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@keyaloding
keyaloding committed Jul 17, 2024
1 parent 8948e92 commit be6ccbc
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114 changes: 114 additions & 0 deletions save_test.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"ename": "KeyError",
"evalue": "'tests/data/slp/minimal_instance.pkg.slp'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[3], line 4\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01msleap_io\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01msio\u001b[39;00m\n\u001b[1;32m 3\u001b[0m labels_original \u001b[38;5;241m=\u001b[39m sio\u001b[38;5;241m.\u001b[39mload_slp(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtests/data/slp/minimal_instance.pkg.slp\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 4\u001b[0m \u001b[43mlabels_original\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msave\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mminimal_instance.pkg.nwb\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mformat\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnwb_training\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5\u001b[0m labels_loaded \u001b[38;5;241m=\u001b[39m sio\u001b[38;5;241m.\u001b[39mload_nwb(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mminimal_instance.pkg.nwb\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
"File \u001b[0;32m~/salk/io_fork/sleap_io/model/labels.py:372\u001b[0m, in \u001b[0;36mLabels.save\u001b[0;34m(self, filename, format, embed, **kwargs)\u001b[0m\n\u001b[1;32m 348\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Save labels to file in specified format.\u001b[39;00m\n\u001b[1;32m 349\u001b[0m \n\u001b[1;32m 350\u001b[0m \u001b[38;5;124;03mArgs:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 368\u001b[0m \u001b[38;5;124;03m This argument is only valid for the SLP backend.\u001b[39;00m\n\u001b[1;32m 369\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 370\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msleap_io\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m save_file\n\u001b[0;32m--> 372\u001b[0m \u001b[43msave_file\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mformat\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mformat\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43membed\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43membed\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/salk/io_fork/sleap_io/io/main.py:241\u001b[0m, in \u001b[0;36msave_file\u001b[0;34m(labels, filename, format, **kwargs)\u001b[0m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mformat\u001b[39m \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mlabelstudio\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 240\u001b[0m save_labelstudio(labels, filename, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[0;32m--> 241\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mformat\u001b[39m \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mjabs\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 242\u001b[0m pose_version \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpose_version\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;241m5\u001b[39m)\n\u001b[1;32m 243\u001b[0m save_jabs(labels, pose_version, filename, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
"File \u001b[0;32m~/salk/io_fork/sleap_io/io/main.py:92\u001b[0m, in \u001b[0;36msave_nwb\u001b[0;34m(labels, filename, as_training, append, **kwargs)\u001b[0m\n\u001b[1;32m 88\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 89\u001b[0m nwb\u001b[38;5;241m.\u001b[39mwrite_nwb(labels, filename)\n\u001b[0;32m---> 92\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mload_labelstudio\u001b[39m(\n\u001b[1;32m 93\u001b[0m filename: \u001b[38;5;28mstr\u001b[39m, skeleton: Optional[Union[Skeleton, \u001b[38;5;28mlist\u001b[39m[\u001b[38;5;28mstr\u001b[39m]]] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 94\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Labels:\n\u001b[1;32m 95\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Read Label Studio-style annotations from a file and return a `Labels` object.\u001b[39;00m\n\u001b[1;32m 96\u001b[0m \n\u001b[1;32m 97\u001b[0m \u001b[38;5;124;03m Args:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 105\u001b[0m \u001b[38;5;124;03m Parsed labels as a `Labels` instance.\u001b[39;00m\n\u001b[1;32m 106\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[1;32m 107\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m labelstudio\u001b[38;5;241m.\u001b[39mread_labels(filename, skeleton\u001b[38;5;241m=\u001b[39mskeleton)\n",
"File \u001b[0;32m~/salk/io_fork/sleap_io/io/nwb.py:388\u001b[0m, in \u001b[0;36mwrite_nwb\u001b[0;34m(labels, nwbfile_path, nwb_file_kwargs, pose_estimation_metadata)\u001b[0m\n\u001b[1;32m 354\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrite_nwb\u001b[39m(\n\u001b[1;32m 355\u001b[0m labels: Labels,\n\u001b[1;32m 356\u001b[0m nwbfile_path: \u001b[38;5;28mstr\u001b[39m,\n\u001b[1;32m 357\u001b[0m nwb_file_kwargs: Optional[\u001b[38;5;28mdict\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 358\u001b[0m pose_estimation_metadata: Optional[\u001b[38;5;28mdict\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 359\u001b[0m ):\n\u001b[1;32m 360\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Write labels to an nwb file and save it to the nwbfile_path given.\u001b[39;00m\n\u001b[1;32m 361\u001b[0m \n\u001b[1;32m 362\u001b[0m \u001b[38;5;124;03m Args:\u001b[39;00m\n\u001b[1;32m 363\u001b[0m \u001b[38;5;124;03m labels: A general `Labels` object.\u001b[39;00m\n\u001b[1;32m 364\u001b[0m \u001b[38;5;124;03m nwbfile_path: The path where the nwb file is to be written.\u001b[39;00m\n\u001b[1;32m 365\u001b[0m \u001b[38;5;124;03m nwb_file_kwargs: A dict containing metadata to the nwbfile. Example:\u001b[39;00m\n\u001b[1;32m 366\u001b[0m \u001b[38;5;124;03m nwb_file_kwargs = {\u001b[39;00m\n\u001b[1;32m 367\u001b[0m \u001b[38;5;124;03m 'session_description: 'your_session_description',\u001b[39;00m\n\u001b[1;32m 368\u001b[0m \u001b[38;5;124;03m 'identifier': 'your session_identifier',\u001b[39;00m\n\u001b[1;32m 369\u001b[0m \u001b[38;5;124;03m }\u001b[39;00m\n\u001b[1;32m 370\u001b[0m \u001b[38;5;124;03m For a full list of possible values see:\u001b[39;00m\n\u001b[1;32m 371\u001b[0m \u001b[38;5;124;03m https://pynwb.readthedocs.io/en/stable/pynwb.file.html#pynwb.file.NWBFile\u001b[39;00m\n\u001b[1;32m 372\u001b[0m \n\u001b[1;32m 373\u001b[0m \u001b[38;5;124;03m Defaults to None and default values are used to generate the nwb file.\u001b[39;00m\n\u001b[1;32m 374\u001b[0m \n\u001b[1;32m 375\u001b[0m \u001b[38;5;124;03m pose_estimation_metadata: This argument has a dual purpose:\u001b[39;00m\n\u001b[1;32m 376\u001b[0m \n\u001b[1;32m 377\u001b[0m \u001b[38;5;124;03m 1) It can be used to pass time information about the video which is\u001b[39;00m\n\u001b[1;32m 378\u001b[0m \u001b[38;5;124;03m necessary for synchronizing frames in pose estimation tracking to other\u001b[39;00m\n\u001b[1;32m 379\u001b[0m \u001b[38;5;124;03m modalities. Either the video timestamps can be passed to\u001b[39;00m\n\u001b[1;32m 380\u001b[0m \u001b[38;5;124;03m This can be used to pass the timestamps with the key `video_timestamps`\u001b[39;00m\n\u001b[1;32m 381\u001b[0m \u001b[38;5;124;03m or the sampling rate with key`video_sample_rate`.\u001b[39;00m\n\u001b[1;32m 382\u001b[0m \n\u001b[1;32m 383\u001b[0m \u001b[38;5;124;03m e.g. pose_estimation_metadata[\"video_timestamps\"] = np.array(timestamps)\u001b[39;00m\n\u001b[1;32m 384\u001b[0m \u001b[38;5;124;03m or pose_estimation_metadata[\"video_sample_rate\"] = 15 # In Hz\u001b[39;00m\n\u001b[1;32m 385\u001b[0m \n\u001b[1;32m 386\u001b[0m \u001b[38;5;124;03m 2) The other use of this dictionary is to ovewrite sleap-io default\u001b[39;00m\n\u001b[1;32m 387\u001b[0m \u001b[38;5;124;03m arguments for the PoseEstimation container.\u001b[39;00m\n\u001b[0;32m--> 388\u001b[0m \u001b[38;5;124;03m see https://github.com/rly/ndx-pose for a full list or arguments.\u001b[39;00m\n\u001b[1;32m 389\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[1;32m 390\u001b[0m nwb_file_kwargs \u001b[38;5;241m=\u001b[39m nwb_file_kwargs \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mdict\u001b[39m()\n\u001b[1;32m 392\u001b[0m \u001b[38;5;66;03m# Add required values for nwbfile if not present\u001b[39;00m\n",
"File \u001b[0;32m~/salk/io_fork/sleap_io/io/nwb.py:471\u001b[0m, in \u001b[0;36mappend_nwb_data\u001b[0;34m(labels, nwbfile, pose_estimation_metadata)\u001b[0m\n\u001b[1;32m 469\u001b[0m labels_data_df = convert_predictions_to_dataframe(labels)\n\u001b[1;32m 470\u001b[0m break\n\u001b[0;32m--> 471\u001b[0m else:\n\u001b[1;32m 472\u001b[0m labels_data_df = pd.DataFrame()\n\u001b[1;32m 474\u001b[0m # For every video create a processing module\n",
"File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/pandas/core/frame.py:4102\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 4100\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcolumns\u001b[38;5;241m.\u001b[39mnlevels \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m 4101\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_getitem_multilevel(key)\n\u001b[0;32m-> 4102\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_loc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 4103\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_integer(indexer):\n\u001b[1;32m 4104\u001b[0m indexer \u001b[38;5;241m=\u001b[39m [indexer]\n",
"File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/pandas/core/indexes/range.py:417\u001b[0m, in \u001b[0;36mRangeIndex.get_loc\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01merr\u001b[39;00m\n\u001b[1;32m 416\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Hashable):\n\u001b[0;32m--> 417\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key)\n\u001b[1;32m 418\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_indexing_error(key)\n\u001b[1;32m 419\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key)\n",
"\u001b[0;31mKeyError\u001b[0m: 'tests/data/slp/minimal_instance.pkg.slp'"
]
}
],
"source": [
"import sleap_io as sio\n",
"\n",
"labels_original = sio.load_slp(\"tests/data/slp/minimal_instance.pkg.slp\")\n",
"labels_original.save(\"minimal_instance.pkg.nwb\", format=\"nwb_training\")\n",
"labels_loaded = sio.load_nwb(\"minimal_instance.pkg.nwb\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"minimal_instance.pkg.nwb_images/img_0.png\n"
]
},
{
"ename": "ValueError",
"evalue": "Can't write images with one color channel.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[2], line 16\u001b[0m\n\u001b[1;32m 14\u001b[0m img_path \u001b[38;5;241m=\u001b[39m save_path \u001b[38;5;241m/\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mimg_\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mi\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m.png\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 15\u001b[0m \u001b[38;5;28mprint\u001b[39m(img_path)\n\u001b[0;32m---> 16\u001b[0m \u001b[43miio\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mimwrite\u001b[49m\u001b[43m(\u001b[49m\u001b[43mimg_path\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlf\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mimage\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 17\u001b[0m img_paths\u001b[38;5;241m.\u001b[39mappend(img_path)\n\u001b[1;32m 18\u001b[0m \u001b[38;5;28mprint\u001b[39m(img_paths)\n",
"File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/imageio/v3.py:147\u001b[0m, in \u001b[0;36mimwrite\u001b[0;34m(uri, image, plugin, extension, format_hint, **kwargs)\u001b[0m\n\u001b[1;32m 105\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Write an ndimage to the given URI.\u001b[39;00m\n\u001b[1;32m 106\u001b[0m \n\u001b[1;32m 107\u001b[0m \u001b[38;5;124;03mThe exact behavior depends on the file type and plugin used. To learn about\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 136\u001b[0m \n\u001b[1;32m 137\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 139\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m imopen(\n\u001b[1;32m 140\u001b[0m uri,\n\u001b[1;32m 141\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mw\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 145\u001b[0m extension\u001b[38;5;241m=\u001b[39mextension,\n\u001b[1;32m 146\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m img_file:\n\u001b[0;32m--> 147\u001b[0m encoded \u001b[38;5;241m=\u001b[39m \u001b[43mimg_file\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwrite\u001b[49m\u001b[43m(\u001b[49m\u001b[43mimage\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 149\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m encoded\n",
"File \u001b[0;32m~/mambaforge3/envs/io_dev/lib/python3.12/site-packages/imageio/plugins/pillow.py:433\u001b[0m, in \u001b[0;36mPillowPlugin.write\u001b[0;34m(self, ndimage, mode, format, is_batch, **kwargs)\u001b[0m\n\u001b[1;32m 431\u001b[0m is_batch \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m 432\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m ndimage\u001b[38;5;241m.\u001b[39mndim \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m3\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m ndimage\u001b[38;5;241m.\u001b[39mshape[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m] \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[0;32m--> 433\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCan\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt write images with one color channel.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 434\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m ndimage\u001b[38;5;241m.\u001b[39mndim \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m3\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m ndimage\u001b[38;5;241m.\u001b[39mshape[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m] \u001b[38;5;129;01min\u001b[39;00m [\u001b[38;5;241m2\u001b[39m, \u001b[38;5;241m3\u001b[39m, \u001b[38;5;241m4\u001b[39m]:\n\u001b[1;32m 435\u001b[0m \u001b[38;5;66;03m# Note: this makes a channel-last assumption\u001b[39;00m\n\u001b[1;32m 436\u001b[0m is_batch \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n",
"\u001b[0;31mValueError\u001b[0m: Can't write images with one color channel."
]
}
],
"source": [
"import imageio.v3 as iio\n",
"from pathlib import Path\n",
"import sleap_io as sio\n",
"\n",
"save_path = Path(\"minimal_instance.pkg.nwb_images\")\n",
"try:\n",
" save_path.mkdir(parents=True, exist_ok=True)\n",
"except Exception as e:\n",
" print(f\"An error {e} occurred. The directory could not be created.\")\n",
"img_paths = []\n",
"\n",
"labels_original = sio.load_slp(\"tests/data/slp/minimal_instance.pkg.slp\")\n",
"for i, lf in enumerate(labels_original):\n",
" img_path = save_path / f\"img_{i}.png\"\n",
" print(img_path)\n",
" iio.imwrite(img_path, lf.image)\n",
" img_paths.append(img_path)\n",
"print(img_paths)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "io_dev",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
3 changes: 0 additions & 3 deletions sleap_io/io/main.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,9 +57,6 @@ def load_nwb(filename: str, as_training: Optional[bool]=None) -> Labels:
Returns:
The dataset as a `Labels` object.
"""
if as_training is None:
return

if as_training:
return nwb.read_nwb_training(filename)
else:
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