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 conventions and scripts used for processing.

Directory Structure

Processing

processing/hyperspectral/atmospheric_correction/<flightline>

ATCOR prefers to have all files for a flightline in a single directory

Delivery

The following directories are included in addition to the ones included with a standard hyperspectral delivery:

flightlines/level2_ac  (the level1 corrected *atm.bil)
flightlines/mappped_ac  (the level3 corrected *atm.bil)
mosaic/                (if a level3 corrected mosaic has been generated - multiple subdirs if required)
doc/                   (standard documentation on procedure - not flight specific)
screenshots/
           fJJJll3b_atm.jpg
AtmosCorr_readme-DATE.pdf   (description of all AC work and parameters, software versions, algorithms, include a table with what
                        has been processed, e.g.  | Topography   | YES   |
                                                  | BRDF         | YES   |
                                                  | Cloud shadow | No    |

Running ATCOR

Running ATCOR comprises generating the .inn parameter file and then running ATCOR through IDL. For files which have entire bands masked out (e.g., Fenix data from late 2014 - 2015) these bands need to be removed before running. The script run_atm_correction_atcor.py will run the entire process on a file which has been masked using aplmask using the NERC-ARF default parameters.

run_atm_correction_atcor.py -d <delivery_directory> <masked_bil_file>

The directory the masked bil file is in will be used for all ATCOR files so it is recommended a separate directory is used for each line.

To run multiple files a separate queue has been set up for ATCOR. To submit ATCOR jobs to the grid a command similar the below can be used:

qsub -q atcor.q -P arsfdan -m n -b y -N acor_test \
         -o /users/rsg/dac/scratch_network/atcor_runs/2017_166/f166071b/  \
         -e /users/rsg/dac/scratch_network/atcor_runs/2017_166/f166071b/  \
         /users/rsg/dac/scratch_network/git_repos/arsf_atcor_scripts/scripts/run_atm_correction_atcor.py \
         -d /users/rsg/arsf/arsf_data/2017/flight_data/spain/RG17_26-2017_166_Albacete/delivery/RG17_26-166-hyperspectral-20170823 \
         /users/rsg/dac/scratch_network/atcor_runs/2017_166/f166071b/f166071b_masked.bil

Note only a single job will run at once.

Non-standard parameters

For more control over the parameters passed to ATCOR, for example to include microtops data to define visibility, the gen_inn_atcor.py script can be used. The .inn files can be opened in the ATCOR GUI and run through that or the batch_run_atcor_inn.py can be used.