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app.R
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app.R
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# ============================================================
# Script Author: [Spaska Forteva]
# Created On: 2021-06-10c
# ============================================================
# ============================================================
# Main Shiny App Distribution Digitization
# ============================================================
#
#
# ============================================================
# # Tab 1 Config Dialog for Book Distribution Digitization
# ============================================================
# This configuration dialog is designed to gather essential
# information about a book before the digitization process.
# Users can input details to create a comprehensive summary
# for proper documentation. The dialog includes the following fields:
#
# 1. Title: Enter the title of the book.
# 2. Author: Provide the name of the book's author.
# 3. Publication Year: Specify the year the book was published.
# 4. Data Input Directory: Specify the directory where the raw
# data for the book digitization is stored.
# 5. Data Output Directory: Specify the directory where the
# digitized output for the book will be stored.
# 6. Number of Book Sites per One Print: Define the number of
# book pages to be included in one printed output.
# 7. All Printed Pages: Indicate whether all pages of the book
# will be included in the digitization process.
# 8. Site Number Position: Specify the placement of the site
# number on each printed page (e.g., top-right, bottom-left).
# 9. Image Format of the Scanned Sites: Choose the format
# (e.g., JPEG, PNG) for the digitized pages.
# 10. Page Color: Indicate the color of the book pages
# (e.g., black and white, color).
#
# This dialog aims to streamline the digitization process by
# ensuring that all relevant information is captured accurately.
# Once the user completes the form, the gathered details can
# be used for cataloging and organizing the digital version of
# the book, preserving its content for future reference.
# ============================================================
library(shiny)
library(shinydashboard)
if(!require(magick)){
install.packages("magick", dependencies = T)
library(magick)
}
if(!require(grid)){
install.packages("grid", dependencies = T)
library(grid)
}
if(!require(rdrop2)){
install.packages("rdrop2", dependencies = T)
library(rdrop2)
}
if(!require(shiny)){
install.packages("shiny",dependencies = T)
library(shiny)
}
if(!require(shinyFiles)){
install.packages("shinyFiles",dependencies = T)
library(shinyFiles)
}
if(!require(reticulate)){
install.packages("reticulate",dependencies = T)
library(reticulate)
}
library(shinyalert)
library(reticulate)
library(tesseract)
if(!require(leaflet)){
install.packages("leaflet",dependencies = T)
library(leaflet)
}
if(!require(raster)){
install.packages("raster",dependencies = T)
library(raster)
}
library(sf)
# Global variables
processEventNumber = 0
# Input variables
# host
options(shiny.host = '127.0.0.1')
# port
options(shiny.port = 8888)
# Change the max uploaf size
options(shiny.maxRequestSize=100*1024^2)
tempImage="temp.png"
scale =20
rescale= (100/scale)
workingDir <- getwd()
print("Working directory 1:")
print(workingDir)
outDir <- ""
inputDir = paste0(workingDir,"/data/input/")
#read config fields from config.csv in .../distribution_digitizer/config directory
fileFullPath = (paste0(workingDir,'/config/config.csv'))
if (file.exists(fileFullPath)){
config <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
if (file.exists(config$dataOutputDir)) {
outDir <- config$dataOutputDir
}
fileFullPath = (paste0(workingDir,'/config/configStartDialog.csv'))
if (file.exists(fileFullPath)){
configStartDialog <- read.csv(fileFullPath, header = TRUE, sep = ';')
} else{
stop("The file configStartDialog.csv was not found, please create them and start the app")
}
# read the shiny text fields
#1 shinyfields_create_templates.csv
fileFullPath = (paste0(workingDir,'/config/shinyfields_create_templates.csv'))
if (file.exists(fileFullPath)){
shinyfields1 <- read.csv(fileFullPath, header = TRUE, sep = ';')
} else{
stop("file shinyfields_create_templates.csv not found, please create them and start the app")
}
#2 shinyfields_detect_maps.csv
fileFullPath = (paste0(workingDir,'/config/shinyfields_detect_maps.csv'))
if (file.exists(fileFullPath)){
shinyfields2 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
#3 shinyfields_detect_points.csv
fileFullPath = (paste0(workingDir,'/config/shinyfields_detect_points.csv'))
if (file.exists(fileFullPath)){
shinyfields3 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
#4 shinyfields_detect_points_using_filtering
fileFullPath = (paste0(workingDir,'/config/shinyfields_detect_points_using_filtering.csv'))
if (file.exists(fileFullPath)){
shinyfields4 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
#4.1 shinyfields_detect_points_using_circle_detection
fileFullPath = (paste0(workingDir,'/config/shinyfields_detect_points_using_circle_detection.csv'))
if (file.exists(fileFullPath)){
shinyfields4.1 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
#5 shinyfields_masking
fileFullPath = (paste0(workingDir,'/config/shinyfields_masking.csv'))
if (file.exists(fileFullPath)){
shinyfields5 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
#5.1 shinyfields_mask_centroids
fileFullPath = (paste0(workingDir,'/config/shinyfields_mask_centroids.csv'))
if (file.exists(fileFullPath)){
shinyfields5.1 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
#6 shinyfields_georeferensing
fileFullPath = (paste0(workingDir,'/config/shinyfields_georeferensing.csv'))
if (file.exists(fileFullPath)){
shinyfields6 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
#7 shinyfields_polygonize
fileFullPath = (paste0(workingDir,'/config/shinyfields_polygonize.csv'))
if (file.exists(fileFullPath)){
shinyfields7 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
# 8 shinyfields_georef_coords_from_csv_file
fileFullPath = (paste0(workingDir,'/config/shinyfields_georef_coords_from_csv_file.csv'))
if (file.exists(fileFullPath)){
shinyfields8 <- read.csv(fileFullPath,header = TRUE, sep = ';')
} else{
stop(paste0("file:", fileFullPath, "not found, please create them and start the app"))
}
header <- dashboardHeader(
tags$li(
class = "dropdown",
tags$style(HTML("
.navbar-custom-menu{float:left !important;}
.sidebar-menu{display:flex;align-items:baseline;}
/* layout of the map images */
.shiny-map-image{margin:7px;}
#message {color: red;}
"))
),
tags$li(
class = "dropdown",
sidebarMenu(
id = "tablist",
menuItem("Environment DD", tabName = "tab0"),
menuItem("Create Templates", tabName = "tab1"),
menuItem("Maps Matching", tabName = "tab2"),
menuItem("Points Matching", tabName = "tab3"),
menuItem("Masking", tabName = "tab4" ),
menuItem("Georeferencing", tabName = "tab5" ),
menuItem("Polygonize", tabName = "tab6" ),
menuItem("Spatial View", tabName = "tab7" ),
menuItem("Download", tabName = "tab8" )
)
)
)
body <- dashboardBody(
# Top Information
# Working directory
titlePanel("Distribution Digitizer"),
p(paste0(config$workingDirInformation,": ",workingDir) , style = "color:black"),
tabItems(
# Tab 0 Config Dialog --------------------------------------------------------------------------------------------------------------
tabItem(
tabName = "tab0",
p("In ", strong("Distribution Digitizer"), " 1.0, certain lines are skipped during species name search. Lines containing special characters like",
strong("doublequotes\""), ",",strong(" point ."),", ", strong("colons :"),", or the word", strong(" \"distribution\"")," are excluded.",
br(),
"The tool also searches for species names in the legend map and uses a specified regular expression for matching the year.",
br(),
"If you've added an extra ",strong("additional keyword"),", indicate if it appears before, after, the species name."
),
fluidRow(
# Linke Spalte
column(
width = 6, # Zum Beispiel die Hälfte der Breite des Containers
wellPanel(
h3(strong("General configuration fields", style = "color:black")),
# Title: Provide the name of the book's author.
fluidRow(textInput("title", label = "Please write the title of the book.", value = config$title)),
# Author: Provide the name of the book's author.
fluidRow(textInput("author", label = "Please write the author of the book.", value = config$autor)),
# Publication Year: Specify the year the book was published.
fluidRow(textInput("pYear", label = "Publication Year", value = config$pYear)),
# Data input directory
fluidRow(textInput("dataInputDir", p("Please write the path to the inputs.",br(),
"This input directory should contain two folders:",br(),
"- 'pages', where the scanned images are stored,",br(),
"- 'templates', which includes four additional folders.",br(),br(),
"-- 'maps' ",br(),
"--- 'map_1.tif' use the next Tab: Create Templates to create this",br(),
"-- 'symbols' ",br(),
"--- 'symbol_1.tif' 'symbol_2.tif' use the next Tab: Create Templates to create this",br(),
"-- 'align_ref' ",br(),
"--- 'map_1_align.tif' make one template map properly aligned (Gimp) and save it here.",br(),
"-- 'geopoints'",br(),
"--- 'gcp_point_map1.points' geopoints data for the georeferens. you can user the program QGIS to extract this",br(),br(),
"To ensure proper functionality of the application,",
"please ensure that the provided path adheres to the aforementioned structure."),
value = config$dataInputDir), verbatimTextOutput("message"),),
# Data output directory
fluidRow(textInput("dataOutputDir", label = "Please write the path to the output environment of the distribution digitizer", value = config$dataOutputDir)),
# numberSitesPrint
# format
fluidRow(selectInput("pFormat", label = "Image iiFormat of the Scanned Sites", c("tif" = 1, "png" = 2, "jpg" = 3), selected = config$pFormat)),
# Page color
fluidRow(selectInput("pColor", label = "Page Color", c("black white" = 1, "color" = 2), selected = config$pColor)),
fluidRow(selectInput("numberSitesPrint", label = "Number of Book Sites per One Print", c("One site per scan" = 1, "Two sites per scan" = 2), selected = config$numberSitesPrint)),
)
),
# Rechte Spalte
column(
width = 6, # Zum Beispiel die Hälfte der Breite des Containers
wellPanel(
h3(strong(" Additional specific configuration input fields", style = "color:black")),
# allprintedPages
fluidRow(textInput("allPrintedPages", label = "Please provide the number of scanned images:", value = config$allPrintedPages)),
# site number position
fluidRow(selectInput("sNumberPosition", label = "Please indicate whether the page number is positioned at the top or bottom of the page.", c("top" = 1, "botom" = 2), selected = config$sNumberPosition)),
# Is the term "species name" inclusive of special patterns such as year, parentheses, or symbols?
fluidRow(selectInput("middle", label = "Is the term shifted to the right, indented?", c( "No" = 0, "Yes" = 1 ), selected = config$middle)),
fluidRow(selectInput("regExYear", label = "Does the term contain a regular expression like a year?", c( "No" = 0, "Yes" = 1), selected = config$regExYear)),# keayword to read species data
fluidRow(textInput("keywordReadSpecies", label = "If there is a keyword related to the term 'species', please write it here. Please note that the word should almost always appear a few lines before, after, or directly on the same line as the species term.", value = config$keywordReadSpecies)),
fluidRow(selectInput("keywordBefore", label = "Is the keyword located a few lines before the species name? If so, how many lines?", c("0" = 0, "1" = 1, "2" = 2, "3" = 3), selected = config$keywordBefore)),
fluidRow(selectInput("keywordThen", label = "Is the keyword located a few lines after the species name? If yes, please specify how many.", c("0" = 0, "1" = 1, "2" = 2, "3" = 3), selected = config$keywordThen)),
#Is the keyword a few lines before the species name? If yes, how many?
#Is the keyword exactly on the line with the species name?
#Is the keyword a few lines after the species name? If yes, please specify how many."
# Save button
fluidRow(actionButton("saveConfig", label = "Save", style = "color:#FFFFFF;background:#999999"))
)
)
)
),
# Tab 1 Create Templates #---------------------------------------------------------------------
tabItem(
tabName = "tab1",
actionButton("listMTemplates", label = "List saved map templates"),
actionButton("listSTemplates", label = "List saved symbol templates"),
fluidRow(
column(4,
wellPanel(
h3(strong(shinyfields1$head, style = "color:black")),
p(shinyfields1$inf4, style = "color:black"),
# Choose the file
fileInput("image", label = h5(shinyfields1$lab1), buttonLabel = "Browse...",
placeholder = "No file selected"),
),
wellPanel(
h4(strong(shinyfields1$save_template, style = "color:black")),
# Add number to the file name of the created template file
fluidRow(column(8, numericInput("imgIndexTemplate", label = h5(shinyfields1$lab2),value = 1),
p(strong(paste0(shinyfields1$inf, workingDir, "/data/templates/maps/"), style = "color:black")),
p(shinyfields1$inf1, style = "color:black"),
# Save the template map image with the given index
downloadButton('saveTemplate', 'Save map template', style="color:#FFFFFF;background:#999999"))),
),
wellPanel(
h4(strong(shinyfields1$save_symbol, style = "color:black")),
# Add number to the file name of the created template file
fluidRow(column(8, numericInput("imgIndexTemplate", label = h5(shinyfields1$lab2),value = 1),
p(strong(paste0(shinyfields1$inf2, workingDir, "/data/templates/symbols"), style = "color:black")),
p(shinyfields1$inf3, style = "color:black"),
# Save the template map image with the given index
downloadButton('saveSymbol', 'Save map symbol/Legende', style="color:#FFFFFF;background:#999999")))
)
), # col 4
column(8,
uiOutput('listMapTemplates', style="width:35%;float:left"),
uiOutput('listSymbolTemplates', style="width:35%;float:left"),
plotOutput("plot", click = "plot_click", # Equiv, to click=clickOpts(id="plot_click")
hover = hoverOpts(id = "plot_hover", delayType = "throttle"),
brush = brushOpts(id = "plot_brush")),
)
) # END fluid Row
), # END tabItem 1
# Tab 2 Maps Matching #----------------------------------------------------------------------
tabItem(
tabName = "tab2",
# which site become overview
fluidRow(column(3,textInput("siteNumberMapsMatching", label=shinyfields6$input, value = ''))),
actionButton("listMapsMatching", label = "List maps"),
actionButton("listAlign", label = "List aligned maps"),
actionButton("listCropped", label = "List cropped maps"),
fluidRow(
column(4,
wellPanel(
# submit action button
h3(strong(shinyfields2$head, style = "color:black")),
p(shinyfields2$inf1, style = "color:black"),
fluidRow(column(8, numericInput("threshold_for_TM", label = shinyfields2$threshold, value = 0.2, min = 0, max = 1, step = 0.05))),
p(shinyfields2$inf2, style = "color:black"),
# Start map matching
fluidRow(column(3,actionButton("templateMatching", label = shinyfields2$start1, style="color:#FFFFFF;background:#999999"))),
),
wellPanel(
# maps align
h3(shinyfields2$head_sub, style = "color:black"),
p(shinyfields2$inf3, style = "color:black"),
fluidRow(column(3, actionButton("alignMaps", label = shinyfields2$start2, style="color:#FFFFFF;background:#999999"))),
),
wellPanel(
# maps species
h3(shinyfields2$head_species, style = "color:black"),
p(shinyfields2$inf4, style = "color:black"),
fluidRow(column(3, actionButton("mapReadRpecies", label = shinyfields2$start3, style="color:#FFFFFF;background:#999999"))),
),
wellPanel(
# page species
h3(shinyfields2$head_page_species, style = "color:black"),
p(shinyfields2$inf5, style = "color:black"),
fluidRow(column(3, actionButton("pageReadRpecies", label = shinyfields2$start4, style="color:#FFFFFF;background:#999999"))),
)
), # col 4
column(8,
uiOutput('listMaps', style="width:30%;float:left"),
uiOutput('listAlign', style="width:30%;float:left"),
uiOutput('listCropped', style="width:30%;float:left")
)
) # END fluid Row
), # END tabItem 2
# Tab 3 Points Matching #----------------------------------------------------------------------
tabItem(
tabName = "tab3",
fluidRow(column(3,textInput("siteNumberPointsMatching", label=shinyfields6$input, value = ''))),
actionButton("listMapsMatching2", label = "List maps"),
actionButton("listPointsM", label = "List points matching"),
actionButton("listPointsF", label = "List points filterng"),
actionButton("listPointsCD", label = "List points circle detection"),
fluidRow(
column(4,
wellPanel(
h3(strong(shinyfields3$head, style = "color:black")),
p(shinyfields3$inf1, style = "color:black"),
p(shinyfields3$inf2, style = "color:black"),
),
wellPanel(
# ----------------------------------------# 3.1 Points detection Using template FILE=shinyfields_detect_points #---------------------------------------------------------------------
h4(shinyfields3$head_sub, style = "color:black"),
p(shinyfields3$inf3, style = "color:black"),
# Threshold for point matching
fluidRow(column(8,numericInput("threshold_for_PM", label = shinyfields3$threshold, value = 0.87, min = 0, max = 1, step = 0.05))),
p(shinyfields3$inf4, style = "color:black"),
fluidRow(column(3, actionButton("pointMatching", label = shinyfields3$lab, style="color:#FFFFFF;background:#999999"))),
),
wellPanel(
# ----------------------------------------# 3.2 Points detection Using filtering FILE=shinyfields_detect_points_using_filtering #---------------------------------------------------
h4(shinyfields4$head, style = "color:black"),
fluidRow(column(8,numericInput("filterK", label = shinyfields4$lab1, value = 5))),#, width = NULL, placeholder = NULL)
p(shinyfields4$inf1, style = "color:black"),
fluidRow(column(8,numericInput("filterG", label = shinyfields4$lab2, value = 9))),#, width = NULL, placeholder = NULL)
p(shinyfields4$inf2, style = "color:black"),
fluidRow(column(3, actionButton("pointFiltering", label = shinyfields4$lab3, style="color:#FFFFFF;background:#999999"))),
),
wellPanel(
# ----------------------------------------# 3.3 Points detection Using circle detection FILE=shinyfields_detect_points_using_circle_detection #------------------------------------
h4(shinyfields4.1$head, style = "color:black"),
fluidRow(column(8,numericInput("Gaussian", label = shinyfields4.1$lab1, value = 5, min = 0))),
p(shinyfields4.1$inf1, style = "color:black"),
fluidRow(column(8,numericInput("minDist", label = shinyfields4.1$lab2, value = 1, min = 0))),
p(shinyfields4.1$inf2, style = "color:black"),
fluidRow(column(8,numericInput("thresholdEdge", label = shinyfields4.1$lab3, value = 100, min = 0))),
p(shinyfields4.1$inf3, style = "color:black"),
fluidRow(column(8,numericInput("thresholdCircles", label = shinyfields4.1$lab4, value = 21, min = 0))),
p(shinyfields4.1$inf4, style = "color:black"),
fluidRow(column(8,numericInput("minRadius", label = shinyfields4.1$lab5, value = 3, min = 0))),
p(shinyfields4.1$inf5, style = "color:black"),
fluidRow(column(8,numericInput("maxRadius", label = shinyfields4.1$lab6, value = 12, min = 0))),
p(shinyfields4.1$inf6, style = "color:black"),
p(shinyfields4.1$inf7, style = "color:black"),
fluidRow(column(3, actionButton("pointCircleDetection", label = shinyfields4.1$lab7, style="color:#FFFFFF;background:#999999"))),
)
), # col 4
column(8,
uiOutput('listMapsMatching2', style="width:25%;float:left"),
uiOutput('listPM', style="width:25%;float:left"),
uiOutput('listPF', style="width:25%;float:left"),
uiOutput('listPCD', style="width:25%;float:left")
)
) # END fluid Row
), # END tabItem 3
# Tab 4 Masking #----------------------------------------------------------------------
tabItem(
tabName = "tab4",
fluidRow(column(3,textInput("siteNumberMasks", label=shinyfields6$input, value = ''))),
actionButton("listMasks", label = "List masks"),
actionButton("listMasksB", label = "List black masks"),
actionButton("listMasksCD", label = "List CD masks"),
# actionButton("listMPointsF", label = "List points filterng"),
fluidRow(
column(4,
wellPanel(
h3(strong(shinyfields5$head, style = "color:black"))
),
wellPanel(
# ----------------------------------------# 4. 1 Masking (white)#----------------------------------------------------------------------
h3(shinyfields5$head_sub, style = "color:black"),
h4("You can extract masks with white background", style = "color:black"),
p(shinyfields5$inf1, style = "color:black"),
# p(shinyfields7$inf2, style = "color:black"),
fluidRow(column(8,numericInput("morph_ellipse", label = shinyfields5$lab1, value = 5))),#, width = NULL, placeholder = NULL)
fluidRow(column(3, actionButton("masking", label = shinyfields5$lab2, style="color:#FFFFFF;background:#999999"))),
),
#wellPanel(
# ----------------------------------------# Masking (black)#----------------------------------------------------------------------
# h4("Or you can extract masks with black background", style = "color:black"),
# p(shinyfields5$inf2, style = "color:black"),
# fluidRow(column(8,numericInput("morph_ellipse", label = shinyfields5$lab1, value = 5))),#, width = NULL, placeholder = NULL)
# fluidRow(column(3, actionButton("maskingBlack", label = shinyfields5$lab2, style="color:#FFFFFF;background:#999999"))),
# ),
# ---------------------------------------- # 4.2 Masking centroids -----------------------------------------------------------------
wellPanel(
h3(shinyfields5.1$head_sub, style = "color:black"),
h4("You can mask the centroids of the points detected by Point Filtering and Circle Detection.", style = "color:black"),
p(shinyfields5.1$inf1, style = "color:black"),
fluidRow(column(3, actionButton("maskingCentroids", label = shinyfields5.1$lab1, style="color:#FFFFFF;background:#999999")))
)
), # col 4
column(8,
uiOutput('listMS', style="float:left"),
uiOutput('listMSB', style="float:left"),
uiOutput('listMCD', style="float:left")
)
) # END fluid Row
), # END tabItem 4
# Tab 5 Georeferencing FILES=shinyfields_georeferensing & shinyfields_georef_coords_from_csv_file.csv #-------------------------------------------------
tabItem(
tabName = "tab5",
wellPanel(
h3(strong(shinyfields6$head, style = "color:black")),
p(shinyfields6$inf1, style = "color:black"),
p(shinyfields6$inf2, style = "color:black"),
# start georeferencing
actionButton("georeferencing", label = shinyfields6$lab1, style="color:#FFFFFF;background:#999999")
),
wellPanel(
# which site become overview
fluidRow(column(3,textInput("siteNumberGeoreferencing", label=shinyfields6$input, value = ''))),
# start overview
actionButton("listGeoreferencing", label = "List georeferenced files"),
),
wellPanel(
uiOutput('leaflet_outputs_GEO')
),
wellPanel(
h4(shinyfields8$head_sub, style = "color:red"),
p(shinyfields8$info1, style = "color:black"),
p(shinyfields8$info2, style = "color:black"),
actionButton("georef_coords_from_csv", label = shinyfields8$lab1, style="color:#FFFFFF;background:#999999")
)
# END fluid Row
),# END tabItem 5
# Tab 6 Polygonize FILE=shinyfields_polygonize #----------------------------------------------------------------------
tabItem(
tabName = "tab6",
wellPanel(
h3(strong(shinyfields7$head, style = "color:black")),
p(shinyfields7$inf1, style = "color:black"),
p(shinyfields7$inf2, style = "color:black"),
actionButton("polygonize", label = shinyfields7$lab1, style="color:#FFFFFF;background:#999999")
),
wellPanel(
# which site become overview
fluidRow(column(3,textInput("siteNumberPolygonize", label=shinyfields6$input, value = ''))),
actionButton("listPolygonize", label = "Listf polygonized files",),
),
wellPanel(
uiOutput("leaflet_outputs_PL")
)
), # END tabItem 6
# 7. Spatial data view #----------------------------------------------------------------------
tabItem(
tabName = "tab7",
# wellPanel(
# h3(strong("Save the outputs in csv file", style = "color:black")),
# p("hier kommt noch mehr Text", style = "color:black"),
# p("hier kommt noch mehr Text", style = "color:black"),
actionButton("startSpatialDataComputing", label ="Spatial Data Computing", style="color:#FFFFFF;background:#999999"),
#),
wellPanel(
# which site become overview
#fluidRow(column(3,textInput("siteNumberSave", label="Test", value = ''))),
actionButton("spatialViewCD", label = "Start View circle detection",),
leafletOutput("mapSpatialViewCD"),
verbatimTextOutput("hoverInfo")
),
wellPanel(
# which site become overview
#fluidRow(column(3,textInput("siteNumberSave", label="Test", value = ''))),
actionButton("spatialViewPF", label = "Start View point detection",),
leafletOutput("mapSpatialViewPF"),
verbatimTextOutput("hoverInfo3")
)
), # END tabItem 6
tabItem(
tabName = "tab8",
actionButton("viewCSV", label ="Overview spatial final data", style="color:#FFFFFF;background:#999999"),
wellPanel(
#downloadButton("downloadCSV", label = "Download CSV", style="color:#FFFFFF;background:#999999"),
downloadButton("download_csv", label = "Download CSV", style="color:#FFFFFF;background:#999999"),
dataTableOutput("view_csv")
),
)
) # END tabItems
) # END BODY
sidebar <-
ui <- dashboardPage(
header = header,
sidebar = dashboardSidebar(disable = TRUE),
body = body,
title = NULL,
skin = "black"
)
################################################################################
# Shiny SERVER CODE
################################################################################
################################################################################
server <- shinyServer(function(input, output, session) {
dataInputDir = ""
# Update the clock every second using a reactiveTimer
current_time <- reactiveTimer(1000)
# SAVE the config
observeEvent(input$saveConfig, {
dataInputDir = input$dataInputDir
tryCatch({
# Check if the directory exists
if (file.exists(dataInputDir) ){#&& file.info(dataInputDir)$isdir) {
output$message <- NULL
# List of subdirectories in the "input" directory
subdirectories <- list.dirs(dataInputDir, full.names = FALSE, recursive = FALSE)
# Required subdirectories
required_subdirectories <- c("pages", "templates")
#required_subdirectories <- c("maps", "symbols", "align", "points")
# Check if all required subdirectories are present
if (all(required_subdirectories %in% subdirectories)) {
print("All required subdirectories of input are present.")
templates <- paste0(dataInputDir,"/templates/")
# List of subdirectories in the "input" directory
subdirectories <- list.dirs(templates, full.names = FALSE, recursive = FALSE)
# Required subdirectories
required_subdirectories <- c("align_ref", "maps","symbols", "geopoints")
#required_subdirectories <- c("maps", "symbols", "align", "points")
if (all(required_subdirectories %in% subdirectories)) {
print("All required subdirectories of templates are present.")
} else {
missing_subdirectories <- required_subdirectories[!required_subdirectories %in% subdirectories]
output$message <- renderPrint(paste("The following subdirectories in templates are missing:", paste(missing_subdirectories, collapse = ", ")))
break
}
} else {
missing_subdirectories <- required_subdirectories[!required_subdirectories %in% subdirectories]
output$message <- renderPrint(paste("The following subdirectories are missing:", paste(missing_subdirectories, collapse = ", ")))
break
}
} else {
#rv$message <- "The 'templates' directory does not exist."
output$message <- renderPrint("The 'templates' directory does not exist.")
break
}
# Generate current date-time string
current_datetime <- format(Sys.time(), "%Y-%m-%d_%H-%M-%S")
# Directory name with current date-time
out_directory_name <- paste("output_", current_datetime, sep = "")
# Concatenate base path with directory name
outDir <- file.path(input$dataOutputDir, out_directory_name)
prepare_base_output(outDir)
webViewMap = paste0(workingDir,"/www/data/")
prepare_www_output(webViewMap)
x <- data.frame(workingDir= workingDir,
workingDirInformation = "Your working directory is the local digitizer repository!",
title = input$title,
autor = input$author,
pYear = input$pYear,
dataInputDir= input$dataInputDir,
dataOutputDir = outDir,
numberSitesPrint = input$numberSitesPrint,
allPrintedPages = input$allPrintedPages,
sNumberPosition = input$sNumberPosition,
middle = input$middle,
regExYear = input$regExYear,
keywordReadSpecies = input$keywordReadSpecies,
keywordBefore = input$keywordBefore,
keywordThen = input$keywordThen,
pFormat = input$pFormat,
pColor = input$pColor)
tf <- tempfile(fileext = ".csv")
## To write a CSV file for input to Excel one might use
write.table(x, file = paste0(workingDir,"/config/config.csv"), sep = ";", row.names = FALSE,
quote=FALSE)
shinyalert::shinyalert(title = "Success", text = "Configuration successfully saved!", type = "success")
},
error = function(e) {
errorMessage <- paste("Ein Fehler ist aufgetreten:", e$message)
stackTrace <- paste("Stapelrückverfolgung:", traceback())
shinyalert::shinyalert(title = "Fehler", text = c(errorMessage, stackTrace), type = "error")
})
})
# -----------------------------------------# 1. Step - Create templates #---------------------------------------------------------------------
#Function to show the ccrop process in the app
plot_png <- function(path, plot_brush, index, add=FALSE)
{
require('png')
#fname=paste0(workingDir, "/", tempImage)
fname=tempImage
png = png::readPNG(fname, native=T) # read the file
# this for tests png <- image_read('DD_shiny/0045.png')
# get the resolution, [x, y]
res = dim(png)[2:1]
# initialize an empty plot area if add==FALSE
if (!add)
plot(1,1,xlim=c(1,res[1]),ylim=c(1,res[2]),asp=1,type='n',xaxs='i',yaxs='i',xaxt='n',yaxt='n',
xlab='',ylab='',bty='n')
img <- as.raster(readPNG(fname))
# rasterImage(img,1,1,res[1],res[2])
#grid.raster(img[1:600,1:500,]) wichtig img[y1:y2,x2:y2]
x1 = plot_brush$xmin
x2 = plot_brush$xmax
y2 = plot_brush$ymin
y1 = plot_brush$ymax
grid.raster(img[y2:y1,x1:x2,])
}
# Render the image in the plot with given dynamical 10%
output$plot <- renderImage({
#only if input$image is given
req(input$image)
temp <- image_read(input$image$datapath)
file <- image_convert(temp, "png")
temp_scale <- image_scale(file, paste0(scale,"%"))
fname = paste0(workingDir, "/", tempImage)
workingDir = workingDir
image_write(temp_scale, path = fname, format = "png", )
req(file)
list(src = fname, alt="alternative text")
shinyalert::shinyalert(title = "Success", text = "Configuration successfully saved!", type = "success")
}, deleteFile = FALSE)
#plot1
output$plot1 <- renderPlot({
req(input$image)
req(input$plot_brush)
d <- data()
if(!is.null(input$image$datapath) && input$image$datapath!=""){
plot_png(input$image$datapath, input$plot_brush, input$imgIndexTemplate)
}
})
# Function to save the cropped tepmlate map image
output$saveTemplate <- downloadHandler(
filename = function() {
paste(workingDir, '/data/templates/maps/map', '_',input$imgIndexTemplate,'.tif', sep='')
},
content = function(file) {
x1 = input$plot_brush$xmin
x2 = input$plot_brush$xmax
y2 = input$plot_brush$ymin
y1 = input$plot_brush$ymax
tempI <- image_read(input$image$datapath)
widht=(x2*rescale-x1*rescale)
height=(y1*rescale-y2*rescale)
geometrie <- paste0(widht, "x", height, "+",x1*rescale,"+", y2*rescale)
#"100x150+0+0")
tempI <- image_crop(tempI, geometrie)
image_write(tempI, file, format = "tif")
#writePNG(tempImage, target = file)
# unlink(paste0(workingDir,"/", tempImage))
i = input$imgIndexTemplate +1
updateNumericInput(session, "imgIndexTemplate", value = i)
})
observeEvent(input$listMTemplates, {
output$listMapTemplates = renderUI({
# Check if the directory already exists
findTemplateResult = paste0(workingDir, "/data/input/templates/maps/")
convertTifToPngSave(findTemplateResult, paste0(workingDir, "/www/data/map_templates_png/"))
prepareImageView("/map_templates_png/", '.png')
})
})
# Function to save the cropped template symbol image
output$saveSymbol <- downloadHandler(
filename = function() {
paste(workingDir, '/data/templates/maps/symbols', '_',input$imgIndexSymbol,'.tif', sep='')
},
content = function(file) {
x1 = input$plot_brush$xmin
x2 = input$plot_brush$xmax
y2 = input$plot_brush$ymin
y1 = input$plot_brush$ymax
tempI <- image_read(input$image$datapath)
widht=(x2*rescale-x1*rescale)
height=(y1*rescale-y2*rescale)
geometrie <- paste0(widht, "x", height, "+",x1*rescale,"+", y2*rescale)
#"100x150+0+0")
tempI <- image_crop(tempI, geometrie)
image_write(tempI, file, format = "tif")
#writePNG(tempImage, target = file)
# unlink(paste0(workingDir,"/", tempImage))
i = input$imgIndexSymbol +1
updateNumericInput(session, "imgIndexSymbol", value = i)
})
observeEvent(input$listSTemplates, {
output$listSymbolTemplates = renderUI({
findTemplateResult = paste0(workingDir, "/data/input/templates/symbols/")
convertTifToPngSave(findTemplateResult, paste0(workingDir, "/www/data/symbol_templates_png/"))
prepareImageView("/symbol_templates_png/", '.png')
})
})
####################
# 2. Maps matching #----------------------------------------------------------------------#
####################
# START th template matching
observeEvent(input$templateMatching, {
# call the function for map matching
manageProcessFlow("mapMatching", "map matching", "matching")
})
observeEvent(input$listMapsMatching, {
if(input$siteNumberMapsMatching != ''){
#print(input$siteNumberMapsMatching)
output$listMaps = renderUI({
prepareImageView("/matching_png/", input$siteNumberMapsMatching)
})
}
else{
output$listMaps = renderUI({
prepareImageView("/matching_png/", '.png')
})
}
})
####################
# 2.1 Maps align #----------------------------------------------------------------------#
####################
# Start Align maps
observeEvent(input$alignMaps, {
# call the function for align maps
manageProcessFlow("alignMaps", "align maps", "allign")
})
# List align maps
observeEvent(input$listAlign, {
if(input$siteNumberMapsMatching != ''){
#print(input$siteNumberMapsMatching)
output$listAlign = renderUI({
prepareImageView("/align_png/", input$siteNumberMapsMatching)
})
}
else{
output$listAlign = renderUI({
prepareImageView("/align_png/", '.png')
})
}
})
####################
# 2.2 Crop map legend species#----------------------------------------------------------------------#
####################
# Start read legend species
observeEvent(input$mapReadRpecies, {
# call the function for cropping
manageProcessFlow("mapReadRpecies", "cropping map species", "align")
})
# List map legend species
observeEvent(input$listCropped, {
if(input$siteNumberMapsMatching != ''){
#print(input$siteNumberMapsMatching)
output$listCropped = renderUI({
prepareImageView("/cropped_png/", input$siteNumberMapsMatching)
})
}
else{
output$listCropped = renderUI({
prepareImageView("/cropped_png/", '.png')
})
}
})
####################
# 2.3 Crop species name of the page content #----------------------------------------------------------------------#
####################
# Start Crop page species
observeEvent(input$pageReadRpecies, {
# call the function for cropping
manageProcessFlow("pageReadRpecies", "read page species", "output")
})
####################
# 3. Points Matching #----------------------------------------------------------------------#
####################
# Start points detection with matching
observeEvent(input$pointMatching, {
# call the function for cropping
manageProcessFlow("pointMatching", "points matching", "pointMatching")
})
observeEvent(input$listPointsM, {
if(input$siteNumberPointsMatching != ''){
#print(input$siteNumberPointsMatching)
output$listPM = renderUI({
prepareImageView("/pointMatching_png/", input$siteNumberPointsMatching)
})
}
else{
output$listPM = renderUI({
prepareImageView("/pointMatching_png/", '.png')
})
}
})
####################
# 3.1 Points Filtering #----------------------------------------------------------------------#
####################
# Start Process point filtering
observeEvent(input$pointFiltering, {
# call the function for filtering
manageProcessFlow("pointFiltering", "points filtering", "pointFiltering")
})
observeEvent(input$listPointsF, {
if(input$siteNumberPointsMatching != ''){
#print(input$siteNumberPointsMatching)
output$listPF = renderUI({
prepareImageView("/pointFiltering_png/", input$siteNumberPointsMatching)
})
}
else{
output$listPF = renderUI({
prepareImageView("/pointFiltering_png/", '.png')
})