UnboundLocalError: local variable 'res0' referenced before assignment when running modified demo_pipeline_cnmfE.py

[michaelfsp]

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Sometimes errors while running CNMF occur during parallel processing which prevents the log to provide a meaningful error message. Please reproduce your error with setting dview=None.

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• Tell us a bit about your setup:

  1. Operating system (Linux/macOS/Windows): Linux
  2. Python version (3.x): 3.7.11
  3. Working environment (Python IDE/Jupyter Notebook/other): IPython
  4. Which of the demo scripts you're using for your analysis (if applicable): A modified version of demos/general/demo_pipeline_cnmfE.py
  5. CaImAn version*: 1.9.2
  6. CaImAn installation process (pip install ./pip install -e ./conda): pip install -e . *You can get the CaImAn version by creating a params object and then typing params.data['caiman_version']. If the field doesn't exist, type N/A and consider upgrading)

• Describe the issue that you are experiencing Running demo_pipeline_cnmfE.py with 'optimize_g': 5 and 's_min': 0 the following error sometimes occurs.

• Copy error log below

  UnboundLocalError Traceback (most recent call last) /mnt/dataz/michael/datalad/ca1cium/code/processing/demo_pipeline_cnmfE_based_off_script.py in 231 # RUN CNMF ON PATCHES 232 cnm = cnmf.CNMF(n_processes=n_processes, dview=dview, Ain=Ain, params=opts) --> 233 cnm.fit(images) 234 235

/mnt/dataz/michael/src/CaImAn/caiman/source_extraction/cnmf/cnmf.py in fit(self, images, indices) 629 else: 630 while len(self.estimates.merged_ROIs) > 0: --> 631 self.merge_comps(Yr, mx=np.Inf, fast_merge=True) 632 #if len(self.estimates.merged_ROIs) > 0: 633 #not_merged = np.setdiff1d(list(range(len(self.estimates.YrA))),

/mnt/dataz/michael/src/CaImAn/caiman/source_extraction/cnmf/cnmf.py in merge_comps(self, Y, mx, fast_merge, max_merge_area) 952 g=self.estimates.g, thr=self.params.get('merging', 'merge_thr'), mx=mx, 953 fast_merge=fast_merge, merge_parallel=self.params.get('merging', 'merge_parallel'), --> 954 max_merge_area=max_merge_area) 955 956 return self

/mnt/dataz/michael/src/CaImAn/caiman/source_extraction/cnmf/merging.py in merge_components(Y, A, b, C, R, f, S, sn_pix, temporal_params, spatial_params, dview, thr, fast_merge, mx, bl, c1, sn, g, merge_parallel, max_merge_area) 245 g_idx = [merged_ROI[indx]] 246 bm, cm, computedA, computedC, gm, sm, ss, yra = merge_iteration(Acsc, C_to_norm, Ctmp, fast_merge, g, g_idx, --> 247 indx, temporal_params) 248 249 A_merged[:, i] = csr_matrix(computedA).T

/mnt/dataz/michael/src/CaImAn/caiman/source_extraction/cnmf/merging.py in merge_iteration(Acsc, C_to_norm, Ctmp, fast_merge, g, g_idx, indx, temporalparams) 349 print("Merge Iteration without g...") 350 deconvC, bm, cm, gm, sm, ss, lam = constrained_foopsi( --> 351 c_in, g=None, **temporal_params) 352 return bm, cm, computedA, deconvC, gm, sm, ss, c_in - deconvC

/mnt/dataz/michael/src/CaImAn/caiman/source_extraction/cnmf/deconvolution.py in constrained_foopsi(fluor, bl, c1, g, sn, p, method_deconvolution, bas_nonneg, noise_range, noise_method, lags, fudge_factor, verbosity, solvers, optimize_g, s_min, **kwargs) 161 c, sp, bl, g, lam = constrained_oasisAR2( 162 fluor.astype(np.float32), g, sn, optimize_b=True, b_nonneg=bas_nonneg, --> 163 optimize_g=optimize_g, penalty=penalty, s_min=smin) 164 else: 165 c, sp, , g, lam = constrained_oasisAR2(

/mnt/dataz/michael/src/CaImAn/caiman/source_extraction/cnmf/deconvolution.py in constrained_oasisAR2(y, g, sn, optimize_b, b_nonneg, optimize_g, decimate, shift, window, tol, max_iter, penalty, s_min) 925 i = (l + u) // 2 926 if i > 0: --> 927 c = res0 928 s = np.append([0, 0], c[2:] - g[0] c[1:-1] - g[1] c[:-2]) 929 else:

UnboundLocalError: local variable 'res0' referenced before assignment

Upon running %debug: ipdb> args y = array([-13.793553 , -21.974134 , -46.97406 , ..., -1.4499683, -23.734684 , -1.0313864], dtype=float32) g = array([ 1.19827518, -0.35684638]) sn = 31.121605 optimize_b = True b_nonneg = False optimize_g = 5 decimate = 5 shift = 100 window = 200 tol = 1e-09 max_iter = 1 penalty = 0 s_min = 0 ipdb> print(spikesizes) [13.16290771 27.83360049]

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[pgunn]

@j-friedrich Looking at deconvolution.py:constrained_oasisAR2() It looks like res0 isn't always given a value before that c = res0 assignment.

I'm not sure how to fix that. Can you give it a look?

[j-friedrich]

I replicated the issue for spike trains that had only 0-2 spikes. I updated the code in the dev branch. @michaelfsp please report back whether the recent commit solves your issue. Thanks

[j-friedrich]

The fix made it into the master branch, thus closing.