Re: [task #7873] Write wrapper function to nmrglue, to read .ft2 files and process them. -- January 15, 2015 - 09:27

So this has nothing to do with nmrglue, I guess?

But to the base64 module of python.

Best
Troels

2015-01-14 19:13 GMT+01:00 Edward d Auvergne <
NO-REPLY.INVALID-ADDRESS@xxxxxxx>:

> Follow-up Comment #94, task #7873 (project relax):
>
> When I run the Nmrglue system tests in Python 2, they pass.  However in
> Python
> 3 I see:
>
> $ python3 ./relax -s --time Nmrglue
> Echoing of user function calls has been enabled.
>
>
> =============================
> = System / functional tests =
> =============================
>
> .     0.00 s for Nmrglue.test_nmrglue_read
> .     0.00 s for Nmrglue.test_nmrglue_read_several
> .     0.16 s for Nmrglue.test_plot_contour
> .     0.10 s for Nmrglue.test_plot_contour_cpmg
> .     0.12 s for Nmrglue.test_plot_correlation
> .     2.90 s for Nmrglue.test_plot_hist_cpmg
> .     3.44 s for Nmrglue.test_plot_hist_cpmg_several
> E     0.00 s for Nmrglue.test_save_state
> .     0.00 s for Nmrglue.test_version
>
> ======================================================================
> ERROR: test_save_state (test_suite.system_tests.nmrglue.Nmrglue)
> Test saving a state with numpy arrays, reset relax, and read the state
> again.
> ----------------------------------------------------------------------
>
> relax> pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)
>
> relax> spectrum.nmrglue_read(file='128_0_FT.ft2',
>
> dir='/data/relax/branches/nmrglue/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data',
> nmrglue_id='test')
> Filesize of .ft2 file is: 527360
> Type of encoding is: <class 'numpy.ndarray'>
> Storing numpy array to: /tmp/tmpl4p2zk/data.npy
> Filesize of .npy file is: 525392
> Shape of data is 256x513
> dtype of data is float32
> Type of data[0][0]:  <class 'numpy.float32'>
>
> relax> state.save(state='state', dir='/tmp/tmpl4p2zk', compress_type=1,
> force=True)
> Opening the file '/tmp/tmpl4p2zk/state.bz2' for writing.
> Traceback (most recent call last):
>   File "/data/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py",
> line
> 569, in test_save_state
>     self.interpreter.state.save('state', dir=dirpath, compress_type=1,
> force=True)
>   File "/data/relax/branches/nmrglue/prompt/uf_objects.py", line 225, in
> __call__
>     self._backend(*new_args, **uf_kargs)
>   File "/data/relax/branches/nmrglue/pipe_control/state.py", line 128, in
> save_state
>     ds.to_xml(file)
>   File "/data/relax/branches/nmrglue/data_store/__init__.py", line 643, in
> to_xml
>     self[pipe].to_xml(xmldoc, pipe_element, pipe_type=self[pipe].pipe_type)
>   File "/data/relax/branches/nmrglue/data_store/pipe_container.py", line
> 335,
> in to_xml
>     self.nmrglue.to_xml(doc, element)
>   File "/data/relax/branches/nmrglue/data_store/data_classes.py", line
> 244, in
> to_xml
>     self[key].to_xml(doc, dict_item_element)
>   File "/data/relax/branches/nmrglue/data_store/nmrglue.py", line 138, in
> to_xml
>     string = b64encode(self.data)
>   File "/usr/lib64/python3.3/base64.py", line 58, in b64encode
>     raise TypeError("expected bytes, not %s" % s.__class__.__name__)
> TypeError: expected bytes, not ndarray
>
> ----------------------------------------------------------------------
> Ran 9 tests in 6.725s
>
> FAILED (errors=1)
>
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>
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>
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