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