knitr::opts_chunk$set(echo = TRUE)
Products generated using sen2r functions follows a precise naming convention, and are organised within a customisable folder structure.
Currently, sen2r can be used to generate the following products:
TOA (Top Of Atmosphere) and BOA (Bottom Of Atmosphere) surface reflectances are multiband rasters containing 12 (TOA) or 11 (BOA) bands, here listed:
Bands are named if an output ENVI format is chosen.
For details about Sentinel-2 bands, refer to this page.
All bands are reshaped with the same resolution. In case the user chose a native resolution (10, 20 or 60 m), bands with a finest resolution are downscaled using an averaged method, while pixels of bands with a coarse resolution are replicated without any interpolation method; conversely, in case the user chose a custom resolution, the chosen resampling method is used.
Bands 8 and 8A are alternatively included, basing on the required output resolution. That is due to the fact that they cover an overlapping spectral window; so, band 8A (finer radiometric resolution, coarse spatial one) is provided when the output spatial resolution is adequate to include it (>= 20m), otherwise band 8 is used. The possibility to include both NIR bands could be included in a future release.
Reflectances values are provided in integer output type (multiplicated by 10000), as well as original values included in SAFE archives.
SCL (Scene Classification Maps) are single band rasters provided within Level-2A SAFE archives. Each 20-metres pixel is classified in one of the following classes:
For further details about this product, see this page.
SCL are used as intermediate layers for cloud masking, but they can be also required as output formats. If cloud masking is required by the user, SCL maps are never masked.
CLD (cloud probability) and SNW (snow probability) are single band rasters provided within Level-2A SAFE archives, representing the percentage probability (0-100 Byte values) of each 20 metres pixel to be cloud- or snow-covered. If cloud masking is required by the user, CLD and SNW maps are never masked. Currently these layers cannot be used for cloud masking (only SCL can).
WVP is a single band raster provided within Level-2A SAFE archives, representing the water vapour column depth. Data type is Int16 (values must be multiplicated by 1000 to obtain floating values in centimetres). Typical ranges of water vapour columns are (sea-level-to space): tropical conditions: WVP = 3-5 cm; mid-altitude summer: WVP = 2-3 cm; dry summer, spring, fall: WVP = 1-1.5 cm; dry desert or winter: WVP = 0.3-0.8 cm.
For further details about this product, see the Sentinel-2 Level 2A Product Definition document.
AOT is a single band raster provided within Level-2A SAFE archives, representing the aerosol optical thickness. It is defined as the integrated extinction coefficient over a vertical column of atmosphere of unit cross section. Extinction coefficient is the fractional depletion of radiance per unit path length (also called attenuation for radar frequencies). Data type is Int16 (values must be multiplicated by 1000 to obtain original values). If cloud masking is required by the user, AOT is never masked.
For further details about this product, see the Sentinel-2 Level 2A Product Definition document.
Spectral indices are single band rasters computed from
BOA (by default)
or TOA images
using function s2_calcindices()
(or the main function sen2r()
).
The list of the indices which can be computed can be seen in the GUI (fourth sheet). In the GUI, the index formula is usually graphically provided. In order to check the formula which is used for index computation, the function `list_indices()' can be used. For example, the following command will return the formula of index NDVI:
list_indices("s2_formula", "^NDVI$")
## [1] "(band_8-band_4)/(band_8+band_4)"
See the function documentation for other examples.
The output type can be both floating (in this case, the actual index value is
provided) or integer (default; in this case, values are multiplicated by a
scaling factor, 10000 by default).
So, if the user did not change the arguments outType
and scaleFactor
of
function s2_calcindices()
, or index_datatype
of function sen2r()
,
raster values will be multiplicated by 10000 respect to the "expected" index values.
RGB are three-bands raster in 24-bit format, computed from
BOA
or TOA images
using function s2_rgb()
(or the main function sen2r()
).
Users can customise the bands used to produce images, as well as the
reflectance ranges of each band and the source
(BOA
or TOA):
the easiest way to do this is to use the GUI (fifth sheet),
or to properly set the arguments of function s2_rgb()
.
If cloud masking is required by the user, RGB are never masked (this because they are thought for visualisation).
The names of RGB products contains information about reflectance source and reproduced bands (see the next section).
ESA Sentinel-2 naming convention is particularly long-winded; so, a different convention was adopted, follows this schema:
S2mll_yyyymmdd_rrr_EXTNAME_PROD_rr.fff
(e.g. S2A2A_20190723_022_Barbellino_BOA_10.tif)
s2_translate()
,
and is kept empty for outputs of function s2_merge()
;list_indices("name")
);The extent name is defined with the argument extent_name
of function sen2r()
.
The user can choose any non-empty alphanumeric string as extent name, as long as it does not contain spaces, points nor underscores, and as long as it is not a five-length string with the same structure of a tile ID (two numeric and three uppercase character values), because this structure is reserved for intermediate layers.
The names of RGB images are 7-length strings following the structure RGBrgbX (e.g. RGBb84B), where:
Processing functions allows setting an output directory using the arguments
path_out
, path_rgb
and path_indices
(sen2r()
) or outdir
(s2_translate()
, s2_merge()
, s2_mask()
, s2_rgb()
and s2_calcindices()
).
These folders are automatically created if their parent directories exist.
By default, functions create a subfolder for each product / index / RGB type,
in which files are stored.
Each product subfolder includes a sub-subfolder named thumbnails
,
which contains small JPEG or PNG images which can be used to rapidly monitor
what was done (see s2_thumbnails()
for further details).
For example, the following command would produce the outputs listed below.
json_path <- build_example_param_file() out_dir_1 <- tempfile(pattern = "sen2r_out_1_") library(sen2r) sen2r( json_path, timewindow = c("2019-07-13","2019-07-23"), path_out = out_dir_1 )
[2020-02-06 09:42:40] #### Starting sen2r execution. #### [2020-02-06 09:42:40] Searching for available SAFE products on SciHub... [2020-02-06 09:42:46] Computing output names... [2020-02-06 09:42:48] Processing group 1 of 5...
Most of output message were skipped; see this vignette for further details.
╔══════════════════════════════════════════════════════════════════════════════ ║ sen2r Processing Report ╟────────────────────────────────────────────────────────────────────────────── ║ Dates to be processed based on processing parameters: 5 ║ Processing completed for: all expected dates. ╚══════════════════════════════════════════════════════════════════════════════ [2020-02-06 09:44:45] #### sen2r session terminated. #### The processing chain can be re-launched with the command: sen2r("/home/lranghetti/.sen2r/proc_par/s2proc_20200206_094240.json")
system(paste("tree", out_dir_1)) # working on Linux with binary "tree" installed
/tmp/RtmpUlAdHw/sen2r_out_1_a55119f4ed09 ├── BOA │ ├── S2A2A_20190713_022_sen2r_BOA_10.tif │ ├── S2A2A_20190716_065_sen2r_BOA_10.tif │ ├── S2A2A_20190723_022_sen2r_BOA_10.tif │ ├── S2B2A_20190718_022_sen2r_BOA_10.tif │ ├── S2B2A_20190721_065_sen2r_BOA_10.tif │ └── thumbnails │ ├── S2A2A_20190713_022_sen2r_BOA_10.jpg │ ├── S2A2A_20190713_022_sen2r_BOA_10.jpg.aux.xml │ ├── S2A2A_20190716_065_sen2r_BOA_10.jpg │ ├── S2A2A_20190716_065_sen2r_BOA_10.jpg.aux.xml │ ├── S2A2A_20190723_022_sen2r_BOA_10.jpg │ ├── S2A2A_20190723_022_sen2r_BOA_10.jpg.aux.xml │ ├── S2B2A_20190718_022_sen2r_BOA_10.jpg │ ├── S2B2A_20190718_022_sen2r_BOA_10.jpg.aux.xml │ ├── S2B2A_20190721_065_sen2r_BOA_10.jpg │ └── S2B2A_20190721_065_sen2r_BOA_10.jpg.aux.xml ├── MSAVI2 │ ├── S2A2A_20190713_022_sen2r_MSAVI2_10.tif │ ├── S2A2A_20190716_065_sen2r_MSAVI2_10.tif │ ├── S2A2A_20190723_022_sen2r_MSAVI2_10.tif │ ├── S2B2A_20190718_022_sen2r_MSAVI2_10.tif │ ├── S2B2A_20190721_065_sen2r_MSAVI2_10.tif │ └── thumbnails │ ├── S2A2A_20190713_022_sen2r_MSAVI2_10.jpg │ ├── S2A2A_20190713_022_sen2r_MSAVI2_10.jpg.aux.xml │ ├── S2A2A_20190716_065_sen2r_MSAVI2_10.jpg │ ├── S2A2A_20190716_065_sen2r_MSAVI2_10.jpg.aux.xml │ ├── S2A2A_20190723_022_sen2r_MSAVI2_10.jpg │ ├── S2A2A_20190723_022_sen2r_MSAVI2_10.jpg.aux.xml │ ├── S2B2A_20190718_022_sen2r_MSAVI2_10.jpg │ ├── S2B2A_20190718_022_sen2r_MSAVI2_10.jpg.aux.xml │ ├── S2B2A_20190721_065_sen2r_MSAVI2_10.jpg │ └── S2B2A_20190721_065_sen2r_MSAVI2_10.jpg.aux.xml ├── NDVI │ ├── S2A2A_20190713_022_sen2r_NDVI_10.tif │ ├── S2A2A_20190716_065_sen2r_NDVI_10.tif │ ├── S2A2A_20190723_022_sen2r_NDVI_10.tif │ ├── S2B2A_20190718_022_sen2r_NDVI_10.tif │ ├── S2B2A_20190721_065_sen2r_NDVI_10.tif │ └── thumbnails │ ├── S2A2A_20190713_022_sen2r_NDVI_10.jpg │ ├── S2A2A_20190713_022_sen2r_NDVI_10.jpg.aux.xml │ ├── S2A2A_20190716_065_sen2r_NDVI_10.jpg │ ├── S2A2A_20190716_065_sen2r_NDVI_10.jpg.aux.xml │ ├── S2A2A_20190723_022_sen2r_NDVI_10.jpg │ ├── S2A2A_20190723_022_sen2r_NDVI_10.jpg.aux.xml │ ├── S2B2A_20190718_022_sen2r_NDVI_10.jpg │ ├── S2B2A_20190718_022_sen2r_NDVI_10.jpg.aux.xml │ ├── S2B2A_20190721_065_sen2r_NDVI_10.jpg │ └── S2B2A_20190721_065_sen2r_NDVI_10.jpg.aux.xml ├── RGB432B │ ├── S2A2A_20190713_022_sen2r_RGB432B_10.tif │ ├── S2A2A_20190716_065_sen2r_RGB432B_10.tif │ ├── S2A2A_20190723_022_sen2r_RGB432B_10.tif │ ├── S2B2A_20190718_022_sen2r_RGB432B_10.tif │ ├── S2B2A_20190721_065_sen2r_RGB432B_10.tif │ └── thumbnails │ ├── S2A2A_20190713_022_sen2r_RGB432B_10.jpg │ ├── S2A2A_20190713_022_sen2r_RGB432B_10.jpg.aux.xml │ ├── S2A2A_20190716_065_sen2r_RGB432B_10.jpg │ ├── S2A2A_20190716_065_sen2r_RGB432B_10.jpg.aux.xml │ ├── S2A2A_20190723_022_sen2r_RGB432B_10.jpg │ ├── S2A2A_20190723_022_sen2r_RGB432B_10.jpg.aux.xml │ ├── S2B2A_20190718_022_sen2r_RGB432B_10.jpg │ ├── S2B2A_20190718_022_sen2r_RGB432B_10.jpg.aux.xml │ ├── S2B2A_20190721_065_sen2r_RGB432B_10.jpg │ └── S2B2A_20190721_065_sen2r_RGB432B_10.jpg.aux.xml ├── RGB843B │ ├── S2A2A_20190713_022_sen2r_RGB843B_10.tif │ ├── S2A2A_20190716_065_sen2r_RGB843B_10.tif │ ├── S2A2A_20190723_022_sen2r_RGB843B_10.tif │ ├── S2B2A_20190718_022_sen2r_RGB843B_10.tif │ ├── S2B2A_20190721_065_sen2r_RGB843B_10.tif │ └── thumbnails │ ├── S2A2A_20190713_022_sen2r_RGB843B_10.jpg │ ├── S2A2A_20190713_022_sen2r_RGB843B_10.jpg.aux.xml │ ├── S2A2A_20190716_065_sen2r_RGB843B_10.jpg │ ├── S2A2A_20190716_065_sen2r_RGB843B_10.jpg.aux.xml │ ├── S2A2A_20190723_022_sen2r_RGB843B_10.jpg │ ├── S2A2A_20190723_022_sen2r_RGB843B_10.jpg.aux.xml │ ├── S2B2A_20190718_022_sen2r_RGB843B_10.jpg │ ├── S2B2A_20190718_022_sen2r_RGB843B_10.jpg.aux.xml │ ├── S2B2A_20190721_065_sen2r_RGB843B_10.jpg │ └── S2B2A_20190721_065_sen2r_RGB843B_10.jpg.aux.xml └── SCL ├── S2A2A_20190713_022_sen2r_SCL_10.tif ├── S2A2A_20190716_065_sen2r_SCL_10.tif ├── S2A2A_20190723_022_sen2r_SCL_10.tif ├── S2B2A_20190718_022_sen2r_SCL_10.tif ├── S2B2A_20190721_065_sen2r_SCL_10.tif └── thumbnails ├── S2A2A_20190713_022_sen2r_SCL_10.png ├── S2A2A_20190713_022_sen2r_SCL_10.png.aux.xml ├── S2A2A_20190716_065_sen2r_SCL_10.png ├── S2A2A_20190716_065_sen2r_SCL_10.png.aux.xml ├── S2A2A_20190723_022_sen2r_SCL_10.png ├── S2A2A_20190723_022_sen2r_SCL_10.png.aux.xml ├── S2B2A_20190718_022_sen2r_SCL_10.png ├── S2B2A_20190718_022_sen2r_SCL_10.png.aux.xml ├── S2B2A_20190721_065_sen2r_SCL_10.png └── S2B2A_20190721_065_sen2r_SCL_10.png.aux.xml 12 directories, 90 files
In each of the 6 subfolders BOA
, MSAVI2
, NDVI
, RGB432B
, RGB843B
and SCL
5 products (one for each date) were created.
Sub-subfolders thumbnails
contains thumbnail images.
Users can skip the creation of products' subfolders setting the argument
sen2r(..., path_subdirs = FALSE)
(default: TRUE
), or doing the same with
the argument subdir
of other processing functions.
The creation of thumbnails can be skipped using sen2r(..., thumbnails = FALSE)
(default: TRUE
).
Both the options can be also set using the sen2r()
GUI.
For example, the following command would produce the outputs listed below.
out_dir_2 <- tempfile(pattern = "sen2r_out_2_") sen2r( json_path, timewindow = c("2019-07-13","2019-07-23"), path_out = out_dir_2, path_subdirs = FALSE, thumbnails = FALSE )
[2020-02-06 09:52:30] #### Starting sen2r execution. #### [2020-02-06 09:52:30] Searching for available SAFE products on SciHub... [2020-02-06 09:52:35] Computing output names... [2020-02-06 09:52:36] Processing group 1 of 5... # most of output message were skipped ╔══════════════════════════════════════════════════════════════════════════════ ║ sen2r Processing Report ╟────────────────────────────────────────────────────────────────────────────── ║ Dates to be processed based on processing parameters: 5 ║ Processing completed for: all expected dates. ╚══════════════════════════════════════════════════════════════════════════════ [2020-02-06 09:54:16] #### sen2r session terminated. #### The processing chain can be re-launched with the command: sen2r("/home/lranghetti/.sen2r/proc_par/s2proc_20200206_095230.json")
system(paste("tree", out_dir_2))
/tmp/RtmpUlAdHw/sen2r_out_2_a5513ad348b0 ├── S2A2A_20190713_022_sen2r_BOA_10.tif ├── S2A2A_20190713_022_sen2r_MSAVI2_10.tif ├── S2A2A_20190713_022_sen2r_NDVI_10.tif ├── S2A2A_20190713_022_sen2r_RGB432B_10.tif ├── S2A2A_20190713_022_sen2r_RGB843B_10.tif ├── S2A2A_20190713_022_sen2r_SCL_10.tif ├── S2A2A_20190716_065_sen2r_BOA_10.tif ├── S2A2A_20190716_065_sen2r_MSAVI2_10.tif ├── S2A2A_20190716_065_sen2r_NDVI_10.tif ├── S2A2A_20190716_065_sen2r_RGB432B_10.tif ├── S2A2A_20190716_065_sen2r_RGB843B_10.tif ├── S2A2A_20190716_065_sen2r_SCL_10.tif ├── S2A2A_20190723_022_sen2r_BOA_10.tif ├── S2A2A_20190723_022_sen2r_MSAVI2_10.tif ├── S2A2A_20190723_022_sen2r_NDVI_10.tif ├── S2A2A_20190723_022_sen2r_RGB432B_10.tif ├── S2A2A_20190723_022_sen2r_RGB843B_10.tif ├── S2A2A_20190723_022_sen2r_SCL_10.tif ├── S2B2A_20190718_022_sen2r_BOA_10.tif ├── S2B2A_20190718_022_sen2r_MSAVI2_10.tif ├── S2B2A_20190718_022_sen2r_NDVI_10.tif ├── S2B2A_20190718_022_sen2r_RGB432B_10.tif ├── S2B2A_20190718_022_sen2r_RGB843B_10.tif ├── S2B2A_20190718_022_sen2r_SCL_10.tif ├── S2B2A_20190721_065_sen2r_BOA_10.tif ├── S2B2A_20190721_065_sen2r_MSAVI2_10.tif ├── S2B2A_20190721_065_sen2r_NDVI_10.tif ├── S2B2A_20190721_065_sen2r_RGB432B_10.tif ├── S2B2A_20190721_065_sen2r_RGB843B_10.tif └── S2B2A_20190721_065_sen2r_SCL_10.tif 0 directories, 30 files
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