BiophysicalOp batch processing from GFP

[chiara]

I am trying to run the BiophysicalOp processor in batch mode on a series of Sentinel-2 images, through the attached files (the graph, the parameters file and the processDataset.bat) on a machine Windows x64:

BiophysicalOp.properties (51 Bytes) BiophysicalOp.xml (1.6 KB) processDataset.bat (1.8 KB)

but by running the processor with the following command:

processDataset.bat BiophysicalOp.xml BiophysicalOp.properties path_to_input_folder path_to_output_folder output_filename_prefix

I get the following error:

Error: Missing source '${source}' in node 'Resample'

I would like the processor to read all the S2 L2A files present in the input folder.
Where am I doing wrong?

Thank you!

[gnwiii]

Per this example, it is convention (perhaps not necessary, but helps others reading your graph) to add “Node” to node id strings. Then try replacing

<sources>
      <sourceProduct refid="Resample"/>
</sources>

with

<sources>
      <source>resampleNode</source>
</sources>

[chiara]

I have finally run the Biophysical Operator, but I get the following messages:

WARNING: org.esa.s2tbx.dataio.s2.ortho.metadata.S2OrthoMetadata: Warning: no image files found for band quality_dense_dark_vegetation

SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\LAI\LAI_TestCases
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients TEST_CASES for variable LAI model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\LAI\LAI_DefinitionDomain_MinMax
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_MINMAX for variable LAI model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\LAI\LAI_DefinitionDomain_Grid
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_GRID for variable LAI model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\FAPAR\FAPAR_TestCases
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients TEST_CASES for variable FAPAR model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\FAPAR\FAPAR_DefinitionDomain_MinMax
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_MINMAX for variable FAPAR model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\FAPAR\FAPAR_DefinitionDomain_Grid
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_GRID for variable FAPAR model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\FCOVER\FCOVER_TestCases
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients TEST_CASES for variable FCOVER model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\FCOVER\FCOVER_DefinitionDomain_MinMax
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_MINMAX for variable FCOVER model S2A. They won’t be available.
SEVERE: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when reading C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0\S2A\FCOVER\FCOVER_DefinitionDomain_Grid
WARNING: org.esa.s2tbx.biophysical.BiophysicalAuxdata: Error when loading coefficients DEFINITION_DOMAIN_GRID for variable FCOVER model S2A. They won’t be available.

But all files are present in the Auxdata folder:

How can I fix this?

In addition, the process ends despite the messages and produces the desired outputs. Are they reliable?

Thanks!

[cchamp]

Hello, I encounter the same issue. I saw the same problem on other question in this forum but unfortunately it was never answered.

Did you find some solution?

Thanks

[chiara]

Hello,

do you mean for the first or for the second issue?

(For the second, no, I have not found a solution, but in my case, as reported in other posts, the outputs seem realistic)

No image files found for band quality_dense_dark_vegetation

Hi, I think they are reliable. After having a quick look in the code, it tries to find such elements but uses a default value if they are not present. I think the message is a bit to frightening. Probably it would be better to set it the level from WARNING to INFO. And I actually wonder why the information is looked up, if it is not necessary. Maybe @kraftek and @obarrilero, the developers of this module can give some insights. I my self will have a look at this message SEVERE: org.esa.sn…

Best regards

[cchamp]

I meant the second. Exactly the outputs are there but the error warning message puts doubt in its reliability.
Thank you for you reply

Regards

[marpet]

Hi,

@cchamp In the log the referred files are located in C:\Users\chiar.snap\auxdata\s2tbx\biophysical\3_0

You have shown the directory C:\Users\chiar.snap\auxdata\s2tbx\biophysical\2_1

But there is one issue with this path. Between chiar and .snap the backslash is missing.
Not sure if it is not shown in the logs only or if this is the reason the auxiliary data can’t be accessed.

It could be that the processor falls back to some default values. And if you don’t change the files it is not important that they are not accesible.

Another point. in my auxdata directory I can’t find the file s2tbx\biophysical\3_0\S2A\LAI\LAI_TestCases it exists only beneath the 2_1 folder.

@FlorianD can you check this?

[FlorianD]

Hi,
@marpet I have checked, indeed, the ‘s2tbx\biophysical\3_0\S2A\LAI\LAI_TestCases’ doesn’t exist in 3_0. This auxdata is not used in the algorithm 3_0 version, the warning is then not be considered.

Best regards

[FlorianD]

I reopen the issue. Unfortunately, the definition domain test, definiton grid test and test cases are missing for S2A. So, it was reliable.
Moreover, there is an issue with the outputRangeTest tolerance sign.

I fix it and I plan to merge the fix in the next s2tbx release.