IndexError: tuple index out of range

[lzj1769]

Hi，

I got the following error when running the function identify_spatial_genes:

`100%|██████████| 128/128 [00:19<00:00, 6.62it/s]

RemoteTraceback Traceback (most recent call last) RemoteTraceback: """ Traceback (most recent call last): File "/data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/site-packages/parmap/parmap.py", line 105, in _func_star_many return func_items_args[0](*list(func_items_args[1]) + func_items_args[2], File "/data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/site-packages/scGCO/Graph_cut.py", line 640, in compute_spatial_genomewise_optimize newLabels, thresholds,label_pred = cut_graph_general_otsu(cellGraph, exp, unary_scale_factor, File "/data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/site-packages/scGCO/Graph_cut.py", line 1348, in cut_graph_general_otsu pair_size = thresholds.shape[0] + 1 IndexError: tuple index out of range """

The above exception was the direct cause of the following exception:

IndexError Traceback (most recent call last) Cell In[17], line 1 ----> 1 df = identify_spatial_genes(locs, data, cellGraph, gmmDict, smooth_factor=5)

File /data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/site-packages/scGCO/Graph_cut.py:729, in identify_spatial_genes(locs, data_norm, cellGraph, gmmDict, smooth_factor, unary_scale_factor, label_cost, algorithm, ncores) 716 ttt = np.array_split(data_norm,num_cores,axis=1) 717 tuples = [(l, d, c, g,ww,nn, s, u, b, a) for l, d, c, g,ww,nn, s, u, b, a in zip( 718 repeat(locs, num_cores), 719 ttt, (...) 726 repeat(label_cost, num_cores), 727 repeat(algorithm, num_cores))] --> 729 results = parmap.starmap(compute_spatial_genomewise_optimize, tuples, 730 pm_processes=num_cores, pm_pbar=True) 732 # pool.close() 733 # p_values, genes, diff_p_values, exp_diff, smooth_factors, pred_labels, model_results 734 nnn = [results[i][0] for i in np.arange(len(results))]

File /data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/site-packages/parmap/parmap.py:317, in starmap(function, iterables, *args, *kwargs) 299 def starmap(function, iterables, args, **kwargs): 300 """ Equivalent to: 301 >>> return ([function(x1,x2,x3,..., args[0], args[1],...) for 302 >>> (x1,x2,x3...) in iterable]) (...) 315 :type pm_pbar: bool or dict 316 """ --> 317 return _map_or_starmap(function, iterables, args, kwargs, "starmap")

File /data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/site-packages/parmap/parmap.py:273, in _map_or_starmap(function, iterable, args, kwargs, map_or_starmap) 271 _do_pbar(result, num_tasks, chunksize, tqdm_options=tqdm_options) 272 finally: --> 273 output = result.get() 274 if close_pool: 275 pool.join()

File /data/pinello/SHARED_SOFTWARE/anaconda_latest/envs/scGCO/lib/python3.9/multiprocessing/pool.py:771, in ApplyResult.get(self, timeout) 769 return self._value 770 else: --> 771 raise self._value

IndexError: tuple index out of range`

How can I solve this issue?

Thanks and best, Zhijian

[fengwanwan]

Dear Zhijian: Thank you for your interest in our study. I've sent you a tiny demo to your google gmail.

Best wishes Wanwan

[lzj1769]

Hi Wanwan,

Thank you very much for sending the demo. With the new code, the method works pretty well!

Best, Zhijian