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b/split_data.py |
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import os |
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import numpy as np |
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import random as rnd |
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import pandas as pd |
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import config |
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from utils import read_csv_column, read_csv, store_to_csv |
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def load_labels(): |
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return read_csv(config.PATIENT_LABELS_CSV) |
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def load_test_ids(): |
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return read_csv_column(config.TEST_PATIENTS_IDS) |
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def get_patient_name(patient_file): |
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return os.path.basename(patient_file).split('.')[0] |
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def load_patient_ids(): |
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test_ids = set(load_test_ids()) |
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patient_ids = [get_patient_name(patient_id) |
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for patient_id in os.listdir(config.ALL_IMGS) |
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if get_patient_name(patient_id) not in test_ids] |
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return patient_ids |
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def get_class(labels, patient_id): |
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return labels.get_value(patient_id, config.COLUMN_NAME) |
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def count_patients_from_class(patient_ids, labels, clazz): |
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return len([patient for patient in patient_ids |
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if get_class(labels, patient) == clazz]) |
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def split_data(): |
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labels = load_labels() |
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total = len(labels) |
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print("Total labels loaded: ", total) |
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patient_ids = load_patient_ids() |
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print("Total patient ids loaded: ", len(patient_ids)) |
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print("Patient with cancer are: ", count_patients_from_class( |
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patient_ids, labels, config.CANCER_CLS)) |
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validation_size = int(0.15 * total) |
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validation_set = rnd.sample(patient_ids, validation_size) |
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train_set = [patient for patient in patient_ids |
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if patient not in validation_set] |
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print("Patients for training: ", len(train_set)) |
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print("Patients for validation: ", len(validation_set)) |
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print("Patients with cancer in validation set {}, no cancer {}.".format( |
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count_patients_from_class(validation_set, labels, config.CANCER_CLS), |
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count_patients_from_class(validation_set, labels, config.NO_CANCER_CLS))) |
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print("Patients with cancer in training set {}, no cancer {}.".format( |
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count_patients_from_class(train_set, labels, config.CANCER_CLS), |
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count_patients_from_class(train_set, labels, config.NO_CANCER_CLS))) |
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validation_labels = [get_class(labels, p) for p in validation_set] |
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store_to_csv(validation_set, validation_labels, |
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config.VALIDATION_PATINETS_IDS) |
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train_labels = [get_class(labels, p) for p in train_set] |
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store_to_csv(train_set, train_labels, |
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config.TRAINING_PATIENTS_IDS) |
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if __name__ == '__main__': |
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split_data() |