Biophysical processor S2_10m: methodology to obtain data

Optical Toolbox
1

Dear SNAP users,

I am new to remote sensing data and I am trying to obtain data in Ireland to derive LAI at 10 m resolution. My undertstanding is that Biophysical Processor toolbox would require simultaneous the following bands:

  • B3,
  • B4,
  • B5,
  • B6,
  • B7,
  • B8A,
  • B11,
  • B12,
  • view_zenith_mean
  • view_azimuth_mean,
  • sun_zenith
  • and sun_azimuth

The question is from what website, or Python or Julia code would be the most appropriate to download the data?

I understand that afterwards I would require to resample the data at 10 m resolution by using bilinear interpolation. Then I would need to Merge the data.

Many thanks for any help you may provide,

Joseph A.P. Pollacco

2

You can download the S2 data from CDSE Copernicus Browser
This is all you need. For computing LAI you can use the Biophysical Processor S2_10m without resampling beforehand or merging. You just need to use the downloaded zip file or the extracted .SAFE directory or the MTD_MSIL2A.xml file inside the SAFE directory.

image
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EOMasters_icon_60 Marco from EOMasters - Mastering Earth Observation

3

Dear Marco,

A great thanks for your great kindness for putting me in the right direction. I followed the different steps you kindly advised and hoping I did it properly and I got the error:

Please consider resampling it so that all rasters have the same size.

I would try and perform resampling, but from my previous experience I woiuld need to convert the .SAFE file into .geoTIFF format.

I am attaching you the different steps in .pdf and I will be more than greatfull if you could correct me if I am doing things not in the correct way?

A great thanks for your kindness,
Joseph A.P. Pollacco
STEPS_Snap.pdf (104.0 KB)

4

Dear Joseph,

You can use the Biophysical Processor S2 and select a 10 m output resolution. This will automatically resample the product.

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https://step.esa.int/main/wp-content/help/versions/13.0.0/snap-toolboxes/eu.esa.opt.opttbx.biophysical/BiophysicalOpProcessorDescription.html

5

Dear @diana_harosa @Marco_EOM

Greetings from cloudy Ireland.

I am ever so grateful for your kindness in helping researchers to make the best use of the comprehensive SNAP software. Thanks to your support, I finally obtained an LAI for the area of interest, with try and error.

Q1) Since I am using the S2A product in cloudy Ireland, will it be beneficial to further perform cloud correction before running the Biophysical processor, such as running the image through sen2cor software?

Q2) My understanding is that it will be best to mask cloud contamination before running the Biophysical processor or is it better to run the Biophysical processor and then remove the clouds, which are flagged given a known issue with the Flag classification?

Q3) If we mask the cloud beforehand, then it is not clear which is the best algorithm to use, as it is not clear for the 10 m resolution derived LAI product, what is the maximum cloudness the S2ToolBox can handle, any recommendation will be welcomed?

Now the next challenge is to automatise the process.

BUGS

Kindly let me know if I should fill out a bug report:

1: In the Biophysical processor, writing to .GeoTIFF fails when opening in QGIS, and therefore, one should use instead GeoTIFF-Big.TIFF

2: if one resampled to 10m before using Biophysical Processor, then one should use Biophysical Processor S2_10 and not S2, as the algorithm resamples again and reduces the image’s sharpness.

3: To save to GeoTIFF, one can only save one variable at a time such as LAI.

Many thanks for all your support,

Joseph A.P. Pollacco