Error while running the algorithm #63
Description
Dear developers,
Thank you for the toolbox!
When trying to run the workshop notebook with its associated SimultaedData.csv file I've been getting the following error during the "Run SuStaIn!" part:
Failed to find pickle file: /Users/ladmin/Downloads/WorkshopOutput/pickle_files/WorkshopOutput_subtype0.pickle. Running SuStaIn model for 0 subtype.
Finding ML solution to 1 cluster problem
Overall ML likelihood is -4738.987014506705
MCMC Iteration: 100%|███████████████████| 10000/10000 [00:02<00:00, 3719.29it/s]
MCMC Iteration: 100%|███████████████████| 10000/10000 [00:02<00:00, 3787.75it/s]
MCMC Iteration: 100%|███████████████████| 10000/10000 [00:02<00:00, 3839.41it/s]
MCMC Iteration: 100%|███████████████████| 10000/10000 [00:02<00:00, 3718.73it/s]
ValueError Traceback (most recent call last)
Cell In[14], line 7
1 samples_sequence,
2 samples_f,
3 ml_subtype,
4 prob_ml_subtype,
5 ml_stage,
6 prob_ml_stage,
----> 7 prob_subtype_stage = sustain_input.run_sustain_algorithm()
File /opt/anaconda3/envs/sustain_env/lib/python3.10/site-packages/pySuStaIn/AbstractSustain.py:186, in AbstractSustain.run_sustain_algorithm(self, plot, plot_format, **kwargs)
178 # max like subtype and stage / subject
179 N_samples = 1000
180 ml_subtype,
181 prob_ml_subtype,
182 ml_stage,
183 prob_ml_stage,
184 prob_subtype,
185 prob_stage,
--> 186 prob_subtype_stage = self.subtype_and_stage_individuals(self.__sustainData, samples_sequence, samples_f, N_samples) #self.subtype_and_stage_individuals(self.__data, samples_sequence, samples_f, N_samples)
187 if not pickle_filepath.exists():
189 if not os.path.exists(self.output_folder):
File /opt/anaconda3/envs/sustain_env/lib/python3.10/site-packages/pySuStaIn/AbstractSustain.py:576, in AbstractSustain.subtype_and_stage_individuals(self, sustainData, samples_sequence, samples_f, N_samples)
573 # if not np.isnan(this_prob_subtype).any()
574 if (np.sum(np.isnan(this_prob_subtype)) == 0):
575 # this_subtype = this_prob_subtype.argmax(
--> 576 this_subtype = np.where(this_prob_subtype == np.max(this_prob_subtype))
578 try:
579 ml_subtype[i] = this_subtype
ValueError: Calling nonzero on 0d arrays is not allowed. Use np.atleast_1d(scalar).nonzero() instead. If the context of this error is of the form arr[nonzero(cond)], just use arr[cond].
Would be grateful for any help!
Tamir