batch-compare-quantised-ctvi.py

import papermill as pm
import os
from os.path import expanduser
import shutil
import json

NB_INPUT_DIR = '{}/repos/HFLung-segmentation'.format(expanduser('~'))
NB_OUTPUT_DIR = '{}/papermill-output/compare-quantised-ctvi'.format(expanduser('~'))
NOTEBOOK_NAME = 'compare patient nnunet predictions with quantised PET and CTVI-DIR'
RAW_BASE_DIR = '/mnt/data/datasets/RNSH_HFlung/nnU-Net-processing/nnUNet_raw'

DATASET_IDS = [160,161,162]
TEST_IDS = [0,1]
CONFIG_SUFFIXES = ['','/2d']

for config in CONFIG_SUFFIXES:
    output_nb_path = '{}{}'.format(NB_OUTPUT_DIR, config.replace('/','-'))

    # make sure the notebook output directory exists
    if os.path.exists(output_nb_path):
        shutil.rmtree(output_nb_path)
        print('deleted {}'.format(output_nb_path))
    os.makedirs(output_nb_path)

    for dataset_id in DATASET_IDS:
        for test_id in TEST_IDS:
            # get the patient ID
            mapping_file = '{}/patient-mapping-Dataset{}_RNSH_HFlung.json'.format(RAW_BASE_DIR, dataset_id)
            with open(mapping_file, 'r') as fp:
                patient_map_d = json.load(fp)
            patient_id = int(patient_map_d['test'][test_id][0].split('/')[-1].split('.')[0].split('Patient')[1])

            input_nb = '{}/{}.ipynb'.format(NB_INPUT_DIR, NOTEBOOK_NAME)
            output_nb = '{}/{} - set {:02d} - tid {:02d} - pid {:02d}.ipynb'.format(output_nb_path, NOTEBOOK_NAME, dataset_id, test_id, patient_id)

            if not os.path.exists(output_nb_path):
                os.makedirs(output_nb_path)

            print('dataset id {:03d}, test id {:02d}, patient id {:02d}: \'{}\''.format(dataset_id, test_id, patient_id, output_nb))
            pm.execute_notebook(
                                input_path=input_nb,
                                output_path=output_nb,
                                parameters=dict(DATASET_ID=dataset_id, TEST_ID=test_id, MODEL_CONFIG_SUFFIX=config)
                                )
            print('-------------\n')