[sen2agri-service@teo-sen4capv2 ~]$ /usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/grassland_mowing.sh --script-path /usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_main.py --site-id 4 --config-file /mnt/archive/grassland_mowing_files/crenetherlandsv1_2/2019/config/S4C_L4B_Config_2019.cfg --input-shape-file /mnt/archive/orchestrator_temp/s4c_l4b/7211/25149-s4c-grassland-gen-input-shp/SEN4CAP_L4B_GeneratedInputShp.shp --output-data-dir /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData --start-date 2019-04-01 --end-date 2019-04-30 --seg-parcel-id-attribute NewID --output-shapefile /mnt/archive/orchestrator_temp/s4c_l4b/7211/25152-product-formatter/SEN4CAP_L4B_S1_S2_MowingDetection.shp --do-cmpl True --test True --input-products-list /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T160019_A20190413T104627 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T161352_A20190327T105622 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T164140_A20190418T104631 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T165404_A20190401T105625 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T001128_A20190416T105625 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T002458_A20190421T105629 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T003558_A20190423T104628
/usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_main.py is absolute!
The parameter s4c-config-file defining the database parameters was not provided!
The default /etc/sen2agri/sen2agri.conf will be used
Activating conda sen4cap for user sen2agri-service
Executing source ~/.bashrc && conda activate sen4cap && python /usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_main.py --s4c-config-file /etc/sen2agri/sen2agri.conf --site-id 4 --config-file /mnt/archive/grassland_mowing_files/crenetherlandsv1_2/2019/config/S4C_L4B_Config_2019.cfg --input-shape-file /mnt/archive/orchestrator_temp/s4c_l4b/7211/25149-s4c-grassland-gen-input-shp/SEN4CAP_L4B_GeneratedInputShp.shp --output-data-dir /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData --new-acq-date 2019-04-30 --older-acq-date 2019-04-01 --seg-parcel-id-attribute NewID --output-shapefile /mnt/archive/orchestrator_temp/s4c_l4b/7211/25152-product-formatter/SEN4CAP_L4B_S1_S2_MowingDetection.shp --do-cmpl True --test True  --input-products-list /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T160019_A20190413T104627 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T161352_A20190327T105622 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T164140_A20190418T104631 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200730T165404_A20190401T105625 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T001128_A20190416T105625 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T002458_A20190421T105629 /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T003558_A20190423T104628
config.prds_are_tif = 0
Extracting NDVI infos from the database for the list of products!!!
tile_list: ['31UFU']
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S2_time_interval 5
locAcqTime 10:30:00
apply_model False
modelDir model
NDVI_nomow_model_perc 95.0
sampling_days 1.0
p_n_th 20
model_temporal_range_str ['20190301 00:00:00', '20190930 23:59:59']
start_params (0.05, 50.0, 0.05, 340.0)
bounds [[0.02, 0.0, 0.02, 180.0], [1, 180.0, 1, 360.0]]
prod_type_list ['SNDVI']
sc_fact [1000.0]
corrupted_th [0.1]
decreasing_abs_th [0.12]
decreasing_rate_th [-1e-06]
increasing_rate_th [0.9]
low_abs_th [0.5]
high_abs_th [0.75]
options_layer_burning ["['ALL_TOUCHED=False']"]
invalid_data [-10000.0]
no_mowing_after_det 60
non_overlap_interval_days 28
erode_pixels 0
stat_smpl_n 0
cnt_crop_TR: [('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019'), ('01/03/2019', '30/09/2019')]
cnt_crop_code ['265', '331', '335', '266', '332', '333', '334', '370', '372', '383', '1921', '3506', '3509', '3512', '3513', '3519', '3522', '3523', '3805', '3807', '3808']
cnt_crop_rule [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
['31UFU']
Run tile: 31UFU
The processing can be run
File list generation from data dir
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path: /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T003558_A20190423T104628/TILES/S2AGRI_L3B_A20190423T104628_T31UFU/IMG_DATA/S2AGRI_L3B_SFCOVERMONO_A20190423T104628_T31UFU.TIF
path: /mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T003558_A20190423T104628/TILES/S2AGRI_L3B_A20190423T104628_T31UFU/IMG_DATA/S2AGRI_L3B_SFAPARMONO_A20190423T104628_T31UFU.TIF
size par_list 28
fill pandas structure
File selection based on dates
validity_temporal_range_str [datetime.datetime(2019, 4, 1, 0, 0), datetime.datetime(2019, 4, 30, 23, 59, 59)]
select_date_interval [datetime.datetime(2019, 4, 1, 0, 0), datetime.datetime(2019, 4, 30, 23, 59, 59)]
6
Filtered file list
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 '/mnt/archive/crenetherlandsv1_2/l3b_lai//S2AGRI_L3B_PRD_S4_20200731T003558_A20190423T104628/TILES/S2AGRI_L3B_A20190423T104628_T31UFU/IMG_DATA/S2AGRI_L3B_SNDVI_A20190423T104628_T31UFU.TIF']
directory  /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData  exists...moving on
directory  /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/tmp  exists...moving on
/mnt/archive/orchestrator_temp/s4c_l4b/7211/25149-s4c-grassland-gen-input-shp/SEN4CAP_L4B_GeneratedInputShp.shp
Make virtual raster of input data (without considering extension of the shape file)
/mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/tmp/data_cube_tmp.vrt
virtual raster extent (92028.60841236264, 470717.4387444006, 205413.32908953947, 584102.1594215775)
shape file extent (171201.8595107137, 522661.5486069781, 189055.1211516279, 531429.8952369813)
intesection extent (171201.8595107137, 522661.5486069781, 189055.1211516279, 531429.8952369813)
Make virtual raster of input data (considering intersection between extensions of i- the shape file, ii- the virtual raster)
/mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/tmp/data_cube.vrt
Images in VRT: 6
Generate segmentation map from input shapefiles
segmentsOutputDir /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/segments
directory  /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/segments  exists...moving on
segmentsOutRaster /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/segments/SEN4CAP_L4B_GeneratedInputShp_raster.tif
layer2mask for segments:  /mnt/archive/orchestrator_temp/s4c_l4b/7211/25149-s4c-grassland-gen-input-shp/SEN4CAP_L4B_GeneratedInputShp.shp /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/tmp/data_cube.vrt /mnt/archive/orchestrator_temp/s4c_l4b/7211/25150-s4c-grassland-mowing/SEN4CAP_L4B_S2_OutputData/segments/SEN4CAP_L4B_GeneratedInputShp_raster.tif
input raster transform (171201.8595107137, 10.000416358897235, 0.0, 531429.8952369813, 0.0, -10.000416358897235)
input raster extent [171201.85951071 189052.60271135 522659.53009023 531429.89523698]
input raster projection PROJCS["Amersfoort / RD New",
    GEOGCS["Amersfoort",
        DATUM["Amersfoort",
            SPHEROID["Bessel 1841",6377397.155,299.1528128,
                AUTHORITY["EPSG","7004"]],
            AUTHORITY["EPSG","6289"]],
        PRIMEM["Greenwich",0,
            AUTHORITY["EPSG","8901"]],
        UNIT["degree",0.0174532925199433,
            AUTHORITY["EPSG","9122"]],
        AUTHORITY["EPSG","4289"]],
    PROJECTION["Oblique_Stereographic"],
    PARAMETER["latitude_of_origin",52.1561605555556],
    PARAMETER["central_meridian",5.38763888888889],
    PARAMETER["scale_factor",0.9999079],
    PARAMETER["false_easting",155000],
    PARAMETER["false_northing",463000],
    UNIT["metre",1,
        AUTHORITY["EPSG","9001"]],
    AXIS["Easting",EAST],
    AXIS["Northing",NORTH],
    AUTHORITY["EPSG","28992"]]
Spatial index file: /mnt/archive/orchestrator_temp/s4c_l4b/7211/25149-s4c-grassland-gen-input-shp/SEN4CAP_L4B_GeneratedInputShp.qix
Traceback (most recent call last):
  File "/usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_main.py", line 971, in <module>
    main()
  File "/usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_main.py", line 965, in main
    do_cmpl=s4cConfig.do_cmpl, test=s4cConfig.test)
  File "/usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_main.py", line 740, in main_run
    test=test)
  File "/usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_main.py", line 222, in run_proc
    burned_pixels, seg_attributes = S2_gmd.layer2mask(segmentsFile, output_vrt, segmentsOutRaster, layer_type='segments', options=options_layer_burning)
  File "/usr/share/sen2agri/S4C_L4B_GrasslandMowing/Bin/src_s2/S2_gmd.py", line 416, in layer2mask
    ogr_data.ExecuteSQL('CREATE SPATIAL INDEX ON %s' % LayerName)
  File "/home/sen2agri-service/miniconda3/envs/sen4cap/lib/python3.6/site-packages/osgeo/ogr.py", line 800, in ExecuteSQL
    return _ogr.DataSource_ExecuteSQL(self, *args, **kwargs)
RuntimeError: CreateSpatialIndex : unsupported operation on a read-only datasource.