ACOLITE

ACOLITE bundles the atmospheric correction algorithms and processing software developed at RBINS (Royal Belgian Institute of Natual Sciences) for aquatic applications of metre and decametre satellite data, including Landsat (5/7/8) and Sentinel-2 (A/B). ACOLITE is in particular suited for processing of turbid waters and small inland water bodies, but can be used with reasonable success over clearer waters and land.

Acolite manual

This has been tested with  Landsat and  Sentinel-2.

• For Sentinel-2, insure that you do not let MICRODEM delete the JP2 files which it converts to Geotiff via GDAL.  The program will warn if this happened.

ACOLITE should mask clouds, even subtle ones, so you can process scenes and get results for the cloud free portions.

This uses the default settings for ACOLITE.  If you want other changes, you should modigy the default settings file  in config\defaults.txt.

Web links

• Program home page: https://odnature.naturalsciences.be/remsem/software-and-data/acolite
• Program forum: https://odnature.naturalsciences.be/remsem/acolite-forum/
• Program download: https://github.com/acolite/acolite
• Old version download: https://github.com/acolite/acolite_ls2   Landsat/Sentinel 2 version (no longer supported)

Set up ACOLITE, one time:

• The simplest solution is to sideload the entire directory from an existing installation, from an external hard drive or a zipped archive.
• If that is not possible:

• Download and uncompress ACOLITE from github.  It does not have to be installed, and does not need admin priviledges.
• In the defaults settings in config\defaults.txt, change the Geotiff settings to true:

• # GeoTIFF export options l1r_export_geotiff=True l2t_export_geotiff=True l2r_export_geotiff=True l2w_export_geotiff=True

• You are likely to have to download the LUTs for the different satellites, from https://github.com/acolite/acolite_luts, and place them in the correct location
• With all lookups (which you don't need, but it's really hard to get just what you do need), this will be about 9 GB.

Set up anaconda, one time

• Download and install anaconda.  You can do this without admin priviledges for the personal edition, but that works only for the single user.
• Open an anaconda prompt from the start menu
• Create a Python environment, by issuing the following commands, and accepting all prompts.  The first and last of the three commands are slow (or very slow, depending on your perspective), but will show progress, and you need to keep an eye open for the prompts.

• conda create -n acolite -c conda-forge python=3 conda activate acolite conda install -c conda-forge numpy matplotlib scipy gdal pyproj scikit-image pyhdf pyresample netcdf4 h5py

Limits when Running ACOLITE

• Strongly considering setting geographic limits. Full scenes take a long time and create very large output files.
• You could reduce the resolution of the product grids from the 10 m default, which runs much faster and with much smaller output files

 ACOLITE L2W Parameters

• Pick the L2W parameters you want.  They are listed in section 5 of the manual, with references. A starting point would be:

• tur_nechad2016,spm_nechad2016,ndci,chl_re_mishra

  • tur, turbidity (units are NFU, Formazin Nephelometric Unit,, log 10 scale)
  • spm, suspended particulate matter (units are g/m³, log 10 scale)
  • chl, chlorphyl concentration (units are ug/l, log 10 scale)
  • ndci, normalized difference chloroph index
• Parameters that cannot be computed with the satellite (for instance NDCI or chlorphyl, which need the red edge band of Sentinel-2 which is not present in Landsat) will be ignored

Running ACOLITE from MICRODEM, obviously the preferred choice

• Get data: Sentinel-2  directions and EarthExplorer download.  Unzip with the MICRODEM tools option.
• Open image for a Sentinel-2 image; use folder directory selection.  Make sure you pick the directory whose name ends with "SAFE"
• Subset & zoom to just the area you want to process
• Imagery options to set parameters
• Image analysis, ACOLITE processing
• If the program cannot find it, you must identify the ACOLITE.EXE file, which will be something like 'G:\acolite_py_win_20210802.0\acolite_py_win\dist\acolite\acolite.exe';
• The output will be placed in a new folder under c:\mapdata\acolite.  You should keep an eye on this folder that it does not kill your hard disk.
• MICRODEM will delete the NC files, and a few other "unneeded" files, but you will still have many GB for each scene.

Running ACOLITE from its GUI

• Start ACOLITE EXE.  A shortcut will be near the top of the directory structure for ACOLITE
• Pick the directory with the satellite image, which should have SAFE at the end of the folder name
• Create and pick an output directory
• Enter the L2W parameters
• Enter geographic limits
• Run

Batch Running ACOLITE

• Open all the images
• Subset one to the desired area
• Use Files, Match other Maps, This coverage area
• Pick the option on the Analyze, Batch processing, ACOLITE
• Use with caution, and probably will not work with Sentinel-2

Output

• You can delete the large NC files, since you want the Geotiffs.  MICRODEM now automatically deletes them as well as several other files, and the next version of ACOLITE will have this as an option.
• Output files will be in c:\mapdata\acolite, with a directory for each run of the program.  The name has the base name for the satellite image, which includes date, location, and sensor, and the subset extent.  You can sort by the creation time to find the most recent one.
• 
• Sentinenel-2 Levels
  • Level-1C processing includes radiometric and geometric corrections including ortho-rectification and spatial registration on a global reference system with sub-pixel accuracy. This is what you download.
  • The Level-2A processing includes a scene classification and an atmospheric correction applied to Top-Of-Atmosphere (TOA) Level-1C orthoimage products. Level-2A main output is an orthoimage Bottom-Of-Atmosphere (BOA) corrected reflectance product. This is what ACOLITE is producing.
• Reflectance files.. These will all be at 10 m resolution (unless you have specfied another resolution), so the files will be huge
  • rhot files from top of atmosphere reflectance
  • rhos files from earth surface reflectance
• Output files named for the wavelength, rather than the band (Table 1)
• To reopen the L2W parameter maps later, open them as a DEM/grid

Table 1.  Sentinel-2 bands used by ACOLITE (some wavelengths differ slighlty from other sources)

ACOLITE Errors and Likely causes

• Key error: 'B1':  you deleted the JP2 files.  If they are not backed up in the the recycle bin, you will have to redownload.
• Ignore these errors:
  • PROJ: utm: Invalid latitude
  • RuntimeWarning: mean of empty slice

Debugging ACOLITE

• Output goes in the folder listed above
• There is a log named "acolite_run_20211108_150946_log_file.txt"which will record the run
• Check that to see what problems are recorded
  

last revised 10/25/2021