v0.2.2, minor improvements

* Automatically expand `path_out`, so abbreviated paths don't cause Zerene Stacker to error out.
* Added `digits` argument to add leading zeros to file numbers in `expand_zs_dataframe`.

DESCRIPTION

@@ -1,14 +1,15 @@
 Package: zerenebatchR
 Type: Package
 Title: Utility for Batch Processing in Zerene Stacker
-Version: 0.2.1
+Version: 0.2.2
 Imports: fs,
 	 magrittr,
-	 xml2
+	 xml2,
+	 stringr
 Author: Ethan Bass
 Maintainer: Ethan Bass <ethanbass@gmail.com>
 Description: Writes Zerene Stacker batch files and executes them from the commandline.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0

NAMESPACE

@@ -11,3 +11,4 @@ importFrom(fs,file_copy)
 importFrom(fs,file_move)
 importFrom(fs,path)
 importFrom(fs,path_home)
+importFrom(stringr,str_pad)

NEWS.md

@@ -1,3 +1,9 @@
+# zerenebatchR 0.2.2
+
+* Allow multiple columns as inputs to `c_id` in `run_zs_batch`.
+* Automatically expand `path_out`, so abbreviated paths don't cause Zerene Stacker to error out.
+* Added `digits` argument to add leading zeros to file numbers in `expand_zs_dataframe`.
+
 # zerenebatchR 0.2.1
 
 * Added check for duplicated ids in `expand_zs_dataframe`.

R/expand_zs_dataframe.R

@@ -2,6 +2,8 @@
 #'
 #' This function facilitates stacking photos that are numbered sequentially. It
 #' must be supplied with a \code{data.frame} with columns containing the
+#' information about the images to be stacked.
+#' @importFrom stringr str_pad
 #' @param df A data.frame containing the first and last photo, file path, and
 #' grouping variable.
 #' @param c_path String or numerical index specifying the column where the file
@@ -15,42 +17,56 @@
 #' @param extension String specifying the file extension of the images. The
 #' extension must be in the correct case so it matches exactly to the extension
 #' of the files to be stacked.
+#' @param digits How many digits should be in the number.
 #' @return Expanded data.frame
 #' @export
 
 expand_zs_dataframe <- function(df, c_path, c_id, c_start, c_end,
-                                extension = "JPG"){
+                                extension = "JPG", digits = 4){
   # check missing lines
-  rm <- which(is.na(df[,c_start]) | is.na(df[,c_end]))
+  df <- as.data.frame(df)
+  df[,c_start] <- as.numeric(df[,c_start])
+  df[,c_end] <- as.numeric(df[,c_end])
+  rm <- which(is.na(df[, c_start]) | is.na(df[, c_end]))
   if (length(rm) > 0){
     df <- df[-rm,]
   }
+  if (length(c_id) > 1){
+    df$id <- apply(df[, c_id], MARGIN = 1, function(x) paste(x, collapse = "-"))
+  } else{
+    df$id <- df[, c_id]
+  }
   # check for duplicated IDs
-  duplicated_ids <- duplicated(df[,c_id])
+  duplicated_ids <- duplicated(df$id)
   if (any(duplicated_ids)){
     stop(paste0("Some identifiers appear to be duplicated. Please double check IDs and try again.
-         Duplicated IDs: ", sQuote(paste0(df[which(duplicated_ids), c_id])), "."))
+         Duplicated IDs: ", paste(sQuote(df[which(duplicated_ids), "id"]), collapse = ", "), "."))
   }
   # check for photos out of order
-  wrong_order <- which(!(df[,c_start] < df[,c_end]))
+  wrong_order <- which(!(df[, c_start] < df[, c_end]))
   if (length(wrong_order) > 0){
-    stop(paste0("Images appear to be out of order. Double check line ",
-                sQuote(paste0(wrong_order,collapse=", ")), "."))
+    stop(paste0("Images appear to be out of order. Double check IDs: ",
+                paste(sQuote(df[wrong_order,"id"]), collapse = ", "), "."))
   }
   extension <- gsub("^\\." ,"", extension)
   pp <- lapply(1:nrow(df), function(i){
-    data.frame(id = paste(df[i, c_id], collapse="_"),
-               path = paste0(df[i,c_path],
-                             seq(df[i, c_start], df[i, c_end], by = 1),
+    data.frame(id = paste(df[i, "id"], collapse = "_"),
+               path = paste0(df[i, c_path],
+                             stringr::str_pad(seq(df[i, c_start], df[i, c_end], by = 1),
+                                              width = digits, side = "left", pad = "0"),
                                                                     ".", extension))
   })
   pp <- do.call(rbind, pp)
   # check for missing files
-  missing_files <- which(!file.exists(pp$path))
-  if (length(missing_files > 0)){
-    warning(paste0("Some image files could not be found: ",
-                   (paste0(sQuote(missing_files), collapse=", ")), "."))
-    pp <- pp[-missing_files,]
+  missing_files <- pp[which(!file.exists(pp$path)), "path"]
+  if (length(missing_files) > 0){
+    if (length(missing_files) == nrow(df)){
+      stop("Files could not be found. Please check path(s) and try again.")
+    } else{
+      warning(paste0("Some image files could not be found: ",
+                     (paste0(sQuote(missing_files), collapse=", ")), "."))
+      pp <- pp[-missing_files,]
+    }
   }
   pp
 }

R/run_zs_batch.R

@@ -30,7 +30,7 @@ globalVariables(c("."))
 #' @author Ethan Bass
 #' @export
 
-run_zs_batch <- function(files, c_path = 1, c_split = 2,
+run_zs_batch <- function(files, c_split = 1, c_path = 2,
                                path_out, stacker = c("pmax", "dmap"),
                                temp, path_template = NULL,
                                path_xml = NULL, stack = TRUE){
@@ -51,7 +51,7 @@ run_zs_batch <- function(files, c_path = 1, c_split = 2,
     if (stack){
       stop("If `stack == TRUE`, a `data.frame` should be provided to the files argument.")
     }
-    exists <- dir_exists(files)
+    exists <- fs::dir_exists(files)
     if (!any(exists)){
       stop("The provided directories do not exist. Please check paths and try again.")
     }
@@ -85,8 +85,8 @@ run_zs_batch <- function(files, c_path = 1, c_split = 2,
   system <- .Platform$OS.type
 
   launch_cmd_path <- switch(system,
-                            "unix" = path_home("Library/Preferences/ZereneStacker/zerenstk.launchcmd"),
-                            "windows" = path_home("AppData\\ZereneStacker\\zerenstk.launchcmd"),
+                            "unix" = fs::path_home("Library/Preferences/ZereneStacker/zerenstk.launchcmd"),
+                            "windows" = fs::path_home("AppData\\ZereneStacker\\zerenstk.launchcmd"),
                             "linux" = "~/.ZereneStacker/zerenstk.launchcmd"
   )
 
@@ -118,13 +118,11 @@ run_zs_batch <- function(files, c_path = 1, c_split = 2,
   l <- x %>% xml_children()  %>% .[[2]] %>% xml_find_all("//Sources") %>% xml_children %>% length
   sources <- x %>% xml_children()  %>% .[[2]] %>% xml_find_all("//Sources")
   xml_attr(sources, "length") <- as.character(l)
-  # x %>% xml_children()  %>% .[[2]] %>% xml_find_all("//Sources")
 
   # set path out
 
   x %>% xml_children()  %>% .[[2]] %>% xml_find_all("//OutputImagesDesignatedFolder") %>%
-    xml_replace(paste0('OutputImagesDesignatedFolder value="', path_out, '"'))
-  # x %>% xml_children %>% .[[4]] %>% xml_add_child(.value=gsub("path_out", path_out, parser))
+    xml_replace(paste0('OutputImagesDesignatedFolder value="', fs::path_expand(path_out), '"'))
 
   # set stacking algorithm
 
@@ -138,7 +136,8 @@ run_zs_batch <- function(files, c_path = 1, c_split = 2,
   # write batch file
 
   if (is.null(path_xml)){
-    path_xml <- paste0(path_out, "batchfile_", strftime(Sys.time(),format = "%Y-%m-%d_%H-%M-%S"), ".xml")
+    path_xml <- paste0(path_out, "batchfile_", strftime(Sys.time(),
+                                                        format = "%Y-%m-%d_%H-%M-%S"), ".xml")
   }
 
   write_xml(x, file = path_xml)
@@ -148,12 +147,11 @@ run_zs_batch <- function(files, c_path = 1, c_split = 2,
   system(paste0(launch_cmd,
                 " -noSplashScreen -runMinimized -exitOnBatchScriptCompletion -batchScript ",
                 path_xml))
-  # , " -sourcePath=", path
 
   # delete temp folders
 
   if (temp){
-    dir_delete(stacks)
+    fs::dir_delete(stacks)
   }
 }
 
@@ -174,22 +172,22 @@ run_zs_batch <- function(files, c_path = 1, c_split = 2,
 stack_files <- function(df, c_path, c_split, temp = TRUE){
 
   if (length(c_split) > 1){
-    df$id <-apply(df[,c_split], MARGIN = 1, function(x) paste(x, collapse="-"))
+    df$id <-apply(df[, c_split], MARGIN = 1, function(x) paste(x, collapse = "-"))
   } else{
-    df$id <- df[,c_split]
+    df$id <- df[, c_split]
   }
 
   df <- split(as.data.frame(df), df[, "id"])
   file_action <- switch(as.character(temp),
-                        "TRUE" = file_copy,
-                        "FALSE" = file_move)
+                        "TRUE" = fs::file_copy,
+                        "FALSE" = fs::file_move)
   paths <- sapply(df, function(x){
     if (any(fs::file_exists(x[, c_path]))){
       path <- x[1, c_path]
       dirn <- dirname(path)
-      dirn <- ifelse(temp, fs::path(dirn,"temp"), dirn)
+      dirn <- ifelse(temp, fs::path(dirn, "temp"), dirn)
       dir_path <- fs::path(dirn, x[, "id"][1])
-      dir_create(dir_path)
+      fs::dir_create(dir_path)
       sapply(x[,c_path], function(file){
         try(file_action(file, dir_path))
       })