json2yolosegment: yolov8.py annotate

annotate yolov8.py @ 4:f6990d85161c draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506

author	bgruening
date	Mon, 21 Jul 2025 15:51:13 +0000
parents	97bc82ee2a61
children

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
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	2 import csv
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	3 import os
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	4 import pathlib
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 # Input arguments
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	17 #
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	18 parser = argparse.ArgumentParser(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	19 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	20 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	21 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	22 \n~~~~Training~~~~ \n\
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	23 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	24 parser.add_argument("--dir_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	25 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	26 "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	27 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	28 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	29 parser.add_argument("--yaml_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	30 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	31 "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	32 " 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	33 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	34 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	35 parser.add_argument("--test_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	36 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	37 "Path to the prediction folder."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	38 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	39 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	40 parser.add_argument("--save_dir",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	41 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	42 "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	43 " would be saved."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	44 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	45 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	46 parser.add_argument("--run_dir",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	47 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	48 "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	49 "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	50 "This should exist."
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	51 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	52 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	53 parser.add_argument("--foldername",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	54 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	55 "For example: FOLDERNAME=batch.\n"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	56 "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	57 " 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	58 " 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	59 " 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	60 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	61 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	62
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	63 # For selecting and loading model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	64 parser.add_argument("--model_name",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	65 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	66 "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	67 "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	68 "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	69 " . Use `yolov8n` for `detect` tasks. "
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	70 "For custom model, use `best`"
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	71 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	72 default='yolov8n', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	73 parser.add_argument("--model_path",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	74 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	75 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	76 parser.add_argument("--model_format",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	77 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	78 default='pt', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	79 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	80 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	81 type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	82 # 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	83 parser.add_argument("--mode",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	84 help=(
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	85 "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	86 " 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	87 ), default='detect', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	88 parser.add_argument('--train',
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	89 help="Do training",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	90 action='store_true')
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	91 parser.add_argument("--confidence",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	92 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	93 default=0.5, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	94 parser.add_argument("--epochs",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	95 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	96 default=100, type=int)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	97 parser.add_argument("--init_lr",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	98 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	99 default=0.01, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	100 parser.add_argument("--weight_decay",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	101 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	102 default=0.0005, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	103
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	104 parser.add_argument("--num_classes",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	105 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	106 default=2, type=int)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	107 parser.add_argument("--iou",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	108 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	109 default=0.7, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	110 parser.add_argument("--image_size",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	111 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	112 "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	113 "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	114 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	115 default=320, type=int)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	116 parser.add_argument("--max_det",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	117 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	118 "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	119 "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	120 ),
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	121 default=300, type=int)
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 # For tracking
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	124 parser.add_argument("--tracker_file",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	125 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	126 default='bytetrack.yaml', type=str)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	127
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	128 # For headless operation
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	129 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	130 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	131
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	132
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	133 # For data augmentation
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	134 parser.add_argument("--hsv_h",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	135 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	136 default=0.015, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	137 parser.add_argument("--hsv_s",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	138 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	139 default=0.7, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	140 parser.add_argument("--hsv_v",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	141 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	142 default=0.4, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	143 parser.add_argument("--degrees",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	144 help="(float) image rotation (+/- deg)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	145 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	146 parser.add_argument("--translate",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	147 help="(float) image translation (+/- fraction)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	148 default=0.1, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	149 parser.add_argument("--scale",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	150 help="(float) image scale (+/- gain)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	151 default=0.5, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	152 parser.add_argument("--shear",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	153 help="(float) image shear (+/- deg)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	154 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	155 parser.add_argument("--perspective",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	156 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	157 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	158 parser.add_argument("--flipud",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	159 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	160 default=0.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	161 parser.add_argument("--fliplr",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	162 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	163 default=0.5, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	164 parser.add_argument("--mosaic",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	165 help="(float) image mosaic (probability)",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	166 default=1.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	167 parser.add_argument("--crop_fraction",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	168 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	169 "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	170 "reducing background distractions",
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	171 default=1.0, type=float)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	172
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 # 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	175 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	176 if "imgsz" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	177 image_size = kwargs['imgsz']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	178 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	179 image_size = 320
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	180
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	181 if "epochs" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	182 n_epochs = kwargs['epochs']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	183 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	184 n_epochs = 100
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	185
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	186 if "hsv_h" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	187 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	188 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	189 aug_hsv_h = 0.015
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	190
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	191 if "hsv_s" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	192 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	193 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	194 aug_hsv_s = 0.7
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	195
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	196 if "hsv_v" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	197 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	198 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	199 aug_hsv_v = 0.4
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	200
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	201 if "degrees" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	202 aug_degrees = kwargs['degrees']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	203 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	204 aug_degrees = 10.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	205
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	206 if "translate" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	207 aug_translate = kwargs['translate']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	208 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	209 aug_translate = 0.1
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	210
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	211 if "scale" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	212 aug_scale = kwargs['scale']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	213 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	214 aug_scale = 0.2
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	215
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	216 if "shear" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	217 aug_shear = kwargs['shear']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	218 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	219 aug_shear = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	220
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	221 if "shear" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	222 aug_shear = kwargs['shear']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	223 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	224 aug_shear = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	225
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	226 if "perspective" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	227 aug_perspective = kwargs['perspective']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	228 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	229 aug_perspective = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	230
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	231 if "fliplr" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	232 aug_fliplr = kwargs['fliplr']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	233 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	234 aug_fliplr = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	235
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	236 if "flipud" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	237 aug_flipud = kwargs['flipud']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	238 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	239 aug_flipud = 0.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	240
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	241 if "mosaic" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	242 aug_mosaic = kwargs['mosaic']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	243 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	244 aug_mosaic = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	245
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	246 if "crop_fraction" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	247 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	248 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	249 aug_crop_fraction = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	250
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	251 if "weight_decay" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	252 weight_decay = kwargs['weight_decay']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	253 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	254 weight_decay = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	255
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	256 if "init_lr" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	257 init_lr = kwargs['init_lr']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	258 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	259 init_lr = 1.0
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	260
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	261 # 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	262 if args.model_format == 'pt':
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	263 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	264 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	265 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	266 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	267 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	268 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	269 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	270 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	271 flipud=aug_flipud, mosaic=aug_mosaic, crop_fraction=aug_crop_fraction,
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	272 weight_decay=weight_decay, lr0=init_lr)
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	273 return model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	274
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	275
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	276 # Validate the trained model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	277 def validateModel(model):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	278 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	279 metrics.box.map # map50-95
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	280 metrics.box.map50 # map50
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	281 metrics.box.map75 # map75
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	282 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	283
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	284
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	285 # 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	286 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	287 if "imgsz" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	288 image_size = kwargs['imgsz']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	289 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	290 image_size = 320
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 if "conf" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	293 confidence = kwargs['conf']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	294 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	295 confidence = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	296
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	297 if "iou" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	298 iou_value = kwargs['iou']
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	299 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	300 iou_value = 0.5
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	301
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	302 if "num_classes" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	303 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	304 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	305 class_array = [0, 1]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	306
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	307 if "max_det" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	308 maximum_detections = args.max_det
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	309 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	310 maximum_detections = 300
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	311
3 97bc82ee2a61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 743c8acf1ea4e4b1e718743d3772b7e592646611 bgruening parents: 2 diff changeset	312 run_save_dir = kwargs['run_dir'] # For Galaxy, run_save_dir is always provided via xml wrapper
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	313 if "foldername" in kwargs:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	314 save_folder_name = kwargs['foldername']
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	315
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	316 # 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	317 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	318 conf=confidence, imgsz=image_size,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	319 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	320 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	321 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	322 return prediction
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	323
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	324
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	325 # Save bounding boxes
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	326 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	327 """
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	328 Function to save YOLO bounding boxes to text files.
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	329
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	330 Parameters:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	331 - 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	332 - 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	333 """
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	334 for result in predictions:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	335 result = result.to("cpu").numpy()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	336 # 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	337 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	338 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	339 class_nums = result.boxes.cls # Class numbers
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	340
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	341 # 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	342 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	343 save_path.mkdir(parents=True, exist_ok=True)
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	344
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	345 # 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	346 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	347 text_filename = save_path / f"{image_filename}.txt"
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	348
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	349 # 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	350 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	351 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	352 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	353 confidence = confidence_scores[i]
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	354 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	355 f.write(f'{class_num:01} {x1:06.2f} {y1:06.2f} {x2:06.2f} {y2:06.2f} {confidence:0.02} \n')
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	356 print(colored(f"Bounding boxes saved in: {text_filename}", 'green'))
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	357
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	358
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	359 # Main code
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	360 if __name__ == '__main__':
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	361 args = parser.parse_args()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	362 os.environ["KMP_DUPLICATE_LIB_OK"] = "TRUE"
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	363
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	364 # Train/load model
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	365 if (args.train):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	366 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	367 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	368 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	369 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	370 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	371 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	372 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	373 validateModel(model)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	374 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	375 t = time.time()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	376 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	377 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	378 "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	379 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	380 "train", "weights", "best.pt"))
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	381 else:
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	382 model = YOLO(os.path.join(args.model_path,
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	383 args.model_name + ".pt"))
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	384 model.info(verbose=True)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	385 elapsed = time.time() - t
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	386 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	387
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	388 if (args.save_dir):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	389 # 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	390 t = time.time()
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	391 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	392 # 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	393 class_names = model.names
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	394 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	395 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	396 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	397 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	398 elapsed = time.time() - t
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	399 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	400
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	401 if (args.mode == "detect"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	402 # Save bounding boxes
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	403 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	404
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	405 # Loop over each result
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	406 for result in predictions:
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	407 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	408 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	409 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	410
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	411 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	412 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	413 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	414 confidence = conf.item()
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	415 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	416
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	417 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	418 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	419 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	420
dfda27273ead planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 9685f843a52451b3416416094cc0e740f8825dcc bgruening parents: 0 diff changeset	421 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	422 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	423 elif (args.mode == "track"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	424 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	425 tracker=args.tracker_file,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	426 conf=args.confidence,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	427 iou=args.iou,
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	428 persist=True,
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	429 show=False,
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	430 save=True,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	431 project=args.run_dir,
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	432 name=args.foldername)
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	433 # Store the track history
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	434 track_history = defaultdict(lambda: [])
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	435
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	436 tsv_path = os.path.join(args.save_dir, "tracks.tsv")
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	437 with open(tsv_path, "w", newline="") as tsvfile:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	438 writer = csv.writer(tsvfile, delimiter='\t')
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	439 writer.writerow(['track_id', 'frame', 'class', 'centroid_x', 'centroid_y'])
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	440 frame_idx = 0
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	441 for result in results:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	442 # Get the boxes and track IDs
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	443 if result.boxes and result.boxes.is_track:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	444 track_ids = result.boxes.id.int().cpu().tolist()
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	445 labels = result.boxes.cls.int().cpu().tolist() if hasattr(result.boxes, "cls") else [0] * len(track_ids)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	446 # Prepare mask image
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	447 img_shape = result.orig_shape if hasattr(result, "orig_shape") else result.orig_img.shape
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	448 mask = np.zeros(img_shape[:2], dtype=np.uint16)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	449 # Check if polygons (masks) are available
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	450 if hasattr(result, "masks") and result.masks is not None and hasattr(result.masks, "xy"):
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	451 polygons = result.masks.xy
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	452 for i, (track_id, label) in enumerate(zip(track_ids, labels)):
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	453 if i < len(polygons):
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	454 contour = polygons[i].astype(np.int32)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	455 contour = contour.reshape(-1, 1, 2)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	456 cv2.drawContours(mask, [contour], -1, int(track_id), cv2.FILLED)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	457 # Calculate centroid of the polygon
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	458 M = cv2.moments(contour)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	459 if M["m00"] != 0:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	460 cx = float(M["m10"] / M["m00"])
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	461 cy = float(M["m01"] / M["m00"])
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	462 else:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	463 cx, cy = 0.0, 0.0
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	464 writer.writerow([track_id, frame_idx, label, cx, cy])
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	465 else:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	466 # Fallback to bounding boxes if polygons are not available
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	467 boxes = result.boxes.xywh.cpu()
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	468 xyxy_boxes = result.boxes.xyxy.cpu().numpy()
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	469 for i, (box, xyxy, track_id, label) in enumerate(zip(boxes, xyxy_boxes, track_ids, labels)):
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	470 x, y, w, h = box
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	471 writer.writerow([track_id, frame_idx, label, float(x), float(y)])
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	472 x1, y1, x2, y2 = map(int, xyxy)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	473 cv2.rectangle(mask, (x1, y1), (x2, y2), int(track_id), thickness=-1)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	474 # Collect masks for TYX stack
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	475 if frame_idx == 0:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	476 mask_stack = []
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	477 mask_stack.append(mask)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	478 frame_idx += 1
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	479 # Save TYX stack (T=frames, Y, X)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	480 if 'mask_stack' in locals() and len(mask_stack) > 0:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	481 tyx_array = np.stack(mask_stack, axis=0)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	482 # Remove string from last underscore in filename
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	483 stem = pathlib.Path(result.path).stem
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	484 stem = stem.rsplit('_', 1)[0] if '_' in stem else stem
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	485 mask_save_as = str(pathlib.Path(os.path.join(args.save_dir, stem + "_mask.tiff")).absolute())
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	486 imwrite(mask_save_as, tyx_array)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	487 print(colored(f"TYX mask stack saved as : '{mask_save_as}'", 'magenta'))
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	488 print(colored(f"Tracking results saved in : '{args.save_dir}' \n", 'green'))
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	489 elif (args.mode == "segment"):
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	490 # 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	491 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	492 class_names = [line.strip() for line in f.readlines()]
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	493 # Create a mapping from class names to indices
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	494 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	495
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	496 # Save polygon coordinates
252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	497 for result in predictions:
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	498 # Create binary mask
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	499 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	500 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	501 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	502 mask_save_as = str(pathlib.Path(os.path.join(args.save_dir, filename + "_mask.tiff")).absolute())
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	503 # Define output file path for text file
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	504 output_filename = os.path.splitext(filename)[0] + ".txt"
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	505 txt_save_as = str(pathlib.Path(os.path.join(args.save_dir, filename + ".txt")).absolute())
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	506 instance_id = 1 # Start instance IDs from 1
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	507 for c, ci in enumerate(result):
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	508 # Extract contour result
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	509 contour = ci.masks.xy.pop()
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	510 contour = contour.astype(np.int32)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	511 contour = contour.reshape(-1, 1, 2)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	512 # Draw contour onto mask with unique instance id
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	513 _ = cv2.drawContours(b_mask, [contour], -1, instance_id, cv2.FILLED)
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	514
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	515 # Normalized polygon points
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	516 points = ci.masks.xyn.pop()
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	517 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	518
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	519 with open(txt_save_as, 'a') as f:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	520 segmentation_points = ['{} {}'.format(points[i][0], points[i][1]) for i in range(len(points))]
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	521 segmentation_points_string = ' '.join(segmentation_points)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	522 line = '{} {} {}\n'.format(instance_id, segmentation_points_string, confidence)
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	523 f.write(line)
0 252fd085940d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 67e0e1d123bcfffb10bab8cc04ae67259caec557 bgruening parents: diff changeset	524
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	525 instance_id += 1 # Increment for next object
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	526
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	527 imwrite(mask_save_as, b_mask, imagej=True) # save label mask image
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	528 print(colored(f"Saved label 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	529 print(colored(f"Polygon coordinates saved as : \n '{txt_save_as}' \n", 'cyan'))
4 f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	530 else:
f6990d85161c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c6c9d43a4ecdc88ebdeaf3451453a550f159c506 bgruening parents: 3 diff changeset	531 raise Exception(("Currently only 'detect', 'segment' and 'track' modes are available"))

Mercurial > repos > bgruening > json2yolosegment

annotate yolov8.py @ 4:f6990d85161c draft default tip