#4 filter has now year and month as args

Author: hurielreichel

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tidyopeneo
 Type: Package
-Title: tidyopeneo : Wrap dplyr functions for openEO datacubes (OpenEOWrap)
+Title: tidyopeneo : Wrap dplyr functions for openEO datacubes (tidyopeneo)
 Version: 0.1.0
 Author: Huriel Reichel
 Maintainer: The package maintainer <huriel.reichel@protonmail.com>
@@ -13,7 +13,7 @@ Encoding: UTF-8
 LazyData: true
 Depends: R (>= 3.3.3), dplyr, openeo, cli, rjson
 Imports: sf, methods
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Suggests: 
     knitr,
     rmarkdown,

R/datacube.R

@@ -4,7 +4,7 @@
 #' openeo::processes()$load_collection() (https://processes.openeo.org/#load_collection).
 #' This is understood as the **starting point** when working with tidyopeneo. (optional)
 #' @param data ProcessNode datacube from openeo (optional)
-#' @param .con (optional) character link to openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) character link to openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import openeo

R/filter.R

@@ -20,6 +20,10 @@
 #' never both.
 #' For **filter_bbox**, the bounding box, which may include a vertical axis
 #' (see `base` and `height`).
+#' @param .year integer or list of integers stating the years you want to filter on the
+#' datacube.
+#' @param .month integer or list of integers referring to the months you want to filter
+#' on the datacube.
 #' @param .dimension (optional) For **filter_temporal** : The name of the temporal dimension
 #' to filter on. If no specific dimension is specified or it is set to `null`,
 #' the filter applies to all temporal dimensions. Fails with a `DimensionNotAvailable`
@@ -28,7 +32,7 @@
 #' filtering, specified as GeoJSON.
 #' @param .context (optional) : any Additional data to be passed to the condition.
 #' Mandatory for filter_labels or array_filter processes.
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli
@@ -39,10 +43,17 @@
 #' library(sf)
 #'
 #' con = connect(host = "https://openeo.cloud")
-#' dc = datacube(id = "SENTINEL_5P_L2")
+#' dc = datacube(id = "SENTINEL1_GRD")
+#'
+#' # filter_temporal
+#' dc_y = dc %>% filter(.year = c(2020, 2021, 2022))
+#'
+#' dc_m = dc %>% filter(.month = c(6,7,8))
+#'
+#' dc_ym = dc %>%  filter(.year = c(2020, 2021, 2022), .month = c(6,7,8))
 #'
 #' # filter_temporal and filter_bbox
-#' dc = dc %>%
+#' dc2 = dc %>%
 #'     filter(.extent = c("2021-01-01", "2021-03-03")) %>%
 #'     filter(.extent = c(west = 6.09, east = 6.99, south = 46.15, north = 46.57))
 #'
@@ -55,7 +66,7 @@
 #'     st_bbox() %>%
 #'     st_as_sfc()
 #'
-#' dc = dc %>% filter(.geometries = pol)
+#' dc = dc2 %>% filter(.geometries = pol)
 #'
 #' # array_filter
 #' # ToDO...
@@ -65,6 +76,7 @@
 filter.datacube <- function(.data = NULL, ...,
                             .condition = NULL, .dimension = NULL, .context = NULL,
                             .extent = NULL, .geometries = NULL,
+                            .year = NULL, .month = NULL,
                             .p = openeo::processes(.con), .con = NULL) {
 
   #check dots ...
@@ -89,6 +101,170 @@ filter.datacube <- function(.data = NULL, ...,
     dc = .p$filter_temporal(data = .data, extent = .extent, dimension = .dimension)
     cli::cli_alert_success("filter_temporal applied")
 
+  ## Working with years
+  } else if (!is.null(.year) & is.null(.month) & is.null(.geometries) & is.null(.condition)&
+             is.null(.context)){
+
+    ### Extract starting year of collection
+    process_json = .p$save_result(data = .data, format = list_file_formats()$output$JSON) %>%
+      as("Process") %>% openeo::toJSON() %>% rjson::fromJSON() %>% suppressWarnings()
+    id = process_json$process_graph[[1]]$arguments$id
+
+    collections = list_collections() %>% suppressWarnings()
+    native_time_ext = c(collections[[id]]$extent$temporal[[1]][[1]] %>% as.Date() %>% format("%04Y-%m-%d"),
+                        collections[[id]]$extent$temporal[[1]][[2]])
+    native_time_ext = ifelse(is.na(native_time_ext), Sys.Date() %>% format("%04Y-%m-%d"), native_time_ext)
+
+    ### stop if year outside of range
+    if (min(.year) < native_time_ext[1] %>% substr(1,4) | max(.year) > native_time_ext[2] %>% substr(1,4)){
+      stop(
+        cli::cli_alert_danger("You're trying to filter outside of the range of the collection {native_time_ext}")
+      )
+    }
+
+    ### Iterate through the called years
+    dcs = list()
+    for (i in 1:length(.year)){
+     dcs[[i]] <- .p$filter_temporal(
+        data = .data,
+        extent = c(paste(.year[i], "01-01", sep = "-"), paste(.year[i], "12-31", sep = "-")),
+        dimension = .dimension)
+    }
+
+    ### merge generated data cubes
+    if (length(dcs) > 1){
+      for (i in 1:length(dcs)){
+        if (i == 1){i = i+1}
+        else if (i == 2){
+          dc = .p$merge_cubes(dcs[[i]], dcs[[i-1]])
+        } else {
+          dc = .p$merge_cubes(dc, dcs[[i]])
+        }
+      }
+      cli::cli_alert_success("merge_cubes applied")
+
+      ### Do not merge --- simple filter for a single year
+    } else {
+      dc = .p$filter_temporal(
+        data = .data,
+        c(paste(.year, "01-01", sep = "-"), paste(.year, "12-31", sep = "-")),
+        dimension = .dimension)
+      cli::cli_alert_success("filter_temporal applied")
+    }
+
+    ## Working with Months
+  } else if (is.null(.year) & !is.null(.month) & is.null(.geometries) & is.null(.condition)&
+             is.null(.context)){
+
+    ### Extract time extent of collection
+    process_json = .p$save_result(data = .data, format = list_file_formats()$output$JSON) %>%
+      as("Process") %>% openeo::toJSON() %>% rjson::fromJSON() %>% suppressWarnings()
+    id = process_json$process_graph[[1]]$arguments$id
+
+    collections = list_collections() %>% suppressWarnings()
+    native_time_ext = c(collections[[id]]$extent$temporal[[1]][[1]] %>% as.Date() %>% format("%04Y-%m-%d"),
+                        collections[[id]]$extent$temporal[[1]][[2]])
+    native_time_ext = ifelse(is.na(native_time_ext), Sys.Date() %>% format("%04Y-%m-%d"), native_time_ext)
+
+    ### Iterate through the existing years and called months
+    years = seq(native_time_ext[1] %>% substr(1, 4), native_time_ext[2] %>% substr(1, 4), 1)
+    months = ifelse(.month < 10, paste0("0", .month), .month) %>% as.character()
+    next_months = ifelse((.month + 1) == 13, 1, .month)
+    next_months =  ifelse(next_months < 10, paste0("0", next_months), next_months) %>% as.character()
+    dcs = list()
+    for (y in 1:length(years)){
+      for (m in 1:length(months)){
+        date1 =  paste(years[y], months[m], "01", sep = "-")
+        date2 = paste(years[y], next_months[m], "01", sep = "-")
+        date2 = as.Date(date2) - 1
+        date2 = date2 %>% format("%04Y-%m-%d")
+
+        if (date1 < native_time_ext[1] | date2 > native_time_ext[2]){
+          next
+        }
+
+      dcs <- append(dcs, .p$filter_temporal(
+        data = .data, extent = c(date1, date2, dimension = .dimension)))
+      }
+    }
+    cli::cli_alert_success("filter_temporal applied")
+
+    ### merge generated data cubes
+      for (i in 1:length(dcs)){
+        if (i == 1){i = i+1}
+        else if (i == 2){
+          dc = .p$merge_cubes(dcs[[i]], dcs[[i-1]])
+        } else {
+          dc = .p$merge_cubes(dc, dcs[[i]])
+        }
+      }
+    cli::cli_alert_success("merge_cubes applied")
+
+    ## Working with Months and Years
+  } else if  (!is.null(.year) & !is.null(.month) & is.null(.geometries) & is.null(.condition)&
+              is.null(.context)){
+
+    ### Extract time extent of collection
+    process_json = .p$save_result(data = .data, format = list_file_formats()$output$JSON) %>%
+      as("Process") %>% openeo::toJSON() %>% rjson::fromJSON() %>% suppressWarnings()
+    id = process_json$process_graph[[1]]$arguments$id
+
+    collections = list_collections() %>% suppressWarnings()
+    native_time_ext = c(collections[[id]]$extent$temporal[[1]][[1]] %>% as.Date() %>% format("%04Y-%m-%d"),
+                        collections[[id]]$extent$temporal[[1]][[2]])
+    native_time_ext = ifelse(is.na(native_time_ext), Sys.Date() %>% format("%04Y-%m-%d"), native_time_ext)
+
+    ### stop if year outside of range
+    if (min(.year) < native_time_ext[1] %>% substr(1,4) | max(.year) > native_time_ext[2] %>% substr(1,4)){
+      stop(
+        cli::cli_alert_danger("You're trying to filter outside of the range of the collection {native_time_ext}")
+      )
+    }
+
+    ### Iterate through the existing years and called months
+    years = .year
+    months = ifelse(.month < 10, paste0("0", .month), .month) %>% as.character()
+    next_months = ifelse((.month + 1) == 13, 1, .month)
+    next_months =  ifelse(next_months < 10, paste0("0", next_months), next_months) %>% as.character()
+    dcs = list()
+    for (y in 1:length(years)){
+      for (m in 1:length(months)){
+        date1 =  paste(years[y], months[m], "01", sep = "-")
+        date2 = paste(years[y], next_months[m], "01", sep = "-")
+        date2 = as.Date(date2) - 1
+        date2 = date2 %>% format(., "%04Y-%m-%d")
+
+        if (date1 < native_time_ext[1] | date2 > native_time_ext[2]){
+          next
+        }
+
+        dcs <- append(dcs, .p$filter_temporal(
+          data = .data, extent = c(date1, date2, dimension = .dimension)))
+      }
+    }
+    cli::cli_alert_success("filter_temporal applied")
+
+    ### merge generated data cubes
+    if (length(dcs) > 1){
+      for (i in 1:length(dcs)){
+        if (i == 1){i = i+1}
+        else if (i == 2){
+          dc = .p$merge_cubes(dcs[[i]], dcs[[i-1]])
+        } else {
+          dc = .p$merge_cubes(dc, dcs[[i]])
+        }
+      }
+      cli::cli_alert_success("merge_cubes applied")
+
+      ### Do not merge --- simple filter for a single year
+    } else {
+      dc = .p$filter_temporal(
+        data = .data,
+        c(paste(.year, "01-01", sep = "-"), paste(.year, "12-31", sep = "-")),
+        dimension = .dimension)
+      cli::cli_alert_success("filter_temporal applied")
+    }
+
     #filter_bbox
   } else if (length(.extent == 4) & is.null(.geometries) & is.null(.condition)&
              is.null(.context)) {

R/group_by.R

@@ -71,7 +71,7 @@
 #' and/or times. Is only required to be specified if the values for the start of
 #' the temporal intervals are not distinct and thus the default labels would not
 #' be unique. The number of labels and the number of groups need to be equal.
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli sf

R/mutate.R

@@ -57,7 +57,7 @@
 #' after, so an overlap of 8 pixels will add 8 pixels on both sides of the window,
 #' so 16 in total.Be aware that large overlaps increase the need for computational
 #' resources and modifying overlapping data in subsequent operations have no effect.
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli

R/rename.R

@@ -9,7 +9,7 @@
 #' `DimensionNotAvailable` exception if the specified dimension does not exist.
 #' @param .target A new Name for the dimension. Fails with a `DimensionExists`
 #' exception if a dimension with the specified name exists.
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli

R/resample.R

@@ -53,7 +53,7 @@
 #' to no-data (`null`).
 #' @param .target_process (optional) either "spatial" to apply **resample_cube_spatial** or
 #' "temporal" to apply **resample_cube_temporal**.
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @details if arg .target is not defined, resample_spatial is gonna be run.

R/select.R

@@ -18,7 +18,7 @@
 #' specified in micrometers. The order of the specified array defines the
 #' order of the bands in the data cube. If multiple bands match the wavelengths,
 #' all matched bands are included in the original order.
-#' @param .con openeo connection. Default to "https://openeo.cloud"
+#' @param .con openeo connection. Default to NULL
 #' @param .p processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli

R/slice.R

@@ -20,7 +20,7 @@
 #' If n is greater than the number of days available in the collection or datacube (or prop > 1), the result
 #' will be truncated to the group size. If the proportion of a group size does not yield an integer number of
 #'rows, the absolute value of prop * ndays(.data) is rounded down.
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli

R/summarise.R

@@ -12,7 +12,7 @@
 #' @param .dimension The name of the dimension over which to reduce. Fails with
 #' a `DimensionNotAvailable` exception if the specified dimension does not exist.
 #' @param .context (optional) Additional data to be passed to the reducer (optional).
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli

R/summarize.R

@@ -12,7 +12,7 @@
 #' @param .dimension The name of the dimension over which to reduce. Fails with
 #' a `DimensionNotAvailable` exception if the specified dimension does not exist.
 #' @param .context (optional) Additional data to be passed to the reducer (optional).
-#' @param .con (optional) openeo connection. Default to "https://openeo.cloud"
+#' @param .con (optional) openeo connection. Default to NULL
 #' @param .p (optional) processes available at .con
 #' @return datacube
 #' @import dplyr openeo cli