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Gemfile

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@@ -2,3 +2,5 @@ source 'https://rubygems.org'
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gem "github-pages", "~> 228", group: :jekyll_plugins
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gem "just-the-docs", "0.4.2"
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gem "webrick"
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gem "rake"
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gem "html-proofer", git: "https://github.com/jonasViehweger/html-proofer"

Gemfile.lock

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This file was deleted.

_config.yml

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color_scheme: sentinel_hub
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footer_content: 'This work is licensed under a <a target="_blank" rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"">Creative Commons Attribution-ShareAlike 4.0 International License</a>'
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footer_content: 'This work is licensed under a <a target="_blank" rel="license" href="https://creativecommons.org/licenses/by-sa/4.0/"">Creative Commons Attribution-ShareAlike 4.0 International License</a>'
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# Footer "Edit this page on GitHub" link text
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gh_edit_link: true # show or hide edit this page link

sentinel-2/mago_water_quality_monitoring_tool/README.md

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The following is the display that can be obtained for concentration of Chrlorophyll-a for the day 2022-01-30 at Barrage Lebna (Tunisia)
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- Configuration of variables:
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<p align="center"><img src="fig/custom_script_index_selection_jan_22.png" width="600"></p>
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<p align="center"><img src="fig/custom_script_index_selection_jan_22.png" alt="Code of custom script" width="600"></p>
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- Map visualization
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<p align="center"><img src="fig/viz_jan_22.png" width="600"></p>
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<p align="center"><img src="fig/viz_jan_22.png" alt="Output of script on January 2022" width="600"></p>
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- Time series plot
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<p align="center"><img src="fig/plot_jan_22.png" width="600"></p>
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<p align="center"><img src="fig/plot_jan_22.png" alt="Output of statistical time series" width="600"></p>
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### Script description
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Scene Classification Map (SCL) aims at providing a pixel classification map, with values from 0 to 11. The labels can be seen in the table below.
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<p align="center"><img src="fig/Description_2_codes.png" width="250"></p>
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<p align="center"><img src="fig/Description_2_codes.png" alt="Scene Classification Codes" width="250"></p>
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Based on this classification, the function will evaluate every pixel and return true for labels 1, 3, 8, 9, 10 and 11. This will allow images with a high percentage of pixels considered as cloudy to be disregarded in the time series plot display.
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<p align="center"><img src="fig/Description_3_filtering.png" width="900"></p>
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<p align="center"><img src="fig/Description_3_filtering.png" alt="Filtering cloudy acquisitions from time series" width="900"></p>
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## Scientific Background
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### Introduction
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The MAGO water quality monitoring tool aims at integrating different water quality parameters calculated by using the formulas listed in the table below - listed by **Index Number** from 0 to 7.
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<p align="center"><img src="fig/Description_4_index.png" width="1000"></p>
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<p align="center"><img src="fig/Description_4_index.png" alt="Table with overview of indices" width="1000"></p>
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The MAGO Water Quality Monitoring Tool was focused on chlorophyll-a and cyanobacteria analysis, as well as some physicochemical parameters were included. A brief explanation of the algorithms selected is the following:
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sentinel-2/ulyssys_water_quality_viewer/README.md

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By default, all pixels identified as "not water" (cloud, snow or land) are shown in true colour. All pixels identifed as water are coloured with an algorithm that evaluates chlorophyll and suspended sediment concentration together. This visualization can be compared to a GIS map with two raster layers, sediment on top and chlorophyll below. The sediment "layer" is semi-transparent and can cover the chlorophyll "layer". Just like clouds in the atmosphere, sediment in the water reduces transparency and obscures chlorophyll. Therefore water pixels with high sediment concentrations are coloured dark brown regardless of their chlorophyll concentration. Medium sediment concentrations are coloured wheat (light brown) with increasing transparency towards lower sediment concentrations. At low sediment concentrations the sediment "layer" is completely transparent. Below the semi-transparent sediment "layer", the chlorophyll concentration is visualized. High chlorophyll concentrations are marked in red, medium concentrations green, and low concentrations dark blue (see palette image below).
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<img src="assets/palette.png" width="500"/>
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<img src="assets/palette.png" alt="Color legend of values" width="500"/>
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By changing input parameters of the script it is also possible to:
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Zlinszky, A.; Padányi-Gulyás, G. Ulyssys Water Quality Viewer Technical Description Supplementary. Preprints 2020, 2020010386 (doi: 10.20944/preprints202001.0386.v1).
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<img src="assets/ulyssys_logo.png" width="250"/>
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<img src="assets/ulyssys_logo.png" alt="Ulyssys Logo" width="250"/>
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## Description of representative images
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