json2yolosegment: yolov8.py annotate

annotate yolov8.py @ 2:158e6ce48345 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9

author	bgruening
date	Fri, 11 Jul 2025 06:49:20 +0000
parents	dfda27273ead
children	97bc82ee2a61

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 #
2 158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	178
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	179 def safe_rmtree(path):
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	180 try:
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	181 shutil.rmtree(path)
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	182 except OSError:
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	183 time.sleep(1)
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	184 shutil.rmtree(path, ignore_errors=True)
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	185
158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	186
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	187 # 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	188 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	189 if "imgsz" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	190 image_size = kwargs['imgsz']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	191 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	192 image_size = 320
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	193
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	194 if "epochs" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	195 n_epochs = kwargs['epochs']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	196 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	197 n_epochs = 100
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	198
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	199 if "hsv_h" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	200 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	201 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	202 aug_hsv_h = 0.015
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	203
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	204 if "hsv_s" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	205 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	206 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	207 aug_hsv_s = 0.7
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	208
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	209 if "hsv_v" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	210 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	211 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	212 aug_hsv_v = 0.4
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	213
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	214 if "degrees" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	215 aug_degrees = kwargs['degrees']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	216 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	217 aug_degrees = 10.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	218
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	219 if "translate" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	220 aug_translate = kwargs['translate']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	221 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	222 aug_translate = 0.1
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	223
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	224 if "scale" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	225 aug_scale = kwargs['scale']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	226 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	227 aug_scale = 0.2
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	228
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	229 if "shear" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	230 aug_shear = kwargs['shear']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	231 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	232 aug_shear = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	233
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	234 if "shear" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	235 aug_shear = kwargs['shear']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	236 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	237 aug_shear = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	238
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	239 if "perspective" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	240 aug_perspective = kwargs['perspective']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	241 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	242 aug_perspective = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	243
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	244 if "fliplr" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	245 aug_fliplr = kwargs['fliplr']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	246 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	247 aug_fliplr = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	248
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	249 if "flipud" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	250 aug_flipud = kwargs['flipud']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	251 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	252 aug_flipud = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	253
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	254 if "mosaic" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	255 aug_mosaic = kwargs['mosaic']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	256 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	257 aug_mosaic = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	258
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	259 if "crop_fraction" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	260 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	261 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	262 aug_crop_fraction = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	263
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	264 if "weight_decay" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	265 weight_decay = kwargs['weight_decay']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	266 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	267 weight_decay = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	268
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	269 if "init_lr" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	270 init_lr = kwargs['init_lr']
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 init_lr = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	273
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	274 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	275 if os.path.isdir(train_save_path):
2 158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	276 safe_rmtree(train_save_path)
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	277 # 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	278 if args.model_format == 'pt':
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	279 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	280 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	281 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	282 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	283 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	284 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	285 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	286 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	287 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	288 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	289 return model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	290
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	291
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	292 # Validate the trained model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	293 def validateModel(model):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	294 # 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	295 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	296 if os.path.isdir(val_save_path):
2 158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	297 safe_rmtree(val_save_path)
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	298 # Validate the model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	299 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	300 metrics.box.map # map50-95
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	301 metrics.box.map50 # map50
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	302 metrics.box.map75 # map75
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	303 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	304
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	305
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	306 # 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	307 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	308 if "imgsz" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	309 image_size = kwargs['imgsz']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	310 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	311 image_size = 320
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	312
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	313 if "conf" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	314 confidence = kwargs['conf']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	315 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	316 confidence = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	317
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	318 if "iou" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	319 iou_value = kwargs['iou']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	320 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	321 iou_value = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	322
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	323 if "num_classes" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	324 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	325 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	326 class_array = [0, 1]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	327
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	328 if "max_det" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	329 maximum_detections = args.max_det
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	330 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	331 maximum_detections = 300
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	332
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	333 if "run_dir" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	334 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	335 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	336 # 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	337 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	338 if os.path.isdir(pred_save_path):
2 158e6ce48345 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 739bcabf09bdb9c291121a6b1f889dabe1a98ea9 bgruening parents: 1 diff changeset	339 safe_rmtree(pred_save_path)
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	340 if "foldername" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	341 save_folder_name = kwargs['foldername']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	342 # 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	343 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	344 conf=confidence, imgsz=image_size,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	345 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	346 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	347 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	348 return prediction
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
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	351 # Save bounding boxes
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	352 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	353 """
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	354 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	355 Parameters:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	356 - 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	357 - 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	358 """
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	359 for result in predictions:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	360 result = result.to("cpu").numpy()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	361 # 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	362 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	363 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	364 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	365 # 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	366 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	367 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	368 # 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	369 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	370 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	371 # 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	372 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	373 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	374 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	375 confidence = confidence_scores[i]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	376 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	377 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	378 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	379
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	380
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	381 if __name__ == '__main__':
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	382 args = parser.parse_args()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	383 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	384 # Train/load model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	385 if (args.train):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	386 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	387 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	388 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	389 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	390 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	391 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	392 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	393 validateModel(model)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	394 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	395 t = time.time()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	396 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	397 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	398 "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	399 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	400 "train", "weights", "best.pt"))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	401 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	402 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	403 args.model_name + ".pt"))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	404 model.info(verbose=True)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	405 elapsed = time.time() - t
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	406 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	407
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	408 if (args.save_dir):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	409 # 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	410 t = time.time()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	411 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	412 # 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	413 class_names = model.names
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	414 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	415 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	416 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	417 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	418 elapsed = time.time() - t
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	419 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	420
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	421 if (args.mode == "detect"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	422 # Save bounding boxes
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	423 save_yolo_bounding_boxes_to_txt(predictions, args.save_dir)
1 dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	424
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	425 # Loop over each result
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	426 for result in predictions:
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	427 img = np.copy(result.orig_img)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	428 image_filename = pathlib.Path(result.path).stem
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	429 overlay_path = os.path.join(args.save_dir, f"{image_filename}_overlay.jpg")
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	430
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	431 for box, cls, conf in zip(result.boxes.xyxy, result.boxes.cls, result.boxes.conf):
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	432 x1, y1, x2, y2 = map(int, box.tolist())
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	433 class_num = int(cls.item())
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	434 confidence = conf.item()
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	435 label = f"{class_names[class_num]} {confidence:.2f}" if class_names else f"{class_num} {confidence:.2f}"
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	436
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	437 cv2.rectangle(img, (x1, y1), (x2, y2), color=(0, 255, 0), thickness=2)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	438 cv2.putText(img, label, (x1, y1 - 10), cv2.FONT_HERSHEY_SIMPLEX,
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	439 0.5, (0, 255, 0), thickness=1)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	440
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	441 cv2.imwrite(overlay_path, img)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	442 print(colored(f"Overlay image saved at: {overlay_path}", 'cyan'))
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	443 elif (args.mode == "track"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	444 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	445 tracker=args.tracker_file,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	446 conf=args.confidence,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	447 iou=args.iou,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	448 persist=False,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	449 show=True,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	450 save=True,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	451 project=args.run_dir,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	452 name=args.foldername)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	453 # Store the track history
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	454 track_history = defaultdict(lambda: [])
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	455
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	456 for result in results:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	457 # 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	458 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	459 boxes = result.boxes.xywh.cpu()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	460 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	461 # 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	462 frame = result.plot()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	463 # Plot the tracks
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	464 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	465 x, y, w, h = box
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	466 track = track_history[track_id]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	467 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	468 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	469 track.pop(0)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	470
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	471 # Draw the tracking lines
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	472 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	473 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	474
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	475 # Display the annotated frame
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	476 cv2.imshow("YOLO11 Tracking", frame)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	477 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	478 elif (args.mode == "segment"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	479 # 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	480 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	481 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	482 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	483
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	484 # Save polygon coordinates
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	485 for result in predictions:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	486 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	487 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	488 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	489 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	490 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	491
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	492 for c, ci in enumerate(result):
1 dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	493 if ci.masks is not None and ci.masks.xy:
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	494 # Extract contour
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	495 contour = ci.masks.xy.pop()
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	496 contour = contour.astype(np.int32).reshape(-1, 1, 2)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	497 _ = cv2.drawContours(b_mask, [contour], -1, (255, 255, 255), cv2.FILLED)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	498
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	499 # Normalized polygon points
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	500 points = ci.masks.xyn.pop()
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	501 obj_class = int(ci.boxes.cls.to("cpu").numpy().item())
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	502 confidence = result.boxes.conf.to("cpu").numpy()[c]
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	503
1 dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	504 with open(txt_save_as, 'a') as f:
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	505 segmentation_points = ['{} {}'.format(points[i][0], points[i][1]) for i in range(len(points))]
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	506 segmentation_points_string = ' '.join(segmentation_points)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	507 line = '{} {} {}\n'.format(obj_class, segmentation_points_string, confidence)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	508 f.write(line)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	509 else:
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	510 print(colored(f"⚠️ No mask found for object {c} in '{filename}'. Skipping.", "yellow"))
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	511
1 dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	512 # Overlay mask onto original image
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	513 colored_mask = cv2.merge([b_mask, np.zeros_like(b_mask), np.zeros_like(b_mask)])
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	514 blended = cv2.addWeighted(img, 1.0, colored_mask, 0.5, 0)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	515 overlay_path = os.path.join(args.save_dir, filename + "_overlay.jpg")
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	516 cv2.imwrite(overlay_path, blended)
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	517
1 dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	518 imwrite(mask_save_as, b_mask, imagej=True)
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	519 print(colored(f"Saved binary mask as : \n '{mask_save_as}' \n", 'magenta'))
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	520 print(colored(f"Polygon coordinates saved as : \n '{txt_save_as}' \n", 'cyan'))

Mercurial > repos > bgruening > json2yolosegment

annotate yolov8.py @ 2:158e6ce48345 draft