Annotate images with areas of interest

Description

Functionality to label areas in images

Usage

annotorious(
  inputId = "annotations",
  src,
  tags = c(),
  type = c("annotorious", "openseadragon", "openseadragon-notoolbar"),
  quickselector = TRUE,
  width = NULL,
  height = NULL,
  elementId = NULL,
  dependencies = NULL
)

Arguments

Value

An object of class htmlwidget as returned by createWidget

See Also

annotorious-shiny

Shiny bindings for annotorious

Description

Output and render functions for using annotorious within Shiny applications.

Usage

annotoriousOutput(outputId, width = "100%", height = "400px")

renderAnnotorious(expr, env = parent.frame(), quoted = FALSE)

openseadragonOutput(outputId, width = "100%", height = "400px")

renderOpenSeaDragon(expr, env = parent.frame(), quoted = FALSE)

openseadragonOutputNoToolbar(outputId, width = "100%", height = "400px")

renderOpenSeaDragonNoToolbar(expr, env = parent.frame(), quoted = FALSE)

Arguments

Value

An output element for use in a Shiny user interface.
Consisting of a toggle button to switch between rectangle / polygon mode and the html-widget (id: outputId) which contains an image (id: outputId-img)

Examples

if(interactive() && require(shiny)){
##
## Annotorious using OpenSeaDragon, allowing to zoom in,
## to select an area, press shift and next select the area
##
library(shiny)
library(recogito)
urls <- paste("https://upload.wikimedia.org/",
              c("wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
                "wikipedia/commons/6/64/Cat_and_dog_standoff_%283926784260%29.jpg"),
              sep = "")
ui <- fluidPage(actionButton(inputId = "ui_switch", label = "Sample image"),
                openseadragonOutput(outputId = "anno"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  current_image <- reactive({
    input$ui_switch
    list(url = sample(urls, size = 1))
  })
  output$anno <- renderOpenSeaDragon({
    info <- current_image()
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = info$url, type = "openseadragon")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

##
## Annotorious using OpenSeaDragon, allowing to zoom in, no selection possibilities
## showing how to load a local image
##
library(shiny)
library(recogito)
url <- system.file(package = "recogito", "examples", "Pamphlet_dutch_tulipomania_1637.jpg")
addResourcePath(prefix = "img", directoryPath = dirname(url))
ui <- fluidPage(openseadragonOutputNoToolbar(outputId = "anno", width = "100%", height = "250px"))
server <- function(input, output) {
  output$anno <- renderOpenSeaDragonNoToolbar({
    annotorious("annotations", src = sprintf("img/%s", basename(url)),
                 type = "openseadragon-notoolbar")
  })
}
shinyApp(ui, server)

##
## Annotorious without openseadragon
##
library(shiny)
library(recogito)
url <- paste("https://upload.wikimedia.org/",
             "wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
             sep = "")

ui <- fluidPage(annotoriousOutput(outputId = "anno", height = "600px"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$anno <- renderAnnotorious({
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = url, type = "annotorious")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

##
## Annotorious, without openseadragon changing the url
##
library(shiny)
library(recogito)
urls <- paste("https://upload.wikimedia.org/",
              c("wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
                "wikipedia/commons/6/64/Cat_and_dog_standoff_%283926784260%29.jpg"),
              sep = "")

ui <- fluidPage(actionButton(inputId = "ui_switch", label = "Sample image"),
                annotoriousOutput(outputId = "anno", height = "600px"),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  current_image <- reactive({
    input$ui_switch
    list(url = sample(urls, size = 1))
  })
  output$anno <- renderAnnotorious({
    info <- current_image()
    annotorious("annotations", tags = c("IMAGE", "TEXT"), src = info$url, type = "annotorious")
  })
  output$annotation_result <- renderPrint({
    read_annotorious(input$annotations)
  })
}
shinyApp(ui, server)

}

Crop annotations to a bounding box

Description

Crop annotations to a bounding box

Usage

ocv_crop_annotorious(data, bbox)

Arguments

Value

data where column polygon and the rectangle information in x, y, width, height is limited to the provided bounding box

Examples

library(opencv)
data(openseadragon_areas)

url  <- attr(openseadragon_areas, "src")
img  <- ocv_read(url)
bbox <- ocv_info(img)
bbox <- c(xmin = 0, ymin = 0, xmax = bbox$width - 1, ymax = bbox$height - 1)
x    <- ocv_crop_annotorious(data = openseadragon_areas)
x    <- ocv_crop_annotorious(data = openseadragon_areas, bbox = bbox)

img
area <- x[2, ]
ocv_polygon(img, pts = area$polygon[[1]], crop = TRUE)
area <- x[1, ]
ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)
area <- x[3, ]
ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)

Extract the areas of interests of an image

Description

Extract the areas of interests of an image

Usage

ocv_read_annotorious(data, image)

Arguments

Value

a list of ocv images with the extracted areas of interest

Examples

library(opencv)
library(magick)
data(openseadragon_areas)

url  <- attr(openseadragon_areas, "src")
img  <- ocv_read(url)

areas <- ocv_read_annotorious(data = openseadragon_areas, image = img)
areas[[1]]
areas[[2]]
img <- lapply(areas, FUN = function(x) image_read(ocv_bitmap(x)))
img <- do.call(c, img)
img <- image_append(img, stack = FALSE)
image_resize(img, "x200")

A dataset of annotations using openseadragon

Description

A dataset of annotations using openseadragon

Examples

data(openseadragon_areas)
openseadragon_areas
attr(openseadragon_areas, "src")

Parse annotorious annotations

Description

Parse annotorious annotations

Usage

read_annotorious(x, src = character())

Arguments

Value

a data.frame with annotations with columns: id, type, label, comment, x, y, width, height, polygon and an attribute src with the provided src

Examples

url <- paste("https://upload.wikimedia.org/",
             "wikipedia/commons/a/a0/Pamphlet_dutch_tulipomania_1637.jpg",
             sep = "")
url <- system.file(package = "recogito", "examples", "Pamphlet_dutch_tulipomania_1637.jpg")
x <- '[
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"IMAGE","purpose":"tagging"}],
"target":{"selector":{
  "type":"FragmentSelector",
  "conformsTo":"http://www.w3.org/TR/media-frags/",
  "value":"xywh=pixel:41,249.5234375,371,245"}},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#58f0096c-4675-4ea8-9f38-bffce0887ab8"
},
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"TEXT","purpose":"tagging"}],
"target":{"selector":{
  "type":"FragmentSelector",
  "conformsTo":"http://www.w3.org/TR/media-frags/",
  "value":"xywh=pixel:46,5.523437976837158,371,239.99999952316284"}},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#50035dda-c62b-4f30-bf95-1879d60288a5"}]'
anno <- read_annotorious(x, src = url)
anno


library(magick)
img  <- image_read(url)
area <- head(anno, n = 1)
image_crop(img, geometry_area(x = area$x, y = area$y,
                              width = area$width, height = area$height))
area <- subset(anno, type == "RECTANGLE")
allrectangles <- Map(
  x      = area$x,
  y      = area$y,
  width  = area$width,
  height = area$height,
  f = function(x, y, width, height){
    image_crop(img, geometry_area(x = x, y = y, width = width, height = height))
})
allrectangles <- do.call(c, allrectangles)
allrectangles



x <- '[
{
  "type":"Annotation",
  "body":[{"type":"TextualBody","value":"IMAGE","purpose":"tagging"}],
  "target":{"selector":{
    "type":"FragmentSelector",
    "conformsTo":"http://www.w3.org/TR/media-frags/",
    "value":"xywh=pixel:43,244.5234375,362,252"
    }},
 "@context":"http://www.w3.org/ns/anno.jsonld",
 "id":"#4eaa8788-0c7e-42d2-b004-4d66b57018a1"},
{
  "type":"Annotation",
  "body":[{"type":"TextualBody","value":"TEXT","purpose":"tagging"}],
  "target":{"selector":{
    "type":"SvgSelector",
    "value":"<svg>
    <polygon points=\\\"75,4 75,58 32,95 32,194 410,195 391,70 373,63 368,3 222,1.5\\\">
    </polygon></svg>"}},
  "@context":"http://www.w3.org/ns/anno.jsonld",
  "id":"#8bf0a557-c847-4a07-91bc-68a98c499615"}]'
x    <- gsub(x, pattern = "\n", replacement = "")
anno <- read_annotorious(x, src = url)
anno
anno$polygon


library(opencv)
img  <- ocv_read(url)
area <- subset(anno, type == "POLYGON")
ocv_polygon(img, pts = area$polygon[[1]])

Parse recogito annotations

Description

Parse recogito annotations

Usage

read_recogito(x, text = character())

Arguments

Value

a data.frame with annotations with columns: id, type, label, chunk_text, chunk_start, chunk_end, relation_from, relation_to, chunk_comment and an attribute text with the provided text

Examples

x <- '[
{
"type":"Annotation",
"body":[
   {"type":"TextualBody","value":"sdfsd","purpose":"commenting"},
   {"type":"TextualBody","value":"Person","purpose":"tagging"}],
"target":{"selector":[
  {"type":"TextQuoteSelector","exact":"ngenious hero"},
  {"type":"TextPositionSelector","start":42,"end":55}]},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#a4ea53d4-69f3-4392-a3dd-cbb7e9ad50cb"
},
{
"type":"Annotation",
"body":[{"type":"TextualBody","value":"Person","purpose":"tagging"},
  {"type":"TextualBody","value":"Location","purpose":"tagging"}],
"target":{"selector":[{"type":"TextQuoteSelector","exact":"far and"},
  {"type":"TextPositionSelector","start":70,"end":77}]},
"@context":"http://www.w3.org/ns/anno.jsonld",
"id":"#d7050196-2537-42bf-9d1b-a3f9e4c9fbc6"
}
]'
read_recogito(x)

Annotate text with tags and relations

Description

Functionality to tag text with entities and relations between these

Usage

recogito(
  inputId = "annotations",
  text,
  type = c("relations", "tags"),
  tags = c("Location", "Person", "Place", "Other"),
  mode = c("html", "pre"),
  annotations = "{}",
  width = NULL,
  height = NULL,
  elementId = NULL,
  dependencies = NULL
)

Arguments

Value

An object of class htmlwidget as returned by createWidget

See Also

recogito-shiny

Examples

txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
x   <- recogito(inputId = "annotations", txt)
x
x   <- recogito(inputId = "annotations", txt, type = "tags",
                tags = c("LOCATION", "TIME", "PERSON"))
x
txt <- "Lorem ipsum dolor sit amet consectetur adipiscing elit Quisque tellus urna
  placerat in tortor ac imperdiet sollicitudin mi Integer vel dolor mollis feugiat
  sem eu porttitor elit Sed aliquam urna sed placerat euismod In risus sem ornare
  nec malesuada eu ornare quis dui Nunc finibus fermentum sollicitudin Fusce vel
  imperdiet mi ac faucibus leo Cras massa massa ultricies et justo vitae molestie
  auctor turpis Vestibulum euismod porta risus euismod dapibus Nullam facilisis
  ipsum sed est tempor et aliquam sapien auctor Aliquam velit ligula convallis a
  dui id varius bibendum quam Cras malesuada nec justo sed
  aliquet Fusce urna magna malesuada"
x   <- recogito(inputId = "annotations", txt)
x
x   <- recogito(inputId = "annotations", txt, type = "tags",
                tags = c("LOCATION", "TIME", "PERSON", "OTHER"))
x

##
## Color the tags by specifying CSS - they should have .tag-{TAGLABEL}
##
library(htmltools)
cat(readLines(system.file(package = "recogito", "examples", "example.css")), sep = "\n")
tagsetcss <- htmlDependency(name = "mytagset", version = "1.0",
                            src = system.file(package = "recogito", "examples"),
                            stylesheet = "example.css")
x   <- recogito(inputId = "annotations", txt,
                tags = c("LOCATION", "TIME", "PERSON", "OTHER"),
                dependencies = tagsetcss)
x

Shiny bindings for recogito

Description

Output and render functions for using recogito within Shiny applications and interactive Rmd documents.

Usage

recogitoOutput(outputId, width = "100%", height = "400px")

renderRecogito(expr, env = parent.frame(), quoted = FALSE)

recogitotagsonlyOutput(outputId, width = "100%", height = "400px")

renderRecogitotagsonly(expr, env = parent.frame(), quoted = FALSE)

Arguments

Value

An output element for use in a Shiny user interface.
Consisting of a div of class plaintext which contains an optional toggle button to switch between annotation / relation mode (id: outputId-toggle) and the html-widget (id: outputId)

Examples

if(interactive() && require(shiny)){

##
## Tagging only, no relations
##
library(shiny)
library(recogito)
txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
ui <- fluidPage(tags$h3("Provide some text to annotate"),
                textAreaInput(inputId = "ui_text", label = "Provide some text", value = txt),
                tags$h3("Annotation area"),
                recogitotagsonlyOutput(outputId = "annotation_text"),
                tags$hr(),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$annotation_text <- renderRecogitotagsonly({
    recogito("annotations", text = input$ui_text, tags = c("LOCATION", "TIME", "PERSON"))
  })
  output$annotation_result <- renderPrint({
    read_recogito(input$annotations)
  })
}
shinyApp(ui, server)

##
## Tagging and relations
##
library(shiny)
library(recogito)
txt <- "Josh went to the bakery in Brussels.\nWhat an adventure!"
ui <- fluidPage(tags$h3("Provide some text to annotate"),
                textAreaInput(inputId = "ui_text", label = "Provide some text", value = txt),
                tags$h3("Annotation area"),
                recogitoOutput(outputId = "annotation_text"),
                tags$hr(),
                tags$h3("Results"),
                verbatimTextOutput(outputId = "annotation_result"))
server <- function(input, output) {
  output$annotation_text <- renderRecogito({
    recogito("annotations", text = input$ui_text, tags = c("LOCATION", "TIME", "PERSON"))
  })
  output$annotation_result <- renderPrint({
    read_recogito(input$annotations)
  })
}
shinyApp(ui, server)

}

recogitoOutput(outputId = "annotation_text")
recogitotagsonlyOutput(outputId = "annotation_text")