| """ |
| Author: Mélanie Gaillochet |
| Date: 2020-10-27 |
| """ |
| import json |
| import os |
| import pickle as pkl |
|
|
| import h5py |
| import nibabel as nib |
| import numpy as np |
|
|
| from Configs.configs import config_folder |
|
|
|
|
| def get_config_from_json(config_filename): |
| """ |
| Get the config from a json file |
| :param config_filename: name of config file (located in Configs.config) |
| :return: config(namespace) or config(dictionary) |
| """ |
| config_filepath = os.path.join(config_folder, config_filename) |
| config_dict = _read_json_file(config_filepath) |
|
|
| return config_dict |
|
|
|
|
| def _read_json_file(file_path): |
| """ |
| We are reading the json file and returning a dictionary |
| :param file_path: |
| :return: |
| """ |
| |
| with open(file_path, 'r') as config_file: |
| output_dict = json.load(config_file) |
| return output_dict |
|
|
|
|
| def load_single_image(folder_path, filename_list, idx): |
| """ |
| We load the data and label for the specific list index given |
| :param folder_path: |
| :param filename_list: |
| :param idx: |
| :return: image (array) |
| """ |
| cur_volume_path = os.path.join(folder_path, filename_list[idx]) |
| ending = cur_volume_path.rpartition('.')[2] |
|
|
| if ending == 'nii': |
| inputImage = nib.load(cur_volume_path) |
| img = inputImage.get_data() |
| img = np.array(img) |
|
|
| elif not os.path.isdir(folder_path): |
| with h5py.File(folder_path + '.hdf5', 'r') as hf: |
| img = hf[filename_list[idx]][:] |
|
|
| return img |
|
|
|
|
| def save_hdf5(data, img_idx, dest_file): |
| """ |
| We are saving an hdf5 object |
| :param data: |
| :param filename: |
| :return: |
| """ |
| with h5py.File(dest_file, "a", libver='latest', swmr=True) as hf: |
| hf.swmr_mode = True |
| hf.create_dataset(name=str(img_idx), data=data, shape=data.shape, dtype=data.dtype) |
|
|
|
|
| def create_unexisting_folder(dir_path): |
| """ |
| We create a folder with the given path. |
| If the folder already exists, we add '_1', '_2', ... to it |
| :param dir_path: |
| """ |
| i = 0 |
| created = False |
| path = dir_path |
| while not created: |
| try: |
| os.makedirs(path) |
| created = True |
| except OSError or FileExistsError: |
| i += 1 |
| path = dir_path + '_' + str(i) |
| |
|
|
| return path |
|
|
|
|
| def save_obj(obj, name): |
| """ |
| Shortcut function to save an object as pkl |
| Args: |
| obj: object to save |
| name: filename of the object |
| """ |
| with open(name + '.pkl', 'wb') as f: |
| pkl.dump(obj, f, pkl.HIGHEST_PROTOCOL) |
|
|
|
|
| def load_obj(name): |
| """ |
| Shortcut function to load an object from pkl file |
| Args: |
| name: filename of the object |
| Returns: |
| obj: object to load |
| """ |
| with open(name + '.pkl', 'rb') as f: |
| return pkl.load(f) |
|
|
|
|
| def unpickle(file): |
| with open(file, 'rb') as fo: |
| dict1 = pkl.load(fo, encoding='bytes') |
| return dict1 |
|
|
