huge update: add some new function and fixed some old ones

Author: haozhu233

.DS_Store

@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^tests$
+^docs$
+^.github$

.Rbuildignore

@@ -1,12 +1,23 @@
 Package: arduino
 Type: Package
-Title: What the Package Does in One 'Title Case' Line
-Version: 1.0
-Date: 2018-02-20
-Author: Your Name
-Maintainer: Your Name <[email protected]>
-Description: One paragraph description of what the package does as one or more full sentences.
+Title: Simple Library for Reading Serial Ports
+Version: 0.1
+Authors@R: c(
+    person('Hao', 'Zhu', email = '[email protected]', role = c('aut', 'cre'),
+    comment = c(ORCID = '0000-0002-3386-6076')),
+    person('Tod', 'Kurt', role = 'aut')
+    )
+Description: Simple C based library for easily reading serial ports. It works 
+    on any POSIX-compatible system, including Mac OS and Linux. 
 License: GPL (>= 2)
-Imports: Rcpp (>= 0.12.15)
+Imports: 
+    Rcpp (>= 0.12.15),
+    progress,
+    glue,
+    shiny,
+    plotly
 LinkingTo: Rcpp
-RoxygenNote: 6.0.1
+VignetteBuilder: knitr
+Encoding: UTF-8
+RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)

DESCRIPTION

@@ -1,9 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
 export(ar_close)
+export(ar_collect)
 export(ar_flush)
+export(ar_flush_hard)
 export(ar_init)
+export(ar_monitor)
+export(ar_plotter)
 export(ar_read)
-export(ar_stream)
+export(ar_sep_comma)
+import(progress)
+import(shiny)
 importFrom(Rcpp,sourceCpp)
+importFrom(glue,glue)
+importFrom(plotly,"%>%")
+importFrom(plotly,add_trace)
+importFrom(plotly,plot_ly)
+importFrom(plotly,plotlyOutput)
+importFrom(plotly,plotlyProxy)
+importFrom(plotly,plotlyProxyInvoke)
+importFrom(plotly,renderPlotly)
 useDynLib(arduino)

NAMESPACE

@@ -27,6 +27,21 @@ ar_init <- function(serialport, baud = 9600L) {
     .Call('_arduino_ar_init', PACKAGE = 'arduino', serialport, baud)
 }
 
+#' Check if a file descriptor is still open
+#' 
+#' @description This function checks whether a stored file descriptor is still
+#' open.
+#' 
+#' @param fd File descriptor returned by `ar_init()`. Should be an integer.
+#' @examples
+#' \dontrun{
+#' con <- ar_init("/dev/cu.SLAB_USBtoUART") 
+#' ar_is_open(con)
+#' }
+ar_is_open <- function(fd) {
+    .Call('_arduino_ar_is_open', PACKAGE = 'arduino', fd)
+}
+
 #' Close Connection to a serial port
 #' 
 #' @description This function closes the connection opened by `ar_init()`.

R/RcppExports.R

@@ -0,0 +1,22 @@
+#' Stream serial port data into R console
+#' 
+#' @description This function wraps around `ar_read()` and will read serial
+#' port data into R console until user stop it.
+#' 
+#' @param size Size
+#' @inheritParams ar_monitor
+#' 
+#' @export
+ar_collect <- function(fd, size = 100, flush_time = 0.5,
+                       eolchar = "\n", buf_max = 256, timeout = 5000) {
+  message("Flushing Port...")
+  ar_flush_hard(fd, flush_time = flush_time)
+  out <- character()
+  pb <- progress::progress_bar$new(total = size)
+  for (i in seq(size)) {
+    out[i] <- ar_read(fd, eolchar, buf_max, timeout)
+    pb$tick()
+  }
+  message("Done")
+  return(out)
+}

R/ar_collect.R

@@ -0,0 +1,18 @@
+#' Flush serial port in the hard way
+#' 
+#' @description In theory `ar_flush` should work but it didn't work out for me 
+#' at least. So I recreated this `flush` feature in R, which basically let the 
+#' data flow for a short time (default 50 ms). The selection of this value 
+#' depends of many factors including the USB port and the size of data so please
+#' pick this value wisely. 
+#' 
+#' @inheritParams ar_monitor
+#' @param include_c_flush T/F for whether to call ar_flush at the beginning
+#' @export
+ar_flush_hard <- function(fd, flush_time = 0.05, include_c_flush = TRUE) {
+  if (include_c_flush)   ar_flush(fd)
+  start_time <- as.numeric(Sys.time())
+  while ((as.numeric(Sys.time()) - start_time) < flush_time) {
+    ar_read(fd)
+  }
+}

R/ar_flush_hard.R

@@ -0,0 +1,15 @@
+#' Stream serial port data into R console
+#' 
+#' @description This function wraps around `ar_read()` and will read serial
+#' port data into R console until user stop it.
+#' @param flush_time Time to flush buffed results in the serial channel
+#' 
+#' @inheritParams ar_read
+#' 
+#' @export
+ar_monitor <- function(fd, flush_time = 0.5, 
+                      eolchar = "\n", buf_max = 256, timeout = 5000) {
+  message("Flushing Port...")
+  ar_flush_hard(fd, flush_time)
+  repeat (cat(ar_read(fd, eolchar, buf_max, timeout)))
+}

R/ar_monitor.R

@@ -0,0 +1,134 @@
+#' Arduino Plotter
+#' 
+#' @param names Labels for variables 
+#' @param sep_fun A function that separates the inline string into different 
+#' variables. By default, it is `ar_sep_comma`, which splits the string by 
+#' comma. You can easily write your own function, which can even do additional
+#' calculation. 
+#' @param reduce_freq T/F. It might be the case that plotly streaming API can't 
+#' process frequency > 25 Hz (40ms delay time) or it might be the case that 
+#' my computer doesn't have enough power. Anyway, I set this option here to
+#' add 40ms delay time to reduce the sampling frequency. 
+#' @inheritParams ar_monitor
+#' 
+#' @export
+ar_plotter <- function(fd, names = NULL, sep_fun = ar_sep_comma,  
+                       reduce_freq = TRUE, flush_time = 0.05,
+                       eolchar = "\n", buf_max = 256, timeout = 5000) {
+  shiny::runApp(
+    ar_app(con = fd, names = names, sep_fun = sep_fun, 
+           flush_time = flush_time, reduce_freq = reduce_freq,
+           eolchar = eolchar, buf_max = buf_max, timeout = timeout), 
+    launch.browser = rstudioapi::viewer
+  )
+}
+
+# con <- ar_init("/dev/cu.SLAB_USBtoUART", baud = 57600)
+
+ar_app <- function(con, names = NULL, sep_fun = ar_sep_comma, 
+                   flush_time = 0.05, reduce_freq = TRUE,
+                   eolchar = "\n", buf_max = 256, timeout = 5000) {
+  message("Flushing Port...")
+  ar_flush_hard(con, flush_time)
+  first_dot <- ar_read(con, eolchar, buf_max, timeout)
+  if (first_dot == "") {
+    stop("Your connection is probably dead. Please use ar_init and start",
+         " a new connection")
+  }
+  first_dot <- sep_fun(first_dot)
+  signal_vars <- seq(length(first_dot))
+  
+  if (is.null(names)) {
+    names(signal_vars) <- paste("Var", signal_vars)
+    names(first_dot) <- paste("Var", signal_vars)
+  } else {
+    if (length(names) != length(first_dot)) {
+      stop(
+        "The amount of names provided is different from the amount of values."
+      )
+    }
+    names(signal_vars) <- names
+    names(first_dot) <- names
+  }
+  
+  save_file_default <- glue("arduino_{format(Sys.time(), '%Y%m%d_%H%M%S')}.csv")
+  
+  ui <- fluidPage(
+    br(),
+    actionButton("power", label = NULL, icon = icon("power-off", "text-danger"),
+                 width = NULL, 
+                 style = "border-radius: 25px; position: absolute; top: 15px; right: 15px;z-index: 20;"),
+    inline_widget(actionButton("start", icon = icon("play"), 
+                               label = NULL, width = "100%"), "50px"),
+    inline_widget(actionButton("reset", icon = icon("undo"), 
+                               label = NULL, width = "100%"), "50px"),
+    inline_widget(h5("Vars:"), "35px"),
+    inline_widget(selectInput(
+      "y_var", label = NULL, choices = signal_vars, 
+      selected = signal_vars, multiple = T
+    ), "calc(95% - 180px);z-index: 15;"),
+    plotlyOutput("plot", height = "250px"),
+    inline_widget(checkboxInput("save", strong("Save to file?")), "30%"),
+    inline_widget(textInput("file", NULL, save_file_default), "65%")
+  )
+  
+  server <- function(input, output, session) {
+    rv <- reactiveValues()
+    rv$state <- 0
+
+    # first_xy <- separateXY(first_dot)
+    
+    output$plot <- renderPlotly({
+      req(input$y_var)
+      input$reset
+      p <- plot_ly(type = 'scatter', mode = 'lines', line = list(width = 3))
+      for (y_i in sort(as.integer(input$y_var))) {
+        p <- add_trace(p, y = first_dot[y_i], name = names(first_dot[y_i]))
+      }
+      return(p)
+    })
+    
+    observeEvent(input$start, {
+      rv$state <- 1 - rv$state
+      start_icon <- icon(c("play", "pause")[rv$state + 1])
+      updateActionButton(session, "start", icon = start_icon)
+      ar_flush_hard(con, flush_time)
+    })
+    
+    observeEvent(input$reset, {
+      rv$state <- 0
+      updateActionButton(session, "start", icon = icon("play"))
+      ar_flush_hard(con, flush_time)
+    })
+    
+    observeEvent(input$save, {
+      if (!file.exists(input$file)) {
+        file.create(input$file)
+        cat(csv_newline(names(first_dot)), file = input$file)
+      }
+    }, ignoreInit = TRUE)
+    
+    observe({
+      invalidateLater(1)
+      if (rv$state) {
+        ar_flush_hard(con, 0.04, FALSE)
+        realtime <- sep_fun(ar_read(con, eolchar, buf_max, timeout))
+        if (input$save) {
+          cat(csv_newline(realtime), file = input$file, append = TRUE)
+        }
+        realtime_y <- lapply(realtime[sort(as.integer(input$y_var))], list)
+        realtime_list <- list(y = realtime_y)
+        to_traces <- as.list(seq(length(input$y_var)))
+        plotlyProxy("plot", session) %>%
+          plotlyProxyInvoke("extendTraces", realtime_list, to_traces)
+      }
+    })
+    
+    observeEvent(input$power, {
+      invisible(stopApp())
+    })
+  }
+  
+  shinyApp(ui, server)
+}
+

R/ar_plotter.R

@@ -0,0 +1,16 @@
+#' Split string by special symbols
+#' 
+#' @description This function determines how the plotter extracts numbers from
+#' the readings. By default, it trims of the "new line" symbol at the end of 
+#' the row and split the string by special symbols (if you have used 
+#' `tidyr::separate`, they are the same). You can write your own function if you
+#' need special processing.
+#' 
+#' @param x Arduino Reading. Usually a string and needs to be chopped and 
+#' converted to numbers. 
+#' 
+#' @export
+ar_sep_comma <- function(x) {
+  x <- sub("\r\n$", "", x)
+  return(as.numeric(strsplit(x, ",")[[1]]))
+}

R/ar_sep.R

@@ -6,4 +6,9 @@
 #' @keywords package
 #' @useDynLib arduino
 #' @importFrom Rcpp sourceCpp
+#' @import progress
+#' @importFrom glue glue
+#' @import shiny
+#' @importFrom plotly plot_ly add_trace renderPlotly plotlyProxy 
+#' plotlyProxyInvoke plotlyOutput %>%
 NULL

R/ar_stream.R

@@ -0,0 +1,9 @@
+inline_widget <- function(x, width = "100px") {
+  shiny::div(
+    style = glue("display: inline-block;vertical-align:top; width: {width};"),
+    x)
+}
+
+csv_newline <- function(x) {
+  paste0(paste(x, collapse = ","), "\r\n")
+}