def initialise_sampler(self): self.sampler = [] if self.is_training: self.sampler.append([ ResizeSampler(reader=reader, data_param=self.data_param, batch_size=self.net_param.batch_size, windows_per_image=1, shuffle_buffer=True, queue_length=self.net_param.queue_length) for reader in self.readers ]) return if self._infer_type in ('encode', 'encode-decode'): self.sampler.append([ ResizeSampler(reader=reader, data_param=self.data_param, batch_size=self.net_param.batch_size, windows_per_image=1, shuffle_buffer=False, queue_length=self.net_param.queue_length) for reader in self.readers ]) return if self._infer_type == 'linear_interpolation': self.sampler.append([ LinearInterpolateSampler( reader=reader, data_param=self.data_param, batch_size=self.net_param.batch_size, n_interpolations=self.autoencoder_param.n_interpolations, queue_length=self.net_param.queue_length) for reader in self.readers ]) return
def initialise_sampler(self): self.sampler = [] if self.is_training: self.sampler.append(ResizeSampler( reader=self.reader, data_param=self.data_param, batch_size=self.net_param.batch_size, windows_per_image=1, shuffle_buffer=True, queue_length=self.net_param.queue_length)) else: self.sampler.append(RandomVectorSampler( names=('vector',), vector_size=(self.gan_param.noise_size,), batch_size=self.net_param.batch_size, n_interpolations=self.gan_param.n_interpolations, repeat=None, queue_length=self.net_param.queue_length)) # repeat each resized image n times, so that each # image matches one random vector, # (n = self.gan_param.n_interpolations) self.sampler.append(ResizeSampler( reader=self.reader, data_param=self.data_param, batch_size=self.net_param.batch_size, windows_per_image=self.gan_param.n_interpolations, shuffle_buffer=False, queue_length=self.net_param.queue_length))
def initialise_resize_sampler(self): self.sampler = [[ResizeSampler( reader=reader, data_param=self.data_param, batch_size=self.net_param.batch_size, shuffle_buffer=self.is_training, queue_length=self.net_param.queue_length) for reader in self.readers]]
def test_inverse_mapping(self): reader = get_label_reader() sampler = ResizeSampler(reader=reader, data_param=MOD_LABEL_DATA, batch_size=1, shuffle_buffer=False, queue_length=50) aggregator = ResizeSamplesAggregator(image_reader=reader, name='label', output_path=os.path.join( 'testing_data', 'aggregated'), interp_order=0) more_batch = True with self.test_session() as sess: coordinator = tf.train.Coordinator() sampler.run_threads(sess, coordinator, num_threads=2) while more_batch: out = sess.run(sampler.pop_batch_op()) more_batch = aggregator.decode_batch(out['label'], out['label_location']) output_filename = '{}_niftynet_out.nii.gz'.format( sampler.reader.get_subject_id(0)) output_file = os.path.join('testing_data', 'aggregated', output_filename) self.assertAllClose(nib.load(output_file).shape, [256, 168, 256, 1, 1]) sampler.close_all()
def test_inverse_mapping(self): reader = get_label_reader() sampler = ResizeSampler(reader=reader, data_param=MOD_LABEL_DATA, batch_size=1, shuffle_buffer=False, queue_length=50) aggregator = ResizeSamplesAggregator( image_reader=reader, name='label', output_path=os.path.join('testing_data', 'aggregated'), interp_order=0) more_batch = True with self.test_session() as sess: coordinator = tf.train.Coordinator() sampler.run_threads(sess, coordinator, num_threads=2) while more_batch: out = sess.run(sampler.pop_batch_op()) more_batch = aggregator.decode_batch( out['label'], out['label_location']) output_filename = '{}_niftynet_out.nii.gz'.format( sampler.reader.get_subject_id(0)) output_file = os.path.join( 'testing_data', 'aggregated', output_filename) self.assertAllClose( nib.load(output_file).shape, [256, 168, 256, 1, 1]) sampler.close_all()
def test_3d_init(self): sampler = ResizeSampler(reader=get_3d_reader(), data_param=MULTI_MOD_DATA, batch_size=1, shuffle_buffer=False, queue_length=1) with self.test_session() as sess: coordinator = tf.train.Coordinator() sampler.run_threads(sess, coordinator, num_threads=2) out = sess.run(sampler.pop_batch_op()) self.assertAllClose(out['image'].shape, [1, 7, 10, 2, 2]) sampler.close_all()
def test_3d_init(self): sampler = ResizeSampler( reader=get_3d_reader(), data_param=MULTI_MOD_DATA, batch_size=1, shuffle_buffer=False, queue_length=1) with self.test_session() as sess: coordinator = tf.train.Coordinator() sampler.run_threads(sess, coordinator, num_threads=2) out = sess.run(sampler.pop_batch_op()) self.assertAllClose(out['image'].shape, [1, 7, 10, 2, 2]) sampler.close_all()