Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Input contains NaN, infinity or a value too large for dtype('float32') #36

Open
Dan-121 opened this issue Nov 3, 2020 · 0 comments
Open

Comments

@Dan-121
Copy link

Dan-121 commented Nov 3, 2020

hello,you really do a good job,but i met some trouble,could ypu tell me how to fix it.and the question is as followed:
ValueError Traceback (most recent call last)
in
----> 1 adata=desc.train(adata,
2 dims=[adata.shape[1],64,32],
3 tol=0.005,
4 n_neighbors=10,
5 batch_size=256,

~/anaconda3/envs/R_env/lib/python3.8/site-packages/desc/models/desc.py in train(data, dims, alpha, tol, init, louvain_resolution, n_neighbors, pretrain_epochs, batch_size, activation, actincenter, drop_rate_SAE, is_stacked, use_earlyStop, use_ae_weights, save_encoder_weights, save_encoder_step, save_dir, max_iter, epochs_fit, num_Cores, num_Cores_tsne, use_GPU, GPU_id, random_seed, verbose, do_tsne, learning_rate, perplexity, do_umap, kernel_clustering)
301 print("Start to process resolution=",str(resolution))
302 use_ae_weights=use_ae_weights if ith==0 else True
--> 303 res=train_single(data=data,
304 dims=dims,
305 alpha=alpha,

~/anaconda3/envs/R_env/lib/python3.8/site-packages/desc/models/desc.py in train_single(data, dims, alpha, tol, init, louvain_resolution, n_neighbors, pretrain_epochs, batch_size, activation, actincenter, drop_rate_SAE, is_stacked, use_earlyStop, use_ae_weights, save_encoder_weights, save_encoder_step, save_dir, max_iter, epochs_fit, num_Cores, num_Cores_tsne, use_GPU, GPU_id, random_seed, verbose, do_tsne, learning_rate, perplexity, do_umap, kernel_clustering)
162 if do_tsne:
163 num_Cores_tsne=int(num_Cores_tsne) if total_cpu>int(num_Cores_tsne) else int(math.ceil(total_cpu/2))
--> 164 sc.tl.tsne(adata,use_rep="X_Embeded_z"+str(louvain_resolution),learning_rate=learning_rate,perplexity=perplexity,n_jobs=num_Cores_tsne)
165 adata.obsm["X_tsne"+str(louvain_resolution)]=adata.obsm["X_tsne"].copy()
166 print('tsne finished and added X_tsne'+str(louvain_resolution),' into the umap coordinates (adata.obsm)\n')

~/anaconda3/envs/R_env/lib/python3.8/site-packages/scanpy/tools/_tsne.py in tsne(adata, n_pcs, use_rep, perplexity, early_exaggeration, learning_rate, random_state, use_fast_tsne, n_jobs, copy)
113 tsne = TSNE(**params_sklearn)
114 logg.info(' using sklearn.manifold.TSNE with a fix by D. DeTomaso')
--> 115 X_tsne = tsne.fit_transform(X)
116 # update AnnData instance
117 adata.obsm['X_tsne'] = X_tsne # annotate samples with tSNE coordinates

~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/manifold/t_sne.py in fit_transform(self, X, y)
889 Embedding of the training data in low-dimensional space.
890 """
--> 891 embedding = self.fit(X)
892 self.embedding
= embedding
893 return self.embedding

~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/manifold/_t_sne.py in _fit(self, X, skip_num_points)
667 raise ValueError("'angle' must be between 0.0 - 1.0")
668 if self.method == 'barnes_hut':
--> 669 X = self._validate_data(X, accept_sparse=['csr'],
670 ensure_min_samples=2,
671 dtype=[np.float32, np.float64])

~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/base.py in _validate_data(self, X, y, reset, validate_separately, **check_params)
418 f"requires y to be passed, but the target y is None."
419 )
--> 420 X = check_array(X, **check_params)
421 out = X
422 else:

~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/utils/validation.py in inner_f(*args, **kwargs)
70 FutureWarning)
71 kwargs.update({k: arg for k, arg in zip(sig.parameters, args)})
---> 72 return f(**kwargs)
73 return inner_f
74

~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/utils/validation.py in check_array(array, accept_sparse, accept_large_sparse, dtype, order, copy, force_all_finite, ensure_2d, allow_nd, ensure_min_samples, ensure_min_features, estimator)
642
643 if force_all_finite:
--> 644 _assert_all_finite(array,
645 allow_nan=force_all_finite == 'allow-nan')
646

~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/utils/validation.py in _assert_all_finite(X, allow_nan, msg_dtype)
94 not allow_nan and not np.isfinite(X).all()):
95 type_err = 'infinity' if allow_nan else 'NaN, infinity'
---> 96 raise ValueError(
97 msg_err.format
98 (type_err,

ValueError: Input contains NaN, infinity or a value too large for dtype('float32').

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant