Usage

Scenarios

Orthorectify pairs of Sentinel-1 images on Sentinel-2 grid

This is the main scenario where pairs of Sentinel-1 images are:

  • calibrated according to β0, γ0 or σ0 calibration

  • then orthorectified onto the Sentinel-2 grid,

  • to be finally concatenated.

The unique elements in this scenario are:

  • the calibration option that must be either one of beta, sigma or gamma

  • the main executable which is S1Processor.

All options go in a request configuration file (e.g. MyS1ToS2.cfg in workingdir). Important options will be:

Then running S1Tiling is as simple as:

cd workingdir
S1Processor MyS1ToS2.cfg

Eventually,

  • The S1 products will be downloaded in s1_images.

  • The orthorectified tiles will be generated in output.

  • Temporary files will be produced in tmp.

Note

S1 Tiling never cleans the tmp directory as its files are cached in between runs. This means you will have to watch this directory and eventually clean it.

Orthorectify pairs of Sentinel-1 images on Sentinel-2 grid with σ0RTC NORMLIM calibration

In this scenario, the calibration applied is the \(σ^0_{RTC}\) NORMLIM calibration described in [Small2011].

[Small2011]

D. Small, “Flattening Gamma: Radiometric Terrain Correction for SAR Imagery,” in IEEE Transactions on Geoscience and Remote Sensing, vol. 49, no. 8, pp. 3081-3093, Aug. 2011, doi: 10.1109/TGRS.2011.2120616.

In S1Tiling, we have chosen to precompute Local Incidence Angle (LIA) maps on Sentinel-2 grid. Given a series of Sentinel-1 images to orthorectify on a Sentinel-2 grid, we select a pair of Sentinel-1 images to compute the LIA in the geometry of these images. The LIA map is then projected, through orthorectification, on a Sentinel-2 tile.

That map will then be used for all series of pairs of Sentinel-1 images that intersect the associated S2 tile.

Regarding options, the only difference with previous scenario are:

S1Tiling will then automatically take care of:

  • producing, or using existing, maps of sin(LIA) for each Sentinel-2 tiles – given an orbit and it direction,

  • producing intermediary products calibrated with β0 LUT.

sine(LIA)

Map of sine(LIA) on 33NWB descending orbit 007

Warning

If you wish to parallelize this scenario and dedicate a different cluster node to each date – as recommended in “Process huge quantities of data” scenario, you will NEED produce all the LIA maps beforehand. Otherwise a same file may be concurrently written to from different nodes, and it will likely end up corrupted.

Note

This scenario requires NORMLIM σ0 binaries. At the moment, NORMLIM σ0 binaries need to be compiled manually. Unless you use either S1Tiling docker images, or S1Tiling on CNES TREX cluster.

Preproduce maps of Local Incidence Angles for σ0RTC NORMLIM calibration

While S1Processor is able to produce the necessary LIA maps on the fly, it is not able to do so when parallelization is done manually over time ranges – as described in “Process huge quantities of data” scenario.

A different program is provided to compute the LIA maps beforehand: S1LIAMap. It takes the exact same parameter files as S1Processor. A few options will be ignored though: calibration type, masking….

cd workingdir
# Yes, the same file works!
S1LIAMap MyS1ToS2.cfg

Note

LIA maps are perfect products to be stored and reused.

Note

This scenario requires NORMLIM σ0 binaries. At the moment, NORMLIM σ0 binaries need to be compiled manually. Unless you use either S1Tiling docker images, or S1Tiling on CNES TREX cluster.

Note

To run S1LIAMap from the official S1Tiling docker, use --lia as the first parameter to the docker execution (just before the the request configuration file and other S1LIAMap related parameters). See Using S1LIAMap with a docker.

Generate masks on final products

Pixel masks of valid data can be produced in all S1Processor scenarios when the option generate_border_mask is True.

Process huge quantities of data

This use case concerns people that:

  • have a lot of images to process over many tiles and over a consequent time-range,

  • and have access to computing resources like HPC clusters

In that case, S1Tiling will be much more efficient if the parallelization is done time-wise. We recommended to cut the full time range in smaller subranges, and to distribute each subrange (with all S2 tiles) to a different node – with jobarrays for instances.

Warning

This scenario is not compatible with normlim calibration where the LIA maps would be computed on-the-fly. For normlim calibration, it’s imperative to precompute (and store LIA maps) before going massively parallel.

Use any other set of DEM inputs

By default S1Tiling comes with a GPKG database that associates SRTM30 geometries to the SRTM tile filename.

In order to use other DEM inputs, we need:

  1. DEM files stored in [PATHS].dem_dir directory.
    The format of these DEM files needs to be supported by OTB/GDAL.

  2. A DEM (GPKG) database that holds a key (or set of keys) that enable(s) to locate/name DEM files associated to a DEM geometry.
    Set the [PATHS].dem_database key accordingly.
    For instance, eotile provides a couple of DEM databases for various types of DEM files.

  3. A naming scheme that will associate an identifier key from the DEM database to a DEM filename (located in [PATHS].dem_dir directory).
    Set the [PATHS].dem_format key accordingly.
    The default {id}.hgt associates the id key to STRM 30m DEM files.
    Using eotile DEM_Union.gpkg as DEM database, we could instead use:

    • {Product10}.tif for Copernicus 30m DEM files, using Product10 key from the GPKG file.

    • {Product30}.tif for Copernicus 90m DEM files, using Product30 key from the GPKG file.

  4. Make sure to use a Geoid file compatible with the chosen DEM. For instance S1Tiling is shipped with EGM96 Geoid with is compatible with SRTM. On the other hand, Copernicus DEM is related to EGM2008 (a.k.a EGM08)

Request Configuration file

The request configuration file passed to S1Processor is in .ini format. It is expected to contain the following entries.

You can use this this template, as a starting point.

[PATHS] section

Option

Description

s1_images

Where S1 images are downloaded thanks to EODAG.
S1Tiling will automatically take care to keep at most 1000 products in that directory – the 1000 last that have been downloaded.
This enables to cache downloaded S1 images in beteen runs.

output

Where products are generated.

lia

Where Local Incidence Maps and sin(LIA) products are generated. Its default value is {output}/_LIA.

tmp

Where intermediary files are produced, and sometimes cached for longer periods.

geoid_file

Path to Geoid model. If left unspecified, it’ll point automatically to the geoid resource shipped with S1 Tiling.

dem_database

Path to DEM (.gpkg) database.
By default points to the internal shapefile/srtm_tiles.gpkg file which knows the geometry of SRTM 30 DEM files.

dem_dir

Path to DEM files.

dem_format

Filename format string to locate the DEM file associated to an identifier within the [PATHS].dem_dir directory.
By default associates the id key of tiles found in the DEM database to {id}.hgt. One may want to use the keys from eotile DEM database like for instance {Product10}.tif for Copernicus 30m DEM.

srtm

(deprecated) Use [PATHS].dem_dir. Path to SRTM files.

[DataSource] section

Option

Description

download

If True, activates the downloading from specified data provider for the ROI, otherwise only local S1 images already in s1_images will be processed.

eodag_config

Designates where the EODAG configuration file is expected to be found.
Default value: %(HOME)s/.config/eodag/eodag.yml.

From S1Tiling point of view, EODAG configuration file will list the authentification credentials for the know providers and their respective priorities.
See EODAG § on Configure EODAG

For instance, given a PEPS account, $HOME/.config/eodag/eodag.yml could contain

peps:
    auth:
        credentials:
            username: THEUSERNAME
            password: THEPASSWORD

nb_parallel_downloads

Number of parallel downloads (+ unzip) of source products.

Warning

Don’t abuse this setting as the data provider may not support too many parallel requests.

roi_by_tiles

The Region of Interest (ROI) for downloading is specified in roi_by_tiles which will contain a list of MGRS tiles. If ALL is specified, the software will download all images needed for the processing (see [Processing] section)

[DataSource]
roi_by_tiles : 33NWB

platform_list

Defines the list of platforms from where come the products to download and process. Valid values are S1A or S1B.

polarisation

Defines the polarisation mode of the products to download and process. Only six values are valid: HH-HV, VV-VH, VV, VH, HV, and HH.

orbit_direction

Download only the products acquired in ascending (ASC) or in descending (DES) order. By default (when left unspecified), no filter is applied.

Warning

Each relative orbit is exclusive to one orbit direction, orbit_direction and relative_orbit_list shall be considered as exclusive.

relative_orbit_list

Download only the products from the specified relative orbits. By default (when left unspecified), no filter is applied.

Warning

Each relative orbit is exclusive to one orbit direction, orbit_direction and relative_orbit_list shall be considered as exclusive.

first_date

Initial date in YYYY-MM-DD format.

last_date

Final date in YYYY-MM-DD format.

tile_to_product_overlap_ratio

Percentage of tile area to be covered for a single or a pair of Sentinel-1 products to be retained.

The number is expected as an integer in the [1..100] range.

[Mask] section

Option

Description

generate_border_mask

This option allows you to choose if you want to generate border masks of the S2 image file produced. Values are True or False.

[Processing] section

Option

Description

cache_dem_by

Tells whether DEM and Geoid files are copied in a temporary directory, or if symbolic links are to be created.

For performance reasons with OTB 7.X, it’s better to regroup the minimal subset of the DEM files required for processing. Symbolic links work fine most of the time, however if the files are on a remote shared filesystem (GPFS, NAS…), performances will be degraded. In those cases, it’s better to copy the required DEM files on a local filesystem.

Geoid file will be also copied (or symlinked), but in {tmp}/geoid/. It won’t be removed automatically. You can also do it manually before running S1Tiling.

Two values are supported for this option: copy and symlink. (default: symlink).

calibration

Defines the calibration type: gamma, beta, sigma, or normlim.

remove_thermal_noise

Activate the thermal noise removal in the images. Values are True or False.

Important

This feature requires a version of OTB >= 7.4.0

lower_signal_value

Noise removal may set some pixel values to 0. However, 0, is currently reserved by S1Tiling chain as a “nodata” value introduced by Margin Cutting and Orthorectification.

This parameter defines which value to use instead of 0 when noise is removed. By default: 1e-7 will be used.

nodata.LIA

Nodata value to use in LIA files

output_spatial_resolution

Pixel size (in meters) of the output images

tiles_shapefile

Path and filename of the tile shape definition (ESRI Shapefile). If left unspecified, it’ll point automatically to the Features.shp shapefile resource shipped with S1 Tiling.

orthorectification_gridspacing

Grid spacing (in meters) for the interpolator in the orthorectification process for more information, please consult the OTB OrthoRectification application.

A nice value is 4 x output_spatial_resolution

orthorectification_interpolation_method

Interpolation method used in the orthorectification process for more information, please consult the OTB OrthoRectification application.

Default value is set to nearest neighbor interpolation (nn) to keep compatibilty with previous results By the way linear method could be more interesting. Note that the bco method is not currently supported

tiles, tiles_list_in_file

Tiles to be processed. The tiles can be given as a list:

  • tiles: list of tiles (comma separated). Ex:

    tiles: 33NWB,33NWC

  • tiles_list_in_file: tile list in a ASCII file. Ex:

    tiles_list_in_file : ~/MyListOfTiles.txt

mode

Running mode:

  • Normal: prints normal, warning and errors on screen

  • debug: also prints debug messages, and forces $OTB_LOGGER_LEVEL=DEBUG

  • logging: saves logs to files

Ex.:

mode : debug logging

nb_parallel_processes

Number of processes to be running in parallel
This number defines the number of Dask Tasks (and indirectly of OTB applications) to be executed in parallel.

Note

For optimal performances, nb_parallel_processes*nb_otb_threads should be <= to the number of cores on the machine.

ram_per_process

RAM allowed per OTB application pipeline, in MB.

nb_otb_threads

Numbers of threads used by each OTB application.

Note

For optimal performances, nb_parallel_processes*nb_otb_threads should be <= to the number of cores on the machine.

produce_lia_map

When LIA sine map is produced, we may also desire the angle values in degrees (x100).

Possible values are:

True:

Do generate the angle map in degrees x 100.

False:

Don’t generate the angle map in degrees x 100.

Note

This option will be ignored when no LIA sine map is required. The LIA sine map is produced by S1LIAMap program , or when calibration mode is "normlim".

dem_warp_resampling_method

DEM files projected on S2 tiles are required to produce LIA maps. This parameters permits to select the resampling method that gdalwarp will use.

The possible values are: near, bilinear, cubic, cubicspline, lanczos, average, rms, mode, max, min, med, q1, q3 and qum.

override_azimuth_cut_threshold_to

Permits to override the analysis on whether top/bottom lines shall be forced to 0 in cutting step.

Possible values are:

True:

Force cutting at the 1600th upper and the 1600th lower lines.

False:

Force to keep every line.

not set/None:

Default analysis heuristic is used.

Warning

This option is not meant to be used. It only makes sense in some very specific scenarios like tests.

fname_fmt.*

Set of filename format templates that permits to override the default filename formats used to generate filenames.

The filename formats can be overridden for both intermediary and final products. Only the final products are documented here. Filename formats for intermediary products are best left alone.

If you change any, make sure to not introduce ambiguity by removing a field that would be used to distinguish two unrelated products.

Available fields come from internal metadata. The main ones of interest are:

Field

Content

Applies to geometry

flying_unit_code

s1a, s1b

S1/S2

tile_name

ex: 33NWB

S2

polarisation

hh, hv, vh, vv

S1/S2

orbit_direction

ASC/DES

S1/S2

orbit

5-digits number that identifies the S1 orbit

S1/S2

acquisition_time

the full timestamp (yymmddthhmmss)

S1/S2

acquisition_day

only the day (yymmddtxxxxxx)

S1/S2

acquisition_stamp

either the full timestamp (yymmddthhmmss), or the day (yymmddtxxxxxx)

S1/S2

LIA_kind

LIA/sin_LIA

S2

basename

Filename of initial S1 image.

S1

rootname

basename without the file extension.

S1

calibration_type

beta/gamma/sigma/dn/Normlim

S1/S2

polarless_basename

Same as basename (with file extension), but without polarisation field. Used when the product only depends on the S1 image geometry and not its content.

S1

polarless_rootname

Same as rootname (without file extension), but without polarisation field. Used when the product only depends on the S1 image geometry and not its content.

S1

fname_fmt.concatenation

File format pattern for concatenation products, for β°, σ° and γ° calibrations.

Default value: {flying_unit_code}_{tile_name}_{polarisation}_{orbit_direction}_{orbit}_{acquisition_stamp}.tif

fname_fmt.s2_lia_corrected

File format pattern for concatenation products when NORMLIM calibrated.

Default value: {flying_unit_code}_{tile_name}_{polarisation}_{orbit_direction}_{orbit}_{acquisition_stamp}_NormLim.tif

fname_fmt.lia_product

File format pattern for LIA and sin(LIA) files

Default value: {LIA_kind}_{flying_unit_code}_{tile_name}_{orbit_direction}_{orbit}.tif

fname_fmt.filtered

File format pattern for filtered files

Default value: {flying_unit_code}_{tile_name}_{polarisation}_{orbit_direction}_{orbit}_{acquisition_stamp}_filtered.tif for β°, σ° and γ° calibrations,

Default value: {flying_unit_code}_{tile_name}_{polarisation}_{orbit_direction}_{orbit}_{acquisition_stamp}_NormLim_filtered.tif when NORMLIM calibrated.

dname_fmt.*

Set of directory format templates that permits to override the default directories where products are generated.

The directory formats can only be overridden for final products.

The only fields available are:

Field

Reference to

{tile_name}

Name of the related tile.

{out_dir}

[PATHS].output

{tmp_dir}

[PATHS].tmp

{lia_dir}

[PATHS].lia

Products from

Option dname_fmt.?

Default value

(β°/σ°/γ°/NORMLIM) Final tiled product

.tiled

{out_dir}/{tile_name}

Masks

.mask

{out_dir}/{tile_name}

degree(LIA) and sin(LIA)

.lia_product

{lia_dir}

Filtering

.filtered

{out_dir}/filtered/{tile_name}

creation_options.*

Set of extra options to create certain products. Creation options take a first and optional pixel type (uint8, float64…) and a list of GDAL creation options.

Products from

Option creation_options.?

Default value

Orthorectification, (β°/σ°/γ°/NORMLIM) Concatenation…

.tiled

COMPRESS=DEFLATE&gdal:co:PREDICTOR=3

Filtering

.filtered

COMPRESS=DEFLATE&gdal:co:PREDICTOR=3

Masks

.mask

uint8 COMPRESS=DEFLATE

LIA (in degrees * 100)

.lia_deg

uint16 COMPRESS=DEFLATE&gdal

sin(LIA)

.lia_sin

COMPRESS=DEFLATE&gdal:co:PREDICTOR=3

[Filtering] section

Note

Multitemporal filtering is not yet integrated in S1Tiling.

Option

Description

filter

If none or empty, then no filtering is done. Otherwise the following spatial speckling filter methods from OTB Despeckle application are supported: Lee, Frost, Gammamap, Kuan.

window_radius

Sets the window radius for the spatial filtering.
Take care that it is a radius, i.e. radius=1 means the filter does an 3x3 pixels averaging.

deramp

Deramp factor – for Frost filter only.
Factor use to control the exponential function used to weight effect of the distance between the central pixel and its neighborhood. Increasing the deramp parameter will lead to take more into account pixels farther from the center and therefore increase the smoothing effects.

nblooks

Number of looks – for all but Frost => Lee, Gammamap and Kuan

keep_non_filtered_products

If not caring for non-filtered product (and if filter method is specified), then the orthorectified and concatenated products won’t be considered as mandatory and they will not be kept at the end of the processing. This (exclusion) feature cannot be used alongside [Mask].generate_border_mask (i.e. keep_non_filtered_products cannot be False if generate_border_mask is True)

Warning

Note: This feature is only supported after LIA calibration as of V1.0 of S1Tiling. See Issue #118.

Log configuration

Default logging configuration is provided in S1Tiling installing directory.

It can be overridden by dropping a file similar to ../s1tiling/logging.conf.yaml in the same directory as the one where the request configuration file is. The file is expected to follow logging configuration file syntax.

Warning

This software expects the specification of:

When mode contains logging, we make sure that file and important handlers are added to the handlers of root and distributed.worker loggers. Note that this is the default configuration.

When mode contains debug the DEBUG logging level is forced into root logger, and $OTB_LOGGER_LEVEL environment variable is set to DEBUG.

Working on clusters

Todo

By default S1Tiling works on single machines. Internally it relies on distributed.LocalCluster a small adaptation would be required to work on a multi-nodes cluster.

Warning

When executing multiple instances of S1Tiling simultaneously, make sure to use different directories for:

  • logs – running S1Tiling in different directories, like $TMPDIR/ on TREX, should be enough

  • storing input files, like for instance $TMPDIR/data_raw/ on TREX for instance.

Process return code

The following exit code are produced when S1Processor returns:

Exit code

Description

0

Execution successful

66

Some OTB tasks could not be executed properly. See the final report in the main log.

67

Downloading error. See the log produced.

68

When offline S1 data could not be retrieved before the configured timeout, the associated S2 products will not be generated and this exit code will be used. See the log produced.

If more critical errors occur, this exit will be superceded.

69

Todo

Output disk full

70

Todo

Cache disk full (when using option --cache-before-ortho)

71

An empty data safe has been found and needs to be removed so it can be fetched again. See the log produced.

72

Error detected in the configuration file. See the log produced.

73

While ALL Sentinel-2 tiles for which there exist an overlapping Sentinel-1 product have been requested, no Sentinel-1 product has been found in the requested time range. See the log produced.

74

No Sentinel-1 product has been found that intersects the requested Sentinel-2 tiles within the requested time range.

If downloading has been disabled, S1 products are searched in the local input directory. See the log produced.

75

Cannot find all the DEM products that cover the requested Sentinel-2 tiles. See the log produced.

76

Geoid file is missing or the specified path is incorrect. See the log produced.

77

Some processing cannot be done because external applications cannot be executed. Likelly OTB and/or NORMLIM related applications aren’t correctly installed. See the log produced.

any other

Unknown error. It could be related to Bash or to Python reserved error codes.