_moments_nontriv.cpp
+	src/nyx/features/2d_geomoments.cpp
+	src/nyx/features/2d_geomoments_basic.cpp
+	src/nyx/features/2d_geomoments_basic_nt.cpp
 	src/nyx/features/intensity.cpp
 	src/nyx/features/intensity_3d.cpp
 	src/nyx/features/neighbors.cpp

README.md

@@ -335,6 +335,9 @@ Apart from defining your feature set by explicitly specifying comma-separated fe
 | \*all_intensity\* | integrated_intensity, mean, median, min, max, range, standard_deviation, standard_error, uniformity, skewness, kurtosis, hyperskewness, hyperflatness, mean_absolute_deviation, energy, root_mean_squared, entropy, mode, uniformity, p01, p10, p25, p75, p90, p99, interquartile_range, robust_mean_absolute_deviation, mass_displacement
 | \*all_morphology\* | area_pixels_count, area_um2, centroid_x, centroid_y, weighted_centroid_y, weighted_centroid_x, compactness, bbox_ymin, bbox_xmin, bbox_height, bbox_width, major_axis_length, minor_axis_length, eccentricity, orientation, num_neighbors, extent, aspect_ratio, equivalent_diameter, convex_hull_area, solidity, perimeter, edge_mean_intensity, edge_stddev_intensity, edge_max_intensity, edge_min_intensity, circularity
 | \*basic_morphology\* | area_pixels_count, area_um2, centroid_x, centroid_y, bbox_ymin, bbox_xmin, bbox_height, bbox_width
+| \*geomoms\* | shape and intensity geometric moments, equivalent to \*igeomoms\* and \*sgeomoms\* combined
+| \*igeomoms\* | intensity raw moments IMOM_RM_pq, central moments IMOM_CM_pq, normalized raw moments IMOM_NRM_pq, normalized central moments IMOM_NCM_pq, Hu invariants IMOM_HUk, weighted raw moments IMOM_WRM_pq, weighted central moments IMOM_WCM_pq, weighted normalized central moments IMOM_WNCM_pq, weighted Hu invariants IMOM_WHUk
+| \*sgeomoms\* | shape raw moments SPAT_MOMENT_pq, central moments CENTRAL_MOMENT_pq, normalized raw moments NORM_SPAT_MOMENT_pq, normalized central moments NORM_CENTRAL_MOMENT_pq, Hu invariants HU_Mk, weighted raw moments WEIGHTED_SPAT_MOMENT_pq, weighted central moments WEIGHTED_CENTRAL_MOMENT_pq, weighted normalized central moments WT_NORM_CTR_MOM_pq, weighted Hu invariants WEIGHTED_HU_Mk
 | \*all_glcm\* | glcm_asm, glcm_acor, glcm_cluprom, glcm_clushade, glcm_clutend, glcm_contrast, glcm_correlation, glcm_difave, glcm_difentro, glcm_difvar, glcm_dis, glcm_energy, glcm_entropy, glcm_hom1, glcm_hom2, glcm_id, glcm_idn, glcm_idm, glcm_idmn, glcm_infomeas1, glcm_infomeas2, glcm_iv, glcm_jave, glcm_je, glcm_jmax, glcm_jvar, glcm_sumaverage, glcm_sumentropy, glcm_sumvariance, glcm_variance
 | \*all_glrlm\* | glrlm_sre, glrlm_lre, glrlm_gln, glrlm_glnn, glrlm_rln, glrlm_rlnn, glrlm_rp, glrlm_glv, glrlm_rv, glrlm_re, glrlm_lglre, glrlm_hglre, glrlm_srlgle, glrlm_srhgle, glrlm_lrlgle, glrlm_lrhgle
 | \*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

docs/source/Math/f_2dmoments.rst

@@ -40,7 +40,7 @@ and
 represent the center of mass of the image :math:`f(x,y)`. Hu's Uniqueness Theorem states that if :math:`f(x,y)` is piecewise continuous and has nonzero values only in the finite part 
 of the :math:`(x,y)` plane, then geometric moments of all orders exist. It can then be shown that the moment set :math:`{\mu_{pq}}` is 
 uniquely determined by :math:`f(x,y)` and conversely, :math:`f(x,y)` is uniquely determined by :math:`{\mu_{pq}}`. Since an image has 
-finite area, a moment set can be evaluated computationally and used to uniquely describe the information contained in the image. 
+finite area, a moment set can be evaluated computationally and used to uniquely describe the information contained in the image. Nyxus calculates 2 sets of geometric moments: moments where :math:`f(x,y)=1` within the ROI mask and 0 outside the ROI mask define shape moments while moments whose :math:`f(x,y)` are intensity at pixel location :math:`x,y` define intensity moments.
 
 Raw moments
 -----------

docs/source/featurelist.rst

@@ -555,7 +555,7 @@ Nyxus provided features
      - A set of Gabor filters of varying frequencies and orientations
 
 
-**2D image moments:**
+**2D shape image moments:**
 
 ----
 
@@ -689,6 +689,139 @@ Nyxus provided features
    * - WEIGHTED_HU_M7
      - Weighted Hu's moment 7
 
+**2D intensity image moments:**
+
+----
+
+.. list-table::
+   :header-rows: 1
+
+   * - Nyxus feature code
+     - Description
+   * - IMOM_RM_00
+     - Spatial (raw) moments 
+   * - IMOM_RM_01
+     - of order 00, 01, 02, etc
+   * - IMOM_RM_02
+     - 
+   * - IMOM_RM_03
+     - 
+   * - IMOM_RM_10
+     - 
+   * - IMOM_RM_11
+     - 
+   * - IMOM_RM_12
+     - 
+   * - IMOM_RM_20
+     - 
+   * - IMOM_RM_21
+     - 
+   * - IMOM_RM_30
+     - 
+   * - IMOM_WRM_00
+     - Spatial moments weighted by pixel distance to ROI edge
+   * - IMOM_WRM_01
+     - 
+   * - IMOM_WRM_02
+     - 
+   * - IMOM_WRM_03
+     - 
+   * - IMOM_WRM_10
+     - 
+   * - IMOM_WRM_11
+     - 
+   * - IMOM_WRM_12
+     - 
+   * - IMOM_WRM_20
+     - 
+   * - IMOM_WRM_21
+     - 
+   * - IMOM_WRM_30
+     - 
+   * - IMOM_СM_02
+     - Central moments 
+   * - IMOM_СM_03
+     - 
+   * - IMOM_СM_11
+     - 
+   * - IMOM_СM_12
+     - 
+   * - IMOM_СM_20
+     - 
+   * - IMOM_СM_21
+     - 
+   * - IMOM_СM_30
+     - 
+   * - IMOM_WСM_02
+     - Central moments weighted by pixel distance to ROI edge
+   * - IMOM_WСM_03
+     - 
+   * - IMOM_WСM_11
+     - 
+   * - IMOM_WСM_12
+     - 
+   * - IMOM_WСM_20
+     - 
+   * - IMOM_WСM_21
+     - 
+   * - IMOM_WСM_30
+     - 
+   * - IMOM_NСM_02
+     - Normalized central moments
+   * - IMOM_NСM_03
+     - 
+   * - IMOM_NСM_11
+     - 
+   * - IMOM_NСM_
+     - 
+   * - IMOM_NСM_20
+     - 
+   * - IMOM_NСM_21
+     - 
+   * - IMOM_NСM_30
+     - 
+   * - IMOM_NRM_00
+     - Normalized (standardized) spatial moments
+   * - IMOM_NRM_01
+     - 
+   * - IMOM_NRM_02
+     - 
+   * - IMOM_NRM_03
+     - 
+   * - IMOM_NRM_10
+     - 
+   * - IMOM_NRM_20
+     - 
+   * - IMOM_NRM_30
+     - 
+   * - IMOM_HU1
+     - Hu's moment 1
+   * - IMOM_HU2
+     - Hu's moment 2
+   * - IMOM_HU3
+     - Hu's moment 3
+   * - IMOM_HU4
+     - Hu's moment 4
+   * - IMOM_HU5
+     - Hu's moment 5
+   * - IMOM_HU6
+     - Hu's moment 6
+   * - IMOM_HU7
+     - Hu's moment 7
+   * - IMOM_WHU1
+     - Weighted Hu's moment 1
+   * - IMOM_WHU2
+     - Weighted Hu's moment 2
+   * - IMOM_WHU3
+     - Weighted Hu's moment 3
+   * - IMOM_WHU4
+     - Weighted Hu's moment 4
+   * - IMOM_WHU5
+     - Weighted Hu's moment 5
+   * - IMOM_WHU6
+     - Weighted Hu's moment 6
+   * - IMOM_WHU7
+     - Weighted Hu's moment 7
 
 **Neighbor features:**
 

src/nyx/env_features.cpp

@@ -27,7 +27,7 @@
 #include "features/gldzm.h"
 #include "features/glrlm.h"
 #include "features/glszm.h"
-#include "features/image_moments.h"
+#include "features/2d_geomoments.h"
 #include "features/intensity.h"
 #include "features/neighbors.h"
 #include "features/ngldm.h"
@@ -248,7 +248,8 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
 		theFeatureSet.enableAll();
 		theFeatureSet.disableFeatures(GaborFeature::featureset);
 		theFeatureSet.disableFeatures(GLCMFeature::featureset);
-		theFeatureSet.disableFeatures(ImageMomentsFeature::featureset);
+		theFeatureSet.disableFeatures(Imoms2D_feature::featureset);
+		theFeatureSet.disableFeatures(Smoms2D_feature::featureset);
 		return true;
 	}
 
@@ -349,9 +350,22 @@ bool Environment::expand_2D_featuregroup (const std::string & s)
 		return true;
 	}
 
-	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_MOMENTS))
+	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GEOMOMENTS))
 	{
-		theFeatureSet.enableFeatures(ImageMomentsFeature::featureset);
+		theFeatureSet.enableFeatures (Smoms2D_feature::featureset);
+		theFeatureSet.enableFeatures (Imoms2D_feature::featureset);
+		return true;
+	}
+
+	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GEOMOMENTS_I))
+	{
+		theFeatureSet.enableFeatures(Imoms2D_feature::featureset);
+		return true;
+	}
+
+	if (s == Nyxus::theFeatureSet.findGroupNameByCode(Fgroup2D::FG2_GEOMOMENTS_S))
+	{
+		theFeatureSet.enableFeatures(Smoms2D_feature::featureset);
 		return true;
 	}
 

src/nyx/feature_mgr_init.cpp

@@ -20,7 +20,7 @@
 #include "features/hexagonality_polygonality.h"
 #include "features/ngldm.h"
 #include "features/ngtdm.h"
-#include "features/image_moments.h"
+#include "features/2d_geomoments.h"
 #include "features/intensity.h"
 #include "features/intensity_3d.h"
 #include "features/moments.h"
@@ -60,7 +60,8 @@ FeatureManager::FeatureManager()
 	register_feature (new GLDMFeature());
 	register_feature (new NGLDMfeature());
 	register_feature (new NGTDMFeature());
-	register_feature (new ImageMomentsFeature());
+	register_feature (new Imoms2D_feature());
+	register_feature (new Smoms2D_feature());
 	register_feature (new GaborFeature());
 	register_feature (new ZernikeFeature());
 	register_feature (new RadialDistributionFeature());