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import os
import os.path as osp
import subprocess
import sys
from pathlib import Path
# custom script arguments
CONFIG_PATH = 'models/swin_base_b32x4-fp16_fungi+val_res_384_cb_epochs_6.py'
CHECKPOINT_PATH = "models/swin_base_b32x4-fp16_fungi+val_res_384_cb_epochs_6_20230524-5197a7e6.pth"
SCORE_THRESHOLD = 0.2
def run_inference(input_csv, output_csv, data_root_path):
"""Load model and dataloader and run inference."""
if not data_root_path.endswith('/'):
data_root_path += '/'
data_cfg_opts = [
f'test_dataloader.dataset.data_root=',
f'test_dataloader.dataset.ann_file={input_csv}',
f'test_dataloader.dataset.data_prefix={data_root_path}']
inference = subprocess.Popen([
'python', '-m',
'tools.test_generate_result_pre-consensus',
CONFIG_PATH, CHECKPOINT_PATH,
output_csv,
'--threshold', str(SCORE_THRESHOLD),
'--no-scores',
'--cfg-options'] + data_cfg_opts)
return_code = inference.wait()
if return_code != 0:
print(f'Inference crashed with exit code {return_code}')
sys.exit(return_code)
print(f'Written {output_csv}')
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument(
"--input-file",
help="Path to a file with observation ids and image paths.",
type=str,
required=True,
)
parser.add_argument(
"--data-root-path",
help="Path to a directory where images are stored.",
type=str,
required=True,
)
parser.add_argument(
"--output-file",
help="Path to a file where predict script will store predictions.",
type=str,
required=True,
)
args = parser.parse_args()
output_csv = os.path.basename(args.output_file)
if not output_csv.endswith(".csv"):
output_csv = output_csv + ".csv"
run_inference(
input_csv=args.input_file,
output_csv=output_csv,
data_root_path=args.data_root_path,
)
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