Version 12 (modified by dac, 6 years ago) (diff)

Added instructions for running atmospheric correction on NERC-ARF system.

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



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


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)
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 will run the entire process on a file which has been masked using aplmask using the NERC-ARF default parameters. -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/ \
         -d /users/rsg/arsf/arsf_data/2017/flight_data/spain/RG17_26-2017_166_Albacete/delivery/RG17_26-166-hyperspectral-20170823 \

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 script can be used. The .inn files can be opened in the ATCOR GUI and run through that or the can be used.