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A DICOM reader sequence object using Tensorflow Keras Sequence API
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class DicomGenerator(tf.keras.utils.Sequence): | |
def __init__(self, dicom_path, batch_size=1, dtype='float32', | |
shuffle=False, drop_remainder=False, | |
preserve_batch_size=False, **kwargs): | |
self.i = 0 | |
self.batch_size = batch_size | |
self.dtype = dtype | |
self.n = len(dicom_path) | |
self.dicom_path = dicom_path | |
self.drop_remainder = drop_remainder | |
self.preserve_batch_size = preserve_batch_size | |
self.shuffle = shuffle | |
self.__dict__.update(**kwargs) | |
self.kwargs = kwargs | |
def __load__(self, dicom_filename): | |
_img = read_dicom(dicom_filename) | |
if _img.max() - _img.min() > 0: _img = (_img - _img.min()) / (_img.max() - _img.min()) | |
_img = np.asarray(_img, dtype=getattr(np, self.dtype)) | |
return _img | |
def __getitem__(self, index): | |
if (index + 1) * self.batch_size <= len(self.dicom_path): | |
_dicom_path_batch = self.dicom_path[index * self.batch_size:(index + 1) * self.batch_size] | |
elif self.drop_remainder: | |
raise StopIteration() | |
elif self.preserve_batch_size and len(self.dicom_path[index * self.batch_size:len(self.dicom_path)]) != self.batch_size: | |
_dicom_path_batch = self.dicom_path[len(self.dicom_path)-self.batch_size:len(self.dicom_path)] | |
else: | |
_dicom_path_batch = self.dicom_path[index * self.batch_size:len(self.dicom_path)] | |
_img_arr = list(map(lambda _dcm_pth: self.__load__(_dcm_pth), _dicom_path_batch)) | |
_img_arr = np.array(_img_arr, dtype=getattr(np, self.dtype)) | |
return _img_arr | |
def __iter__(self): | |
return self | |
def __next__(self): | |
if self.i*self.batch_size < len(self.dicom_path): | |
_img_arr = self.__getitem__(self.i) | |
self.i += 1 | |
else: raise StopIteration() | |
_img_arr = tf.cast(_img_arr, dtype=getattr(tf, self.dtype)) | |
return _img_arr | |
def __call__(self): | |
self.i = 0 | |
return self | |
def on_epoch_end(self): | |
if self.shuffle: random.SystemRandom().shuffle(self.dicom_path) | |
def __len__(self): | |
return self.n // self.batch_size |
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