From 06d0d8cea4b2ac1cd6ccd14e6fe818208bf78ee7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 24 Mar 2024 12:47:01 +0100 Subject: [PATCH] smaller corrections --- .../climate/tutorials/argo_pangeo/tutorial.md | 75 +++++++++++-------- 1 file changed, 45 insertions(+), 30 deletions(-) diff --git a/topics/climate/tutorials/argo_pangeo/tutorial.md b/topics/climate/tutorials/argo_pangeo/tutorial.md index 19b53ec0265440..a92fc5712497ca 100644 --- a/topics/climate/tutorials/argo_pangeo/tutorial.md +++ b/topics/climate/tutorials/argo_pangeo/tutorial.md @@ -3,13 +3,13 @@ layout: tutorial_hands_on title: Analyse Argo data questions: -- How to use Pangeo ecosystem to analyse ocean data? -- How to process Argo data to visulise ocean temperature variations? +- How to use the Pangeo ecosystem to analyse ocean data? +- How to process Argo data to visualise ocean temperature variations? objectives: -- How to fetch Argo Data ? -- How to get metadata with xarray netcdf tools ? +- How to fetch Argo Data? +- How to get metadata with xarray netcdf tools? - Learn to get temperature variations. -- Learn to use an interactive tool to visualise Argo temperature variable on a interactive map. +- Learn to use an interactive tool to visualise Argo temperature variable on an interactive map. time_estimation: 1H requirements: - type: "internal" @@ -31,18 +31,21 @@ contributions: funding: - fairease - eurosciencegateway - --- -The ocean is a key component of the Earth climate system. It thus needs a continuous real-time monitoring to help scientists better understand its dynamic and predict its evolution. All around the world, oceanographers have managed to join their efforts and set up a Global Ocean Observing System among which Argo is a key component. +The ocean is a key component of the Earth's climate system. It thus needs continuous real-time monitoring to help scientists better understand its dynamics and predict its evolution. +All around the world, oceanographers have managed to join their efforts and set up a Global Ocean Observing System among which Argo is a key component. Argo is an international program that collects information from inside the ocean using a fleet of robotic instruments that drift with the ocean currents and move up and down between the surface and a mid-water level. -The data used in this tutorial are from the Argo gliders network. We are interested in the following variables: water temperature, latitude, longitude and time. Our main objective is to plot the water temperature with respect to time. For this we will be using the netCDF xarray tools available in the Galaxy Europe (or your favourite Galaxy Instance) server. +The data used in this tutorial are from the Argo gliders network. We are interested in the following variables: water temperature, latitude, longitude and time. +Our main objective is to plot the water temperature with respect to time. For this, we will be using the netCDF xarray tools available in the Galaxy Europe (or your favourite Galaxy Instance) server. -These tools are part of the Pangeo ecosystem in which the next generation of open-source analysis tools for ocean, atmosphere and climate science can be developed, distributed, and sustained. These tools must be scalable in order to meet the current and future challenges of big data, and these solutions should leverage the existing expertise outside of the geoscience community. +These tools are part of the Pangeo ecosystem in which the next generation of open-source analysis tools for ocean, atmosphere and climate science can be developed, distributed, +and sustained. These tools must be scalable to meet the current and future challenges of big data, and these solutions should leverage the existing expertise outside of +the geoscience community. -This tutorial is part of set of tutorials on the [Galaxy Earth System](https://earth-system.usegalaxy.eu/) supported by the [EOSC FAIR-EASE project](https://fairease.eu/). +This tutorial is part of a set of tutorials on the [Galaxy Earth System](https://earth-system.usegalaxy.eu/) supported by the [EOSC FAIR-EASE project](https://fairease.eu/). > > @@ -60,7 +63,7 @@ This tutorial is part of set of tutorials on the [Galaxy Earth System](https://e > > Log in to Galaxy > > 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** +> > 3. On the top go to **Login or Register** > > > > > {: .hands_on} @@ -77,15 +80,20 @@ This tutorial is part of set of tutorials on the [Galaxy Earth System](https://e --- - # Argo gliders data -Argo is a global network of nearly 4000 autonomous probes measuring pressure, temperature and salinity from the surface to 2000m depth every 10 days. The localisation of these probes is nearly random between the 60th parallels. All probes data are collected by satellite in real-time, processed by several data centers and finally merged in a single dataset (collecting more than 2 millions of vertical profiles data) made freely available to anyone through a ftp server or monthly zip snapshots. +Argo is a global network of nearly 4000 autonomous probes measuring pressure, temperature and salinity from the surface to 2000m depth every 10 days. +The localisation of these probes is nearly random between the 60th parallels. All probes data are collected by satellite in real-time, processed by several data +centers and finally merged in a single dataset (collecting more than 2 million vertical profiles) made freely available to anyone through an FTP server or monthly zip snapshots. -Each Argo probe is an autonomous, free drifting, profiling float, i.e. a probe that canโ€™t control its trajectory but is able to control its buoyancy and thus to move up and down the water column as it wishes. Argo floats continuously operate the same program, or cycle, illustrated in the figure below. After 9 to 10 days of free drift at a parking depth of about 1000m, a typical Argo float dives down to 2000m and then shoals back to the surface while measuring pressure, temperature and salinity. Once it reaches the surface, the float sends by satellite its measurements to a data center where they are processed in real time and made freely available on the web in less than 24h00. +Each Argo probe is an autonomous, free drifting, profiling float, i.e. a probe that canโ€™t control its trajectory but can control its buoyancy and thus move up and down the water +column as it wishes. Argo floats continuously operate the same program, or cycle, illustrated in the figure below. After 9 to 10 days of free drift at a parking depth of about 1000m, +a typical Argo float dives down to 2000m and then shoals back to the surface while measuring pressure, temperature and salinity. Once it reaches the surface, +the float sends by satellite its measurements to a data center where they are processed in real-time and made freely available on the web in less than 24h00. ![Schema of a typical 10 days program, cycle, of an Argo float](../../images/argo_pangeo/argofloats_cycle.png "10 days program, cycle, of an Argo float") -Here we will focus on the Caribbean sea surrounding the Antilles during April and May. The 9th of April 2021 an eruption of the volcano La Soufriere Saint Vincent (Antilles) occured. Another tutorials on this event is available on the [Galaxy Training Network]({% link topics/climate/tutorials/sentinel5_data/tutorial.md %}). +Here we will focus on the Caribbean Sea surrounding the Antilles during April and May. On the 9th of April 2021 an eruption of the volcano La Soufriere Saint Vincent (Antilles) occurred. +Another tutorial on this event is available on the [Galaxy Training Network]({% link topics/climate/tutorials/sentinel5_data/tutorial.md %}). ## Get Argo data @@ -102,7 +110,7 @@ Here we will focus on the Caribbean sea surrounding the Antilles during April an > > > 1. {% tool [Argo data access](toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0) %} with the following parameters: -> - {% icon param-select %} *"We have preconfigured some mode of operations for you. What mode do you want to use?"*: `๐ŸŠ standard mode simplifies the dataset, remove most of its jargon and return a priori good data` +> - {% icon param-select %} *"We have preconfigured some mode of operations for you. What mode do you want to use?"*: `๐ŸŠ standard mode simplifies the dataset, removes most of its jargon and returns a priori good data` > - {% icon param-select %} *"How do you want to select your data of interest ?"*: `๐Ÿ—บ For a space/time domain` > - *"Input longitude min (+east/-west)"*: `-75.0` > - *"Input longitude max (+east/-west)"*: `-45.0` @@ -115,20 +123,24 @@ Here we will focus on the Caribbean sea surrounding the Antilles during April an > - {% icon param-select %} *"Which kind of dataset do you want ?"*: `Physical parameters: temperature, salinity, pressure` > > 2. **Run Tool** -> 3. After a couple minutes an `Argo data` output will appear green in your history. +> 3. After a couple of minutes, an `Argo data` output will appear green in your history. > 4. Check that your data are in netcdf format with {% icon galaxy-pencil %}, it should be `netcdf` > > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="nectdf" box_type="tip" %} {: .hands_on} -# Argo data analysed, managed, and visualised by th Pangeo tools +# Argo data analysed, managed, and visualised by the Pangeo tools ## Xarray tools -First, we'll use 2 xarray netcdf tools. xarray, formerly known as xray, is a python package which enables us to play with gridded data. This package shares most of its features from numpy, but in a more convenient manner by keeping track of labels in arrays. The gridded data is mainly available in netCDF data format. Thus xarray comes very handy while dealing with netCDF files. +First, we'll use 2 xarray netcdf tools. xarray, formerly known as xray, is a Python package which enables us to play with gridded data. +This package shares most of its features from numpy, but in a more convenient manner by keeping track of labels in arrays. +The gridded data is mainly available in netCDF data format. Thus xarray comes in very handy while dealing with netCDF files. ## Knowing more about hour data -After fetching the required Argo data, the following stage is to obtain the meta info or meta data of the file. The very purpose of these steps are to obtain the information about dimensions, variables, global attributes, etc. The coordinate info helps to know about the actual data entries present under the various variables. +After fetching the required Argo data, the following stage is to obtain the meta info or metadata of the file. +The very purpose of these steps is to obtain information about dimensions, variables, global attributes, etc. The coordinate info helps to +know about the actual data entries present under the various variables. ## Get metadata @@ -139,7 +151,7 @@ After fetching the required Argo data, the following stage is to obtain the meta > {: .hands_on} -In info file output file, we can identify 4 different sections: +In the info output file, we can identify 4 different sections: 1. Dimensions: name of dimensions and corresponding number of elements; 2. Coordinates: contains coordinate arrays (longitude, latitude, level and time) with their values. @@ -184,7 +196,9 @@ View {% icon galaxy-eye %} the 5 generated outputs: # Visualisation mapping with a Galaxy Earth System's tool -The Earth System is a complex and dynamic system that encompasses the interactions between the atmosphere, oceans, land, and biosphere. Understanding and analyzing data from the Earth System Model (ESM) are essential, for example to predict and mitigate the impacts of climate change. The ESM that the project tries to implement includes coastal water dynamics, ocean bio-geochemical in-situ data, marine omics observations, volcano activities and land degradation. +The Earth System is a complex and dynamic system that encompasses the interactions between the atmosphere, oceans, land, and biosphere. +Understanding and analyzing data from the Earth System Model (ESM) is essential, for example, to predict and mitigate the impacts of climate change. +The ESM that the project tries to implement includes coastal water dynamics, ocean bio-geochemical in-situ data, marine omics observations, volcano activities and land degradation. To know more keep an {% icon galaxy-eye %} open for all related blogs on the [Galaxy Community Hub](https://galaxyproject.org/news/) or go try the tools directly on [Galaxy Earth System](https://earth-system.usegalaxy.eu/). @@ -193,7 +207,7 @@ To know more keep an {% icon galaxy-eye %} open for all related blogs on the [Ga ## Ocean Data View (ODV) Ocean Data View (ODV) is a software package for the interactive exploration, analysis and visualization of oceanographic and other geo-referenced profile, time-series, trajectory or sequence data. To know more about ODV go check the [official page](https://odv.awi.de/). -ODV is now integrated in Galaxy as an interactive tool. This kind of tools is working 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. +ODV is now integrated with Galaxy as an interactive tool. This kind of tool works differently than classical tools as it allows the user to interact with a dedicated graphical interface. Those tools are used to give access to Jupyter Notebooks, RStudio or R Shiny apps for example. > Launch ODV > @@ -206,11 +220,11 @@ ODV is now integrated in Galaxy as an interactive tool. This kind of tools is wo > {% snippet faqs/galaxy/interactive_tools_open.md tool="ODV" %} > > > ODV - Disconnected -> > If at one point your ODV interface becomes grey with a red panel on the top "X ODV - Disconnected", do NOT panic ;) you just need to reload your tab (circular arrow top left) +> > If at one point your ODV interface becomes grey with a red panel on the top "X ODV - Disconnected", do NOT panic ;) you just need to reload your tab (circular arrow on top left) > {: .tip} > > > Copy pasting between computer and ODV -> > You can expand the ODV left panel (where there are 3 dots, vertically) to access the "clipboard" menu, and paste the content you want to paste on a ODV form. From there you can copy paste everything from one side to the other. Then, click outside of this panel to collapse it. +> > You can expand the ODV left panel (where there are 3 dots, vertically) to access the "clipboard" menu, and paste the content you want to paste on an ODV form. From there you can copy-paste everything from one side to the other. Then, click outside of this panel to collapse it. > > > > ![Image showing in transparent on the left of the ODV interface the clipboard](../../images/argo_pangeo/clipboard.png) > {: .tip} @@ -224,7 +238,7 @@ ODV is now integrated in Galaxy as an interactive tool. This kind of tools is wo > > 2. Go the top left and click on **File**, then on **Open...** > -> 3. On the pop-up screen on the left pannel select **ODV**, then the folder **galaxy**, then **data**. +> 3. On the pop-up screen on the left panel select **ODV**, then the folder **galaxy**, then **data**. > You should see a folder open it (double clicking) > > 4. In the bottom of the pop-up window in **Files of type** select **All Files (*)** @@ -239,7 +253,7 @@ ODV is now integrated in Galaxy as an interactive tool. This kind of tools is wo > > 9. Once you're happy with your selection click on **Enter** on your keyboard. > -> There your data should be openning an you can now visualise them ! +> There your data should be opening and you can now visualise them! > {: .hands_on} @@ -255,9 +269,9 @@ ODV is now integrated in Galaxy as an interactive tool. This kind of tools is wo > 6. Then, click on **OK**. > > > Change your visualisation properties -> > 1. Go on the central map +> > 1. Go to the central map > > 2. Click right and select **Properties...** -> > 3. For example make your data dots bigger in "Display Style" increase the number below "Symbol Size" to 30, click **OK** +> > 3. For example, make your data dots bigger in "Display Style" increase the number below "Symbol Size" to 30, and click **OK** > > > > You can now see bigger dots representing your data. > {: .tip} @@ -278,7 +292,8 @@ ODV is now integrated in Galaxy as an interactive tool. This kind of tools is wo # Conclusion -Awesome ! You now know how to get Argo data, then get meta data and other information within the Pangeo ecosystem and finally visualise these data with an Earth System tool, Ocean Data View. +Awesome! You now know how to get Argo data, then get metadata and other information within the Pangeo ecosystem and finally visualise these data with an Earth System tool, +Ocean Data View. ![The full workflow](../../images/argo_pangeo/workflow.png)