new version 0.3.0

SFB-ELAINE · Nov 30, 2023 · 747f438 · 747f438
1 parent d6e79b3
commit 747f438
Show file tree

Hide file tree

Showing 9 changed files with 86 additions and 240 deletions.
diff --git a/CITATION.cff b/CITATION.cff
@@ -7,24 +7,36 @@ cff-version: 1.2.0
 message: 'To cite package "readCzi" in publications use:'
 type: software
 license: GPL-3.0-or-later
-title: 'readCzi: Read czi image files, convert them to tifs, and save metadata'
-version: 0.2.4
-abstract: The package reads (z-stack) czi microscopy files, edits them, and stores
-  the results in the tif format. The metadata is also read and saved and transformed
-  into a tibble.
+title: 'readCzi: Read CZI image files, convert them to tifs, and save metadata'
+version: 0.3.0
+doi: NN
+abstract: The package reads (z-stack) CZI microscopy files, edits them, and stores
+  the results in the tif format. The metadata is also read, transformed into a tibble,
+  and saved as a CSV file.
 authors:
-- family-names: Budde
+- family-names: Budde-Sagert
   given-names: Kai
   email: [email protected]
-- name: c
-- family-names: c)
-  given-names: comment =
+  orcid: https://orcid.org/0000-0001-6836-9865
+preferred-citation:
+  type: manual
+  title: 'readCzi: Read CZI image files, convert them to tifs, and save metadata'
+  authors:
+  - family-names: Budde-Sagert
+    given-names: Kai
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-6836-9865
+  year: '2023'
+  notes: R package version 0.3.0
+  doi: NN
+  url: https://github.com/SFB-ELAINE/readCzi
 repository-code: https://github.com/SFB-ELAINE/readCzi
 url: https://github.com/SFB-ELAINE/readCzi
 contact:
-- family-names: Budde
+- family-names: Budde-Sagert
   given-names: Kai
   email: [email protected]
+  orcid: https://orcid.org/0000-0001-6836-9865
 references:
 - type: software
   title: 'R: A Language and Environment for Statistical Computing'
@@ -50,26 +62,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-5874-8148
   year: '2023'
-  version: '>='
-- type: software
-  title: reticulate
-  abstract: 'reticulate: Interface to ''Python'''
-  notes: Imports
-  url: https://rstudio.github.io/reticulate/
-  repository: https://CRAN.R-project.org/package=reticulate
-  authors:
-  - family-names: Ushey
-    given-names: Kevin
-    email: [email protected]
-  - family-names: Allaire
-    given-names: JJ
-    email: [email protected]
-  - family-names: Tang
-    given-names: Yuan
-    email: [email protected]
-    orcid: https://orcid.org/0000-0001-5243-233X
-  year: '2023'
-  version: '>='
+  version: '>= 1.30.19'
 - type: software
   title: EBImage
   abstract: 'EBImage: Image processing and analysis toolbox for R'
@@ -92,7 +85,41 @@ references:
   - family-names: Marais
     given-names: Philip A.
   year: '2023'
-  version: '>='
+  version: '>= 4.40.0'
+- type: software
+  title: reticulate
+  abstract: 'reticulate: Interface to ''Python'''
+  notes: Imports
+  url: https://rstudio.github.io/reticulate/
+  repository: https://CRAN.R-project.org/package=reticulate
+  authors:
+  - family-names: Ushey
+    given-names: Kevin
+    email: [email protected]
+  - family-names: Allaire
+    given-names: JJ
+    email: [email protected]
+  - family-names: Tang
+    given-names: Yuan
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-5243-233X
+  year: '2023'
+  version: '>= 1.26'
+- type: software
+  title: tibble
+  abstract: 'tibble: Simple Data Frames'
+  notes: Imports
+  url: https://tibble.tidyverse.org/
+  repository: https://CRAN.R-project.org/package=tibble
+  authors:
+  - family-names: Müller
+    given-names: Kirill
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  year: '2023'
+  version: '>= 3.1.8'
 - type: software
   title: xml2
   abstract: 'xml2: Parse XML'
@@ -108,4 +135,4 @@ references:
   - family-names: Ooms
     given-names: Jeroen
   year: '2023'
-  version: '>='
+  version: '>= 1.3.3'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,24 @@
 Package: readCzi
 Type: Package
-Title: Read czi image files, convert them to tifs, and save metadata
-Version: 0.2.3
-Author: c(person("Kai", "Budde", email = "[email protected]",
-    role = c("aut", "cre"))
-Maintainer: Kai Budde <[email protected]>
-Description: This package may read (z-stack) czi image data, edit them,
-    and store the results in the tif-format. The metadata is also read and
-    saved and transformed into a data frame.
-License: LICENSE
+Title: Read CZI image files, convert them to tifs, and save metadata
+Version: 0.3.0
+Authors@R: person("Kai", "Budde-Sagert", email = "[email protected]",
+    role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6836-9865"))
+Maintainer: Kai Budde-Sagert <[email protected]>
+Description: The package reads (z-stack) CZI microscopy files, edits them,
+    and stores the results in the tif format. The metadata is also read,
+    transformed into a tibble, and saved as a CSV file.
+URL: https://github.com/SFB-ELAINE/readCzi
+BugReports: https://github.com/SFB-ELAINE/readCzi/issues
+License: GPL (>= 3)
+Depends: 
+    R (>= 4.0.0)
+Imports:
+    BiocManager (>= 1.30.19),
+    EBImage (>= 4.40.0),
+    reticulate (>= 1.26),
+    tibble (>= 3.1.8),
+    xml2 (>= 1.3.3)
 Encoding: UTF-8
 LazyData: true
-Imports: BiocManager, reticulate, EBImage, xml2
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
diff --git a/R/addScaleBar.R b/R/addScaleBar.R
@@ -18,18 +18,6 @@ addScaleBar <- function(image = NULL,
                         distance_from_border = 20,
                         number_size_factor = 1){
 
-  # if(class(image) == "EBImage"){
-  #   # Convert to array for faster manipulation
-  #   image <- as.array(image)
-  #   image_was_EBImage <- TRUE
-  # }else{
-  #   image_was_EBImage <- FALSE
-  # }
-
-
-  # dim_x <- dim(image)[2]
-  # dim_y <- dim(image)[1]
-  # dim_c <- dim(image)[3]
   dim_x <- dim(image)[1]
   dim_y <- dim(image)[2]
   dim_c <- dim(image)[3]
@@ -63,9 +51,6 @@ addScaleBar <- function(image = NULL,
   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_c] <- 1
   if(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),
@@ -78,8 +63,6 @@ addScaleBar <- function(image = NULL,
 
 
   # Add length of scale bar 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
 
@@ -89,9 +72,6 @@ addScaleBar <- function(image = NULL,
 
   scale_legend_image <- EBImage::readImage(files = scale_legend_path,
                                            type = "tiff")
-  # 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]
@@ -103,27 +83,10 @@ addScaleBar <- function(image = NULL,
 
   dim_legend_x <- dim(scale_legend_image)[1]
   dim_legend_y <- dim(scale_legend_image)[2]
-  # dim_legend_x <- dim(scale_legend_image)[1]
-  # dim_legend_y <- dim(scale_legend_image)[2]
 
   # Add number images to image
   start_x <- floor(dim_x-distance_from_border-0.5*length_scale_bar_pixels-0.5*dim_legend_x)
   start_y <- floor(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_c] <- scale_legend_image[row, col]
-  #       image[start_x+col, start_y+row, 1:dim_c] <- scale_legend_image[row, col]
-  #     }
-  #   }
-  # }
 
   # Add \um image to original image
   scale_legend_image_copy <- scale_legend_image
@@ -132,22 +95,16 @@ addScaleBar <- function(image = NULL,
   if(dim_z == 1){
     scale_legend_image[start_x:(start_x+dim_legend_x-1),
                        start_y:(start_y+dim_legend_y-1),] <-
-      # EBImage::transpose(scale_legend_image_copy)
       scale_legend_image_copy
   }else{
     scale_legend_image[start_x:(start_x+dim_legend_x-1),
                        start_y:(start_y+dim_legend_y-1),,] <-
-      # EBImage::transpose(scale_legend_image_copy)
       scale_legend_image_copy
   }
 
 
   image <- scale_legend_image + image
   image[image > 1] <- 1
 
-  # if(image_was_EBImage){
-  #   image <- EBImage::Image(data = image_data, colormode = "Color")
-  # }
-
   return(image)
 }
diff --git a/R/convertCziToTif.R b/R/convertCziToTif.R
@@ -213,12 +213,6 @@ convertCziToTif <- function(input_file = NULL,
 
     if(dim_z > 1){
 
-      # for(i in 1:3){
-      #   if(max(Image_Stack[,,i]) > 0){
-      #     Image_Stack_normalized[,,i] <- Image_Stack_normalized[,,i]/max(Image_Stack_normalized[,,i])
-      #   }
-      # }
-
       disregarded_layers <- c()
       for(i in 1:3){
         if(max(Image_Stack[,,i]) == 0){
@@ -232,12 +226,6 @@ convertCziToTif <- function(input_file = NULL,
       output_file_name <- paste(output_dir, "/", image_name_wo_czi, "_zstack_histogram_equalized_normalized.tif", sep="")
     }else{
 
-      # for(i in 1:3){
-      #   if(max(Image_Data[,,i]) > 0){
-      #     Image_Stack_normalized[,,i] <- Image_Stack_normalized[,,i]/max(Image_Stack_normalized[,,i])
-      #   }
-      # }
-
       disregarded_layers <- c()
       for(i in 1:3){
         if(max(Image_Data[,,i]) == 0){

diff --git a/R/readCzi.R b/R/readCzi.R
@@ -141,53 +141,6 @@ readCzi <- function(input_file = NULL) {
 
     color_axis <- "C"
 
-    # if(number_of_channels == 3){
-    #   wavelengths <- gsub(
-    #     pattern =  paste(".+<EmissionWavelength>(.+)</EmissionWavelength>.+",
-    #                      ".+<EmissionWavelength>(.+)</EmissionWavelength>.+",
-    #                      ".+<EmissionWavelength>(.+)</EmissionWavelength>.+",
-    #                      sep=""),
-    #     replacement = "\\1,\\2,\\3",
-    #     x = metadata)
-    # }else if(number_of_channels == 2){
-    #   wavelengths <- gsub(
-    #     pattern =  paste(".+<EmissionWavelength>(.+)</EmissionWavelength>.+",
-    #                      ".+<EmissionWavelength>(.+)</EmissionWavelength>.+",
-    #                      sep=""),
-    #     replacement = "\\1,\\2",
-    #     x = metadata)
-    # }else if(number_of_channels == 1){
-    #   wavelengths <- gsub(
-    #     pattern =  paste(".+<EmissionWavelength>(.+)</EmissionWavelength>.+",
-    #                      sep=""),
-    #     replacement = "\\1",
-    #     x = metadata)
-    # }
-
-    # wavelengths <- as.numeric(strsplit(wavelengths, split = ",")[[1]])
-
-    # Upper and lower limits of wavelengths to determine the colors
-    # red: > 600nm
-    # green: >= 500nm and <= 600nm
-    # blue: < 500nm
-
-    # upper_limit_blue <- 450#500
-    # lower_limit_red <- 550#600
-    #
-    # test_red <- any(wavelengths > lower_limit_red)
-    # red_id <- ifelse(test = test_red, yes = which(wavelengths > lower_limit_red), no = 0)
-    # if(length(red_id) > 1){print("More than one red channel!?")}
-    #
-    # test_green <- any( (upper_limit_blue) <= wavelengths & (wavelengths <= lower_limit_red))
-    # green_id <- ifelse(test = test_green, yes = which((upper_limit_blue <= wavelengths) & (wavelengths <= lower_limit_red)), no = 0)
-    # if(length(green_id) > 1){print("More than one green channel!?")}
-    #
-    # test_blue <- any(wavelengths < upper_limit_blue)
-    # blue_id <- ifelse(test = test_blue, yes = which(upper_limit_blue > wavelengths), no = 0)
-    # if(length(blue_id) > 1){print("More than one blue channel!?")}
-#
-#     rgb_layers <- c(red_id, green_id, blue_id)
-
     rgb_layers <- c(df_metadata$red_channel,
                     df_metadata$green_channel,
                     df_metadata$blue_channel)
@@ -275,9 +228,6 @@ readCzi <- function(input_file = NULL) {
     # Reorganize the array according according to: "X","Y", "C"/"0", "Z"
     new_array_order <- c("X", "Y", color_axis, "Z")
   }else{
-    # print(paste("The image is one-dimensional in z-direction (no z-stack).",
-    #             sep=""))
-
     # Reorganize the array according according to: "X","Y", "C"/"0"
     new_array_order <- c("X", "Y", color_axis)
   }
@@ -300,10 +250,6 @@ readCzi <- function(input_file = NULL) {
     copy_image_loaded <- image_loaded
     image_loaded <- array(data = 0, dim = c(dim_x, dim_y, 3, dim_z))
 
-    # if(number_of_channels != 3){
-    #   image_loaded[,,-which(rgb_layers == 0),] <- copy_image_loaded
-    # }
-
     # Copy image layers in the correct order depending on which dimension
     # the original image has
     if(length(dim(copy_image_loaded)) == 12){
@@ -377,13 +323,6 @@ readCzi <- function(input_file = NULL) {
         check_array_dims <- length(new_array_order)
       }
 
-      # # Remove z dimension in array if it is 1
-      # if(!zstack){
-      #   # Drop all arrays with dim=1
-      #   image_loaded <- drop(image_loaded)
-      # }
-
-
       if(length(dim(image_loaded)) != check_array_dims){
         print("There is more or less information than thought in the image.")
         return()
@@ -437,12 +376,6 @@ readCzi <- function(input_file = NULL) {
     print(paste("There is no color axis.", sep=""))
   }
 
-  # Check if we have a (Transmitted light detector (T-PMT)) which needs to
-  # be saved in a different color (to not overwrite the other ones)
-
-  # Reverse y-axis (It will go from top to bottom instead from bottom to top)
-  #image_loaded <- EBImage::flip(image_loaded)
-
   rm(copy_image_loaded)
 
   rm(list= c("czi_class"))