Accuracy with Structural similarity index

NEWS.md

@@ -2,6 +2,11 @@
 
 -   Both x and y coordinates of SIFT/ORB landmarks are now checked after 
     alignment with `registerSpatialData`.  
+-   Intersection, Bhattacharyya, and newly added Structural Similarity index
+    measure is now calculated for chunks of image pairs and visualized as
+    `Local SSIM` to show regions of good and bad alignment. Aggregate 
+    values of these three measures are also used to report on the global 
+    alignment score.
 
 # VoltRon 0.3.0
 

R/RcppExports.R

@@ -1,12 +1,12 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-accuracy_rawvector <- function(ref_image, query_image, mask, width, height, type, overlay_images = TRUE, compute_matte_map = TRUE) {
-    .Call('_VoltRon_accuracy_rawvector', PACKAGE = 'VoltRon', ref_image, query_image, mask, width, height, type, overlay_images, compute_matte_map)
+accuracy_rawvector <- function(ref_image, query_image, mask, width, height, type, overlay_images = TRUE, compute_ssim_map = TRUE) {
+    .Call('_VoltRon_accuracy_rawvector', PACKAGE = 'VoltRon', ref_image, query_image, mask, width, height, type, overlay_images, compute_ssim_map)
 }
 
-automated_registeration_rawvector <- function(ref_image, query_image, width1, height1, width2, height2, GOOD_MATCH_PERCENT, MAX_FEATURES, invert_query, invert_ref, flipflop_query, flipflop_ref, rotate_query, rotate_ref, matcher, method, nonrigid, compute_matte_map = TRUE) {
-    .Call('_VoltRon_automated_registeration_rawvector', PACKAGE = 'VoltRon', ref_image, query_image, width1, height1, width2, height2, GOOD_MATCH_PERCENT, MAX_FEATURES, invert_query, invert_ref, flipflop_query, flipflop_ref, rotate_query, rotate_ref, matcher, method, nonrigid, compute_matte_map)
+automated_registeration_rawvector <- function(ref_image, query_image, width1, height1, width2, height2, GOOD_MATCH_PERCENT, MAX_FEATURES, invert_query, invert_ref, flipflop_query, flipflop_ref, rotate_query, rotate_ref, matcher, method, nonrigid, compute_ssim_map = TRUE) {
+    .Call('_VoltRon_automated_registeration_rawvector', PACKAGE = 'VoltRon', ref_image, query_image, width1, height1, width2, height2, GOOD_MATCH_PERCENT, MAX_FEATURES, invert_query, invert_ref, flipflop_query, flipflop_ref, rotate_query, rotate_ref, matcher, method, nonrigid, compute_ssim_map)
 }
 
 replaceNaMatrix <- function(mat, replace) {
@@ -25,8 +25,8 @@ warpImageManual <- function(ref_image, query_image, mapping, width1, height1, wi
     .Call('_VoltRon_warpImageManual', PACKAGE = 'VoltRon', ref_image, query_image, mapping, width1, height1, width2, height2)
 }
 
-manual_registeration_rawvector <- function(ref_image, query_image, reference_landmark, query_landmark, width1, height1, width2, height2, invert_query, invert_ref, method, nonrigid, compute_matte_map = TRUE) {
-    .Call('_VoltRon_manual_registeration_rawvector', PACKAGE = 'VoltRon', ref_image, query_image, reference_landmark, query_landmark, width1, height1, width2, height2, invert_query, invert_ref, method, nonrigid, compute_matte_map)
+manual_registeration_rawvector <- function(ref_image, query_image, reference_landmark, query_landmark, width1, height1, width2, height2, invert_query, invert_ref, method, nonrigid, compute_ssim_map = TRUE) {
+    .Call('_VoltRon_manual_registeration_rawvector', PACKAGE = 'VoltRon', ref_image, query_image, reference_landmark, query_landmark, width1, height1, width2, height2, invert_query, invert_ref, method, nonrigid, compute_ssim_map)
 }
 
 manual_registeration_matrix <- function(query_data, reference_landmark, query_landmark, method, nonrigid) {

R/auxiliary.R

@@ -80,9 +80,10 @@ fixVoltRon <- function(object) {
 ####
 
 .ALIGNMENT_ACCURACY_METRICS <- c(
+  "SSIM",
+  "Matte's MI",
   "Intersection",
-  "Bhattacharyya",
-  "Matte's MI"
+  "Bhattacharyya"
 )
 
 .ALIGNMENT_KEYPOINT_METRICS <- c(