Alignment accuracy

NEWS.md

@@ -1,13 +1,15 @@
 # VoltRon 0.2.7
 
--   `transferData` now allows integrating single cell data object (`Seurat` or `SingleCellExperiment`)
-    for transfering features (e.g. gene expression) or metadata features (e.g. cell types, annotations).
 -   `registerSpatialData` now allows registering assays with no images. In case of either one of the assays, 
     do not have images, assays can be registered with only the manual approach. 
+-   The Shiny interface for `registerSpatialData` now reports on the accuracy of the alignment using multiple
+    metrics such as Intersection, Bhattacharyya and Matte's Mutual Information.
 -   An image-free alignment tutorial has been added where DBIT-Seq and a QuPath processed mIF experiment are
     aligned using manually selected landmarks.
+-   `transferData` now allows integrating single cell data object (`Seurat` or `SingleCellExperiment`)
+    for transfering features (e.g. gene expression) or metadata features (e.g. cell types, annotations).
 -   Now `importImageData` and `importQuPathIF` functions only work with segments already converted to a
-    list by the user, or the `generateSegments` function whose arguement is an **sf** object. 
+    list by the user, or the `generateSegments` function whose argument is an **sf** object. 
 -   The `formAssay` function now accepts only segments without the user manually generating coordinates 
     (or centroids).
 -   The `name` argument in functions like `vrImages`, `vrCoordinates` and `vrSegments` is replaced

R/RcppExports.R

@@ -1,8 +1,12 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-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) {
-    .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)
+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)
+}
+
+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)
 }
 
 replaceNaMatrix <- function(mat, replace) {
@@ -21,8 +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, method, nonrigid) {
-    .Call('_VoltRon_manual_registeration_rawvector', PACKAGE = 'VoltRon', ref_image, query_image, reference_landmark, query_landmark, width1, height1, width2, height2, method, nonrigid)
+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_matrix <- function(query_data, reference_landmark, query_landmark, method, nonrigid) {
@@ -33,6 +37,10 @@ applyRcppMapping <- function(coords, mapping) {
     .Call('_VoltRon_applyRcppMapping', PACKAGE = 'VoltRon', coords, mapping)
 }
 
+generateOverlapMask <- function(dsize, trans_mat, ssize) {
+    .Call('_VoltRon_generateOverlapMask', PACKAGE = 'VoltRon', dsize, trans_mat, ssize)
+}
+
 build_snn_rank <- function(neighbors) {
     .Call('_VoltRon_build_snn_rank', PACKAGE = 'VoltRon', neighbors)
 }

R/auxiliary.R

@@ -58,6 +58,43 @@ fixVoltRon <- function(object) {
   object
 }
 
+####
+# Bioformats extensions for image pyramids ####
+####
+
+.PYRAMID_FORMATS <- c(
+  ".ome.tiff",    # OME-TIFF pyramidal TIFF variants (OME-TIFF and related) 
+  ".ome.tif",
+  ".ome.tf2",
+  ".ome.tf8",
+  ".ome.btf",
+  ".svs",         # Aperio SVS
+  ".afi",         # Aperio AFI
+  ".ndpi",        # Hamamatsu NDPI
+  ".ndpis",       # Hamamatsu NDPI variants
+  ".qptiff"       # CODEX ?
+)
+
+####
+# Alignment Metrics ####
+####
+
+.ALIGNMENT_ACCURACY_METRICS <- c(
+  "Intersection",
+  "Bhattacharyya",
+  "Matte's MI"
+)
+
+.ALIGNMENT_KEYPOINT_METRICS <- c(
+  "#Keypoints",
+  "Inlier Perc.",
+  "sd ref. kpts (>1?)",
+  "sd query kpts (>1?)",
+  "sd grid (in [w,h]?)",
+  "Median distance",
+  "Degenerate"
+)
+
 ####
 # Matrix Operations ####
 ####
@@ -326,24 +363,6 @@ getBasilisk <- function() {
   py_env
 }
 
-####
-# Bioformats extensions for pyramids ####
-####
-
-.PYRAMID_FORMATS <- c(
-  ".ome.tiff",    # OME-TIFF pyramidal TIFF variants (OME-TIFF and related) 
-  ".ome.tif",
-  ".ome.tf2",
-  ".ome.tf8",
-  ".ome.btf",
-  ".svs",         # Aperio SVS
-  ".afi",         # Aperio AFI
-  ".ndpi",        # Hamamatsu NDPI
-  ".ndpis",       # Hamamatsu NDPI variants
-  ".qptiff"       # CODEX ?
-)
-
-
 ####
 # Other Auxiliary tools ####
 ####