Error while running the algorithm

[TamirEisenstein]

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

[noxtoby]

Did you try Troubleshooting? Wondering if this might be a numpy version issue (version 1.18 seems to work)