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Changeset 0:81b0ca76435d (2021-12-30)

Commit message:
"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

[

b'@@ -0,0 +1,363 @@\n+<tool id="eodie" name="EODIE" version="@VERSION@" profile="20.09">\r\n+ <description>converts simple features data between file formats</description>\r\n+ <macros>\r\n+ <import>macros.xml</import>\r\n+ </macros>\r\n+ <expand macro="edam_ontology"/>\r\n+ <requirements>\r\n+ <requirement type="package" version="@VERSION@">eodie</requirement>\r\n+ <requirement type="package" version="3.9">python</requirement>\r\n+ <requirement type="package" version="1.8">shapely</requirement>\r\n+ <requirement type="package" version="1.2">rasterio</requirement>\r\n+ <requirement type="package" version="0.16">rasterstats</requirement>\r\n+ <requirement type="package" version="1.8">fiona</requirement>\r\n+ <requirement type="package" version="1.21">numpy</requirement>\r\n+ <requirement type="package" version="3.4.0">gdal</requirement>\r\n+ <requirement type="package" version="6.0">pyyaml</requirement>\r\n+ <requirement type="package" version="6.0">unzip</requirement>\r\n+ <requirement type="package" version="1.34">tar</requirement>\r\n+ </requirements>\r\n+ <command detect_errors="exit_code"><![CDATA[\r\n+ mkdir -p work/data_collection work/results results_csv results_tiffs &&\r\n+ cp \'$config_tif\' config_tif.yml && \r\n+ cp \'$config_s2\' config_s2.yml && \r\n+ cp \'$config_ls8\' config_ls8.yml && \r\n+ cp \'$user_config\' user_config.yml && \r\n+ cp \'${input.extra_files_path}\'/* work/ &&\r\n+ cd work &&\r\n+ ln -s \'${input_type.input_file}\' \'${input_type.input_file.element_identifier}\' &&\r\n+ #if $input_type.input_file.is_of_type("zip")\r\n+ unzip \'$input_type.input_file\' -d data_collection/ &&\r\n+ #elif $input_type.input_file.is_of_type("tar")\r\n+ tar -xf \'$input_type.input_file\' -C data_collection &&\r\n+ #end if\r\n+ #if str($input_type.platform) == \'s2\'\r\n+ mkdir -p sentinel2_tiles_world &&\r\n+ (cp \'$input_type.s2_shp.extra_files_path\'/shapefile.shp sentinel2_tiles_world/sentinel2_tiles_world.shp || true ) &&\r\n+ (cp \'$input_type.s2_shp.extra_files_path\'/shapefile.shx sentinel2_tiles_world/sentinel2_tiles_world.shx || true ) &&\r\n+ (cp \'$input_type.s2_shp.extra_files_path\'/shapefile.dbf sentinel2_tiles_world/sentinel2_tiles_world.dbf || true ) &&\r\n+ (cp \'$input_type.s2_shp.extra_files_path\'/shapefile.prj sentinel2_tiles_world/sentinel2_tiles_world.prj || true ) &&\r\n+ #elif str($input_type.platform) == \'ls8\'\r\n+ mkdir -p WRS2_descending &&\r\n+ (cp \'$input_type.ls8_shp.extra_files_path\'/shapefile.shp WRS2_descending/WRS2_descending.shp || true ) &&\r\n+ (cp \'$input_type.ls8_shp.extra_files_path\'/shapefile.shx WRS2_descending/WRS2_descending.shx || true ) &&\r\n+ (cp \'$input_type.ls8_shp.extra_files_path\'/shapefile.dbf WRS2_descending/WRS2_descending.dbf || true ) &&\r\n+ (cp \'$input_type.ls8_shp.extra_files_path\'/shapefile.prj WRS2_descending/WRS2_descending.prj || true ) &&\r\n+ #end if\r\n+\r\n+ eodie_process.py\r\n+ --platform $input_type.platform\r\n+ #if str($input_type.platform) == \'tif\'\r\n+ --file ${input_type.input_file.element_identifier}\r\n+ #else\r\n+ --dir data_collection\r\n+ --out ./results\r\n+ #end if\r\n+ --shp shapefile\r\n+ #for $i, $s in enumerate( $adv_options.statistics )\r\n+ #if str($i) == \'0\'\r\n+ --statistics_out\r\n+ --statistics \r\n+ #end if\r\n+ #if $s.stats_input.stats and str($s.stats_input.stats) != \'\':\r\n+ #if str($s.stats_input.stats) == \'percentile\':\r\n+ \'$s.stats_input.stats\'_\'$s.stats_input.p_value\'\r\n+ #else\r\n+ \'$s.stats_input.stats\'\r\n+ #end if\r\n+ #end if\r\n+ #end for\r\n+ #if $adv_options.indices and str($adv_op'..b' </assert_contents>\r\n+ </element>\r\n+ </output_collection>\r\n+ </test>\r\n+ <test>\r\n+ <conditional name="input_type">\r\n+ <param name="platform" value="s2" />\r\n+ <param name="input_file" ftype="tar" value="S2.tar" />\r\n+ <param name="s2_shp" ftype="shp" value="sentinel2_tiles_world/sentinel2_tiles_world.html">\r\n+ <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.shp"/>\r\n+ <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.shx"/>\r\n+ <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.dbf"/>\r\n+ <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.prj"/>\r\n+ </param>\r\n+ </conditional>\r\n+ <param name="input" value="test_parcels_32635/test_parcels_32635.html" ftype="shp">\r\n+ <composite_data value="test_parcels_32635/test_parcels_32635.shp"/>\r\n+ <composite_data value="test_parcels_32635/test_parcels_32635.shx"/>\r\n+ <composite_data value="test_parcels_32635/test_parcels_32635.dbf"/>\r\n+ <composite_data value="test_parcels_32635/test_parcels_32635.prj"/>\r\n+ </param>\r\n+ <param name="identifier" value="ID"/>\r\n+ <section name="adv_options">\r\n+ <repeat name="statistics">\r\n+ <conditional name="stats_input">\r\n+ <param name="stats" value="mean"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <repeat name="statistics">\r\n+ <conditional name="stats_input">\r\n+ <param name="stats" value="median"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <repeat name="statistics">\r\n+ <conditional name="stats_input">\r\n+ <param name="stats" value="std"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <param name="indices" value="ndvi"/>\r\n+ </section>\r\n+ <output file="20211217-210343.log" name="logfile" compare="sim_size" delta="100"/>\r\n+ <output_collection name="csv_files" type="list" count="1">\r\n+ <element name="ndvi_20200626_34VFN_statistics.csv" ftype="tabular" file="ndvi_20200626_34VFN_statistics.csv" compare="diff" lines_diff="1">\r\n+ <assert_contents>\r\n+ <has_text text="204" />\r\n+ <has_text text="551" />\r\n+ <has_text text="335" />\r\n+ <has_text text=".321" />\r\n+ <has_text text=".293" />\r\n+ <has_text text=".661" />\r\n+ <has_text text=".302" />\r\n+ <has_text text=".294" />\r\n+ <has_text text=".686" />\r\n+ <has_text text=".091" />\r\n+ <has_text text=".088" />\r\n+ <has_text text=".091" />\r\n+ <has_n_columns n="5" />\r\n+ </assert_contents>\r\n+ </element>\r\n+ </output_collection>\r\n+ </test>\r\n+ </tests>\r\n+ <help><![CDATA[\r\n+\r\n+**EODIE - Earth Observation Data Information Extractor**\r\n+=======================================================================================================\r\n+\r\n+Toolkit to extract object based timeseries from Earth Observation data such as Copernicus Sentinel 2, Landsat 8 and more generally geotiff files. \r\n+\r\n+EODIE takes the objects in as polygons in a shapefile as well as the timeframe of interest and the features (eg vegetation indices) to be extracted.\r\n+The output is a per polygon timeseries of the selected features over the timeframe of interest.\r\n+\r\n+ ]]> </help>\r\n+ <expand macro="citations" />\r\n+</tool>\r\n'

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 @@
+<macros>
+    <token name="@VERSION@">1.0.2</token>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0610</edam_topic>
+            <edam_topic>topic_3050</edam_topic>
+        </edam_topics>
+    </xml>
+    <xml name="configfiles">
+        <configfiles>
+            <configfile name="config_tif"><![CDATA[
+platform: tif
+
+##the first that is found is used
+datepattern: '20[1-2][0-9][0-1][0-9][0-3][0-9]'
+
+##name to write into output statistics filename
+name: 'testrgb'
+        ]]>            </configfile>
+            <configfile name="config_s2"><![CDATA[
+####
+
+## Configuration file for the use of Sentinel-2 ##
+
+## Know what you do before you change anything here ##
+
+####
+
+platform: 's2'
+
+## Mask conditions are stored as values, not as bitflags
+bitmask: 0
+## Values to be to be included in cloudmask
+## default [9,8,3,10,0,1]
+tobemaskedlist:
+  - 9 ## cloud high probability
+  - 8 ## cloud medium probability
+  - 3 ## cloud shadow
+  - 10 ## cirrus
+  - 0 ## no data
+  - 1 ## saturated and defective
+
+##pattern to find all data files
+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$'
+
+## Sentinel-2 bands
+red : 'B04'
+green: 'B03'
+blue: 'B02'
+nir: 'B08'
+r_edge: 'B05'
+swir1: 'B11'
+swir2: 'B12'
+
+## some part of the products file name that identifies them as product to be used
+productnameidentifier: 'S2*.SAFE'
+
+## parts to build path towards bands
+bandlocation: ['.','*','*','IMG_DATA']
+
+## path building set after imgpath to get the bandfile
+pathbuildinglist: ['R', 'pixelsize' , 'm','*', 'bandname', '_' , 'pixelsize' ,'m.jp2']
+
+##indicator for cloudfile
+cloudfilename: 'SCL'
+
+tilepattern: '(?<=T)[0-9]{2}[A-Z]{3}'
+
+##the first that is found is used
+datepattern: '20[1-2][0-9][0-1][0-9][0-3][0-9]'
+
+band_designation: 'B[0-1]?\dA?'
+
+## Quantification value used to multiple the reflectance to get DN
+## This could be read from metadata but for now at least is here
+quantification_value: 10000
+
+## available resolutions per band
+B01: [60]
+B02: [10,20,60]
+B03: [10,20,60]
+B04: [10,20,60]
+B05: [20,60]
+B06: [20,60]
+B07: [20,60]
+B08: [10]
+B8A: [20,60]
+B09: [60]
+B11: [20,60]
+B12: [20,60]
+SCL: [20,60]
+AOT: [10,20,60]
+TCI: [10,20,60]
+WVP: [10,20,60]
+     ]]>            </configfile>
+            <configfile name="config_ls8"><![CDATA[
+platform: 'ls8'
+
+## Process only files with less than xx % cloudcover
+maxcloudcover: 10
+
+
+## Mask conditions are not stored as values, but as individual 0/1 flags in bits
+bitmask: 1
+## Bits to be to be included in cloudmask
+## https://prd-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/atoms/files/LSDS-1328_Landsat8-9-OLI-TIRS-C2-L2-DFCB-v6.pdf
+tobemaskedlist:
+  - 0 ## Fill data
+  - 1 ## Dilated cloud
+  - 2 ## Cirrus
+  - 3 ## Cloud
+  - 4 ## Cloud shadow
+  - 5 ## Snow
+  - 9 ## Cloud medium to high confidence
+  - 11 ## Cloud shadow high confidence
+  - 13 ## Snow/Ice high confidence
+  - 15 ## Cirrus high confidence
+
+
+##pattern to find all data files
+filepattern: 'LC08_L\d.._\d{6}_\d{8}_\d{8}_02_[TR][12T]$'
+
+##all bands are located in parent directory directly
+bandlocation: ['.']
+
+##indicator for cloudfile
+cloudfilename: 'QA_PIXEL'
+
+## LS8 bands
+## https://www.usgs.gov/media/images/landsat-8-band-designations
+red : 'B4'
+green: 'B3'
+blue: 'B2'
+nir: 'B5'
+swir1: 'B6'
+swir2: 'B7'
+
+tilepattern: '[0-9]{6}'
+
+## the first that is found is used
+datepattern: '20[1-2][0-9][0-1][0-9][0-3][0-9]'
+
+band_designation: 'B\d?\d'
+
+##???????????
+## Quantification value used to multiple the reflectance to get DN
+## This could be read from metadata but for now at least is here
+quantification_value: 65535
+
+## available resolutions per band
+B1: [30]
+B2: [30]
+B3: [30]
+B4: [30]
+B5: [30]
+B6: [30]
+B7: [30]
+QA_PIXEL: [30]
+## to be continued
+
+##upsampling (converting to higher resolution/smaller cells) / downsampling (converting to lower resolution/larger cellsize)
+##available: ‘nearest’, ‘bilinear’, ‘cubic’, ‘cubic_spline’, ‘lanczos’, ‘average’, ‘mode’, and ‘gauss’,
+## from https://rasterio.readthedocs.io/en/latest/api/rasterio.enums.html#rasterio.enums.Resampling
+
+resampling_method: 'bilinear'
+
+
+## path building set *after inpath* to get the bandfile
+
+pathbuildinglist: ['*', 'bandname', '*' , '.TIF']
+     ]]>            </configfile>
+            <configfile name="user_config"><![CDATA[
+####
+
+## Configuration file for adjusting the process/results and give paths ##
+
+####
+
+## Process only files with less than xx % cloudcover
+maxcloudcover: 99
+
+## Extract files with xx m pixel size
+## options: 10,20 (for Sentinel-2)
+## options: 30 (for Landsat8)
+
+#if str($input_type.platform) == 'ls8'
+pixelsize: 30
+#else
+pixelsize: 10
+#end if
+
+##resampling (converting to higher/lower resolution/smaller cells)
+##available: 'biliner','nearest','cubic','average', ...
+## from https://rasterio.readthedocs.io/en/latest/api/rasterio.enums.html#rasterio.enums.Resampling
+
+resampling_method: 'bilinear'
+
+##location of the shapefile with tiles (Sentinel2-tiles-world in case of Sentinel-2, WRS2_descending in case of Landsat 8)
+#if str($input_type.platform) == 's2'
+tileshp: './sentinel2_tiles_world/sentinel2_tiles_world'
+#elif str($input_type.platform) == 'ls8'
+tileshp: './WRS2_descending/WRS2_descending'
+#end if
+
+##name of field where tilenames are stored in shapefile ('Name' in case of sentinel2_tiles_world, 'PR' in case of WRS2_descending )
+#if str($input_type.platform) == 'ls8'
+fieldname: 'PR'
+#else
+fieldname: 'Name'
+#end if
+
+## Lookup table for storing the tiles and the IDs they include for every tile processed by EODIE with --array_out
+## Table needed for array plotting
+lookup: './postprocesses/lookuptable.txt'
+    ]]>            </configfile>
+        </configfiles>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.5281/zenodo.4762323</citation>
+        </citations>
+    </xml>
+</macros>

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 @@
+<html><head><title>Shapefile Galaxy Composite Dataset</title></head><p/>
+<div>This composite dataset is composed of the following files:<p/><ul>
+<li><a href="WRS2_descending.shp" type="application/binary">shapefile.shp (Geometry File (shp))</a></li>
+<li><a href="WRS2_descending.shx" type="application/binary">shapefile.shx (Geometry index File (shx))</a></li>
+<li><a href="WRS2_descending.dbf" type="application/binary">shapefile.dbf (Columnar attributes for each shape (dbf))</a></li>
+<li><a href="WRS2_descending.prj" type="application/binary">shapefile.prj (Projection description (prj))</a> (optional)</li>
+<li><a href="WRS2_descending.sbn" type="application/binary">shapefile.sbn (Spatial index of the features (sbn))</a> (optional)</li>
+<li><a href="WRS2_descending.sbx" type="application/binary">shapefile.sbx (Spatial index of the features (sbx))</a> (optional)</li>
+</ul></div></html>

diff -r 000000000000 -r 81b0ca76435d test-data/WRS2_descending/WRS2_descending.dbf

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diff -r 000000000000 -r 81b0ca76435d test-data/WRS2_descending/WRS2_descending.prj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/WRS2_descending/WRS2_descending.prj Thu Dec 30 15:24:09 2021 +0000

[

@@ -0,0 +1,1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
\ No newline at end of file

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diff -r 000000000000 -r 81b0ca76435d test-data/WRS2_descending/WRS2_descending.shp

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diff -r 000000000000 -r 81b0ca76435d test-data/ndvi_20190628_189017_statistics.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ndvi_20190628_189017_statistics.csv Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,4 @@
+id count mean median std
+0 32 0.384 0.387 0.033
+1 81 0.304 0.295 0.078
+2 48 0.424 0.432 0.031

diff -r 000000000000 -r 81b0ca76435d test-data/ndvi_20200626_34VFN_statistics.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ndvi_20200626_34VFN_statistics.csv Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,4 @@
+id count mean median std
+0 204 0.321 0.302 0.091
+1 551 0.293 0.294 0.088
+2 335 0.661 0.686 0.091

diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sentinel2_tiles_world.html Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,7 @@
+<html><head><title>Shapefile Galaxy Composite Dataset</title></head><p/>
+<div>This composite dataset is composed of the following files:<p/><ul>
+<li><a href="sentinel2_tiles_world.shp" type="application/binary">shapefile.shp (Geometry File (shp))</a></li>
+<li><a href="sentinel2_tiles_world.shx" type="application/binary">shapefile.shx (Geometry index File (shx))</a></li>
+<li><a href="sentinel2_tiles_world.dbf" type="application/binary">shapefile.dbf (Columnar attributes for each shape (dbf))</a></li>
+<li><a href="sentinel2_tiles_world.prj" type="application/binary">shapefile.prj (Projection description (prj))</a> (optional)</li>
+</ul></div></html>

diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/COPYING.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sentinel2_tiles_world/COPYING.txt Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,3 @@
+© Copernicus Sentinel data 2016 downloaded from https://scihub.copernicus.eu/
+
+Read the TERMS AND CONDITIONS
\ No newline at end of file

diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/TERMS AND CONDITIONS.pdf

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diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/readme.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sentinel2_tiles_world/readme.txt Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,3 @@
+© Copernicus Sentinel data 2016 downloaded from https://scihub.copernicus.eu/
+
+Sentinel-2 tiling grid adapted from the kml file downloaded from ESA (https://sentinel.esa.int/web/sentinel/missions/sentinel-2/data-products) at the link https://sentinel.esa.int/documents/247904/1955685/S2A_OPER_GIP_TILPAR_MPC__20151209T095117_V20150622T000000_21000101T000000_B00.kml
\ No newline at end of file

diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/sentinel2_tiles_world.dbf

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diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/sentinel2_tiles_world.prj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sentinel2_tiles_world/sentinel2_tiles_world.prj Thu Dec 30 15:24:09 2021 +0000

[

@@ -0,0 +1,1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]
\ No newline at end of file

diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/sentinel2_tiles_world.qpj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sentinel2_tiles_world/sentinel2_tiles_world.qpj Thu Dec 30 15:24:09 2021 +0000

[

@@ -0,0 +1,1 @@
+GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]]

diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/sentinel2_tiles_world.shp

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diff -r 000000000000 -r 81b0ca76435d test-data/sentinel2_tiles_world/sentinel2_tiles_world.shx

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diff -r 000000000000 -r 81b0ca76435d test-data/smaller_area_20100401.tif

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diff -r 000000000000 -r 81b0ca76435d test-data/test_parcels_32635.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_parcels_32635.html Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,7 @@
+<html><head><title>Shapefile Galaxy Composite Dataset</title></head><p/>
+<div>This composite dataset is composed of the following files:<p/><ul>
+<li><a href="test_parcels_32635.shp" type="application/binary">shapefile.shp (Geometry File (shp))</a></li>
+<li><a href="test_parcels_32635.shx" type="application/binary">shapefile.shx (Geometry index File (shx))</a></li>
+<li><a href="test_parcels_32635.dbf" type="application/binary">shapefile.dbf (Columnar attributes for each shape (dbf))</a></li>
+<li><a href="test_parcels_32635.prj" type="application/binary">shapefile.prj (Projection description (prj))</a> (optional)</li>
+</ul></div></html>

diff -r 000000000000 -r 81b0ca76435d test-data/test_parcels_32635/test_parcels_32635.cpg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_parcels_32635/test_parcels_32635.cpg Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,1 @@
+UTF-8
\ No newline at end of file

diff -r 000000000000 -r 81b0ca76435d test-data/test_parcels_32635/test_parcels_32635.dbf

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diff -r 000000000000 -r 81b0ca76435d test-data/test_parcels_32635/test_parcels_32635.prj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_parcels_32635/test_parcels_32635.prj Thu Dec 30 15:24:09 2021 +0000

[

@@ -0,0 +1,1 @@
+PROJCS["WGS_1984_UTM_Zone_35N",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",27.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]
\ No newline at end of file

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diff -r 000000000000 -r 81b0ca76435d test-data/test_polygons.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_polygons.html Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,7 @@
+<html><head><title>Shapefile Galaxy Composite Dataset</title></head><p/>
+<div>This composite dataset is composed of the following files:<p/><ul>
+<li><a href="test_polygons.shp" type="application/binary">shapefile.shp (Geometry File (shp))</a></li>
+<li><a href="test_polygons.shx" type="application/binary">shapefile.shx (Geometry index File (shx))</a></li>
+<li><a href="test_polygons.dbf" type="application/binary">shapefile.dbf (Columnar attributes for each shape (dbf))</a></li>
+<li><a href="test_polygons.prj" type="application/binary">shapefile.prj (Projection description (prj))</a> (optional)</li>
+</ul></div></html>

diff -r 000000000000 -r 81b0ca76435d test-data/test_polygons/test_polygons.dbf

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diff -r 000000000000 -r 81b0ca76435d test-data/test_polygons/test_polygons.prj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_polygons/test_polygons.prj Thu Dec 30 15:24:09 2021 +0000

[

@@ -0,0 +1,1 @@
+PROJCS["EUREF_FIN_TM35FIN",GEOGCS["GCS_ETRS_1989",DATUM["D_ETRS_1989",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",27.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]
\ No newline at end of file

diff -r 000000000000 -r 81b0ca76435d test-data/test_polygons/test_polygons.shp

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diff -r 000000000000 -r 81b0ca76435d test-data/test_polygons/test_polygons.shx

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diff -r 000000000000 -r 81b0ca76435d test-data/testrgb_20100401__statistics.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testrgb_20100401__statistics.csv Thu Dec 30 15:24:09 2021 +0000

@@ -0,0 +1,4 @@
+id count mean percentile_10
+3 20508 154.641 110.000
+1 12049 181.347 147.000
+2 4508 89.314 32.000