# HG changeset patch
# User climate
# Date 1640877849 0
# Node ID 81b0ca76435dce311034ff868739368f84d3ebd6
"planemo upload for repository https://gitlab.com/eetun-tiimi/EODIE commit c4a5672398bc878dd2bc0bf4f3a26f59b3f6395c"
diff -r 000000000000 -r 81b0ca76435d eodie.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/eodie.xml Thu Dec 30 15:24:09 2021 +0000
@@ -0,0 +1,363 @@
+
+ converts simple features data between file formats
+
+ macros.xml
+
+
+
+ eodie
+ python
+ shapely
+ rasterio
+ rasterstats
+ fiona
+ numpy
+ gdal
+ pyyaml
+ unzip
+ tar
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diff -r 000000000000 -r 81b0ca76435d macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Dec 30 15:24:09 2021 +0000
@@ -0,0 +1,223 @@
+
+ 1.0.2
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+ topic_0610
+ topic_3050
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+ 10.5281/zenodo.4762323
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diff -r 000000000000 -r 81b0ca76435d postprocess_csv.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/postprocess_csv.sh Thu Dec 30 15:24:09 2021 +0000
@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+WORKDIR=$1
+RESDIR=$2
+
+echo "===================================================================="
+echo " Convert EODIE csv to tabular "
+echo "===================================================================="
+
+nb_csv=$(find $WORKDIR -type f -name "*.csv" | wc -l)
+echo "Number of csv file to convert: $nb_csv"
+if [[ $nb_csv -gt 0 ]]; then
+ echo "Start"
+ for infile in $WORKDIR/*.csv; do
+ echo "processing $infile"
+ sed -i.bak -e "s/,/\t/g" $infile
+ mv $infile $RESDIR/.
+ done
+fi
+
+echo "EODIE Tabular saved."
diff -r 000000000000 -r 81b0ca76435d test-data/20211213-104427.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/20211213-104427.log Thu Dec 30 15:24:09 2021 +0000
@@ -0,0 +1,6 @@
+INFO:root:All inputs for this process: dict_items([('platform', 'tif'), ('config', {'platform': 'tif', 'datepattern': '20[1-2][0-9][0-1][0-9][0-3][0-9]', 'name': 'testrgb', 'maxcloudcover': 99, 'pixelsize': 10, 'resampling_method': 'bilinear', 'fieldname': 'Name', 'lookup': './postprocesses/lookuptable.txt'}), ('mydir', None), ('myfile', 'smaller_area_20100401.tif'), ('input', ['smaller_area_20100401.tif']), ('shpbase', 'shapefile'), ('outpath', './results'), ('idname', 'id'), ('statistics_out', True), ('array_out', False), ('indexlist', None), ('statistics', ['count', 'mean', 'percentile_10']), ('startdate', '20160101'), ('enddate', '20211221'), ('keep_shp', False), ('geotiff_out', False), ('test', False), ('exclude_border', False), ('extmask', None), ('exclude_splitshp', True), ('verbose', False), ('format', ['statistics'])])
+INFO:root:File to be processed smaller_area_20100401.tif
+INFO:root:Checking the projection of the inputfile now
+INFO:root:Reprojectcommand: ogr2ogr -t_srs EPSG:3067 shapefile_reprojected_3067.shp shapefile.shp
+INFO:root:input shapefile had other than EPSG 3067 but was reprojected and works now
+INFO:root:stat to csv in: ./results/testrgb_20100401__statistics.csv
diff -r 000000000000 -r 81b0ca76435d test-data/20211217-210343.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/20211217-210343.log Thu Dec 30 15:24:09 2021 +0000
@@ -0,0 +1,21 @@
+INFO:root:All inputs for this process: dict_items([('platform', 's2'), ('config', {'platform': 's2', 'bitmask': 0, 'tobemaskedlist': [9, 8, 3, 10, 0, 1], 'filepattern': 'S2[A-C]_MSIL2A_\\d{8}T\\d{6}_N\\d{4}_R\\d{3}_T\\d{2}[A-Z]{3}_\\d{8}T\\d{6}.SAFE$', 'red': 'B04', 'green': 'B03', 'blue': 'B02', 'nir': 'B08', 'r_edge': 'B05', 'swir1': 'B11', 'swir2': 'B12', 'productnameidentifier': 'S2*.SAFE', 'bandlocation': ['.', '*', '*', 'IMG_DATA'], 'pathbuildinglist': ['R', 'pixelsize', 'm', '*', 'bandname', '_', 'pixelsize', 'm.jp2'], 'cloudfilename': 'SCL', 'tilepattern': '(?<=T)[0-9]{2}[A-Z]{3}', 'datepattern': '20[1-2][0-9][0-1][0-9][0-3][0-9]', 'band_designation': 'B[0-1]?\\dA?', 'quantification_value': 10000, 'B01': [60], 'B02': [10, 20, 60], 'B03': [10, 20, 60], 'B04': [10, 20, 60], 'B05': [20, 60], 'B06': [20, 60], 'B07': [20, 60], 'B08': [10], 'B8A': [20, 60], 'B09': [60], 'B11': [20, 60], 'B12': [20, 60], 'SCL': [20, 60], 'AOT': [10, 20, 60], 'TCI': [10, 20, 60], 'WVP': [10, 20, 60], 'maxcloudcover': 99, 'pixelsize': 10, 'resampling_method': 'bilinear', 'tileshp': './sentinel2_tiles_world/sentinel2_tiles_world', 'fieldname': 'Name', 'lookup': './postprocesses/lookuptable.txt'}), ('mydir', 'data_collection'), ('myfile', None), ('input', ['data_collection/S2B_MSIL2A_20200626T095029_N0214_R079_T34VFN_20200626T123234.SAFE']), ('shpbase', 'shapefile'), ('outpath', './results'), ('idname', 'ID'), ('statistics_out', True), ('array_out', False), ('indexlist', ['ndvi']), ('statistics', ['count', 'mean', 'median', 'std']), ('startdate', '20160101'), ('enddate', '20211221'), ('keep_shp', False), ('geotiff_out', False), ('test', False), ('exclude_border', False), ('extmask', None), ('exclude_splitshp', False), ('verbose', False), ('format', ['statistics'])])
+INFO:root:checking the projection of the inputfile now
+INFO:root:input shapefile had other than EPSG 4326 but was reprojected and works now
+INFO:root:checking the projection of the inputfile now
+INFO:root:input shapefile had other than EPSG 4326 but was reprojected and works now
+INFO:root:checking the projection of the inputfile now
+INFO:root:input shapefile had other than EPSG 4326 but was reprojected and works now
+INFO:root:number of usable cores for shapesplitting is 2
+INFO:root:splitted shapefiles now exist
+INFO:root:deleted splitted worldtiles
+INFO:root:Imagepath is data_collection/S2B_MSIL2A_20200626T095029_N0214_R079_T34VFN_20200626T123234.SAFE/./GRANULE/L2A_T34VFN_A017265_20200626T095032/IMG_DATA
+INFO:root:Tile is 34VFN
+INFO:root:Date is 20200626
+INFO:root:Shape of cloudmask is (10980, 10980)
+INFO:root:Checking the projection of the inputfile now
+INFO:root:Reprojectcommand: ogr2ogr -t_srs EPSG:32634 EODIE_temp_shp/shapefile_34VFN_reprojected_32634.shp EODIE_temp_shp/shapefile_reprojected_4326_34VFN.shp
+INFO:root:input shapefile had other than EPSG 32634 but was reprojected and works now
+INFO:root:Cloudcover below 99: True
+INFO:root:Data withing area of interest: True
+INFO:root:stat to csv in: ./results/ndvi_20200626_34VFN_statistics.csv
+INFO:root:deleted splitted shapefiles
diff -r 000000000000 -r 81b0ca76435d test-data/20211218-102629.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/20211218-102629.log Thu Dec 30 15:24:09 2021 +0000
@@ -0,0 +1,19 @@
+INFO:root:All inputs for this process: dict_items([('platform', 'ls8'), ('config', {'platform': 'ls8', 'maxcloudcover': 99, 'bitmask': 1, 'tobemaskedlist': [0, 1, 2, 3, 4, 5, 9, 11, 13, 15], 'filepattern': 'LC08_L\\d.._\\d{6}_\\d{8}_\\d{8}_02_[TR][12T]$', 'bandlocation': ['.'], 'cloudfilename': 'QA_PIXEL', 'red': 'B4', 'green': 'B3', 'blue': 'B2', 'nir': 'B5', 'swir1': 'B6', 'swir2': 'B7', 'tilepattern': '[0-9]{6}', 'datepattern': '20[1-2][0-9][0-1][0-9][0-3][0-9]', 'band_designation': 'B\\d?\\d', 'quantification_value': 65535, 'B1': [30], 'B2': [30], 'B3': [30], 'B4': [30], 'B5': [30], 'B6': [30], 'B7': [30], 'QA_PIXEL': [30], 'resampling_method': 'bilinear', 'pathbuildinglist': ['*', 'bandname', '*', '.TIF'], 'pixelsize': 30, 'tileshp': './WRS2_descending/WRS2_descending', 'fieldname': 'PR', 'lookup': './postprocesses/lookuptable.txt'}), ('mydir', 'data_collection'), ('myfile', None), ('input', ['data_collection/LC08_L2SP_189017_20190628_20200827_02_T1']), ('shpbase', 'shapefile'), ('outpath', './results'), ('idname', 'ID'), ('statistics_out', True), ('array_out', False), ('indexlist', ['ndvi']), ('statistics', ['count', 'mean', 'median', 'std']), ('startdate', '20160101'), ('enddate', '20211221'), ('keep_shp', False), ('geotiff_out', False), ('test', False), ('exclude_border', False), ('extmask', None), ('exclude_splitshp', False), ('verbose', False), ('format', ['statistics'])])
+INFO:root:checking the projection of the inputfile now
+INFO:root:input shapefile had other than EPSG 4326 but was reprojected and works now
+INFO:root:checking the projection of the inputfile now
+INFO:root:input shapefile had other than EPSG 4326 but was reprojected and works now
+INFO:root:checking the projection of the inputfile now
+INFO:root:input shapefile had other than EPSG 4326 but was reprojected and works now
+INFO:root:number of usable cores for shapesplitting is 2
+INFO:root:splitted shapefiles now exist
+INFO:root:deleted splitted worldtiles
+INFO:root:Imagepath is data_collection/LC08_L2SP_189017_20190628_20200827_02_T1/.
+INFO:root:Tile is 189017
+INFO:root:Date is 20190628
+INFO:root:Shape of cloudmask is (40, 27)
+INFO:root:Checking the projection of the inputfile now
+INFO:root:Reprojectcommand: ogr2ogr -t_srs EPSG:32635 EODIE_temp_shp/shapefile_189017_reprojected_32635.shp EODIE_temp_shp/shapefile_reprojected_4326_189017.shp
+INFO:root:input shapefile had other than EPSG 32635 but was reprojected and works now
+INFO:root:stat to csv in: ./results/ndvi_20190628_189017_statistics.csv
+INFO:root:deleted splitted shapefiles
diff -r 000000000000 -r 81b0ca76435d test-data/WRS2_descending.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/WRS2_descending.html Thu Dec 30 15:24:09 2021 +0000
@@ -0,0 +1,9 @@
+Shapefile Galaxy Composite Dataset
+This composite dataset is composed of the following files:
This composite dataset is composed of the following files:
This composite dataset is composed of the following files:
This composite dataset is composed of the following files: