version 0.2.0 contains the possibility to draw scale bars when conver…

…ting from czi to tif

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: readCzi
 Type: Package
 Title: Read czi image files, convert them to tifs, and save metadata
-Version: 0.1.17
+Version: 0.2.0
 Author: c(person("Kai", "Budde", email = "kai.budde@uni-rostock.de",
     role = c("aut", "cre"))
 Maintainer: Kai Budde <kai.budde@uni-rostock.de>

NAMESPACE

@@ -1,7 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+export(addScaleBar)
 export(convertCziToTif)
 export(normalizeIntensity)
 export(readCzi)
 export(readCziMetadata)
+export(resizeImage)
 export(stackLayers)

R/addScaleBar.R

@@ -0,0 +1,103 @@
+#' @title addScaleBar
+#' @description Add a horizontal scale bare to image
+#' @details Add a scale bar to a tiff image depending on the meta data of
+#' the czi file
+#' @aliases addscaleBar addScalebar addscalebar
+#' @author Kai Budde
+#' @export addScaleBar
+#' @param image An array (2 or 3 dimensional array, could also be of
+#' formal class Image by package EBImage)
+#' @param length_per_pixel_in_um A number (length per pixel in um)
+#' @param distance_from_border A number (distance in pixels for the scale bar)
+#' @param number_size_factor A number (factor for resizing the number)
+
+
+addScaleBar <- function(image = NULL,
+                        length_per_pixel_in_um = NULL,
+                        distance_from_border = 20,
+                        number_size_factor = 1){
+
+  # dim_x <- dim(image)[2]
+  # dim_y <- dim(image)[1]
+  # dim_z <- dim(image)[3]
+  dim_x <- dim(image)[1]
+  dim_y <- dim(image)[2]
+  dim_z <- dim(image)[3]
+
+
+  dim_x_microns <- dim_x * length_per_pixel_in_um
+  length_scale_bar_microns <- round(dim_x_microns / 10)
+
+  if(length_scale_bar_microns < 10){
+    length_scale_bar_microns <- 10
+  }else if(length_scale_bar_microns < 20){
+    length_scale_bar_microns <- 20
+  }else if(length_scale_bar_microns < 50){
+    length_scale_bar_microns <- 50
+  }else if(length_scale_bar_microns < 100){
+    length_scale_bar_microns <- 100
+  }else if(length_scale_bar_microns < 200){
+    length_scale_bar_microns <- 200
+  }else if(length_scale_bar_microns < 500){
+    length_scale_bar_microns <- 500
+  }
+
+  length_scale_bar_pixels <- length_scale_bar_microns /
+    (length_per_pixel_in_um)
+
+  length_scale_bar_pixels <- as.integer(round(length_scale_bar_pixels))
+  heigth_scale_bar_pixels <- as.integer(round(dim_y/150))
+
+  # Add the scale_bar
+  # image[(dim_y-distance_from_border-heigth_scale_bar_pixels):(dim_y-distance_from_border),
+  #       (dim_x-distance_from_border-length_scale_bar_pixels):(dim_x-distance_from_border),
+  #       1:dim_z] <- 1
+  image[(dim_x-distance_from_border-length_scale_bar_pixels):(dim_x-distance_from_border),
+        (dim_y-distance_from_border-heigth_scale_bar_pixels):(dim_y-distance_from_border),
+        1:dim_z] <- 1
+
+  # Add length and unit
+  # number_pos_x <- dim_y-distance_from_border-heigth_scale_bar_pixels
+  # number_pos_y <- dim_x-distance_from_border-0.5*length_scale_bar_pixels
+  number_pos_x <- dim_x-distance_from_border-0.5*length_scale_bar_pixels
+  number_pos_y <- dim_y-distance_from_border-heigth_scale_bar_pixels
+
+  # Get the file names with the text
+  scale_legend_path <- paste(length_scale_bar_microns, "microns.tif", sep="")
+  scale_legend_path <- system.file("scale", scale_legend_path, package = "cellPixels")
+
+  scale_legend_image <- tiff::readTIFF(source = scale_legend_path, convert = TRUE,
+                                       info = FALSE)
+  # Only keep the black layer
+  scale_legend_image <- scale_legend_image[,,4]
+
+  # Rescale image
+  resize_factor <- dim_x/15/dim(scale_legend_image)[2]
+  scale_legend_image <- resizeImage(image = scale_legend_image,
+                                    resize_factor = resize_factor)
+
+  dim_legend_x <- dim(scale_legend_image)[2]
+  dim_legend_y <- dim(scale_legend_image)[1]
+  # dim_legend_x <- dim(scale_legend_image)[1]
+  # dim_legend_y <- dim(scale_legend_image)[2]
+
+  # Add number images to image
+  start_x <- dim_x-distance_from_border-0.5*length_scale_bar_pixels-0.5*dim_legend_x
+  start_y <- dim_y-distance_from_border-heigth_scale_bar_pixels-1.1*dim_legend_y
+  # start_x <- dim_x-distance_from_border-0.5*length_scale_bar_pixels-0.5*dim_legend_x
+  # start_y <- dim_y-distance_from_border-heigth_scale_bar_pixels-1.1*dim_legend_y
+
+  # for(row in 1:dim_legend_y){
+  #   for(col in 1:dim_legend_x){
+  for(col in 1:dim_legend_x){
+    for(row in 1:dim_legend_y){
+      if(scale_legend_image[row, col] > 0){
+        # if(scale_legend_image[col, row] > 0){
+        # image[start_y+row, start_x+col, 1:dim_z] <- scale_legend_image[row, col]
+        image[start_x+col, start_y+row, 1:dim_z] <- scale_legend_image[row, col]
+      }
+    }
+  }
+
+  return(image)
+}

R/convertCziToTif.R

@@ -18,6 +18,8 @@
 #' of the z-stack or original image if it is not a z stack)
 #' @param normalize_stack A logical (T/F for normalizing intensities of stack)
 #' @param change_layers A character (either "none" or, e.g., "green<->red")
+#' @param add_scale_bar A logic (add scale bar to all images that are saved
+#' if true)
 
 # TODO: stack_method: average OR max (instead of maxprojection)
 
@@ -28,7 +30,8 @@ convertCziToTif <- function(input_file = NULL,
                             higher_contrast_slices = FALSE,
                             higher_contrast_stack = TRUE,
                             normalize_stack = TRUE,
-                            change_layers = "none") {
+                            change_layers = "none",
+                            add_scale_bar = TRUE) {
   if(is.null(input_file)){
     print("Please call function with input file.")
     return()
@@ -43,7 +46,7 @@ convertCziToTif <- function(input_file = NULL,
 
   # Load image and convert it to Image class -------------------------------
   # Dimensions of the image: 1: row, 2: col, 3: channels (r,g,b), 4: z-layer,
-  image_data <- readCzi(input_file = input_file)
+  image_data <- readCzi::readCzi(input_file = input_file)
   dim_z <- dim(image_data)[4]
 
   # Drop z-layer of multidimensional array if dim_z == 1
@@ -92,12 +95,28 @@ convertCziToTif <- function(input_file = NULL,
   # Convert to EBImage
   Image_Data <- EBImage::Image(data = image_data, colormode = "Color")
 
+  # Save length per pixel in x-direction
+  df_metadata <- readCzi::readCziMetadata(input_file = input_file, save_metadata = FALSE)
+  length_per_pixel_x_in_um <- df_metadata$scaling_x_in_um[1]
+
+  # Check that pixels in x and y direction have the same lengths
+  length_per_pixel_y_in_um <- df_metadata$scaling_y_in_um[1]
+
+  if(length_per_pixel_x_in_um != length_per_pixel_y_in_um){
+    print("Dimension in x- and y-directions are different! ERROR!")
+  }
+
   # Save all slices --------------------------------------------------------
 
   if(dim_z > 1 && convert_all_slices){
     tif_file_names <- rep(image_name_wo_czi, dim(image_data)[4])
     tif_file_names <- paste(output_dir, "/", tif_file_names, "_z", 1:dim(image_data)[4], ".tif", sep="")
 
+    if(add_scale_bar){
+      Image_Data <- addScaleBar(image = Image_Data,
+                                length_per_pixel = length_per_pixel_x_in_um)
+    }
+
     EBImage::writeImage(x = Image_Data, files = tif_file_names, type = "tiff", bits.per.sample = 8)
   }
 
@@ -108,12 +127,22 @@ convertCziToTif <- function(input_file = NULL,
                                stack_method = stack_method)
 
     stack_file_name <- paste(output_dir, "/", image_name_wo_czi, "_zstack.tif", sep="")
+
+    if(add_scale_bar){
+      Image_Stack <- addScaleBar(image = Image_Stack,
+                                length_per_pixel = length_per_pixel_x_in_um)
+    }
     EBImage::writeImage(x = Image_Stack, files = stack_file_name, type = "tiff", bits.per.sample = 8)
 
   }else{
     # Not a z-stack image (dim_z==1)
 
     output_file_name <- paste(output_dir, "/", image_name_wo_czi, ".tif", sep="")
+
+    if(add_scale_bar){
+      Image_Data <- addScaleBar(image = Image_Data,
+                                 length_per_pixel = length_per_pixel_x_in_um)
+    }
     EBImage::writeImage(x = Image_Data, files = output_file_name, type = "tiff", bits.per.sample = 8)
 
   }
@@ -128,6 +157,10 @@ convertCziToTif <- function(input_file = NULL,
     tif_file_names <- rep(image_name_wo_czi, dim(image_data)[4])
     tif_file_names <- paste(output_dir, "/", tif_file_names, "_z", 1:dim(image_data)[4], "_histogram_equalized.tif", sep="")
 
+    if(add_scale_bar){
+      Image_Data <- addScaleBar(image = Image_Data,
+                                length_per_pixel = length_per_pixel_x_in_um)
+    }
     EBImage::writeImage(x = Image_Data, files = tif_file_names, type = "tiff", bits.per.sample = 8)
 
   }
@@ -145,6 +178,10 @@ convertCziToTif <- function(input_file = NULL,
       output_file_name <- paste(output_dir, "/", image_name_wo_czi, "_histogram_equalized.tif", sep="")
     }
 
+    if(add_scale_bar){
+      Image_Stack_histogram_equalization <- addScaleBar(image = Image_Stack_histogram_equalization,
+                                length_per_pixel = length_per_pixel_x_in_um)
+    }
     EBImage::writeImage(x = Image_Stack_histogram_equalization, files = output_file_name, type = "tiff", bits.per.sample = 8)
 
   }
@@ -194,6 +231,10 @@ convertCziToTif <- function(input_file = NULL,
       output_file_name <- paste(output_dir, "/", image_name_wo_czi, "_histogram_equalized_normalized.tif", sep="")
     }
 
+    if(add_scale_bar){
+      Image_Stack_normalized <- addScaleBar(image = Image_Stack_normalized,
+                                            length_per_pixel = length_per_pixel_x_in_um)
+    }
     EBImage::writeImage(x = Image_Stack_normalized, files = output_file_name, type = "tiff", bits.per.sample = 8)
 
   }

R/resizeImage.R

@@ -0,0 +1,50 @@
+#' @title resizeImage
+#' @description Resizes an image
+#' @details Resizes an image with a given scaling factor
+#' @aliases resizeimage
+#' @author Kai Budde
+#' @export resizeImage
+#' @param image An one to three-dimensional array of numbers between 0 and 1
+#' @param resize_factor A number (factor for resizing an image)
+
+resizeImage <- function(image = NULL,
+                        resize_factor = 1){
+
+  # Default values for missing arguments -----------------------------------
+  if(is.null(image)){
+    print(paste("Please call the function with an image.", sep=""))
+    return()
+  }
+  if(is.null(resize_factor)){
+    print(paste("Please call the function with a number", sep=""))
+    return()
+  }
+
+  if(resize_factor < 0){
+    print(paste("The factor may only be a number > 0", sep=""))
+    return()
+  }
+
+  # Leave image as is if factor == 1 ---------------------------------------
+  if(resize_factor == 1){
+    return(image)
+  }
+
+  # Shrink image if resize_factor </> 1 ---------------------------------
+  if(resize_factor > 0){
+
+    new_height <-  round(resize_factor * dim(image)[1])
+    new_width  <-  round(resize_factor * dim(image)[2])
+
+    new_img = apply(image, 2, function(y){return (stats::spline(y, n = new_height)$y)})
+    new_img = t(apply(new_img, 1, function(y){return (stats::spline(y, n = new_width)$y)}))
+
+    new_img[new_img < 0] = 0
+    new_img = round(new_img)
+
+    return(new_img)
+  }
+
+  print("Something went wrong.")
+  return(0)
+}