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@dalessioluca
dalessioluca committed Mar 18, 2022
1 parent 7ad6b06 commit 44e32ed
Showing 1 changed file with 20 additions and 4 deletions.
24 changes: 20 additions & 4 deletions notebooks/notebook3_all.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -552,16 +552,29 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 15,
"id": "c0ad7278-39ac-45ec-91df-979063079ced",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0 gr_barlow_dataset.pt gr_barlow_l2_10.0.pt\n",
"1 gr_simclr_dataset.pt gr_simclr_l2_None.pt\n"
"0 gr_barlow_dataset.pt gr_barlow_l2_10.0.pt\n"
]
},
{
"ename": "MemoryError",
"evalue": "Unable to allocate 1.61 GiB for an array with shape (20760, 1604) and data type <U13",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mMemoryError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/tmp/ipykernel_1582/3322125257.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0mnum_samples\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m100\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 12\u001b[0m \u001b[0msubsample_size_cells\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m200\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m subsample_size_genes=None)\n\u001b[0m\u001b[1;32m 14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 15\u001b[0m df_metric_tmp_test, df_count_tmp_test = gr.predict(\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/torch/autograd/grad_mode.py\u001b[0m in \u001b[0;36mdecorate_context\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 27\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 28\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 29\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mcast\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mF\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 30\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/mnt/disks/persistent_disk/REPOS/tissue_purifier/src/tissue_purifier/genex/pyro_model.py\u001b[0m in \u001b[0;36mpredict\u001b[0;34m(self, dataset, num_samples, subsample_size_cells, subsample_size_genes)\u001b[0m\n\u001b[1;32m 706\u001b[0m \u001b[0mcell_type_ids_ng\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcell_type_ids\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mview\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexpand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 707\u001b[0m \u001b[0mcell_names_ng\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnumpy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_inverse_cell_type_mapping\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mcell_type_ids_ng\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcpu\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnumpy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 708\u001b[0;31m \u001b[0mgene_names_ng\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_gene_names_kg\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcell_names_ng\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 709\u001b[0m \u001b[0;32massert\u001b[0m \u001b[0mcell_names_ng\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mdataset\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcounts\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mpred_counts_ng\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mcell_names_ng\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 710\u001b[0m \"Shape mismatch {0} vs {1} vs {2} vs {3}\".format(cell_names_ng.shape,\n",
"\u001b[0;32m/mnt/disks/persistent_disk/REPOS/tissue_purifier/src/tissue_purifier/genex/pyro_model.py\u001b[0m in \u001b[0;36m_get_gene_names_kg\u001b[0;34m(self, k)\u001b[0m\n\u001b[1;32m 176\u001b[0m \u001b[0mlen_genes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgene_names_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 177\u001b[0m \u001b[0mgene_codes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen_genes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mview\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexpand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlen_genes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 178\u001b[0;31m \u001b[0mgene_names_kg\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnumpy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgene_names_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mgene_codes\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcpu\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnumpy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 179\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mgene_names_kg\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mMemoryError\u001b[0m: Unable to allocate 1.61 GiB for an array with shape (20760, 1604) and data type <U13"
]
}
],
Expand All @@ -588,11 +601,14 @@
" \n",
" df_tmp_test = df_metric_tmp_test.groupby([\"cell_type\", \"gene\"]).mean()\n",
" df_tmp_test[\"q_ratio\"] = df_tmp_test[\"q_dist\"] / df_baseline_test[\"q_dist\"]\n",
" \n",
" # BIN HERE. SAVE THE BINNED STUFF OTHERWISE IT IS TOO BIG\n",
" \n",
" result_dict[\"test_\"+ckpt_file] = df_tmp_test[\"q_ratio\"].values \n",
" \n",
" df_tmp_train = df_metric_tmp_train.groupby([\"cell_type\", \"gene\"]).mean()\n",
" df_tmp_train[\"q_ratio\"] = df_tmp_train[\"q_dist\"] / df_baseline_train[\"q_dist\"]\n",
" result_dict[\"test_\"+ckpt_file] = df_tmp_train[\"q_ratio\"].values "
" result_dict[\"train_\"+ckpt_file] = df_tmp_train[\"q_ratio\"].values "
]
},
{
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