diff --git a/docs/_static/img/YOLOVisualizer_2.webm b/docs/_static/img/YOLOVisualizer_2.webm
new file mode 100644
index 000000000..b25651ef4
Binary files /dev/null and b/docs/_static/img/YOLOVisualizer_2.webm differ
diff --git a/docs/nb/yolo_ex_2.ipynb b/docs/nb/yolo_ex_2.ipynb
index db49571c9..f7ed53e41 100644
--- a/docs/nb/yolo_ex_2.ipynb
+++ b/docs/nb/yolo_ex_2.ipynb
@@ -335,7 +335,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 7,
"id": "71ff3b83-d631-45f4-b400-9cec5bcca469",
"metadata": {
"scrolled": true
@@ -1098,7 +1098,112 @@
"name": "stderr",
"output_type": "stream",
"text": [
- " 23/25 2.14G 0.8963 0.8309 1.226 16 640: 48%|████▊ | 58/122 [00:04<00:04, 14.08it/s]"
+ " 23/25 2.14G 0.8959 0.8062 1.218 14 640: 100%|██████████| 122/122 [00:08<00:00, 14.03it/s]\n",
+ " Class Images Instances Box(P R mAP50 mAP50-95): 100%|██████████| 9/9 [00:00<00:00, 10.68it/s]"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " all 278 278 0.845 0.863 0.891 0.699\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ " Epoch GPU_mem box_loss cls_loss dfl_loss Instances Size\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ " 24/25 2.06G 0.8613 0.7794 1.2 14 640: 100%|██████████| 122/122 [00:08<00:00, 13.87it/s]\n",
+ " Class Images Instances Box(P R mAP50 mAP50-95): 100%|██████████| 9/9 [00:00<00:00, 10.37it/s]"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " all 278 278 0.786 0.883 0.883 0.698\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ " Epoch GPU_mem box_loss cls_loss dfl_loss Instances Size\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ " 25/25 2.14G 0.8329 0.7644 1.189 14 640: 100%|██████████| 122/122 [00:08<00:00, 14.38it/s]\n",
+ " Class Images Instances Box(P R mAP50 mAP50-95): 100%|██████████| 9/9 [00:00<00:00, 9.79it/s]"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " all 278 278 0.834 0.885 0.894 0.711\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "25 epochs completed in 0.069 hours.\n",
+ "Optimizer stripped from /mnt/c/troubleshooting/yolo_mdl/train/weights/last.pt, 6.2MB\n",
+ "Optimizer stripped from /mnt/c/troubleshooting/yolo_mdl/train/weights/best.pt, 6.2MB\n",
+ "\n",
+ "Validating /mnt/c/troubleshooting/yolo_mdl/train/weights/best.pt...\n",
+ "Ultralytics 8.3.19 🚀 Python-3.10.15 torch-2.5.0+cu124 CUDA:0 (NVIDIA GeForce RTX 4070, 12282MiB)\n",
+ "Model summary (fused): 168 layers, 3,005,843 parameters, 0 gradients, 8.1 GFLOPs\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ " Class Images Instances Box(P R mAP50 mAP50-95): 100%|██████████| 9/9 [00:01<00:00, 7.17it/s]\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " all 278 278 0.834 0.885 0.894 0.71\n",
+ "Speed: 0.2ms preprocess, 0.9ms inference, 0.0ms loss, 0.6ms postprocess per image\n",
+ "Results saved to \u001b[1m/mnt/c/troubleshooting/yolo_mdl/train\u001b[0m\n"
]
}
],
@@ -1114,10 +1219,7064 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 8,
"id": "182f0071-2cd5-4c21-9087-b606aa909804",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "WARNING ⚠️ TensorRT requires GPU export, automatically assigning device=0\n",
+ "Ultralytics 8.3.19 🚀 Python-3.10.15 torch-2.5.0+cu124 CUDA:0 (NVIDIA GeForce RTX 4070, 12282MiB)\n",
+ "Model summary (fused): 168 layers, 3,005,843 parameters, 0 gradients, 8.1 GFLOPs\n",
+ "\n",
+ "\u001b[34m\u001b[1mPyTorch:\u001b[0m starting from '/mnt/c/troubleshooting/yolo_mdl/train/weights/best.pt' with input shape (1, 3, 640, 640) BCHW and output shape(s) (1, 5, 8400) (6.0 MB)\n",
+ "\n",
+ "\u001b[34m\u001b[1mONNX:\u001b[0m starting export with onnx 1.17.0 opset 19...\n",
+ "\u001b[34m\u001b[1mONNX:\u001b[0m slimming with onnxslim 0.1.35...\n",
+ "\u001b[34m\u001b[1mONNX:\u001b[0m export success ✅ 0.7s, saved as '/mnt/c/troubleshooting/yolo_mdl/train/weights/best.onnx' (11.7 MB)\n",
+ "\n",
+ "\u001b[34m\u001b[1mTensorRT:\u001b[0m starting export with TensorRT 10.5.0...\n",
+ "[11/16/2024-12:37:05] [TRT] [I] [MemUsageChange] Init CUDA: CPU +1, GPU +0, now: CPU 2100, GPU 1583 (MiB)\n",
+ "[11/16/2024-12:37:14] [TRT] [I] [MemUsageChange] Init builder kernel library: CPU +2238, GPU +426, now: CPU 4494, GPU 2009 (MiB)\n",
+ "[11/16/2024-12:37:14] [TRT] [I] ----------------------------------------------------------------\n",
+ "[11/16/2024-12:37:14] [TRT] [I] Input filename: /mnt/c/troubleshooting/yolo_mdl/train/weights/best.onnx\n",
+ "[11/16/2024-12:37:14] [TRT] [I] ONNX IR version: 0.0.10\n",
+ "[11/16/2024-12:37:14] [TRT] [I] Opset version: 19\n",
+ "[11/16/2024-12:37:14] [TRT] [I] Producer name: pytorch\n",
+ "[11/16/2024-12:37:14] [TRT] [I] Producer version: 2.5.0\n",
+ "[11/16/2024-12:37:14] [TRT] [I] Domain: \n",
+ "[11/16/2024-12:37:14] [TRT] [I] Model version: 0\n",
+ "[11/16/2024-12:37:14] [TRT] [I] Doc string: \n",
+ "[11/16/2024-12:37:14] [TRT] [I] ----------------------------------------------------------------\n",
+ "\u001b[34m\u001b[1mTensorRT:\u001b[0m input \"images\" with shape(1, 3, 640, 640) DataType.FLOAT\n",
+ "\u001b[34m\u001b[1mTensorRT:\u001b[0m output \"output0\" with shape(1, 5, 8400) DataType.FLOAT\n",
+ "\u001b[34m\u001b[1mTensorRT:\u001b[0m building FP32 engine as /mnt/c/troubleshooting/yolo_mdl/train/weights/best.engine\n",
+ "[11/16/2024-12:39:12] [TRT] [I] Local timing cache in use. Profiling results in this builder pass will not be stored.\n",
+ "[11/16/2024-12:40:09] [TRT] [I] Detected 1 inputs and 3 output network tensors.\n",
+ "[11/16/2024-12:40:10] [TRT] [I] Total Host Persistent Memory: 331408 bytes\n",
+ "[11/16/2024-12:40:10] [TRT] [I] Total Device Persistent Memory: 819200 bytes\n",
+ "[11/16/2024-12:40:10] [TRT] [I] Max Scratch Memory: 4608 bytes\n",
+ "[11/16/2024-12:40:10] [TRT] [I] [BlockAssignment] Started assigning block shifts. This will take 178 steps to complete.\n",
+ "[11/16/2024-12:40:10] [TRT] [I] [BlockAssignment] Algorithm ShiftNTopDown took 4.03146ms to assign 8 blocks to 178 nodes requiring 17204224 bytes.\n",
+ "[11/16/2024-12:40:10] [TRT] [I] Total Activation Memory: 17203200 bytes\n",
+ "[11/16/2024-12:40:10] [TRT] [I] Total Weights Memory: 14263360 bytes\n",
+ "[11/16/2024-12:40:10] [TRT] [I] Engine generation completed in 57.8062 seconds.\n",
+ "[11/16/2024-12:40:10] [TRT] [I] [MemUsageStats] Peak memory usage of TRT CPU/GPU memory allocators: CPU 1 MiB, GPU 133 MiB\n",
+ "[11/16/2024-12:40:10] [TRT] [I] [MemUsageStats] Peak memory usage during Engine building and serialization: CPU: 8904 MiB\n",
+ "\u001b[34m\u001b[1mTensorRT:\u001b[0m export success ✅ 186.3s, saved as '/mnt/c/troubleshooting/yolo_mdl/train/weights/best.engine' (17.1 MB)\n",
+ "\n",
+ "Export complete (186.4s)\n",
+ "Results saved to \u001b[1m/mnt/c/troubleshooting/yolo_mdl/train/weights\u001b[0m\n",
+ "Predict: yolo predict task=detect model=/mnt/c/troubleshooting/yolo_mdl/train/weights/best.engine imgsz=640 \n",
+ "Validate: yolo val task=detect model=/mnt/c/troubleshooting/yolo_mdl/train/weights/best.engine imgsz=640 data=/mnt/c/troubleshooting/yolo_data_split_animal/map.yaml \n",
+ "Visualize: https://netron.app\n",
+ "\n",
+ "video 1/1 (frame 1/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 2/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 3/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 4/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 5/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 6/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 7/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 8/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 9/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 10/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 11/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 12/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 13/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 14/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 2.7ms\n",
+ "video 1/1 (frame 15/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 2.7ms\n",
+ "video 1/1 (frame 16/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 2.7ms\n",
+ "video 1/1 (frame 17/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.7ms\n",
+ "video 1/1 (frame 18/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.7ms\n",
+ "video 1/1 (frame 19/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.7ms\n",
+ "video 1/1 (frame 20/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.7ms\n",
+ "video 1/1 (frame 21/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 22/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 23/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 24/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 25/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 26/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 27/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.7ms\n",
+ "video 1/1 (frame 28/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.7ms\n",
+ "video 1/1 (frame 29/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 30/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 31/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 32/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 33/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 34/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 35/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 36/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 37/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 38/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 39/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 40/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 41/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 42/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.6ms\n",
+ "video 1/1 (frame 43/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 44/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 45/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 46/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 47/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 48/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.6ms\n",
+ "video 1/1 (frame 49/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.5ms\n",
+ "video 1/1 (frame 50/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 51/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 52/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 53/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 54/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 3 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 55/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 56/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 57/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 58/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.5ms\n",
+ "video 1/1 (frame 59/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.5ms\n",
+ "video 1/1 (frame 60/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
+ "video 1/1 (frame 61/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.5ms\n",
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+ "video 1/1 (frame 1974/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1975/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1976/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1977/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1978/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1979/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1980/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1981/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1982/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1983/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1984/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1985/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1986/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1987/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1988/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1989/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1990/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1991/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1992/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1993/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1994/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1995/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1996/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1997/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1998/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 1999/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 2000/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
+ "video 1/1 (frame 2001/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.7ms\n",
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+ "video 1/1 (frame 6917/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6918/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6919/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6920/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6921/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6922/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6923/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6924/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6925/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6926/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6927/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6928/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6929/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6930/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6931/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6932/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6933/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6934/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6935/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6936/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6937/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6938/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6939/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6940/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 1.1ms\n",
+ "video 1/1 (frame 6941/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6942/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 1.1ms\n",
+ "video 1/1 (frame 6943/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 1.1ms\n",
+ "video 1/1 (frame 6944/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 1.1ms\n",
+ "video 1/1 (frame 6945/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6946/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6947/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6948/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6949/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6950/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6951/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6952/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6953/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6954/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6955/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6956/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6957/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6958/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6959/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6960/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6961/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6962/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6963/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6964/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6965/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6966/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6967/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6968/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6969/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6970/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6971/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6972/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6973/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6974/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6975/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6976/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6977/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6978/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6979/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6980/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6981/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6982/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6983/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 2 Animal_1s, 0.9ms\n",
+ "video 1/1 (frame 6984/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6985/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6986/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6987/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6988/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6989/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6990/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6991/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6992/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 0.9ms\n",
+ "video 1/1 (frame 6993/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "video 1/1 (frame 6994/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "video 1/1 (frame 6995/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "video 1/1 (frame 6996/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "video 1/1 (frame 6997/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "video 1/1 (frame 6998/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "video 1/1 (frame 6999/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "video 1/1 (frame 7000/7000) /mnt/c/troubleshooting/mitra/project_folder/videos/clipped/FRR_gq_Saline_0626.mp4: 576x640 1 Animal_1, 4.4ms\n",
+ "Speed: 1.1ms preprocess, 0.7ms inference, 0.7ms postprocess per image at shape (16, 3, 576, 640)\n"
+ ]
+ }
+ ],
"source": [
"#NEXT, WE USE THE TRAINED MODEL TO FIND THE ROIS IN A NEW VIDEO\n",
"INFERENCE_RESULTS = \"/mnt/c/troubleshooting/yolo_results\" #DIRECTORY WHERE TO STORE THE RESULTS IN CSV FORMAT\n",
@@ -1127,10 +8286,115 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 9,
"id": "a32acdbc-574c-4328-a7d3-ad5e5795c897",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Section 0/32 complete...\n",
+ "Section 1/32 complete...\n",
+ "Section 2/32 complete...\n",
+ "Section 3/32 complete...\n",
+ "Section 4/32 complete...\n",
+ "Section 5/32 complete...\n",
+ "Section 6/32 complete...\n",
+ "Section 7/32 complete...\n",
+ "Section 8/32 complete...\n",
+ "Section 9/32 complete...\n",
+ "Section 10/32 complete...\n",
+ "Section 11/32 complete...\n",
+ "Section 12/32 complete...\n",
+ "Section 13/32 complete...\n",
+ "Section 14/32 complete...\n",
+ "Section 15/32 complete...\n",
+ "Section 16/32 complete...\n",
+ "Section 17/32 complete...\n",
+ "Section 18/32 complete...\n",
+ "Section 19/32 complete...\n",
+ "Section 20/32 complete...\n",
+ "Section 21/32 complete...\n",
+ "Section 22/32 complete...\n",
+ "Section 23/32 complete...\n",
+ "Section 24/32 complete...\n",
+ "Section 25/32 complete...\n",
+ "Section 26/32 complete...\n",
+ "Section 27/32 complete...\n",
+ "Section 28/32 complete...\n",
+ "Section 29/32 complete...\n",
+ "Section 30/32 complete...\n",
+ "Section 31/32 complete...\n",
+ "Joining FRR_gq_Saline_0626 geometry video...\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "Trailing option(s) found in the command: may be ignored.\n",
+ "Input #0, concat, from '/mnt/c/troubleshooting/yolo_videos/FRR_gq_Saline_0626/temp/files.txt':\n",
+ " Duration: N/A, start: 0.000000, bitrate: 978 kb/s\n",
+ " Stream #0:0(und): Video: mpeg4 (Simple Profile) (mp4v / 0x7634706D), yuv420p, 628x538 [SAR 1:1 DAR 314:269], 978 kb/s, 30 fps, 30 tbr, 15360 tbn\n",
+ " Metadata:\n",
+ " handler_name : VideoHandler\n",
+ " vendor_id : [0][0][0][0]\n",
+ "Stream mapping:\n",
+ " Stream #0:0 -> #0:0 (mpeg4 (native) -> h264 (libx264))\n",
+ "Press [q] to stop, [?] for help\n",
+ "[libx264 @ 0x5627ab992240] using SAR=1/1\n",
+ "[libx264 @ 0x5627ab992240] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 BMI2 AVX2\n",
+ "[libx264 @ 0x5627ab992240] profile High, level 3.1, 4:2:0, 8-bit\n",
+ "[libx264 @ 0x5627ab992240] 264 - core 164 r3108 31e19f9 - H.264/MPEG-4 AVC codec - Copyleft 2003-2023 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=17 lookahead_threads=2 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00\n",
+ "Output #0, mp4, to '/mnt/c/troubleshooting/yolo_videos/FRR_gq_Saline_0626.mp4':\n",
+ " Metadata:\n",
+ " encoder : Lavf60.16.100\n",
+ " Stream #0:0(und): Video: h264 (avc1 / 0x31637661), yuv420p(progressive), 628x538 [SAR 1:1 DAR 314:269], q=2-31, 30 fps, 15360 tbn\n",
+ " Metadata:\n",
+ " handler_name : VideoHandler\n",
+ " vendor_id : [0][0][0][0]\n",
+ " encoder : Lavc60.31.102 libx264\n",
+ " Side data:\n",
+ " cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: N/A\n",
+ "frame= 6411 fps=912 q=29.0 size= 10496kB time=00:03:33.63 bitrate= 402.5kbits/s speed=30.4x \r"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "SIMBA COMPLETE: Video concatenated (elapsed time: 8.0335s) \tcomplete\n",
+ "SIMBA COMPLETE: Geometry video /mnt/c/troubleshooting/yolo_videos/FRR_gq_Saline_0626.mp4 complete! (elapsed time: 74.6498s) \tcomplete\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "[out#0/mp4 @ 0x5627ab984e00] video:11665kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.643653%\n",
+ "frame= 7000 fps=917 q=-1.0 Lsize= 11740kB time=00:03:53.23 bitrate= 412.3kbits/s speed=30.5x \n",
+ "[libx264 @ 0x5627ab992240] frame I:28 Avg QP:18.69 size: 11674\n",
+ "[libx264 @ 0x5627ab992240] frame P:2849 Avg QP:20.90 size: 2929\n",
+ "[libx264 @ 0x5627ab992240] frame B:4123 Avg QP:22.75 size: 794\n",
+ "[libx264 @ 0x5627ab992240] consecutive B-frames: 14.8% 11.5% 25.1% 48.6%\n",
+ "[libx264 @ 0x5627ab992240] mb I I16..4: 30.8% 60.2% 9.0%\n",
+ "[libx264 @ 0x5627ab992240] mb P I16..4: 5.3% 14.0% 0.2% P16..4: 40.6% 4.6% 2.2% 0.0% 0.0% skip:33.1%\n",
+ "[libx264 @ 0x5627ab992240] mb B I16..4: 0.5% 1.0% 0.0% B16..8: 32.8% 1.2% 0.0% direct: 0.6% skip:63.9% L0:56.6% L1:42.7% BI: 0.7%\n",
+ "[libx264 @ 0x5627ab992240] 8x8 transform intra:71.0% inter:93.1%\n",
+ "[libx264 @ 0x5627ab992240] coded y,uvDC,uvAC intra: 35.6% 43.0% 2.8% inter: 3.4% 8.1% 0.2%\n",
+ "[libx264 @ 0x5627ab992240] i16 v,h,dc,p: 40% 26% 19% 15%\n",
+ "[libx264 @ 0x5627ab992240] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 31% 22% 43% 2% 1% 0% 0% 1% 1%\n",
+ "[libx264 @ 0x5627ab992240] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 42% 25% 22% 2% 2% 2% 2% 2% 1%\n",
+ "[libx264 @ 0x5627ab992240] i8c dc,h,v,p: 46% 25% 27% 2%\n",
+ "[libx264 @ 0x5627ab992240] Weighted P-Frames: Y:0.0% UV:0.0%\n",
+ "[libx264 @ 0x5627ab992240] ref P L0: 69.4% 3.9% 18.6% 8.1% 0.0%\n",
+ "[libx264 @ 0x5627ab992240] ref B L0: 79.4% 17.4% 3.2%\n",
+ "[libx264 @ 0x5627ab992240] ref B L1: 94.9% 5.1%\n",
+ "[libx264 @ 0x5627ab992240] kb/s:409.51\n"
+ ]
+ }
+ ],
"source": [
"#FINALLY, WE VISUALIZE THE RESULTS TO CHECK THAT THE PREDICTIONS ARE ACCURATE\n",
"DATA_PATH = r\"/mnt/c/troubleshooting/yolo_results/FRR_gq_Saline_0626.csv\" #PATH TO ONE OF THE CSV FILES CREATED IN THE PRIOR STEP.\n",
@@ -1143,14 +8407,29 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 11,
"id": "14f805bd-8e07-4801-8b52-6f046a853d78",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ " \n"
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
"#EXPECTED RESULTS\n",
- "\n",
- "video_url = 'https://raw.githubusercontent.com/sgoldenlab/simba/master/docs/_static/img/YOLOVisualizer.webm'\n",
+ "from ipywidgets import Video\n",
+ "from IPython.display import HTML\n",
+ "video_url = 'https://raw.githubusercontent.com/sgoldenlab/simba/master/docs/_static/img/YOLOVisualizer_2.webm'\n",
"HTML(f''' \n",
"''')"
]
diff --git a/docs/notebooks.rst b/docs/notebooks.rst
index 3c3f57267..4bac90ca4 100644
--- a/docs/notebooks.rst
+++ b/docs/notebooks.rst
@@ -48,6 +48,7 @@ Some example operations pertaining to working with animals and environments as g
nb/geometry_example_6
nb/geometry_example_7
nb/yolo_ex_1
+ nb/yolo_ex_2
Miscellaneous
-------------------
diff --git a/simba/data_processors/gibbs_sampler.py b/simba/data_processors/gibbs_sampler.py
index 4ffe1ccb1..f04e79b62 100644
--- a/simba/data_processors/gibbs_sampler.py
+++ b/simba/data_processors/gibbs_sampler.py
@@ -1,194 +1,130 @@
-__author__ = "Simon Nilsson"
-__email__ = "sronilsson@gmail.com"
-
import os
-import random
-from typing import Union
-
+from typing import Union, Tuple
import numpy as np
import pandas as pd
-from simba.mixins.config_reader import ConfigReader
-from simba.utils.printing import stdout_success
-
-
-class GibbsSampler(ConfigReader):
- """
- Gibbs sampling for finding "motifs" in categorical sequences.
-
- :parameter str config_path: path to SimBA project config file in Configparser format
- :parameter pd.DataFrame data: Dataframe where each row represents videos and each column represents behavior sequence.
- :parameter float pseudo_number: Small error value for fuzzy search. Default: 0.001.
- :parameter int sequence_length: The length of the motif sequence searched for.
- :parameter int iterations: Number of iterations per epoch. Default: 1000.
- :parameter int epochs: Number of epochs of iterations. Default: 5.
- :parameter int plateau_val: Terminate epoch when error rate has remained unchanged for ``plateau_val`` count of interations.
-
- :example:
- >>> df = pd.read_csv('/tests/data/gibbs_sample_data/gibbs_sample_ver_7.csv', index_col=0)
- >>> gibbs_sampler = GibbsSampler(data=df)
- >>> gibbs_sampler.run()
-
-
- :References:
- .. [1] Lawrence et.al, Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment,
- Science, vol. 262, pp. 208-214, 1993.
- .. [2] `Great YouTube course by Xiaole Shirley Liu `_.
- """
-
- def __init__(
- self,
- config_path: Union[str, os.PathLike],
- data: pd.DataFrame,
- pseudo_number: int = 0.001,
- sequence_length: int = 4,
- iterations: int = 1500,
- epochs: int = 2,
- stop_val: float = 0.001,
- plateau_val: int = 50,
- ):
- ConfigReader.__init__(self, config_path=config_path, read_video_info=False)
- self.unique_vals = sorted(list(pd.unique(data.values.ravel("K"))))
- self.target_probability = 1 * sequence_length + (
- pseudo_number * (sequence_length + 1)
- )
-
- self.holdout_cols = ["H_{}".format(i) for i in range(0, sequence_length)]
- self.non_holdout_cols = ["C_{}".format(i) for i in range(sequence_length)]
- self.output_cols = ["Behavior_{}".format(i + 1) for i in range(sequence_length)]
-
- self.data, self.pseudo_num, self.sequence_len = (
- data,
- pseudo_number,
- sequence_length,
- )
- self.iterations, self.stop_val = [iterations] * epochs, stop_val
- self.plateau_val = plateau_val
- self.summary_df = pd.DataFrame(columns=self.output_cols)
- self.data.columns = ["F_{}".format(x) for x in range(len(self.data.columns))]
- self.save_path = os.path.join(
- self.logs_path, f"gibbs_sampling_results_{self.datetime}.csv"
- )
-
- def __get_start_positions(self):
- start_positions = []
- for val in range(len(self.data)):
- start_positions.append(
- random.randint(0, len(self.data.columns) - self.sequence_len)
- )
- return start_positions
-
- def __make_probability_table(self, df: pd.DataFrame, unique_vals: np.ndarray):
- prob_df = pd.DataFrame(columns=unique_vals)
- for column in df:
- occurance_lst = []
- for value in unique_vals:
- occurance_lst.append(
- (len(df[df[column] == value]) + self.pseudo_num) / len(df[column])
- + self.pseudo_num
- )
- prob_df.loc[len(prob_df)] = occurance_lst
+from simba.utils.printing import SimbaTimer, stdout_success
+from simba.utils.checks import check_valid_array, check_float, check_int, check_if_dir_exists
+
+class GibbSampler():
+ def __init__(self,
+ data: np.ndarray,
+ save_path: Union[str, os.PathLike],
+ sequence_length: int = 4,
+ iterations: int = 1500,
+ epochs: int = 2,
+ stop_val: float = 0.001,
+ pseudo_number: float = 10e-6,
+ plateau_val: int = 50):
+
+ """
+ Gibbs sampling for finding "motifs" in categorical sequences.
+
+ :param np.ndarray data: 2-dimensional array where observations are organised by row and each sequential sample in the observation is organized by column.
+ :param Union[str, os.PathLike] save_path: The path location where to save the CSV results.
+ :param int sequence_length: The length of the motif sequence searched for.
+ :param int iterations: Number of iterations per epoch. Default: 1500.
+ :param int epochs: Number of epochs of iterations. Default: 4.
+ :param float stop_val: Terminate once the error value reaches below this threshold. Default 0.001.
+ :param int plateau_val: Terminate epoch when error rate has remained unchanged for ``plateau_val`` count of iterations. Default 50.
+ :param float pseudo_number: Small error value for fuzzy search and avoid division by zero errors. Default: 10e-6.
+
+ :example:
+ >>> data = pd.read_csv(r"/Users/simon/Desktop/envs/simba/simba/tests/data/sample_data/gibbs_sample_cardinal.csv", index_col=0).values
+ >>> sampler = GibbSampler(data=data, save_path=r'/Users/simon/Desktop/gibbs.csv', epochs=5, iterations=600)
+ >>> sampler.run()
+
+ :references:
+ .. [1] Lawrence et.al, Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment, Science, vol. 262, pp. 208-214, 1993.
+ .. [2] Great YouTube tutorial / explanation by Xiaole Shirley Liu - `https://www.youtube.com/watch?v=NRjhfyXWHuQ `_.
+ .. [3] Weinreb et al. Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics, Nature Methods, 21, 1329–1339 (2024).
+ """
+
+
+ check_valid_array(data=data, source=f'{self.__class__.__name__} data', accepted_ndims=(2,))
+ check_float(name=f'{self.__class__.__name__} stop_val', value=stop_val, min_value=0.0)
+ check_float(name=f'{self.__class__.__name__} pseudo_number', value=pseudo_number, min_value=10e-16)
+ check_int(name=f'{self.__class__.__name__} epochs', value=epochs, min_value=1)
+ check_int(name=f'{self.__class__.__name__} iterations', value=iterations, min_value=1)
+ check_int(name=f'{self.__class__.__name__} sequence_length', value=sequence_length, min_value=2)
+ check_if_dir_exists(in_dir=os.path.dirname(save_path), source=f'{self.__class__.__name__} save_path')
+ self.unique_vals = np.sort(np.unique(data.flatten()))
+ self.target_probability = 1 * sequence_length + (pseudo_number * (sequence_length + 1))
+ self.holdout_fields = [f"H_{i}" for i in range(sequence_length)]
+ self.non_holdout_cols = [f"C_{i}" for i in range(sequence_length)]
+ self.out_cols = [f"Behavior_{i+1}" for i in range(sequence_length)]
+ self.summary_df = pd.DataFrame(columns=self.out_cols)
+ self.data, self.pseudo_num, self.sequence_len, self.plateau_val = (data, pseudo_number, sequence_length, plateau_val)
+ self.iterations, self.stop_val, self.epochs = [iterations] * epochs, stop_val, epochs
+ self.save_path = save_path
+
+ def __make_probability_table(self, data: np.ndarray) -> pd.DataFrame:
+ prob_df = pd.DataFrame(columns=self.unique_vals)
+ for field_idx in range(data.shape[1]):
+ idx_data = data[:, field_idx].flatten()
+ for unique_val in self.unique_vals:
+ val_idx = np.argwhere(idx_data == unique_val).flatten()
+ pct = (val_idx.shape[0] + self.pseudo_num) / (idx_data.shape[0] + self.pseudo_num)
+ prob_df.loc[field_idx, unique_val] = pct
return prob_df
- def __iterate_through_possible_seq_in_hold_out(
- self,
- hoObs: pd.DataFrame,
- bgDf: pd.DataFrame,
- probDf: pd.DataFrame,
- start_hold_no: int,
- ):
- df_holdout_seqs = pd.DataFrame(columns=self.holdout_cols + ["Prob_weight"])
- for startv in range(0, len(hoObs.columns) - self.sequence_len + 1):
- cols = [
- "F_{}".format(ind) for ind in range(startv, startv + self.sequence_len)
- ]
- seq = hoObs.loc[:, cols]
- ptot = 1
- for ind in range(self.sequence_len):
- prob_table_cols = seq.loc[start_hold_no][ind]
- ptot *= probDf.loc[ind][prob_table_cols] / bgDf.loc[prob_table_cols]
- seq["Prob_weight"] = ptot
- seq.columns = self.holdout_cols + ["Prob_weight"]
- df_holdout_seqs = df_holdout_seqs.append(seq, ignore_index=True)
- return df_holdout_seqs
-
- def __sum_results(self, full_sequence_set, summary_df):
- for i in range(self.sequence_len):
- full_sequence_set = full_sequence_set.rename(
- columns={f"C_{i}": self.output_cols[i]}
- )
-
- summary_df = pd.concat([summary_df, full_sequence_set], axis=0).reset_index(
- drop=True
- )
- output = (
- summary_df.groupby(summary_df.columns.tolist())
- .size()
- .reset_index()
- .rename(columns={0: "records"})
- .sort_values(by=["records"], ascending=False)
- )
+ def __iterate_through_possible_seq_in_hold_out(self,
+ holdout_obs: np.ndarray,
+ bg_dict: dict,
+ probability_df: pd.DataFrame) -> pd.DataFrame:
+
+ out_df = pd.DataFrame(columns=self.holdout_fields + ["weight"])
+ for r in range(self.sequence_len, holdout_obs.shape[0]+1):
+ sequence = holdout_obs[r - self.sequence_len:r]
+ prob_tot = 1
+ for i in range(self.sequence_len):
+ val = sequence[i]
+ prob_tot *= probability_df.loc[i][val] / bg_dict[val]
+ out_df.loc[len(out_df)] = np.append(sequence, prob_tot)
+ return out_df
+
+ def __sum_results(self, full_sequence_set, summary_df) -> Tuple[pd.DataFrame, pd.DataFrame]:
+ full_sequence_set = pd.DataFrame(full_sequence_set, columns=self.out_cols)
+ summary_df = pd.concat([summary_df, full_sequence_set], axis=0).reset_index(drop=True)
+ output = (summary_df.groupby(summary_df.columns.tolist()).size().reset_index().rename(columns={0: "records"}).sort_values(by=["records"], ascending=False))
output["percent"] = output["records"] / output["records"].sum()
-
return summary_df, output.reset_index(drop=True)
def run(self):
- # calculate background constants
- bg_df = self.data.stack().value_counts()
- bg_df = bg_df / bg_df.sum()
- bg_df = bg_df.sort_index()
- full_sequence_set, output = None, None
- prior_error, stable_error_cnt = np.inf, 0
-
- for iteration_counter, iterations in enumerate(self.iterations):
- holdout_idx = np.random.randint(0, len(self.data) - 2)
- start_positions = self.__get_start_positions()
+ timer = SimbaTimer(start=True)
+ unique_elements, counts = np.unique(self.data, return_counts=True)
+ counts_dict = dict(zip(unique_elements, counts))
+ bg_dict = {k: (v / np.sum(counts)) for k, v in counts_dict.items()}
+ prior_error, stable_error_cnt, full_sequence, output = np.inf, 0, None, None
+
+ for epoch_cnt, iterations in enumerate(self.iterations):
+ holdout_idx = np.random.randint(0, self.data.shape[0]-1)
for iteration in range(0, iterations):
- hold_out_observation_df = self.data.iloc[[holdout_idx]]
+ hold_out_obs = self.data[holdout_idx]
if iteration == 0:
- df_it = self.data.drop(hold_out_observation_df.index)
- idx_lst, seq_lst = [], []
- for index, row in df_it.iterrows():
- seq_lst.append(
- list(
- row[
- start_positions[index] : start_positions[index]
- + self.sequence_len
- ]
- )
- )
- idx_lst.append(index)
- non_holdout_df = pd.DataFrame(
- seq_lst, columns=self.non_holdout_cols, index=idx_lst
- )
+ start_pos = np.random.randint(low=0, high=self.data.shape[1] - self.sequence_len, size=(self.data.shape[0]))
+ end_pos = np.array([x + self.sequence_len for x in start_pos])
+ slices = np.array([[x, y] for x, y in zip(start_pos, end_pos)])
+ epoch_sample = np.delete(self.data, [holdout_idx], axis=0)
+ sequences = np.full(shape=(epoch_sample.shape[0], self.sequence_len), fill_value='-1.0')
+ for idx in range(epoch_sample.shape[0]):
+ i = slices[idx]
+ sequences[idx] = epoch_sample[idx][i[0]: i[1]]
else:
- non_holdout_df = full_sequence_set.loc[
- full_sequence_set.index != holdout_idx
- ]
-
- probability_df = self.__make_probability_table(
- non_holdout_df, self.unique_vals
- )
- df_holdout_seqs = self.__iterate_through_possible_seq_in_hold_out(
- hold_out_observation_df, bg_df, probability_df, holdout_idx
- )
- new_seq = df_holdout_seqs.sample(1, weights="Prob_weight")
- new_seq = new_seq[self.holdout_cols]
- new_seq.columns = self.non_holdout_cols
- new_seq.index = [holdout_idx]
- full_sequence_set = pd.concat([new_seq, non_holdout_df])
- error = self.target_probability - probability_df.max(axis=1).sum()
- # self.summary_df, output = self.__sum_results(full_sequence_set, self.summary_df, iteration_counter)
- print(
- f"Current error: {error}, iteration: {iteration}, epoch: {iteration_counter}"
- )
+ sequences = np.delete(full_sequence, [holdout_idx], axis=0)
+ probability_df = self.__make_probability_table(sequences)
+ df_holdout_seqs = self.__iterate_through_possible_seq_in_hold_out(hold_out_obs, bg_dict, probability_df)
+ new_sequence = df_holdout_seqs.sample(1, weights="weight")[self.holdout_fields].values[0]
+ full_sequence = np.insert(sequences, 0, new_sequence, axis=0)
+ error = round(self.target_probability - probability_df.max(axis=1).sum(), 4)
+ print(f"Current error: {error}, iteration: {iteration+1}/{iterations}, epoch: {epoch_cnt+1}/{self.epochs}")
if error <= self.stop_val:
- print(f"Convergence reached in {iteration} iterations")
+ print(f"Convergence reached. Error: {error}, Stop value: {self.stop_val}")
break
if error == prior_error:
stable_error_cnt += 1
if stable_error_cnt >= self.plateau_val - 1:
- print(f"Platea reached {self.plateau_val}")
+ print(f"Plateau reached. Stable error count: {stable_error_cnt}. Plateau value: {self.plateau_val}")
break
else:
stable_error_cnt = 0
@@ -197,18 +133,18 @@ def run(self):
holdout_idx += 1
else:
holdout_idx = 0
- self.summary_df, output = self.__sum_results(
- full_sequence_set, self.summary_df
- )
+ self.summary_df, output = self.__sum_results(full_sequence, self.summary_df)
output.to_csv(self.save_path)
- self.timer.stop_timer()
- stdout_success(
- msg=f"Gibbs sampling results saved @{self.save_path}",
- elapsed_time=self.timer.elapsed_time_str,
- )
+ timer.stop_timer()
+ stdout_success(msg=f"Gibbs sampling results saved @{self.save_path}", elapsed_time=timer.elapsed_time_str)
+
+
+# data = pd.read_csv(r"C:\projects\simba\simba\tests\data\sample_data\gibbs_sample_cardinal.csv", index_col=0).values
+# sampler = GibbSampler(data=data, save_path=r'C:\Users\sroni\OneDrive\Desktop\gibbs.csv', iterations=5)
+# sampler.run()
-# df = pd.read_csv('/Users/simon/Desktop/envs/simba_dev/tests/data/gibbs_sample_data/gibbs_sample_7.csv', index_col=0)
-# test = GibbsSampler(config_path='/Users/simon/Desktop/envs/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini', data=df)
-# test.run()
+# data = pd.read_csv(r"/Users/simon/Desktop/envs/simba/simba/tests/data/sample_data/gibbs_sample_cardinal.csv", index_col=0).values
+# sampler = GibbSampler(data=data, save_path=r'/Users/simon/Desktop/gibbs.csv', epochs=5, iterations=600)
+# sampler.run()
\ No newline at end of file
diff --git a/simba/mixins/circular_statistics.py b/simba/mixins/circular_statistics.py
index b275e56be..0d19df532 100644
--- a/simba/mixins/circular_statistics.py
+++ b/simba/mixins/circular_statistics.py
@@ -4,6 +4,10 @@
import numpy as np
from numba import float32, float64, int64, jit, njit, prange, typed, types
+from simba.utils.checks import check_valid_array, check_float
+from simba.utils.enums import Formats
+from simba.utils.errors import InvalidInputError
+from simba.utils.data import get_mode
class CircularStatisticsMixin(object):
@@ -1202,9 +1206,10 @@ def rotational_direction(data: np.ndarray, stride: int = 1) -> np.ndarray:
:align: center
The result array contains values:
- - `0` where there is no change between points.
- - `1` where the angle has increased in the positive direction.
- - `2` where the angle has decreased in the negative direction.
+ - `-1`: Indicates no rotation is possible for the first frame. This serves as a placeholder since there is no prior frame to compare to.
+ - `0`: Represents no change in the angular value between consecutive frames
+ - `1`: Indicates an increase in the angular value (rotation in the positive direction, counterclockwise)
+ - `2`: Indicates a decrease in the angular value (rotation in the negative direction, clockwise)
:param np.ndarray data: 1D array of size len(frames) representing degrees.
:return: An array of directional indicators.
@@ -1330,6 +1335,84 @@ def fit_circle(data: np.ndarray, max_iterations: Optional[int] = 400) -> np.ndar
return results
+ @staticmethod
+ def preferred_turning_direction(x: np.ndarray) -> int:
+ """
+ Determines the preferred turning direction from a 1D array of circular directional data.
+
+ .. note::
+ The input ``x`` can be created using any of the following methods:
+ - :func:`simba.mixins.circular_statistics.CircularStatisticsMixin.direction_two_bps`
+ - :func:`simba.data_processors.cuda.circular_statistics.direction_from_two_bps`
+ - :func:`simba.data_processors.cuda.circular_statistics.direction_from_three_bps`
+ - :func:`simba.mixins.circular_statistics.CircularStatisticsMixin.direction_three_bps`
+
+ .. seealso::
+ :func:`simba.mixins.circular_statistics.CircularStatisticsMixin.rotational_direction`, :func:`~simba.data_processors.cuda.circular_statistics.rotational_direction`,
+ :func:`simba.mixins.circular_statistics.CircularStatisticsMixin.sliding_preferred_turning_direction`
+
+ :param np.ndarray x: 1D array of circular directional data (values between 0 and 360, inclusive). The array represents angular directions measured in degrees.
+ :return:
+ The most frequent turning direction from the input data:
+ - `0`: No change in the angular value between consecutive frames.
+ - `1`: An increase in the angular value (rotation in the positive direction, counterclockwise).
+ - `2`: A decrease in the angular value (rotation in the negative direction, clockwise).
+ :rtype: int
+
+ :example:
+ >>> x = np.random.randint(0, 361, (200,))
+ >>> CircularStatisticsMixin.preferred_turning_direction(x=x)
+ """
+
+ check_valid_array(data=x, source=CircularStatisticsMixin.preferred_turning_direction.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ if np.max(x) > 360 or np.min(x) < 0:
+ raise InvalidInputError(msg='x has to be values between 0 and 360 inclusive', source=CircularStatisticsMixin.preferred_turning_direction.__name__)
+ rotational_direction = CircularStatisticsMixin.rotational_direction(data=x.astype(np.float32))
+ return get_mode(x=rotational_direction)
+
+ @staticmethod
+ def sliding_preferred_turning_direction(x: np.ndarray,
+ time_window: float,
+ sample_rate: float) -> np.ndarray:
+ """
+ Computes the sliding preferred turning direction over a given time window from a 1D array of circular directional data.
+
+ Calculates the most frequent turning direction (mode) within a sliding window of a specified duration.
+
+ .. seealso::
+ :func:`simba.mixins.circular_statistics.CircularStatisticsMixin.rotational_direction`, :func:`~simba.data_processors.cuda.circular_statistics.rotational_direction`,
+ :func:`simba.mixins.circular_statistics.CircularStatisticsMixin.preferred_turning_direction`
+
+
+ :param np.ndarray x: A 1D array of circular directional data (values between 0 and 360, inclusive). Each value represents an angular direction in degrees.
+ :param float time_window: The duration of the sliding window in seconds.
+ :param float sample_rate: The sampling rate of the data in Hz (samples per second) or FPS (frames per seconds)
+ :return:
+ A 1D array of integers indicating the preferred turning direction for each window:
+ - `0`: No change in angular values within the window.
+ - `1`: An increase in angular values (counterclockwise rotation).
+ - `2`: A decrease in angular values (clockwise rotation).
+ For indices before the first full window, the value is `-1`.
+ :rtype: np.ndarray
+
+ :example:
+ >>> x = np.random.randint(0, 361, (213,))
+ >>> CircularStatisticsMixin.sliding_preferred_turning_direction(x=x, time_window=1, sample_rate=10)
+ """
+ check_valid_array(data=x, source=CircularStatisticsMixin.sliding_preferred_turning_direction.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ if np.max(x) > 360 or np.min(x) < 0:
+ raise InvalidInputError(msg='x has to be values between 0 and 360 inclusive', source=CircularStatisticsMixin.sliding_preferred_turning_direction.__name__)
+ check_float(name=f'{CircularStatisticsMixin.sliding_preferred_turning_direction.__name__} time_window', value=time_window)
+ check_float(name=f'{CircularStatisticsMixin.sliding_preferred_turning_direction.__name__} sample_rate', value=sample_rate)
+ rotational_directions = CircularStatisticsMixin.rotational_direction(data=x.astype(np.float32))
+ window_size = np.int64(np.max((1.0, (time_window * sample_rate))))
+ results = np.full(shape=(x.shape[0]), fill_value=-1, dtype=np.int32)
+ for r in range(window_size, x.shape[0] + 1):
+ l = r - window_size
+ sample = rotational_directions[l:r]
+ results[r - 1] = get_mode(x=sample)
+ return results.astype(np.int32)
+
# data = np.array([260, 280, 300, 340, 360, 0, 10, 350, 0, 15]).astype(np.float32)
diff --git a/simba/mixins/timeseries_features_mixin.py b/simba/mixins/timeseries_features_mixin.py
index caf409427..71f2f7af6 100644
--- a/simba/mixins/timeseries_features_mixin.py
+++ b/simba/mixins/timeseries_features_mixin.py
@@ -2409,4 +2409,22 @@ def radial_dispersion_index(x: np.ndarray, reference_point: np.ndarray) -> float
radial_distances = np.linalg.norm(x - reference_point, axis=1)
return np.std(radial_distances) / np.mean(radial_distances)
+ @staticmethod
+ def avg_kinetic_energy(x: np.ndarray, mass: float, sample_rate: float) -> float:
+ """
+ Calculate the average kinetic energy of an object based on its velocity.
+
+ :param np.ndarray x: A 2D NumPy array of shape (n, 2), where each row contains the x and y position coordinates of the object at each time step.
+ :param float mass: The mass of the object.
+ :param float sample_rate: The sampling rate (Hz), i.e., the number of data points per second.
+ :return: The average kinetic energy of the object.
+ :rtype: float: The mean kinetic energy calculated from the velocity data.
+ """
+ delta_t = np.round(1 / sample_rate, 2)
+ vx, vy = np.gradient(x[:, 0], delta_t), np.gradient(x[:, 1], delta_t)
+ speed = np.sqrt(vx ** 2 + vy ** 2)
+ kinetic_energy = 0.5 * mass * speed ** 2
+
+ return np.mean(kinetic_energy).astype(np.float32)
+
diff --git a/simba/model/regression/__init__.py b/simba/model/regression/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/simba/model/regression/metrics.py b/simba/model/regression/metrics.py
new file mode 100644
index 000000000..d54b02907
--- /dev/null
+++ b/simba/model/regression/metrics.py
@@ -0,0 +1,139 @@
+from typing import Optional
+import numpy as np
+from simba.utils.checks import check_valid_array, check_float
+from simba.utils.enums import Formats
+
+def mean_absolute_percentage_error(y_true: np.ndarray,
+ y_pred: np.ndarray,
+ epsilon=1e-10,
+ weights: Optional[np.ndarray] = None) -> float:
+ """
+ Compute the Mean Absolute Percentage Error (MAPE)
+
+ :param np.ndarray y_true: The array containing the true values (dependent variable) of the dataset. Should be a 1D numeric array of shape (n,).
+ :param np.ndarray y_pred: The array containing the predicted values for the dataset. Should be a 1D numeric array of shape (n,) and of the same length as `y_true`.
+ :param float epsilon: A small pseudovalue to replace zeros in `y_true` to avoid division by zero errors.
+ :param Optional[np.ndarray] weights: An optional 1D array of weights to apply to each error. If provided, the weighted mean absolute percentage error is computed.
+ :return: The Mean Absolute Percentage Error (MAPE) as a float, in percentage format. A lower value indicates better prediction accuracy.
+ :rtype: float
+
+ :example:
+ >>> x, y = np.random.random(size=(100000,)), np.random.random(size=(100000,))
+ >>> mean_absolute_percentage_error(y_true=x, y_pred=y)
+ """
+
+ check_valid_array(data=y_true, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_array(data=y_pred, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0],accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_float(name=mean_absolute_percentage_error.__name__, value=epsilon)
+ y_true = np.where(y_true == 0, epsilon, y_true)
+ se = np.abs((y_true - y_pred) / y_true)
+ if weights is not None:
+ check_valid_array(data=weights, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ se = se * weights
+ return (np.sum(se) / np.sum(weights)) * 100
+ else:
+ return np.mean(se * 100)
+
+
+def mean_squared_error(y_true: np.ndarray,
+ y_pred: np.ndarray,
+ weights: Optional[np.ndarray] = None) -> float:
+
+ """
+ Compute the Mean Squared Error (MSE) between the true and predicted values.
+
+ :param np.ndarray y_true: The array containing the true values (dependent variable) of the dataset. Should be a 1D numeric array of shape (n,).
+ :param np.ndarray y_pred: The array containing the predicted values for the dataset. Should be a 1D numeric array of shape (n,) and of the same length as `y_true`.
+ :param Optional[np.ndarray] weights: An optional 1D array of weights to apply to each squared error. If provided, the weighted mean squared error is computed.
+ :return: The Mean Squared Error (MSE) as a float. A lower value indicates better model accuracy.
+ :rtype: float
+ """
+
+ check_valid_array(data=y_true, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_array(data=y_pred, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0],accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ se = (y_true - y_pred) ** 2
+ if weights is not None:
+ check_valid_array(data=weights, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ se = se * weights
+ return np.sum(se) / np.sum(weights)
+ else:
+ return np.mean(se)
+
+def mean_absolute_error(y_true: np.ndarray,
+ y_pred: np.ndarray,
+ weights: Optional[np.ndarray] = None) -> float:
+ """
+ Compute the Mean Absolute Error (MAE) between the true and predicted values.
+
+ :param np.ndarray y_true: A 1D array of true values (ground truth).
+ :param np.ndarray y_pred: A 1D array of predicted values.
+ :param np.ndarray weights: An optional 1D array of weights for each observation. If provided, the weighted MAE is computed.
+ :return: The Mean Absolute Error (MAE) as a float. A lower value indicates a better fit.
+ :rtype: float
+ """
+
+ check_valid_array(data=y_true, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_array(data=y_pred, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ absolute_error = np.abs(y_true - y_pred)
+ if weights is not None:
+ check_valid_array(data=weights, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ absolute_error = absolute_error * weights
+ return np.sum(absolute_error) / np.sum(weights)
+ else:
+ return np.mean(absolute_error)
+
+
+def r2_score(y_true: np.ndarray, y_pred: np.ndarray, weights: Optional[np.ndarray] = None) -> float:
+ """
+ Compute the R^2 (coefficient of determination) score.
+
+ :param np.ndarray y_true: 1D array of true values (dependent variable).
+ :param np.ndarray y_pred: 1D array of predicted values, same length as `y_true`.
+ :param np.ndarray weights: Optional 1D array of weights for each observation.
+ :return: The R^2 score as a float. A value closer to 1 indicates better fit.
+ :rtype: float
+
+ """
+
+ check_valid_array(data=y_true, source=r2_score.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_array(data=y_pred, source=r2_score.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+
+ if weights is not None:
+ check_valid_array(data=weights, source=r2_score.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0])
+
+ y_mean = np.average(y_true, weights=weights) if weights is not None else np.mean(y_true)
+ residuals, total = (y_true - y_pred) ** 2, (y_true - y_mean) ** 2
+
+ if weights is not None:
+ ss_residual = np.sum(residuals * weights)
+ ss_total = np.sum(total * weights)
+ else:
+ ss_residual = np.sum(residuals)
+ ss_total = np.sum(total)
+
+ return 1 - (ss_residual / ss_total)
+
+
+def root_mean_squared_error(y_true: np.ndarray,
+ y_pred: np.ndarray,
+ weights: Optional[np.ndarray] = None) -> float:
+
+ """
+ Compute the Root Mean Squared Error (RMSE) between the true and predicted values.
+
+ :param np.ndarray y_true: The array containing the true values (dependent variable) of the dataset. Should be a 1D numeric array of shape (n,).
+ :param np.ndarray y_pred: The array containing the predicted values for the dataset. Should be a 1D numeric array of shape (n,) and of the same length as `y_true`.
+ :param Optional[np.ndarray] weights: An optional 1D array of weights to apply to each squared error. If provided, the weighted mean squared error is computed.
+ :return: The Root Mean Squared Error (MSE) as a float. A lower value indicates better model accuracy.
+ :rtype: float
+ """
+
+ check_valid_array(data=y_true, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_array(data=y_pred, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0],accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ se = (y_true - y_pred) ** 2
+ if weights is not None:
+ check_valid_array(data=weights, source=mean_absolute_percentage_error.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ weighted_mse = np.sum(se * weights) / np.sum(weights)
+ return np.sqrt(weighted_mse)
+ else:
+ return np.sqrt(np.mean(se))
\ No newline at end of file
diff --git a/simba/model/regression/model.py b/simba/model/regression/model.py
new file mode 100644
index 000000000..08ea664cf
--- /dev/null
+++ b/simba/model/regression/model.py
@@ -0,0 +1,155 @@
+from typing import Optional, Dict, List
+import numpy as np
+import pandas as pd
+import xgboost as xgb
+from sklearn.model_selection import StratifiedKFold
+from simba.utils.checks import check_valid_array, check_int, check_valid_lst, check_str, check_float, check_instance, check_valid_dataframe
+from simba.utils.enums import Formats
+from simba.utils.errors import DataHeaderError
+from simba.model.regression.metrics import (mean_absolute_percentage_error,
+ mean_squared_error,
+ mean_absolute_error,
+ r2_score,
+ root_mean_squared_error)
+
+def fit_xgb(x: pd.DataFrame,
+ y: np.ndarray,
+ objective: Optional[str] = 'reg:squarederror',
+ n_estimators: Optional[int] = 100,
+ max_depth: Optional[int] = 6,
+ verbosity: Optional[int] = 1,
+ learning_rate: Optional[float] = 0.3,
+ tree_method: Optional[str] = 'auto'):
+ """
+ :example:
+ >>> x = pd.DataFrame(np.random.randint(0, 500, (100, 20)))
+ >>> y = np.random.randint(1, 6, (100,))
+ >>> mdl = fit_xgb(x=x, y=y)
+ """
+ OBJECTIVES = ('reg:squarederror', 'reg:squaredlogerror', 'reg:logistic', 'reg:pseudohubererror')
+ TREE_METHODS = ('auto', 'exact', 'approx', 'hist', 'gpu_hist')
+
+ check_valid_dataframe(df=x, source=f'{fit_xgb.__name__} x', valid_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_array(data=y, source=f'{fit_xgb.__name__} y', accepted_ndims=(1,), accepted_axis_0_shape=[x.shape[0]], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_str(name=f'{fit_xgb.__name__} objective', value=objective, options=OBJECTIVES)
+ check_str(name=f'{fit_xgb.__name__} tree_method', value=tree_method, options=TREE_METHODS)
+ check_int(name=f'{fit_xgb.__name__} n_estimators', value=n_estimators, min_value=1)
+ check_int(name=f'{fit_xgb.__name__} max_depth', value=max_depth, min_value=1)
+ check_int(name=f'{fit_xgb.__name__} verbosity', value=verbosity, min_value=0, max_value=3)
+ check_float(name=f'{fit_xgb.__name__} learning_rate', value=learning_rate, min_value=0.1, max_value=1.0)
+ xgb_reg = xgb.XGBRegressor(objective=objective, max_depth=max_depth, n_estimators=n_estimators, verbosity=verbosity)
+ return xgb_reg.fit(X=x, y=y)
+
+def transform_xgb(x: pd.DataFrame, model: xgb.XGBRegressor):
+
+ """
+ :example:
+ >>> x, y = pd.DataFrame(np.random.randint(0, 500, (100, 20))), np.random.randint(1, 6, (100,))
+ >>> mdl = fit_xgb(x=x, y=y)
+ >>> new_x = pd.DataFrame(np.random.randint(0, 500, (100, 20)))
+ >>> results = transform_xgb(x=new_x, model=mdl)
+ """
+
+ check_instance(source=transform_xgb.__name__, instance=model, accepted_types=(xgb.XGBRegressor,))
+ check_valid_dataframe(df=x, source=f'{transform_xgb.__name__} x', valid_dtypes=Formats.NUMERIC_DTYPES.value)
+ expected_x_names = model.get_booster().feature_names
+ new_x_names = [str(i) for i in list(x.columns)]
+ missing_x_names = set([i for i in expected_x_names if i not in new_x_names])
+ additional_x_names = set([i for i in new_x_names if i not in expected_x_names])
+ if len(additional_x_names) > 0:
+ raise DataHeaderError(msg=f'The new data has {len(additional_x_names)} features not expected by the model: {additional_x_names}', source=transform_xgb.__name__)
+ if len(missing_x_names) > 0:
+ raise DataHeaderError(msg=f'The new data are missing {len(missing_x_names)} features expected by the model: {missing_x_names}', source=transform_xgb.__name__)
+ if expected_x_names != new_x_names:
+ raise DataHeaderError(msg=f'The new data contains features in the wrong order from the expected features', source=transform_xgb.__name__)
+ return np.round(model.predict(x), 2)
+
+
+def evaluate_xgb(y_pred: np.ndarray,
+ y_true: np.ndarray,
+ metrics: List[str],
+ stratified: Optional[bool] = False) -> dict:
+ """
+ Evaluates the performance of a regression model (e.g., XGBoost) by calculating selected metrics. Optionally, the evaluation can be stratified by unique
+ values in the true target variable (`y_true`), where performance is computed separately for each class/level.
+
+ :param np.ndarray y_pred: Predicted values generated by the model, must have the same shape as `y_true`.
+ :param np.ndarray y_true: True target values to compare the predictions against.
+ :param List[str] metrics: List of metrics to compute.
+ :param stratified: If True, computes the metric for each unique class/level in `y_true`. If False (default), computes the metric for the entire dataset.
+ :return: A dictionary containing the computed metrics.
+ :rtype: dict
+
+ :example:
+ >>> x = pd.DataFrame(np.random.randint(0, 500, (100, 20)))
+ >>> y = np.random.randint(1, 6, (100,))
+ >>> mdl = fit_xgb(x=x, y=y)
+ >>> new_x = pd.DataFrame(np.random.randint(0, 500, (100, 20)))
+ >>> y_pred = transform_xgb(x=new_x, model=mdl)
+ >>> evaluate_xgb(y_pred=y_pred, y_true=y, metrics=['MAE', 'MAPE', 'RMSE', 'MSE'])
+ """
+ METRICS = {'MAPE': mean_absolute_percentage_error, 'MSE': mean_squared_error, 'MAE': mean_absolute_error, 'R2': r2_score, 'RMSE': root_mean_squared_error}
+ check_valid_array(data=y_true, source=evaluate_xgb.__name__, accepted_ndims=(1,), accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_array(data=y_pred, source=evaluate_xgb.__name__, accepted_ndims=(1,), min_axis_0=y_true.shape[0],accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ check_valid_lst(data=metrics, source=f'{evaluate_xgb.__name__} metrics', valid_values=list(METRICS.keys()))
+ results = {}
+ for metric in metrics:
+ if not stratified:
+ results[metric] = METRICS[metric](y_true=y_true, y_pred=y_pred)
+ else:
+ results[metric] = {}
+ for unique_true in (np.unique(y_true)):
+ sample_idx = np.argwhere(y_true == unique_true)
+ sample_y_true, sample_y_pred = y_true[sample_idx].flatten(), y_pred[sample_idx].flatten()
+ results[metric][unique_true] = METRICS[metric](y_true=sample_y_true, y_pred=sample_y_pred)
+
+ return results
+
+
+def kfold_fit_xgb(x: pd.DataFrame,
+ y: np.ndarray,
+ objective: Optional[str] = 'reg:squarederror',
+ n_estimators: Optional[int] = 100,
+ max_depth: Optional[int] = 6,
+ verbosity: Optional[int] = 1,
+ learning_rate: Optional[float] = 0.3,
+ tree_method: Optional[str] = 'auto',
+ k: Optional[int] = 5):
+
+ # USE xgb.cv
+ #
+ # OBJECTIVES = ('reg:squarederror', 'reg:squaredlogerror', 'reg:logistic', 'reg:pseudohubererror')
+ # TREE_METHODS = ('auto', 'exact', 'approx', 'hist', 'gpu_hist')
+ #
+ # check_valid_dataframe(df=x, source=f'{fit_xgb.__name__} x', valid_dtypes=Formats.NUMERIC_DTYPES.value)
+ # check_valid_array(data=y, source=f'{fit_xgb.__name__} y', accepted_ndims=(1,), accepted_axis_0_shape=[x.shape[0]], accepted_dtypes=Formats.NUMERIC_DTYPES.value)
+ # check_str(name=f'{fit_xgb.__name__} objective', value=objective, options=OBJECTIVES)
+ # check_str(name=f'{fit_xgb.__name__} tree_method', value=tree_method, options=TREE_METHODS)
+ # check_int(name=f'{fit_xgb.__name__} n_estimators', value=n_estimators, min_value=1)
+ # check_int(name=f'{fit_xgb.__name__} max_depth', value=max_depth, min_value=1)
+ # check_int(name=f'{fit_xgb.__name__} verbosity', value=verbosity, min_value=0, max_value=3)
+ # check_float(name=f'{fit_xgb.__name__} learning_rate', value=learning_rate, min_value=0.1, max_value=1.0)
+ # check_int(name=f'{fit_xgb.__name__} k', value=k, min_value=2)
+ # k_fold = StratifiedKFold(n_splits=k, shuffle=True)
+ # for fold_cnt, (train_index, test_index) in enumerate(k_fold.split(x, y)):
+ # x_fold, y_fold = x.loc[train_index], y[test_index]
+
+ pass
+
+
+# x = pd.DataFrame(np.random.randint(0, 500, (100, 20)))
+# y = np.random.randint(1, 6, (100,))
+# mdl = fit_xgb(x=x, y=y)
+# new_x = pd.DataFrame(np.random.randint(0, 500, (100, 20)))
+# y_pred = transform_xgb(x=new_x, model=mdl)
+# evaluate_xgb(y_pred=y_pred, y_true=y, metrics=['MAE', 'MAPE', 'RMSE', 'MSE'], stratified=True)
+#
+
+
+# x = pd.DataFrame(np.random.randint(0, 500, (100, 20)))
+# y = np.random.randint(1, 6, (100,))
+# #mdl = fit_xgb(x=x, y=y)
+#
+# kfold_fit_xgb(x=x, y=y)
+
+ #for fold_cnt, (train_index, test_index) in enumerate(k_fold.split(x_data, y_data)):
\ No newline at end of file