Merge pull request #4635 from Marie59/ndvi

From NDVI satellite data to timeseries

topics/ecology/tutorials/ndvi_openeo/faqs/index.md

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+---
+layout: faq-page
+---

topics/ecology/tutorials/ndvi_openeo/tutorial.bib

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+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
+           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
+           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
+           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
+           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
+           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}

topics/ecology/tutorials/ndvi_openeo/tutorial.md

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+---
+layout: tutorial_hands_on
+
+title: From NDVI data with OpenEO to time series visualisation with Holoviews
+questions:
+- What's the NDVI ?
+- How to evaluate the NDVI through out time ?
+objectives:
+- Use OpenEo technologies and learn how to download data with them
+- Learn to use Holoviz environment to process csv data
+- Create timeseries and visualisation of the NDVI 
+- Handle going form one interactive tool to another
+time_estimation: 1H
+key_points:
+- Manage NDVI data
+- Handle jupyterlab tools
+tags:
+  - earth-system
+  - land degradation
+  - NDVI
+  - copernicus
+  - holoviews
+contributions:
+  authorship:
+    - Marie59
+  funding:
+    - fairease
+    - eurosciencegateway
+---
+
+
+
+Through this tutorial you will learn here how to access and download Copernicus Data Space Ecosystem (CDSE) data through a jupyterlab Galaxy interactive tool :
+
+This tool enables you to leverage the Copernicus Data Space Ecosystem services and access data effortlessly.
+The JupyterLab service allows you to dive into data exploration, visualization, and analysis without the hassle of installing dependencies or downloading large data sets.
+
+You will also apprehend how to use the Holoviz ecosysytem by plotting and visualising NDVI (from the CDSE) timeseries :
+HoloViz provides high-level Python tools that are designed to work together to solve the entire problem of visualization, from conducting exploratory data analysis to deploying complex dashboards.
+
+> <agenda-title></agenda-title>
+>
+> In this tutorial, we will cover:
+>
+> 1. TOC
+> {:toc}
+>
+{: .agenda}
+
+## Context on Galaxy
+Interactive tools work differently than classical tools as it allows the user to interact with a dedicated graphical interface. This kind of tools is used to give access to Jupyter notebooks, RStudio or R Shiny apps for example. 
+
+> <details-title>Short introduction on how Galaxy works</details-title>
+>
+> You can come back to where you left off the tutorial anytime by clicking {% icon level %}.
+>
+> > <hands-on-title>Log in to Galaxy</hands-on-title>
+> > 1. Open your favorite browser (Chrome, Safari or Firefox as your browser, not Internet Explorer!)
+> > 2. Browse to your [Galaxy instance](https://earth-system.usegalaxy.eu/)
+> > 3. On the top pannel go to **Login or Register**
+> >
+> >
+> {: .hands_on}
+>
+> The Galaxy homepage is divided into three panels:
+> * Tools on the left
+> * Viewing panel in the middle
+> * History of analysis and files on the right
+>
+> ![Screenshot of the Galaxy interface, the tools panel is on the left, the main panel is in the center, and the history is on the right.]({% link shared/images/galaxy_interface.png %} "Galaxy interface explanation")
+>
+> The first time you use Galaxy, there will be no files in your history panel.
+{: .details}
+
+# Copernicus Data Space Ecosystem
+
+> <hands-on-title> Launch the interactive tool </hands-on-title>
+>
+> 1. {% tool [Copernicus Data Space Ecosystem](interactive_tool_copernicus) %} with the following parameters:
+>    - *"Do you already have a notebook?"*: `Start with a fresh notebook`
+>    - *"Include data into the environment - optional "*: You don't need anything
+> 2. Click on **Run Tool**
+>
+> 3. {% snippet faqs/galaxy/interactive_tools_open.md tool="Copernicus Data Space Ecosystem" %}
+{: .hands_on}
+
+> <hands-on-title> Navigate the jupyterlab </hands-on-title>
+> 1. Once you are in the jupyterlab go to :
+>    - **notebooks**
+>    - Then, **openeo** 
+>    - Open the notebook **NDVI_Timeseries.ipynb**
+> 2. You can start running your notebook. To do so you can go on the pannel displaying button right above the notebook and click on the {% icon workflow-run %}. 
+>    Everytime you press this button you can excecute a one by one the cells. 
+> 3. In the **Setup** section when you execute the connection cell you'll have some actions to conduct.
+> 4. First click ont the link appearing, you're notebook should look like the following :
+> ![Begining of the NDVI notebook  with the connection link visible](../../images/ndvi_openeo_holoviz/ndvi_notebook.png)
+> 5. Once you clicked a new window opens. If you don't have a copernicus account please create one and follow the instructions given. 
+> 6. If you have an account sign in and then press the green **YES**
+> ![Image of how does the connection page looks like](../../images/ndvi_openeo_holoviz/connection.png)
+> 7. You'll be redirected to a page letting you know the connection was a success
+> ![Image of the successful connection](../../images/ndvi_openeo_holoviz/connection_ok.png)
+> 8. Now, you can go back on your jupyterlab and execute the rest of the notebook.
+> 9. Once you executed the entire notebook you should have a new folder in the left pannel named **ndvi-results** go in it.
+> 10. Select the 3 files there and click right, and then copy
+> ![The copy command on the 3 files in the ndvi-results folder](../../images/ndvi_openeo_holoviz/copy_paste.png)
+> 11. Then go back to the root of your path and go in the **ouputs** folder. There you can click right and paste the 3 NDVI files. 
+> ![The resulting 3 files in the outputs folder](../../images/ndvi_openeo_holoviz/outputs.png)
+> 12. This part is now finished you just have to correctly close this notebook. On the top left click on **files** and then on **Shut down**.
+> ![The shut down button to correctly close the jupyterlab](../../images/ndvi_openeo_holoviz/shut_down.png)
+{: .hands_on}
+
+Go back on your Galaxy window. After a couple minutes you should see your outputs turning green in your history.
+
+Check that your data are in csv format. 
+
+> <tip-title> Check datatype </tip-title>
+>
+> {% icon galaxy-pencil %}, it should be `csv`
+>
+> {% snippet faqs/galaxy/datasets_change_datatype.md datatype="csv" %}
+{: .tip}
+
+
+# Holoviz
+
+> <hands-on-title> Launch Holoviz </hands-on-title>
+>
+> 1. {% tool [Holoviz](interactive_tool_holoviz) %} with the following parameters:
+>    - *"Do you already have a notebook?"*: `Start with a fresh notebook`
+>    - *"Include data into the environment - optional "*: Select `timeseries-basic`, `timeseries-masked` and `timeseries-smoothed`
+> 2. Click on **Run Tool**
+>
+> 3. {% snippet faqs/galaxy/interactive_tools_open.md tool="Holoviz" %}
+> 
+> 4. Once, you are in the jupyterlab go in the the **notebooks** folder
+> 5. Open a terminal in bash and write the following
+> > <code-in-title>Download the notebook</code-in-title>
+> > ```bash
+> > wget https://raw.githubusercontent.com/fair-ease/Holoviz/main/Tabular_Datasets_NDVI.ipynb
+> > ```
+> {: .code-in}
+> Now that you have your notebook you can just follow the instructions.
+{: .hands_on}
+
+Enjoy discovering the rest of the notebook. 
+
+# Conclusion
+The tutorial ends there and with that you have the basis on how to use jupyterlab tools and more particularly the copernicus and holoviz ones.

topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO-tests.yml

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+- doc: Test outline for NDVI-with-OpenEO
+  job: {}
+  outputs: {}

topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.ga

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+{
+    "a_galaxy_workflow": "true",
+    "annotation": "",
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "0009-0008-0622-604X",
+            "name": "Marie Joss\u00e9",
+            "url": "https://github.com/Marie59"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "CC-BY-4.0",
+    "name": "NDVI with OpenEO",
+    "steps": {
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+            "annotation": "",
+            "content_id": "interactive_tool_copernicus_notebook",
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [],
+            "label": null,
+            "name": "Copernicus Data Space Ecosystem",
+            "outputs": [
+                {
+                    "name": "output_collection",
+                    "type": "input"
+                },
+                {
+                    "name": "jupyter_notebook",
+                    "type": "ipynb"
+                }
+            ],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_copernicus_notebook",
+            "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": null, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.0.1",
+            "type": "tool",
+            "uuid": "0266bd4e-8767-4f1b-949d-d413ac698602",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "interactive_tool_holoviz",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
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+                    "id": 0,
+                    "output_name": "output_collection"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Holoviz",
+            "outputs": [
+                {
+                    "name": "output_collection",
+                    "type": "input"
+                },
+                {
+                    "name": "jupyter_notebook",
+                    "type": "ipynb"
+                }
+            ],
+            "position": {
+                "left": 344,
+                "top": 0
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_holoviz",
+            "tool_state": "{\"__input_ext\": \"csv\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.0.1",
+            "type": "tool",
+            "uuid": "b0ea1c4d-46bd-4d4f-9843-97e5251c3d8e",
+            "when": null,
+            "workflow_outputs": []
+        }
+    },
+    "tags": [],
+    "uuid": "1e8b66e1-d310-46ae-89a5-5e98939f0e9b",
+    "version": 3
+}

topics/ecology/tutorials/ndvi_openeo/workflows/index.md

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+---
+layout: workflow-list
+---

topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga

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+{"a_galaxy_workflow": "true", "annotation": "", "creator": [{"class": "Person", "identifier": "0009-0008-0622-604X", "name": "Marie Joss\u00e9", "url": "https://github.com/Marie59"}], "format-version": "0.1", "license": "CC-BY-4.0", "name": "NDVI with OpenEO", "steps": {"0": {"annotation": "", "content_id": "interactive_tool_copernicus_notebook", "errors": null, "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Copernicus Data Space Ecosystem", "outputs": [{"name": "output_collection", "type": "input"}, {"name": "jupyter_notebook", "type": "ipynb"}], "position": {"left": 0, "top": 0}, "post_job_actions": {}, "tool_id": "interactive_tool_copernicus_notebook", "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": null, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.1", "type": "tool", "uuid": "0266bd4e-8767-4f1b-949d-d413ac698602", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": "interactive_tool_holoviz", "errors": null, "id": 1, "input_connections": {"input": {"id": 0, "output_name": "output_collection"}}, "inputs": [], "label": null, "name": "Holoviz", "outputs": [{"name": "output_collection", "type": "input"}, {"name": "jupyter_notebook", "type": "ipynb"}], "position": {"left": 344, "top": 0}, "post_job_actions": {}, "tool_id": "interactive_tool_holoviz", "tool_state": "{\"__input_ext\": \"csv\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.1", "type": "tool", "uuid": "b0ea1c4d-46bd-4d4f-9843-97e5251c3d8e", "when": null, "workflow_outputs": []}}, "tags": [], "uuid": "1e8b66e1-d310-46ae-89a5-5e98939f0e9b", "version": 3}