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Commit 9e20074d authored by Jean-Karim Heriche's avatar Jean-Karim Heriche
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Fix bug caused by the difference between aws.s3 and paws.storage (used by... 

Fix bug caused by the difference between aws.s3 and paws.storage (used by Rarr), revert arbitrary dimensions order (it's fixed in NGFF specs).
parent 642fb14f
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Tags v1.5.1
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Pipeline #46562 passed
Stage: build
    Stage: deploy
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      R/explore_image.R
      + 21
      − 16
      View file @ 9e20074d
      ......@@ -34,28 +34,26 @@ explore_image_server <-function(input, output, session, rv, parent_input){
      img.idx <- 1
      if(class(rv$imgRoot)[1] == "s3_bucket") { # Images are in a S3 bucket
      bucketName <- rv$imgRoot$Contents$Bucket
      endPoint <- Sys.getenv("AWS_S3_ENDPOINT")
      s3.client <- omeRarr::get_s3_client() # use AWS_S3 env variables
      filePath1 <- file.path("https:/", endPoint, bucketName, rv$imgPath1[1])
      # paws.storage requires protocol prefix to endpoint contrary to aws.s3
      endPoint <- file.path("https:/", Sys.getenv("AWS_S3_ENDPOINT"))
      s3.client <- omeRarr::get_s3_client(endPoint = endPoint,
      accessKey = Sys.getenv("AWS_ACCESS_KEY_ID"),
      secretKey = Sys.getenv("AWS_SECRET_ACCESS_KEY"),
      region = Sys.getenv("AWS_DEFAULT_REGION"))
      filePath1 <- file.path(endPoint, bucketName, rv$imgPath1[1])
      } else if(!is.null(rv$imgRoot)) { # Images are on a filesystem
      ## Deal with eventual Windows-style paths
      rootDir <- file.path(strsplit(rv$imgRoot,'\\\\'))
      filePath1 <- file.path(rootDir, strsplit(rv$imgPath1[1], '\\\\'))
      }
      multiscale.info <- omeRarr::get_multiscale_info(rv$imgPath1[1], s3.client)
      ## If this is a multiresolution container, use the second level
      if(length(multiscale.info$datasets[[1]]$path)>1) {
      img.idx <- 2
      }
      if(!is.null(rv$roiFrame) && rv$roiFrame != "") {
      ## Figure out what the 3rd dimension is
      ## NGFF dimensions order is arbitrary and defined in metadata
      size <- omeRarr::get_image_dims(dirname(filePath1), image.idx = img.idx, s3.client)
      ## NGFF dimensions order is t,c,z,y,x
      size <- omeRarr::get_image_dims(filePath1, image.idx = img.idx, s3.client)
      ## Reorder as x,y,z,t,c
      size <- as.list(size[c("x","y","z","t","c")])
      size <- as.list(c(rev(size), rep(0, 5 - length(size))))
      names(size) <- c("x","y","z","t","c")
      size[is.na(size)] <- 0
      slice <- size
      slice <- slice <- rev(size)
      slice$x <- 1:slice$x
      slice$y <- 1:slice$y
      if(size$z == 0 && size$t > 0 && size$c == 0) {
      ......@@ -80,6 +78,7 @@ explore_image_server <-function(input, output, session, rv, parent_input){
      return(omeRarr::get_image(filePath1, image.idx = img.idx, slice = slice, s3.client = s3.client))
      }
      )
      I <- aperm(I, length(dim(I)):1) # re-order as (x, y, z, t, c)
      I <- EBImage::as.Image(I)
      } else { # Other formats, use RBioFormats
      if(class(rv$imgRoot)[1] == "s3_bucket"){ # Images are in a S3 bucket
      ......@@ -108,11 +107,17 @@ explore_image_server <-function(input, output, session, rv, parent_input){
      if(!is.null(rv$roiFrame) && rv$roiFrame != "") {
      ## Figure out what the 3rd dimension is
      if(metadata$sizeZ == 1 && metadata$sizeT > 1 && metadata$sizeC == 1) {
      slice.def = list(T = unique(rv$selectedFrame))
      if(unique(rv$selectedFrame) <= metadata$sizeT) {
      slice.def = list(T = unique(rv$selectedFrame))
      }
      } else if(metadata$sizeZ > 1 && metadata$sizeT == 1 && metadata$sizeC == 1) {
      slice.def = list(Z = unique(rv$selectedFrame))
      if(unique(rv$selectedFrame) <= metadata$sizeZ) {
      slice.def = list(Z = unique(rv$selectedFrame))
      }
      } else if(metadata$sizeZ == 1 && metadata$sizeT == 1 && metadata$sizeC > 1) {
      slice.def = list(C = unique(rv$selectedFrame))
      if(unique(rv$selectedFrame) <= metadata$sizeC) {
      slice.def = list(C = unique(rv$selectedFrame))
      }
      }
      }
      }
      ......
      R/explore_image2.R
      + 22
      − 17
      View file @ 9e20074d
      ......@@ -30,28 +30,26 @@ explore_image_server2 <-function(input, output, session, rv){
      img.idx <- 1
      if(class(rv$imgRoot)[1] == "s3_bucket") { # Images are in a S3 bucket
      bucketName <- rv$imgRoot$Contents$Bucket
      endPoint <- Sys.getenv("AWS_S3_ENDPOINT")
      s3.client <- omeRarr::get_s3_client() # use AWS_S3 env variables
      filePath2 <- file.path("https:/", endPoint, bucketName, rv$imgPath2[1])
      # paws.storage requires protocol prefix to endpoint contrary to aws.s3
      endPoint <- file.path("https:/", Sys.getenv("AWS_S3_ENDPOINT"))
      s3.client <- omeRarr::get_s3_client(endPoint = endPoint,
      accessKey = Sys.getenv("AWS_ACCESS_KEY_ID"),
      secretKey = Sys.getenv("AWS_SECRET_ACCESS_KEY"),
      region = Sys.getenv("AWS_DEFAULT_REGION"))
      filePath2 <- file.path(endPoint, bucketName, rv$imgPath2[1])
      } else if(!is.null(rv$imgRoot)) { # Images are on a filesystem
      ## Deal with eventual Windows-style paths
      rootDir <- file.path(strsplit(rv$imgRoot,'\\\\'))
      filePath2 <- file.path(rootDir, strsplit(rv$imgPath2[1], '\\\\'))
      }
      multiscale.info <- omeRarr::get_multiscale_info(rv$imgPath2[1], s3.client)
      ## If this is a multiresolution container, use the second level
      if(length(metadata$datasets[[1]]$path)>1) {
      img.idx <- 2
      }
      if(!is.null(rv$roiFrame) && rv$roiFrame != "") {
      ## Figure out what the 3rd dimension is
      ## NGFF dimensions order is arbitrary and defined in metadata
      size <- omeRarr::get_image_dims(dirname(filePath2), image.idx = img.idx, s3.client)
      ## NGFF dimensions order is t,c,z,y,x
      size <- omeRarr::get_image_dims(filePath2, image.idx = img.idx, s3.client)
      ## Reorder as x,y,z,t,c
      size <- as.list(size[c("x","y","z","t","c")])
      size <- as.list(c(rev(size), rep(0, 5 - length(size))))
      names(size) <- c("x","y","z","t","c")
      size[is.na(size)] <- 0
      slice <- size
      slice <- rev(size)
      slice$x <- 1:slice$x
      slice$y <- 1:slice$y
      if(size$z == 0 && size$t > 0 && size$c == 0) {
      ......@@ -76,6 +74,7 @@ explore_image_server2 <-function(input, output, session, rv){
      return(omeRarr::get_image(filePath2, image.idx = img.idx, slice = slice, s3.client = s3.client))
      }
      )
      I <- aperm(I, length(dim(I)):1) # re-order as (x, y, z, t, c)
      I <- EBImage::as.Image(I)
      } else { # Other formats, use RBioFormats
      if(class(rv$imgRoot)[1] == "s3_bucket"){ # Images are in a S3 bucket
      ......@@ -103,11 +102,17 @@ explore_image_server2 <-function(input, output, session, rv){
      if(!is.null(rv$roiFrame) && rv$roiFrame != "") {
      ## Figure out what the 3rd dimension is
      if(metadata2$sizeZ == 1 && metadata2$sizeT > 1 && metadata2$sizeC == 1) {
      slice.def = list(T = unique(rv$selectedFrame))
      if(unique(rv$selectedFrame) <= metadata2$sizeT) {
      slice.def = list(T = unique(rv$selectedFrame))
      }
      } else if(metadata2$sizeZ > 1 && metadata2$sizeT == 1 && metadata2$sizeC == 1) {
      slice.def = list(Z = unique(rv$selectedFrame))
      if(unique(rv$selectedFrame) <= metadata2$sizeZ) {
      slice.def = list(Z = unique(rv$selectedFrame))
      }
      } else if(metadata2$sizeZ == 1 && metadata2$sizeT == 1 && metadata2$sizeC > 1) {
      slice.def = list(C = unique(rv$selectedFrame))
      if(unique(rv$selectedFrame) <= metadata2$sizeC) {
      slice.def = list(C = unique(rv$selectedFrame))
      }
      }
      }
      }
      ......@@ -125,7 +130,7 @@ explore_image_server2 <-function(input, output, session, rv){
      image2 <- img2()
      if(!is.null(image2)) {
      if(!is.null(rv$pixelPosition) && !is.null(rv$roiX) && rv$roiX != "") { # input$roiX != "" => ROI selection enabled
      if(!grepl("\\.ome\\.zarr$", rv$imgPath1[1])) { # Not NGFF
      if(!grepl("\\.ome\\.zarr$", rv$imgPath2[1])) { # Not NGFF
      res.level <- 1
      if(seriesCount(rv$metadataImg2) > 3) {
      # Image is likely a multi-resolution pyramid
      ......
      image_data_explorer.R
      + 1
      − 1
      View file @ 9e20074d
      ......@@ -4,7 +4,7 @@
      ## Main application file ##
      ###########################
      VERSION <- "v1.5.0" # Update this when creating a new version
      VERSION <- "v1.5.1" # Update this when creating a new version
      # Increase max upload size to 1 GB
      options(shiny.maxRequestSize=1000*1024^2)
      ......
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