example scripts update

script_examples/process_l2a_and_indices_by_identifier_multiprocessing.csv

 pre1_pre2_starttime_pre3_pre4_tile_pre5_endtime_maxclouds_site_nom_indices
-#~ S2A_MSIL1C_20161023T070232_N0204_R120_T39LUG_20161023T070234
-#~ S2A_MSIL1C_20160611T072212_N0202_R063_T38KLB_20160611T072355
-#~ S2A_MSIL1C_20160621T072212_N0204_R063_T38KME_20160621T072212
-#~ S2A_MSIL1C_20160608T071222_N0202_R020_T38KLV_20160608T071512
-#~ S2A_MSIL1C_20160608T071222_N0202_R020_T38KMD_20160608T071219
-#~ S2A_MSIL1C_20160621T072212_N0204_R063_T38KLF_20160621T072212
-#~ S2A_MSIL1C_20160628T071222_N0204_R020_T38JMT_20160628T071217
-#~ S2A_MSIL1C_20160611T072212_N0202_R063_T38KMC_20160611T072355
-#~ S2A_MSIL1C_20160608T071222_N0202_R020_T38KLU_20160608T071512
-#~ S2A_MSIL1C_20160628T071222_N0204_R020_T38JLT_20160628T071217
-#~ S2A_MSIL1C_20161108T072212_N0204_R063_T38KLA_20161108T072535
-#~ S2A_MSIL1C_20160516T070242_N0202_R120_T39LTG_20160516T070240
-#~ S2A_MSIL1C_20160516T070242_N0202_R120_T39LTF_20160516T070240
-#~ S2A_MSIL1C_20160516T070242_N0202_R120_T38LRK_20160516T070240
-#~ S2A_MSIL1C_20160708T071222_N0204_R020_T38LRK_20160708T071218
-#~ S2A_MSIL1C_20160715T070242_N0204_R120_T38LRL_20160715T070238
-#~ S2A_MSIL1C_20160715T070242_N0204_R120_T39LTF_20160715T070238
-#~ S2A_MSIL1C_20160830T072212_N0204_R063_T38KMG_20160830T072348
-#~ S2A_MSIL1C_20160817T071222_N0204_R020_T38LNH_20160817T071218
-#~ S2A_MSIL1C_20160817T071222_N0204_R020_T38LPJ_20160817T071218
-#~ S2A_MSIL1C_20160817T071222_N0204_R020_T38LQJ_20160817T071218
-#~ S2A_MSIL1C_20160827T071222_N0204_R020_T38LQH_20160827T071227
-#~ S2A_MSIL1C_20160827T071222_N0204_R020_T38LPH_20160827T071401
-#~ S2A_MSIL1C_20160827T071222_N0204_R020_T38LPH_20160827T071227
-#~ S2A_MSIL1C_20160830T072212_N0204_R063_T38LMH_20160830T072348
-#~ S2A_MSIL1C_20160906T071212_N0204_R020_T38LRJ_20160906T071214
-#~ S2A_MSIL1C_20160926T071212_N0204_R020_T38KMC_20160926T071210
-#~ S2A_MSIL1C_20160926T071212_N0204_R020_T38KLC_20160926T071210
-#~ S2A_MSIL1C_20161108T072212_N0204_R063_T38KLA_20161108T072535
+
+# L1C identifier list
 S2A_MSIL1C_20160830T072212_N0204_R063_T38KLE_20160830T072348
-S2A_MSIL1C_20160909T072212_N0204_R063_T38KLF_20160909T072258
-S2A_MSIL1C_20161029T072212_N0204_R063_T38KME_20161029T072230
-S2A_MSIL1C_20161003T070232_N0204_R120_T39LUC_20161003T070230
-S2A_MSIL1C_20161003T070232_N0204_R120_T39LVC_20161003T070230
-S2A_MSIL1C_20161003T070232_N0204_R120_T39LUC_20161003T070230
+

script_examples/process_l2a_and_indices_by_identifier_multiprocessing.py

 # -*- coding:utf-8 -*-
 
-""" lance les traitements sur les fichiers L1C qui ont
-été téléchargés mais qui n'ont pas été traités 
+""" Process L1C products by identifiers 
+    
+    Input : - an identifier list in a csv file
+            - a Sen2chain L1C library 
+    Output : L2A / indices
+    
+    If any argument is supplied nothiing is done, this script outputs only a product list to process but without any processing
+    
+    This script uses multiprocessing to process files. 
+    Please adapt the number of process lines 65, 79, 96 according to your hardware
+    
+    Please refer to sen2chain wiki for more info : https://framagit.org/jebins/sen2chain/wikis/home
 """
+
 import logging
 import datetime
 import pandas as pd
@@ -19,18 +30,18 @@ except:
     arg = []
 print(arg)
 
-logger = logging.getLogger("Traitement L2A")
+logger = logging.getLogger("L2A Processing")
 logging.basicConfig(level=logging.INFO)
 logger.setLevel(logging.INFO)
 
 
-# default nombre de jours à requeter à partir de today
-# si le champs n'est pas renseingné ds le csv
+# default number of days to check before today 
+# if this field is empty in the csv file
 delta_t = 15
 
-# liste de tuiles à traiter
+# file path to tile identifiers list to process
 fwd = os.path.dirname(os.path.realpath(__file__))
-tiles_file = fwd + "/97_02_traitement_l2a_identifier_multiprocessing.csv"
+tiles_file = fwd + "/process_l2a_and_indices_by_identifier_multiprocessing.csv"
 
 tiles_list = pd.read_csv(tiles_file, sep = '_', na_values="", na_filter=False, comment='#')
 
@@ -45,15 +56,7 @@ for index, row in tiles_list.iterrows():
 logger.info("\n{}".format(tiles_list))
 
 
-# Nettoyage de la librairie
-clean_list = []
-for index, row in tiles_list.iterrows():
-    clean_list.append(row.tile)
-lib = Library()
-lib.clean(clean_list, remove=True)
-
-
-# Traitement des L1C en L2A
+# Processing L1C to L2A
 l1c_process_list =  []
 for index, row in tiles_list.iterrows():
     t = Tile(row.tile)
@@ -67,7 +70,7 @@ if l1c_process_list:
         l2a_res = l2a_multiprocessing(l1c_process_list, nb_proc=12)
 
 
-# Traitement des L2A (clouds)
+# Processing L2A cloud masks
 cld_l2a_process_list =  []
 for index, row in tiles_list.iterrows():
     t = Tile(row.tile)
@@ -81,7 +84,7 @@ if cld_l2a_process_list:
         cld_res = cld_multiprocessing(cld_l2a_process_list, nb_proc=4)
 
 
-# Traitement des L2A (indices)
+# Processing L2A indices
 indices_l2a_process_list =  []
 for index, row in tiles_list.iterrows():
     t = Tile(row.tile)

script_examples/process_l2a_and_indices_multiprocessing.csv

 tile;start_time;end_time;max_clouds;site;nom;indices
-
-40KCB;2018-10-01;;;France;Reunion;NDVI/NDWIGAO/NDWIMCF/MNDWI/BIGR/BIRNIR/BIBG
-#~ 40KEC;2019-01-01;;;Maurice;Maurice
-#~ 41KNU;2019-03-01;;;Maurice;Rodrigues;NDVI/NDWIGAO/NDWIMCF/BIGR/BIRNIR/BIBG
-#~ 38LML;2019-01-01;;;France;Mayotte
-#~ 38LNL;2019-01-01;;;France;Mayotte
-#~ 38LNM;2019-01-01;;;France;Mayotte
-#~ 38LMM;2019-01-01;;;Comores;Anjouan_MAY
-#~ 38LLN;2019-01-01;;;Comores;Grande_Comores
-#~ 38LLM;2019-01-01;;;Comores;GC_Moheli
-
-#~ #37KFR;2015-01-01;2020-01-01;;TAAF_Eparses;Europa
-#~ #37KES;2015-01-01;2020-01-01;;TAAF_Eparses;Bassas
-#~ #38KKG;;;;TAAF_Eparses;Juan
-#~ #38LPM;20190101;;;TAAF_Eparses;Geyser_Zelee
-#~ #38LQN;;;;TAAF_Eparses;Glorieuses
-#~ #40MCV;;;;Seychelles;Mahe
-#~ #40MCA;;;;Seychelles;Praslin
-
-#~ 38LPQ;2019-01-01;;;Seychelles;Aldabra
-
-#~ #38LQQ;;;;Seychelles;Cosmoledo_Cosmoledo
-#~ #38LQP;;;;Seychelles;Cosmoledo_Astove
-#~ #39GWJ;;;;TAAF_Subantarctique;Crozet_Possession
-#~ #39GVJ;;;;TAAF_Subantarctique;Crozet_Cochons_Manchots
-#~ #39GVK;;;;TAAF_Subantarctique;Crozet_Cochons_Apotres
-#~ #42FXL;;;;TAAF_Subantarctique;Kerguelen_E
-#~ #42FWL;;;;TAAF_Subantarctique;Kerguelen_C
-#~ #42FVL;;;;TAAF_Subantarctique;Kerguelen_W
-#~ #42FVM;;;;TAAF_Subantarctique;Kerguelen_NW
-#~ #42FWM;;;;TAAF_Subantarctique;Kerguelen_NC
-#~ 38KLA;2019-01-01;;;Madagascar;Morombe;NDVI/NDWIGAO/NDWIMCF/MNDWI/BIGR/BIRNIR/BIBG
-
-#~ 38KQE;;;;Madagascar;Tana
-#~ 38KQD;;;;Madagascar;Sud_Tana
-#~ 38KRE;;;;Madagascar;Est_Tana
-#~ 38KRD;;;;Madagascar;Sud-Est_Tana
+# max_clouds parameter not implemented yet
+40KCB;2018-10-01;2018-11-01;;France;Reunion;NDVI/NDWIGAO/NDWIMCF/MNDWI/BIGR/BIRNIR/BIBG

script_examples/process_l2a_and_indices_multiprocessing.py

 # -*- coding:utf-8 -*-
 
-""" lance les traitements sur les fichiers L1C qui ont
-été téléchargés mais qui n'ont pas été traités 
+""" Process L1C products 
+    
+    Input : - a tile list in a csv file (tile;start_time;end_time;max_clouds;site;nom;indices)
+            - a Sen2chain L1C library 
+    Output : L2A / indices
+    
+    If any argument is supplied nothiing is done, this script outputs only a product list to process but without any processing
+    
+    This script uses multiprocessing to process files. 
+    Adapt the number of process (lines 65, 79, 96) according to your hardware
+    
+    Please refer to sen2chain wiki for more info : https://framagit.org/jebins/sen2chain/wikis/home
 """
+
 import logging
 import datetime
 import pandas as pd
-from sen2chain import Tile, L1cProduct, L2aProduct
-from sen2chain import l2a_multiprocessing, cldidx_multiprocessing, cld_multiprocessing, idx_multiprocessing
-import os, shutil, sys
-import glob
-import math
+from sen2chain import Tile
+from sen2chain import l2a_multiprocessing, cld_multiprocessing, idx_multiprocessing
+import os, sys
 from itertools import chain
 
 try:
@@ -19,18 +28,18 @@ except:
     arg = []
 print(arg)
 
-logger = logging.getLogger("Traitement L2A")
+logger = logging.getLogger("L2A Prcessing")
 logging.basicConfig(level=logging.INFO)
 logger.setLevel(logging.INFO)
 
 
-# default nombre de jours à requeter à partir de today
-# si le champs n'est pas renseingné ds le csv
+# default number of days to check before today 
+# if this field is empty in the csv file
 delta_t = 15
 
-# liste de tuiles à traiter
+# file path to tile list to process
 fwd = os.path.dirname(os.path.realpath(__file__))
-tiles_file = fwd + "/99_traitement_l2a_multiprocessing.csv"
+tiles_file = fwd + "/process_l2a_and_indices_multiprocessing.csv"
 
 tiles_list = pd.read_csv(tiles_file, sep = ';', na_values="", na_filter=False, comment='#')
 
@@ -45,7 +54,7 @@ for index, row in tiles_list.iterrows():
 logger.info("\n{}".format(tiles_list))
 
 
-# Traitement des L1C en L2A
+# Processing L1C to L2A
 l1c_process_list =  []
 for index, row in tiles_list.iterrows():
     t = Tile(row.tile)
@@ -59,7 +68,7 @@ if l1c_process_list:
         l2a_res = l2a_multiprocessing(l1c_process_list, nb_proc=12)
 
 
-# Traitement des L2A (clouds)
+# Processing L2A cloud masks
 cld_l2a_process_list =  []
 for index, row in tiles_list.iterrows():
     t = Tile(row.tile)
@@ -73,7 +82,7 @@ if cld_l2a_process_list:
         cld_res = cld_multiprocessing(cld_l2a_process_list, nb_proc=4)
 
 
-# Traitement des L2A (indices)
+# Processing L2A indices
 indices_l2a_process_list =  []
 for index, row in tiles_list.iterrows():
     t = Tile(row.tile)