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""" |
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Code copied from AGXNet: |
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https://github.com/batmanlab/AGXNet |
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""" |
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"""Create adjacency matrix for representing the relations between anatomical landmarks and observations.""" |
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import argparse |
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import pandas as pd |
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import numpy as np |
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import pickle |
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from tqdm import tqdm, trange |
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from torch.utils.data import Dataset, DataLoader |
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parser = argparse.ArgumentParser(description="Create Adjacency matrix Matrix.") |
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parser.add_argument( |
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"--input-path", |
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default="/PROJECT DIR/preprocessing/mimic-cxr-radgraph-sentence-parsed.csv", |
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help="Itemized input data path.", |
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) |
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NORM_OBS = [ |
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"normal", |
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"clear", |
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"sharp", |
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"sharply", |
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"unremarkable", |
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"intact", |
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"stable", |
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"free", |
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] |
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EXCLUDED_OBS = [ |
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"none", |
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"unchanged", |
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"change", |
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"great", |
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"similar", |
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"large", |
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"small", |
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"moderate", |
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"mild", |
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"median", |
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"decrease", |
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"bad", |
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"more", |
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"constant", |
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"worsen", |
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"new", |
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"improve", |
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"status", |
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"position", |
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"sternotomy", |
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"cabg", |
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"replacement", |
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"postoperative", |
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"assessment", |
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"patient", |
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] |
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ABNORM_OBS = [ |
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"effusion", |
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"opacity", |
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"pneumothorax", |
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"edema", |
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"atelectasis", |
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"tube", |
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"consolidation", |
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"process", |
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"abnormality", |
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"enlarge", |
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"tip", |
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"low", |
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"pneumonia", |
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"line", |
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"congestion", |
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"catheter", |
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"cardiomegaly", |
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"fracture", |
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"air", |
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"tortuous", |
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"lead", |
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"disease", |
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"calcification", |
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"prominence", |
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"device", |
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"engorgement", |
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"picc", |
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"clip", |
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"elevation", |
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"expand", |
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"nodule", |
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"wire", |
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"fluid", |
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"degenerative", |
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"pacemaker", |
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"thicken", |
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"marking", |
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"scar", |
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"hyperinflate", |
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"blunt", |
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"loss", |
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"widen", |
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"collapse", |
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"density", |
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"emphysema", |
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"aerate", |
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"mass", |
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"crowd", |
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"infiltrate", |
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"obscure", |
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"deformity", |
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"hernia", |
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"drainage", |
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"distention", |
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"shift", |
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"stent", |
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"pressure", |
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"lesion", |
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"finding", |
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"borderline", |
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"hardware", |
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"dilation", |
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"chf", |
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"redistribution", |
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"aspiration", |
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] |
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LANDMARK_NAME = [ |
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"trachea", |
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"left_hilar", |
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"right_hilar", |
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"hilar_unspec", |
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"left_pleural", |
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"right_pleural", |
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"pleural_unspec", |
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"heart_size", |
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"heart_border", |
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"left_diaphragm", |
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"right_diaphragm", |
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"diaphragm_unspec", |
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"retrocardiac", |
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"lower_left_lobe", |
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"upper_left_lobe", |
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"lower_right_lobe", |
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"middle_right_lobe", |
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"upper_right_lobe", |
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"left_lower_lung", |
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"left_mid_lung", |
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"left_upper_lung", |
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"left_apical_lung", |
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"left_lung_unspec", |
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"right_lower_lung", |
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"right_mid_lung", |
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"right_upper_lung", |
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"right_apical_lung", |
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"right_lung_unspec", |
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"lung_apices", |
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"lung_bases", |
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"left_costophrenic", |
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"right_costophrenic", |
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"costophrenic_unspec", |
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"cardiophrenic_sulcus", |
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"mediastinal", |
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"spine", |
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"clavicle", |
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"rib", |
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"stomach", |
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"right_atrium", |
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"right_ventricle", |
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"aorta", |
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"svc", |
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"interstitium", |
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"parenchymal", |
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"cavoatrial_junction", |
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"cardiopulmonary", |
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"pulmonary", |
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"lung_volumes", |
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"unspecified", |
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"other", |
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] |
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OBSERVATION_CLASS = [ |
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"normal", |
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"clear", |
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"sharp", |
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"sharply", |
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"unremarkable", |
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"intact", |
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"stable", |
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"free", |
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"effusion", |
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"opacity", |
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"pneumothorax", |
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"edema", |
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"atelectasis", |
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"tube", |
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"consolidation", |
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"process", |
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"abnormality", |
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"enlarge", |
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"tip", |
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"low", |
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"pneumonia", |
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"line", |
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"congestion", |
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"catheter", |
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"cardiomegaly", |
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"fracture", |
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"air", |
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"tortuous", |
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"lead", |
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"disease", |
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"calcification", |
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"prominence", |
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"device", |
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"engorgement", |
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"picc", |
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"clip", |
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"elevation", |
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"expand", |
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"nodule", |
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"wire", |
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"fluid", |
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"degenerative", |
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"pacemaker", |
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"thicken", |
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"marking", |
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"scar", |
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"hyperinflate", |
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"blunt", |
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"loss", |
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"widen", |
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"collapse", |
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"density", |
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"emphysema", |
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"aerate", |
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"mass", |
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"crowd", |
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"infiltrate", |
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"obscure", |
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"deformity", |
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"hernia", |
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"drainage", |
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"distention", |
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"shift", |
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"stent", |
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"pressure", |
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"lesion", |
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"finding", |
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"borderline", |
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"hardware", |
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"dilation", |
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"chf", |
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"redistribution", |
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"aspiration", |
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"tail_abnorm_obs", |
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"excluded_obs", |
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] |
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DICT_ANATOMICAL_LANDMARKS = { |
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"trachea": {"a": ["trachea", "tracheal"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
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"left_hilar": { |
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"a": ["hilar", "hilum", "perihilar", "infrahilar"], |
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"m1": ["left"], |
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"m2": ["right"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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"right_hilar": { |
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"a": ["hilar", "hilum", "perihilar", "infrahilar"], |
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"m1": ["right"], |
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"m2": ["left"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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"hilar_unspec": { |
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"a": ["hilar", "hilum", "perihilar", "infrahilar"], |
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"m1": ["left", "right"], |
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"m2": [], |
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"sc": ["hila", "perihilar|right|left", "perihilar|left|right"], |
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"t": "m1-", |
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}, |
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"left_pleural": { |
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"a": ["pleural"], |
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"m1": ["left"], |
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"m2": ["right"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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"right_pleural": { |
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"a": ["pleural"], |
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"m1": ["right"], |
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"m2": ["left"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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"pleural_unspec": { |
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"a": ["pleural"], |
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"m1": ["left", "right"], |
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"m2": [], |
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"sc": [ |
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"pleural|left|right", |
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"pleural|right|left", |
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"pleural|bilateral|right|left", |
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"pleural|bilateral|left|right", |
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], |
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"t": "m1-", |
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}, |
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"heart_size": { |
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"a": ["heart", "cardiac"], |
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"m1": ["border", "borders"], |
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"m2": [], |
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"sc": [], |
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"t": "m1-", |
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}, |
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"heart_border": { |
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"a": ["heart", "cardiac"], |
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"m1": ["border", "borders"], |
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"m2": [], |
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"sc": [], |
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"t": "m1+", |
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}, |
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"left_diaphragm": { |
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"a": ["diaphragm", "hemidiaphragm"], |
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"m1": ["left"], |
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"m2": ["right"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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"right_diaphragm": { |
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"a": ["diaphragm", "hemidiaphragm"], |
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"m1": ["right"], |
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"m2": ["left"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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"diaphragm_unspec": { |
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"a": ["diaphragm", "diaphragms", "hemidiaphragms", "hemidiaphragm"], |
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"m1": ["left", "right"], |
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"m2": [], |
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"sc": ["hemidiaphragm|left|right", "hemidiaphragm|right|left"], |
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"t": "m1-", |
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}, |
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"retrocardiac": {"a": ["retrocardiac"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
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"lower_left_lobe": { |
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"a": ["lobe"], |
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"m1": ["left"], |
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"m2": ["lower"], |
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"sc": [], |
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"t": "m1+m2+", |
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}, |
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"upper_left_lobe": { |
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"a": ["lobe"], |
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"m1": ["left"], |
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"m2": ["upper"], |
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"sc": ["lingula", "lingular"], |
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"t": "m1+m2+", |
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}, |
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"lower_right_lobe": { |
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"a": ["lobe"], |
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"m1": ["right"], |
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"m2": ["lower"], |
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"sc": [], |
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"t": "m1+m2+", |
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}, |
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"middle_right_lobe": { |
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"a": ["lobe"], |
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"m1": ["right"], |
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"m2": ["middle"], |
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"sc": [], |
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"t": "m1+m2+", |
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}, |
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"upper_right_lobe": { |
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"a": ["lobe"], |
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"m1": ["right"], |
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"m2": ["upper"], |
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"sc": [], |
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"t": "m1+m2+", |
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}, |
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"left_lower_lung": { |
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"a": ["lung"], |
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"m1": ["left"], |
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"m2": ["lower", "base", "basilar", "basal", "basis"], |
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"sc": ["base|left", "basilar|left", "basal|left", "lung|left|bases"], |
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"t": "m1+m2+", |
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}, |
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"left_mid_lung": { |
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"a": ["lung"], |
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"m1": ["left"], |
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"m2": ["middle", "mid"], |
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"sc": ["midlung|left"], |
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"t": "m1+m2+", |
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}, |
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"left_upper_lung": { |
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"a": ["lung"], |
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"m1": ["left"], |
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"m2": ["upper"], |
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"sc": [], |
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"t": "m1+m2+", |
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}, |
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"left_apical_lung": { |
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"a": ["apex", "apical", "apical", "apicolateral"], |
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"m1": ["left"], |
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"m2": ["right"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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"left_lung_unspec": { |
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"a": ["lung", "hemithorax"], |
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"m1": ["left", "left-sided"], |
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"m2": [ |
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"volume", |
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"volumes", |
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"right", |
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"lower", |
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"base", |
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"bases", |
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"basilar", |
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"basilar", |
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"basal", |
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"basis", |
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"middle", |
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"mid", |
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"upper", |
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"apex", |
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"apical", |
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"perihilar", |
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], |
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"sc": ["left", "left side", "thorax|left|hemi"], |
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"t": "m1+m2-", |
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}, |
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"right_lower_lung": { |
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"a": ["lung"], |
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"m1": ["right"], |
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"m2": ["lower", "base", "basilar", "basal", "basis"], |
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"sc": ["base|right", "basilar|right", "basal|right", "lung|right|bases"], |
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"t": "m1+m2+", |
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}, |
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"right_mid_lung": { |
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"a": ["lung"], |
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"m1": ["right"], |
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"m2": ["middle", "mid"], |
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"sc": [], |
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"t": "m1+m2+", |
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}, |
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"right_upper_lung": { |
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"a": ["lung"], |
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"m1": ["right"], |
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"m2": ["upper"], |
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"sc": [], |
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"t": "m1+m2+", |
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}, |
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"right_apical_lung": { |
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"a": ["apex", "apical", "apical", "apicolateral"], |
|
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"m1": ["right"], |
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"m2": ["left"], |
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"sc": [], |
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"t": "m1+m2-", |
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}, |
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|
"right_lung_unspec": { |
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|
"a": ["lung", "hemithorax"], |
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|
"m1": ["right", "right-sided"], |
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"m2": [ |
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"volume", |
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"volumes", |
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"left", |
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"lower", |
|
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"base", |
|
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"bases", |
|
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"basilar", |
|
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"basilar", |
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"basal", |
|
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"basis", |
|
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"middle", |
|
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"mid", |
|
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"upper", |
|
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"apex", |
|
|
"apical", |
|
|
"perihilar", |
|
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], |
|
|
"sc": ["right", "right side", "thorax|right|hemi"], |
|
|
"t": "m1+m2-", |
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|
}, |
|
|
"lung_apices": { |
|
|
"a": ["apices", "apical"], |
|
|
"m1": ["left", "right"], |
|
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"m2": [], |
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"sc": ["biapical", "lungs|upper"], |
|
|
"t": "m1-", |
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|
}, |
|
|
"lung_bases": { |
|
|
"a": ["lung", "lungs"], |
|
|
"m1": ["left", "right"], |
|
|
"m2": ["bibasilar", "basilar", "base", "bases", "bibasal", "basal"], |
|
|
"sc": [ |
|
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"lung|lower", |
|
|
"lungs|lower", |
|
|
"bibasilar", |
|
|
"basilar", |
|
|
"bases", |
|
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"bibasal", |
|
|
"basal", |
|
|
"basal|bilateral", |
|
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"lobe|lower", |
|
|
"lobes|lower", |
|
|
"lobe|bilateral|lower", |
|
|
"bases|both", |
|
|
"bibasilar|left|right", |
|
|
"bibasilar|right|left", |
|
|
], |
|
|
"t": "m1-m2+", |
|
|
}, |
|
|
"left_costophrenic": { |
|
|
"a": ["costophrenic"], |
|
|
"m1": ["left"], |
|
|
"m2": ["right"], |
|
|
"sc": [], |
|
|
"t": "m1+m2-", |
|
|
}, |
|
|
"right_costophrenic": { |
|
|
"a": ["costophrenic"], |
|
|
"m1": ["right"], |
|
|
"m2": ["left"], |
|
|
"sc": [], |
|
|
"t": "m1+m2-", |
|
|
}, |
|
|
"costophrenic_unspec": { |
|
|
"a": ["costophrenic"], |
|
|
"m1": ["left", "right"], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m1-", |
|
|
}, |
|
|
"cardiophrenic_sulcus": { |
|
|
"a": ["cardiophrenic"], |
|
|
"m1": [], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m0", |
|
|
}, |
|
|
"mediastinal": { |
|
|
"a": ["mediastinal", "cardiomediastinal", "mediastinum", "cardiomediastinum"], |
|
|
"m1": [], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m0", |
|
|
}, |
|
|
"spine": {"a": ["spine", "spinal"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
|
|
"clavicle": { |
|
|
"a": ["clavicle", "clavicles"], |
|
|
"m1": [], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m0", |
|
|
}, |
|
|
"rib": {"a": ["rib", "ribs"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
|
|
"stomach": { |
|
|
"a": ["stomach", "abdomen", "abdominal"], |
|
|
"m1": [], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m0", |
|
|
}, |
|
|
"right_atrium": { |
|
|
"a": ["atrium", "atrial"], |
|
|
"m1": ["right"], |
|
|
"m2": ["left"], |
|
|
"sc": [], |
|
|
"t": "m1+m2-", |
|
|
}, |
|
|
"right_ventricle": { |
|
|
"a": ["ventricle", "ventricular"], |
|
|
"m1": ["right"], |
|
|
"m2": ["left"], |
|
|
"sc": [], |
|
|
"t": "m1+m2-", |
|
|
}, |
|
|
"aorta": {"a": ["aorta", "aortic"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
|
|
"svc": {"a": ["svc"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
|
|
"interstitium": { |
|
|
"a": ["interstitium", "interstitial"], |
|
|
"m1": [], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m0", |
|
|
}, |
|
|
"parenchymal": {"a": ["parenchymal"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
|
|
"cavoatrial_junction": { |
|
|
"a": ["cavoatrial junction"], |
|
|
"m1": [], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m0", |
|
|
}, |
|
|
"cardiopulmonary": { |
|
|
"a": ["cardiopulmonary"], |
|
|
"m1": [], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m0", |
|
|
}, |
|
|
"pulmonary": {"a": ["pulmonary"], "m1": [], "m2": [], "sc": [], "t": "m0"}, |
|
|
"lung_volumes": { |
|
|
"a": ["lungs", "lung", "volume", "volumes"], |
|
|
"m1": [ |
|
|
"left", |
|
|
"right", |
|
|
"lower", |
|
|
"base", |
|
|
"bases", |
|
|
"basilar", |
|
|
"basal", |
|
|
"basis", |
|
|
"middle", |
|
|
"mid", |
|
|
"upper", |
|
|
"apex", |
|
|
"apical", |
|
|
"apical", |
|
|
], |
|
|
"m2": [], |
|
|
"sc": [], |
|
|
"t": "m1-", |
|
|
}, |
|
|
} |
|
|
|
|
|
|
|
|
class LandmarkObservationAdjacentMatrix(Dataset): |
|
|
def __init__(self, LANDMARK_NAME, OBSERVATION_CLASS, df_anatomy_label): |
|
|
self.LANDMARK_NAME = LANDMARK_NAME |
|
|
self.OBSERVATION_CLASS = OBSERVATION_CLASS |
|
|
self.df_anatomy_label = df_anatomy_label |
|
|
|
|
|
|
|
|
self.sids = list(self.df_anatomy_label["study_id"].unique()) |
|
|
|
|
|
def __getitem__(self, idx): |
|
|
sid = self.sids[idx] |
|
|
df_sid = self.df_anatomy_label[self.df_anatomy_label["study_id"] == sid] |
|
|
landmark_observation_adj_mtx = ( |
|
|
np.zeros((len(LANDMARK_NAME), len(OBSERVATION_CLASS))) - 1.0 |
|
|
) |
|
|
for index, row in df_sid.iterrows(): |
|
|
try: |
|
|
observation_idx = self.OBSERVATION_CLASS.index( |
|
|
row.obs_lemma_grp |
|
|
) |
|
|
landmark_idx = self.LANDMARK_NAME.index(row.landmark_name) |
|
|
|
|
|
curr_val = landmark_observation_adj_mtx[landmark_idx, observation_idx] |
|
|
|
|
|
|
|
|
|
|
|
if row.label == "OBS-DP": |
|
|
landmark_observation_adj_mtx[landmark_idx, observation_idx] = 1.0 |
|
|
elif row.label == "OBS-DA": |
|
|
landmark_observation_adj_mtx[ |
|
|
landmark_idx, observation_idx |
|
|
] = np.maximum(curr_val, 0.0) |
|
|
except: |
|
|
pass |
|
|
return sid, landmark_observation_adj_mtx |
|
|
|
|
|
def __len__(self): |
|
|
return len(self.sids) |
|
|
|
|
|
|
|
|
def anatomy_to_landmark(x, a, m1=[], m2=[], sc=[], t="m0"): |
|
|
""" |
|
|
Args: |
|
|
x: input anatomy, e.g., "lobe|left|lower" |
|
|
a: base anatomy set, e.g., ["hilar", "hilum", "perihilar"] |
|
|
m1: level 1 modifier, e.g., ["left", "right"] |
|
|
m2: level 2 modifier, e.g., ["upper", "middle", "lower"] |
|
|
s: special cases, e.g., ["chest"] |
|
|
t: type, ["m2+", "m1+m2-"] |
|
|
Return: |
|
|
flag: boolean, matched or not matched |
|
|
""" |
|
|
s = set(x.split("|")) |
|
|
if t == "m1+m2+": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m1)) > 0) & (len(s & set(m2)) > 0) |
|
|
elif t == "m1+m2-": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m1)) > 0) & (len(s & set(m2)) == 0) |
|
|
elif t == "m1-m2+": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m1)) == 0) & (len(s & set(m2)) > 0) |
|
|
elif t == "m1-m2-": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m1)) == 0) & (len(s & set(m2)) == 0) |
|
|
elif t == "m1+": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m1)) > 0) |
|
|
elif t == "m2+": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m2)) > 0) |
|
|
elif t == "m1-": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m1)) == 0) |
|
|
elif t == "m2-": |
|
|
flag = (len(s & set(a)) > 0) & (len(s & set(m2)) == 0) |
|
|
elif t == "m0": |
|
|
flag = len(s & set(a)) > 0 |
|
|
|
|
|
if sc: |
|
|
flag = flag | (x in sc) |
|
|
return flag |
|
|
|
|
|
|
|
|
def create_adj_matrix(args): |
|
|
|
|
|
print("Loading parsed RadGraph data...") |
|
|
df_anatomy_label = pd.read_csv(args.input_path, dtype=str) |
|
|
|
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["enlargement", "increase"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "enlarge" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["engorge"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "engorgement" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["opacification", "opacity-"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "opacity" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["calcify"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "calcification" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["effusion ;"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "effusion" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin( |
|
|
["atelectatic", "atelectasis ;", "atelectase"] |
|
|
) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "atelectasis" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["aeration"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "aerate" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["distend", "distension"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "distention" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["wide"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "widen" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["prominent"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "prominence" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["haze"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "haziness" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["masse"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "mass" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["kyphotic"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "kyphosis" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["degenerate"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "degenerative" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["obscuration"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "obscure" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["fibrotic"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "fibrosis" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["nodular", "nodularity"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "nodule" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["ventilate"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "ventilation" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["tortuosity"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "tortuous" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["elongate"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "elongation" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["elevate"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "elevation" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["drain"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "drainage" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["deviate"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "deviation" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["consolidative", "consolidate"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "consolidation" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["dilate", "dilatation"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "dilation" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin( |
|
|
["hydropneumothorax", "pneumothoraces", "pneumothorace"] |
|
|
) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "pneumothorax" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin(["improvement", "improved"]) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "improve" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin( |
|
|
[ |
|
|
"can not be assess", |
|
|
"can not be evaluate", |
|
|
"not well see", |
|
|
"not well assess", |
|
|
"can not be accurately assess", |
|
|
"not well evaluate", |
|
|
"not well visualize", |
|
|
"difficult to evaluate", |
|
|
"poorly see", |
|
|
] |
|
|
) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "difficult to assess" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"] == "pacer" |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "pacemaker" |
|
|
|
|
|
idx_replace = df_anatomy_label["obs_lemma"].isin( |
|
|
["infection", "infectious", "infectious process"] |
|
|
) |
|
|
df_anatomy_label.loc[idx_replace, "obs_lemma"] = "pneumonia" |
|
|
|
|
|
df_anatomy_label.loc[df_anatomy_label["label"].isna(), "label"] = "OBS-NA" |
|
|
|
|
|
|
|
|
landmark_name = [] |
|
|
for index, row in tqdm( |
|
|
df_anatomy_label.iterrows(), total=df_anatomy_label.shape[0] |
|
|
): |
|
|
x = row.anatomy |
|
|
flag = False |
|
|
for k, v in DICT_ANATOMICAL_LANDMARKS.items(): |
|
|
flag = anatomy_to_landmark(x, v["a"], v["m1"], v["m2"], v["sc"], v["t"]) |
|
|
if flag: |
|
|
landmark_name.append(k) |
|
|
break |
|
|
if (not flag) & (row.anatomy == "unspecified"): |
|
|
landmark_name.append("unspecified") |
|
|
elif (not flag) & (row.anatomy != "unspecified"): |
|
|
landmark_name.append("other") |
|
|
|
|
|
df_anatomy_label["landmark_name"] = landmark_name |
|
|
|
|
|
|
|
|
df_anatomy_label["obs_lemma_grp"] = df_anatomy_label["obs_lemma"] |
|
|
|
|
|
idx1 = df_anatomy_label["obs_lemma"].isin(NORM_OBS) |
|
|
idx2 = df_anatomy_label["obs_lemma"].isin(ABNORM_OBS) |
|
|
idx3 = df_anatomy_label["obs_lemma"].isin(EXCLUDED_OBS) |
|
|
|
|
|
df_anatomy_label.loc[idx3, "obs_lemma_grp"] = "excluded_obs" |
|
|
|
|
|
idx = (~idx1) & (~idx2) & (~idx3) |
|
|
df_anatomy_label.loc[idx, "obs_lemma_grp"] = "tail_abnorm_obs" |
|
|
|
|
|
|
|
|
dataset = LandmarkObservationAdjacentMatrix( |
|
|
LANDMARK_NAME, OBSERVATION_CLASS, df_anatomy_label |
|
|
) |
|
|
loader = DataLoader( |
|
|
dataset, batch_size=32, shuffle=False, num_workers=8, drop_last=False |
|
|
) |
|
|
|
|
|
sid_lst = [] |
|
|
adj_mtx_lst = [] |
|
|
for index, data in tqdm(enumerate(loader), total=len(loader)): |
|
|
sid, landmark_observation_adj_mtx = data |
|
|
sid_lst.append(sid) |
|
|
adj_mtx_lst.append(landmark_observation_adj_mtx) |
|
|
|
|
|
|
|
|
full_sids = np.concatenate(sid_lst, axis=0) |
|
|
full_adj_mtx = np.concatenate(adj_mtx_lst, axis=0) |
|
|
dict_adj_mtx = {} |
|
|
for i in trange(len(full_sids)): |
|
|
sid = full_sids[i] |
|
|
dict_adj_mtx[sid] = full_adj_mtx[i] |
|
|
|
|
|
np.save("landmark_observation_sids.npy", full_sids) |
|
|
print("landmark_observation_sids.npy has been saved!") |
|
|
np.save("landmark_observation_adj_mtx.npy", full_adj_mtx) |
|
|
print("landmark_observation_sids.npy has been saved!") |
|
|
|
|
|
|
|
|
if __name__ == "__main__": |
|
|
args = parser.parse_args() |
|
|
create_adj_matrix(args) |
|
|
|
