Ok, now I can reproduce it :) It is the Map.map_3D_text() method of the pipe_control.opendx module where the problem really is.
Regards, Edward On 5 May 2014 17:37, Troels Emtekær Linnet <[email protected]> wrote: > When reverting the change, you can get the bug by: > > relax test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py > > 2014-05-05 17:36 GMT+02:00 Troels Emtekær Linnet <[email protected]>: >> Hi Edward. >> >> Sorry for being unclear. >> >> It is this comment: >> https://gna.org/bugs/?22012#comment3 >> >> >> >> dx.map(params=['dw', 'pA', 'kex'], map_type='Iso3D', spin_id=':1@N', >> inc=20, lower=None, upper=None, axis_incs=5, file_prefix='map', >> dir=None, point=None, point_file='point', remap=None) >> >> Creating the OpenDX .net program file. >> Opening the file 'map.net' for writing. >> >> Creating the OpenDX .cfg program configuration file. >> Opening the file 'map.cfg' for writing. >> >> Creating the OpenDX .general file. >> Opening the file 'map.general' for writing. >> >> Creating the map. >> Opening the file 'map' for writing. >> Progress: 0.000% >> RelaxWarning: invalid value encountered in double_scalars >> debug> Execution lock: Release by 'script UI' ('script' mode). >> Traceback (most recent call last): >> File "/Users/tlinnet/software/relax_trunk/multi/processor.py", line 494, in >> run >> self.callback.init_master(self) >> File "/Users/tlinnet/software/relax_trunk/multi/__init__.py", line >> 318, in default_init_master >> self.master.run() >> File "/Users/tlinnet/software/relax_trunk/relax.py", line 194, in run >> self.interpreter.run(self.script_file) >> File "/Users/tlinnet/software/relax_trunk/prompt/interpreter.py", line >> 275, in run >> return run_script(intro=self.__intro_string, local=locals(), >> script_file=script_file, show_script=self.__show_script, >> raise_relax_error=self.__raise_relax_error) >> File "/Users/tlinnet/software/relax_trunk/prompt/interpreter.py", line >> 569, in run_script >> return console.interact(intro, local, script_file, >> show_script=show_script, raise_relax_error=raise_relax_error) >> File "/Users/tlinnet/software/relax_trunk/prompt/interpreter.py", line >> 468, in interact_script >> exec_script(script_file, local) >> File "/Users/tlinnet/software/relax_trunk/prompt/interpreter.py", line >> 347, in exec_script >> runpy.run_module(module, globals) >> File >> "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/runpy.py", >> line 180, in run_module >> fname, loader, pkg_name) >> File >> "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/runpy.py", >> line 72, in _run_code >> exec code in run_globals >> File >> "/Users/tlinnet/software/relax_trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py", >> line 277, in <module> >> dx.map(params=['dw', 'pA', 'kex'], map_type='Iso3D', spin_id=":1@N", >> inc=20, lower=None, upper=None, axis_incs=5, file_prefix='map', >> dir=ds.resdir, point=None, point_file='point', remap=None) >> File "/Users/tlinnet/software/relax_trunk/prompt/uf_objects.py", line >> 221, in _call_ >> self._backend(*new_args, **uf_kargs) >> File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py", >> line 88, in map >> Map(params, spin_id, inc, lower, upper, axis_incs, file_prefix, dir, >> point, point_file, remap) >> File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py", >> line 184, in _init_ >> self.create_map() >> File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py", >> line 197, in create_map >> self.map_3D_text(map_file) >> File "/Users/tlinnet/software/relax_trunk/pipe_control/opendx.py", >> line 255, in map_3D_text >> k, n, chi2 = self.model_statistics(spin_id=self.spin_id) >> File >> "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", >> line 683, in model_statistics >> spins = spin_ids_to_containers(spin_ids) >> File >> "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/data.py", >> line 3620, in spin_ids_to_containers >> for id in spin_ids: >> TypeError: 'NoneType' object is not iterable >> >> 2014-05-05 17:27 GMT+02:00 Edward d'Auvergne <[email protected]>: >>> The argument checking is reasonable, but the code: >>> >>> + #spins = spin_ids_to_containers(spin_ids) >>> + >>> + spins_list = [] >>> + for spin_id in self.model_loop(): >>> + spins_list.append(spin_id[0]) >>> + >>> + spins = spin_ids_to_containers(spins_list) >>> >>> breaks the logic. This cannot be done, as the code calling >>> model_statistics() must be looping over the models (i.e. the >>> model_loop()), so you cannot have the model_loop() inside it. Any API >>> method which accepts the model_info argument will follow this logic. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> On 5 May 2014 17:23, Edward d'Auvergne <[email protected]> wrote: >>>> The original code was correct. The full test suite passes when this >>>> change is not included. Why did you make this change? What was the >>>> purpose? I'm a little confused. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 5 May 2014 17:15, Troels Emtekær Linnet <[email protected]> wrote: >>>>> Ehhhh. >>>>> >>>>> Can you suggest a change? >>>>> >>>>> Best >>>>> Troels >>>>> >>>>> 2014-05-05 17:05 GMT+02:00 Edward d'Auvergne <[email protected]>: >>>>>> Hi, >>>>>> >>>>>> I now have the failure when running: >>>>>> >>>>>> $ ./relax -s Relax_disp.test_hansen_cpmg_data_auto_analysis >>>>>> >>>>>> This is because the change is incorrect. The model_statistics() >>>>>> method is called once for each individual model - for each iteration >>>>>> of the model_loop(), which for the dispersion analysis is each spin >>>>>> cluster (or individual spins). The logic: >>>>>> >>>>>> spins_list = [] >>>>>> for spin_id in self.model_loop(): >>>>>> spins_list.append(spin_id[0]) >>>>>> >>>>>> spins = spin_ids_to_containers(spins_list) >>>>>> >>>>>> is incorrect as the model_loop() loops over all spin clusters. >>>>>> Therefore the 'spins' object will now be a list of the first spin >>>>>> system from all clusters. Previously it was simply a list of all the >>>>>> spins for the current spin cluster. I hope this makes sense. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> >>>>>> On 5 May 2014 16:52, Troels Emtekær Linnet <[email protected]> wrote: >>>>>>> Now ready to be tested with: >>>>>>> >>>>>>> relax -s Relax_disp.test_hansen_cpmg_data_auto_analysis -d >>>>>>> >>>>>>> >>>>>>> ---------- Forwarded message ---------- >>>>>>> From: <[email protected]> >>>>>>> Date: 2014-05-05 16:46 GMT+02:00 >>>>>>> Subject: r22958 - /trunk/specific_analyses/relax_disp/api.py >>>>>>> To: [email protected] >>>>>>> >>>>>>> >>>>>>> Author: tlinnet >>>>>>> Date: Mon May 5 16:46:10 2014 >>>>>>> New Revision: 22958 >>>>>>> >>>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=22958&view=rev >>>>>>> Log: >>>>>>> Inserted commit r22954 to fix the AIC method selection. >>>>>>> >>>>>>> The command used was: >>>>>>> svn merge -r22953:r22954 . >>>>>>> >>>>>>> ..... >>>>>>> Attempt to fix function model_statistics() in API for relax_disp. >>>>>>> >>>>>>> bug #22012(https://gna.org/bugs/?22012): dx.map not implemented >>>>>>> for pipe type relax_disp. >>>>>>> >>>>>>> Modified: >>>>>>> trunk/specific_analyses/relax_disp/api.py >>>>>>> ..... >>>>>>> >>>>>>> >>>>>>> Modified: >>>>>>> trunk/specific_analyses/relax_disp/api.py >>>>>>> >>>>>>> Modified: trunk/specific_analyses/relax_disp/api.py >>>>>>> URL: >>>>>>> http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=22958&r1=22957&r2=22958&view=diff >>>>>>> ============================================================================== >>>>>>> --- trunk/specific_analyses/relax_disp/api.py (original) >>>>>>> +++ trunk/specific_analyses/relax_disp/api.py Mon May 5 16:46:10 2014 >>>>>>> @@ -678,9 +678,21 @@ >>>>>>> @rtype: tuple of (int, int, float) >>>>>>> """ >>>>>>> >>>>>>> + # Bad argument combination. >>>>>>> + if model_info == None and spin_id == None: >>>>>>> + raise RelaxError("Either the model_info or spin_id >>>>>>> argument must be supplied.") >>>>>>> + elif model_info != None and spin_id != None: >>>>>>> + raise RelaxError("The model_info arg " + repr(model_info) >>>>>>> + " and spin_id arg " + repr(spin_id) + " clash. Only one should be >>>>>>> supplied.") >>>>>>> + >>>>>>> # Unpack the data. >>>>>>> spin_ids = model_info >>>>>>> - spins = spin_ids_to_containers(spin_ids) >>>>>>> + #spins = spin_ids_to_containers(spin_ids) >>>>>>> + >>>>>>> + spins_list = [] >>>>>>> + for spin_id in self.model_loop(): >>>>>>> + spins_list.append(spin_id[0]) >>>>>>> + >>>>>>> + spins = spin_ids_to_containers(spins_list) >>>>>>> >>>>>>> # The number of parameters for the cluster. >>>>>>> k = param_num(spins=spins) >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> relax (http://www.nmr-relax.com) >>>>>>> >>>>>>> This is the relax-commits mailing list >>>>>>> [email protected] >>>>>>> >>>>>>> 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 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> relax (http://www.nmr-relax.com) >>>>>>> >>>>>>> This is the relax-devel mailing list >>>>>>> [email protected] >>>>>>> >>>>>>> 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-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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-devel
