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PeyracheLab / miniscoPy

A package to analyse calcium imaging data recorded with the Miniscope.
GNU General Public License v2.0
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update_temporal_components() problem in main_cnmfe_e.ipynb cnm.fit() #18

Open lyprince opened 6 years ago

lyprince commented 6 years ago

Rerunning main_cnmfe_e.ipynb after new pull and I run into the following error at cnm.fit(procs)

TypeError Traceback (most recent call last)

in () 4 5 cnm = CNMFE(data, parameters['cnmfe']) ----> 6 cnm.fit(procs) ~/Downloads/miniscoPy/miniscopy/cnmf_e/cnmfe.py in fit(self, procs) 429 # 2. Fit for each patch by calling the class Patch 430 ################################################################################################# --> 431 self.fit_patch(procs) 432 433 ################################################################################################# ~/Downloads/miniscoPy/miniscopy/cnmf_e/cnmfe.py in fit_patch(self, procs) 139 # fitting it 140 for i in tqdm(range(len(self.patch_index))): --> 141 self.patch_object[i].fit(procs) 142 return 143 ~/Downloads/miniscoPy/miniscopy/cnmf_e/cnmfe.py in fit(self, procs) 59 # 2. Initialize components / CALL greedyROI_corr in CAIMAN PACKAGE 60 ################################################################################################# ---> 61 initialize_components(self, **self.parameters['init_params']) 62 63 ################################################################################################# ~/Downloads/miniscoPy/miniscopy/cnmf_e/initialization.py in initialize_components(patch, gSig, gSiz, ssub, tsub, **kwargs) 764 kwargs_copy['ssub'] = ssub 765 --> 766 greedyROI_corr(patch, Yc, **kwargs_copy) 767 768 K = patch.A.shape[0] # number of neurons initialized ~/Downloads/miniscoPy/miniscopy/cnmf_e/initialization.py in greedyROI_corr(patch, Yc, tsub, ssub, ring_size_factor, **kwargs) 650 if nr: 651 # # Update temporal --> 652 patch.C[...] = update_temporal_components(patch.B, patch.A, patch.C, **patch.parameters['temporal_params']) 653 654 # # Update spatial h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() ~/anaconda2/envs/calcium/lib/python3.6/site-packages/h5py/_hl/dataset.py in __setitem__(self, args, val) 629 mshape_pad = mshape 630 mspace = h5s.create_simple(mshape_pad, (h5s.UNLIMITED,)*len(mshape_pad)) --> 631 for fspace in selection.broadcast(mshape): 632 self.id.write(mspace, fspace, val, mtype, dxpl=self._dxpl) 633 ~/anaconda2/envs/calcium/lib/python3.6/site-packages/h5py/_hl/selections.py in broadcast(self, target_shape) 297 tshape.append(t) 298 else: --> 299 raise TypeError("Can't broadcast %s -> %s" % (target_shape, count)) 300 tshape.reverse() 301 tshape = tuple(tshape) TypeError: Can't broadcast (2,) -> (1000, 4)