Loss persistence colombian forests

.gitignore

@@ -3,3 +3,8 @@
 .Rhistory
 **/.cache
 **/.config
+scripts/1_IAvH_functions/01_pp.R
+scripts/1_IAvH_functions/01_pp.yml
+scripts/IAvH_inputs/p&p_collection/metadata.json
+scripts/IAvH_inputs/p&p_collection/metadata.csv
+*.tif

http-proxy/conf.d/ngnix.conf

@@ -2,6 +2,8 @@
 server {
 
     listen 80;
+    client_max_body_size 8M;
+    add_header Access-Control-Allow-Origin "localhost:3000";
     server_name boninabox.com;
 
     location /script/ {

pipelines/01_pp.R

@@ -0,0 +1,97 @@
+### funci?n check_collections
+
+# Cargar librerias
+packages_list<-list("magrittr", "terra", "raster")
+invisible(lapply(packages_list, library, character.only = TRUE))
+
+# Organizar directorios
+args <- commandArgs(trailingOnly=TRUE)
+outputFolder <- args[1]
+
+# Cargar archivos de entrada
+input <- rjson::fromJSON(file=file.path(outputFolder, "input.json"))
+
+dir_wkt<- input$dir_wkt_polygon
+dir_colection<- input$dir_colection
+
+epsg_polygon<- input$epsg_polygon
+resolution<- input$resolution
+folder_output<- input$folder_output
+
+wkt_polygon<- readLines(dir_wkt)
+layers <- list.files(dir_colection, "\\.tif$", recursive = TRUE, full.names = TRUE)
+json_colleciton_file <- list.files(dir_colection, "\\.json$", recursive = TRUE, full.names = TRUE)
+meadata_collecion_file <- list.files(dir_colection, "\\.csv$", recursive = TRUE, full.names = TRUE)
+metadata<- read.csv(meadata_collecion_file)
+
+# Especificar carpea donmde guardar resultados
+folder_results<- paste0(dirname(dirname(dirname(outputFolder))), "/", folder_output)
+dir.create(folder_results)
+
+
+# Especificar info area de estudio
+vector_polygon<- terra::vect(wkt_polygon, crs= sf::st_crs(epsg_polygon)$proj4string ) %>% terra::as.polygons()
+crs_polygon<- terra::crs(vector_polygon)
+box_polygon<-  sf::st_bbox(vector_polygon)
+
+
+# Alinear con colecci?on
+stac_collection<- gdalcubes::create_image_collection(files= layers, format= json_colleciton_file) 
+
+# Cargar cubo
+cube_collection<- gdalcubes::cube_view(srs = crs_polygon,  extent = list(t0 = gdalcubes::extent(stac_collection)$t0, t1 = gdalcubes::extent(stac_collection)$t1,
+                                                left = box_polygon[1], right = box_polygon[3],
+                                                top = box_polygon[4], bottom = box_polygon[2]),
+              dx = resolution, dy = resolution, dt = "P1Y", aggregation = "first", resampling = "first", keep.asp= F)
+
+cube <- gdalcubes::raster_cube(stac_collection, cube_collection)
+
+# Cortar cubo por area de estudio
+cube_mask<- gdalcubes::filter_geom(cube, geom= wkt_polygon, srs = crs_polygon )
+
+
+# Convertir cubo a raster
+cube_stars <- stars::st_as_stars(cube_mask) %>% terra::rast() %>% setNames(names(cube))
+
+collection_rast<- lapply(cube_stars, function(x) { if(any( is.na(summary(raster::raster(x))) )){NULL}else{x} } ) %>%
+  {Filter(function(x) !is.null(x), .)} %>% {setNames(., unlist(sapply(., function(x) names(x))) )} %>% terra::rast()
+
+# estimar metricas de area
+data_sum<- terra::freq(collection_rast, usenames=T) %>% dplyr::mutate(area_m2= count*resolution) %>% dplyr::select(-count) %>%
+  dplyr::rename(collection= layer) %>% dplyr::mutate(layer= sapply(.$collection, function(x) stringr::str_split(x, "_B*time")[[1]][1]) ) %>%
+  list(metadata) %>% plyr::join_all() %>% dplyr::group_by(layer)  %>% dplyr::mutate(porcentaje=  area_m2/sum(area_m2) )
+
+data_sum$periodo<-  unlist(strsplit(data_sum$layer, "_") %>% sapply(function(x) paste(x[c(2:3)], collapse = "_")), recursive = T)
+
+names(data_sum)<-c("collection", "value", "area", "layer", "key", "percentage", "period")
+
+
+
+# partir y guardar raster acorde a los valores
+setwd(folder_results)
+saveraster<- lapply( seq(nrow(data_sum)), function(i) {
+
+  x<- data_sum[i, ]
+
+  raster_val<- collection_rast[x$layer]
+  raster_val[!raster_val %in% x$value]= NA
+  raster_val[raster_val %in% x$value]= 1
+
+  terra::writeRaster(raster_val, paste0(x$layer, "_class_",x$class,  ".tif"), overwrite=T)
+
+} )
+
+
+
+
+# guardar tabla resumen
+setwd(folder_results)
+write.csv(data_sum,"data_summ.csv")
+
+# Imprimir resultado en logs
+print(data_sum)
+
+## Imprimir resultado - Formao json
+output <- list("folder_output" = folder_results)
+jsonData <- rjson::toJSON(output, indent=2)
+write(jsonData, file.path(outputFolder,"output.json"))

pipelines/01_pp.yml

@@ -0,0 +1,35 @@
+script: 01_pp.R
+description: "This sample script shows how it works."
+external_link: https://github.com/GEO-BON/biab-2.0
+inputs:
+  dir_wkt_polygon:
+    label: dir_wkt_polygon
+    description: dir_wkt_polygon
+    type: text
+    example: '/scripts/IAvH_inputs/wkt_polygon_test.txt'
+  epsg_polygon:
+    label: epsg_polygon
+    description: epsg_polygon
+    type: numeric
+    example: 3395   
+  dir_colection:
+    label: dir_colection
+    description: dir_colection
+    type: text
+    example: '/scripts/IAvH_inputs/p&p_collection'
+  resolution:
+    label: resolution
+    description: value in meters
+    type: numeric
+    example: 1000
+  folder_output:
+    label: folder_output
+    description: folder_output
+    type: text
+    example: 'p_p_studyarea_1000m2'
+
+outputs:
+  folder_output:
+    label: folder_output
+    description: folder_output
+    type: text

scripts/lossPersistence/input/Colombia_pp_collection/Colombia_pp-2000_12_31-pp_2000_2005.tfw

@@ -0,0 +1,6 @@
+0.0002500000
+0.0000000000
+0.0000000000
+-0.0002500000
+-79.0074509690
+12.4582381791

scripts/lossPersistence/input/Colombia_pp_collection/Colombia_pp-2005_12_31-pp_2000_2005.tfw

@@ -0,0 +1,6 @@
+0.0002500000
+0.0000000000
+0.0000000000
+-0.0002500000
+-79.0074509690
+12.4582381791

scripts/lossPersistence/input/Colombia_pp_collection/Colombia_pp-2010_12_31-pp_2006_2010.tfw

@@ -0,0 +1,6 @@
+0.0002500000
+0.0000000000
+0.0000000000
+-0.0002500000
+-79.0074509690
+12.4582381791

scripts/lossPersistence/input/Colombia_pp_collection/Colombia_pp-2015_12_31-pp_2011_2015.tfw

@@ -0,0 +1,6 @@
+0.0002500000
+0.0000000000
+0.0000000000
+-0.0002500000
+-79.0074509690
+12.4582381791

scripts/lossPersistence/input/Colombia_pp_collection/Colombia_pp-2021_12_31-pp_2016_2021.tfw

@@ -0,0 +1,6 @@
+0.0002500000
+0.0000000000
+0.0000000000
+-0.0002500000
+-79.0074509690
+12.4582381791

scripts/lossPersistence/input/Colombia_pp_collection/catalog.json

@@ -0,0 +1,177 @@
+{
+  "id": "Colombia_pp",
+  "type": "Collection",
+  "description": "Collection format for Biotablero (IAvH, 2022)",
+  "pattern": ".+\\.tif",
+  "images": {
+    "pattern": ".*(Colombia_pp-.{4}_.{2}_.{2}-.*)\\.tif"
+  },
+  "datetime": {
+    "pattern": ".*Colombia_pp-(.{4}_.{2}_.{2})-.*\\.tif",
+    "format": "%Y_%m_%d"
+  },
+  "features": {
+    "Colombia_pp-2005_12_31-pp_2000_2005": {
+      "id": "Colombia_pp-2005_12_31-pp_2000_2005",
+      "pattern": ".+Colombia_pp-2005_12_31-pp_2000_2005+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2005_12_31-pp_2000_2005": {
+          "href": "Colombia_pp-2005_12_31-pp_2000_2005.tif",
+          "classes": {
+            "period_layer": ["2000-2005", "2000-2005", "2000-2005"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    },
+    "Colombia_pp-2010_12_31-pp_2006_2010": {
+      "id": "Colombia_pp-2010_12_31-pp_2006_2010",
+      "pattern": ".+Colombia_pp-2010_12_31-pp_2006_2010+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2010_12_31-pp_2006_2010": {
+          "href": "Colombia_pp-2010_12_31-pp_2006_2010.tif",
+          "classes": {
+            "period_layer": ["2006-2010", "2006-2010", "2006-2010"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    },
+    "Colombia_pp-2015_12_31-pp_2011_2015": {
+      "id": "Colombia_pp-2015_12_31-pp_2011_2015",
+      "pattern": ".+Colombia_pp-2015_12_31-pp_2011_2015+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2015_12_31-pp_2011_2015": {
+          "href": "Colombia_pp-2015_12_31-pp_2011_2015.tif",
+          "classes": {
+            "period_layer": ["2011-2015", "2011-2015", "2011-2015"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    },
+    "Colombia_pp-2021_12_31-pp_2016_2021": {
+      "id": "Colombia_pp-2021_12_31-pp_2016_2021",
+      "pattern": ".+Colombia_pp-2021_12_31-pp_2016_2021+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2021_12_31-pp_2016_2021": {
+          "href": "Colombia_pp-2021_12_31-pp_2016_2021.tif",
+          "classes": {
+            "period_layer": ["2016-2021", "2016-2021", "2016-2021"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    }
+  },
+  "bands": {
+    "Colombia_pp-2005_12_31-pp_2000_2005": {
+      "id": "Colombia_pp-2005_12_31-pp_2000_2005",
+      "pattern": ".+Colombia_pp-2005_12_31-pp_2000_2005+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2005_12_31-pp_2000_2005": {
+          "href": "Colombia_pp-2005_12_31-pp_2000_2005.tif",
+          "classes": {
+            "period_layer": ["2000-2005", "2000-2005", "2000-2005"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    },
+    "Colombia_pp-2010_12_31-pp_2006_2010": {
+      "id": "Colombia_pp-2010_12_31-pp_2006_2010",
+      "pattern": ".+Colombia_pp-2010_12_31-pp_2006_2010+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2010_12_31-pp_2006_2010": {
+          "href": "Colombia_pp-2010_12_31-pp_2006_2010.tif",
+          "classes": {
+            "period_layer": ["2006-2010", "2006-2010", "2006-2010"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    },
+    "Colombia_pp-2015_12_31-pp_2011_2015": {
+      "id": "Colombia_pp-2015_12_31-pp_2011_2015",
+      "pattern": ".+Colombia_pp-2015_12_31-pp_2011_2015+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2015_12_31-pp_2011_2015": {
+          "href": "Colombia_pp-2015_12_31-pp_2011_2015.tif",
+          "classes": {
+            "period_layer": ["2011-2015", "2011-2015", "2011-2015"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    },
+    "Colombia_pp-2021_12_31-pp_2016_2021": {
+      "id": "Colombia_pp-2021_12_31-pp_2016_2021",
+      "pattern": ".+Colombia_pp-2021_12_31-pp_2016_2021+.*\\.tif",
+      "assets": {
+        "Colombia_pp-2021_12_31-pp_2016_2021": {
+          "href": "Colombia_pp-2021_12_31-pp_2016_2021.tif",
+          "classes": {
+            "period_layer": ["2016-2021", "2016-2021", "2016-2021"],
+            "col": ["#c65453", "#92ab58", "#c5b599"],
+            "value": [0, 1, 2],
+            "classes": ["Perdida", "Persistencia", "No Bosque"]
+          }
+        }
+      },
+      "bbox": [-180, -90, 180, 90],
+      "properties": {
+        "proj:epsg": null,
+        "resolution": [300, 300]
+      }
+    }
+  }
+}