Hi Edward,
Thank you very much for your suggestions. Should I separate the the
questions about test suite and cmpg_analysis.py and resubmit them ?
For the cpmy_analysis.py, I have change it to
'..\..\test_suite\shared_data\dispersion\Hansen' as your suggestion,
and try to run the script
Hi Mengjun.
There is missing a \
.\\..\test_suite
should be
.\\..\\test_suite
2014-04-23 10:23 GMT+02:00 mengjun@mailbox.tu-berlin.de:
Hi Edward,
Thank you very much for your suggestions. Should I separate the the
questions about test suite and cmpg_analysis.py and resubmit them ? For
Update of bug #21954 (project relax):
Priority: 5 - Normal = 9 - Immediate
Severity: 3 - Normal = 4 - Important
Status:None = Fixed
Open/Closed:
Update of bug #21953 (project relax):
Priority: 5 - Normal = 7 - High
Severity: 3 - Normal = 4 - Important
Status:None = Fixed
Open/Closed:
Hi,
There's no need to separate them now. I've fixed both in relax. For
the error you see now, if I run:
$ ./relax sample_scripts/relax_disp/cpmg_analysis.py
from the base relax directory, then it will find the data in the test
suite directories and perform the test analysis. Also in the
Awesome! That's exactly the change I would have made.
I would also suggest to try to increase the system test coverage of
this to make sure it works in all cases, as well as to make sure that
any future code refactorisation or expansion doesn't break this. The
easiest way is to simply add more
URL:
http://gna.org/bugs/?21959
Summary: cpmg_analysis
Project: relax
Submitted by: None
Submitted on: Wed 23 Apr 2014 09:43:15 AM UTC
Category: relax sample scripts
Specific analysis category: None
URL:
http://gna.org/bugs/?21960
Summary: systemtest
Relax_disp.test_hansen_cpmg_data_missing_auto_analysis highly unstable
Project: relax
Submitted by: tlinnet
Submitted on: Wed 23 Apr 2014 10:33:17 AM UTC
Category:
Hi Edward.
I see some errors:
The key 'relax_disp.cpmg_frq' does not exist.
it is from this block.
if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2
(classic)':
analysis.peak_intensity.action_relax_disp_cpmg_frq(item=4)
Hi,
Does this GUI test not pass on your system? Or have you modified the
test and it now no longer works?
Cheers,
Edward
On 23 April 2014 12:46, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
Hi Edward.
I see some errors:
The key 'relax_disp.cpmg_frq' does not exist.
it is from
Update of bug #21959 (project relax):
Status:None = Invalid
Assigned to:None = bugman
Open/Closed:Open = Closed
Hi Troels,
Maybe it would be better to hardcode the two variance averaged
standard deviations (126.05227793927868 and 265.7619655474242)
directly into the test. This would be just in case cdp.var_I somehow
changed and propagated the bug into cdp.sigma_I. The current tests
are great and should
Update of bug #21960 (project relax):
Assigned to:None = bugman
___
Follow-up Comment #1:
I'll have a look at this one. It looks like that the optimisation was just
terminated early and
Follow-up Comment #2, bug #21960 (project relax):
Actually, it is simply because of the fix for bug #21954. The absolute peak
intensity errors are bigger. But this is the same for all data - i.e. the
errors are scaled by some factor X. Therefore the optimised parameters are
identical, but the
Hi Edward,
Thank you so much for the detailed information about setting data
path, as you suggested I have set data path in cpmg_analysis.py to:
DATA_PATH = 'C:\Program
files\Relax-3.1.7\\test_suite\shared_data\dispersion\Hansen' or
DATA_PATH = 'C:\Program
Hi,
Could you list the entire contents of the '500_MHz' folder? I must
absolutely contain that file! You can do this by running dir log
and opening the 'log' text file. I have done this on a virtual
machine and see:
Directory:
Hi Mengjun,
I also just checked the contents of the officially released relax
3.1.7 MS Windows distribution zip file. The reference.in_sparky file
is in that directory. Note that 'fake_sequence.in' is not in that
directory - it is in the parent
test_suite/shared_data/dispersion/Hansen/
Update of bug #21960 (project relax):
Status:None = Fixed
Open/Closed:Open = Closed
___
Reply to this item at:
Hi Edward,
Thank you. I have made the log file for dir, it seems it is same to yours:
Directory of C:\Program
Files\relax-3.1.7\test_suite\shared_data\dispersion\Hansen\500_MHz
04/23/2014 03:24 PMDIR .
04/23/2014 03:24 PMDIR ..
03/17/2014 03:11 PM
Hi,
There is no '500_reference.in' file. This is not the name of the file
but is the spectrum ID string used in relax to handle spectral data
from different spectra. Therefore all the data read out of the
'reference.in_sparky' file will be associated with the ID
'500_reference.in'. So if you
Hi Edward,
Thank you. Should I run debug command in this way:
C:\program files\relax-3.1.7\relax --debug --tee log_debug cpmg_analysis.py,?
Best regards,
Mengjun
Quoting Edward d'Auvergne edw...@nmr-relax.com:
Hi Mengjun,
Could you also run the script in debugging mode - with the
Hi,
That should work. It will record the source of the error.
Cheers,
Edward
On 23 April 2014 15:56, mengjun@mailbox.tu-berlin.de wrote:
Hi Edward,
Thank you. Should I run debug command in this way:
C:\program files\relax-3.1.7\relax --debug --tee log_debug
cpmg_analysis.py,?
Hi Edward,
I have set data path in cpmg_analysis.py to:
DATA_PATH = 'C:\Program
files\Relax-3.1.7\test_suite\shared_data\dispersion\Hansen'
and run the cpmg_analysis.py under cmd,C:\program
files\relax-3.1.7\relax --debug --tee log_debug cpmg_analysis.py,
please see following output of
Hi Mengjun,
Looking at which user functions have been run, I can now see that the
following one is missing:
sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1, res_name_col=2)
From the log files attached to https://gna.org/bugs/?21959, I can see
that this line has been deleted from
Hi Edward,
I have downloaded relax-3.1.7 again, and copy the new
cpmg_analysis.py, which include # Load the sequence.
sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1,
res_name_col=2), and run again, C:\program files\relax-3.1.7\relax
--debug --tee log_debug cpmg_analysis.py,
Hi,
One failure source in Python with paths is sometimes if there is a
space in a file or directory name. Is it possible to copy the entire
relax-3.1.7 directory to C:\ so it is not in 'Program files', and then
run this again? I'll look into the relax lib\io.py file tomorrow to
see if that
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