scv.tl.velocity_graph(adata, n_jobs=8)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[16], line 1
----> 1 scv.tl.velocity_graph(vel0, n_jobs=8)
File [~/miniconda3/envs/deepvelo/lib/python3.9/site-packages/scvelo/tools/velocity_graph.py:363](http://192.168.2.10:8001/user/dengzhen/lab/tree/code_old/newcode/miniconda3/envs/deepvelo/lib/python3.9/site-packages/scvelo/tools/velocity_graph.py#line=362), in velocity_graph(data, vkey, xkey, tkey, basis, n_neighbors, n_recurse_neighbors, random_neighbors_at_max, sqrt_transform, variance_stabilization, gene_subset, compute_uncertainties, approx, mode_neighbors, copy, n_jobs, backend)
359 n_jobs = get_n_jobs(n_jobs=n_jobs)
360 logg.info(
361 f"computing velocity graph (using {n_jobs}/{os.cpu_count()} cores)", r=True
362 )
--> 363 vgraph.compute_cosines(n_jobs=n_jobs, backend=backend)
365 adata.uns[f"{vkey}_graph"] = vgraph.graph
366 adata.uns[f"{vkey}_graph_neg"] = vgraph.graph_neg
File [~/miniconda3/envs/deepvelo/lib/python3.9/site-packages/scvelo/tools/velocity_graph.py:175](http://192.168.2.10:8001/user/dengzhen/lab/tree/code_old/newcode/miniconda3/envs/deepvelo/lib/python3.9/site-packages/scvelo/tools/velocity_graph.py#line=174), in VelocityGraph.compute_cosines(self, n_jobs, backend)
172 n_obs = self.X.shape[0]
174 # TODO: Use batches and vectorize calculation of dX in self._calculate_cosines
--> 175 res = parallelize(
176 self._compute_cosines,
177 range(self.X.shape[0]),
178 n_jobs=n_jobs,
179 unit="cells",
180 backend=backend,
181 )()
182 uncertainties, vals, rows, cols = map(_flatten, zip(*res))
184 vals = np.hstack(vals)
File [~/miniconda3/envs/deepvelo/lib/python3.9/site-packages/scvelo/core/_parallelize.py:138](http://192.168.2.10:8001/user/dengzhen/lab/tree/code_old/newcode/miniconda3/envs/deepvelo/lib/python3.9/site-packages/scvelo/core/_parallelize.py#line=137), in parallelize.<locals>.wrapper(*args, **kwargs)
126 pbar, queue, thread = None, None, None
128 res = Parallel(n_jobs=n_jobs, backend=backend)(
129 delayed(callback)(
130 *((i, cs) if use_ixs else (cs,)),
(...)
135 for i, cs in enumerate(collections)
136 )
--> 138 res = np.array(res) if as_array else res
139 if thread is not None:
140 thread.join()
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (8, 4) + inhomogeneous part.
I search that upgrade the scvelo can solve the issue. However, upgraded scvelo are not match deepvelo in other issue. How to deal with it? THANKS
Hi, great module!
I get a issue like this
I search that upgrade the scvelo can solve the issue. However, upgraded scvelo are not match deepvelo in other issue. How to deal with it? THANKS