Added postproc.R

R/postproc.R

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+
+# Function to find Cropped Image Segment of Segment Anything Model (SAM) output
+# y: original grayscale image in matrix/rip format
+# box: same as `bbox` in SAM output
+# mask: same as `segmentation` in SAM output
+# seg: logical flag. If TRUE then returns cropped image segment based on both box and mask and
+#       If FALSE only cropped image based on box
+
+# See https://github.com/facebookresearch/segment-anything/blob/main/segment_anything/automatic_mask_generator.py
+# for details related to `box` and `mask` argument
+
+findSeg <- function(y,box,mask = NULL,seg = T){
+
+  # To adjust for indexes starting from 0 in python
+  ycrop <- y[(box[[2]] + 1):(box[[2]] + box[[4]] + 1),
+             (box[[1]] + 1):(box[[1]] + box[[3]] + 1)]
+
+  if(seg){
+    maskcrop <- mask[box[[2]]:(box[[2]] + box[[4]]),
+                     box[[1]]:(box[[1]] + box[[3]])]
+    ycrop[!maskcrop] <- 0
+  }
+
+  return(as.rip(ycrop))
+}
+
+# Function to Spatially Deblur an Image based on blur map
+# img: Original RGB channel image
+# blurMap: A matrix of blurkernel of parameters similar in size to `img` dimension
+# lamb: Similar to rip.deconv `lambda` argument
+
+# For more details see https://github.com/deepayan/rip/blob/main/rip.recover/R/nonblind.R
+
+spatDeblur <- function(img, blurMap, kern = c("norm","circnorm","cauchy","disc"),
+                       kap = 1, lamb = 0.01) {
+
+  radMap <- unique(as.vector(blurMap))
+  ydeblur <- img
+
+  for(i in 1:length(radMap)) {
+    kk <- blurkernel(kern = kern, rad = radMap[i],kap = kap)
+    temp1 <- rip.deconv(as.rip(img[,,1]),k = kk, method = "direct", lambda = lamb,
+                        rho = list(along = 0, across = 0), patch = 150, verbose = TRUE)
+    temp1[temp1 > 1] <- 1
+
+    temp2 <- rip.deconv(as.rip(img[,,2]),k = kk, method = "direct", lambda = lamb,
+                        rho = list(along = 0, across = 0), patch = 150, verbose = TRUE)
+    temp2[temp2 > 1] <- 1
+
+    temp3 <- rip.deconv(as.rip(img[,,3]),k = kk, method = "direct", lambda = lamb,
+                        rho = list(along = 0, across = 0), patch = 150, verbose = TRUE)
+    temp3[temp3 > 1] <- 1
+
+    mask <- (blurMap == radMap[i])
+    ydeblur[,,1][mask] <- temp1[mask]
+    ydeblur[,,2][mask] <- temp2[mask]
+    ydeblur[,,3][mask] <- temp3[mask]
+  }
+  return(ydeblur)
+}
+
+
+
+
+