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Copy file name to clipboardexpand all lines: _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
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.
<palign="center"><imgsrc="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.
<palign="center"><imgsrc="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:
Copy file name to clipboardexpand all lines: 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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<imgsrc="assets/palette.png"width="500"/>
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<imgsrc="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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