EBVCubeVisualizer

EBVCubeVisualizer is a QGIS plugin tailored for exploring Essential Biodiversity Variables (EBVs) stored as EBVCube netCDF files and available at EBV Data Portal. This plugin enables users to extract and visualize specific slices of ebv data cubes, allowing flexible selection based on time, entity, scenario, and metric. While not designed for in-depth biodiversity analysis, EBVCubeVisualizer serves as a powerful and intuitive GIS tool for exploring datasets and preparing data for further analysis.

Features

• Load and Visualize EBVCube netCDF files: Seamlessly load EBVCube data stored in netCDF format and visualize them directly in QGIs.
• Flexible Data Subsetting: Extract specific slices of data by selecting time, entity, scenario, and metric, providing targeted views of biodiversity information.
• Metadata and Data Structure Discovery: Explore the full metadata and hierarchical strcuture of EBVCube netCDF file, making it easier to understand and navigate complex biodiversity data.
• Automatic CRS Application: Automatically apply the correct Coordinate Refrence System (CRS) based on the metadata embedded in the netCDF files.
• Clear and Informative Layer Naming: Display selected data on the QGIS canvas with meaningful layer names that incorporate entity and time details for easy identification.

Installation

1. Download this repository as zip file.
2. Open QGIS and go to Plugins > Manage and Install Plugins....
3. Click on Install from ZIP and select the downloaded file.
4. Activate the plugin by checking the box next to "EBVCubeVisualizer" in the Installed tab.

Usage

1. Open the Plugin:

   • After installation, go to Plugins > EBVCubeVisualizer to open the plugin interface.

2. Plugin Interface Overview:

   • The plugin interface consists of three main sections:

     • Dataset Explorer: Located on the left, it displays the hierarchical structure of the loaded dataset, including scenarios, metrics, and the data cube.
     • Metadata Panel: Positioned on the top-right, it dinamically updates to show the metadata of the selected data set, scenario, metric or data cube
     • Map Panel: Found on the buttom-rigth, it allows users to select specific parameters (e.g., Scenario, Metric, Entity, and Time) and visualize the data by clicking the Add Layer button.

     Below the plugin interface

     

3. Load a EBVCube netCDF File:

   • Use the file browser to select a EBVCube netCDF file.

   • Once loaded, the structure of the dataset is displayed in the Dataset Explorer on the left, showing entity, scnenarios (if available), metrics and the data cube.

     Example of the loaded dataset

     

4. Explore the Hierarchical Structure of the Dataset:

   • The Dataset Explorer displays the hierarchical structure, organized into:

     • File name: Represent the root of the dataset.
     • Entity: Provides attributes about enititis analyzed in the dataset (e.g., species, taxonomic groups)
     • Scenarios (e.g., scenario_1): Represent different modeling or simulation scenarios in the dataset.
     • Metrics (e.g., metric_1): Represent specific biodiversity measurements or calculations.
     • Data cube: Represent the four-dimensional EBVdata cube.

   • To view details:

     • File name: Click to display the global attributes of the data set (e.g., doi, summary, project_name, data_created)
     • Entity: Click to display the entity attibutes (e.g.,ebv_entity_type, ebv_entity_scope)
     • Scenarios: Click to view associated attributes (e.g., standard_name, long_name).
     • Metric: Click to see specific attributes (e.g., standard_name, long_name, units).
     • Data cube: Click to explore its attibures (e.g., units, FillValue, long_name, coverage_content_type)

     Example of attributes displayed when you click 'metric_1'

     

     

   • Tip: The metadata panel updates dynamically based on your selection in the Dataset Explorer.

5. Select Parameters:

   • Use the dropdown menus under Map Panel to select:

     • Scenario: e.g., SSP1 (if available).
     • Metric: e.g., Biodiversity metric such as Weighted Mean habitat suitability.
     • Entity: e.g., species like Hyla arborea.
     • Time: e.g., 2020-01-01.

     Example of selecting parameters

     

6. Visualize Data:

   • Click the Add Layer button to display the selected subset of data on the QGIS canvas.

   • The layer will include an automatically generated color ramp based on the data values.

     Example of a visualized layer on the QGIS canvas

     

7. Customize Visualization:

   • Use QGIS layer properties to further refine the visualization:
     • Adjust the color ramp for better interpretation.
     • Apply spatial analysis tools for advanced exploration.

Dependencies

• QGIS 3.0 or later
• Python 3.6 or later
• Required Python Libraries:
  • netCDF4: Handles netCDF file loading and data extraction.
  • numpy: Supports array operations and data handling.
  • gdal: Facilitates raster data management and processing.

if you encounter issues with missing libraries, follow the instructions below to install them:

Installing Libraries via OSGeo4W Shell

1. Open the OSGeo4W Shell.
2. Run the following commands to install the required libraries:

   python -m pip install netCDF4 numpy gdal 

3. Restart QGIS to ensure the new libraries are recognized

Troubleshooting

If you encounter any issues with the plugin, please follow these steps:

1. Ensure that all dependencies are installed and correctly configured.
2. Verify that the netCDF file you are using is properly formatted and contains the required dimensions (e.g., entity, time, lat, lon).
3. Check the QGIS Python console for any error messages and provide them when seeking help.

Example Dataset

The examples in this README use the publicly available dataset entitled "Species habitat suitability of European terrestrial vertebrates for contemporary climate and land use", provided by the EBV Data Portal. It is stored as an EBVCube netCDF file and can be accessed directly through the following link:

• EBV Data Portal Link: Species habitat suitability of European terrestrial vertebrates for contemporary climate and land use

This dataset serves as an example to showcase the functionality of the plugin. You are encouraged to explore additional datasets available on the EBV Data Portal for your analyses.

Contributing

We welcome contributions to this project! If you have an idea for a new feature or have found a bug, feel free to open an issue or submit a pull request.

License

TThis project is licensed under the GNU General Public License v3.0 or later (GPL-3.0-or-later). For more details, please refer to the LICENSE file.

Future Enhancements

• User Interface Improvements: Implement new features to enhance the user experience and make the plugin more intuitive.
• Data Availability: Integrate the EBV Portal catalog within the plugin to facilitate data retrieval.

Stay tuned for future updates and enhancements!