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:
2025-01-02]
--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
-t, --conf_threshold_list FLOAT
List of thresholds used as bins to
discretize the confidence index into several
classes
-c, --conf_classes_list TEXT 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 extract_reflectance
Extracts reflectance from Sentinel-2 data using a vector file containing points, exports the data to a csv file. If new acquisitions are added to the Sentinel-2 directory, new data is extracted and added to the existing csv file.
Usage:
fordead extract_reflectance [OPTIONS]
Options:
--obs_path TEXT Path to a vector file containing observation
points, must have an ID column corresponding to
name_column parameter, an 'area_name' column
with the name of the Sentinel-2 tile from which
to extract reflectance, and a 'espg' column
containing the espg integer corresponding to
the CRS of the Sentinel-2 tile.
--sentinel_dir TEXT Path of the directory containing Sentinel-2
data.
--export_path TEXT Path to write csv file with extracted
reflectance
--name_column TEXT Name of the ID column [default: id]
-b, --bands_to_extract LIST Bands to extract ex : -b B2 -b B3 -b B11
[default: B2, B3, B4, B5, B6, B7, B8, B8A, B11,
B12, Mask]
--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/
Parameters
data_directory x y shape_path name_column ymin ymax chunks
Returns
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
--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.
--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]
--compress_vi Stores the vegetation index as low-resolution
floating-point data as small integers in a
netCDF file. Uses less disk space but can
lead to very small difference in results as
the vegetation is rounded to three decimal
places
--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 obs_to_s2_grid
Attributes intersecting Sentinel-2 tiles to observation points or polygons, adding their epsg and name. If polygons are used, they are converted to grid points located at the centroid of Sentinel-2 pixels. If points or polygons intersect several Sentinel-2 tiles, they are duplicated for each of them. If some intersect no Sentinel-2 tiles, they are removed and their IDs are printed.
Usage:
fordead obs_to_s2_grid [OPTIONS]
Options:
--obs_path TEXT Path to a vector file containing observation points or
polygons, must have an ID column corresponding to
name_column parameter
--sentinel_dir TEXT Path of the directory containing Sentinel-2 data
--export_path TEXT Path used to write resulting vector file, with added
'epsg','area_name' and 'id_pixel' columns
--name_column TEXT Name of the ID column [default: id]
--overwrite Overwrites file at obs_path
--help Show this message and exit.
fordead preprocess_obs
Used as a preprocessing function for a vector file containing observation points or polygons. Can add an ID column if one does not already exist, and can also apply a buffer to erode or dilate observations.
Usage:
fordead preprocess_obs [OPTIONS]
Options:
--obs_path TEXT Path of vector file containing observation points or
polygons to preprocess
--export_path TEXT Path used to export the resulting preprocessed
observation points or polygons
--buffer INTEGER Length in meters of the buffer used to dilate (positive
integer) or erode (negative integer) the observations.
If None, no buffer is applied. Some observations may
disappear completely if a negative buffer is applied
--name_column TEXT Name of the column used to identify observations. If the
column doesn't already exists, it is added as an integer
between 1 and the number of observations [default: id]
--help Show this message and exit.
fordead read_tileinfo
Prints parameters, all dates used and last anomaly date computed to the console
Parameters
data_directory : str Path of the output directory containing the saved TileInfo object Returns
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.
--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/
Parameters
data_directory shape_path name_column x y buffer vector_display_path hover_column_list max_date show_confidence_class zip_results
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/)
--zip_results If True, puts timelapses in a zip file
--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
--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.