Ad-hoc Sequence Processing

This section provides a user guide for running the hypernets_processor module to process specified field acquisitions, or sequences, on an ad-hoc basis outside of any automated processing.

Prerequisites

hypernets_processor is distributed using Git, from the project’s GitHub repository. Git can be installed from the from the Git website.

Python 3 is required to run the software, the Anaconda distribution provides a convenient way to install this.

Installation

First clone the project repository from GitHub:

$ git clone https://github.com/HYPERNETS/hypernets_processor.git

Then install the module with pip:

$ pip install -e hypernets_processor/

This will also automatically install any dependencies.

If you are installing the module to contribute to its development, it is recommended you follow the install instructions on the Getting Started page.

Sequence Processing

Once installed the hypernets_sequence_processor command-line tool provides the means to process raw sequence data, it is run as follows:

$ hypernets_sequence_processor -i <input_directory> -o <output_directory> -n <network>

where:

  • input_directory - directory of raw sequence product, or directory containing a number of raw sequence products, to process.

  • output_directory - directory to write output data to.

  • network - network name, land or water. The default configuration for this network is applied for the processing.

To see more options, try:

$ hypernets_sequence_processor --help

Alternatively, the processing can be specified with a job configuration file as follows:

$ hypernets_sequence_processor -j <job_config_path>

where:

  • job_config_path - path of a job configuration file. See Job Setup for information on initialising a job configuration file.

Specifying processing with a custom job configuration file allows non-network-default configuration values to be set, for example, chosen calibration function. See also Processing Configuration for more details about the processing parameters that can be given.

Examples

Ad-hoc processing of a single sequence for a site called M1BE can be done with the following command:

$ hypernets_sequence_processor -i /home/waterhypernet/HYPSTAR/Raw/M1BE/DATA/SEQ20231031T182051 -o /home/waterhypernet/HYPSTAR/Processed/test/ -n water --max-level L2A

While processing all sequences within a single directory can be done with:

$ hypernets_sequence_processor -i /home/waterhypernet/HYPSTAR/Raw/M1BE/DATA/ -o /home/waterhypernet/HYPSTAR/Processed/test/ -n water  --max-level L2A

If the adhoc processing arguments do not refer to a user defined job configuration path, input parameters for the processing configuration are taken by default from:

  • /hypernets_processor/hypernets_processor/etc/processor_land_defaults.config, or,

  • /hypernets_processor/hypernets_processor/etc/processor_water_defaults.config,

for the land and water network respectively. More details about the input parameters for the processing configuration can be found in Processing Configuration.