Although the easiest way to set-up and launch a processing chain is probably by setting parameters with the GUI and launching it right away, it is often very useful to be able to launch a processing from the command line without opening the GUI.
This allows using
sen2r
functionalities (provided both by the main function sen2r() or other package
functions) as part of more complex scripts, or scheduling a processing so to
automatically update a time series of S2 products.
Three main processing modes are available:
sen2r();sen2r().sen2r()In this case, the user is expected to specify all arguments required for
processing within the call to sen2r()
(see sen2r() documentation for a detailed description of each option –
note that unspecified arguments will be set to default values, when possible).
For example, the following code chunk would perform the following operations:
barbellino.geojson spatial file between 1 and 15 July 2019;"cloud_and_shadow", in this case)
shows that less than 10% of the area of interest was covered by clouds;# Set paths
out_dir_1 <- tempfile(pattern = "sen2r_out_1_") # output folder
safe_dir <- tempfile(pattern = "sen2r_safe_") # folder to store downloaded SAFE
myextent_1 <- system.file("extdata/vector/barbellino.geojson", package = "sen2r")
library(sen2r)
out_paths_1 <- sen2r(
gui = FALSE,
step_atmcorr = "l2a",
extent = myextent_1,
extent_name = "Barbellino",
timewindow = c(as.Date("2020-11-13"), as.Date("2020-11-25")),
list_prods = c("BOA","SCL"),
list_indices = c("NDVI","MSAVI2"),
list_rgb = c("RGB432B"),
mask_type = "cloud_and_shadow",
max_mask = 10,
path_l2a = safe_dir,
path_out = out_dir_1
)
[2020-11-27 16:59:58] #### Starting sen2r execution. ####
[2020-11-27 16:59:59] Searching for available SAFE products on SciHub...
[2020-11-27 17:00:10] Computing output names...
Linking to GEOS 3.7.1, GDAL 2.2.3, PROJ 4.9.3
[2020-11-27 17:00:11] Processing group 1 of 5...
[2020-11-27 17:00:11] Starting to download the required level-2A SAFE products.
[2020-11-27 17:00:11] Check if products are available for download...
[2020-11-27 17:00:11] Downloading Sentinel-2 image 1 of 1
(S2A_MSIL2A_20201114T101301_N0214_R022_T32TNS_20201114T120346.SAFE)...
[2020-11-27 17:00:59] Download of level-2A SAFE products terminated.
# (skipping most processing messages here)
After subsequent messages describing the processing operations which are being done, a report summarising the conducted processing is issued at the end:
╔══════════════════════════════════════════════════════════════════════════════
║ sen2r Processing Report
╟──────────────────────────────────────────────────────────────────────────────
║ Dates to be processed based on processing parameters: 5
║ Processing completed for: all expected dates.
╚══════════════════════════════════════════════════════════════════════════════
[2020-11-27 17:10:30] #### sen2r session terminated. ####
The processing chain can be re-launched with the command:
sen2r("/home/lranghetti/.sen2r/proc_par/s2proc_20201127_165959.json")
In this case, it shows that all the 5 S2 images satisfying the spatial-temporal query were downloaded and properly processed.
S2 original SAFE images are stored in the folder specified by safe_dir,
and are not deleted after processing (unless the user sets also the argument
rm_safe to TRUE).
list.files(safe_dir)
[1] "S2A_MSIL2A_20201114T101301_N0214_R022_T32TNS_20201114T120346.SAFE"
[2] "S2A_MSIL2A_20201117T102321_N0214_R065_T32TNS_20201117T130408.SAFE"
[3] "S2A_MSIL2A_20201124T101341_N0214_R022_T32TNS_20201124T115339.SAFE"
[4] "S2B_MSIL2A_20201119T101319_N0214_R022_T32TNS_20201119T120649.SAFE"
[5] "S2B_MSIL2A_20201122T102339_N0214_R065_T32TNS_20201122T122607.SAFE"
Outputs are automatically subsetted and masked over the study area,
and stored in appropriate subfolders of out_dir.
list.files(out_dir_1)
[1] "BOA" "MSAVI2" "NDVI" "RGB432B" "SCL"
list.files(file.path(out_dir_1, "NDVI"))
[1] "S2A2A_20201114_022_Barbellino_NDVI_10.tif"
[2] "S2A2A_20201117_065_Barbellino_NDVI_10.tif"
[3] "S2A2A_20201124_022_Barbellino_NDVI_10.tif"
[4] "S2B2A_20201119_022_Barbellino_NDVI_10.tif"
[5] "S2B2A_20201122_065_Barbellino_NDVI_10.tif"
[6] "thumbnails"
See this vignette for more info about folder structure
and naming conventions of sen2r() outputs.
Users can set the desired parameters with the GUI, export them to a JSON file
and run the command sen2r() specifying the JSON path in the argument
param_list to specify processing options.
For example, the command would launch sen2r() using settings specified in file
"myparams.json" (or "file30ac6089ea3_sen2r_params.json" in the reproducible case):
# set the path to an existing JSON file
# (commented here, and substituted with an instruction that creates
# a test JSON file)
# json_path <- "/path/to/myparams.json"
json_path_2 <- build_example_param_file()
json_path_2
[1] "/tmp/RtmpHUtF1k/file9a625065871c_sen2r_params.json"
out_paths_2 <- sen2r(param_list = json_path_2)
[2020-11-27 17:25:23] #### Starting sen2r execution. ####
[2020-11-27 17:25:23] Searching for available SAFE products on SciHub...
[2020-11-27 17:25:26] Computing output names...
[2020-11-27 17:25:28] Starting to download the required level-2A SAFE products.
# (skipping most processing messages here)
╔══════════════════════════════════════════════════════════════════════════════
║ sen2r Processing Report
╟──────────────────────────────────────────────────────────────────────────────
║ Dates to be processed based on processing parameters: 1
║ Processing completed for: all expected dates.
╚══════════════════════════════════════════════════════════════════════════════
[2020-11-27 17:26:43] #### sen2r session terminated. ####
The processing chain can be re-launched with the command:
sen2r("/home/lranghetti/.sen2r/proc_par/s2proc_20201127_172523.json")
This is for example particularly useful if a sen2r() processing requires
ordering images from the LTA archive
(see https://scihub.copernicus.eu/userguide/LongTermArchive).
The user can in fact, in that case:
sen2r() will process
all already online dates, and automatically order the missing ones;See https://luigi.ranghetti.info/post/order-s2-lta/ for a more detailed
discussion about how LTA orders are dealt with in sen2r().
sen2r()This allows users to use a previously saved JSON file as a “template” for a processing, but changing “manually” any desired parameter.
For example, the following instructions would execute the same processing as in the previous example, but changing both the extent and time window of the analysis.
# use the previously saved JSON path
json_path_2
[1] "/tmp/RtmpDLx7qh/file30ac6089ea3_sen2r_params.json"
out_dir_3 <- tempfile(pattern = "sen2r_out_3_") # new output folder
myextent_3 <- system.file("extdata/vector/scalve.kml", package = "sen2r")
out_paths_3 <- sen2r(
param_list = json_path_2,
extent = myextent_3,
extent_name = "newxtent",
timewindow = c(as.Date("2020-10-01"), as.Date("2020-10-30")),
path_out = out_dir_3
)
This allows for example to easily run the same processing over different spatial/temporal extents.