Fix handling of ome-zarr.

R/explore_image.R

@@ -29,7 +29,7 @@ explore_image_server <-function(input, output, session, rv, parent_input){
     if(!is.null(rv$imgPath1) && length(unique(rv$imgPath1)) == 1 &&
        length(unique(rv$selectedFrame)) <= 1 &&
        !is.null(rv$fileCol1) && rv$fileCol1 != ""){
-      if(grepl("\\.ome\\.zarr\\/", rv$imgPath1[1])) { # NGFF, use omeRarr
+      if(grepl("\\.ome\\.zarr", rv$imgPath1[1])) { # NGFF, use omeRarr
         s3.client <- NULL
         img.idx <- 1 # Assume object coordinates refer to highest resolution level
         if(class(rv$imgRoot)[1] == "s3_bucket") { # Images are in a S3 bucket
@@ -48,25 +48,28 @@ explore_image_server <-function(input, output, session, rv, parent_input){
         }
         ## NGFF dimensions order is t,c,z,y,x
         size <- as.list(omeRarr::get_image_dims(filePath1, image.idx = img.idx, s3.client))
-        ## Set a dimension to NA to get everything in this dimension
-        slice <- list(t = NA, c = NA, z = NA, y = NA, x = NA)
+        # Some older files only specify dimensions > 1
+        if(is.null(size$z)) {size$z <- 1}
+        if(is.null(size$c)) {size$c <- 1}
+        if(is.null(size$t)) {size$t <- 1}
+        ## Set a dimension to NULL to get everything in this dimension
+        slice <- list(t = NA, c = NA, z = NA, y = NULL, x = NULL)
         if(!is.null(rv$roiFrame) && rv$roiFrame != "") {
           ## Figure out what the 3rd dimension is
           if(size$z == 1 && size$t > 1 && size$c == 1) {
             slice$t <- unique(rv$selectedFrame)
-            slice$z <- NA
-            slice$c <- NA
+            slice$z <- NULL
+            slice$c <- NULL
           } else if(size$z > 1 && size$t == 1 && size$c == 1) {
             slice$z <- unique(rv$selectedFrame)
-            slice$t <- NA
-            slice$c <- NA
+            slice$t <- NULL
+            slice$c <- NULL
           } else if(size$z == 1 && size$t == 1 && size$c > 1) {
             slice$c <- unique(rv$selectedFrame)
-            slice$z <- NA
-            slice$t <- NA
+            slice$z <- NULL
+            slice$t <- NULL
           }
         }
-        print(slice)
         I <- tryCatch(
           { omeRarr::get_image(filePath1, image.idx = img.idx, slice = slice, s3.client = s3.client) },
           error = function(e) {

R/explore_image2.R

@@ -25,7 +25,7 @@ explore_image_server2 <-function(input, output, session, rv){
     if(!is.null(rv$imgPath2) && length(unique(rv$imgPath2)) == 1 &&
        length(unique(rv$selectedFrame)) <= 1 &&
        !is.null(rv$fileCol2) && rv$fileCol2 != ""){
-      if(grepl("\\.ome\\.zarr\\/", rv$imgPath2[1])) { # NGFF, use omeRarr
+      if(grepl("\\.ome\\.zarr", rv$imgPath2[1])) { # NGFF, use omeRarr
         s3.client <- NULL
         img.idx <- 1 # Assume object coordinates refer to highest resolution level
         if(class(rv$imgRoot)[1] == "s3_bucket") { # Images are in a S3 bucket
@@ -44,22 +44,26 @@ explore_image_server2 <-function(input, output, session, rv){
         }
         ## NGFF dimensions order is t,c,z,y,x
         size <- as.list(omeRarr::get_image_dims(filePath1, image.idx = img.idx, s3.client))
+        # Some older files only specify dimensions > 1
+        if(is.null(size$z)) {size$z <- 1}
+        if(is.null(size$c)) {size$c <- 1}
+        if(is.null(size$t)) {size$t <- 1}
         ## Set a dimension to NA to get everything in this dimension
-        slice <- list(t = NA, c = NA, z = NA, y = NA, x = NA)
+        slice <- list(t = NA, c = NA, z = NA, y = NULL, x = NULL)
         if(!is.null(rv$roiFrame) && rv$roiFrame != "") {
           ## Figure out what the 3rd dimension is
           if(size$z == 1 && size$t > 1 && size$c == 1) {
             slice$t <- unique(rv$selectedFrame)
-            slice$z <- NA
-            slice$c <- NA
+            slice$z <- NULL
+            slice$c <- NULL
           } else if(size$z > 1 && size$t == 1 && size$c == 1) {
             slice$z <- unique(rv$selectedFrame)
-            slice$t <- NA
-            slice$c <- NA
+            slice$t <- NULL
+            slice$c <- NULL
           } else if(size$z == 1 && size$t == 1 && size$c > 1) {
             slice$c <- unique(rv$selectedFrame)
-            slice$z <- NA
-            slice$t <- NA
+            slice$z <- NULL
+            slice$t <- NULL
           }
         }
         I <- tryCatch(