Add new scripts to analyze BIDS compliant datasets #40
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valosekj
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Nov 14, 2023
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| parser = argparse.ArgumentParser(description='Analyse config file') | ||
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| ## Parameters | ||
| parser.add_argument('--paths-to-bids', default='', nargs='+', | ||
| help='Paths to BIDS compliant datasets (You can add multiple paths using spaces)') | ||
| parser.add_argument('--config', default='', | ||
| help='Path to JSON config file that contains all the training splits') | ||
| parser.add_argument('--paths-to-csv', default='', nargs='+', | ||
| help='Paths to csv files with already computed metrics (You can add multiple paths using spaces)') | ||
| parser.add_argument('--split', default='ALL', choices=('TRAINING', 'VALIDATION', 'TESTING', 'ALL'), | ||
| help='Split of the data that will be analysed (default="ALL")') | ||
| parser.add_argument('--create-csv', default=True, | ||
| help='Store computed metrics using a csv file in results/files (default=True)') |
valosekj
reviewed
Nov 14, 2023
| help='Store computed metrics using a csv file in results/files (default=True)') | ||
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| # Start analysis | ||
| run_analysis(parser.parse_args()) |
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I would add a main() function (example here) and call run_analysis from it.
valosekj
reviewed
Nov 14, 2023
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| from utils import get_img_path_from_mask_path, get_mask_path_from_img_path, edit_metric_dict, save_graphs, change_mask_suffix, get_deriv_sub_from_img_path, str_to_float_list, str_to_str_list, mergedict | ||
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| def run_analysis(args): |
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This function is slightly "heavy".
Would it be possible to split it into several smaller functions (10-20 lines per function)? Each one with a self-explaning docstring.
Also, some nested for loops and if-else conditions are hard to follow. Adding comments would make them easier to follow.
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Thank you for the initiative, @NathanMolinier! I will try the scripts and take a closer look next week (after the workshop and course). |
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Description
Add new scripts to analyze BIDS compliant datasets