[6969be]: / rocaseg / describe.py

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import os
import logging
from collections import defaultdict
import click
import torch
from torch.utils.data.dataloader import DataLoader
from rocaseg.datasets import sources_from_path
from rocaseg.preproc import *
from rocaseg.repro import set_ultimate_seed
logging.basicConfig()
logger = logging.getLogger('train')
logger.setLevel(logging.DEBUG)
set_ultimate_seed()
if torch.cuda.is_available():
maybe_gpu = 'cuda'
else:
maybe_gpu = 'cpu'
class Describer:
def __init__(self, config):
self.config = config
def run(self, loader):
metrics_avg = defaultdict(float)
for i, data_batch in enumerate(loader):
metrics_curr = dict()
xs, ys_true = data_batch
# xs, ys_true = xs.to(maybe_gpu), ys_true.to(maybe_gpu)
# Calculate metrics
with torch.no_grad():
e = self.config['metrics_skip_edge']
if e != 0:
metrics_curr['mean'] = xs[:, :, e:-e, e:-e].mean()
metrics_curr['std'] = xs[:, :, e:-e, e:-e].std()
metrics_curr['var'] = xs[:, :, e:-e, e:-e].var()
else:
metrics_curr['mean'] = xs.mean()
metrics_curr['std'] = xs.std()
metrics_curr['var'] = xs.var()
for k, v in metrics_curr.items():
metrics_avg[k] += v
# Add metrics logging
logger.info('Metrics:')
metrics_avg = {k: v / len(loader)
for k, v in metrics_avg.items()}
for k, v in metrics_avg.items():
logger.info(f'{k}: {v}')
@click.command()
@click.option('--path_data_root', default='../../data')
@click.option('--path_experiment_root', default='../../results/temporary')
@click.option('--dataset', type=click.Choice(
['oai_imo', 'okoa', 'maknee']))
@click.option('--mask_mode', default='all_unitibial_unimeniscus', type=str)
@click.option('--sample_mode', default='x_y', type=str)
@click.option('--batch_size', default=64, type=int)
@click.option('--num_workers', default=1, type=int)
@click.option('--seed_trainval_test', default=0, type=int)
@click.option('--metrics_skip_edge', default=0, type=int)
def main(**config):
config['path_logs'] = os.path.join(
config['path_experiment_root'], f"logs_{config['dataset']}_describe")
os.makedirs(config['path_logs'], exist_ok=True)
logging_fh = logging.FileHandler(
os.path.join(config['path_logs'], 'main.log'))
logging_fh.setLevel(logging.DEBUG)
logger.addHandler(logging_fh)
# Collect the available and specified sources
sources = sources_from_path(path_data_root=config['path_data_root'],
selection=config['dataset'],
with_folds=False,
seed_trainval_test=config['seed_trainval_test'])
if config['dataset'] == 'oai_imo':
from rocaseg.datasets import DatasetOAIiMoSagittal2d as DatasetSagittal2d
elif config['dataset'] == 'okoa':
from rocaseg.datasets import DatasetOKOASagittal2d as DatasetSagittal2d
elif config['dataset'] == 'maknee':
from rocaseg.datasets import DatasetMAKNEESagittal2d as DatasetSagittal2d
else:
raise ValueError('Unknown dataset')
for subset in ('trainval', 'test'):
name = subset
df = sources[config['dataset']][f"{subset}_df"]
dataset = DatasetSagittal2d(
df_meta=df, mask_mode=config['mask_mode'], name=name,
sample_mode=config['sample_mode'],
transforms=[
PercentileClippingAndToFloat(cut_min=10, cut_max=99),
ToTensor()
])
loader = DataLoader(dataset,
batch_size=config['batch_size'],
shuffle=False,
num_workers=config['num_workers'],
pin_memory=True,
drop_last=False)
describer = Describer(config=config)
describer.run(loader)
loader.dataset.describe()
if __name__ == '__main__':
main()