def test_DATAIO_BASE_savePrediction(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path=os.path.join(self.tmp_dir.name, "pred"),
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_0",
backup=False,
load_seg=True,
load_pred=False)
self.assertIsNone(sample.pred_data)
data_io.save_prediction(sample.seg_data, sample.index)
self.assertTrue(os.path.exists(os.path.join(self.tmp_dir.name,
"pred")))
sample = data_io.sample_loader("TEST.sample_0",
backup=False,
load_seg=True,
load_pred=True)
self.assertTrue(np.array_equal(sample.seg_data, sample.pred_data))
def test_DATAIO_SampleLoader_Prediction(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path="",
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_5",
backup=False,
load_seg=False,
load_pred=True)
self.assertTrue(
np.array_equal(np.reshape(sample.pred_data, (16, 16, 16)),
self.dataset["TEST.sample_5"][2]))
self.assertEqual(sample.pred_data.shape, (16, 16, 16, 1))
self.assertIsNotNone(sample.img_data)
self.assertIsNone(sample.seg_data)
with self.assertRaises(Exception):
sample = data_io.sample_loader("TEST.sample_2",
backup=False,
load_seg=False,
load_pred=True)
def test_DATAIO_BATCHES_sampleStorage(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path="",
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_0",
backup=False,
load_seg=True,
load_pred=False)
data_io.backup_sample(sample)
self.assertEqual(len(os.listdir(self.tmp_batches)), 1)
data_io.batch_cleanup()
def test_DATAIO_SampleLoader_Imaging(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path="",
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_0",
backup=False,
load_seg=False,
load_pred=False)
self.assertTrue(
np.array_equal(np.reshape(sample.img_data, (16, 16, 16)),
self.dataset["TEST.sample_0"][0]))
self.assertEqual(sample.img_data.shape, (16, 16, 16, 1))
def test_DATAIO_BATCHES_sampleLoading(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path="",
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_0",
backup=False,
load_seg=True,
load_pred=False)
data_io.backup_sample(sample)
sample_new = data_io.load_sample_pickle(sample.index)
data_io.batch_cleanup()
self.assertTrue(np.array_equal(sample_new.img_data, sample.img_data))
self.assertTrue(np.array_equal(sample_new.seg_data, sample.seg_data))
def test_DATAIO_SampleLoader_Combined(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path="",
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_3",
backup=False,
load_seg=True,
load_pred=True)
self.assertIsNotNone(sample.img_data)
self.assertIsNotNone(sample.seg_data)
self.assertIsNotNone(sample.pred_data)
self.assertEqual(sample.img_data.shape, sample.seg_data.shape)
self.assertEqual(sample.seg_data.shape, sample.pred_data.shape)
def test_DATAIO_BATCHES_loading(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path="",
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_0",
backup=False,
load_seg=True,
load_pred=False)
data_io.backup_batches(sample.img_data, sample.seg_data, "abc")
img = data_io.batch_load(pointer="abc", img=True)
self.assertTrue(np.array_equal(sample.img_data, img))
seg = data_io.batch_load(pointer="abc", img=False)
self.assertTrue(np.array_equal(sample.seg_data, seg))
data_io.batch_cleanup()
def test_DATAIO_BATCHES_cleanup(self):
data_io = Data_IO(self.io_interface,
input_path="",
output_path="",
batch_path=self.tmp_batches,
delete_batchDir=False)
sample = data_io.sample_loader("TEST.sample_0",
backup=False,
load_seg=True,
load_pred=False)
data_io.backup_batches(sample.img_data, sample.seg_data, "abc")
data_io.backup_batches(sample.img_data, sample.seg_data, "def")
data_io.backup_batches(sample.img_data, None, pointer="ghi")
self.assertEqual(len(os.listdir(self.tmp_batches)), 5)
data_io.batch_cleanup(pointer="def")
self.assertEqual(len(os.listdir(self.tmp_batches)), 3)
data_io.batch_cleanup()
self.assertEqual(len(os.listdir(self.tmp_batches)), 0)
def test_SUBFUNCTIONS_postprocessing(self):
ds = dict()
for i in range(0, 10):
img = np.random.rand(16, 16, 16) * 255
img = img.astype(int)
seg = np.random.rand(16, 16, 16) * 3
seg = seg.astype(int)
sample = (img, seg)
ds["TEST.sample_" + str(i)] = sample
io_interface = Dictionary_interface(ds, classes=3, three_dim=True)
self.tmp_dir = tempfile.TemporaryDirectory(prefix="tmp.CESP.")
tmp_batches = os.path.join(self.tmp_dir.name, "batches")
dataio = Data_IO(io_interface,
input_path="",
output_path="",
batch_path=tmp_batches,
delete_batchDir=False)
sf = [Resize((9, 9, 9)), Normalization(), Clipping(min=-1.0, max=0.0)]
pp = Preprocessor(dataio,
batch_size=1,
prepare_subfunctions=False,
analysis="patchwise-grid",
subfunctions=sf,
patch_shape=(4, 4, 4))
sample_list = dataio.get_indiceslist()
for index in sample_list:
sample = dataio.sample_loader(index)
for sf in pp.subfunctions:
sf.preprocessing(sample, training=False)
pp.cache["shape_" + str(index)] = sample.img_data.shape
sample.seg_data = np.random.rand(9, 9, 9) * 3
sample.seg_data = sample.seg_data.astype(int)
sample.seg_data = to_categorical(sample.seg_data, num_classes=3)
data_patches = pp.analysis_patchwise_grid(sample,
training=True,
data_aug=False)
seg_list = []
for i in range(0, len(data_patches)):
seg_list.append(data_patches[i][1])
seg = np.stack(seg_list, axis=0)
self.assertEqual(seg.shape, (27, 4, 4, 4, 3))
pred = pp.postprocessing(index, seg)
self.assertEqual(pred.shape, (16, 16, 16))
self.tmp_dir.cleanup()
class DataGeneratorTEST(unittest.TestCase):
# Create random imaging and segmentation data
@classmethod
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.CESP.")
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()
# Delete all temporary files
@classmethod
def tearDownClass(self):
self.tmp_dir.cleanup()
#-------------------------------------------------#
# Base Functionality #
#-------------------------------------------------#
# Class Creation
def test_DATAGENERATOR_create(self):
pp_fi = Preprocessor(self.data_io,
batch_size=4,
data_aug=self.data_aug,
prepare_subfunctions=False,
prepare_batches=False,
analysis="fullimage")
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=False,
validation=False,
shuffle=False,
iterations=None)
self.assertIsInstance(data_gen, DataGenerator)
# Run data generation for training
def test_DATAGENERATOR_runTraining(self):
pp_fi = Preprocessor(self.data_io,
batch_size=4,
data_aug=self.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(len(data_gen), 3)
for batch in data_gen:
self.assertIsInstance(batch, tuple)
self.assertEqual(batch[0].shape, (4, 16, 16, 16, 1))
self.assertEqual(batch[1].shape, (4, 16, 16, 16, 3))
pp_pc = Preprocessor(self.data_io,
batch_size=3,
data_aug=self.data_aug,
prepare_subfunctions=False,
prepare_batches=False,
patch_shape=(5, 5, 5),
analysis="patchwise-crop")
data_gen = DataGenerator(self.sample_list,
pp_pc,
training=True,
shuffle=False,
iterations=None)
self.assertEqual(len(data_gen), 4)
for batch in data_gen:
self.assertIsInstance(batch, tuple)
self.assertEqual(batch[0].shape, (3, 5, 5, 5, 1))
self.assertEqual(batch[1].shape, (3, 5, 5, 5, 3))
# Run data generation for prediction
def test_DATAGENERATOR_runPrediction(self):
pp_fi = Preprocessor(self.data_io,
batch_size=4,
data_aug=self.data_aug,
prepare_subfunctions=False,
prepare_batches=False,
analysis="fullimage")
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=False,
shuffle=False,
iterations=None)
self.assertEqual(len(data_gen), 10)
for batch in data_gen:
self.assertNotIsInstance(batch, tuple)
self.assertEqual(batch.shape, (1, 16, 16, 16, 1))
pp_pc = Preprocessor(self.data_io,
batch_size=3,
data_aug=self.data_aug,
prepare_subfunctions=False,
prepare_batches=False,
patch_shape=(5, 5, 5),
analysis="patchwise-crop")
data_gen = DataGenerator(self.sample_list,
pp_pc,
training=False,
shuffle=False,
iterations=None)
self.assertEqual(len(data_gen), 220)
for batch in data_gen:
self.assertNotIsInstance(batch, tuple)
self.assertIn(batch.shape, [(3, 5, 5, 5, 1), (1, 5, 5, 5, 1)])
# Check if full images without data augmentation are consistent
def test_DATAGENERATOR_consistency(self):
pp_fi = Preprocessor(self.data_io,
batch_size=1,
data_aug=None,
prepare_subfunctions=False,
prepare_batches=False,
analysis="fullimage")
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=False,
iterations=None)
i = 0
for batch in data_gen:
sample = self.data_io.sample_loader(self.sample_list[i],
load_seg=True)
self.assertTrue(np.array_equal(batch[0][0], sample.img_data))
seg = to_categorical(sample.seg_data, num_classes=3)
self.assertTrue(np.array_equal(batch[1][0], seg))
i += 1
# Iteration fixation test
def test_DATAGENERATOR_iterations(self):
pp_fi = Preprocessor(self.data_io,
batch_size=1,
data_aug=None,
prepare_subfunctions=False,
prepare_batches=False,
analysis="fullimage")
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=False,
iterations=None)
self.assertEqual(10, len(data_gen))
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=False,
iterations=5)
self.assertEqual(5, len(data_gen))
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=False,
iterations=50)
self.assertEqual(50, len(data_gen))
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=False,
iterations=100)
self.assertEqual(100, len(data_gen))
# Iteration fixation test
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))
# Check if shuffling is functional
def test_DATAGENERATOR_shuffle(self):
pp_fi = Preprocessor(self.data_io,
batch_size=1,
data_aug=None,
prepare_subfunctions=False,
prepare_batches=False,
analysis="fullimage")
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=False,
iterations=None)
list_ordered = []
for batch in data_gen:
list_ordered.append(batch)
for batch in data_gen:
list_ordered.append(batch)
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=True,
iterations=None)
list_shuffled = []
for batch in data_gen:
list_shuffled.append(batch)
data_gen.on_epoch_end()
for batch in data_gen:
list_shuffled.append(batch)
size = len(data_gen)
o_counter = 0
s_counter = 0
for i in range(0, size):
oa_img = list_ordered[i][0]
oa_seg = list_ordered[i][1]
ob_img = list_ordered[i + size][0]
ob_seg = list_ordered[i + size][1]
sa_img = list_shuffled[i][0]
sa_seg = list_shuffled[i][1]
sb_img = list_shuffled[i + size][0]
sb_seg = list_shuffled[i + size][1]
if np.array_equal(oa_img, ob_img) and \
np.array_equal(oa_seg, ob_seg):
o_counter += 1
if not np.array_equal(sa_img, sb_img) and \
not np.array_equal(sa_seg, sb_seg):
s_counter += 1
o_ratio = o_counter / size
self.assertTrue(o_ratio == 1.0)
s_ratio = s_counter / size
self.assertTrue(1.0 >= s_ratio and s_ratio >= 0.5)
# Run data generation with preparation of subfunctions and batches
def test_DATAGENERATOR_prepareData(self):
pp_fi = Preprocessor(self.data_io,
batch_size=4,
data_aug=None,
prepare_subfunctions=True,
prepare_batches=True,
analysis="fullimage")
data_gen = DataGenerator(self.sample_list,
pp_fi,
training=True,
shuffle=True,
iterations=None)
self.assertEqual(len(data_gen), 3)
for batch in data_gen:
self.assertIsInstance(batch, tuple)
self.assertEqual(batch[0].shape[1:], (16, 16, 16, 1))
self.assertEqual(batch[1].shape[1:], (16, 16, 16, 3))
self.assertIn(batch[0].shape[0], [2, 4])
class NeuralNetworkTEST(unittest.TestCase):
# Create random imaging and segmentation data
@classmethod
def setUpClass(self):
np.random.seed(1234)
# Create 2D imgaging and segmentation data set
self.dataset2D = dict()
for i in range(0, 6):
img = np.random.rand(16, 16) * 255
self.img = img.astype(int)
seg = np.random.rand(16, 16) * 3
self.seg = seg.astype(int)
self.dataset2D["TEST.sample_" + str(i)] = (self.img, self.seg)
# Initialize Dictionary IO Interface
io_interface2D = Dictionary_interface(self.dataset2D,
classes=3,
three_dim=False)
# Initialize temporary directory
self.tmp_dir2D = tempfile.TemporaryDirectory(prefix="tmp.CESP.")
tmp_batches = os.path.join(self.tmp_dir2D.name, "batches")
# Initialize Data IO
self.data_io2D = Data_IO(io_interface2D,
input_path=os.path.join(self.tmp_dir2D.name),
output_path=os.path.join(self.tmp_dir2D.name),
batch_path=tmp_batches,
delete_batchDir=False)
# Initialize Preprocessor
self.pp2D = Preprocessor(self.data_io2D,
batch_size=2,
data_aug=None,
analysis="fullimage")
# Get sample list
self.sample_list2D = self.data_io2D.get_indiceslist()
# Create 3D imgaging and segmentation data set
self.dataset3D = dict()
for i in range(0, 6):
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)
self.dataset3D["TEST.sample_" + str(i)] = (self.img, self.seg)
# Initialize Dictionary IO Interface
io_interface3D = Dictionary_interface(self.dataset3D,
classes=3,
three_dim=True)
# Initialize temporary directory
self.tmp_dir3D = tempfile.TemporaryDirectory(prefix="tmp.CESP.")
tmp_batches = os.path.join(self.tmp_dir3D.name, "batches")
# Initialize Data IO
self.data_io3D = Data_IO(io_interface3D,
input_path=os.path.join(self.tmp_dir3D.name),
output_path=os.path.join(self.tmp_dir3D.name),
batch_path=tmp_batches,
delete_batchDir=False)
# Initialize Preprocessor
self.pp3D = Preprocessor(self.data_io3D,
batch_size=2,
data_aug=None,
analysis="fullimage")
# Get sample list
self.sample_list3D = self.data_io3D.get_indiceslist()
# Delete all temporary files
@classmethod
def tearDownClass(self):
self.tmp_dir2D.cleanup()
self.tmp_dir3D.cleanup()
#-------------------------------------------------#
# Base Functionality #
#-------------------------------------------------#
# Class Creation
def test_MODEL_create(self):
nn2D = Neural_Network(preprocessor=self.pp2D)
self.assertIsInstance(nn2D, Neural_Network)
self.assertFalse(nn2D.three_dim)
self.assertIsNotNone(nn2D.model)
nn3D = Neural_Network(preprocessor=self.pp3D)
self.assertIsInstance(nn3D, Neural_Network)
self.assertTrue(nn3D.three_dim)
self.assertIsNotNone(nn3D.model)
# Model storage
def test_MODEL_storage(self):
nn = Neural_Network(preprocessor=self.pp3D)
model_path = os.path.join(self.tmp_dir3D.name, "my_model.hdf5")
nn.dump(model_path)
self.assertTrue(os.path.exists(model_path))
# Model loading
def test_MODEL_loading(self):
nn = Neural_Network(preprocessor=self.pp3D)
model_path = os.path.join(self.tmp_dir3D.name, "my_model.hdf5")
nn.dump(model_path)
nn_new = Neural_Network(preprocessor=self.pp3D)
nn_new.load(model_path)
# Reseting weights
def test_MODEL_resetWeights(self):
nn = Neural_Network(preprocessor=self.pp3D)
nn.reset_weights()
#-------------------------------------------------#
# Training #
#-------------------------------------------------#
def test_MODEL_training2D(self):
nn = Neural_Network(preprocessor=self.pp2D)
nn.train(self.sample_list2D, epochs=3)
def test_MODEL_training3D(self):
nn = Neural_Network(preprocessor=self.pp3D)
nn.train(self.sample_list3D, epochs=3)
#-------------------------------------------------#
# Prediction #
#-------------------------------------------------#
def test_MODEL_prediction2D(self):
nn = Neural_Network(preprocessor=self.pp2D)
nn.predict(self.sample_list2D)
for index in self.sample_list2D:
sample = self.data_io2D.sample_loader(index,
load_seg=True,
load_pred=True)
self.assertIsNotNone(sample.pred_data)
def test_MODEL_prediction3D(self):
nn = Neural_Network(preprocessor=self.pp3D)
nn.predict(self.sample_list3D)
for index in self.sample_list3D:
sample = self.data_io3D.sample_loader(index,
load_seg=True,
load_pred=True)
self.assertIsNotNone(sample.pred_data)
def test_MODEL_prediction_returnOutput(self):
nn = Neural_Network(preprocessor=self.pp2D)
pred_list = nn.predict(self.sample_list2D, return_output=True)
for pred in pred_list:
self.assertIsNotNone(pred)
self.assertEqual(pred.shape, (16, 16))
def test_MODEL_prediction_activationOutput(self):
nn = Neural_Network(preprocessor=self.pp2D)
pred_list = nn.predict(self.sample_list2D,
return_output=True,
activation_output=True)
for pred in pred_list:
self.assertIsNotNone(pred)
self.assertEqual(pred.shape, (16, 16, 3))
#-------------------------------------------------#
# Validation #
#-------------------------------------------------#
def test_MODEL_validation2D(self):
nn = Neural_Network(preprocessor=self.pp2D)
history = nn.evaluate(self.sample_list2D[0:4],
self.sample_list2D[4:6],
epochs=3)
self.assertIsNotNone(history)
def test_MODEL_validation3D(self):
nn = Neural_Network(preprocessor=self.pp3D)
history = nn.evaluate(self.sample_list3D[0:4],
self.sample_list3D[4:6],
epochs=3)
self.assertIsNotNone(history)
class PreprocessorTEST(unittest.TestCase):
# Create random imaging and segmentation data
@classmethod
def setUpClass(self):
np.random.seed(1234)
# Create 2D imgaging and segmentation data set
self.dataset2D = dict()
for i in range(0, 10):
img = np.random.rand(16, 16) * 255
self.img = img.astype(int)
seg = np.random.rand(16, 16) * 2
self.seg = seg.astype(int)
self.dataset2D["TEST.sample_" + str(i)] = (self.img, self.seg)
# Initialize Dictionary IO Interface
io_interface2D = Dictionary_interface(self.dataset2D,
classes=3,
three_dim=False)
# Initialize temporary directory
self.tmp_dir2D = tempfile.TemporaryDirectory(prefix="tmp.CESP.")
tmp_batches = os.path.join(self.tmp_dir2D.name, "batches")
# Initialize Data IO
self.data_io2D = Data_IO(io_interface2D,
input_path="",
output_path="",
batch_path=tmp_batches,
delete_batchDir=False)
# Create 3D imgaging and segmentation data set
self.dataset3D = 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)
if i in range(8, 10): sample = (self.img, None)
else: sample = (self.img, self.seg)
self.dataset3D["TEST.sample_" + str(i)] = sample
# Initialize Dictionary IO Interface
io_interface3D = Dictionary_interface(self.dataset3D,
classes=3,
three_dim=True)
# Initialize temporary directory
self.tmp_dir3D = tempfile.TemporaryDirectory(prefix="tmp.CESP.")
tmp_batches = os.path.join(self.tmp_dir3D.name, "batches")
# Initialize Data IO
self.data_io3D = Data_IO(io_interface3D,
input_path="",
output_path="",
batch_path=tmp_batches,
delete_batchDir=False)
# Delete all temporary files
@classmethod
def tearDownClass(self):
self.tmp_dir2D.cleanup()
self.tmp_dir3D.cleanup()
#-------------------------------------------------#
# Base Functionality #
#-------------------------------------------------#
# Class Creation
def test_PREPROCESSOR_BASE_create(self):
with self.assertRaises(Exception):
Preprocessor()
Preprocessor(self.data_io3D, batch_size=1, analysis="fullimage")
Preprocessor(self.data_io3D,
batch_size=1,
analysis="patchwise-crop",
patch_shape=(16, 16, 16))
Preprocessor(self.data_io3D,
batch_size=1,
analysis="patchwise-grid",
patch_shape=(16, 16, 16),
data_aug=None)
# Simple Prepreossor run
def test_PREPROCESSOR_BASE_run(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
data_aug=None,
batch_size=1,
analysis="fullimage")
batches = pp.run(sample_list[8:10], training=False, validation=False)
self.assertEqual(len(batches), 2)
self.assertEqual(batches[0][0].shape, (1, 16, 16, 16, 1))
self.assertIsNone(batches[0][1])
batches = pp.run(sample_list[0:8], training=True, validation=False)
self.assertEqual(batches[0][0].shape, (1, 16, 16, 16, 1))
self.assertEqual(batches[0][1].shape, (1, 16, 16, 16, 3))
batches = pp.run(sample_list[0:8], training=True, validation=True)
self.assertEqual(batches[0][0].shape, (1, 16, 16, 16, 1))
self.assertEqual(batches[0][1].shape, (1, 16, 16, 16, 3))
# Prepreossor run with data augmentation
def test_PREPROCESSOR_BASE_dataaugmentation(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D, batch_size=1, analysis="fullimage")
batches = pp.run(sample_list[8:10], training=False, validation=False)
self.assertEqual(len(batches), 2)
self.assertEqual(batches[0][0].shape, (1, 16, 16, 16, 1))
self.assertIsNone(batches[0][1])
sample = self.data_io3D.sample_loader(sample_list[8], load_seg=False)
self.assertFalse(np.array_equal(batches[0][0], sample.img_data))
# Different batchsizes run
def test_PREPROCESSOR_BASE_batchsizes(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D, batch_size=1, analysis="fullimage")
batches = pp.run(sample_list[0:8], training=True, validation=False)
self.assertEqual(len(batches), 8)
self.assertEqual(batches[0][0].shape, (1, 16, 16, 16, 1))
pp = Preprocessor(self.data_io3D, batch_size=2, analysis="fullimage")
batches = pp.run(sample_list[0:8], training=True, validation=False)
self.assertEqual(len(batches), 4)
self.assertEqual(batches[0][0].shape, (2, 16, 16, 16, 1))
pp = Preprocessor(self.data_io3D, batch_size=3, analysis="fullimage")
batches = pp.run(sample_list[0:8], training=True, validation=False)
self.assertEqual(len(batches), 3)
self.assertEqual(batches[0][0].shape, (3, 16, 16, 16, 1))
self.assertEqual(batches[-1][0].shape, (2, 16, 16, 16, 1))
pp = Preprocessor(self.data_io3D, batch_size=8, analysis="fullimage")
batches = pp.run(sample_list[0:8], training=True, validation=False)
self.assertEqual(len(batches), 1)
self.assertEqual(batches[0][0].shape, (8, 16, 16, 16, 1))
pp = Preprocessor(self.data_io3D, batch_size=100, analysis="fullimage")
batches = pp.run(sample_list[0:8], training=True, validation=False)
self.assertEqual(len(batches), 1)
self.assertEqual(batches[0][0].shape, (8, 16, 16, 16, 1))
# Batch preparation check
def test_PREPROCESSOR_BASE_prepareBatches(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
batch_size=1,
analysis="fullimage",
prepare_batches=True)
batch_pointer = pp.run(sample_list[0:8],
training=True,
validation=False)
self.assertEqual(batch_pointer, 7)
tmp_batches = os.path.join(self.tmp_dir3D.name, "batches")
batch_list = []
for batch_file in os.listdir(tmp_batches):
if batch_file.startswith(str(pp.data_io.seed)):
batch_list.append(batch_file)
self.assertEqual(len(batch_list), 16)
#-------------------------------------------------#
# Postprocessing #
#-------------------------------------------------#
def test_PREPROCESSOR_postprocessing_(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
batch_size=1,
analysis="fullimage",
data_aug=None)
batches = pp.run(sample_list[0:3], training=True, validation=False)
for i in range(0, 3):
pred_postprec = pp.postprocessing(sample_list[i], batches[i][1])
self.assertEqual(pred_postprec.shape, (16, 16, 16))
sam = self.data_io3D.sample_loader(sample_list[i], load_seg=True)
self.assertTrue(
np.array_equal(pred_postprec,
np.reshape(sam.seg_data, (16, 16, 16))))
#-------------------------------------------------#
# Analysis: Patchwise-crop #
#-------------------------------------------------#
def test_PREPROCESSOR_patchwisecrop_2D(self):
sample_list = self.data_io2D.get_indiceslist()
pp = Preprocessor(self.data_io2D,
data_aug=None,
batch_size=1,
analysis="patchwise-crop",
patch_shape=(4, 4))
batches = pp.run(sample_list[0:3], training=True, validation=False)
self.assertEqual(len(batches), 3)
batches = pp.run(sample_list[0:1], training=False, validation=False)
self.assertEqual(len(batches), 16)
sample = self.data_io2D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
ready_data = pp.analysis_patchwise_crop(sample, data_aug=False)
self.assertEqual(len(ready_data), 1)
self.assertEqual(ready_data[0][0].shape, (4, 4, 1))
self.assertEqual(ready_data[0][1].shape, (4, 4, 3))
def test_PREPROCESSOR_patchwisecrop_3D(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
data_aug=None,
batch_size=1,
analysis="patchwise-crop",
patch_shape=(4, 4, 4))
batches = pp.run(sample_list[0:3], training=True, validation=False)
self.assertEqual(len(batches), 3)
batches = pp.run(sample_list[0:1], training=False, validation=False)
self.assertEqual(len(batches), 64)
sample = self.data_io3D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
ready_data = pp.analysis_patchwise_crop(sample, data_aug=False)
self.assertEqual(len(ready_data), 1)
self.assertEqual(ready_data[0][0].shape, (4, 4, 4, 1))
self.assertEqual(ready_data[0][1].shape, (4, 4, 4, 3))
def test_PREPROCESSOR_patchwisecrop_skipBlanks(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
data_aug=None,
batch_size=1,
analysis="patchwise-crop",
patch_shape=(4, 4, 4))
pp.patchwise_skip_blanks = True
batches = pp.run(sample_list[0:3], training=True, validation=False)
sample = self.data_io3D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
ready_data = pp.analysis_patchwise_crop(sample, data_aug=False)
self.assertEqual(len(ready_data), 1)
self.assertEqual(ready_data[0][0].shape, (4, 4, 4, 1))
self.assertEqual(ready_data[0][1].shape, (4, 4, 4, 3))
#-------------------------------------------------#
# Analysis: Patchwise-grid #
#-------------------------------------------------#
def test_PREPROCESSOR_patchwisegrid_2D(self):
sample_list = self.data_io2D.get_indiceslist()
pp = Preprocessor(self.data_io2D,
data_aug=None,
batch_size=1,
analysis="patchwise-grid",
patch_shape=(4, 4))
batches = pp.run(sample_list[0:1], training=False, validation=False)
self.assertEqual(len(batches), 16)
sample = self.data_io2D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
pp = Preprocessor(self.data_io2D,
data_aug=None,
batch_size=1,
analysis="patchwise-grid",
patch_shape=(5, 5))
ready_data = pp.analysis_patchwise_grid(sample,
data_aug=False,
training=True)
self.assertEqual(len(ready_data), 16)
self.assertEqual(ready_data[0][0].shape, (5, 5, 1))
self.assertEqual(ready_data[0][1].shape, (5, 5, 3))
def test_PREPROCESSOR_patchwisegrid_3D(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
data_aug=None,
batch_size=1,
analysis="patchwise-grid",
patch_shape=(4, 4, 4))
batches = pp.run(sample_list[0:1], training=False, validation=False)
self.assertEqual(len(batches), 64)
sample = self.data_io3D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
pp = Preprocessor(self.data_io3D,
data_aug=None,
batch_size=1,
analysis="patchwise-grid",
patch_shape=(5, 5, 5))
ready_data = pp.analysis_patchwise_grid(sample,
data_aug=False,
training=True)
self.assertEqual(len(ready_data), 64)
self.assertEqual(ready_data[0][0].shape, (5, 5, 5, 1))
self.assertEqual(ready_data[0][1].shape, (5, 5, 5, 3))
def test_PREPROCESSOR_patchwisegrid_skipBlanks(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
data_aug=None,
batch_size=1,
analysis="patchwise-grid",
patch_shape=(4, 4, 4))
pp.patchwise_skip_blanks = True
batches = pp.run(sample_list[0:3], training=True, validation=False)
sample = self.data_io3D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
ready_data = pp.analysis_patchwise_grid(sample,
data_aug=False,
training=True)
self.assertEqual(len(ready_data), 64)
self.assertEqual(ready_data[0][0].shape, (4, 4, 4, 1))
self.assertEqual(ready_data[0][1].shape, (4, 4, 4, 3))
#-------------------------------------------------#
# Analysis: Fullimage #
#-------------------------------------------------#
def test_PREPROCESSOR_fullimage_2D(self):
sample_list = self.data_io2D.get_indiceslist()
pp = Preprocessor(self.data_io2D,
data_aug=None,
batch_size=2,
analysis="fullimage")
batches = pp.run(sample_list[0:3], training=True, validation=False)
self.assertEqual(len(batches), 2)
batches = pp.run(sample_list[0:1], training=False, validation=False)
self.assertEqual(len(batches), 1)
sample = self.data_io2D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
ready_data = pp.analysis_fullimage(sample,
data_aug=False,
training=True)
self.assertEqual(len(ready_data), 1)
self.assertEqual(ready_data[0][0].shape, (16, 16, 1))
self.assertEqual(ready_data[0][1].shape, (16, 16, 3))
def test_PREPROCESSOR_fullimage_3D(self):
sample_list = self.data_io3D.get_indiceslist()
pp = Preprocessor(self.data_io3D,
data_aug=None,
batch_size=2,
analysis="fullimage")
batches = pp.run(sample_list[0:3], training=True, validation=False)
self.assertEqual(len(batches), 2)
batches = pp.run(sample_list[0:1], training=False, validation=False)
self.assertEqual(len(batches), 1)
sample = self.data_io3D.sample_loader(sample_list[0], load_seg=True)
sample.seg_data = to_categorical(sample.seg_data,
num_classes=sample.classes)
ready_data = pp.analysis_fullimage(sample,
data_aug=False,
training=True)
self.assertEqual(len(ready_data), 1)
self.assertEqual(ready_data[0][0].shape, (16, 16, 16, 1))
self.assertEqual(ready_data[0][1].shape, (16, 16, 16, 3))
class PatchOperationsTEST(unittest.TestCase):
# Create random imaging and segmentation data
@classmethod
def setUpClass(self):
np.random.seed(1234)
# Create 2D imgaging and segmentation data set
self.dataset2D = dict()
for i in range(0, 10):
img = np.random.rand(16, 16) * 255
self.img = img.astype(int)
seg = np.random.rand(16, 16) * 2
self.seg = seg.astype(int)
self.dataset2D["TEST.sample_" + str(i)] = (self.img, self.seg)
# Initialize Dictionary IO Interface
io_interface2D = Dictionary_interface(self.dataset2D,
classes=3,
three_dim=False)
# Initialize temporary directory
self.tmp_dir2D = tempfile.TemporaryDirectory(prefix="tmp.CESP.")
tmp_batches = os.path.join(self.tmp_dir2D.name, "batches")
# Initialize Data IO
self.data_io2D = Data_IO(io_interface2D,
input_path="",
output_path="",
batch_path=tmp_batches,
delete_batchDir=False)
# Create 3D imgaging and segmentation data set
self.dataset3D = 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)
self.dataset3D["TEST.sample_" + str(i)] = (self.img, self.seg)
# Initialize Dictionary IO Interface
io_interface3D = Dictionary_interface(self.dataset3D,
classes=3,
three_dim=True)
# Initialize temporary directory
self.tmp_dir3D = tempfile.TemporaryDirectory(prefix="tmp.CESP.")
tmp_batches = os.path.join(self.tmp_dir3D.name, "batches")
# Initialize Data IO
self.data_io3D = Data_IO(io_interface3D,
input_path="",
output_path="",
batch_path=tmp_batches,
delete_batchDir=False)
# Delete all temporary files
@classmethod
def tearDownClass(self):
self.tmp_dir2D.cleanup()
self.tmp_dir3D.cleanup()
#-------------------------------------------------#
# Slice Matrix #
#-------------------------------------------------#
def test_PATCHOPERATIONS_slicing(self):
sample_list = self.data_io2D.get_indiceslist()
for index in sample_list:
sample = self.data_io2D.sample_loader(index)
patches = slice_matrix(sample.img_data,
window=(5, 5),
overlap=(2, 2),
three_dim=False)
self.assertEqual(len(patches), 25)
self.assertEqual(patches[0].shape, (5, 5, 1))
sample_list = self.data_io3D.get_indiceslist()
for index in sample_list:
sample = self.data_io3D.sample_loader(index)
patches = slice_matrix(sample.img_data,
window=(5, 5, 5),
overlap=(2, 2, 2),
three_dim=True)
self.assertEqual(len(patches), 125)
self.assertEqual(patches[0].shape, (5, 5, 5, 1))
#-------------------------------------------------#
# Concatenate Matrices #
#-------------------------------------------------#
def test_PATCHOPERATIONS_concatenate(self):
sample_list = self.data_io2D.get_indiceslist()
for index in sample_list:
sample = self.data_io2D.sample_loader(index)
patches = slice_matrix(sample.img_data,
window=(5, 5),
overlap=(2, 2),
three_dim=False)
concat = concat_matrices(patches=patches,
image_size=(16, 16),
window=(5, 5),
overlap=(2, 2),
three_dim=False)
self.assertEqual(concat.shape, (16, 16, 1))
sample_list = self.data_io3D.get_indiceslist()
for index in sample_list:
sample = self.data_io3D.sample_loader(index)
patches = slice_matrix(sample.img_data,
window=(5, 5, 5),
overlap=(2, 2, 2),
three_dim=True)
concat = concat_matrices(patches=patches,
image_size=(16, 16, 16),
window=(5, 5, 5),
overlap=(2, 2, 2),
three_dim=True)
self.assertEqual(concat.shape, (16, 16, 16, 1))
#-------------------------------------------------#
# Patch Padding #
#-------------------------------------------------#
def test_PATCHOPERATIONS_padding(self):
sample_list = self.data_io2D.get_indiceslist()
for index in sample_list:
sample = self.data_io2D.sample_loader(index)
img_padded = pad_patch(np.expand_dims(sample.img_data, axis=0),
patch_shape=(8, 20),
return_slicer=False)
self.assertEqual(img_padded.shape, (1, 16, 20, 1))
sample_list = self.data_io3D.get_indiceslist()
for index in sample_list:
sample = self.data_io3D.sample_loader(index)
img_padded = pad_patch(np.expand_dims(sample.img_data, axis=0),
patch_shape=(8, 16, 32),
return_slicer=False)
self.assertEqual(img_padded.shape, (1, 16, 16, 32, 1))
#-------------------------------------------------#
# Patch Cropping #
#-------------------------------------------------#
def test_PATCHOPERATIONS_cropping(self):
sample_list = self.data_io2D.get_indiceslist()
for index in sample_list:
sample = self.data_io2D.sample_loader(index)
img_padded, slicer = pad_patch(np.expand_dims(sample.img_data,
axis=0),
patch_shape=(8, 20),
return_slicer=True)
img_processed = crop_patch(img_padded, slicer)
self.assertEqual(img_processed.shape, (1, 16, 16, 1))
sample_list = self.data_io3D.get_indiceslist()
for index in sample_list:
sample = self.data_io3D.sample_loader(index)
img_padded, slicer = pad_patch(np.expand_dims(sample.img_data,
axis=0),
patch_shape=(8, 16, 32),
return_slicer=True)
img_processed = crop_patch(img_padded, slicer)
self.assertEqual(img_processed.shape, (1, 16, 16, 16, 1))