json2yolosegment: yolov8.py annotate

author	bgruening
date	Fri, 13 Jun 2025 11:23:35 +0000
parents
children	dfda27273ead

rev	line source
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	1 import argparse
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	2 import os
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	3 import pathlib
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	4 import shutil
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	5 import time
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	6 from argparse import RawTextHelpFormatter
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	7 from collections import defaultdict
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	8
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	9 import cv2
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	10 import numpy as np
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	11 from termcolor import colored
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	12 from tifffile import imwrite
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	13 from ultralytics import YOLO
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	14
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	15
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	16 #
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	17 # Input arguments
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	18 #
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	19 parser = argparse.ArgumentParser(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	20 description='train/predict dataset with YOLOv8',
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	21 epilog="""USAGE EXAMPLE:\n\n~~~~Prediction~~~~\n\
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	22 python yolov8.py --test_path=/g/group/user/data --model_path=/g/cba/models --model_name=yolov8n --save_dir=/g/group/user/results --iou=0.7 --confidence=0.5 --image_size=320 --run_dir=/g/group/user/runs --foldername=batch --headless --num_classes=1 max_det=1 --class_names_file=/g/group/user/class_names.txt\n\
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	23 \n~~~~Training~~~~ \n\
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	24 python yolov8.py --train --yaml_path=/g/group/user/example.yaml --model_path=/g/cba/models --model_name=yolov8n --run_dir=/g/group/user/runs/ --image_size=320 --epochs=150 --scale=0.3 --hsv_v=0.5 --model_format=pt --degrees=180 --class_names_file=/g/group/user/class_names.txt""", formatter_class=RawTextHelpFormatter)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	25 parser.add_argument("--dir_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	26 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	27 "Path to the training data directory."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	28 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	29 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	30 parser.add_argument("--yaml_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	31 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	32 "YAML file with all the data paths"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	33 " i.e. for train, test, valid data."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	34 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	35 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	36 parser.add_argument("--test_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	37 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	38 "Path to the prediction folder."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	39 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	40 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	41 parser.add_argument("--save_dir",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	42 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	43 "Path to the directory where bounding boxes text files"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	44 " would be saved."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	45 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	46 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	47 parser.add_argument("--run_dir",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	48 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	49 "Path where overlaid images would be saved."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	50 "For example: `RUN_DIR=projectName/results`."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	51 "This should exist."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	52 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	53 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	54 parser.add_argument("--foldername",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	55 help=("Folder to save overlaid images.\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	56 "For example: FOLDERNAME=batch.\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	57 "This should not exist as a new folder named `batch`\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	58 " will be created in RUN_DIR.\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	59 " If it exists already then, a new folder named `batch1`\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	60 " will be created automatically as it does not overwrite\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	61 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	62 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	63
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	64 # For selecting and loading model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	65 parser.add_argument("--model_name",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	66 help=("Models for task `detect` can be seen here:\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	67 "https://docs.ultralytics.com/tasks/detect/#models \n\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	68 "Models for task `segment` can be seen here:\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	69 "https://docs.ultralytics.com/tasks/segment/#models \n\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	70 " . Use `yolov8n` for `detect` tasks. "
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	71 "For custom model, use `best`"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	72 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	73 default='yolov8n', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	74 parser.add_argument("--model_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	75 help="Full absolute path to the model directory",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	76 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	77 parser.add_argument("--model_format",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	78 help="Format of the YOLO model i.e pt, yaml etc.",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	79 default='pt', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	80 parser.add_argument("--class_names_file",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	81 help="Path to the text file containing class names.",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	82 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	83
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	84 # For training the model and prediction
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	85 parser.add_argument("--mode",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	86 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	87 "detection, segmentation, classification, and pose \n. "
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	88 " Only detection mode available currently i.e. `detect`"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	89 ), default='detect', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	90 parser.add_argument('--train',
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	91 help="Do training",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	92 action='store_true')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	93 parser.add_argument("--confidence",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	94 help="Confidence value (0-1) for each detected bounding box",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	95 default=0.5, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	96 parser.add_argument("--epochs",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	97 help="Number of epochs for training. Default: 100",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	98 default=100, type=int)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	99 parser.add_argument("--init_lr",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	100 help="Number of epochs for training. Default: 100",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	101 default=0.01, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	102 parser.add_argument("--weight_decay",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	103 help="Number of epochs for training. Default: 100",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	104 default=0.0005, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	105
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	106 parser.add_argument("--num_classes",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	107 help="Number of classes to be predicted. Default: 2",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	108 default=2, type=int)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	109 parser.add_argument("--iou",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	110 help="Intersection over union (IoU) threshold for NMS",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	111 default=0.7, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	112 parser.add_argument("--image_size",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	113 help=("Size of input image to be used only as integer of w,h. \n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	114 "For training choose <= 1000. \n\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	115 "Prediction will be done on original image size"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	116 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	117 default=320, type=int)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	118 parser.add_argument("--max_det",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	119 help=("Maximum number of detections allowed per image. \n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	120 "Limits the total number of objects the model can detect in a single inference, \n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	121 "preventing excessive outputs in dense scenes.\n\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	122 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	123 default=300, type=int)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	124
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	125 # For tracking
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	126 parser.add_argument("--tracker_file",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	127 help=("Path to the configuration file of the tracker used. \n"),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	128 default='bytetrack.yaml', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	129
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	130 # For headless operation
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	131 parser.add_argument('--headless', action='store_true')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	132 parser.add_argument('--nextflow', action='store_true')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	133
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	134 # For data augmentation
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	135 parser.add_argument("--hsv_h",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	136 help="(float) image HSV-Hue augmentation (fraction)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	137 default=0.015, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	138 parser.add_argument("--hsv_s",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	139 help="(float) image HSV-Saturation augmentation (fraction)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	140 default=0.7, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	141 parser.add_argument("--hsv_v",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	142 help="(float) image HSV-Value augmentation (fraction)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	143 default=0.4, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	144 parser.add_argument("--degrees",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	145 help="(float) image rotation (+/- deg)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	146 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	147 parser.add_argument("--translate",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	148 help="(float) image translation (+/- fraction)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	149 default=0.1, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	150 parser.add_argument("--scale",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	151 help="(float) image scale (+/- gain)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	152 default=0.5, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	153 parser.add_argument("--shear",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	154 help="(float) image shear (+/- deg)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	155 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	156 parser.add_argument("--perspective",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	157 help="(float) image perspective (+/- fraction), range 0-0.001",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	158 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	159 parser.add_argument("--flipud",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	160 help="(float) image flip up-down (probability)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	161 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	162 parser.add_argument("--fliplr",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	163 help="(float) image flip left-right (probability)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	164 default=0.5, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	165 parser.add_argument("--mosaic",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	166 help="(float) image mosaic (probability)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	167 default=1.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	168 parser.add_argument("--crop_fraction",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	169 help="(float) crops image to a fraction of its size to "
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	170 "emphasize central features and adapt to object scales, "
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	171 "reducing background distractions",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	172 default=1.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	173
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	174
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	175 #
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	176 # Functions
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	177 #
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	178 # Train a new model on the dataset mentioned in yaml file
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	179 def trainModel(model_path, model_name, yaml_filepath, **kwargs):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	180 if "imgsz" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	181 image_size = kwargs['imgsz']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	182 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	183 image_size = 320
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	184
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	185 if "epochs" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	186 n_epochs = kwargs['epochs']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	187 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	188 n_epochs = 100
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	189
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	190 if "hsv_h" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	191 aug_hsv_h = kwargs['hsv_h']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	192 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	193 aug_hsv_h = 0.015
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	194
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	195 if "hsv_s" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	196 aug_hsv_s = kwargs['hsv_s']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	197 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	198 aug_hsv_s = 0.7
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	199
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	200 if "hsv_v" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	201 aug_hsv_v = kwargs['hsv_v']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	202 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	203 aug_hsv_v = 0.4
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	204
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	205 if "degrees" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	206 aug_degrees = kwargs['degrees']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	207 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	208 aug_degrees = 10.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	209
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	210 if "translate" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	211 aug_translate = kwargs['translate']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	212 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	213 aug_translate = 0.1
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	214
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	215 if "scale" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	216 aug_scale = kwargs['scale']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	217 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	218 aug_scale = 0.2
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	219
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	220 if "shear" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	221 aug_shear = kwargs['shear']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	222 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	223 aug_shear = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	224
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	225 if "shear" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	226 aug_shear = kwargs['shear']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	227 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	228 aug_shear = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	229
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	230 if "perspective" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	231 aug_perspective = kwargs['perspective']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	232 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	233 aug_perspective = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	234
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	235 if "fliplr" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	236 aug_fliplr = kwargs['fliplr']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	237 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	238 aug_fliplr = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	239
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	240 if "flipud" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	241 aug_flipud = kwargs['flipud']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	242 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	243 aug_flipud = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	244
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	245 if "mosaic" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	246 aug_mosaic = kwargs['mosaic']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	247 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	248 aug_mosaic = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	249
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	250 if "crop_fraction" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	251 aug_crop_fraction = kwargs['crop_fraction']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	252 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	253 aug_crop_fraction = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	254
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	255 if "weight_decay" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	256 weight_decay = kwargs['weight_decay']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	257 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	258 weight_decay = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	259
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	260 if "init_lr" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	261 init_lr = kwargs['init_lr']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	262 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	263 init_lr = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	264
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	265 train_save_path = os.path.expanduser('~/runs/' + args.mode + '/train/')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	266 if os.path.isdir(train_save_path):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	267 shutil.rmtree(train_save_path)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	268 # Load a pretrained YOLO model (recommended for training)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	269 if args.model_format == 'pt':
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	270 model = YOLO(os.path.join(model_path, model_name + "." + args.model_format))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	271 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	272 model = YOLO(model_name + "." + args.model_format)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	273 model.train(data=yaml_filepath, epochs=n_epochs, project=args.run_dir,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	274 imgsz=image_size, verbose=True, hsv_h=aug_hsv_h,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	275 hsv_s=aug_hsv_s, hsv_v=aug_hsv_v, degrees=aug_degrees,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	276 translate=aug_translate, shear=aug_shear, scale=aug_scale,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	277 perspective=aug_perspective, fliplr=aug_fliplr,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	278 flipud=aug_flipud, mosaic=aug_mosaic, crop_fraction=aug_crop_fraction,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	279 weight_decay=weight_decay, lr0=init_lr, seed=42)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	280 return model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	281
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	282
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	283 # Validate the trained model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	284 def validateModel(model):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	285 # Remove prediction save path if already exists
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	286 val_save_path = os.path.expanduser('~/runs/' + args.mode + '/val/')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	287 if os.path.isdir(val_save_path):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	288 shutil.rmtree(val_save_path)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	289 # Validate the model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	290 metrics = model.val() # no args needed, dataset & settings remembered
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	291 metrics.box.map # map50-95
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	292 metrics.box.map50 # map50
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	293 metrics.box.map75 # map75
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	294 metrics.box.maps # a list contains map50-95 of each category
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	295
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	296
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	297 # Do predictions on images/videos using trained/loaded model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	298 def predict(model, source_datapath, **kwargs):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	299 if "imgsz" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	300 image_size = kwargs['imgsz']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	301 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	302 image_size = 320
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	303
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	304 if "conf" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	305 confidence = kwargs['conf']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	306 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	307 confidence = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	308
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	309 if "iou" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	310 iou_value = kwargs['iou']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	311 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	312 iou_value = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	313
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	314 if "num_classes" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	315 class_array = list(range(kwargs['num_classes']))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	316 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	317 class_array = [0, 1]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	318
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	319 if "max_det" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	320 maximum_detections = args.max_det
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	321 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	322 maximum_detections = 300
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	323
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	324 if "run_dir" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	325 run_save_dir = kwargs['run_dir']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	326 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	327 # Remove prediction save path if already exists
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	328 pred_save_path = os.path.expanduser('~/runs/' + args.mode + '/predict/')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	329 if os.path.isdir(pred_save_path):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	330 shutil.rmtree(pred_save_path)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	331 if "foldername" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	332 save_folder_name = kwargs['foldername']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	333 # infer on a local image or directory containing images/videos
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	334 prediction = model.predict(source=source_datapath, save=True, stream=True,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	335 conf=confidence, imgsz=image_size,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	336 save_conf=True, iou=iou_value, max_det=maximum_detections,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	337 classes=class_array, save_txt=False,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	338 project=run_save_dir, name=save_folder_name, verbose=True)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	339 return prediction
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	340
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	341
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	342 # Save bounding boxes
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	343 def save_yolo_bounding_boxes_to_txt(predictions, save_dir):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	344 """
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	345 Function to save YOLO bounding boxes to text files.
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	346 Parameters:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	347 - predictions: List of results from YOLO model inference.
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	348 - save_dir: Directory where the text files will be saved.
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	349 """
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	350 for result in predictions:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	351 result = result.to("cpu").numpy()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	352 # Using bounding_boxes, confidence_scores, and class_num which are defined in the list
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	353 bounding_boxes = result.boxes.xyxy # Bounding boxes in xyxy format
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	354 confidence_scores = result.boxes.conf # Confidence scores
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	355 class_nums = result.boxes.cls # Class numbers
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	356 # Create save directory if it doesn't exist
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	357 save_path = pathlib.Path(save_dir).absolute()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	358 save_path.mkdir(parents=True, exist_ok=True)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	359 # Construct filename for the text file
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	360 image_filename = pathlib.Path(result.path).stem
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	361 text_filename = save_path / f"{image_filename}.txt"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	362 # Write bounding boxes info into the text file
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	363 with open(text_filename, 'w') as f:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	364 for i in range(bounding_boxes.shape[0]):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	365 x1, y1, x2, y2 = bounding_boxes[i]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	366 confidence = confidence_scores[i]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	367 class_num = int(class_nums[i])
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	368 f.write(f'{class_num:01} {x1:06.2f} {y1:06.2f} {x2:06.2f} {y2:06.2f} {confidence:0.02} \n')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	369 print(colored(f"Bounding boxes saved in: {text_filename}", 'green'))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	370
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	371
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	372 if __name__ == '__main__':
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	373 args = parser.parse_args()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	374 os.environ["KMP_DUPLICATE_LIB_OK"] = "TRUE"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	375 # Train/load model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	376 if (args.train):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	377 model = trainModel(args.model_path, args.model_name, args.yaml_path,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	378 imgsz=args.image_size, epochs=args.epochs,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	379 hsv_h=args.hsv_h, hsv_s=args.hsv_s, hsv_v=args.hsv_v,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	380 degrees=args.degrees, translate=args.translate,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	381 shear=args.shear, scale=args.scale,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	382 perspective=args.perspective, fliplr=args.fliplr,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	383 flipud=args.flipud, mosaic=args.mosaic)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	384 validateModel(model)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	385 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	386 t = time.time()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	387 train_save_path = os.path.expanduser('~/runs/' + args.mode + '/')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	388 if os.path.isfile(os.path.join(train_save_path,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	389 "train", "weights", "best.pt")) and (args.model_name == 'sam'):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	390 model = YOLO(os.path.join(train_save_path,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	391 "train", "weights", "best.pt"))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	392 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	393 model = YOLO(os.path.join(args.model_path,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	394 args.model_name + ".pt"))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	395 model.info(verbose=True)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	396 elapsed = time.time() - t
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	397 print(colored(f"\nYOLO model loaded in : '{elapsed}' sec \n", 'white', 'on_yellow'))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	398
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	399 if (args.save_dir):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	400 # Do predictions (optionally show image results with bounding boxes)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	401 t = time.time()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	402 datapath_for_prediction = args.test_path
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	403 # Extracting class names from the model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	404 class_names = model.names
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	405 predictions = predict(model, datapath_for_prediction,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	406 imgsz=args.image_size, conf=args.confidence,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	407 iou=args.iou, run_dir=args.run_dir,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	408 foldername=args.foldername, num_classes=args.num_classes, max_det=args.max_det)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	409 elapsed = time.time() - t
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	410 print(colored(f"\nYOLO prediction done in : '{elapsed}' sec \n", 'white', 'on_cyan'))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	411
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	412 if (args.mode == "detect"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	413 # Save bounding boxes
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	414 save_yolo_bounding_boxes_to_txt(predictions, args.save_dir)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	415 elif (args.mode == "track"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	416 results = model.track(source=datapath_for_prediction,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	417 tracker=args.tracker_file,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	418 conf=args.confidence,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	419 iou=args.iou,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	420 persist=False,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	421 show=True,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	422 save=True,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	423 project=args.run_dir,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	424 name=args.foldername)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	425 # Store the track history
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	426 track_history = defaultdict(lambda: [])
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	427
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	428 for result in results:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	429 # Get the boxes and track IDs
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	430 if result.boxes and result.boxes.is_track:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	431 boxes = result.boxes.xywh.cpu()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	432 track_ids = result.boxes.id.int().cpu().tolist()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	433 # Visualize the result on the frame
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	434 frame = result.plot()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	435 # Plot the tracks
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	436 for box, track_id in zip(boxes, track_ids):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	437 x, y, w, h = box
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	438 track = track_history[track_id]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	439 track.append((float(x), float(y))) # x, y center point
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	440 if len(track) > 30: # retain 30 tracks for 30 frames
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	441 track.pop(0)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	442
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	443 # Draw the tracking lines
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	444 points = np.hstack(track).astype(np.int32).reshape((-1, 1, 2))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	445 cv2.polylines(frame, [points], isClosed=False, color=(230, 230, 230), thickness=2)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	446
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	447 # Display the annotated frame
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	448 cv2.imshow("YOLO11 Tracking", frame)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	449 print(colored(f"Tracking results saved in : '{args.save_dir}' \n", 'green'))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	450 elif (args.mode == "segment"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	451 # Read class names from the file
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	452 with open(args.class_names_file, 'r') as f:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	453 class_names = [line.strip() for line in f.readlines()]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	454 # Create a mapping from class names to indices
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	455 class_to_index = {class_name: i for i, class_name in enumerate(class_names)}
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	456
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	457 # Save polygon coordinates
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	458 for result in predictions:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	459 # Create binary mask
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	460 img = np.copy(result.orig_img)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	461 filename = pathlib.Path(result.path).stem
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	462 b_mask = np.zeros(img.shape[:2], np.uint8)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	463 mask_save_as = str(pathlib.Path(os.path.join(args.save_dir, filename + "_mask.tiff")).absolute())
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	464 # Define output file path for text file
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	465 output_filename = os.path.splitext(filename)[0] + ".txt"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	466 txt_save_as = str(pathlib.Path(os.path.join(args.save_dir, filename + ".txt")).absolute())
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	467
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	468 for c, ci in enumerate(result):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	469 # Extract contour result
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	470 contour = ci.masks.xy.pop()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	471 # Changing the type
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	472 contour = contour.astype(np.int32)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	473 # Reshaping
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	474 contour = contour.reshape(-1, 1, 2)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	475 # Draw contour onto mask
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	476 _ = cv2.drawContours(b_mask, [contour], -1, (255, 255, 255), cv2.FILLED)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	477
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	478 # Normalized polygon points
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	479 points = ci.masks.xyn.pop()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	480 obj_class = int(ci.boxes.cls.to("cpu").numpy().item())
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	481 confidence = result.boxes.conf.to("cpu").numpy()[c]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	482
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	483 with open(txt_save_as, 'a') as f:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	484 segmentation_points = ['{} {}'.format(points[i][0], points[i][1]) for i in range(len(points))]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	485 segmentation_points_string = ' '.join(segmentation_points)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	486 line = '{} {} {}\n'.format(obj_class, segmentation_points_string, confidence)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	487 f.write(line)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	488
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	489 imwrite(mask_save_as, b_mask, imagej=True) # save image
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	490 print(colored(f"Saved cropped image as : \n '{mask_save_as}' \n", 'magenta'))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	491 print(colored(f"Polygon coordinates saved as : \n '{txt_save_as}' \n", 'cyan'))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	492
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	493 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	494 raise Exception(("Currently only 'detect' and 'segment' modes are available"))

0

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1 import argparse

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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2 import os

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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3 import pathlib

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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4 import shutil

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5 import time

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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6 from argparse import RawTextHelpFormatter

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7 from collections import defaultdict

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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8

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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9 import cv2

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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10 import numpy as np

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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11 from termcolor import colored

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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12 from tifffile import imwrite

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13 from ultralytics import YOLO

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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14

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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15

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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16 #

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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17 # Input arguments

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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18 #

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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19 parser = argparse.ArgumentParser(

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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20 description='train/predict dataset with YOLOv8',

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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21 epilog="""USAGE EXAMPLE:\n\n~~~~Prediction~~~~\n\

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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22 python yolov8.py --test_path=/g/group/user/data --model_path=/g/cba/models --model_name=yolov8n --save_dir=/g/group/user/results --iou=0.7 --confidence=0.5 --image_size=320 --run_dir=/g/group/user/runs --foldername=batch --headless --num_classes=1 max_det=1 --class_names_file=/g/group/user/class_names.txt\n\

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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23 \n~~~~Training~~~~ \n\

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24 python yolov8.py --train --yaml_path=/g/group/user/example.yaml --model_path=/g/cba/models --model_name=yolov8n --run_dir=/g/group/user/runs/ --image_size=320 --epochs=150 --scale=0.3 --hsv_v=0.5 --model_format=pt --degrees=180 --class_names_file=/g/group/user/class_names.txt""", formatter_class=RawTextHelpFormatter)

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25 parser.add_argument("--dir_path",

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26 help=(

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27 "Path to the training data directory."

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28 ),

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29 type=str)

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30 parser.add_argument("--yaml_path",

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31 help=(

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32 "YAML file with all the data paths"

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33 " i.e. for train, test, valid data."

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34 ),

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35 type=str)

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36 parser.add_argument("--test_path",

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37 help=(

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38 "Path to the prediction folder."

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39 ),

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40 type=str)

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41 parser.add_argument("--save_dir",

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42 help=(

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43 "Path to the directory where bounding boxes text files"

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44 " would be saved."

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45 ),

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46 type=str)

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47 parser.add_argument("--run_dir",

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48 help=(

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49 "Path where overlaid images would be saved."

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50 "For example: `RUN_DIR=projectName/results`."

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51 "This should exist."

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52 ),

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53 type=str)

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54 parser.add_argument("--foldername",

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55 help=("Folder to save overlaid images.\n"

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56 "For example: FOLDERNAME=batch.\n"

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57 "This should not exist as a new folder named `batch`\n"

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58 " will be created in RUN_DIR.\n"

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59 " If it exists already then, a new folder named `batch1`\n"

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60 " will be created automatically as it does not overwrite\n"

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61 ),

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62 type=str)

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63

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64 # For selecting and loading model

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65 parser.add_argument("--model_name",

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66 help=("Models for task `detect` can be seen here:\n"

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67 "https://docs.ultralytics.com/tasks/detect/#models \n\n"

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68 "Models for task `segment` can be seen here:\n"

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69 "https://docs.ultralytics.com/tasks/segment/#models \n\n"

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70 " . Use `yolov8n` for `detect` tasks. "

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71 "For custom model, use `best`"

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72 ),

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73 default='yolov8n', type=str)

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74 parser.add_argument("--model_path",

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75 help="Full absolute path to the model directory",

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76 type=str)

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77 parser.add_argument("--model_format",

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78 help="Format of the YOLO model i.e pt, yaml etc.",

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79 default='pt', type=str)

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80 parser.add_argument("--class_names_file",

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81 help="Path to the text file containing class names.",

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82 type=str)

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83

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84 # For training the model and prediction

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85 parser.add_argument("--mode",

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86 help=(

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87 "detection, segmentation, classification, and pose \n. "

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88 " Only detection mode available currently i.e. `detect`"

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89 ), default='detect', type=str)

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90 parser.add_argument('--train',

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91 help="Do training",

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92 action='store_true')

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93 parser.add_argument("--confidence",

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94 help="Confidence value (0-1) for each detected bounding box",

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95 default=0.5, type=float)

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96 parser.add_argument("--epochs",

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97 help="Number of epochs for training. Default: 100",

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98 default=100, type=int)

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99 parser.add_argument("--init_lr",

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100 help="Number of epochs for training. Default: 100",

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101 default=0.01, type=float)

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102 parser.add_argument("--weight_decay",

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103 help="Number of epochs for training. Default: 100",

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104 default=0.0005, type=float)

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105

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106 parser.add_argument("--num_classes",

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107 help="Number of classes to be predicted. Default: 2",

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108 default=2, type=int)

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109 parser.add_argument("--iou",

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110 help="Intersection over union (IoU) threshold for NMS",

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111 default=0.7, type=float)

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112 parser.add_argument("--image_size",

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113 help=("Size of input image to be used only as integer of w,h. \n"

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114 "For training choose <= 1000. \n\n"

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115 "Prediction will be done on original image size"

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116 ),

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117 default=320, type=int)

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118 parser.add_argument("--max_det",

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119 help=("Maximum number of detections allowed per image. \n"

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120 "Limits the total number of objects the model can detect in a single inference, \n"

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121 "preventing excessive outputs in dense scenes.\n\n"

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122 ),

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123 default=300, type=int)

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124

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125 # For tracking

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126 parser.add_argument("--tracker_file",

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127 help=("Path to the configuration file of the tracker used. \n"),

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128 default='bytetrack.yaml', type=str)

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129

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130 # For headless operation

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131 parser.add_argument('--headless', action='store_true')

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132 parser.add_argument('--nextflow', action='store_true')

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133

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134 # For data augmentation

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135 parser.add_argument("--hsv_h",

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136 help="(float) image HSV-Hue augmentation (fraction)",

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137 default=0.015, type=float)

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138 parser.add_argument("--hsv_s",

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139 help="(float) image HSV-Saturation augmentation (fraction)",

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140 default=0.7, type=float)

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141 parser.add_argument("--hsv_v",

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142 help="(float) image HSV-Value augmentation (fraction)",

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143 default=0.4, type=float)

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144 parser.add_argument("--degrees",

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145 help="(float) image rotation (+/- deg)",

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146 default=0.0, type=float)

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147 parser.add_argument("--translate",

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148 help="(float) image translation (+/- fraction)",

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149 default=0.1, type=float)

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150 parser.add_argument("--scale",

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151 help="(float) image scale (+/- gain)",

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152 default=0.5, type=float)

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153 parser.add_argument("--shear",

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154 help="(float) image shear (+/- deg)",

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155 default=0.0, type=float)

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156 parser.add_argument("--perspective",

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157 help="(float) image perspective (+/- fraction), range 0-0.001",

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158 default=0.0, type=float)

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159 parser.add_argument("--flipud",

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160 help="(float) image flip up-down (probability)",

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161 default=0.0, type=float)

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162 parser.add_argument("--fliplr",

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163 help="(float) image flip left-right (probability)",

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164 default=0.5, type=float)

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165 parser.add_argument("--mosaic",

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166 help="(float) image mosaic (probability)",

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167 default=1.0, type=float)

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168 parser.add_argument("--crop_fraction",

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169 help="(float) crops image to a fraction of its size to "

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170 "emphasize central features and adapt to object scales, "

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171 "reducing background distractions",

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172 default=1.0, type=float)

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173

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174

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175 #

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176 # Functions

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177 #

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178 # Train a new model on the dataset mentioned in yaml file

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179 def trainModel(model_path, model_name, yaml_filepath, **kwargs):

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180 if "imgsz" in kwargs:

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181 image_size = kwargs['imgsz']

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182 else:

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183 image_size = 320

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184

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185 if "epochs" in kwargs:

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186 n_epochs = kwargs['epochs']

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187 else:

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188 n_epochs = 100

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189

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190 if "hsv_h" in kwargs:

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191 aug_hsv_h = kwargs['hsv_h']

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192 else:

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193 aug_hsv_h = 0.015

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194

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195 if "hsv_s" in kwargs:

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196 aug_hsv_s = kwargs['hsv_s']

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197 else:

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198 aug_hsv_s = 0.7

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199

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200 if "hsv_v" in kwargs:

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201 aug_hsv_v = kwargs['hsv_v']

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diff changeset

202 else:

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203 aug_hsv_v = 0.4

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204

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205 if "degrees" in kwargs:

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206 aug_degrees = kwargs['degrees']

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diff changeset

207 else:

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208 aug_degrees = 10.0

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209

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210 if "translate" in kwargs:

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211 aug_translate = kwargs['translate']

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212 else:

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213 aug_translate = 0.1

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214

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215 if "scale" in kwargs:

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216 aug_scale = kwargs['scale']

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217 else:

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218 aug_scale = 0.2

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219

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220 if "shear" in kwargs:

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221 aug_shear = kwargs['shear']

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222 else:

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223 aug_shear = 0.0

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224

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225 if "shear" in kwargs:

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226 aug_shear = kwargs['shear']

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227 else:

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228 aug_shear = 0.0

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229

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230 if "perspective" in kwargs:

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231 aug_perspective = kwargs['perspective']

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232 else:

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233 aug_perspective = 0.0

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234

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235 if "fliplr" in kwargs:

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236 aug_fliplr = kwargs['fliplr']

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diff changeset

237 else:

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238 aug_fliplr = 0.5

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239

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240 if "flipud" in kwargs:

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241 aug_flipud = kwargs['flipud']

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diff changeset

242 else:

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243 aug_flipud = 0.0

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244

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245 if "mosaic" in kwargs:

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246 aug_mosaic = kwargs['mosaic']

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247 else:

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248 aug_mosaic = 1.0

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249

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250 if "crop_fraction" in kwargs:

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251 aug_crop_fraction = kwargs['crop_fraction']

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252 else:

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253 aug_crop_fraction = 1.0

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254

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255 if "weight_decay" in kwargs:

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256 weight_decay = kwargs['weight_decay']

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257 else:

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258 weight_decay = 1.0

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259

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260 if "init_lr" in kwargs:

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261 init_lr = kwargs['init_lr']

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262 else:

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263 init_lr = 1.0

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264

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265 train_save_path = os.path.expanduser('~/runs/' + args.mode + '/train/')

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266 if os.path.isdir(train_save_path):

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267 shutil.rmtree(train_save_path)

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268 # Load a pretrained YOLO model (recommended for training)

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269 if args.model_format == 'pt':

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270 model = YOLO(os.path.join(model_path, model_name + "." + args.model_format))

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271 else:

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272 model = YOLO(model_name + "." + args.model_format)

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273 model.train(data=yaml_filepath, epochs=n_epochs, project=args.run_dir,

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274 imgsz=image_size, verbose=True, hsv_h=aug_hsv_h,

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275 hsv_s=aug_hsv_s, hsv_v=aug_hsv_v, degrees=aug_degrees,

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276 translate=aug_translate, shear=aug_shear, scale=aug_scale,

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277 perspective=aug_perspective, fliplr=aug_fliplr,

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278 flipud=aug_flipud, mosaic=aug_mosaic, crop_fraction=aug_crop_fraction,

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279 weight_decay=weight_decay, lr0=init_lr, seed=42)

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280 return model

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281

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282

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283 # Validate the trained model

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284 def validateModel(model):

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285 # Remove prediction save path if already exists

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286 val_save_path = os.path.expanduser('~/runs/' + args.mode + '/val/')

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287 if os.path.isdir(val_save_path):

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288 shutil.rmtree(val_save_path)

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289 # Validate the model

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290 metrics = model.val() # no args needed, dataset & settings remembered

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291 metrics.box.map # map50-95

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292 metrics.box.map50 # map50

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293 metrics.box.map75 # map75

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294 metrics.box.maps # a list contains map50-95 of each category

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295

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296

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297 # Do predictions on images/videos using trained/loaded model

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298 def predict(model, source_datapath, **kwargs):

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299 if "imgsz" in kwargs:

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300 image_size = kwargs['imgsz']

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301 else:

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302 image_size = 320

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303

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304 if "conf" in kwargs:

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305 confidence = kwargs['conf']

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306 else:

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307 confidence = 0.5

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308

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309 if "iou" in kwargs:

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310 iou_value = kwargs['iou']

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311 else:

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312 iou_value = 0.5

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313

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314 if "num_classes" in kwargs:

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315 class_array = list(range(kwargs['num_classes']))

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316 else:

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317 class_array = [0, 1]

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318

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319 if "max_det" in kwargs:

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320 maximum_detections = args.max_det

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321 else:

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322 maximum_detections = 300

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323

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324 if "run_dir" in kwargs:

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325 run_save_dir = kwargs['run_dir']

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326 else:

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327 # Remove prediction save path if already exists

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328 pred_save_path = os.path.expanduser('~/runs/' + args.mode + '/predict/')

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329 if os.path.isdir(pred_save_path):

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330 shutil.rmtree(pred_save_path)

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331 if "foldername" in kwargs:

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332 save_folder_name = kwargs['foldername']

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333 # infer on a local image or directory containing images/videos

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334 prediction = model.predict(source=source_datapath, save=True, stream=True,

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335 conf=confidence, imgsz=image_size,

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336 save_conf=True, iou=iou_value, max_det=maximum_detections,

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337 classes=class_array, save_txt=False,

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338 project=run_save_dir, name=save_folder_name, verbose=True)

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339 return prediction

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340

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341

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342 # Save bounding boxes

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343 def save_yolo_bounding_boxes_to_txt(predictions, save_dir):

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344 """

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345 Function to save YOLO bounding boxes to text files.

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346 Parameters:

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347 - predictions: List of results from YOLO model inference.

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348 - save_dir: Directory where the text files will be saved.

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349 """

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350 for result in predictions:

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351 result = result.to("cpu").numpy()

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352 # Using bounding_boxes, confidence_scores, and class_num which are defined in the list

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353 bounding_boxes = result.boxes.xyxy # Bounding boxes in xyxy format

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354 confidence_scores = result.boxes.conf # Confidence scores

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355 class_nums = result.boxes.cls # Class numbers

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356 # Create save directory if it doesn't exist

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357 save_path = pathlib.Path(save_dir).absolute()

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358 save_path.mkdir(parents=True, exist_ok=True)

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359 # Construct filename for the text file

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360 image_filename = pathlib.Path(result.path).stem

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361 text_filename = save_path / f"{image_filename}.txt"

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362 # Write bounding boxes info into the text file

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363 with open(text_filename, 'w') as f:

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364 for i in range(bounding_boxes.shape[0]):

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365 x1, y1, x2, y2 = bounding_boxes[i]

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366 confidence = confidence_scores[i]

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367 class_num = int(class_nums[i])

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368 f.write(f'{class_num:01} {x1:06.2f} {y1:06.2f} {x2:06.2f} {y2:06.2f} {confidence:0.02} \n')

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369 print(colored(f"Bounding boxes saved in: {text_filename}", 'green'))

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370

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371

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372 if __name__ == '__main__':

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373 args = parser.parse_args()

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374 os.environ["KMP_DUPLICATE_LIB_OK"] = "TRUE"

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375 # Train/load model

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376 if (args.train):

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377 model = trainModel(args.model_path, args.model_name, args.yaml_path,

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378 imgsz=args.image_size, epochs=args.epochs,

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379 hsv_h=args.hsv_h, hsv_s=args.hsv_s, hsv_v=args.hsv_v,

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380 degrees=args.degrees, translate=args.translate,

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381 shear=args.shear, scale=args.scale,

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382 perspective=args.perspective, fliplr=args.fliplr,

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383 flipud=args.flipud, mosaic=args.mosaic)

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384 validateModel(model)

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385 else:

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386 t = time.time()

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387 train_save_path = os.path.expanduser('~/runs/' + args.mode + '/')

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388 if os.path.isfile(os.path.join(train_save_path,

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389 "train", "weights", "best.pt")) and (args.model_name == 'sam'):

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390 model = YOLO(os.path.join(train_save_path,

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391 "train", "weights", "best.pt"))

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392 else:

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393 model = YOLO(os.path.join(args.model_path,

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394 args.model_name + ".pt"))

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395 model.info(verbose=True)

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396 elapsed = time.time() - t

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397 print(colored(f"\nYOLO model loaded in : '{elapsed}' sec \n", 'white', 'on_yellow'))

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398

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399 if (args.save_dir):

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400 # Do predictions (optionally show image results with bounding boxes)

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401 t = time.time()

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402 datapath_for_prediction = args.test_path

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403 # Extracting class names from the model

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404 class_names = model.names

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405 predictions = predict(model, datapath_for_prediction,

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406 imgsz=args.image_size, conf=args.confidence,

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407 iou=args.iou, run_dir=args.run_dir,

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408 foldername=args.foldername, num_classes=args.num_classes, max_det=args.max_det)

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409 elapsed = time.time() - t

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410 print(colored(f"\nYOLO prediction done in : '{elapsed}' sec \n", 'white', 'on_cyan'))

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411

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412 if (args.mode == "detect"):

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413 # Save bounding boxes

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414 save_yolo_bounding_boxes_to_txt(predictions, args.save_dir)

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415 elif (args.mode == "track"):

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416 results = model.track(source=datapath_for_prediction,

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417 tracker=args.tracker_file,

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418 conf=args.confidence,

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419 iou=args.iou,

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420 persist=False,

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421 show=True,

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422 save=True,

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423 project=args.run_dir,

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424 name=args.foldername)

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425 # Store the track history

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426 track_history = defaultdict(lambda: [])

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427

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428 for result in results:

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429 # Get the boxes and track IDs

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430 if result.boxes and result.boxes.is_track:

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431 boxes = result.boxes.xywh.cpu()

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432 track_ids = result.boxes.id.int().cpu().tolist()

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433 # Visualize the result on the frame

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434 frame = result.plot()

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435 # Plot the tracks

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436 for box, track_id in zip(boxes, track_ids):

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437 x, y, w, h = box

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438 track = track_history[track_id]

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439 track.append((float(x), float(y))) # x, y center point

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440 if len(track) > 30: # retain 30 tracks for 30 frames

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441 track.pop(0)

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442

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443 # Draw the tracking lines

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444 points = np.hstack(track).astype(np.int32).reshape((-1, 1, 2))

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445 cv2.polylines(frame, [points], isClosed=False, color=(230, 230, 230), thickness=2)

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446

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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447 # Display the annotated frame

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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448 cv2.imshow("YOLO11 Tracking", frame)

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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449 print(colored(f"Tracking results saved in : '{args.save_dir}' \n", 'green'))

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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450 elif (args.mode == "segment"):

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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451 # Read class names from the file

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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452 with open(args.class_names_file, 'r') as f:

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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453 class_names = [line.strip() for line in f.readlines()]

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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454 # Create a mapping from class names to indices

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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455 class_to_index = {class_name: i for i, class_name in enumerate(class_names)}

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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456

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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457 # Save polygon coordinates

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

bgruening

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458 for result in predictions:

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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459 # Create binary mask

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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460 img = np.copy(result.orig_img)

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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461 filename = pathlib.Path(result.path).stem

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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462 b_mask = np.zeros(img.shape[:2], np.uint8)

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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463 mask_save_as = str(pathlib.Path(os.path.join(args.save_dir, filename + "_mask.tiff")).absolute())

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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464 # Define output file path for text file

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465 output_filename = os.path.splitext(filename)[0] + ".txt"

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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466 txt_save_as = str(pathlib.Path(os.path.join(args.save_dir, filename + ".txt")).absolute())

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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467

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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468 for c, ci in enumerate(result):

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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469 # Extract contour result

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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470 contour = ci.masks.xy.pop()

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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471 # Changing the type

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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472 contour = contour.astype(np.int32)

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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473 # Reshaping

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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474 contour = contour.reshape(-1, 1, 2)

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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475 # Draw contour onto mask

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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476 _ = cv2.drawContours(b_mask, [contour], -1, (255, 255, 255), cv2.FILLED)

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477

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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478 # Normalized polygon points

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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479 points = ci.masks.xyn.pop()

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480 obj_class = int(ci.boxes.cls.to("cpu").numpy().item())

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481 confidence = result.boxes.conf.to("cpu").numpy()[c]

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482

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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483 with open(txt_save_as, 'a') as f:

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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484 segmentation_points = ['{} {}'.format(points[i][0], points[i][1]) for i in range(len(points))]

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485 segmentation_points_string = ' '.join(segmentation_points)

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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486 line = '{} {} {}\n'.format(obj_class, segmentation_points_string, confidence)

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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487 f.write(line)

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488

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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489 imwrite(mask_save_as, b_mask, imagej=True) # save image

252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557

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490 print(colored(f"Saved cropped image as : \n '{mask_save_as}' \n", 'magenta'))

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491 print(colored(f"Polygon coordinates saved as : \n '{txt_save_as}' \n", 'cyan'))

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492

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493 else:

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494 raise Exception(("Currently only 'detect' and 'segment' modes are available"))

Mercurial > repos > bgruening > json2yolosegment

annotate yolov8.py @ 0:252fd085940d draft