removed a bug

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: readCzi
 Type: Package
 Title: Read czi image files, convert them to tifs, and save metadata
-Version: 0.1.1
+Version: 0.1.2
 Author: c(person("Kai", "Budde", email = "[email protected]",
     role = c("aut", "cre"))
 Maintainer: Kai Budde <[email protected]>

R/readCzi.R

@@ -126,7 +126,7 @@ readCzi <- function(input_file = NULL) {
   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 <- all( (upper_limit_blue) <= wavelengths & (wavelengths <= lower_limit_red))
+  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!?")}
 
@@ -159,22 +159,28 @@ readCzi <- function(input_file = NULL) {
     # not existing colors
     copy_image_loaded <- image_loaded
 
+    image_loaded <- array(data = 0, dim = c(dim_x, dim_y, 3, dim_z))
+
     # add missing channel(s)
     if(number_of_channels != 3){
-      image_loaded <- array(data = 0, dim = c(dim_x, dim_y, 3, dim_z))
       image_loaded[,,-which(rgb_layers == 0),] <- copy_image_loaded
     }
 
-    if(rgb_layers[1] != 0){
-      image_loaded[,,1,] <- copy_image_loaded[,,rgb_layers[1],,,,,]
-    }
-    if(rgb_layers[2] != 0){
-      image_loaded[,,2,] <- copy_image_loaded[,,rgb_layers[2],,,,,]
-    }
-    if(rgb_layers[3] != 0){
-      image_loaded[,,3,] <- copy_image_loaded[,,rgb_layers[3],,,,,]
+    if(length(dim(copy_image_loaded)) == 8){
+      if(rgb_layers[1] != 0){
+        image_loaded[,,1,] <- copy_image_loaded[,,rgb_layers[1],,,,,]
+      }
+      if(rgb_layers[2] != 0){
+        image_loaded[,,2,] <- copy_image_loaded[,,rgb_layers[2],,,,,]
+      }
+      if(rgb_layers[3] != 0){
+        image_loaded[,,3,] <- copy_image_loaded[,,rgb_layers[3],,,,,]
+      }
+    }else{
+      print("The dimensions of the image does not fit.")
     }
 
+
     # Drop all arrays with dim=1 (except the channel, if C=1)
     #image_loaded <- drop(image_loaded)
 

inst/testscriptDevelop.R

@@ -9,7 +9,7 @@ rm(list = ls())
 # close all open plots in RStudio
 graphics.off()
 
-# Load packages #############################################################
+# Load packages ############################################################
 
 list.of.packages <- c("BiocManager", "reticulate")
 #list.of.packages <- c("tiff", "dplyr", "devtools", "BiocManager", "xlsx", "zis", "reticulate")
@@ -54,7 +54,8 @@ load_all()
 
 # Please adapt the following parameters ####################################
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-input_file <- "tests/EV52_6_links_63x_zstack_3 nur rot.czi"
+input_file <- "tests/190815_EV38_2_Kollagen mit Asc u Dexa_63x_zstack_6.czi"
+#input_file <- "tests/210301_EV38_Kollagen + WF_1_1024x1024_z-stack_1.czi"
 input_folder <- "tests/"
 
 # <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -68,7 +69,7 @@ image_data <- readCzi(input_file <- input_file)
 df_metadata <- readCziMetadata(input_file <- input_file)
 
 # Test script for converting a czi file into a tif file --------------------
-convertCziToTif(input_file <- input_file)
+convertCziToTif(input_file <- input_file, convert_all_slices = FALSE)
 
 ### Test with files in folder ----------------------------------------------