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RE: Running the toolbox on Octave

HE
Hisham Elsafti, modified 4 Years ago.

Running the toolbox on Octave

Capillary Posts: 10 Join Date: 2/8/16 Recent Posts
Greetings,

I have installed Xbeach on a Linux box with OpenMPI. I am trying to run the tutorials using the Matlab toolbox from OpenEarthTools on Octave. It seems they may be incompatible!! Does anyone use the toolbox on Octave. When I run oetsettings I get this error message:


octave:1> oetsettings
Adding <a href="http://OpenEarth.deltares.nl">openearthtools</a>, please wait ...

warning: addpath: /home/hisham/openearthtools/trunk/matlab/;/home/hisham/openearthtools/trunk/matlab/applications/;/home/hisham/openearthtools/trunk/matlab/apps/;/home/hisham/openearthtools/trunk/matlab/conf/;/home/hisham/openearthtools/trunk/matlab/db/;/home/hisham/openearthtools/trunk/matlab/deprecated/;/home/hisham/openearthtools/trunk/matlab/docs/;/home/hisham/openearthtools/trunk/matlab/general/;/home/hisham/openearthtools/trunk/matlab/hooks/;/home/hisham/openearthtools/trunk/matlab/io/;/home/hisham/openearthtools/trunk/matlab/locks/;/home/hisham/openearthtools/trunk/matlab/maintenance/;/home/hisham/openearthtools/trunk/matlab/tutorials/;/home/hisham/openearthtools/trunk/matlab/applications/CoastalMorphologyModeling/;/home/hisham/openearthtools/trunk/matlab/applications/DGeoStability/;/home/hisham/openearthtools/trunk/matlab/applications/DUROS/;/home/hisham/openearthtools/trunk/matlab/applications/DelftDashBoard/;/home/hisham/openearthtools/trunk/matlab/applications/DigitalGrainSizeAnalysis/;/home/hisham/openearthtools/trunk/matlab/applications/DuneErosionLibrary/;/home/hisham/openearthtools/trunk/matlab/applications/FEWS-World/;/home/hisham/openearthtools/trunk/matlab/applications/GustChamperExperiment/;/home/hisham/openearthtools/trunk/matlab/applications/ITHK/;/home/hisham/openearthtools/trunk/matlab/applications/KNMI/;/home/hisham/openearthtools/trunk/matlab/applications/OceanDataView/;/home/hisham/openearthtools/trunk/matlab/applications/POD-4Dvar_toolbox/;/home/hisham/openearthtools/trunk/matlab/applications/POLCOMS-WAM/;/home/hisham/openearthtools/trunk/matlab/applications/Rijkswaterstaat/;/home/hisham/openearthtools/trunk/matlab/applications/SuperTrans/;/home/hisham/openearthtools/trunk/matlab/applications/aeolian/;/home/hisham/openearthtools/trunk/matlab/applications/bmi/;/home/hisham/openearthtools/trunk/matlab/applications/cBathy/;/home/hisham/openearthtools/trunk/matlab/applications/cmg/;/home/hisham/openearthtools/trunk/matlab/applications/cosmos/;/home/hisham/openearthtools/trunk/matlab/applications/delft3d/;/home/hisham/openearthtools/trunk/matlab/applications/delft3d_matlab/;/home/hisham/openearthtools/trunk/matlab/applications/detran/;/home/hisham/openearthtools/trunk/matlab/applications/drifters/;/home/hisham/openearthtools/trunk/matlab/applications/durosta/;/home/hisham/openearthtools/trunk/matlab/applications/gis/;/home/hisham/openearthtools/trunk/matlab/applications/googleplot/;/home/hisham/openearthtools/trunk/matlab/applications/grid_2D_orthogonal/;/home/hisham/openearthtools/trunk/matlab/applications/ices/;/home/hisham/openearthtools/trunk/matlab/applications/knowledgegraphs/;/home/hisham/openearthtools/trunk/matlab/applications/ldbTool/;/home/hisham/openearthtools/trunk/matlab/applications/m_map/;/home/hisham/openearthtools/trunk/matlab/applications/meander/;/home/hisham/openearthtools/trunk/matlab/applications/mm/;/home/hisham/openearthtools/trunk/matlab/applications/modelvalidation/;/home/hisham/openearthtools/trunk/matlab/applications/muppet/;/home/hisham/openearthtools/trunk/matlab/applications/muppet_v4/;/home/hisham/openearthtools/trunk/matlab/applications/nc_processing/;/home/hisham/openearthtools/trunk/matlab/applications/ncgen/;/home/hisham/openearthtools/trunk/matlab/applications/netica/;/home/hisham/openearthtools/trunk/matlab/applications/nourishment/;/home/hisham/openearthtools/trunk/matlab/applications/oceancolor/;/home/hisham/openearthtools/trunk/matlab/applications/opti/;/home/hisham/openearthtools/trunk/matlab/applications/polygons/;/home/hisham/openearthtools/trunk/matlab/applications/pontos/;/home/hisham/openearthtools/trunk/matlab/applications/probabilistic/;/home/hisham/openearthtools/trunk/matlab/applications/sal_decomposition_tool/;/home/hisham/openearthtools/trunk/matlab/applications/salinity_conversion/;/home/hisham/openearthtools/trunk/matlab/applications/simona/;/home/hisham/openearthtools/trunk/matlab/applications/sobek/;/home/hisham/openearthtools/trunk/matlab/applications/statistic/;/home/hisham/openearthtools/trunk/matlab/applications/swan/;/home/hisham/openearthtools/trunk/matlab/applications/tass/;/home/hisham/openearthtools/trunk/matlab/applications/textpad/;/home/hisham/openearthtools/trunk/matlab/applications/tide/;/home/hisham/openearthtools/trunk/matlab/applications/ucit/;/home/hisham/openearthtools/trunk/matlab/applications/unibest/;/home/hisham/openearthtools/trunk/matlab/applications/waves/;/home/hisham/openearthtools/trunk/matlab/applications/xbeach/;/home/hisham/openearthtools/trunk/matlab/applications/CoastalMorphologyModeling/1dHump/;/home/hisham/openearthtools/trunk/matlab/applications/CoastalMorphologyModeling/BottomScheme/;/home/hisham/openearthtools/trunk/matlab/applications/CoastalMorphologyModeling/ChannelSimulation/;/home/hisham/openearthtools/trunk/matlab/applications/CoastalMorphologyModeling/GenericCoastlineModel/;/home/hisham/openearthtools/trunk/matlab/applications/CoastalMorphologyModeling/ProfileModel/;/home/hisham/openearthtools/trunk/m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t/css/images/;: 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So my questions are:
1. Is anyone running the toolbox on Octave or should I just save my time and find a different path?
2. Does anyone use a Python option for pre-/post-processing of Xbeach? I thought BMI could be the way but it is not clear how to use it and if it is actually a good idea to use BMI, which seems to be not supported by the official Xbeach developments.


I would appreciate your input for these questions!

Best regards,
Hisham
Bas Hoonhout, modified 4 Years ago.

RE: Running the toolbox on Octave

Infra-gravity Posts: 362 Join Date: 5/20/11 Recent Posts
Hi Hisham,

I'm not aware of any attempts to use OpenEarthTools in Octave. Given the great extent of the toolbox it would surprise me if it will work. Ever.

The XBeach Matlab Toolbox does a lot of work for you. For example, the xb_generate_model function contains many features that make it easy to setup a working XBeach model, like straitening the borders and defining an optimal grid. These functions are only available in Matlab.

However, I'm working mainly on Unix machines and do use Python for the pre- and post-processing. The preprocessing is not "automated" like in Matlab, but possible. For example, writing a linear bathymetry:

import numpy as np

x = np.arange(0, 100, 0.5)
z = np.linspace(-10, 10, len(x))

np.savetxt('x.grd', x)
np.savetxt('bed.dep', z)


Reading output is especially easy when using netCDF output:

import netCDF4
import matplotlib.pyplot as plt

with netCDF4.Dataset('xboutput.nc', 'r') as ds:
    fig, axs = plt.subplots()
    axs.plot(ds.variables['x'][...], ds.variables['zb'][0,:,:], ':k', label='initial profile')
    axs.plot(ds.variables['x'][...], ds.variables['zb'][-1,:,:], '-k', label='final profile')
    axs.legend(loc='upper left')


How are your Python skills? We could start a Python toolbox :-)

BMI is not really meant for these daily pre- and post-processing tasks. BMI is suitable to interact with the model *during* the simulation. This is quite different. Note that BMI is currently only implemented in the trunk and not in any stable release of XBeach.

Bas
HE
Hisham Elsafti, modified 4 Years ago.

RE: Running the toolbox on Octave

Capillary Posts: 10 Join Date: 2/8/16 Recent Posts
Hi Bas,

Thanks a lot for your quick reply. Indeed a Python toolbox will be a nice thing and thanks for your pointers, neat snippets by the way :-)

I think the code you provide can help as a start to look at the tutorials. I would gladly participate in writing a Python tool. I think transforming the matlab code into Python is easier than starting from scratch.

Best regards
Hisham
Bas Hoonhout, modified 4 Years ago.

RE: Running the toolbox on Octave

Infra-gravity Posts: 362 Join Date: 5/20/11 Recent Posts
Hi Hisham,

Well, Python is quite different from Matlab. I would setup a Python toolbox totally different from what we currently have in Matlab. Even for Matlab the toolbox is slightly outdated in terms of code structure.

Bas
HE
Hisham Elsafti, modified 4 Years ago.

RE: Running the toolbox on Octave

Capillary Posts: 10 Join Date: 2/8/16 Recent Posts
Hi Bas,

Well, you know what you're doing, so it is easier to have an overview over things. For me as an Xbeach noob, I still need to know what are the needed functionalists, here reading the matlab code can help. I agree of course that a different paradigm would be ideal with heavy use of OOP.

If you would like to start a repo and structure it with a todo list, I would be happy to participate in doing the work. I would love to have a python toolbox after all and have no problem to do some coding.

Best regards,
Hisham
Bas Hoonhout, modified 4 Years ago.

RE: Running the toolbox on Octave

Infra-gravity Posts: 362 Join Date: 5/20/11 Recent Posts
Ok. I'll set something up.
Currently I'm working on another Python toolbox for XBeach, so it might not be tomorrow or next week :-)

Bas
HE
Hisham Elsafti, modified 4 Years ago.

RE: Running the toolbox on Octave

Capillary Posts: 10 Join Date: 2/8/16 Recent Posts
I don't see the logic behind having two toolboxes. I can help you with "the" Python toolbox you are developing if you want.
ED
ethan dabney, modified 8 Days ago.

RE: Running the toolbox on Octave

Capillary Posts: 1 Join Date: 3/23/20 Recent Posts
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Leah Johnson, modified 7 Days ago.

RE: Running the toolbox on Octave

Capillary Posts: 6 Join Date: 3/6/20 Recent Posts
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therouting therouting, modified 6 Days ago.

RE: Running the toolbox on Octave

Capillary Posts: 1 Join Date: 3/25/20 Recent Posts
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