def test_padding():
# create test 2D array
R = 5
C = 10
x = np.array(range(R * C)).reshape(R, C)
# array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
# [10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
# [20, 21, 22, 23, 24, 25, 26, 27, 28, 29],
# [30, 31, 32, 33, 34, 35, 36, 37, 38, 39],
# [40, 41, 42, 43, 44, 45, 46, 47, 48, 49]])
# split into blocks
block_slices, blocks, xout = pymg.block_split(x,
nblocks=(1, 4),
pad_width=(2, 3),
mode='constant',
constant_values=0)
# check number of blocks
assert (1 * 4 == len(blocks))
# check that array has been padded
assert ((np.pad(x, pad_width=(2, 3), mode='constant') == xout).all())
# load ground truth
expected_blocks = example_padded_2D_array_blocks()
# check that all blocks were computed as expected
for eb, b in zip(expected_blocks, blocks):
assert ((eb == b).all())
def test_3d_array():
S = 3
R = 7
C = 5
# create 3D array
x = np.array(range(R * C * S)).reshape(S, R, C)
# array([[[ 0, 1, 2],
# [ 3, 4, 5],
# [ 6, 7, 8],
# [ 9, 10, 11],
# [ 12, 13, 14]],
#
# ...
#
# [[ 90, 91, 92],
# [ 93, 94, 95],
# [ 96, 97, 98],
# [ 99, 100, 101],
# [102, 103, 104]]])
# split into blocks
block_slices, blocks, _ = pymg.block_split(x,
nblocks=(3, 3, 2),
by_reference=True)
# load ground truth
expected_blocks = example_3D_array_blocks()
# check that all blocks were computed as expected
for eb, b in zip(expected_blocks, blocks):
assert ((eb == b).all())
def test_blocks_by_value():
# create test 2D array
R = 5
C = 10
x = np.array(range(R * C)).reshape(R, C)
# array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
# [10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
# [20, 21, 22, 23, 24, 25, 26, 27, 28, 29],
# [30, 31, 32, 33, 34, 35, 36, 37, 38, 39],
# [40, 41, 42, 43, 44, 45, 46, 47, 48, 49]])
# split into blocks
block_slices, blocks, xout = pymg.block_split(x,
nblocks=(2, 3),
by_reference=False)
# check number of blocks
assert (2 * 3 == len(blocks))
# check that array hasn't changed
assert ((x == xout).all())
# load ground truth
expected_blocks = example_2D_array_blocks()
# check that all blocks were computed as expected
for eb, b in zip(expected_blocks, blocks):
assert ((eb == b).all())
# set one block to zeros, and check that the original array does not change
blocks[3][...] = 0
assert ((x[block_slices[3]] == expected_blocks[3]).all())
def aux_split_stack(R,
C,
nblocks,
S=1,
pad_width=0,
mode='constant',
constant_values=0):
if (S == 1):
x = np.array(range(R * C)).reshape(R, C)
else:
x = np.array(range(S * R * C)).reshape(S, R, C)
# array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
# [10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
# [20, 21, 22, 23, 24, 25, 26, 27, 28, 29],
# [30, 31, 32, 33, 34, 35, 36, 37, 38, 39],
# [40, 41, 42, 43, 44, 45, 46, 47, 48, 49]])
# split into blocks
block_slices, blocks, xout = pymg.block_split(
x,
nblocks=nblocks,
pad_width=pad_width,
mode=mode,
constant_values=constant_values)
# check number of blocks
assert (np.prod(nblocks) == len(blocks))
# check that array has been padded
assert ((np.pad(x, pad_width=pad_width, mode='constant') == xout).all())
# stack blocks
x2, block_slices2 = pymg.block_stack(blocks,
block_slices,
pad_width=pad_width)
# check that the array is correctly recovered
assert ((x == x2).all())
def test_no_reference_with_padding():
# create test 2D array
R = 5
C = 10
x = np.array(range(R * C)).reshape(R, C)
# array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
# [10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
# [20, 21, 22, 23, 24, 25, 26, 27, 28, 29],
# [30, 31, 32, 33, 34, 35, 36, 37, 38, 39],
# [40, 41, 42, 43, 44, 45, 46, 47, 48, 49]])
# split into blocks
try:
block_slices, blocks, xout = pymg.block_split(x,
nblocks=(2, 3),
pad_width=3,
by_reference=True)
except Exception:
pass
else:
raise Exception('Exception not raised')
pad_xy = 30
# create image
im = np.ones(shape=(1, 2, 200, 200))
im[:, :, 0:50, 0:50] = 2
im[:, :, 100:150, 100:150] = 2
# apply DeepCell's preprocessing
im[0, 0, :, :] = deepcell.process_image(im[0, 0, :, :], 30, 30)
im[0, 1, :, :] = deepcell.process_image(im[0, 1, :, :], 30, 30)
# split into blocks
block_slices, blocks, im_padded = pymproc.block_split(
im,
nblocks=(1, 1, 1, 2),
pad_width=((0, 0), (0, 0), (pad_xy, pad_xy), (pad_xy, pad_xy)),
mode='reflect')
# load a model
j = 0 # model index
model = deepcell_models.sparse_bn_feature_net_61x61(batch_input_shape=im.shape)
model = deepcell.set_weights(
model, os.path.join(netdir, model_dir,
model_weights_file + str(j) + '.h5'))
# process image and blocks
im_out = model.predict(im)
im_out = np.pad(im_out,
pad_width=((0, 0), (0, 0), (pad_xy, pad_xy), (pad_xy, pad_xy)),
mode='constant',
plt.ion()
plt.clf()
plt.imshow(im_crop)
plt.draw()
plt.show()
plt.pause(0.1)
# remove alpha channel
im_crop = np.array(im_crop)
im_crop = im_crop[:, :, 0:3]
# split image into overlapping blocks
im_crop_slices, im_crop_blocks, xout = pystoim.block_split(
im_crop, (10, 10, 1),
pad_width=((100, 100), (100, 100), (0, 0)),
mode='reflect',
reflect_type='even')
# init memory and correct slices for the predictor output (input images are RGB, and predictions have 4 channels)
im_crop_blocks_predicted = im_crop_blocks.copy()
im_crop_slices_predicted = im_crop_slices.copy()
for i, sl in enumerate(im_crop_slices_predicted):
sl[2] = slice(0, 4, 1)
im_crop_slices_predicted[i] = sl
# apply trained model to the cropped image
for i, block in enumerate(im_crop_blocks):
if DEBUG:
print("Processing block " + str(i) + "/" + str(len(im_crop_blocks)))
aux = model.predict(block.reshape((1, ) + block.shape))
'''
for fold_i, model_file in enumerate(model_files):
# select test data (data not used for training)
idx_test = idx_test_all[fold_i]
im_test = im[idx_test, ...]
dmap_test = dmap[idx_test, ...]
mask_test = mask[idx_test, ...]
# split data into blocks
dmap_test = dmap_test[:, 0:-1, 0:-1, :]
mask_test = mask_test[:, 0:-1, 0:-1, :]
im_test = im_test[:, 0:-1, 0:-1, :]
_, dmap_test, _ = pystoim.block_split(dmap_test, nblocks=(1, 2, 2, 1))
_, im_test, _ = pystoim.block_split(im_test, nblocks=(1, 2, 2, 1))
_, mask_test, _ = pystoim.block_split(mask_test, nblocks=(1, 2, 2, 1))
dmap_test = np.concatenate(dmap_test, axis=0)
im_test = np.concatenate(im_test, axis=0)
mask_test = np.concatenate(mask_test, axis=0)
# load model
model = cytometer.models.fcn_sherrah2016_regression(
input_shape=im_test.shape[1:])
model.load_weights(model_file)
# visualise results
if DEBUG:
for i in range(im_test.shape[0]):
'''
for fold_i, model_file in enumerate(model_files):
# select test data (data not used for training)
idx_test = idx_test_all[fold_i]
im_test = im[idx_test, ...]
seg_test = seg[idx_test, ...]
mask_test = mask[idx_test, ...]
# split data into blocks
seg_test = seg_test[:, 0:-1, 0:-1, :]
mask_test = mask_test[:, 0:-1, 0:-1, :]
im_test = im_test[:, 0:-1, 0:-1, :]
_, seg_test, _ = pystoim.block_split(seg_test, nblocks=(1, 2, 2, 1))
_, im_test, _ = pystoim.block_split(im_test, nblocks=(1, 2, 2, 1))
_, mask_test, _ = pystoim.block_split(mask_test, nblocks=(1, 2, 2, 1))
seg_test = np.concatenate(seg_test, axis=0)
im_test = np.concatenate(im_test, axis=0)
mask_test = np.concatenate(mask_test, axis=0)
# load model
model = cytometer.models.fcn_sherrah2016_contour(
input_shape=im_test.shape[1:])
model.load_weights(model_file)
# visualise results
if DEBUG:
for i in range(im_test.shape[0]):