AutoSeg4ETICA / nnunet /dataset_conversion /Task027_AutomaticCardiacDetectionChallenge.py

Chris Xiao

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#    Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
#    Licensed under the Apache License, Version 2.0 (the "License");
#    you may not use this file except in compliance with the License.
#    You may obtain a copy of the License at
#
#        http://www.apache.org/licenses/LICENSE-2.0
#
#    Unless required by applicable law or agreed to in writing, software
#    distributed under the License is distributed on an "AS IS" BASIS,
#    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#    See the License for the specific language governing permissions and
#    limitations under the License.

from collections import OrderedDict
from batchgenerators.utilities.file_and_folder_operations import *
import shutil
import numpy as np
from sklearn.model_selection import KFold


def convert_to_submission(source_dir, target_dir):
    niftis = subfiles(source_dir, join=False, suffix=".nii.gz")
    patientids = np.unique([i[:10] for i in niftis])
    maybe_mkdir_p(target_dir)
    for p in patientids:
        files_of_that_patient = subfiles(source_dir, prefix=p, suffix=".nii.gz", join=False)
        assert len(files_of_that_patient)
        files_of_that_patient.sort()
        # first is ED, second is ES
        shutil.copy(join(source_dir, files_of_that_patient[0]), join(target_dir, p + "_ED.nii.gz"))
        shutil.copy(join(source_dir, files_of_that_patient[1]), join(target_dir, p + "_ES.nii.gz"))


if __name__ == "__main__":
    folder = "/media/fabian/My Book/datasets/ACDC/training"
    folder_test = "/media/fabian/My Book/datasets/ACDC/testing/testing"
    out_folder = "/media/fabian/My Book/MedicalDecathlon/MedicalDecathlon_raw_splitted/Task027_ACDC"

    maybe_mkdir_p(join(out_folder, "imagesTr"))
    maybe_mkdir_p(join(out_folder, "imagesTs"))
    maybe_mkdir_p(join(out_folder, "labelsTr"))

    # train
    all_train_files = []
    patient_dirs_train = subfolders(folder, prefix="patient")
    for p in patient_dirs_train:
        current_dir = p
        data_files_train = [i for i in subfiles(current_dir, suffix=".nii.gz") if i.find("_gt") == -1 and i.find("_4d") == -1]
        corresponding_seg_files = [i[:-7] + "_gt.nii.gz" for i in data_files_train]
        for d, s in zip(data_files_train, corresponding_seg_files):
            patient_identifier = d.split("/")[-1][:-7]
            all_train_files.append(patient_identifier + "_0000.nii.gz")
            shutil.copy(d, join(out_folder, "imagesTr", patient_identifier + "_0000.nii.gz"))
            shutil.copy(s, join(out_folder, "labelsTr", patient_identifier + ".nii.gz"))

    # test
    all_test_files = []
    patient_dirs_test = subfolders(folder_test, prefix="patient")
    for p in patient_dirs_test:
        current_dir = p
        data_files_test = [i for i in subfiles(current_dir, suffix=".nii.gz") if i.find("_gt") == -1 and i.find("_4d") == -1]
        for d in data_files_test:
            patient_identifier = d.split("/")[-1][:-7]
            all_test_files.append(patient_identifier + "_0000.nii.gz")
            shutil.copy(d, join(out_folder, "imagesTs", patient_identifier + "_0000.nii.gz"))


    json_dict = OrderedDict()
    json_dict['name'] = "ACDC"
    json_dict['description'] = "cardias cine MRI segmentation"
    json_dict['tensorImageSize'] = "4D"
    json_dict['reference'] = "see ACDC challenge"
    json_dict['licence'] = "see ACDC challenge"
    json_dict['release'] = "0.0"
    json_dict['modality'] = {
        "0": "MRI",
    }
    json_dict['labels'] = {
        "0": "background",
        "1": "RV",
        "2": "MLV",
        "3": "LVC"
    }
    json_dict['numTraining'] = len(all_train_files)
    json_dict['numTest'] = len(all_test_files)
    json_dict['training'] = [{'image': "./imagesTr/%s.nii.gz" % i.split("/")[-1][:-12], "label": "./labelsTr/%s.nii.gz" % i.split("/")[-1][:-12]} for i in
                             all_train_files]
    json_dict['test'] = ["./imagesTs/%s.nii.gz" % i.split("/")[-1][:-12] for i in all_test_files]

    save_json(json_dict, os.path.join(out_folder, "dataset.json"))

    # create a dummy split (patients need to be separated)
    splits = []
    patients = np.unique([i[:10] for i in all_train_files])
    patientids = [i[:-12] for i in all_train_files]

    kf = KFold(5, True, 12345)
    for tr, val in kf.split(patients):
        splits.append(OrderedDict())
        tr_patients = patients[tr]
        splits[-1]['train'] = [i[:-12] for i in all_train_files if i[:10] in tr_patients]
        val_patients = patients[val]
        splits[-1]['val'] = [i[:-12] for i in all_train_files if i[:10] in val_patients]

    save_pickle(splits, "/media/fabian/nnunet/Task027_ACDC/splits_final.pkl")

	# Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
	#
	# Licensed under the Apache License, Version 2.0 (the "License");
	# you may not use this file except in compliance with the License.
	# You may obtain a copy of the License at
	#
	# http://www.apache.org/licenses/LICENSE-2.0
	#
	# Unless required by applicable law or agreed to in writing, software
	# distributed under the License is distributed on an "AS IS" BASIS,
	# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	# See the License for the specific language governing permissions and
	# limitations under the License.

	from collections import OrderedDict
	from batchgenerators.utilities.file_and_folder_operations import *
	import shutil
	import numpy as np
	from sklearn.model_selection import KFold


	def convert_to_submission(source_dir, target_dir):
	niftis = subfiles(source_dir, join=False, suffix=".nii.gz")
	patientids = np.unique([i[:10] for i in niftis])
	maybe_mkdir_p(target_dir)
	for p in patientids:
	files_of_that_patient = subfiles(source_dir, prefix=p, suffix=".nii.gz", join=False)
	assert len(files_of_that_patient)
	files_of_that_patient.sort()
	# first is ED, second is ES
	shutil.copy(join(source_dir, files_of_that_patient[0]), join(target_dir, p + "_ED.nii.gz"))
	shutil.copy(join(source_dir, files_of_that_patient[1]), join(target_dir, p + "_ES.nii.gz"))


	if __name__ == "__main__":
	folder = "/media/fabian/My Book/datasets/ACDC/training"
	folder_test = "/media/fabian/My Book/datasets/ACDC/testing/testing"
	out_folder = "/media/fabian/My Book/MedicalDecathlon/MedicalDecathlon_raw_splitted/Task027_ACDC"

	maybe_mkdir_p(join(out_folder, "imagesTr"))
	maybe_mkdir_p(join(out_folder, "imagesTs"))
	maybe_mkdir_p(join(out_folder, "labelsTr"))

	# train
	all_train_files = []
	patient_dirs_train = subfolders(folder, prefix="patient")
	for p in patient_dirs_train:
	current_dir = p
	data_files_train = [i for i in subfiles(current_dir, suffix=".nii.gz") if i.find("_gt") == -1 and i.find("_4d") == -1]
	corresponding_seg_files = [i[:-7] + "_gt.nii.gz" for i in data_files_train]
	for d, s in zip(data_files_train, corresponding_seg_files):
	patient_identifier = d.split("/")[-1][:-7]
	all_train_files.append(patient_identifier + "_0000.nii.gz")
	shutil.copy(d, join(out_folder, "imagesTr", patient_identifier + "_0000.nii.gz"))
	shutil.copy(s, join(out_folder, "labelsTr", patient_identifier + ".nii.gz"))

	# test
	all_test_files = []
	patient_dirs_test = subfolders(folder_test, prefix="patient")
	for p in patient_dirs_test:
	current_dir = p
	data_files_test = [i for i in subfiles(current_dir, suffix=".nii.gz") if i.find("_gt") == -1 and i.find("_4d") == -1]
	for d in data_files_test:
	patient_identifier = d.split("/")[-1][:-7]
	all_test_files.append(patient_identifier + "_0000.nii.gz")
	shutil.copy(d, join(out_folder, "imagesTs", patient_identifier + "_0000.nii.gz"))


	json_dict = OrderedDict()
	json_dict['name'] = "ACDC"
	json_dict['description'] = "cardias cine MRI segmentation"
	json_dict['tensorImageSize'] = "4D"
	json_dict['reference'] = "see ACDC challenge"
	json_dict['licence'] = "see ACDC challenge"
	json_dict['release'] = "0.0"
	json_dict['modality'] = {
	"0": "MRI",
	}
	json_dict['labels'] = {
	"0": "background",
	"1": "RV",
	"2": "MLV",
	"3": "LVC"
	}
	json_dict['numTraining'] = len(all_train_files)
	json_dict['numTest'] = len(all_test_files)
	json_dict['training'] = [{'image': "./imagesTr/%s.nii.gz" % i.split("/")[-1][:-12], "label": "./labelsTr/%s.nii.gz" % i.split("/")[-1][:-12]} for i in
	all_train_files]
	json_dict['test'] = ["./imagesTs/%s.nii.gz" % i.split("/")[-1][:-12] for i in all_test_files]

	save_json(json_dict, os.path.join(out_folder, "dataset.json"))

	# create a dummy split (patients need to be separated)
	splits = []
	patients = np.unique([i[:10] for i in all_train_files])
	patientids = [i[:-12] for i in all_train_files]

	kf = KFold(5, True, 12345)
	for tr, val in kf.split(patients):
	splits.append(OrderedDict())
	tr_patients = patients[tr]
	splits[-1]['train'] = [i[:-12] for i in all_train_files if i[:10] in tr_patients]
	val_patients = patients[val]
	splits[-1]['val'] = [i[:-12] for i in all_train_files if i[:10] in val_patients]

	save_pickle(splits, "/media/fabian/nnunet/Task027_ACDC/splits_final.pkl")