Hi Troels,
Class instances cannot be saved in the relax data store. The only
exception are special objects in the data_store package which have
to_xml() and from_xml() methods. These paired methods are essential
for packing the data into a reasonable XML tag structure and fully
recreating the special object when reading the XML.
Maybe you should discuss these issues with Jonathan on the nmrglue
forums (https://groups.google.com/forum/#!forum/nmrglue-discuss). You
can instead store the cdp.ngdata[key].data (a numpy ndarray), the
cdp.ngdata[key].dic (a Python dictionary), cdp.ngdata[key].udic (again
a Python dictionary), and cdp.ngdata[key].file_path (a Python
string/unicode object). But you'd need to talk to Jonathan about how
this can be restored into the nmrglue data container. It might even
be possible that you contribute to_xml() and from_xml() methods to
nmrglue (or we monkey patch them). The class instance seems pretty
basic, so this should be quite easy to handle. Look at the modules in
the relax data_store package for inspiration.
Oh, looking at this more closely, I can see that you have created the
Assignment data container in lib/spectrum/objects.py, so this is on
our side! Then you should shift this into data_store/nmrglue.py.
Then you just need to add the to_xml() and from_xml() methods. This
is very easy, just subclass the data_store.data_classes.Element class
and you will instantly have all the required methods. You then need
to modify the data_store.pipe_container to_xml() and from_xml()
methods to recognise this 'cdp.ngdata' structure as a special object
with these methods. Just copy the example of the 'cdp.exp_info' or
'cdp.diff_tensor' objects. Having the Assignment data container
rather than using Element directly will be useful if you'd like to add
more advanced data structures to cdp.ngdata. I.e. new classes that
are Element instances.
Regards,
Edward
On 3 December 2014 at 23:29, <tlinnet@xxxxxxxxxxxxx> wrote:
Author: tlinnet
Date: Wed Dec 3 23:28:59 2014
New Revision: 26954
URL: http://svn.gna.org/viewcvs/relax?rev=26954&view=rev
Log:
Added systemtest Nmrglue.test_save_state, which fails.
This is to test saving a state after reading nmrglue data, and then reset
and restore the state.
This failure shows, that data cannot be saved as Class instances.
Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to
nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion:
https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html
Modified:
branches/nmrglue/test_suite/system_tests/nmrglue.py
Modified: branches/nmrglue/test_suite/system_tests/nmrglue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py?rev=26954&r1=26953&r2=26954&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/nmrglue.py (original)
+++ branches/nmrglue/test_suite/system_tests/nmrglue.py Wed Dec 3 23:28:59
2014
@@ -345,6 +345,42 @@
self.setup_plot_hist_cpmg_several(show=False)
+ def test_save_state(self):
+ """Test saving a state with numpy arrays, reset relax, and read
the state again."""
+
+ # Read the spectrum.
+ fname = 'freq_real.ft2'
+ sp_id = 'test'
+ self.interpreter.spectrum.nmrglue_read(file=fname, dir=ds.ng_test,
spectrum_id=sp_id)
+
+ # Test that the spectrum id has been stored.
+ self.assertEqual(cdp.spectrum_ids[0], sp_id)
+
+ # Extract the data.
+ dic = cdp.ngdata[sp_id].dic
+ udic = cdp.ngdata[sp_id].udic
+ data = cdp.ngdata[sp_id].data
+
+ # Store the directory path, before reset of the controller.
+ dirpath = ds.tmpdir
+
+ cdp.hello = "HELLO WORLD"
+ print(cdp)
+ print(type(cdp.ngdata))
+ print(type(cdp.ngdata[sp_id]))
+
+ # Save the results.
+ self.interpreter.state.save('state', dir=dirpath, compress_type=1,
force=True)
+
+ # Reset of the controller.
+ self.interpreter.reset()
+
+ # Load the state again.
+ self.interpreter.state.load(dirpath+sep+'state')
+
+ print(cdp.hello)
+
+
def test_version(self):
"""Test version of nmrglue."""
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
relax-commits@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
Re: r26954 - /branches/nmrglue/test_suite/system_tests/nmrglue.py