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Add background
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.gitignore

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etc/nextcloud
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etc/nextcloud

RQADeforestationTestData

website/content/.gitignore

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docs
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.vitepress/dist
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.vitepress/cache
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*.md
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*.rmarkdown
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out.zarr
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*_files

website/content/.vitepress/config.mts

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import { defineConfig } from 'vitepress'
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import mathjax3 from 'markdown-it-mathjax3';
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const customElements = [
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'mjx-container',
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'mjx-assistive-mml',
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'math',
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'maction',
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'maligngroup',
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'malignmark',
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'menclose',
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'merror',
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'mfenced',
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'mfrac',
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'mi',
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'mlongdiv',
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'mmultiscripts',
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'mn',
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'mo',
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'mover',
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'mpadded',
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'mphantom',
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'mroot',
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'mrow',
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'ms',
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'mscarries',
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'mscarry',
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'mscarries',
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'msgroup',
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'mstack',
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'mlongdiv',
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'msline',
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'mstack',
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'mspace',
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'msqrt',
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'msrow',
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'mstack',
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'mstack',
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'mstyle',
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'msub',
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'msup',
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'msubsup',
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'mtable',
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'mtd',
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'mtext',
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'mtr',
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'munder',
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'munderover',
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'semantics',
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'math',
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'mi',
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'mn',
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'mo',
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'ms',
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'mspace',
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'mtext',
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'menclose',
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'merror',
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'mfenced',
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'mfrac',
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'mpadded',
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'mphantom',
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'mroot',
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'mrow',
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'msqrt',
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'mstyle',
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'mmultiscripts',
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'mover',
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'mprescripts',
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'msub',
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'msubsup',
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'msup',
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'munder',
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'munderover',
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'none',
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'maligngroup',
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'malignmark',
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'mtable',
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'mtd',
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'mtr',
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'mlongdiv',
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'mscarries',
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'mscarry',
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'msgroup',
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'msline',
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'msrow',
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'mstack',
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'maction',
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'semantics',
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'annotation',
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'annotation-xml',
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];
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// https://vitepress.dev/reference/site-config
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export default defineConfig({
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title: "FAIRSenDD",
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markdown: {
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config: (md) => {
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md.use(mathjax3);
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},
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},
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vue: {
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template: {
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compilerOptions: {
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isCustomElement: (tag) => customElements.includes(tag),
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},
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},
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},
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themeConfig: {
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// https://vitepress.dev/reference/default-theme-config
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{
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items: [
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{text: "Overview", link: "overview.md"},
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{text: "Background", link: "background.md"},
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{text: "Julia Library", link: "julia-library.md"},
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{text: "CWL Workflow", link: "cwl-workflow.md"},
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{text: "OGC API - Processes", link: "ogc-api.md"},
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<a href="https://nor-discover.org/"><img src="assets/ESA_NoR_logo.svg" class = "footer-logo"/></a>
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`,
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copyright: `© Copyright ${new Date().getUTCFullYear()}.`
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}
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},
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}
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})

website/content/.vitepress/theme/custom.css

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code {
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font-size: small;
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white-space: pre-wrap;
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}

website/content/FAIRSenDD documentation.qmd

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website/content/background.md

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# Background
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This page shows scientific background information about the workflow.
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Further information is provided in the publication [(Cremer et al. 2020)](https://doi.org/10.1109/JSTARS.2020.3019333).
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## Introduction
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Tropical forests help stabilize the global climate and protect biodiversity.
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Remote sensing technologies, like optical sensors, have been used to monitor these forests, but they struggle with cloud cover, especially during rainy seasons.
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Synthetic Aperture Radar (SAR) can penetrate clouds and is used to map forest changes.
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SAR data can vary due to environmental conditions, thus using time series data helps improve accuracy.
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Current methods for detecting deforestation with Sentinel-1 data fall into two groups: one uses single or few images to detect changes, while the other uses time series to predict changes.
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Various techniques, like using radar shadows or Bayesian updating, help identify deforestation.
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## Methods
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The underlying algorithm is based on Recurrence quantification analysis (RQA).
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Hereby, one counts signal change across every possible time point pair.
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Recurrence plots visualize all comparisons:
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![](assets/creme1-3019333-large.gif)
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Recurrence plots for (a) the sum of two sine waves with different frequencies, (b) a step function with noise, and (c) a sine wave with trend. (b) shows a deforestation event whereas the other two just show seasonal effects or trends.
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A location is considered as deforested if a change was detected often enough (threshold approach).
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In particular, the TREND metric is used to make this decision:
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$$
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\text{TREND}= \frac{\sum _{\tau =1}^{\tilde{N}}(\tau - \tilde{N}/2)(\text{RR}_\tau - \langle \text{RR}_\tau \rangle)}
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{\sum _{\tau =1}^{\tilde{N}}(\tau - \tilde{N}/2)}
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$$
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Hereby, $\tilde{N}$ is the number of time steps and $RR_i$ is the number of recurrent values on the ith diagonal.
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It represents the linear regression coefficient over the $RR$ of the diagonals in comparison to their distance to the main diagonal.
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It indicates whether the process is drifting or not.
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The $TREND$ value is computed for each location individually and reported in the final result data cube.
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## Data
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Up to now, this algorithm was only applied to Sentinel-1 Sigma Nought backscatter data as processed using [Wagner et al. 2021](https://www.mdpi.com/2072-4292/13/22/4622) in [Equi7Grid projection](https://github.com/TUW-GEO/Equi7Grid).
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Using less corrected imagery may be possible but has not been tested yet.
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## Parameters
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First, the workflow is executed on a given spatiotemporal extent.
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The spatial extent doesn't influence the result of individual locations, since neighboring pixels are not considered.
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For the Sentinel-1 Sigma Nought dataset in Equi7Grid projection, the area to be analyzed is given as a list of tiles.
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The time span should be a multiple of a year to reduce potential seasonal bias.
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The algorithm itself can be tuned by setting the threshold value that determines whether to count a time point par change or not.

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