Merge pull request #3 from npernat/master

update with no-reject parameter

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: plantnet
 Type: Package
 Title: Automated Plant Identification with PlantNet
-Version: 0.1.0
+Version: 1.0.0
 Date: 2019-07-25
-Author: Tom August
+Author: Tom August, Nadja Pernat
 Maintainer: Tom August <tomaug@ceh.ac.uk>
 Description: Using the PlantNet API (https://my.plantnet.org/) this package will assign a plant species name to images.
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.2
 Imports: httr
 Suggests: 
     testthat,

R/buildURL.R

@@ -6,27 +6,30 @@
 #' @param key character, your API key (get from my-api.plantnet.org)
 #' @param imageURL character, the URL path top the image you want to identify
 #' @param organs character, the organ in the image. Must be one of,
-#' leaf, flower, fruit, or bark. Currently this does not effect the result.
+#' auto, leaf, flower, fruit, or bark. Currently this does not effect the result.
 #' You can also use the tags habit (the overall form of the plant), or other,
 #' but you can only have an image labelled as one of these if you also have
-#' an image labelled as one of the primay organs (i.e. leaf, flower, fruit, bark).
+#' an image labelled as one of the primary organs (i.e. auto, leaf, flower, fruit, bark).
 #' @param lang can be one of 'en' (English), 'fr' (French), 'de' (German)
+#' @param no_reject character, can be one of 'true' or 'false' (default), 
+#' if 'true' 'no results' are disabled in case of reject class match
 #' @return The URL required, as a character of length 1
 #' @importFrom utils URLencode
 #' @export
 
-buildURL <- function(key, imageURL, organs = 'leaf', lang = 'en'){
+buildURL <- function(key, imageURL, organs = 'auto', 
+                     lang = 'en', no_reject = 'false'){
 
   if(length(imageURL) != length(organs)){
     stop('imageURL and organs must be the same length')
   }
 
-  if(!all(organs %in% c('flower','leaf','fruit','bark','habit','other'))){
-    stop("The only allowed values of organs are 'flower','leaf','fruit','bark','habit','other'")
+  if(!all(organs %in% c('auto', 'flower','leaf','fruit','bark','habit','other'))){
+    stop("The only allowed values of organs are 'auto', 'flower','leaf','fruit','bark','habit','other'")
   }
 
-  if(!any(organs %in% c('flower','leaf','fruit','bark'))){
-    stop("At leaset one image must be tagged as 'flower','leaf','fruit','bark'")
+  if(!any(organs %in% c('auto', 'flower','leaf','fruit','bark'))){
+    stop("At leaset one image must be tagged as 'auto', 'flower','leaf','fruit','bark'")
   }
 
   if(length(lang) > 1){
@@ -36,13 +39,20 @@ buildURL <- function(key, imageURL, organs = 'leaf', lang = 'en'){
   if(!lang %in% c('en', 'fr', 'de')){
     stop("lang must be one of 'en', 'fr', 'de'")
   }
-
+
+  if(!no_reject %in% c('true','false'))
+    stop("no_reject must be one of 'true' or 'false'(default)")
+
   URLencoded <- sapply(imageURL, FUN = URLencode, reserved = TRUE, repeated = TRUE)
 
-  paste0("https://my-api.plantnet.org/v1/identify/all?",
-         "images=", paste(URLencoded, collapse = "&images="),
-         "&organs=", paste(organs, collapse = "&organs="),
-         "&lang=", lang,
-         "&api-key=", key)
+  url_string <- paste0("https://my-api.plantnet.org/v2/identify/all?",
+                       "images=", paste(URLencoded, collapse = "&images="),
+                       "&organs=", paste(organs, collapse = "&organs="),
+                       "&no-reject=", no_reject,
+                       "&lang=", lang,
+                       "&api-key=", key)
+
+  print(url_string)
+  return(url_string)
 
-}
+  }

R/identify.R

@@ -12,16 +12,18 @@
 #' @param simplify logical, if `TRUE` the output will be simplified into a
 #' data.frame
 #' @param organs character, the organ in the image. Must be one of,
-#' leaf, flower, fruit, or bark. Must be the same length as `imageURL`.
+#' auto, leaf, flower, fruit, or bark. Must be the same length as `imageURL`.
 #' You can also use the tags habit (the overall form of the plant), or other,
 #' but you can only have an image labelled as one of these if you also have
-#' an image labelled as one of the primay organs (i.e. leaf, flower, fruit, bark).
+#' an image labelled as one of the primary organs (i.e. auto, leaf, flower, fruit, bark).
 #' @param lang can be one of 'en' (English), 'fr' (French), 'de' (German)
+#' @param no_reject character, can be one of 'true' or 'false' (default), 
+#' if 'true' 'no results' are disabled in case of reject class match
 #' @details The function uses the PlantNet API. To use this service you need
 #' to have registered an account and generated an API key. All this can be
 #' done here: https://my.plantnet.org/.
 #' @return If `simplify` is set to `FALSE` then a list is returned. The
-#' structure of this list can be explored using hte tool at
+#' structure of this list can be explored using the tool at
 #' https://my-api.plantnet.org. If `simplify` is set to `TRUE` (default)
 #' then a data.frame is with three columns for the score, latin name,
 #' and common name. There are as many rows as there are species predictions
@@ -60,12 +62,16 @@
 #'}
 
 identify <- function(key, imageURL, simplify = TRUE,
-                     organs = rep('leaf', length(imageURL)), lang = 'en'){
+                     organs = rep('auto', length(imageURL)), 
+                     lang = 'en', no_reject = 'false'){
 
   if(!is.character(key)) stop('key should be a character')
   if(!is.character(imageURL)) stop('image should be a character')
+  if(!is.character(no_reject)) stop('no_reject should be a character')
+
 
-  URL <- buildURL(key = key, imageURL = imageURL, organs = organs, lang = lang)
+  URL <- buildURL(key = key, imageURL = imageURL, organs = organs, 
+                  lang = lang, no_reject = no_reject)
 
   # Hit the API
   response <- httr::GET(URL)

README.md

@@ -7,7 +7,7 @@
 # PlantNet
 
 ### Developed by Tom August
-last built 2019-07-23
+last built 09/03/2022
 
 The R-package interfaces with the PlantNet image classification API. This API is designed to receive images and return species classifications. You can find out more about the PlantNet project here: https://plantnet.org. To use the API you need to have registered an account and generated an API key. All this can be done here: https://my.plantnet.org/.
 

tests/testthat/testbuildURL.R

@@ -21,7 +21,7 @@ test_that("test warnings and errors", {
                         imageURL = imageURL,
                         organs = 'head',
                         lang = lang),
-               "The only allowed values of organs are 'flower','leaf','fruit','bark','habit','other'")
+               "The only allowed values of organs are 'auto', 'flower','leaf','fruit','bark','habit','other'")
   expect_error(buildURL(key = key,
                         imageURL = imageURL,
                         organs = c('flower', 'flower'),
@@ -31,7 +31,7 @@ test_that("test warnings and errors", {
                         imageURL = imageURL,
                         organs = c('habit'),
                         lang = lang),
-               "At leaset one image must be tagged as 'flower','leaf','fruit','bark'")
+               "At leaset one image must be tagged as 'auto', 'flower','leaf','fruit','bark'")
   expect_error(buildURL(key = key,
                         imageURL = c(imageURL, imageURL),
                         organs = organs,
@@ -46,7 +46,7 @@ test_that("test built URL is as expected", {
                      imageURL = c(imageURL, imageURL),
                      organs = c(organs, organs),
                      lang = lang)
-  expected <- "https://my-api.plantnet.org/v1/identify/all?images=IMAGEURL&images=IMAGEURL&organs=flower&organs=flower&lang=en&api-key=MYKEY"
+  expected <- "https://my-api.plantnet.org/v2/identify/all?images=IMAGEURL&images=IMAGEURL&organs=flower&organs=flower&no-reject=false&lang=en&api-key=MYKEY"
   expect_equal(tested, expected)
 
 })