def test_DATAAUGMENTATION_parameter_classification(self):
data_aug = Data_Augmentation()
data_aug.config_p_per_sample = 1
data_aug.seg_augmentation = False
img_aug, seg_aug = data_aug.run(self.img3D, self.seg3D)
self.assertFalse(np.array_equal(img_aug, self.img3D))
self.assertTrue(np.array_equal(seg_aug, self.seg3D))
def test_DATAAUGMENTATION_BASE_create(self):
data_Aug = Data_Augmentation()
self.assertIsInstance(data_Aug, Data_Augmentation)
Data_Augmentation(cycles=5)
Data_Augmentation(cycles=1,
scaling=True,
rotations=True,
elastic_deform=False,
mirror=False,
brightness=True,
contrast=True,
gamma=True,
gaussian_noise=True)
def test_DATAAUGMENTATION_parameter_gaussiannoise(self):
data_aug = Data_Augmentation(cycles=1,
scaling=False,
rotations=False,
elastic_deform=False,
mirror=False,
brightness=False,
contrast=False,
gamma=False,
gaussian_noise=True)
data_aug.config_p_per_sample = 1
img_aug, seg_aug = data_aug.run(self.img3D, self.seg3D)
self.assertFalse(np.array_equal(img_aug, self.img3D))
self.assertTrue(np.array_equal(seg_aug, self.seg3D))
def test_DATAAUGMENTATION_parameter_cropping(self):
data_aug = Data_Augmentation(cycles=1,
scaling=False,
rotations=False,
elastic_deform=False,
mirror=False,
brightness=False,
contrast=False,
gamma=False,
gaussian_noise=False)
data_aug.cropping = True
data_aug.cropping_patch_shape = (4, 4, 4)
img_aug, seg_aug = data_aug.run(self.img3D, self.seg3D)
self.assertEqual(img_aug.shape, (1, 4, 4, 4, 1))
self.assertEqual(seg_aug.shape, (1, 4, 4, 4, 3))
def setUpClass(self):
np.random.seed(1234)
# Create imgaging and segmentation data set
self.dataset = dict()
for i in range(0, 10):
img = np.random.rand(16, 16, 16) * 255
self.img = img.astype(int)
seg = np.random.rand(16, 16, 16) * 3
self.seg = seg.astype(int)
sample = (self.img, self.seg)
self.dataset["TEST.sample_" + str(i)] = sample
# Initialize Dictionary IO Interface
io_interface = Dictionary_interface(self.dataset,
classes=3,
three_dim=True)
# Initialize temporary directory
self.tmp_dir = tempfile.TemporaryDirectory(prefix="tmp.miscnn.")
tmp_batches = os.path.join(self.tmp_dir.name, "batches")
# Initialize Data IO
self.data_io = Data_IO(io_interface,
input_path="",
output_path="",
batch_path=tmp_batches,
delete_batchDir=False)
# Initialize Data Augmentation
self.data_aug = Data_Augmentation()
# Get sample list
self.sample_list = self.data_io.get_indiceslist()
def test_DATAAUGMENTATION_parameter_percentage(self):
data_aug = Data_Augmentation(cycles=100,
scaling=True,
rotations=False,
elastic_deform=False,
mirror=False,
brightness=False,
contrast=False,
gamma=False,
gaussian_noise=False)
data_aug.config_p_per_sample = 0.3
img_aug, seg_aug = data_aug.run(self.img3D, self.seg3D)
counter_equal = 0
for i in range(0, 100):
is_equal = np.array_equal(img_aug[i], self.img3D[0])
if is_equal: counter_equal += 1
ratio = counter_equal / 100
self.assertTrue(ratio >= 0.5 and ratio <= 0.9)
def test_MODEL_predictionAugmentated_2D(self):
data_aug = Data_Augmentation()
pp = Preprocessor(self.data_io2D,
batch_size=2,
data_aug=data_aug,
analysis="fullimage")
nn = Neural_Network(preprocessor=pp)
for sample in self.sample_list2D:
predictions = nn.predict_augmentated(sample)
self.assertEqual(len(predictions), 2)
for pred in predictions:
self.assertEqual(pred.shape, (16, 16, 3))
def test_DATAAUGMENTATION_BASE_cycles(self):
with self.assertRaises(Exception):
data_aug = Data_Augmentation(cycles=0)
img_aug, seg_aug = data_aug.run(self.img2D, self.seg2D)
for i in range(1, 50, 5):
data_aug = Data_Augmentation(cycles=i)
img_aug, seg_aug = data_aug.run(self.img2D, self.seg2D)
self.assertEqual(img_aug.shape[0], i)
def test_DATAGENERATOR_augcyling(self):
data_aug = Data_Augmentation(cycles=20)
pp_fi = Preprocessor(self.data_io,
batch_size=4,
data_aug=data_aug,
prepare_subfunctions=False,
prepare_batches=False,
analysis="fullimage")
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=False,
iterations=None)
self.assertEqual(50, len(data_gen))
def test_MODEL_predictionAugmentated_3D(self):
data_aug = Data_Augmentation()
pp = Preprocessor(self.data_io3D,
batch_size=1,
patch_shape=(8, 8, 8),
data_aug=data_aug,
analysis="patchwise-crop")
nn = Neural_Network(preprocessor=pp,
architecture=UNet_standard(depth=2))
for sample in self.sample_list3D:
predictions = nn.predict_augmentated(sample)
self.assertEqual(len(predictions), 3)
for pred in predictions:
self.assertEqual(pred.shape, (16, 16, 16, 3))
def test_DATAAUGMENTATION_BASE_infauf(self):
data_aug = Data_Augmentation()
data_aug.infaug = True
for axis in data_aug.infaug_flip_list:
data_aug.infaug_flip_current = axis
img_aug = data_aug.run_infaug(self.img3D)
self.assertFalse(np.array_equal(img_aug, self.img3D))
img_aug = data_aug.run_infaug(img_aug)
self.assertTrue(np.array_equal(img_aug, self.img3D))
def test_DATAGENERATOR_inferenceAug(self):
data_aug = Data_Augmentation()
pp_fi = Preprocessor(self.data_io,
batch_size=4,
data_aug=data_aug,
prepare_subfunctions=False,
prepare_batches=False,
analysis="fullimage")
data_gen = DataGenerator([self.sample_list[0]],
pp_fi,
training=False,
shuffle=False,
iterations=None)
pred_list_inactive = []
for batch in data_gen:
pred_list_inactive.append(batch)
data_aug.infaug = True
pred_list_active = []
for batch in data_gen:
pred_list_active.append(batch)
for i in range(0, len(pred_list_active)):
ba = pred_list_active[i]
bi = pred_list_inactive[i]
self.assertFalse(np.array_equal(ba, bi))
def test_DATAAUGMENTATION_BASE_run2D(self):
data_aug = Data_Augmentation()
data_aug.config_p_per_sample = 1
img_aug, seg_aug = data_aug.run(self.img2D, self.seg2D)
self.assertEqual(img_aug.shape, self.img2D.shape)
self.assertFalse(np.array_equal(img_aug, self.img2D))
self.assertEqual(seg_aug.shape, self.seg2D.shape)
self.assertFalse(np.array_equal(seg_aug, self.seg2D))
data_aug = Data_Augmentation(cycles=1,
scaling=False,
rotations=False,
elastic_deform=False,
mirror=False,
brightness=False,
contrast=False,
gamma=False,
gaussian_noise=False)
img_aug, seg_aug = data_aug.run(self.img2D, self.seg2D)
self.assertTrue(np.array_equal(img_aug, self.img2D))
# Setup of MIScnn Pipeline #
#-----------------------------------------------------#
# Initialize Data IO Interface for NIfTI data
## We are using 4 classes due to [background, lung_left, lung_right, covid-19]
interface = NIFTI_interface(channels=1, classes=4)
# Create Data IO object to load and write samples in the file structure
data_io = Data_IO(interface, input_path="data", delete_batchDir=False)
# Access all available samples in our file structure
sample_list = data_io.get_indiceslist()
sample_list.sort()
# Create and configure the Data Augmentation class
data_aug = Data_Augmentation(cycles=1, scaling=True, rotations=True,
elastic_deform=True, mirror=True,
brightness=True, contrast=True, gamma=True,
gaussian_noise=True)
# Create a clipping Subfunction to the lung window of CTs (-1250 and 250)
sf_clipping = Clipping(min=-1250, max=250)
# Create a pixel value normalization Subfunction to scale between 0-255
sf_normalize = Normalization(mode="grayscale")
# Create a resampling Subfunction to voxel spacing 1.58 x 1.58 x 2.70
sf_resample = Resampling((1.58, 1.58, 2.70))
# Create a pixel value normalization Subfunction for z-score scaling
sf_zscore = Normalization(mode="z-score")
# Assemble Subfunction classes into a list
sf = [sf_clipping, sf_normalize, sf_resample, sf_zscore]
# Create and configure the Preprocessor class
