correct create_viewer(); close #10

NEWS

@@ -7,8 +7,9 @@ phonfieldwork 0.0.6 (20.06.2020)
   - add text_size argument to the "draw_sound()" function
   - add zoom argument to the "draw_sound()" function
   - add the "get_sound_duration()" function
-  - fix ploting of multiple sounds with multiple .TextGrid
+  - fix ploting of multiple sounds with multiple .TextGrids
   - add an argument "title_as_filename" to the "draw_sound()" function
+  - change textgrid asociated arguments of the "create_viewer()" function to "table" argument; as a result users now need to provide a table for the annotation viewer and not a TextGrid
 
 phonfieldwork 0.0.5 (07.06.2020)
   - add "textgrid_to_df()" function for reading Praat files

R/create_image_look_up.R

@@ -14,14 +14,20 @@
 #'
 
 create_image_look_up <- function(img_src,
-                                 img_caption = "",
+                                 img_caption = NULL,
                                  text = "&#x1f441;"){
+  if(is.null(img_caption)){
+    img_caption <- rep("", length(img_src))
+  }
+
+
   if(length(img_src) != length(img_caption)){
     stop(paste0("It looks like the img_src variable contains ",
                 length(img_src),
                 " objects and the img_caption variable contains ",
                 length(img_caption)))
   }
+
   paste0("<a ",
         "onmouseover=\"resize(this, '200%')\" ",
         "onmouseout=\"resize(this, '100%')\" ",

R/create_viewer.R

@@ -6,10 +6,9 @@
 #'
 #' @param audio_dir path to the directory with sounds
 #' @param picture_dir path to the directory with pictures
-#' @param textgrid string with a filename or path to the TextGrid
-#' @param tiers vecors of numbers or names of TextGrid tiers. They merged into a table and used in the created viewer.
-#' @param merge_column string with a column name that will be used for merging stimuli and video and audio viewer.
-#' @param caption_column string with a column name that will be used for captions for a picture (by default is the same as merge_column).
+#' @param table data frame with data ordered according to files in the audio folder
+#' @param captions vector of strings that will be used for captions for a picture.
+#' @param sorting_columns vector of strings for sorting the result column
 #' @param output_file the name of the result .html file (by default stimuli_viewer)
 #' @param output_dir the output directory for the rendered file
 #' @param render the logical argument, if \code{TRUE} renders the created R Markdown viewer to the \code{output_dir} folder, otherwise returns the path to the temporary file with a .csv file.
@@ -22,18 +21,15 @@
 #' @importFrom utils installed.packages
 #' @importFrom utils write.csv
 
-
 create_viewer <- function(audio_dir,
                           picture_dir,
-                          textgrid,
-                          tiers = 1,
-                          merge_column,
-                          caption_column = NULL,
+                          table,
+                          captions = NULL,
+                          sorting_columns = NULL,
                           about = "Created with the `phonfieldworks` package (Moroz 2020).",
                           output_dir,
                           output_file = "stimuli_viewer",
                           render = TRUE){
-  if(is.null(caption_column)){caption_column =  merge_column}
   if(!("DT" %in% utils::installed.packages()[,"Package"])){
     stop('For this function you need to install DT package with a command install.packages("DT").')
   }
@@ -46,37 +42,25 @@ create_viewer <- function(audio_dir,
     stop("The number of audio files is less then number of pictures.")
   }
 
-  result_df <- lapply(seq_along(tiers), function(i){
-    df <- tier_to_df(textgrid = textgrid, tier = tiers[i])
-    return(df$annotation[df$annotation != ""])
-  })
-  result_df <- as.data.frame(result_df)
-
-
-# check whether there is an empty names -----------------------------------
-  tier_names <- get_textgrid_names(textgrid)[tiers]
-  tier_names <- lapply(seq_along(tier_names), function(i){
-    ifelse(tier_names[i] == "", paste0("X", i), tier_names[i])
-  })
-  tier_names <- unlist(tier_names)
-
-# make a column names ------------------------------------------------------
-  colnames(result_df) <- tier_names
-
 # create correct relative paths -------------------------------------------
   audio_dir <- strsplit(normalizePath(audio_dir),
                         normalizePath(output_dir))[[1]][2]
   audio_dir <- substr(audio_dir, 2, nchar(audio_dir))
-  result_df$audio <- paste0(audio_dir, "/", audio)
+  table$audio <- paste0(audio_dir, "/", audio)
 
   picture_dir <- strsplit(normalizePath(picture_dir),
                           normalizePath(output_dir))[[1]][2]
   picture_dir <- substr(picture_dir, 2, nchar(picture_dir))
-  result_df$pictures <- paste0(picture_dir, "/", pictures)
+  table$pictures <- paste0(picture_dir, "/", pictures)
+
+  # sort rows according to sorting_columns
+  if(!is.null(sorting_columns)){
+    table <- table[do.call(order, table[sorting_columns]), ]
+  }
 
 # create a .csv file ------------------------------------------------------
   tmp1 <- tempfile(fileext = ".csv")
-  utils::write.csv(result_df, tmp1, row.names = FALSE)
+  utils::write.csv(table, tmp1, row.names = FALSE)
 
 # create about file -------------------------------------------------------
   if(substr(about, nchar(about)-3, nchar(about)) == ".Rmd"){
@@ -92,8 +76,7 @@ create_viewer <- function(audio_dir,
 "/phonfieldwork/rmarkdown/templates/annotation_viewer/skeleton/skeleton.Rmd"),
                     params = list(data = tmp1,
                                   about = tmp2,
-                                  merge_column = merge_column,
-                                  caption_column = caption_column),
+                                  captions = captions),
                     output_dir = output_dir,
                     quiet = TRUE,
                     output_file = output_file)

R/draw_sound.R

@@ -29,6 +29,9 @@
 #'
 #' @return Oscilogram and spectrogram plot (and possibly TextGrid annotation).
 #'
+#' @examples
+#' draw_sound(system.file("extdata", "test.wav", package = "phonfieldwork"))
+#'
 #' @export
 #'
 #' @importFrom tuneR readWave
@@ -74,7 +77,8 @@ draw_sound <- function(file_name,
       if(class(file_name) == "Wave"){
         s <- file_name
       } else{
-        ext <- tolower(substring(file_name, regexpr("\\..*$", file_name) + 1))
+        ext <- unlist(strsplit(file_name, "\\."))
+        ext <- ext[length(ext)]
 
         if(ext == "wave"|ext == "wav"){
           s <- tuneR::readWave(file_name)

R/get_sound_durations.R

@@ -7,6 +7,10 @@
 #' @param file_name a sound file
 #' @param sounds_from_folder path to a folder with multiple sound files. If this argument is not \code{NULL}, then the function goes through all files and calculates duration for all of them.
 #'
+#' @examples
+#' get_sound_duration(
+#'   sounds_from_folder = system.file("extdata", package = "phonfieldwork"))
+#'
 #' @export
 #'
 #' @importFrom tuneR readWave
@@ -18,7 +22,8 @@ get_sound_duration <- function(file_name,
     if(class(file_name) == "Wave"){
       s <- file_name
     } else{
-      ext <- tolower(substring(file_name, regexpr("\\..*$", file_name) + 1))
+      ext <- unlist(strsplit(file_name, "\\."))
+      ext <- ext[length(ext)]
 
       if(ext == "wave"|ext == "wav"){
         s <- tuneR::readWave(file_name)

docs/index.Rmd

@@ -364,28 +364,6 @@ tree | tail -n 25 | head -n 23
 
 It is also possible to use the argument `textgrid_from_folder` in order to specify the folder where .TextGrids for annotation are (could be the same folder as the sound one). By default the `draw_sound()` function with the `sounds_from_folder` argument adds a title with the file name to each pictures' title, but it is possible to turn it off using the argument `title_as_filename = FALSE`.
 
-## Create a viewer
-
-It is possible to create an annotation viewer.
-
-```{r, message= FALSE, warning=FALSE}
-create_viewer(audio_dir = "s1/s1_sounds/",
-              picture_dir = "s1/s1_pics/", 
-              textgrid = "s1/s1_all.TextGrid",
-              tiers = c(1, 3),
-              merge_column = "labels",
-              output_dir = "s1/",
-              output_file = "stimuli_viewer")
-```
-
-As a result, a `stimuli_viewer.html` was created in the `s1` folder.
-
-```{bash, echo = FALSE}
-tree | tail -n 26 | head -n 24
-```
-
-You can find the created example [here](https://agricolamz.github.io/phonfieldwork/s1/stimuli_viewer.html).
-
 # Read linguistic files into R
 
 The `phonfieldwork` package provides also several methods for reading different file types into R. This makes it possible to analyze them and convert into `.csv` files (e. g. using the `write.csv()` function):
@@ -423,4 +401,93 @@ create_glossed_document(flextext = "files/zilo_test.flextext",
 file.copy("files/glossed_document.html", to = "glossed_document.html", overwrite = TRUE)
 ```
 
+# Create a viewer
+
+In oredr to create a sound viewer you need three things:
+
+* folder with sounds
+* folder with pictures
+* dataframe with some details (e. g. annotation, utterance number etc.)
+
+We will start with the previous folder structure:
+
+```{bash, echo = FALSE}
+tree | tail -n 25 | head -n 23
+```
+
+We have all folders:
+
+```{r}
+list.files("s1/s1_sounds/") # sounds
+list.files("s1/s1_pics/") # pictures
+```
+
+So what is left is the table. It is possible to create manually (or upload it form .csv or .xlsx files, see section 4.1):
+
+```{r}
+df <- data.frame(word  = c("tap", "tip", "top"),
+                 sounds = c("æ", "ı", "ɒ"))
+df
+```
+
+This table could be used in order to create an annotation viewer:
+
+```{r, warning = FALSE}
+create_viewer(audio_dir = "s1/s1_sounds/",
+              picture_dir = "s1/s1_pics/", 
+              table = df,
+              output_dir = "s1/",
+              output_file = "stimuli_viewer")
+```
+
+As a result, a `stimuli_viewer.html` was created in the `s1` folder.
+
+```{bash, echo = FALSE}
+tree | tail -n 26 | head -n 24
+```
+
+You can find the created example [here](https://agricolamz.github.io/phonfieldwork/s1/stimuli_viewer.html).
+
+Unfortunately, the way of table creation for the annotation viewer presented in this section is not a good solution for the huge amount of sounds. It is possible to derive such a table from annotation TextGrid, that we have created earlier. Here is a TextGrid:
+
+```{r}
+textgrid_to_df("s1/s1_all.TextGrid")
+```
+
+So in order to create desired table we can use `tier_to_df()` function:
+
+```{r}
+t1 <- tier_to_df("s1/s1_all.TextGrid", tier = 1)
+t1
+t3 <- tier_to_df("s1/s1_all.TextGrid", tier = 3)
+t3
+```
+
+As we see the first tier is ready, but the third tier contains empty annotations. Let's remove them:
+
+```{r}
+t3 <- t3[t3$annotation != "",]
+t3
+```
+
+So from this point it is possible to create the table that we wanted:
+
+```{r}
+new_df <- data.frame(words = t1$annotation,
+                 sounds = t3$annotation)
+new_df
+```
+
+So now we are ready to run our code for creating an annotation viewer:
+
+```{r, warning = FALSE}
+create_viewer(audio_dir = "s1/s1_sounds/",
+              picture_dir = "s1/s1_pics/", 
+              table = new_df,
+              output_dir = "s1/",
+              output_file = "stimuli_viewer")
+```
+
+By default sorting in the result annotation viewer will be according file names in the system, so if you want to have another default sorting you can specify column names that the result table should be sorted by using the `sorting_columns` argument.
+
 # References

docs/s1/stimuli_viewer.html

@@ -3252,8 +3252,8 @@ <h1 class="title toc-ignore">Sound Viewer</h1>
 <h1></h1>
 <div id="data" class="section level2">
 <h2>data</h2>
-<div id="htmlwidget-6f1c50ef636fa007e550" style="width:100%;height:auto;" class="datatables html-widget"></div>
-<script type="application/json" data-for="htmlwidget-6f1c50ef636fa007e550">{"x":{"filter":"top","filterHTML":"<tr>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[["tap <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'pic_appear(\"s1_pics/1_s1_æ.png\", \"tap\")'> &#x1f441;<a> <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'sound_play(\"s1_sounds/1_s1_æ.wav\")'> &#x1f442;<a>","tip <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'pic_appear(\"s1_pics/2_s1_ı.png\", \"tip\")'> &#x1f441;<a> <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'sound_play(\"s1_sounds/2_s1_ı.wav\")'> &#x1f442;<a>","top <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'pic_appear(\"s1_pics/3_s1_ɒ.png\", \"top\")'> &#x1f441;<a> <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'sound_play(\"s1_sounds/3_s1_ɒ.wav\")'> &#x1f442;<a>"],["æ","ı","ɒ"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>labels<\/th>\n      <th>X2<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":50,"dom":"tip","order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-7c19380a1ffc7b1a7a15" style="width:100%;height:auto;" class="datatables html-widget"></div>
+<script type="application/json" data-for="htmlwidget-7c19380a1ffc7b1a7a15">{"x":{"filter":"top","filterHTML":"<tr>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[["tap","tip","top"],["æ","ı","ɒ"],["<a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'pic_appear(\"s1_pics/1_s1_æ.png\", \"\")'> &#x1f441;<a> <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'sound_play(\"s1_sounds/1_s1_æ.wav\")'> &#x1f442;<a>","<a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'pic_appear(\"s1_pics/2_s1_ı.png\", \"\")'> &#x1f441;<a> <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'sound_play(\"s1_sounds/2_s1_ı.wav\")'> &#x1f442;<a>","<a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'pic_appear(\"s1_pics/3_s1_ɒ.png\", \"\")'> &#x1f441;<a> <a onmouseover=\"resize(this, '200%')\" onmouseout=\"resize(this, '100%')\" onclick = 'sound_play(\"s1_sounds/3_s1_ɒ.wav\")'> &#x1f442;<a>"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>words<\/th>\n      <th>sounds<\/th>\n      <th>viewer<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":50,"dom":"tip","order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true}},"evals":[],"jsHooks":[]}</script>
 <div id="my_block" class="my_block" onclick="pic_disappear()">
 <span class="close">×</span> <img class="my_img" id="my_img">
 <div id="caption" class="caption">

inst/rmarkdown/templates/annotation_viewer/skeleton/skeleton.Rmd

@@ -3,8 +3,7 @@ title: "Sound Viewer"
 output: html_document
 params:
   data: your_file.csv
-  merge_column: "merge_column"
-  caption_column: "caption_column"
+  captions: "caption_for_pictures"
   about: about.Rmd
 editor_options: 
   chunk_output_type: console
@@ -44,15 +43,12 @@ editor_options:
 ## data
 
 ```{r make_viewer, echo=FALSE, message=FALSE, warning=FALSE}
-df <- read.csv(params$data, stringsAsFactors = FALSE)
-merge <- which(colnames(df) %in% params$merge_column)
-captions <- which(colnames(df) %in% params$caption_column)
+df <- read.csv(tmp1, stringsAsFactors = FALSE)
 
-df[,merge] <- 
-  paste(df[,merge],
-         phonfieldwork::create_image_look_up(img_src = df$pictures,
-                                             img_caption = df[,captions]),
-         phonfieldwork::create_sound_play(snd_src = df$audio))
+df$viewer <- 
+  paste(phonfieldwork::create_image_look_up(img_src = df$pictures,
+                                            img_caption = captions),
+        phonfieldwork::create_sound_play(snd_src = df$audio))
 
 df <- df[, -which(colnames(df) %in% c("audio", "pictures"))]