Closed nsplattner closed 9 years ago
thanks. I will look at this.
Am 20/07/15 um 18:12 schrieb nsplattner:
The function cktest() in msm.bayesian_markov_model fails if applied to a model where not all states are in the largest connected set. (Tested on Trypsin/Benzamidine data) The error message is something like 'index XXX is out of bounds for axis 1 with size YYY'
— Reply to this email directly or view it on GitHub https://github.com/markovmodel/PyEMMA/issues/431.
Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354 Web: research.franknoe.de
can you please post the full python exception?
Am 20/07/15 um 18:12 schrieb nsplattner:
The function cktest() in msm.bayesian_markov_model fails if applied to a model where not all states are in the largest connected set. (Tested on Trypsin/Benzamidine data) The error message is something like 'index XXX is out of bounds for axis 1 with size YYY'
— Reply to this email directly or view it on GitHub https://github.com/markovmodel/PyEMMA/issues/431.
Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354 Web: research.franknoe.de
Here the full exception:
----> 2 cktest = M.cktest(4)
3 mpl.plot_cktest(cktest);
/storage/mi/nplattner/miniconda/envs/PyE-devR/lib/python2.7/site-packages/pyemma/msm/estimators/maximum_likelihood_msm.pyc in cktest(self, nsets, memberships, mlags)
251 self.pcca(nsets)
252 memberships = self.metastable_memberships
--> 253 ck = ChapmanKolmogorovValidator(self, self, memberships, mlags=mlags)
254 ck.estimate(self._dtrajs_full)
255 return ck
/storage/mi/nplattner/miniconda/envs/PyE-devR/lib/python2.7/site-packages/pyemma/msm/estimators/lagged_model_validators.pyc in __init__(self, model, estimator, memberships, mlags, conf, err_est)
314 self.active_set = types.ensure_ndarray(np.array(estimator.active_set), kind='i') # create a copy
315 self._full2active = np.zeros(self.nstates, dtype=int)
--> 316 self._full2active[self.active_set] = np.arange(self.nstates)
317 # define starting distribution
318 self.P0 = memberships * model.stationary_distribution[:, None]
IndexError: index 271 is out of bounds for axis 1 with size 271
thanks!
Am 21/07/15 um 17:36 schrieb nsplattner:
Here the full exception:
----> 2 cktest = M.cktest(4) 3 mpl.plot_cktest(cktest);
/storage/mi/nplattner/miniconda/envs/PyE-devR/lib/python2.7/site-packages/pyemma/msm/estimators/maximum_likelihood_msm.pyc in cktest(self, nsets, memberships, mlags) 251 self.pcca(nsets) 252 memberships = self.metastable_memberships --> 253 ck = ChapmanKolmogorovValidator(self, self, memberships, mlags=mlags) 254 ck.estimate(self._dtrajs_full) 255 return ck
/storage/mi/nplattner/miniconda/envs/PyE-devR/lib/python2.7/site-packages/pyemma/msm/estimators/lagged_model_validators.pyc in init(self, model, estimator, memberships, mlags, conf, err_est) 314 self.active_set = types.ensure_ndarray(np.array(estimator.active_set), kind='i') # create a copy 315 self._full2active = np.zeros(self.nstates, dtype=int) --> 316 self._full2active[self.active_set] = np.arange(self.nstates) 317 # define starting distribution 318 self.P0 = memberships * model.stationary_distribution[:, None]
IndexError: index 271 is out of bounds for axis 1 with size 271
— Reply to this email directly or view it on GitHub https://github.com/markovmodel/PyEMMA/issues/431#issuecomment-123374885.
Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354 Web: research.franknoe.de
I think I have fixed this now in dev_release_1.3. Please try.
Now it works! :-)
great! thanks.
Am 23/07/15 um 10:43 schrieb nsplattner:
Now it works! :-)
— Reply to this email directly or view it on GitHub https://github.com/markovmodel/PyEMMA/issues/431#issuecomment-124023435.
Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354 Web: research.franknoe.de
The function cktest() in msm.bayesian_markov_model fails if applied to a model where not all states are in the largest connected set. (Tested on Trypsin/Benzamidine data) The error message is something like 'index XXX is out of bounds for axis 1 with size YYY'