dhi-gras / fmaskilicious Goto Github PK

We used to call docker fmask like this:

       uid, gid = os.getuid(), os.getgid()
        shell(
            'docker run'
            f' -u {uid}:{gid}'
            f' -v {indir!s}:/mnt/input-dir:ro'
            f' -v {outdir!s}:/mnt/output-dir:rw'
            ' --rm '
            '-t fmask '
            f'{wildcards.scene_id} {granule_wildcard}'
)

But since the recent update, I get the following error:

Processing granule L1C_T19LDD_A008173_20180929T145000
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v95/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v95/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v95/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v95/sys/opengl/lib/glnxa64
Cloud/cloud shadow/snow dilated by 3/3/0 pixels.
Cloud probability threshold of 20.00%.

Load or calculate TOA reflectances, Error using mkdir
Read-only file system

Error in LoadAuxiData (line 87)

Error in autoFmask (line 101)

Error in Fmask_4_0 (line 10)

MATLAB:MKDIR:OSError

The error is gone if I mount the input directory rw, i.e.

            f' -v {indir!s}:/mnt/input-dir:rw'

I can live with this workaround, but it is not nice.

FMask 4.4 is out.

Note the changes in the installation - using a newer version of Matlab: GERSL/Fmask#21 (comment)

Fmask 4.2 is out GERSL/Fmask#14 (comment)

I have no clue which parameters we can pass to /usr/GERS/Fmask_4_0/application/run_Fmask_4_0.sh. Our run_fmask.sh entrypoint script passes any options on - but which are there?

I tried to run the docker image interactively and /usr/GERS/Fmask_4_0/application/run_Fmask_4_0.sh --help etc, but that fails for some technical reasons, at least on my first brief attempts.

When available (GERSL/Fmask#3)