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{
"cells": [
{
"cell_type": "markdown",
"id": "d9814eee-f863-42d5-80a0-3d7256d62ea5",
"metadata": {},
"source": [
"Testing the pipeline from sleap nn and train the UNet model"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "f68e1de7-5c06-4f30-83af-6fbae1f8a2c4",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "f68e1de7-5c06-4f30-83af-6fbae1f8a2c4",
"outputId": "4796108c-23fb-450c-8656-970d3651e887",
"tags": []
},
"outputs": [],
"source": [
"# !pip install sleap-io>=0.0.7\n",
"# !pip install Lightning\n",
"# !pip install pytorch-lightning"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "608b5174-f047-4201-9038-696bdc8f3964",
"metadata": {
"id": "608b5174-f047-4201-9038-696bdc8f3964",
"tags": []
},
"outputs": [],
"source": [
"import torch\n",
"import sleap_io as sio\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"from torch.utils.data import DataLoader\n",
"from torch.utils.data.datapipes.datapipe import IterDataPipe\n",
"import lightning.pytorch as pl\n",
"import torch.nn.functional as F\n",
"from pytorch_lightning.loggers import WandbLogger"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "c0b7fbd1-84a3-4664-9f0a-62957181f193",
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"'0.0.11'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sio.__version__"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "bbe5e47a-3f2f-41ed-9f8d-29ebeb554fa4",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: wandb in /opt/conda/envs/python37/lib/python3.7/site-packages (0.13.10)\n",
"Requirement already satisfied: GitPython>=1.0.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (3.1.31)\n",
"Requirement already satisfied: protobuf!=4.21.0,<5,>=3.12.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (3.19.6)\n",
"Requirement already satisfied: typing-extensions in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (3.10.0.2)\n",
"Requirement already satisfied: psutil>=5.0.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (5.9.3)\n",
"Requirement already satisfied: pathtools in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (0.1.2)\n",
"Requirement already satisfied: PyYAML in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (6.0)\n",
"Requirement already satisfied: requests<3,>=2.0.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (2.28.2)\n",
"Requirement already satisfied: sentry-sdk>=1.0.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (1.16.0)\n",
"Requirement already satisfied: docker-pycreds>=0.4.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (0.4.0)\n",
"Requirement already satisfied: appdirs>=1.4.3 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (1.4.4)\n",
"Requirement already satisfied: Click!=8.0.0,>=7.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (8.1.3)\n",
"Requirement already satisfied: setuptools in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (67.4.0)\n",
"Requirement already satisfied: setproctitle in /opt/conda/envs/python37/lib/python3.7/site-packages (from wandb) (1.3.2)\n",
"Requirement already satisfied: importlib-metadata in /opt/conda/envs/python37/lib/python3.7/site-packages (from Click!=8.0.0,>=7.0->wandb) (4.2.0)\n",
"Requirement already satisfied: six>=1.4.0 in /opt/conda/envs/python37/lib/python3.7/site-packages (from docker-pycreds>=0.4.0->wandb) (1.15.0)\n",
"Requirement already satisfied: gitdb<5,>=4.0.1 in /opt/conda/envs/python37/lib/python3.7/site-packages (from GitPython>=1.0.0->wandb) (4.0.10)\n",
"Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/envs/python37/lib/python3.7/site-packages (from requests<3,>=2.0.0->wandb) (2021.10.8)\n",
"Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/envs/python37/lib/python3.7/site-packages (from requests<3,>=2.0.0->wandb) (1.26.14)\n",
"Requirement already satisfied: idna<4,>=2.5 in /opt/conda/envs/python37/lib/python3.7/site-packages (from requests<3,>=2.0.0->wandb) (3.4)\n",
"Requirement already satisfied: charset-normalizer<4,>=2 in /opt/conda/envs/python37/lib/python3.7/site-packages (from requests<3,>=2.0.0->wandb) (2.1.1)\n",
"Requirement already satisfied: smmap<6,>=3.0.1 in /opt/conda/envs/python37/lib/python3.7/site-packages (from gitdb<5,>=4.0.1->GitPython>=1.0.0->wandb) (5.0.0)\n",
"Requirement already satisfied: zipp>=0.5 in /opt/conda/envs/python37/lib/python3.7/site-packages (from importlib-metadata->Click!=8.0.0,>=7.0->wandb) (3.15.0)\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Failed to detect the name of this notebook, you can set it manually with the WANDB_NOTEBOOK_NAME environment variable to enable code saving.\n",
"\u001b[34m\u001b[1mwandb\u001b[0m: Currently logged in as: \u001b[33mdsmurali\u001b[0m (\u001b[33mteam-ucsd\u001b[0m). Use \u001b[1m`wandb login --relogin`\u001b[0m to force relogin\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"!pip install wandb\n",
"import wandb\n",
"wandb.login()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "263b4722-1d21-422d-8ca3-3a0d1ccca5e7",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# from sleap_nn.data.providers import LabelsReader\n",
"from sleap_nn.data.normalization import Normalizer\n",
"from sleap_nn.data.augmentation import KorniaAugmenter\n",
"from sleap_nn.data.instance_centroids import InstanceCentroidFinder\n",
"from sleap_nn.data.instance_cropping import InstanceCropper\n",
"from sleap_nn.data.confidence_maps import ConfidenceMapGenerator\n",
"\n",
"import itertools"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "FdlxcnxJNKKl",
"metadata": {
"id": "FdlxcnxJNKKl",
"tags": []
},
"outputs": [],
"source": [
"'''This class returns the image and the corresponding confidence map for the DataLoader'''\n",
"class SleapDataset(IterDataPipe):\n",
" \"\"\" Returns image and corresponding heatmap for the DataLoader\n",
"\n",
" This class is to return the image and its corresponding confidence map\n",
" to load the dataset with the DataLoader class\n",
"\n",
" Attributes:\n",
" source_dp: The previous `DataPipe` with samples that contain an `instances` key.\n",
"\n",
" \"\"\"\n",
" def __init__(self, source_dp: IterDataPipe):\n",
" \"\"\"Initialize SleapDataset with the source `DataPipe.\"\"\"\n",
" self.dp = source_dp\n",
"\n",
" def __iter__(self):\n",
" \"\"\"Returns a tuple with the cropped image and the heatmap\"\"\"\n",
" i=0\n",
" for example in self.dp:\n",
" example[\"instance_image\"] = example[\"instance_image\"].squeeze(dim=0)\n",
" yield example[\"instance_image\"], example[\"confidence_maps\"]\n",
" "
]
},
{
"cell_type": "markdown",
"id": "iTHJqI2QOW-j",
"metadata": {
"id": "iTHJqI2QOW-j",
"tags": []
},
"source": [
"#### Download Dataset and create the Data pipeline"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "-jqYG_TGKYlu",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "-jqYG_TGKYlu",
"outputId": "c5ba72cd-0508-456e-a06e-9a142e1c8674",
"tags": []
},
"outputs": [],
"source": [
"# path to dataset : \n",
"# train_dataset_loc = \"../../datasets/sleap-data/datasets/wt_gold.13pt/tracking_split2/train.pkg.slp\"\n",
"train_dataset_loc = \"../210205.sleap_wt_gold.13pt.local_paths.slp\"\n",
"# dataset_loc = \"train.pkg.slp\""
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "a88675e7-aa1e-472d-9a31-35157a2ebca8",
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"Labels(labeled_frames=3000, videos=30, skeletons=1, tracks=2)"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"train_labels = sio.load_slp(train_dataset_loc)\n",
"train_labels"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "aa1ee3a1-1155-45da-82bb-5673834b6a9a",
"metadata": {},
"outputs": [],
"source": [
"\"\"\"This module implements pipeline blocks for reading input data such as labels.\"\"\"\n",
"from torch.utils.data.datapipes.datapipe import IterDataPipe\n",
"import torch\n",
"from typing import List\n",
"\n",
"class LabelsReader(IterDataPipe):\n",
" \"\"\"Datapipe for reading frames from Labels object.\n",
"\n",
" This DataPipe will produce examples containing a window of frames and an sleap_io.Instance for the center frame\n",
" from a sleap_io.Labels instance.\n",
"\n",
" Attributes:\n",
" labels: sleap_io.Labels object that contains LabeledFrames that will be\n",
" accessed through a torchdata DataPipe\n",
" deltas: window indices, e.g.:`[-1, 0, 1]`\n",
" \"\"\"\n",
"\n",
" def __init__(self, labels: sio.Labels, deltas: List):\n",
" \"\"\"Initialize labels and deltas attributes of the class.\"\"\"\n",
" self.labels = labels\n",
" self.deltas = deltas\n",
"\n",
" @classmethod\n",
" def from_filename(cls, filename: str, deltas: List):\n",
" \"\"\"Create LabelsReader from a .slp filename.\"\"\"\n",
" labels = sio.load_slp(filename)\n",
" return cls(labels, deltas)\n",
"\n",
" def __iter__(self):\n",
" \"\"\"Return an example dictionary containing the following elements.\n",
"\n",
" \"image\": A torch.Tensor containing full raw frame image as a uint8 array\n",
" of shape (len(deltas), channels, height, width).\n",
" \"instances\": Keypoint coordinates for all instances in the frame as a\n",
" float32 torch.Tensor of shape (1, num_instances, num_nodes, 2).\n",
" \"\"\"\n",
" # filter labels with labeled frames\n",
" self.labels.labeled_frames = [lf for lf in self.labels.labeled_frames if len(lf) > 0]\n",
" for lf in self.labels:\n",
" lf.instances = lf.user_instances\n",
" instances = []\n",
" for inst in lf:\n",
" instances.append(inst.numpy())\n",
" # load the keypoints for the center frame\n",
" instances = np.stack(instances, axis=0)\n",
"\n",
" # get the frame indices from the source video\n",
" fidx = lf.frame_idx\n",
" video = lf.video\n",
" finds = np.array(self.deltas) + fidx\n",
" finds = np.maximum(np.minimum(finds, len(lf.video) - 1), 0)\n",
" imgs = np.stack([np.transpose(l, (2, 0, 1)) for l in video[finds]],axis=0)\n",
"\n",
" yield {\n",
" \"image\": torch.from_numpy(imgs),\n",
" \"instances\": torch.from_numpy(instances.astype(\"float32\")).unsqueeze(dim=0),\n",
" }\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "ced8e738-4d6a-43bb-a2cd-1936efceaadb",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"\"\"\"This module stacks the images in the window into the channels dimension\"\"\"\n",
"\n",
"class StackImage(IterDataPipe):\n",
"\n",
" \"\"\"DataPipe for stacking the images in the window.\n",
"\n",
" This DataPipe will stack the images in the frame window into the channel dimension.\n",
"\n",
" Attributes:\n",
" source_dp: The input `IterDataPipe` with examples that contain `\"instances\"` and\n",
" `\"image\"` keys.\n",
" deltas: window indices, e.g.:`[-1, 0, 1]`\n",
"\n",
" Notes:\n",
" This block expects the \"image\" and \"instances\" keys to be present in the input\n",
" examples.\n",
"\n",
" The `\"image\"` key should contain a torch.Tensor of dtype torch.float32\n",
" and of shape `(..., 1, C, H, W)`, i.e., rank >= 3.\n",
"\n",
" \"\"\"\n",
"\n",
" def __init__(self, source_dp: IterDataPipe, deltas: List):\n",
" \"\"\"Initialize the block\"\"\"\n",
" self.dp = source_dp\n",
" self.deltas = deltas\n",
"\n",
" def __iter__(self):\n",
" \"\"\"Return an example dictionary with the stacked image (..., C * len(deltas), H, W) and instances.\"\"\"\n",
" for dict in self.dp:\n",
" images = dict[\"image\"]\n",
" instances = dict[\"instances\"]\n",
" image = torch.cat(images.chunk(len(self.deltas)),dim=1)\n",
" # image = image.squeeze(dim=0)\n",
" yield {\"image\": image, \"instances\": instances}"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "925246d3-6d89-47a9-99c9-9f447f654117",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 1000
},
"id": "925246d3-6d89-47a9-99c9-9f447f654117",
"outputId": "46dd4a79-dfe6-4766-b999-a4fa6cd4831a",
"tags": []
},
"outputs": [],
"source": [
"from torchdata.datapipes.iter import Shuffler, InMemoryCacheHolder, Prefetcher, Batcher\n",
"\n",
"deltas = [-1,0,1]\n",
"datapipe = LabelsReader.from_filename(filename=train_dataset_loc, deltas = [-1, 0, 1])\n",
"datapipe = StackImage(datapipe, deltas)\n",
"datapipe = Normalizer(datapipe) \n",
"datapipe = KorniaAugmenter(datapipe, rotation=180, mixup_p=0, erase_p=0)\n",
"datapipe = InstanceCentroidFinder(datapipe) \n",
"datapipe = InstanceCropper(datapipe, 160, 160) \n",
"train_datapipe = ConfidenceMapGenerator(datapipe, sigma=1.5, output_stride=2) \n",
"dataset = SleapDataset(train_datapipe)\n"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "82152207-448f-4d13-8ac7-6aa48c4ac945",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"\n",
"import multiprocessing\n",
"\n",
"cores = multiprocessing.cpu_count()\n",
"cores = 2"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "VkenBdZVeziv",
"metadata": {
"id": "VkenBdZVeziv",
"tags": []
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/opt/conda/envs/py39_pth2_3/lib/python3.9/site-packages/torch/utils/data/graph_settings.py:103: UserWarning: `shuffle=True` was set, but the datapipe does not contain a `Shuffler`. Adding one at the end. Be aware that the default buffer size might not be sufficient for your task.\n",
" warnings.warn(\n"
]
}
],
"source": [
"# train, valid, test = dataset.random_split(total_length=3000, weights={\"train\": 0.8, \"valid\": 0.1, \"test\":0.1}, seed=0)\n",
"# from torch.utils.data.backward_compatibility import worker_init_fn\n",
"\n",
"\n",
"# val_dataset = val_dataset.sharding_filter()\n",
"\n",
"# train_data_loader = DataLoader(dataset, batch_size=4, shuffle=True, pin_memory=True, drop_last=True, prefetch_factor=2, num_workers=cores)\n",
"# # val_data_loader = DataLoader( val_dataset, batch_size=4, shuffle=False, pin_memory=True, drop_last=True, prefetch_factor=2, num_workers=cores)\n",
"# # test_data_loader = DataLoader(test, batch_size=4, shuffle=False)\n",
"\n",
"\n",
"train, valid, test = dataset.random_split(total_length=4000, weights={\"train\": 0.8, \"valid\": 0.1, \"test\":0.1}, seed=0)\n",
"train = train.sharding_filter()\n",
"valid = valid.sharding_filter()\n",
"test = test.sharding_filter() \n",
"\n",
"train_data_loader = DataLoader(train, batch_size=4, shuffle=True, num_workers=8)\n",
"val_data_loader = DataLoader(valid, batch_size=4, shuffle=False, num_workers=8)\n",
"test_data_loader = DataLoader(test, batch_size=4, shuffle=False, num_workers=8)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "6ba56c28-7f8f-49a7-8993-fcf58d2aae82",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Invalid NAL unit size (-268431284 > 532).\n",
"missing picture in access unit with size 536\n",
"Invalid NAL unit size (-1399290930 > 532).\n",
"missing picture in access unit with size 536\n"
]
},
{
"ename": "KeyboardInterrupt",
"evalue": "",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[15], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m viz_imgs, viz_cms \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mnext\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43miter\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mval_data_loader\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28mprint\u001b[39m(viz_imgs\u001b[38;5;241m.\u001b[39mshape, viz_cms\u001b[38;5;241m.\u001b[39mshape)\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/site-packages/torch/utils/data/dataloader.py:633\u001b[0m, in \u001b[0;36m_BaseDataLoaderIter.__next__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 630\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_sampler_iter \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 631\u001b[0m \u001b[38;5;66;03m# TODO(https://github.com/pytorch/pytorch/issues/76750)\u001b[39;00m\n\u001b[1;32m 632\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reset() \u001b[38;5;66;03m# type: ignore[call-arg]\u001b[39;00m\n\u001b[0;32m--> 633\u001b[0m data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_next_data\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 634\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_num_yielded \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 635\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_dataset_kind \u001b[38;5;241m==\u001b[39m _DatasetKind\u001b[38;5;241m.\u001b[39mIterable \u001b[38;5;129;01mand\u001b[39;00m \\\n\u001b[1;32m 636\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_IterableDataset_len_called \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m \\\n\u001b[1;32m 637\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_num_yielded \u001b[38;5;241m>\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_IterableDataset_len_called:\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/site-packages/torch/utils/data/dataloader.py:1328\u001b[0m, in \u001b[0;36m_MultiProcessingDataLoaderIter._next_data\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1325\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_process_data(data)\n\u001b[1;32m 1327\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_shutdown \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_tasks_outstanding \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m-> 1328\u001b[0m idx, data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_data\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1329\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_tasks_outstanding \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 1330\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_dataset_kind \u001b[38;5;241m==\u001b[39m _DatasetKind\u001b[38;5;241m.\u001b[39mIterable:\n\u001b[1;32m 1331\u001b[0m \u001b[38;5;66;03m# Check for _IterableDatasetStopIteration\u001b[39;00m\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/site-packages/torch/utils/data/dataloader.py:1294\u001b[0m, in \u001b[0;36m_MultiProcessingDataLoaderIter._get_data\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1290\u001b[0m \u001b[38;5;66;03m# In this case, `self._data_queue` is a `queue.Queue`,. But we don't\u001b[39;00m\n\u001b[1;32m 1291\u001b[0m \u001b[38;5;66;03m# need to call `.task_done()` because we don't use `.join()`.\u001b[39;00m\n\u001b[1;32m 1292\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1293\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[0;32m-> 1294\u001b[0m success, data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_try_get_data\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1295\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m success:\n\u001b[1;32m 1296\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m data\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/site-packages/torch/utils/data/dataloader.py:1132\u001b[0m, in \u001b[0;36m_MultiProcessingDataLoaderIter._try_get_data\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 1119\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_try_get_data\u001b[39m(\u001b[38;5;28mself\u001b[39m, timeout\u001b[38;5;241m=\u001b[39m_utils\u001b[38;5;241m.\u001b[39mMP_STATUS_CHECK_INTERVAL):\n\u001b[1;32m 1120\u001b[0m \u001b[38;5;66;03m# Tries to fetch data from `self._data_queue` once for a given timeout.\u001b[39;00m\n\u001b[1;32m 1121\u001b[0m \u001b[38;5;66;03m# This can also be used as inner loop of fetching without timeout, with\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1129\u001b[0m \u001b[38;5;66;03m# Returns a 2-tuple:\u001b[39;00m\n\u001b[1;32m 1130\u001b[0m \u001b[38;5;66;03m# (bool: whether successfully get data, any: data if successful else None)\u001b[39;00m\n\u001b[1;32m 1131\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 1132\u001b[0m data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_data_queue\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1133\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m (\u001b[38;5;28;01mTrue\u001b[39;00m, data)\n\u001b[1;32m 1134\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 1135\u001b[0m \u001b[38;5;66;03m# At timeout and error, we manually check whether any worker has\u001b[39;00m\n\u001b[1;32m 1136\u001b[0m \u001b[38;5;66;03m# failed. Note that this is the only mechanism for Windows to detect\u001b[39;00m\n\u001b[1;32m 1137\u001b[0m \u001b[38;5;66;03m# worker failures.\u001b[39;00m\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/multiprocessing/queues.py:113\u001b[0m, in \u001b[0;36mQueue.get\u001b[0;34m(self, block, timeout)\u001b[0m\n\u001b[1;32m 111\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m block:\n\u001b[1;32m 112\u001b[0m timeout \u001b[38;5;241m=\u001b[39m deadline \u001b[38;5;241m-\u001b[39m time\u001b[38;5;241m.\u001b[39mmonotonic()\n\u001b[0;32m--> 113\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_poll\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m:\n\u001b[1;32m 114\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m Empty\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_poll():\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/multiprocessing/connection.py:257\u001b[0m, in \u001b[0;36m_ConnectionBase.poll\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 255\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_closed()\n\u001b[1;32m 256\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_readable()\n\u001b[0;32m--> 257\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_poll\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/multiprocessing/connection.py:424\u001b[0m, in \u001b[0;36mConnection._poll\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 423\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_poll\u001b[39m(\u001b[38;5;28mself\u001b[39m, timeout):\n\u001b[0;32m--> 424\u001b[0m r \u001b[38;5;241m=\u001b[39m \u001b[43mwait\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mbool\u001b[39m(r)\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/multiprocessing/connection.py:931\u001b[0m, in \u001b[0;36mwait\u001b[0;34m(object_list, timeout)\u001b[0m\n\u001b[1;32m 928\u001b[0m deadline \u001b[38;5;241m=\u001b[39m time\u001b[38;5;241m.\u001b[39mmonotonic() \u001b[38;5;241m+\u001b[39m timeout\n\u001b[1;32m 930\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[0;32m--> 931\u001b[0m ready \u001b[38;5;241m=\u001b[39m \u001b[43mselector\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mselect\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 932\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ready:\n\u001b[1;32m 933\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [key\u001b[38;5;241m.\u001b[39mfileobj \u001b[38;5;28;01mfor\u001b[39;00m (key, events) \u001b[38;5;129;01min\u001b[39;00m ready]\n",
"File \u001b[0;32m/opt/conda/envs/py39_pth2_3/lib/python3.9/selectors.py:416\u001b[0m, in \u001b[0;36m_PollLikeSelector.select\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 414\u001b[0m ready \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 416\u001b[0m fd_event_list \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_selector\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpoll\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 417\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mInterruptedError\u001b[39;00m:\n\u001b[1;32m 418\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ready\n",
"\u001b[0;31mKeyboardInterrupt\u001b[0m: "
]
}
],
"source": [
"# sleap_io v0.0.11\n",
"\n",
"viz_imgs, viz_cms = next(iter(val_data_loader))\n",
"print(viz_imgs.shape, viz_cms.shape)"
]
},
{
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"execution_count": null,
"id": "06570fde-1854-4549-84bd-962844690d79",
"metadata": {
"tags": []
},
"outputs": [],
"source": []
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