import os import random import pandas as pd def get_training_batch(root): """ the proportional distribution of training data across each batch for classification, disease localization, report generation, and segmentation tasks to be 0.15/0.2/0.5/0.15 """ classification_label = ['Atelectasis', 'Calcification of the Aorta', 'Cardiomegaly', 'Consolidation', 'Edema', \ 'Emphysema', 'Enlarged Cardiomediastinum', 'Fibrosis', 'Fracture', 'Hernia', 'Infiltration', 'Lung Lesion', \ 'Lung Opacity', 'Mass', 'No Finding', 'Nodule', 'Pleural Effusion', 'Pleural Other', 'Pleural Thickening', \ 'Pneumomediastinum', 'Pneumonia', 'Pneumoperitoneum', 'Pneumothorax', 'Subcutaneous Emphysema', 'Support Devices', 'Tortuous Aorta'] batch_size = 256 cla_num = int(batch_size * 0.15) loc_num = int(batch_size * 0.2) report_num = int(batch_size * 0.5) seg_num = batch_size - (cla_num + loc_num + report_num) read = lambda x, y : pd.read_csv(x, sep='\t', header=None, chunksize=y) ### classification and report generation # Instruction: # what disease does this image have? # is {} in this image? mimic = f'{root}/MIMIC_classification_report-generation_train.tsv' mimic_chunck = read(mimic, max(cla_num, report_num)) cla_mimic_info = [] report_mimic_info = [] for chunck in mimic_chunck: for info in chunck.values.tolist(): report = info[1] label = info[2] dicom_id = info[-1] if len(report_mimic_info) < report_num: report_mimic_info.append( ['describe the image', report, dicom_id, 'report generation'] ) if len(cla_mimic_info) < int(cla_num*0.6): if random.randint(0, 1): cur_info = ['what disease does this image have?', f"there are {', '.join(label.split('&&'))}", dicom_id, 'classification'] else: vqa_label = classification_label[random.randint(0, len(classification_label)-1)] if vqa_label in label: cur_info = [f'Is {vqa_label} in this image?', f'yes, there is {vqa_label}.', dicom_id, 'classification'] else: cur_info = [f'Is {vqa_label} in this image?', f'no {vqa_label}.', dicom_id, 'classification'] cla_mimic_info.append(cur_info) break del mimic_chunck def organize_data(file, chunck_size, task, instruction, label_index, image_index, instruction_index=None, label_format=None): res = [] chunck_size = max(chunck_size, 1) chuncks = read(file, chunck_size) for chunck in chuncks: for info in chunck.values.tolist(): if instruction_index is not None: instruction = instruction.format(info[instruction_index]) ans = info[label_index] elif label_format is not None: label_ans_list = label_format(info[label_index]) label_ans = label_ans_list[random.randint(0, len(label_ans_list)-1)].split(',') if len(label_ans) == 1: label, ans = label_ans_list[0].split(',')[0], label_ans[0] else: label, ans = label_ans label = label.strip() instruction = instruction.format(label) ans = ans.strip() if len(res) < chunck_size: res.append( [instruction, ans, info[image_index], task] ) break return res ### classification: severity # Instruction: # what is the level of {}? mimic_severity = f'{root}/MIMIC_classification-severity_train.tsv' cla_sev_mimic_info = organize_data( mimic_severity, int(cla_num*0.2), 'classification_sev', 'what is the level of {}?', 1, -1, label_format=lambda x:x.split('&&') ) ### classification: location # Instruction: # where is {}? mimic_location = f'{root}/MIMIC_classification-location_train.tsv' cla_loc_mimic_info = organize_data( mimic_location, int(cla_num*0.2), 'classification_loc', 'where is {}?', 1, -1, label_format=lambda x:x.split('&') ) ### localization # Instruction: # give the accurate bbox of {}. chestX_det = f'{root}/ChestX_Det_localization.tsv' chestX_det_info = organize_data( chestX_det, loc_num, 'localization', 'where is {}?', 2, -1, instruction_index=1, ) ### segmentation # Instruction: # describe the image. cheXmask_heart = f'{root}/CheXmask_heart_segmentation.tsv' cheXmask_heart_info = organize_data( cheXmask_heart, seg_num, 'segmentation', 'please segment the {} from the given image.', 2, -1, instruction_index=1 ) batch_info = cla_mimic_info + report_mimic_info + cla_loc_mimic_info + cla_sev_mimic_info + chestX_det_info + cheXmask_heart_info random.shuffle(batch_info) batch_df = pd.DataFrame(batch_info) return batch_df if __name__ == '__main__': root = '' get_training_batch(root)