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## Major changes * **`sen2r`** package directory is no more used to store files, but a subfolder `.sen2r` of the user Home directory is created and used. In this way, reinstalling sen2r will not require anymore to reinstall runtime dependencies / to reconfigure the package. The permission to write on this folder is asked to the user when the package is loaded for the first time. ## Other changes * Small base example files were added to the package for testing purposes. * Sen2Cor version which the user wants to install can be chosen in the GUI. * Documentation was updated and improved, in particular adding function examples. ## New functions * `build_example_param_file()` (not exported) to build an example parameter file. ## Fixes * Fix generation of thumbnails in case of multiple product types.
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| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| ^\.travis\.yml$ | ||
| ^\.covrignore\.yml$ | ||
| ^.*\.yaml$ | ||
| ^README\.R?md$ | ||
| ^WIP$ | ||
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| This package was submitted to CRAN on 2019-09-13. | ||
| Once it is accepted, delete this file and tag the release (commit 48f043460c). |
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@@ -2,25 +2,26 @@ Package: sen2r | |
| Type: Package | ||
| Title: Find, Download and Process Sentinel-2 Data | ||
| Version: 1.1.0 | ||
| Authors@R: c(person("Luigi", "Ranghetti", | ||
| email = "ranghetti.[email protected]", | ||
| role = c("aut", "cre"), | ||
| Authors@R: c(person("Luigi", "Ranghetti", | ||
| email = "luigi@ranghetti.info", | ||
| role = c("aut", "cre"), | ||
| comment = c(ORCID = "0000-0001-6207-5188")), | ||
| person("Lorenzo", "Busetto", | ||
| email = "[email protected]", | ||
| person("Lorenzo", "Busetto", | ||
| email = "[email protected]", | ||
| role = c("aut"), | ||
| comment = c(ORCID = "0000-0001-9634-6038"))) | ||
| Description: Functions to download Sentinel-2 optical images | ||
| and perform preliminary processing operations. | ||
| 'sen2r' provides the instruments required to easily perform | ||
| (and eventually automate) the steps necessary to build a complete | ||
| Description: Functions to download Sentinel-2 optical images | ||
| and perform preliminary processing operations. | ||
| 'sen2r' provides the instruments required to easily perform | ||
| (and eventually automate) the steps necessary to build a complete | ||
| Sentinel-2 processing chain. | ||
| A Graphical User Interface to facilitate data processing is also provided. | ||
| License: GPL-3 | ||
| Encoding: UTF-8 | ||
| URL: http://sen2r.ranghetti.info, https://github.com/ranghetti/sen2r | ||
| BugReports: https://github.com/ranghetti/sen2r/issues | ||
| Imports: | ||
| Depends: R (>= 3.5.0) | ||
| Imports: | ||
| reticulate, | ||
| methods, | ||
| digest, | ||
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@@ -46,7 +47,7 @@ Imports: | |
| units, | ||
| httr | ||
| Suggests: | ||
| spelling, | ||
| spelling, | ||
| geojsonlint, | ||
| httptest, | ||
| knitr, | ||
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| FROM rocker/geospatial:3.5.1 | ||
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| LABEL maintainer="Luigi Ranghetti <ranghetti.[email protected]>" | ||
| LABEL maintainer="Luigi Ranghetti <luigi@ranghetti.info>" | ||
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| # Install external dependencies | ||
| RUN apt-get update && apt-get install -y \ | ||
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| #' @title Ask permission to write settings on disk | ||
| #' @description Ask users for permission to create a .sen2r settings directory, | ||
| #' in which to store the files paths.json and apihub.txt. | ||
| #' @return 'logical' if TRUE, the user authorised saving in this directory. | ||
| #' @author Lorenzo Busetto, phD (2019) \email{lbusett@@gmail.com} | ||
| #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info} | ||
| #' @note License: GPL 3.0 | ||
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| ask_permission <- function() { | ||
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| settings_dir <- normalize_path("~/.sen2r", mustWork = FALSE) | ||
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| if (!dir.exists(settings_dir)) { | ||
| message(paste( | ||
| "\nsen2r would like to create a hidden folder in your home directory, ", | ||
| paste0("named '",settings_dir,"', "), | ||
| "in which storing some files required by the package:", | ||
| "- 'paths.json', containing the paths of sen2r runtime dependencies ", | ||
| " (GDAL, aria2, Sen2Cor);", | ||
| "- 'apihub.txt', in which saving the user's SciHub credentials;", | ||
| "- 's2_tiles.rds', containing the Sentinel-2 tile boundaries;", | ||
| "- the 'log' subfolder, used to keep trace of temporary files created ", | ||
| " during processing operations.\n", | ||
| "Do you authorise this?\n", | ||
| "Yes: folder '.sen2r' will be created permanently, and the files ", | ||
| " will be created and updated when needed. ", | ||
| " You will not see this message anymore.\n", | ||
| "No: a temporary folder will be used and will be lost when exiting ", | ||
| " R. You will see this message every time you will restart R.\n", | ||
| sep = "\n" | ||
| )) | ||
| choice <- "" | ||
| while (!tolower(choice) %in% c("y", "yes", "n", "no")) { | ||
| choice <- readline(prompt = "Choice (y/n): ") | ||
| } | ||
| if (tolower(choice) %in% c("y", "yes")) { | ||
| dir.create(settings_dir) | ||
| } | ||
| } else { | ||
| choice <- "y" | ||
| } | ||
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| return(tolower(choice) %in% c("y", "yes")) | ||
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| } |
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| #' @title Build an example JSON parameter file | ||
| #' @description Function used to write JSON parameter file. | ||
| #' A function is provided instead than a json file to ensure | ||
| #' directories to match the user folder tree. | ||
| #' @param json_path Path of the output file. Default is to save it on a | ||
| #' temporary file, whose path is returned. | ||
| #' @param overwrite Logical value: should existing output file be | ||
| #' overwritten? (default: TRUE) | ||
| #' @return The path of the created file. | ||
| #' | ||
| #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info} | ||
| #' @note License: GPL 3.0 | ||
| #' @importFrom jsonlite toJSON | ||
| #' @examples | ||
| #' sen2r:::build_example_param_file() | ||
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| build_example_param_file <- function( | ||
| json_path = tempfile(fileext = "_sen2r_params.json"), | ||
| overwrite = TRUE | ||
| ) { | ||
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| # Check json_path | ||
| if (json_path == "") {json_path <- NULL} | ||
| if (!attr(path_check(dirname(json_path)), "isvalid")) { | ||
| print_message( | ||
| type = "error", | ||
| "Path '",dirname(json_path),"' is missing or not writable." | ||
| ) | ||
| } | ||
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| # Delete existing file | ||
| if (file.exists(json_path)) { | ||
| if (overwrite == TRUE) { | ||
| file.remove(json_path) | ||
| } else { | ||
| print_message( | ||
| type = "error", | ||
| "File '",json_path,"' already exists." | ||
| ) | ||
| } | ||
| } | ||
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| writeLines( | ||
| jsonlite::toJSON( | ||
| list( | ||
| "preprocess" = TRUE, | ||
| "s2_levels" = c("l1c", "l2a"), | ||
| "sel_sensor" = c("s2a", "s2b"), | ||
| "online" = TRUE, | ||
| "downloader" = "builtin", | ||
| "overwrite_safe" = FALSE, | ||
| "rm_safe" = "no", | ||
| "max_cloud_safe" =100, | ||
| "step_atmcorr" = "l2a", | ||
| "timewindow" = c("2017-07-03", "2017-07-03"), | ||
| "timeperiod" = "full", | ||
| "extent" = system.file("extdata/vector/barbellino.geojson", package = "sen2r"), | ||
| "s2tiles_selected" = NA, | ||
| "s2orbits_selected" = NA, | ||
| "list_prods" = c("TOA", "BOA", "SCL"), | ||
| "list_indices" = c("MSAVI2", "NDVI"), | ||
| "list_rgb" = c("RGB432B", "RGB432T", "RGB843B"), | ||
| "rgb_ranges" = list( | ||
| c(0, 2500), | ||
| c(0, 2500), | ||
| matrix(c(0, 0, 0, 7500, 2500, 2500), ncol = 2) | ||
| ), | ||
| "index_source" = "BOA", | ||
| "mask_type" = NA, | ||
| "max_mask" = 80, | ||
| "mask_smooth" = 0, | ||
| "mask_buffer" = 0, | ||
| "clip_on_extent" = TRUE, | ||
| "extent_as_mask" = FALSE, | ||
| "extent_name" = "sen2r", | ||
| "reference_path" = NA, | ||
| "res" = NA, | ||
| "res_s2" ="10m", | ||
| "unit" = "Meter", | ||
| "proj"= NA, | ||
| "resampling" = "near", | ||
| "resampling_scl" = "near", | ||
| "outformat" = "GTiff", | ||
| "rgb_outformat" = "GTiff", | ||
| "index_datatype" = "Int16", | ||
| "compression" = "DEFLATE", | ||
| "rgb_compression" = "DEFLATE", | ||
| "overwrite" = FALSE, | ||
| "path_l1c" = file.path(dirname(attr(load_binpaths(), "path")), "safe"), | ||
| "path_l2a" = file.path(dirname(attr(load_binpaths(), "path")), "safe"), | ||
| "path_tiles"= NA, | ||
| "path_merged"= NA, | ||
| "path_out" = tempfile(pattern = "sen2r_out_"), | ||
| "path_rgb" = "", | ||
| "path_indices" = "", | ||
| "path_subdirs"= TRUE, | ||
| "thumbnails" = TRUE, | ||
| "log"= NA, | ||
| "parallel" = FALSE, | ||
| "processing_order" = "by_groups", | ||
| "pkg_version" = as.character(packageVersion("sen2r")) | ||
| ), | ||
| pretty = TRUE | ||
| ), | ||
| json_path | ||
| ) | ||
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| return(json_path) | ||
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| } |
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