make_k_folds_tvt_bbbc021.py

from email.mime import image
from make_k_folds_tvt import MakeTVTSets
# Make K-folds, including their train and validation parts, with csv files as outpus


class MakeKFoldsTVTBBBC021(MakeTVTSets):

    def __init__(self,
                 labels_path="/home/jovyan/Data/BBBC021/BBBC021_Labels.csv",
                 output_dir='/home/jovyan/Inputs/TEST_BBBC021_leave_one_out/',
                 include_groups=[],  # Empty for everything included,
                 include_header="moa",
                 class_column_header="moa",
                 excluded_groups=[
                     ["DMSO", "Cholesterol-lowering", "Eg5 inhibitors"]],
                 #excluded_groups = [["DMSO"]],
                 excluded_groups_headers=["moa"],
                 exclude_images_path="",
                 intact_group_header='compound',
                 unique_sample_headers=["ImageNumber"],
                 image_number_heading="ImageNumber",
                 k_folds="3",
                 divide_on_header='compound',
                 make_train_valid=True,
                 # 1 = 100%,  Percentage of images remaining afte the test set has been excluded
                 valid_fraction=0.25,
                 leave_one_out=True,
                 make_unique_validation=True,
                 non_unique_divider=['concentration',
                                     'moa', 'compound', 'Replicate']
                 ):
        super().__init__(labels_path=labels_path,
                         output_dir=output_dir,
                         include_groups=include_groups,
                         include_header=include_header,
                         class_column_header=class_column_header,
                         excluded_groups=excluded_groups,
                         excluded_groups_headers=excluded_groups_headers,
                         exclude_images_path=exclude_images_path,
                         intact_group_header=intact_group_header,
                         unique_sample_headers=unique_sample_headers,
                         image_number_heading=image_number_heading,
                         k_folds=k_folds,
                         divide_on_header=divide_on_header,
                         valid_fraction=valid_fraction,
                         non_unique_divider=non_unique_divider)
        self.leave_one_out = leave_one_out
        self.make_unique_validation = make_unique_validation

    def main(self):
        print("Started making divisions for runs for BBBC021.")
        if self.leave_one_out:
            if self.make_unique_validation:
                self.make_leave_one_out()
            else:
                self.make_leave_one_out_train_test()
        else:
            if self.make_unique_validation:
                self.make_k_folds()
            else:
                self.make_k_folds_train_test()

        print("Finished. Find output in: " + self.output_dir)


if __name__ == "__main__":
    MakeKFoldsTVTBBBC021().main()