Skip to content

CLI Reference

This page provides documentation for our command line tools.

fordead

fordead - Remote sensing time series processing to detect forest anomalies

The usual workflow is : masked_vi --> train_model --> dieback_detection --> forest_mask --> export_results

Usage:

fordead [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

fordead dieback_detection

Detects anomalies by comparing the vegetation index and its prediction from the model. Detects pixels suffering from dieback when there are 3 successive anomalies. If pixels detected as suffering from dieback have 3 successive dates without anomalies, they are considered healthy again. If stress_index_mode parameter is given, Those periods between detection and return to normal are saved, with the date of first anomaly, date of return to normal, number of dates, and an associated stress index. Anomalies and dieback data are written in the data_directory See details here : https://fordead.gitlab.io/fordead_package/docs/user_guides/english/03_dieback_detection/

Usage:

fordead dieback_detection [OPTIONS]

Options:

  -o, --data_directory TEXT       Path of the output directory
  -s, --threshold_anomaly FLOAT   Minimum threshold for anomaly detection
                                  [default: 0.16]
  --max_nb_stress_periods INTEGER
                                  Maximum number of stress periods  [default:
                                  5]
  --stress_index_mode TEXT        Chosen stress index, if 'mean', the index is
                                  the mean of the difference between the
                                  vegetation index and the predicted
                                  vegetation index for all unmasked dates
                                  after the first anomaly subsequently
                                  confirmed. If 'weighted_mean', the index is
                                  a weighted mean, where for each date used,
                                  the weight corresponds to the number of the
                                  date (1, 2, 3, etc...) from the first
                                  anomaly. If None, the stress periods are not
                                  detected, and no informations are saved.
  --vi TEXT                       Chosen vegetation index, only useful if
                                  step1 was skipped
  --path_dict_vi TEXT             Path of text file to add vegetation index
                                  formula, only useful if step1 was skipped
  --help                          Show this message and exit.

fordead export_results

Export results to a vectorized shapefile format.

Usage:

fordead export_results [OPTIONS]

Options:

  -o, --data_directory TEXT       Path of the output directory
  --start_date TEXT               Start date for exporting results  [default:
                                  2015-06-23]
  --end_date TEXT                 End date for exporting results  [default:
                                  2022-01-02]
  --frequency TEXT                Frequency used to aggregate results, if
                                  value is 'sentinel', then periods correspond
                                  to the period between sentinel dates used in
                                  the detection, or it can be the frequency as
                                  used in pandas.date_range. e.g. 'M'
                                  (monthly), '3M' (three months), '15D'
                                  (fifteen days)  [default: M]
  --multiple_files                If True, one shapefile is exported for each
                                  period containing the areas in dieback at
                                  the end of the period. Else, a single
                                  shapefile is exported containing diebackd
                                  areas associated with the period of dieback
                                  [default: False]
  -t, --conf_threshold_list LIST  List of thresholds used as bins to
                                  discretize the confidence index into several
                                  classes
  -c, --conf_classes_list LIST    List of classes names, if
                                  conf_threshold_list has n values,
                                  conf_classes_list must have n+1 values
  --help                          Show this message and exit.

fordead forest_mask

Compute forest mask from IGN's BDFORET or CESBIO's OSO map See details here : https://fordead.gitlab.io/fordead_package/docs/user_guides/english/04_compute_forest_mask/

Usage:

fordead forest_mask [OPTIONS]

Options:

  -o, --data_directory TEXT      Path of the output directory
  -f, --forest_mask_source TEXT  Source of the forest mask, can be 'vector' to
                                 use a vector file at vector_path, or the path
                                 to a binary raster of 10m resolution with the
                                 value 1 on the pixels of interest, 'BDFORET'
                                 to use the BD Foret of the IGN, 'OSO' to use
                                 the CESBIO's land use map, or None to not use
                                 a forest mask and to extend the area of
                                 interest to all pixels
  --dep_path TEXT                Path to shapefile containg departements with
                                 code insee. Optionnal, only used if
                                 forest_mask_source equals 'BDFORET'
  --bdforet_dirpath TEXT         Path to directory containing BD FORET.
                                 Optionnal, only used if forest_mask_source
                                 equals 'BDFORET'
  --list_forest_type TEXT        List of forest types to be kept in the forest
                                 mask, corresponds to the CODE_TFV of the BD
                                 FORET. Optionnal, only used if
                                 forest_mask_source equals 'BDFORET'
                                 [default: FF2-00-00, FF2-90-90, FF2-91-91,
                                 FF2G61-61]
  --path_oso TEXT                Path to soil occupation raster, only used if
                                 forest_mask_source = 'OSO'
  --list_code_oso INTEGER        List of values used to filter the soil
                                 occupation raster. Only used if
                                 forest_mask_source = 'OSO'  [default: 17]
  --vector_path TEXT             path of shapefile whose polygons will be
                                 rasterized as a binary raster with
                                 resolution, extent and crs of the raster at
                                 path_example_raster. Only used if
                                 forest_mask_source = 'vector'
  --path_example_raster TEXT     Path to raster from which to copy the extent,
                                 resolution, CRS...
  --help                         Show this message and exit.

fordead graph_series

From previously computed results, graphs the results for specific pixels showing the vegetation index for each dates, the model and the detection. By specifying 'shape_path' and 'name_column' parameters, it can be used with a shapefile containing points with a column containing a unique ID used to name the exported image. By specifying 'x' and 'y' parameters, it can be used with coordinates in the Sentinel-2 data CRS. If neither shape_path or x and y parameters are specified, the user will be prompted to give coordinates in the system of projection of the tile. Graphs can also be plotted for random pixels inside the forest mask. The user can also choose to specify pixels by their indices from the top left hand corner of the computed area (If only a small region of interest was computed (for example by using extent_shape_path parameter in the step 01_compute_masked_vegetationindex (https://fordead.gitlab.io/fordead_package/docs/user_guides/english/01_compute_masked_vegetationindex/)), then create a timelapse on this whole region of interest (https://fordead.gitlab.io/fordead_package/docs/user_guides/Results_visualization/#creer-des-timelapses), then these indices correspond to the indices in the timelapse) The graphs are exported in the data_directory/TimeSeries directory as png files. See details here : https://fordead.gitlab.io/fordead_package/docs/user_guides/Results_visualization/

Usage:

fordead graph_series [OPTIONS]

Options:

  -o, --data_directory TEXT  Path of the directory containing results from the
                             region of interest
  -x, --x FLOAT              x coordinate in the Sentinel-2 data CRS of the
                             pixel of interest. Not used if shape_path
                             parameter is used.
  -y, --y FLOAT              y coordinate in the Sentinel-2 data CRS of the
                             pixel of interest. Not used if shape_path
                             parameter is used.
  --shape_path TEXT          Path to shapefile containing points whose data
                             will be plotted. If None, indexes or coordinates
                             for x and y can be given
  --name_column TEXT         Name of the column containing the name of the
                             point, used to name the exported image. Not used
                             if pixel is selected from indexes or coordinates
  --ymin FLOAT               ymin limit of graph
  --ymax FLOAT               ymax limit of graph
  --chunks INTEGER           Chunk length to import data as dask arrays and
                             save RAM, advised if computed area in
                             data_directory is large
  --help                     Show this message and exit.

fordead masked_vi

Computes masks and masked vegetation index for each SENTINEL date under a cloudiness threshold. The mask includes pixels ouside satellite swath, some shadows, and the mask from SENTINEL data provider if the option is chosen. Also, if soil detection is activated, the mask includes bare ground detection and cloud detection, but the process might only be adapted to THEIA data in France's coniferous forests. If it is not activated, then the user can choose a mask of his own using the formula_mask parameter. Results are written in the chosen directory. See details here : https://fordead.gitlab.io/fordead_package/docs/user_guides/english/01_compute_masked_vegetationindex/

Usage:

fordead masked_vi [OPTIONS]

Options:

  -i, --input_directory TEXT     Path of the directory with Sentinel dates
  -o, --data_directory TEXT      Path of the output directory
  -n, --lim_perc_cloud FLOAT     Maximum cloudiness at the tile scale, used to
                                 filter used SENTINEL dates. Set parameter as
                                 -1 to not filter based on cloudiness
                                 [default: 0.4]
  --interpolation_order INTEGER  interpolation order for bands at 20m
                                 resolution : 0 = nearest neighbour, 1 =
                                 linear, 2 = bilinéaire, 3 = cubique
                                 [default: 0]
  --sentinel_source TEXT         Source of data, can be 'THEIA' et 'Scihub' et
                                 'PEPS'  [default: THEIA]
  --apply_source_mask            If True, applies the mask from SENTINEL-data
                                 supplier  [default: False]
  --soil_detection               If True, bare ground is detected and used as
                                 mask, but the process has not been tested on
                                 other data than THEIA data in France (see htt
                                 ps://fordead.gitlab.io/fordead_package/docs/u
                                 ser_guides/english/01_compute_masked_vegetati
                                 onindex/). If False, mask from formula_mask
                                 is applied.  [default: False]
  --formula_mask TEXT            formula whose result would be binary, as
                                 described here https://fordead.gitlab.io/ford
                                 ead_package/reference/fordead/masking_vi/#com
                                 pute_vegetation_index. Is only used if
                                 soil_detection is False.  [default: (B2 >=
                                 700)]
  --vi TEXT                      Chosen vegetation index  [default: CRSWIR]
  --ignored_period LIST          Period whose Sentinel dates to ignore (format
                                 'MM-DD', ex : --ignored_period 11-01
                                 --ignored_period 05-01
  --extent_shape_path TEXT       Path of shapefile used as extent of
                                 detection, if None, the whole tile is used
  --path_dict_vi TEXT            Path of text file to add vegetation index
                                 formula, if None, only built-in vegetation
                                 indices can be used (CRSWIR, NDVI)
  --help                         Show this message and exit.

fordead read_tileinfo

Prints parameters, all dates used and last anomaly date computed to the console

Usage:

fordead read_tileinfo [OPTIONS]

Options:

  -o, --data_directory TEXT  Path of the output directory containing the saved
                             TileInfo object
  --help                     Show this message and exit.

fordead theia_preprocess

Automatically downloads all Sentinel-2 data from THEIA between two dates under a cloudiness threshold. Then this data is unzipped, keeping only chosen bands from Flat REflectance data, and zip files can be emptied as a way to save storage space. Finally, if two Sentinel-2 directories come from the same acquisition date, they are merged by replacing no data pixels from one directory with pixels with data in the other, before removing the latter directory.

Usage:

fordead theia_preprocess [OPTIONS]

Options:

  -i, --zipped_directory TEXT     Path of the directory with zipped theia data
  -o, --unzipped_directory TEXT   Path of the output directory
  -t, --tiles TEXT                Name of the tiles to be downloaded (format :
                                  T31UFQ)
  --login_theia TEXT              Login of your theia account
  --password_theia TEXT           Password of your theia account
  --level [LEVEL1C|LEVEL2A|LEVEL3A]
                                  Product level for reflectance products
                                  [default: LEVEL2A]
  --start_date TEXT               start date, fmt('2015-12-22')  [default:
                                  2015-06-23]
  --end_date TEXT                 end date, fmt('2015-12-22')  [default:
                                  2023-06-23]
  -n, --lim_perc_cloud INTEGER    Maximum cloudiness in SENTINEL dates
                                  downloaded (%)  [default: 50]
  -b, --bands TEXT                List of bands to extracted (B2, B3, B4, B5,
                                  B6, B7, B8, B8A, B11, B12, as well as CLMR2,
                                  CLMR2, EDGR1, EDGR2, SATR1, SATR2 for
                                  LEVEL2A data, and DTS1, DTS2, FLG1, FLG2,
                                  WGT1, WGT2 for LEVEL3A)  [default: B2, B3,
                                  B4, B5, B6, B7, B8, B8A, B11, B12, CLMR2]
  --correction_type [SRE|FRE|FRC]
                                  Chosen correction type (SRE or FRE for
                                  LEVEL2A data, FRC for LEVEL3A)  [default:
                                  FRE]
  --empty_zip                     If True, the zip files are emptied as a way
                                  to save space.  [default: False]
  --help                          Show this message and exit.

fordead timelapse

Create timelapse allowing navigation through Sentinel-2 dates with detection results superimposed. By specifying 'shape_path' and 'name_column' parameters, it can be used with a shapefile containing one or multiple polygons or points with a column containing a unique ID used to name the export. By specifying 'x' and 'y' parameters, it can be used by specifying coordinates in the system of projection of the tile. The timelapse is exported in the data_directory/Timelapses directory as an html file. See details https://fordead.gitlab.io/fordead_package/docs/user_guides/Results_visualization/

Usage:

fordead timelapse [OPTIONS]

Options:

  -o, --data_directory TEXT   Path of the directory containing results from
                              the region of interest
  --shape_path TEXT           Path of the shapefile of the area, or points, to
                              convert to timelapse. Not used if timelapse made
                              from x and y coordinates
  --name_column TEXT          Name of the column containing the name of the
                              export. Not used if timelapse made from x and y
                              coordinates  [default: id]
  -x, --x INTEGER             Coordinate x in the crs of the Sentinel-2 tile.
                              Not used if timelapse is made using a shapefile
  -y, --y INTEGER             Coordinate y in the crs of the Sentinel-2 tile.
                              Not used if timelapse is made using a shapefile
  --buffer INTEGER            Buffer around polygons or points for the extent
                              of the timelapse  [default: 100]
  --vector_display_path TEXT  Path of the shapefile with ground observations
  --hover_column_list TEXT    List of columns to display when hovering mouse
                              over vectors of vector_display_path
  --max_date TEXT             Last date used in the timelapse
  --show_confidence_class     If True, detected dieback is shown with the
                              confidence class at the last date used, as
                              vectorized in the step [05_export_results](https
                              ://fordead.gitlab.io/fordead_package/docs/user_g
                              uides/english/05_export_results/)  [default:
                              False]
  --zip_results               If True, puts timelapses in a zip file
                              [default: False]
  --help                      Show this message and exit.

fordead train_model

Uses first SENTINEL dates to train a periodic vegetation index model capable of predicting the vegetation index at any date. If there aren't nb_min_date at min_last_date_training, later dates between min_last_date_training and max_last_date_training can be used. See details here : https://fordead.gitlab.io/fordead_package/docs/user_guides/english/02_train_model/

Usage:

fordead train_model [OPTIONS]

Options:

  -o, --data_directory TEXT      Path of the output directory
  --nb_min_date INTEGER          Minimum number of valid dates to compute a
                                 vegetation index model for the pixel
                                 [default: 10]
  --min_last_date_training TEXT  First date that can be used for detection
                                 [default: 2018-01-01]
  --max_last_date_training TEXT  Last date that can be used for training
                                 [default: 2018-06-01]
  --correct_vi                   If True, corrects vi using large scale median
                                 vi  [default: False]
  --path_vi TEXT                 Path of directory containing vegetation
                                 indices for each date. If None, the
                                 information has to be saved from a previous
                                 step
  --path_masks TEXT              Path of directory containing masks for each
                                 date.  If None, the information has to be
                                 saved from a previous step
  --help                         Show this message and exit.