Working With HDF file and SeaDAS in UBUNTU

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Introduction to SeaDAS

Satellite ocean color analysis is a powerful tool for studying the health, dynamics, and productivity of Earth’s oceans. One of the key software packages used in this field is SeaDAS (SeaWiFS Data Analysis System). SeaDAS is an open-source software developed by NASA (National Aeronautics and Space Administration) to process, analyze, and visualize satellite-derived ocean color data.

SeaDAS provides a comprehensive suite of tools and algorithms that facilitate the extraction of valuable information from satellite imagery. By harnessing the data captured by sensors such as SeaWiFS, MODIS, and VIIRS, SeaDAS enables researchers, scientists, and oceanographers to explore and understand various oceanographic parameters.

Key Features and Capabilities:

  1. Data Processing: SeaDAS offers a range of functionalities for importing and processing satellite ocean color data. It supports different file formats, including HDF (Hierarchical Data Format) and netCDF (Network Common Data Form). The software handles tasks such as atmospheric correction, geolocation, and calibration, ensuring that the data is ready for analysis.
  2. Oceanographic Parameter Retrieval: SeaDAS incorporates advanced algorithms for the retrieval of oceanographic parameters from satellite data. These parameters include chlorophyll-a concentration, sea surface temperature, turbidity, and primary productivity. By applying bio-optical models and inversion techniques, SeaDAS estimates these parameters, providing valuable insights into the marine ecosystem.
  3. Data Visualization and Analysis: SeaDAS offers a rich set of visualization and analysis tools to explore and interpret ocean color data. It enables the generation of color composites, scatterplots, time series plots, and geographic maps. These visualizations aid in identifying spatial and temporal patterns, understanding ecosystem dynamics, and detecting anomalies.
  4. Quality Control and Validation: SeaDAS includes features for quality control and validation of satellite-derived ocean color data. It allows users to compare the satellite data with in-situ measurements and ground truth data, ensuring the reliability and accuracy of the results. Quality assessment flags embedded in the data help identify potential issues and anomalies.
  5. Customization and Extensibility: SeaDAS is an open-source software, providing users with the flexibility to customize and extend its capabilities. Users can develop and integrate their own algorithms, plugins, and workflows to address specific research needs and objectives. This adaptability makes SeaDAS a powerful tool for diverse applications in marine science.

Understanding MOD09Q1 HDF Files

Satellite remote sensing plays a crucial role in monitoring and understanding the Earth’s oceans. The MOD09Q1 HDF (Hierarchical Data Format) file is an important data product that contains valuable information derived from satellite sensors such as MODIS (Moderate Resolution Imaging Spectroradiometer). In this article, we will delve into the structure, contents, and significance of MOD09Q1 HDF files in the context of satellite ocean color analysis.

  1. Overview of MOD09Q1 HDF Files:
    • Explanation of MOD09Q1 as a specific MODIS data product.
    • Introduction to the hierarchical structure of HDF files.
    • Significance of MOD09Q1 for ocean color analysis and its applications in marine research.
  2. Contents of MOD09Q1 HDF Files:
    • Surface Reflectance: The MOD09Q1 file contains bands representing the surface reflectance of the Earth’s surface in various spectral regions. These bands capture information about the amount of light reflected by the ocean, providing insights into water properties.
    • Atmospheric Correction Parameters: MOD09Q1 HDF files also include parameters derived from atmospheric correction algorithms. These parameters compensate for atmospheric effects, such as scattering and absorption, ensuring more accurate surface reflectance measurements.
    • Quality Assessment Flags: Quality assessment flags embedded in the HDF file indicate the reliability and quality of the data. These flags help identify potential issues, such as cloud cover, aerosol contamination, or data anomalies, enabling data filtering and selection of high-quality information.
  3. Hierarchical Structure of MOD09Q1 HDF Files:
    • Overview of the hierarchical organization of MOD09Q1 files.
    • Explanation of different levels within the hierarchy, including groups, datasets, and attributes.
    • Understanding the metadata associated with MOD09Q1 files, such as acquisition time, geolocation information, and sensor characteristics.
  4. Accessing and Working with MOD09Q1 HDF Files:
    • Introduction to software tools and libraries that can be used to access and process HDF files, such as HDFView, h5py, or PyHDF.
    • Exploring and extracting specific data layers from MOD09Q1 files.
    • Visualizing MOD09Q1 data using specialized software packages or programming languages like Python.
  5. Applications of MOD09Q1 HDF Files in Ocean Color Analysis:
    • Highlighting the significance of MOD09Q1 data in studying oceanographic phenomena.
    • Discussing how MOD09Q1 information can be used to derive key oceanographic parameters, such as chlorophyll-a concentration, sea surface temperature, or turbidity.
    • Demonstrating the value of MOD09Q1 in research areas like marine ecology, fisheries management, and climate studies.
  6. Limitations and Considerations:
    • Addressing potential limitations of MOD09Q1 data, such as spatial resolution or atmospheric variability.
    • Discussing factors that may affect data accuracy and interpretation, including cloud cover, sensor calibration, and data gaps.

Installation of SeaDAS on Ubuntu

SeaDAS (SeaWiFS Data Analysis System) is a powerful open-source software package developed by NASA (National Aeronautics and Space Administration) for processing and analyzing satellite ocean color data. If you’re using Ubuntu, here is a step-by-step guide on how to install SeaDAS on your system:

  1. System Requirements:
    • Ubuntu operating system (version 16.04 or later recommended).
    • Java Development Kit (JDK) version 8 or higher.
    • Sufficient disk space for installation and data storage.
  2. Install Java:
    • Open the Terminal application on Ubuntu.
    • Check if Java is already installed by running the command: ‘java -version‘.
    • If Java is not installed, run the command: ‘sudo apt install default-jdk‘ to install the default JDK package.
  3. Download SeaDAS:
    • Visit the SeaDAS website at and navigate to the “Downloads” section.
    • Choose the appropriate version of SeaDAS for Ubuntu and download the installation package (e.g., seadas.x.x.x-linux64-install.bin).
  4. Make the Installer Executable:
    • In the Terminal, navigate to the directory where the installer file is located.
    • Run the following command to make the installer executable: “chmod +x seadas.x.x.x-linux64-install.bin“.
  5. Run the Installer:
    • Execute the installer by running the command: “./seadas.x.x.x-linux64-install.bin“.
    • Follow the on-screen instructions to proceed with the installation.
    • You may be prompted to accept the license agreement and specify the installation directory. Choose an appropriate location (e.g., /opt/seadas) or use the default path.
  6. Configure SeaDAS Environment:
    • Once the installation is complete, open the Terminal and navigate to the SeaDAS installation directory (e.g., /opt/seadas).
    • Run the command: “source” to set up the necessary environment variables for SeaDAS.
  7. Launch SeaDAS:
    • In the Terminal, run the command: seadas to launch the SeaDAS graphical user interface (GUI).
    • The SeaDAS interface should open, providing access to various tools and functionalities for satellite ocean color analysis.

Congratulations! You have successfully installed SeaDAS on Ubuntu. You can now start exploring its features and capabilities for processing, analyzing, and visualizing satellite ocean color data. Remember to refer to the SeaDAS documentation and user guides for further assistance with specific tasks and workflows.

Working with MOD09Q1 HDF Files in SeaDAS

SeaDAS (SeaWiFS Data Analysis System) is a powerful software package developed by NASA for processing and analyzing satellite ocean color data. In this article, we will explore how to work with MOD09Q1 HDF (Hierarchical Data Format) files in SeaDAS to extract valuable information about ocean color and related parameters.

  1. Importing MOD09Q1 HDF Files into SeaDAS:
    • Launch SeaDAS on your system.
    • In the SeaDAS interface, go to the “File” menu and select “Open”.
    • Navigate to the directory where your MOD09Q1 HDF file is located.
    • Select the MOD09Q1 HDF file and click “Open” to import it into SeaDAS.
  2. Preprocessing Steps:
    • Atmospheric Correction: SeaDAS provides algorithms for atmospheric correction to remove atmospheric effects from the satellite data. Explore the atmospheric correction options and choose the appropriate method based on your study area and objectives.
    • Geolocation: SeaDAS allows you to geolocate the data, ensuring accurate spatial referencing. Use the geolocation tools in SeaDAS to align the satellite data with the corresponding geographic coordinates.
  3. Exploring Data Layers:
    • SeaDAS provides a variety of tools to explore the different data layers available in MOD09Q1 HDF files.
    • Use the “Layers” panel in SeaDAS to select and visualize specific data layers of interest, such as surface reflectance bands or atmospheric correction parameters.
    • Experiment with different color scales and enhancements to visualize the data effectively.
  4. Data Visualization:
    • SeaDAS offers a range of visualization tools to help you explore and interpret the satellite ocean color data.
    • Generate color composites to visualize different combinations of bands, enabling the identification of specific features or phenomena.
    • Create scatterplots to analyze the relationships between different oceanographic parameters, such as chlorophyll-a concentration and sea surface temperature.
  5. Analysis and Extraction of Parameters:
    • SeaDAS provides algorithms and tools for the extraction of various oceanographic parameters from satellite data.
    • Explore the available algorithms for parameter retrieval, such as chlorophyll-a concentration, turbidity, or primary productivity.
    • Apply the selected algorithms to your MOD09Q1 HDF file to derive the desired parameters.
  6. Quality Control and Validation:
    • SeaDAS allows you to perform quality control checks and validation of the processed data.
    • Compare the satellite-derived data with in-situ measurements or ground truth data to assess the accuracy and reliability of the results.
    • Pay attention to quality assessment flags embedded in the MOD09Q1 HDF file to identify potential issues or anomalies in the data.
  7. Saving and Exporting Results:
    • Once you have processed and analyzed the MOD09Q1 HDF file in SeaDAS, you can save the results for further analysis or visualization.
    • SeaDAS provides options to export the data in various formats, such as GeoTIFF or netCDF, allowing compatibility with other software or GIS tools.
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