Atmospheric correction with ATCOR

The latest version of our atmospheric correction procedure is being developed in a private GitHub repository - email us if you require access. The process is still being refined to cope with the variety of environments and conditions flown by NERC-ARF and feedback is welcome.

NERC-ARF Specific Instructions

For running on the NERC-ARF systems there are a number of utilities to make batch processing easier.

Work in progress - more documentation will be added as it is written

Generating the .inn file

To generate the .inn file for ATCOR use the gen_inn_atcor.py script.

• --calfile needs to point to the .cal file ATCOR users, this wil be ~arsf/usr/opt/atcor_4/sensor/SENSOR/*.cal where SENSOR is the name used for the sensor definition in ATCOR (e.g., f17_b2).
• inputbil needs to point to the bil file in the delivery folder directory.
• --outputdir should be the directory used or ATCOR processing.

If microtops data has been provided pass this in using --microtops to read using the ​https://github.com/robintw/PyMicrotops library and set a constant visibility based on this. Note if the microtops data has a number of header lines these need to be removed before PyMicrotops can read the file, there should just be one header line with the column names.

After generating the .inn file it should be renamed to use the same name as the image (without the .bsq extension). For example if the file being processed in ATCOR is 'f168043b_masked_resampled_utm31n.bsq' name 'f168043b_masked_resampled_utm31n.inn'.

Currently ATCOR doesn't always read all the parameters correctly open the .inn file (plain text) and update the values in the ATCOR GUI if needed.

Batch running .inn files

Once .inn files have been generated and checked using the ATCOR GUI it is possible to run in batch using the script batch_run_atcor_inn.py. To do so ssh onto 'rsg-atcor' and run:

batch_run_atcor_inn.py /path/to/files/to/process

This will recursively search for .inn files and run them through ATCOR.