Starting biophysical processor via command line

Optical Toolbox
#1

Hello,

is there a way to start the biophysical processor through a command line interface? If yes how is it done?

#2

I see two different ways of doing it here:

  1. Use the “GraphBuilder” tool in the SNAP Interface and create your process from reading the input data to calculating the biophysical parameters to finally write the output into a new file. Simply call the created .xml file through the command line.

  2. Use the SNAP Command-Line and call ‘gpt BiophysicalOP …’. There is also some help available.

Cheers

#3

some questions regarding the two different ways

  1. can I vary the input variables this way? e.g: select different images programmatically
  2. how can I acess the SNAP command line (and give inputs) from e.g. python?
#4

@unnic: 1) You can simply create a pyhton (or whatever you like) and use loops to read Image after Image until you reached the end. 2) You can access the SNAP commands from python using ''os.system(‘here is your SNAP command’). At leeast that is the way it works for the L2A process.

Hope this is helpful

#5

reading the images is not the problem.
sen2cor is a standalone process so L2A_process is something different. but thanks for your input, I’ll give it a try.

#6

Hello, I am running the biophysical processor with snappy and I get a warning/error message. The file is created though and everything seems fine with it. Is there something to worry about then?

Thank you

Chloe

I run:

HashMap = snappy.jpy.get_type(‘java.util.HashMap’)
snappy.GPF.getDefaultInstance().getOperatorSpiRegistry().loadOperatorSpis()
parameters = HashMap()
parameters.put(‘computeCab’, True)
parameters.put(‘computeCw’, True)
parameters.put(‘computeFapar’, True)
parameters.put(‘computeFcover’, True)
parameters.put(‘computeLAI’, True)
biophysical_indexes = GPF.createProduct(‘BiophysicalOp’, parameters, Sent2_image_subset)

The message I get is:
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chbr.snap\auxdata\s2tbx\biophysical\2_1\LAI_Cw\LAI_Cw_TestCases
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients TEST_CASES for variable LAI_Cw. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chbr.snap\auxdata\s2tbx\biophysical\2_1\FCOVER\FCOVER_TestCases
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients TEST_CASES for variable FCOVER. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chbr.snap\auxdata\s2tbx\biophysical\2_1\FCOVER\FCOVER_DefinitionDomain_MinMax
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_MINMAX for variable FCOVER. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chbr.snap\auxdata\s2tbx\biophysical\2_1\FCOVER\FCOVER_DefinitionDomain_Grid
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_GRID for variable FCOVER. They won’t be available.

#7

Hello,
I have the same problem, when using snappy. I dont find LAI_Cw_TestCases, FCOVER_TestCases, FCOVER_DefinitionDomain_MinMax and COVER_DefinitionDomain_Grid files!! Help?

Thank you

WARNING: org.esa.snap.core.gpf.common.SubsetOp: No intersection with source product boundary S2A_MSIL2A_20171026T110131_N0206_R094_T30SWJ_20171026T144303_resampled
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading /home/ndjamai/.snap/auxdata/s2tbx/biophysical/2_1/LAI_Cw/LAI_Cw_TestCases
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients TEST_CASES for variable LAI_Cw. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading /home/ndjamai/.snap/auxdata/s2tbx/biophysical/2_1/FCOVER/FCOVER_TestCases
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients TEST_CASES for variable FCOVER. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading /home/ndjamai/.snap/auxdata/s2tbx/biophysical/2_1/FCOVER/FCOVER_DefinitionDomain_MinMax
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_MINMAX for variable FCOVER. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading /home/ndjamai/.snap/auxdata/s2tbx/biophysical/2_1/FCOVER/FCOVER_DefinitionDomain_Grid
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_GRID for variable FCOVER. They won’t be available.