update to v0.8.0 (clean up functions)

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: detectCilia
 Title: Detect and measure the lengths of primary cilia in microsopy images
-Version: 0.7.6
+Version: 0.8.0
 Authors@R: 
     person("Kai", "Budde-Sagert", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6836-9865"))

NAMESPACE

@@ -1,10 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(addNumberToImage)
 export(detectCilia)
-export(editImage)
-export(getLayer)
-export(summarizeCiliaInformation)
 import(graphics)
 import(stats)
 importFrom(magrittr,"%>%")

R/addNumberToImage.R

@@ -14,7 +14,6 @@
 #' added.
 #'
 #' @return An array (image) with added number.
-#' @export addNumberToImage
 
 addNumberToImage <- function(image = NULL,
                              number = NULL,

R/editImage.R

@@ -1,16 +1,14 @@
-#' @title editImage
-#' @description Get the layer of the primary cilia
-#' @details By using an x-y-3(rgb)-representation of an image, you can
-#' extract the information of the cilia in an image and only use those pixel
-#' that are above a certain threshold.
-#' @aliases editimage imageedit imageEdit
-#' @author Kai Budde-Sagert
-#' @export editImage
-#' @param image An three-dimensional array of numbers between 0 and 1
-#' @param object_color A character (color of the staining of the object)
-#' @param threshold A number (that determines the brightness of a pixel to
-#' be counted as cilium pixel)
-#' @returns An array (changed image).
+#' Calculate binary mask
+#' 
+#' `editImage()` masks an image layer depending on a threshold.
+#' 
+#' @param image An three-dimensional array of numbers between 0 and 1.
+#' @param object_color A character being the color of the staining of the
+#' object to be masked.
+#' @param threshold A number that determines the brightness of a pixel to
+#' be counted as a cilium pixel.
+#' 
+#' @returns A binary image.
 
 editImage <- function(image = NULL,
                       object_color = NULL,
@@ -45,12 +43,8 @@ editImage <- function(image = NULL,
     return()
   }
 
-  # higher contrast of the cilia -------------------------------------------
-  #threshold <- threshold * sum(image_cilia[,])/sum(image_cilia[,]>0)
-  #print(threshold)
-  #print(sum(image_cilia[,])/sum(image_cilia[,]>0))
-  #print(threshold)
-
+  # Calculate binary mask of cilia pixels ----------------------------------
+
   # Making sure that the calculated threshold is not above 1 or below 0
   if(threshold > 1){
     threshold <- 1

R/getLayer.R

@@ -1,12 +1,11 @@
-#' @title getLayer
-#' @description Get a specific layer of the image
-#' @details By using an x-y-3(rgb)-representation of an image, you can
-#' extract one layer.
-#' @aliases getlayer
-#' @author Kai Budde-Sagert
-#' @export getLayer
-#' @param image An three-dimensional array of numbers between 0 and 1
-#' @param layer A character (color of the layer)
+#' Get a specific layer of the image
+#' 
+#' `getLayer()` extracts a specific layer of an image (being x-y-3(rgb)-
+#' representation).
+
+#' @param image An three-dimensional array of numbers between 0 and 1.
+#' @param layer A character being the color of the layer.
+
 #' @returns An array (specific channel of image).
 
 getLayer <- function(image = NULL,

R/resizeImage.R

@@ -1,11 +1,11 @@
-#' @title resizeImage
-#' @description Resizes an image
-#' @details Resizes an image with a given scaling factor
-#' @aliases resizeimage
-#' @author Kai Budde-Sagert
-#' @export addNumberToImage
-#' @param image An one to three-dimensional array of numbers between 0 and 1
-#' @param number_size_factor A number (factor for resizing the number)
+#' Resizes an image
+#' 
+#' `resizeImage()` eesizes an image with a given scaling factor
+#' 
+#' @param image A one to three-dimensional array of numbers between 0 and 1
+#' @param number_size_factor A number being the factor for resizing the
+#' image of a number.
+#' 
 #' @returns An array (resized image).
 
 resizeImage <- function(image = NULL,

R/summarizeCiliaInformation.R

@@ -1,17 +1,19 @@
-#' @title summarizeCiliaInformation
-#' @description Summarizes the information of found cilia in images
-#' @details Input should be the result of detectCilia.R.
-#' The output is a data frame with the lengths of the found cilia.
-#' @aliases summarizeCiliumInformation summarizeciliainformation
-#' @author Kai Budde-Sagert
-#' @export summarizeCiliaInformation
+#' Summarize the information of found cilia
+#' 
+#' `summarizeCiliaInformation()` summarizes the information of cilia found
+#' by the main function detectCilia.R. The output is a data frame with the
+#' lengths of the found cilia.
+
+#' @param df_cilium_information A data frame with found cilia.
+#' @param min_cilium_area A number for the minimum number of pixels needed
+#' to represent a cilium.
+#' @param pixel_size A number depicting the size of one pixel in micrometers.
+#' @param slice_distance A number depicting the distance of two consecutive
+#' z-stack layers in micrometers.
+#' 
 #' @import graphics
 #' @import stats
-#' @param df_cilium_information A data frame
-#' @param min_cilium_area A number (min number of pixels needed for a layer being part of a cilium)
-#' @param pixel_size A number (size of one pixel in micrometer)
-#' @param slice_distance A number (distance of two consecutive slices in
-#' z-direction in micrometer)
+#' 
 #' @returns A tibble with summarized cilium information (lengths).
 
 summarizeCiliaInformation <- function(
@@ -58,9 +60,6 @@ summarizeCiliaInformation <- function(
       vertical_length_in_um     <- NA
     }
 
-
-
-
     # Find pixels of z-projection ##
     # Only keep non-duplicated columns pos_x and pos_y (all unique positions)
     df_cilium_projection <- df_cilium_projection[,c(1,2)]