def test_pad_too_many_axes(self):
arr = np.arange(30).reshape(5, 6)
# Attempt to pad using a 3D array equivalent
bad_shape = (((3,), (4,), (5,)), ((0,), (1,), (2,)))
with testing.raises(ValueError):
pad(arr, bad_shape, mode='constant')
def test_check_wrong_pad_amount(self):
arr = np.arange(30)
arr = np.reshape(arr, (6, 5))
kwargs = dict(mode='mean', stat_length=(3, ))
with pytest.raises(TypeError):
pad(arr, ((2, 3, 4), (3, 2)),
**kwargs)
def prefilt(img, fc=4):
"""
assume greyscale (c==1), individual image(N==1)
"""
w = 5
s1 = fc/np.sqrt(np.log(2.0))
# pad images to reduce boundary artifacts
img = np.log(img+1)
img = util.pad(img, w, mode='symmetric')
sn, sm = img.shape
n = max(sn, sm)
n += np.mod(n, 2)
img = util.pad(img, ((0, n-sn), (0, n-sm)), mode='symmetric')
# filter
fx, fy = np.meshgrid(np.arange(-n/2, n/2), np.arange(-n/2, n/2))
gf = np.fft.fftshift(np.exp(-(fx**2+fy**2)/(s1**2)))
# whitening
output = img - np.real(np.fft.ifft2(np.fft.fft2(img)*gf))
# local contrast normalization
localstd = np.sqrt(
np.abs(np.fft.ifft2(np.fft.fft2(output**2)*gf)))
output = output / (0.2+localstd)
# crop output to have the same size as the input
output = output[w:sn-w, w:sm-w]
return output
def test_check_simple(self):
arr = np.arange(30)
arr = np.reshape(arr, (6, 5))
kwargs = dict(mode='mean', stat_length=(3, ))
with pytest.raises(ValueError):
pad(arr, ((2, 3), (3, 2), (4, 5)),
**kwargs)
def sliding_concentric_windows(self, img):
n_rows, n_cols = img.shape[:2]
y_a, x_a = 5, 5
y_b, x_b = 11, 11
new_img = np.zeros((n_rows, n_cols), dtype=np.uint)
img_a = util.pad(img, ((y_a/2, y_a/2), (x_a/2, x_a/2)), mode='constant')
img_b = util.pad(img, ((y_b/2, y_b/2), (x_b/2, x_b/2)), mode='constant')
blocks_a = util.view_as_windows(img_a, (y_a, x_a), step=1)
blocks_b = util.view_as_windows(img_b, (y_b, x_b), step=1)
for row in xrange(n_rows):
for col in xrange(n_cols):
mean_a = blocks_a[row, col].mean()
mean_b = blocks_b[row, col].mean()
r_mean = 0
if mean_a != 0:
r_mean = mean_b/float(mean_a)
if r_mean > 1.0:
new_img[row, col] = 0
else:
new_img[row, col] = 255
return new_img
def test_check_negative_pad_amount(self):
arr = np.arange(30)
arr = np.reshape(arr, (6, 5))
kwargs = dict(mode='mean', stat_length=(3, ))
with pytest.raises(ValueError):
pad(arr, ((-2, 3), (3, 2)),
**kwargs)
def test_shallow_statistic_range(self):
test = np.arange(120).reshape(4, 5, 6)
pad_amt = [(1, 1) for axis in test.shape]
modes = ['maximum',
'mean',
'median',
'minimum',
]
for mode in modes:
assert_array_equal(pad(test, pad_amt, mode='edge'),
pad(test, pad_amt, mode=mode, stat_length=1))
def test_clip_statistic_range(self):
test = np.arange(30).reshape(5, 6)
pad_amt = [(3, 3) for axis in test.shape]
modes = ['maximum',
'mean',
'median',
'minimum',
]
for mode in modes:
assert_array_equal(pad(test, pad_amt, mode=mode),
pad(test, pad_amt, mode=mode, stat_length=30))
def data_augmentation_test(img_id=1, crop_size=200, pad_size=100):
Xb = np.array(Image.open('data/images/train/' + str(img_id) + '.jpg'),
dtype=np.uint8) / np.float32(255.)
im_size = Xb.shape[0]
frame_size = im_size + 2 * pad_size
print "X shape ", Xb.shape
padded = np.zeros((3, frame_size, frame_size))
for i in range(3):
padded[i] = pad(np.swapaxes(Xb, 0, 2)[i], (pad_size, pad_size), 'reflect')
padded = np.swapaxes(padded, 0, 2)
print "Padded shape ", padded.shape
lower_cut = (im_size - crop_size) / 2 + pad_size
upper_cut = (im_size + crop_size) / 2 + pad_size
shift_x = frame_size / 2
shift_y = shift_x
tf_shift = AffineTransform(translation=[-shift_x, -shift_y])
tf_shift_inv = AffineTransform(translation=[shift_x, shift_y])
scaling_factor = 0.2 * np.random.random() + 0.9
angle = 2 * pi * (np.random.random() - 0.5)
trans_x = np.random.randint(-5, 5)
trans_y = np.random.randint(-5, 5)
tf = AffineTransform(scale=(scaling_factor, scaling_factor),
rotation=angle, shear=None,
translation=(trans_x, trans_y))
padded = warp(padded, (tf_shift + (tf + tf_shift_inv)).inverse)
print "Padded shape after transform ", padded.shape
# Crop to desired size
tmp = padded[lower_cut:upper_cut, lower_cut:upper_cut, :]
print "Finally, cuts and shape: ", lower_cut, upper_cut, padded.shape
plt.imshow(tmp)
def gist_gabor(img, param):
"""
Assume single image
Assume greyscale image
"""
w = param.number_blocks
G = param.G
be = param.boundary_extension
n_rows, n_cols = img.shape
c = 1
N = c
ny, nx, n_filters = G.shape
W = w*w
g = np.zeros((W*n_filters, N))
# pad image
img = util.pad(img, be, mode='symmetric')
img = np.fft.fft2(img)
k = 0
for n in range(n_filters):
ig = np.abs(np.fft.ifft2(img*G[:,:,n]))
ig = ig[be:ny-be, be:nx-be]
v = downN(ig, w)
g[k:k+W] = np.reshape(v.T, [W, N])
k = k + W
return g
def test_check_median_stat_length(self):
a = np.arange(100).astype('f')
a[1] = 2.
a[97] = 96.
a = pad(a, (25, 20), 'median', stat_length=(3, 5))
b = np.array(
[ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.,
2., 2., 2., 2., 2., 2., 2., 2., 2., 2.,
2., 2., 2., 2., 2.,
0., 2., 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.,
50., 51., 52., 53., 54., 55., 56., 57., 58., 59.,
60., 61., 62., 63., 64., 65., 66., 67., 68., 69.,
70., 71., 72., 73., 74., 75., 76., 77., 78., 79.,
80., 81., 82., 83., 84., 85., 86., 87., 88., 89.,
90., 91., 92., 93., 94., 95., 96., 96., 98., 99.,
96., 96., 96., 96., 96., 96., 96., 96., 96., 96.,
96., 96., 96., 96., 96., 96., 96., 96., 96., 96.]
)
assert_array_equal(a, b)
def test_check_large_pad(self):
a = np.arange(12)
a = np.reshape(a, (3, 4))
a = pad(a, (10, 12), 'wrap')
b = np.array(
[[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11],
[2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2,
3, 0, 1, 2, 3, 0, 1, 2, 3],
[6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6,
7, 4, 5, 6, 7, 4, 5, 6, 7],
[10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10,
11, 8, 9, 10, 11, 8, 9, 10, 11]]
)
assert_array_equal(a, b)
def image_padding(img, padding_value=0, crop_size=None, ismask=0):
h, w = img.shape[:2]
if crop_size is None:
pad_h = h
pad_w = w
else:
if h > w:
pad_h = int(crop_size/2.)
pad_w = int(1.*pad_h*w/h)
else:
pad_w = int(crop_size/2.)
pad_h = int(1.*pad_w*h/w)
if not ismask:
return pad(img, ((pad_h, pad_h), (pad_w, pad_w), (0, 0)), mode='constant', constant_values=int(padding_value)), pad_h, pad_w
else:
return pad(img, ((pad_h, pad_h), (pad_w, pad_w)), mode='constant', constant_values=0), pad_h, pad_w
def adj_matrix(Graph, skel_mat):
"""
Returns adjacency matrix for the given skeleton
binary matrix and the corresponding graph of nodes.
Parameters
--------
Graph : a graph of nodes; each node correspond to the
nonzero element of skeleton matrix and has the attrubutes
'index' and 'neig'
skel_mat : 3d binary matrix
Returns
-------
a_m : 2d array of the dimentions n by n, where n is equal to
the number of nodes; matrix is symmetric, nonzero elements
indicate the connections between the nodes.
Examples
-------
>>>b = np.zeros((3,3,3))
>>>b[1,1,:] = 1
>>>b
array([[[ 0., 0., 0.],
[ 0., 0., 0.],
[ 0., 0., 0.]],
[[ 0., 0., 0.],
[ 1., 1., 1.],
[ 0., 0., 0.]],
[[ 0., 0., 0.],
[ 0., 0., 0.],
[ 0., 0., 0.]]])
>>>G = label(b)
>>>adj_m = adj_matrix(G,b)
>>>adj_m
array([[ 0., 1., 0.],
[ 1., 0., 1.],
[ 0., 1., 0.]])
"""
point = nx.get_node_attributes(Graph, 'index')
node_label = dict( (j,i) for i,j in point.iteritems())
a_pad = util.pad(skel_mat,((1,1),(1,1),(1,1)), 'constant')
n = nx.number_of_nodes(Graph)
a_m = np.zeros((n,n))
for i in Graph.nodes():
vol = np.zeros(a_pad.shape)
co = point[i]
vol[co[0]:co[0]+3, co[1]:co[1]+3,
co[2]:co[2]+3] = a_pad[co[0]:co[0]+3, co[1]:co[1]+3, co[2]:co[2]+3]
nz_vol = np.transpose(np.nonzero(vol)) - 1
el = tuple(map(tuple,nz_vol))
for elem in el:
j = node_label[elem]
a_m [i-1,j-1] = 1
a_m = a_m - np.eye(n)
return a_m
def read_img_file_PIL(file_path, size=(32,32)):
img = Image.open(file_path).convert('L')
img.thumbnail(size, Image.NEAREST)
data = np.array(img)
shape = data.shape
append_top = int(ceil(max(0, size[0] - shape[0])/2.0))
append_bot = int(floor(max(0, size[0] - shape[0])/2.0))
data = util.pad(data, ((append_top, append_bot),
(0,0)), mode='constant', constant_values=0)
return data
def center_crop_reflect(img, size):
"""Center crop with mirror padding if necessary"""
a0 = max(0, size[0] - img.shape[0])
a1 = max(0, size[1] - img.shape[1])
v = ((a0//2, a0-a0//2), (a1//2, a1-a1//2))
if img.ndim == 3:
v = v + ((0, 0),)
pimg = util.pad(img, v, mode='reflect')
return center_crop(pimg, size)
def test_check_median_02(self):
a = np.array([[3, 1, 4], [4, 5, 9], [9, 8, 2]])
a = pad(a.T, 1, 'median').T
b = np.array([
[5, 4, 5, 4, 5],
[3, 3, 1, 4, 3],
[5, 4, 5, 9, 5],
[8, 9, 8, 2, 8],
[5, 4, 5, 4, 5]])
assert_array_equal(a, b)
def transform(self, Xb, yb):
Xb, yb = super(DataAugmentationBatchIterator, self).transform(Xb, yb)
# Flip half of the images in this batch at random:
bs = Xb.shape[0]
indices = np.random.choice(bs, bs / 2, replace=False)
Xb[indices] = Xb[indices, :, :, ::-1]
# Divide pixels values by 255 to make it fit in [-1;1], for SimilarityTransform compatibility
Xb /= np.float32(255.)
# Change shape from [Batch_size, nb_channels, width, height] to [Batch_size, width, height, nb_channels]
Xb = np.swapaxes(Xb, 1, 3)
# Define relevant shapes
im_size = Xb.shape[1]
frame_size = im_size + 2 * self.pad_size
lower_cut = (frame_size - self.crop_size) / 2
upper_cut = (frame_size + self.crop_size) / 2
shift_x = frame_size / 2
shift_y = shift_x
# Necessary shifts to allow rotation around center
tf_shift = SimilarityTransform(translation=[-shift_x, -shift_y])
tf_shift_inv = SimilarityTransform(translation=[shift_x, shift_y])
# Xb_new = np.zeros((bs,self.crop_size,self.crop_size,self.nb_channels))
for i in xrange(bs):
pic = Xb[i] # Picture as a [width, height, nb_channels] np.array
# Pad image to avoid black regions after zoom/rotation/translation
padded = np.zeros((self.nb_channels, frame_size, frame_size))
for j in xrange(self.nb_channels):
padded[j] = pad(np.swapaxes(pic, 0, 2)[j], (self.pad_size, self.pad_size), 'reflect')
padded = np.swapaxes(padded, 0, 2)
# Pick random values
scaling_factor_tmp = 2 * np.random.random() * self.scale_delta + (1. - self.scale_delta)
scaling_factor = random.choice([1./scaling_factor_tmp, 1., scaling_factor_tmp])
angle = 2 * pi * (np.random.random() - 0.5) * self.angle_factor
trans_x = np.random.randint(-self.max_trans, self.max_trans)
trans_y = np.random.randint(-self.max_trans, self.max_trans)
# Apply similarity transform to zoom, rotate and translate
tf = SimilarityTransform(scale=scaling_factor, rotation=angle, translation=(trans_x, trans_y))
padded = warp(padded, (tf_shift + (tf + tf_shift_inv)).inverse)
# Crop to desired size
Xb[i] = padded[lower_cut:upper_cut, lower_cut:upper_cut, :]
Xb = np.swapaxes(Xb, 1, 3)
Xb *= np.float32(255.)
return Xb, yb
def test_check_2d(self):
arr = np.arange(20).reshape(4, 5).astype(np.float64)
test = pad(arr, (2, 2), mode='linear_ramp', end_values=(0, 0))
expected = np.array(
[[0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0.5, 1., 1.5, 2., 1., 0.],
[0., 0., 0., 1., 2., 3., 4., 2., 0.],
[0., 2.5, 5., 6., 7., 8., 9., 4.5, 0.],
[0., 5., 10., 11., 12., 13., 14., 7., 0.],
[0., 7.5, 15., 16., 17., 18., 19., 9.5, 0.],
[0., 3.75, 7.5, 8., 8.5, 9., 9.5, 4.75, 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0.]])
assert_allclose(test, expected)
def test_blob_dog():
r2 = math.sqrt(2)
img = np.ones((512, 512))
xs, ys = circle(400, 130, 5)
img[xs, ys] = 255
xs, ys = circle(100, 300, 25)
img[xs, ys] = 255
xs, ys = circle(200, 350, 45)
img[xs, ys] = 255
blobs = blob_dog(img, min_sigma=5, max_sigma=50)
radius = lambda x: r2 * x[2]
s = sorted(blobs, key=radius)
thresh = 5
b = s[0]
assert abs(b[0] - 400) <= thresh
assert abs(b[1] - 130) <= thresh
assert abs(radius(b) - 5) <= thresh
b = s[1]
assert abs(b[0] - 100) <= thresh
assert abs(b[1] - 300) <= thresh
assert abs(radius(b) - 25) <= thresh
b = s[2]
assert abs(b[0] - 200) <= thresh
assert abs(b[1] - 350) <= thresh
assert abs(radius(b) - 45) <= thresh
# Testing no peaks
img_empty = np.zeros((100,100))
assert blob_dog(img_empty).size == 0
# Testing 3D
r = 10
pad = 10
im3 = ellipsoid(r, r, r)
im3 = util.pad(im3, pad, mode='constant')
blobs = blob_dog(im3, min_sigma=3, max_sigma=10,
sigma_ratio=1.2, threshold=0.1)
b = blobs[0]
assert b[0] == r + pad + 1
assert b[1] == r + pad + 1
assert b[2] == r + pad + 1
assert abs(math.sqrt(3) * b[3] - r) < 1
def test_blob_overlap():
img = np.ones((256, 256), dtype=np.uint8)
xs, ys = circle(100, 100, 20)
img[xs, ys] = 255
xs, ys = circle(120, 100, 30)
img[xs, ys] = 255
blobs = blob_doh(
img,
min_sigma=1,
max_sigma=60,
num_sigma=10,
threshold=.05)
assert len(blobs) == 1
r1, r2 = 7, 6
pad1, pad2 = 11, 12
blob1 = ellipsoid(r1, r1, r1)
blob1 = util.pad(blob1, pad1, mode='constant')
blob2 = ellipsoid(r2, r2, r2)
blob2 = util.pad(blob2, [(pad2, pad2), (pad2 - 9, pad2 + 9),
(pad2, pad2)],
mode='constant')
im3 = np.logical_or(blob1, blob2)
blobs = blob_log(im3, min_sigma=2, max_sigma=10, overlap=0.1)
assert len(blobs) == 1
# Two circles with distance between centers equal to radius
overlap = _blob_overlap(np.array([0, 0, 10 / math.sqrt(2)]),
np.array([0, 10, 10 / math.sqrt(2)]))
assert_almost_equal(overlap,
1./math.pi * (2 * math.acos(1./2) - math.sqrt(3)/2.))
def test_zero_padding_shortcuts(self):
test = np.arange(120).reshape(4, 5, 6)
pad_amt = [(0, 0) for axis in test.shape]
modes = ['constant',
'edge',
'linear_ramp',
'maximum',
'mean',
'median',
'minimum',
'reflect',
'symmetric',
'wrap',
]
for mode in modes:
assert_array_equal(test, pad(test, pad_amt, mode=mode))
def test_check_constant_odd_pad_amount(self):
arr = np.arange(30).reshape(5, 6)
test = pad(arr, ((1,), (2,)), mode='constant',
constant_values=3)
expected = np.array(
[[ 3, 3, 3, 3, 3, 3, 3, 3, 3, 3],
[ 3, 3, 0, 1, 2, 3, 4, 5, 3, 3],
[ 3, 3, 6, 7, 8, 9, 10, 11, 3, 3],
[ 3, 3, 12, 13, 14, 15, 16, 17, 3, 3],
[ 3, 3, 18, 19, 20, 21, 22, 23, 3, 3],
[ 3, 3, 24, 25, 26, 27, 28, 29, 3, 3],
[ 3, 3, 3, 3, 3, 3, 3, 3, 3, 3]]
)
assert_allclose(test, expected)
def test_check_simple(self):
a = np.arange(12)
a = np.reshape(a, (4, 3))
a = pad(a, ((2, 3), (3, 2)), 'edge')
b = np.array([
[0, 0, 0, 0, 1, 2, 2, 2],
[0, 0, 0, 0, 1, 2, 2, 2],
[0, 0, 0, 0, 1, 2, 2, 2],
[3, 3, 3, 3, 4, 5, 5, 5],
[6, 6, 6, 6, 7, 8, 8, 8],
[9, 9, 9, 9, 10, 11, 11, 11],
[9, 9, 9, 9, 10, 11, 11, 11],
[9, 9, 9, 9, 10, 11, 11, 11],
[9, 9, 9, 9, 10, 11, 11, 11]])
assert_array_equal(a, b)
def numb(skel_mat) :
"""
Counts the number of neighboring 1 for every nonzero
element in 3D.
Parameters
------
skel_mat : 3d binary array
Returns
------
arr : The array of uint8 of the same size as skel_mat
with the elements equal to the number of neighbors
for the current point.
Examples
------
>>> a = np.random.random_integers(0,1,(3,3,3))
>>> a
array([[[0, 0, 1],
[0, 1, 1],
[1, 0, 1]],
[[1, 0, 1],
[1, 0, 1],
[1, 1, 0]],
[[1, 1, 1],
[1, 0, 0],
[1, 1, 0]]])
>>> neigh = numb(a)
>>> neigh
array([[[ 0, 0, 4],
[ 0, 10, 6],
[ 4, 0, 4]],
[[ 5, 0, 6],
[10, 0, 9],
[ 7, 10, 0]],
[[ 4, 7, 3],
[ 8, 0, 0],
[ 5, 6, 0]]], dtype=uint8)
"""
c_pad = util.pad(skel_mat,((1,1),(1,1),(1,1)), 'constant')
mask = c_pad > 0
fil = 3**3 * ndimage.uniform_filter(c_pad.astype('float'),
size = (3,3,3)) - 1
arr = (fil * mask)[1:-1,1:-1,1:-1].astype('uint8')
return arr
def fill_holes_with_contour_filling(gray_mask,inverse=False):
'''
Input: Grayscale image
Returns: Image with holes filled by contour mapping
'''
filled = gray_mask.copy()
filled = pad(filled,((5,5),(0,0)),'constant',constant_values=255)
if inverse:
filled = cv2.bitwise_not(filled)
image, contour, _ = cv2.findContours(filled, cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE)
for cnt in contour:
cv2.drawContours(filled,[cnt], 0, 255, -1)
if inverse:
filled = cv2.bitwise_not(filled)
filled = crop(filled,((5,5),(0,0)))
return filled
def test_check_simple(self):
a = np.arange(30)
a = np.reshape(a, (6, 5))
a = pad(a, ((2, 3), (3, 2)), mode='mean', stat_length=(3,))
b = np.array([[ 6, 6, 6, 5, 6, 7, 8, 9, 8, 8],
[ 6, 6, 6, 5, 6, 7, 8, 9, 8, 8],
[ 1, 1, 1, 0, 1, 2, 3, 4, 3, 3],
[ 6, 6, 6, 5, 6, 7, 8, 9, 8, 8],
[11, 11, 11, 10, 11, 12, 13, 14, 13, 13],
[16, 16, 16, 15, 16, 17, 18, 19, 18, 18],
[21, 21, 21, 20, 21, 22, 23, 24, 23, 23],
[26, 26, 26, 25, 26, 27, 28, 29, 28, 28],
[21, 21, 21, 20, 21, 22, 23, 24, 23, 23],
[21, 21, 21, 20, 21, 22, 23, 24, 23, 23],
[21, 21, 21, 20, 21, 22, 23, 24, 23, 23]])
assert_array_equal(a, b)
def test_legacy_vector_functionality(self):
def _padwithtens(vector, pad_width, iaxis, kwargs):
vector[:pad_width[0]] = 10
vector[-pad_width[1]:] = 10
return vector
a = np.arange(6).reshape(2, 3)
a = pad(a, 2, _padwithtens)
b = np.array(
[[10, 10, 10, 10, 10, 10, 10],
[10, 10, 10, 10, 10, 10, 10],
[10, 10, 0, 1, 2, 10, 10],
[10, 10, 3, 4, 5, 10, 10],
[10, 10, 10, 10, 10, 10, 10],
[10, 10, 10, 10, 10, 10, 10]]
)
assert_array_equal(a, b)
def test_check_constant_float(self):
# If input array is int, but constant_values are float, the dtype of
# the array to be padded is kept
arr = np.arange(30).reshape(5, 6)
test = pad(arr, (1, 2), mode='constant',
constant_values=1.1)
expected = np.array(
[[ 1, 1, 1, 1, 1, 1, 1, 1, 1],
[ 1, 0, 1, 2, 3, 4, 5, 1, 1],
[ 1, 6, 7, 8, 9, 10, 11, 1, 1],
[ 1, 12, 13, 14, 15, 16, 17, 1, 1],
[ 1, 18, 19, 20, 21, 22, 23, 1, 1],
[ 1, 24, 25, 26, 27, 28, 29, 1, 1],
[ 1, 1, 1, 1, 1, 1, 1, 1, 1],
[ 1, 1, 1, 1, 1, 1, 1, 1, 1]]
)
assert_allclose(test, expected)
def test_check_constant_float2(self):
# If input array is float, and constant_values are float, the dtype of
# the array to be padded is kept - here retaining the float constants
arr = np.arange(30).reshape(5, 6)
arr_float = arr.astype(np.float64)
test = pad(arr_float, ((1, 2), (1, 2)), mode='constant',
constant_values=1.1)
expected = np.array(
[[ 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1],
[ 1.1, 0. , 1. , 2. , 3. , 4. , 5. , 1.1, 1.1],
[ 1.1, 6. , 7. , 8. , 9. , 10. , 11. , 1.1, 1.1],
[ 1.1, 12. , 13. , 14. , 15. , 16. , 17. , 1.1, 1.1],
[ 1.1, 18. , 19. , 20. , 21. , 22. , 23. , 1.1, 1.1],
[ 1.1, 24. , 25. , 26. , 27. , 28. , 29. , 1.1, 1.1],
[ 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1],
[ 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1]]
)
assert_allclose(test, expected)
def test_blob_dog():
r2 = math.sqrt(2)
img = np.ones((512, 512))
xs, ys = circle(400, 130, 5)
img[xs, ys] = 255
xs, ys = circle(100, 300, 25)
img[xs, ys] = 255
xs, ys = circle(200, 350, 45)
img[xs, ys] = 255
blobs = blob_dog(img, min_sigma=5, max_sigma=50)
radius = lambda x: r2 * x[2]
s = sorted(blobs, key=radius)
thresh = 5
b = s[0]
assert abs(b[0] - 400) <= thresh
assert abs(b[1] - 130) <= thresh
assert abs(radius(b) - 5) <= thresh
b = s[1]
assert abs(b[0] - 100) <= thresh
assert abs(b[1] - 300) <= thresh
assert abs(radius(b) - 25) <= thresh
b = s[2]
assert abs(b[0] - 200) <= thresh
assert abs(b[1] - 350) <= thresh
assert abs(radius(b) - 45) <= thresh
# Testing no peaks
img_empty = np.zeros((100, 100))
assert blob_dog(img_empty).size == 0
# Testing 3D
r = 10
pad = 10
im3 = ellipsoid(r, r, r)
im3 = util.pad(im3, pad, mode='constant')
blobs = blob_dog(im3,
min_sigma=3,
max_sigma=10,
sigma_ratio=1.2,
threshold=0.1)
b = blobs[0]
assert b.shape == (4, )
assert b[0] == r + pad + 1
assert b[1] == r + pad + 1
assert b[2] == r + pad + 1
assert abs(math.sqrt(3) * b[3] - r) < 1
# Testing 3D anisotropic
r = 10
pad = 10
im3 = ellipsoid(r / 2, r, r)
im3 = util.pad(im3, pad, mode='constant')
blobs = blob_dog(im3,
min_sigma=[1.5, 3, 3],
max_sigma=[5, 10, 10],
sigma_ratio=1.2,
threshold=0.1)
b = blobs[0]
assert b.shape == (6, )
assert b[0] == r / 2 + pad + 1
assert b[1] == r + pad + 1
assert b[2] == r + pad + 1
assert abs(math.sqrt(3) * b[3] - r / 2) < 1
assert abs(math.sqrt(3) * b[4] - r) < 1
assert abs(math.sqrt(3) * b[5] - r) < 1
# Testing exclude border
# image where blob is 5 px from borders, radius 5
img = np.ones((512, 512))
xs, ys = circle(5, 5, 5)
img[xs, ys] = 255
blobs = blob_dog(
img,
min_sigma=1.5,
max_sigma=5,
sigma_ratio=1.2,
)
assert blobs.shape[0] == 1
b = blobs[0]
assert b[0] == b[1] == 5, "blob should be 5 px from x and y borders"
blobs = blob_dog(img,
min_sigma=1.5,
max_sigma=5,
sigma_ratio=1.2,
exclude_border=5)
msg = "zero blobs should be detected, as only blob is 5 px from border"
assert blobs.shape[0] == 0, msg
def rgb(folder):
palm_location_file = "/s/red/a/nobackup/cwc/skeleton/ChaLearn17/frames/palm_location/valid/%03d/K_%05d.npy"
image_root = "/s/red/a/nobackup/cwc/skeleton/ChaLearn17/frames/valid/%03d/M_%05d"
hand_root = "/s/red/a/nobackup/cwc/skeleton/ChaLearn17/frames/hands/rgb/individual/valid/%03d/M_%05d"
start = (folder - 1) * 200 + 1
end = start + 200
print start, end
for video in range(start, end):
hand_dir = hand_root % (folder, video)
try:
os.makedirs(hand_dir)
except:
pass
palm_location = np.load(palm_location_file % (folder, video))
depth_images = get_all_frames(image_root % (folder, video),False)
print folder, video, palm_location.shape, depth_images.shape, hand_dir
image_name = ["%d_right.png", "%d_left.png"]
for frame, (palm, image) in enumerate(zip(palm_location, depth_images)):
for i in range(2):
if np.sum(palm[i]) != -2:
x_start = palm[i, 0] - 55
x_end = x_start + 110
y_start = palm[i, 1] - 55
y_end = y_start + 110
width = [[0, 0], [0, 0],[0,0]]
#print frame,
if x_end > 240:
width[0][1] = x_end - 240
x_end = 240
if y_end > 320:
width[1][1] = y_end - 320
y_end = 320
if x_start < 0:
width[0][0] = -x_start
x_start = 0
if y_start < 0:
width[1][0] = -y_start
y_start = 0
hand = np.copy(image[x_start:x_end, y_start:y_end])
hand = pad(hand, width, 'constant', constant_values=255)
hand = hand.astype("uint8")
skimage.io.imsave(os.path.join(hand_dir, image_name[i] % frame), hand)
#plt.imshow(hand)
#plt.show()
print
def corner_subpix(image, corners, window_size=11, alpha=0.99):
"""Determine subpixel position of corners.
Parameters
----------
image : ndarray
Input image.
corners : (N, 2) ndarray
Corner coordinates `(row, col)`.
window_size : int, optional
Search window size for subpixel estimation.
alpha : float, optional
Significance level for point classification.
Returns
-------
positions : (N, 2) ndarray
Subpixel corner positions. NaN for "not classified" corners.
References
----------
.. [1] http://www.ipb.uni-bonn.de/uploads/tx_ikgpublication/\
foerstner87.fast.pdf
.. [2] http://en.wikipedia.org/wiki/Corner_detection
Examples
--------
>>> from skimage.feature import corner_harris, corner_peaks, corner_subpix
>>> img = np.zeros((10, 10))
>>> img[:5, :5] = 1
>>> img[5:, 5:] = 1
>>> img.astype(int)
array([[1, 1, 1, 1, 1, 0, 0, 0, 0, 0],
[1, 1, 1, 1, 1, 0, 0, 0, 0, 0],
[1, 1, 1, 1, 1, 0, 0, 0, 0, 0],
[1, 1, 1, 1, 1, 0, 0, 0, 0, 0],
[1, 1, 1, 1, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1]])
>>> coords = corner_peaks(corner_harris(img), min_distance=2)
>>> coords_subpix = corner_subpix(img, coords, window_size=7)
>>> coords_subpix
array([[ 4.5, 4.5]])
"""
# window extent in one direction
wext = (window_size - 1) // 2
image = pad(image, pad_width=wext, mode='constant', constant_values=0)
# add pad width, make sure to not modify the input values in-place
corners = corners + wext
# normal equation arrays
N_dot = np.zeros((2, 2), dtype=np.double)
N_edge = np.zeros((2, 2), dtype=np.double)
b_dot = np.zeros((2, ), dtype=np.double)
b_edge = np.zeros((2, ), dtype=np.double)
# critical statistical test values
redundancy = window_size**2 - 2
t_crit_dot = stats.f.isf(1 - alpha, redundancy, redundancy)
t_crit_edge = stats.f.isf(alpha, redundancy, redundancy)
# coordinates of pixels within window
y, x = np.mgrid[-wext:wext + 1, -wext:wext + 1]
corners_subpix = np.zeros_like(corners, dtype=np.double)
for i, (y0, x0) in enumerate(corners):
# crop window around corner + border for sobel operator
miny = y0 - wext - 1
maxy = y0 + wext + 2
minx = x0 - wext - 1
maxx = x0 + wext + 2
window = image[miny:maxy, minx:maxx]
winx, winy = _compute_derivatives(window, mode='constant', cval=0)
# compute gradient suares and remove border
winx_winx = (winx * winx)[1:-1, 1:-1]
winx_winy = (winx * winy)[1:-1, 1:-1]
winy_winy = (winy * winy)[1:-1, 1:-1]
# sum of squared differences (mean instead of gaussian filter)
Axx = np.sum(winx_winx)
Axy = np.sum(winx_winy)
Ayy = np.sum(winy_winy)
# sum of squared differences weighted with coordinates
# (mean instead of gaussian filter)
bxx_x = np.sum(winx_winx * x)
bxx_y = np.sum(winx_winx * y)
bxy_x = np.sum(winx_winy * x)
bxy_y = np.sum(winx_winy * y)
byy_x = np.sum(winy_winy * x)
byy_y = np.sum(winy_winy * y)
# normal equations for subpixel position
N_dot[0, 0] = Axx
N_dot[0, 1] = N_dot[1, 0] = -Axy
N_dot[1, 1] = Ayy
N_edge[0, 0] = Ayy
N_edge[0, 1] = N_edge[1, 0] = Axy
N_edge[1, 1] = Axx
b_dot[:] = bxx_y - bxy_x, byy_x - bxy_y
b_edge[:] = byy_y + bxy_x, bxx_x + bxy_y
# estimated positions
est_dot = np.linalg.solve(N_dot, b_dot)
est_edge = np.linalg.solve(N_edge, b_edge)
# residuals
ry_dot = y - est_dot[0]
rx_dot = x - est_dot[1]
ry_edge = y - est_edge[0]
rx_edge = x - est_edge[1]
# squared residuals
rxx_dot = rx_dot * rx_dot
rxy_dot = rx_dot * ry_dot
ryy_dot = ry_dot * ry_dot
rxx_edge = rx_edge * rx_edge
rxy_edge = rx_edge * ry_edge
ryy_edge = ry_edge * ry_edge
# determine corner class (dot or edge)
# variance for different models
var_dot = np.sum(winx_winx * ryy_dot - 2 * winx_winy * rxy_dot \
+ winy_winy * rxx_dot)
var_edge = np.sum(winy_winy * ryy_edge + 2 * winx_winy * rxy_edge \
+ winx_winx * rxx_edge)
# test value (F-distributed)
t = var_edge / var_dot
# 1 for edge, -1 for dot, 0 for "not classified"
corner_class = (t < t_crit_edge) - (t > t_crit_dot)
if corner_class == -1:
corners_subpix[i, :] = y0 + est_dot[0], x0 + est_dot[1]
elif corner_class == 0:
corners_subpix[i, :] = np.nan, np.nan
elif corner_class == 1:
corners_subpix[i, :] = y0 + est_edge[0], x0 + est_edge[1]
# subtract pad width
corners_subpix -= wext
return corners_subpix
def describe(self, image, test_image: bool, sigma_psd=70/255, cutoff_freq=10, a=0.75, b=1.0):
if isinstance(image, DatasetManager.Image):
if test_image:
image_data = image.test_data
else:
image_data = image.data
else:
image_data = image.copy()
# Perform BM3D Filter
image_bm3d_filtered = SharedFunctions.bm3d_filter(image_data, 70/255)
# Perform Homomorphic filter, Note: This requires images to be normalised in range [0, 255]
image_scaled_255 = ImageUtils.convert_float32_image_uint8(image_data)
cutoff, a, b = 10, 0.75, 0.1
image_homomorphic_filtered = SharedFunctions.homomorphic_filter(image_scaled_255, cutoff, a, b)
image_homomorphic_filtered = ImageUtils.convert_uint8_image_float32(image_homomorphic_filtered)
# Perform Median filter. Padding is required for median filter.
image_padded = pad(array=image_data, pad_width=1, mode='constant', constant_values=0)
image_median_filtered = np.zeros(image_padded.shape, dtype=np.float32)
SharedFunctions.median_filter(image_padded, 3, 1, image_median_filtered)
image_median_filtered = image_median_filtered[1:-1, 1:-1] # Remove padding now median filter done
# Subtract original image from filtered image to get noise only
bm3d_noise = image_data - image_bm3d_filtered
homomorphic_noise = image_data - image_homomorphic_filtered
median_noise = image_data - image_median_filtered
if self.save_img:
if isinstance(image, DatasetManager.Image):
GenerateExamples.write_image(ImageUtils.convert_float32_image_uint8(image_bm3d_filtered),
os.path.join('BM3DELBP', 'NoiseClassifier', 'Filtered Images'),
'{}-{}-{}-BM3D-filtered.png'.format(image.name, image.test_noise,
image.test_noise_val))
GenerateExamples.write_image(ImageUtils.convert_float32_image_uint8(image_homomorphic_filtered),
os.path.join('BM3DELBP', 'NoiseClassifier', 'Filtered Images'),
'{}-{}-{}-homomorphic-filtered-cutoff_{}-a_{}-b_{}.png'.format(image.name,
image.test_noise,
image.test_noise_val,
cutoff, a,
b))
GenerateExamples.write_image(ImageUtils.convert_float32_image_uint8(image_median_filtered),
os.path.join('BM3DELBP', 'NoiseClassifier', 'Filtered Images'),
'{}-{}-{}-median-filtered.png'.format(image.name, image.test_noise,
image.test_noise_val))
GenerateExamples.write_image(ImageUtils.convert_float32_image_uint8(bm3d_noise),
os.path.join('BM3DELBP', 'NoiseClassifier', 'Noise Estimates'),
'{}-{}-{}-BM3D-noise-estimate.png'.format(image.name, image.test_noise,
image.test_noise_val))
GenerateExamples.write_image(ImageUtils.convert_float32_image_uint8(homomorphic_noise),
os.path.join('BM3DELBP', 'NoiseClassifier', 'Noise Estimates'),
'{}-{}-{}-homomorphic-filtered-cutoff_{}-a_{}-b_{}.png'.format(image.name,
image.test_noise,
image.test_noise_val,
cutoff, a,
b))
GenerateExamples.write_image(ImageUtils.convert_float32_image_uint8(median_noise),
os.path.join('BM3DELBP', 'NoiseClassifier', 'Noise Estimates'),
'{}-{}-{}-median-noise-estimate.png'.format(image.name, image.test_noise,
image.test_noise_val))
else:
raise ValueError('save_img set but not passed as DatasetManager.Image or BM3DELBPImage')
kurtosis_bm3d = kurtosis(a=bm3d_noise, axis=None, fisher=False, nan_policy='raise')
skewness_bm3d = skew(a=bm3d_noise, axis=None, nan_policy='raise')
kurtosis_homomorphic = kurtosis(a=homomorphic_noise, axis=None, fisher=False, nan_policy='raise')
skewness_homomorphic = skew(a=homomorphic_noise, axis=None, nan_policy='raise')
kurtosis_median = kurtosis(a=median_noise, axis=None, fisher=False, nan_policy='raise')
skewness_median = skew(a=median_noise, axis=None, nan_policy='raise')
if GlobalConfig.get('debug'):
print("BM3D Filtered Kurtosis:", kurtosis_bm3d, ", Skewness: ", skewness_bm3d)
print("Homomorphic Filtered Kurtosis:", kurtosis_homomorphic, ", Skewness: ", skewness_homomorphic)
print("Median Filtered Kurtosis:", kurtosis_median, ", Skewness: ", skewness_median)
# Generate image featurevector of 6 characteristics
featurevector = np.array([kurtosis_bm3d, skewness_bm3d,
kurtosis_homomorphic, skewness_homomorphic,
kurtosis_median, skewness_median])
return featurevector
avg, std = image.mean(), image.std()
logging.info(f"intensity: {avg:.4f}+-{std:.4f}")
image = image > avg + std
# remove small spot
image = median(image, disk(1))
# rotate +90d
image = rotate(image, 90, resize=True, preserve_range=True)
imageio.imwrite("sobel.tif", image.astype(np.uint8))
# pad to destination shape
src_shape = image.shape[:2] # potentially colored
pad_shape = tuple(d - s for d, s in zip(dst_shape, src_shape))
# update pad shape to before/after
pad_shape = tuple((p // 2, p - p // 2) for p in pad_shape)
logging.info(f"pad width: {pad_shape}")
if len(image.shape) == 3:
# color dimension does not need padding
pad_shape += ((0, 0), )
image = pad(image, pad_shape, mode="constant", constant_values=0)
# gray scale
image = rescale_intensity(image, out_range=np.uint8)
image = image.astype(np.uint8)
logging.info(f"{len(image > 0)} active pixels")
imageio.imwrite("hashimoto_slm_simple.bmp", image)
##
# Read in image and convert it to boolean
image = util.img_as_bool(io.imread(sys.argv[1]))
# Read in the structuring element (SE) and convert it to boolean
se = util.img_as_bool(io.imread(sys.argv[2]))
# Get the height and width of the SE
se_height, se_width = se.shape
# Find the center indices
pad_v = se_height // 2
pad_h = se_width // 2
# Pad the input image with numpy.util.pad
padded = util.pad(image, (pad_v, pad_h), mode="constant")
# Create output image
out = numpy.zeros(image.shape, dtype=bool)
# Loop through the image (follow image indices)
for i in range(image.shape[0]):
for j in range(image.shape[1]):
# Retrieve subimage from padded image (not index-aligned with the image)
subimage = padded[i:i + se_height, j:j + se_width]
# Determine whether or not we have an overlap at the current position
# We use numpy.array_equal to determine if product of the se and the subimage
# is the same as the se
out[i, j] = numpy.array_equal(subimage * se, se)
# Save output image
model = load_model(path_to_model)
# get input shape of model
_, input_rows, input_cols, input_channels = model.layers[0].input_shape
_, output_classes = model.layers[-1].output_shape
in_rows_half = int(input_rows/2)
in_cols_half = int(input_cols/2)
# import correct preprocessing
if input_channels is 3:
from image_functions import preprocessing_image_rgb as preprocessing_image
else:
from image_functions import preprocessing_image_ms as preprocessing_image
# pad image
image = pad(image, ((input_rows, input_rows),
(input_cols, input_cols),
(0, 0)), 'symmetric')
# don't forget to preprocess
image = preprocessing_image(image)
num_rows, num_cols, _ = image.shape
# sliding window over image
image_classified_prob = np.zeros((num_rows, num_cols, output_classes))
row_images = np.zeros((num_cols_unpadded, input_rows,
input_cols, input_channels))
for row in tqdm(range(input_rows, num_rows-input_rows), desc="Processing..."):
# get all images along one row
for idx, col in enumerate(range(input_cols, num_cols-input_cols)):
# cut smal image patch
row_images[idx, ...] = image[row-in_rows_half:row+in_rows_half,
def save_canny_save_fit(path, sig, low, high): #sig=3,low = 0, high = 30
zstack = io.imread(path)
image = img_as_ubyte(zstack[:, :, 0])
mask = image > 20
fprefix = os.path.basename(path).strip('.jpg')
bn = fprefix + '_CANNY.jpg'
current_dir = os.getcwd()
cannysavepath = current_dir + '/' + plate_dir.strip('/') + '_canny/' + bn
edges = canny(image, sigma=sig, low_threshold=low, high_threshold=high)
#plt.imsave(fname=str(p + fprefix + '_ubyte.jpg'), arr=image)
#plt.imsave(fname=str(p + fprefix + '_bounded.jpg'), arr=mask)
bn = fprefix + '_dropfinder2.jpg'
fitsavepath = current_dir + '/' + plate_dir.strip('/') + '_fit/' + bn
try:
plt.imsave(fname=cannysavepath, arr=edges)
plt.close()
except FileNotFoundError:
print('FileNotFoundError: making ' + plate_dir.strip('/') + '_canny')
os.mkdir(current_dir + '/' + plate_dir.strip('/') + '_canny/')
print('writing ' + cannysavepath)
plt.imsave(fname=cannysavepath, arr=edges)
plt.close()
print(cannysavepath)
accum_d, cx_d, cy_d, radii_d = circular_hough_transform(
135, 145, 2, edges, 1) #edge detection on drop
accum_w, cx_w, cy_w, radii_w = circular_hough_transform(
479, 495, 1, edges, 1) #edge detection on well
try:
im = image
padsize = np.array([(0, 100), (0, 100)])
pad_im = pad(image, padsize, mode='constant')
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(20, 8))
draw_circles_on_image(pad_im, cx_d, cy_d, radii_d, 255, 2)
draw_circles_on_image(pad_im, cx_w, cy_w, radii_w, 255, 2)
### Code to draw the inner circle
r_inner = 0.73701 * radii_w
r_inner = r_inner.astype(int)
draw_circles_on_image(pad_im, cx_w, cy_w, r_inner, 255, 2)
cx = 641
cy = 553
rad = 487
c, r = circle_perimeter(cx, cy, rad)
#pad_im[r,c] = 255
#pad_im[cx-2:cx+2,cy-2:cy+2]=255
try:
plt.imsave(fname=fitsavepath, arr=pad_im, cmap='Greys_r')
plt.close()
except FileNotFoundError:
print('making ' + plate_dir.strip('/') + '_fit/')
os.mkdir(current_dir + '/' + plate_dir.strip('/') + '_fit/')
print('writing' + bn)
plt.imsave(fname=fitsavepath, arr=pad_im, cmap='Greys_r')
plt.close()
print(fitsavepath)
except IndexError:
print('IndexError' + ' ' + fitsavepath)
#plt.imshow(pad_im)
return cx_d, cy_d, radii_d, cx_w, cy_w, radii_w
def iradonT(radon_image,
theta=None,
output_size=None,
filter="ramp",
interpolation="linear",
circle=False):
"""
Inverse radon transform.
Reconstruct an image from the radon transform, using the filtered
back projection algorithm.
Parameters
----------
radon_image : array_like, dtype=float
Image containing radon transform (sinogram). Each column of
the image corresponds to a projection along a different angle. The
tomography rotation axis should lie at the pixel index
``radon_image.shape[0] // 2`` along the 0th dimension of
``radon_image``.
theta : array_like, dtype=float, optional
Reconstruction angles (in degrees). Default: m angles evenly spaced
between 0 and 180 (if the shape of `radon_image` is (N, M)).
output_size : int
Number of rows and columns in the reconstruction.
filter : str, optional (default ramp)
Filter used in frequency domain filtering. Ramp filter used by default.
Filters available: ramp, shepp-logan, cosine, hamming, hann.
Assign None to use no filter.
interpolation : str, optional (default 'linear')
Interpolation method used in reconstruction. Methods available:
'linear', 'nearest', and 'cubic' ('cubic' is slow).
circle : boolean, optional
Assume the reconstructed image is zero outside the inscribed circle.
Also changes the default output_size to match the behaviour of
``radon`` called with ``circle=True``.
Returns
-------
reconstructed : ndarray
Reconstructed image. The rotation axis will be located in the pixel
with indices
``(reconstructed.shape[0] // 2, reconstructed.shape[1] // 2)``.
Notes
-----
It applies the Fourier slice theorem to reconstruct an image by
multiplying the frequency domain of the filter with the FFT of the
projection data. This algorithm is called filtered back projection.
"""
if radon_image.ndim != 2:
raise ValueError('The input image must be 2-D')
if theta is None:
m, n = radon_image.shape
theta = np.linspace(0, 180, n, endpoint=False)
else:
theta = np.asarray(theta)
if len(theta) != radon_image.shape[1]:
raise ValueError("The given ``theta`` does not match the number of "
"projections in ``radon_image``.")
interpolation_types = ('linear', 'nearest', 'cubic')
if not interpolation in interpolation_types:
raise ValueError("Unknown interpolation: %s" % interpolation)
if not output_size:
# If output size not specified, estimate from input radon image
if circle:
output_size = radon_image.shape[0]
else:
output_size = int(
np.floor(np.sqrt((radon_image.shape[0])**2 / 2.0)))
if circle:
radon_image = _sinogram_circle_to_square(radon_image)
th = (np.pi / 180.0) * theta
# resize image to next power of two (but no less than 64) for
# Fourier analysis; speeds up Fourier and lessens artifacts
projection_size_padded = \
max(64, int(2**np.ceil(np.log2(2 * radon_image.shape[0]))))
pad_width = ((0, projection_size_padded - radon_image.shape[0]), (0, 0))
img = util.pad(radon_image, pad_width, mode='constant', constant_values=0)
# Construct the Fourier filter
#delta = 1
l1 = (2 * np.pi)**(-4 / 5) * (delta)**(8 / 5) / 5
l2 = (2 * np.pi)**(-4 / 5) * (delta)**(-2 / 5) * 4 / 5
f = fftfreq(projection_size_padded).reshape(-1, 1) # digital frequency
omega = 2 * np.pi * f # angular frequency
fourier_filter = 2 * np.abs(f) # ramp filter
if filter == "ramp":
pass
elif filter == "tigran":
g = fftfreq(projection_size_padded).reshape(-1, 1)
w = abs(omega)
g[1:] = l2 / (l1 * (
(w[1:])**5 /
(2 * np.pi)) + l2) + np.sqrt(l1 * l2) * (w[1:])**2 * np.sqrt(l1 * (
(w[1:])**5 /
(2 * np.pi)) + l2 - w[1:] / (2 * np.pi)) / (l1 *
((w[1:])**5 /
(2 * np.pi)) + l2)
fourier_filter[1:] = fourier_filter[1:] * g[1:]
elif filter == "shepp-logan":
# Start from first element to avoid divide by zero
fourier_filter[1:] = fourier_filter[1:] * np.sin(omega[1:]) / omega[1:]
elif filter == "cosine":
fourier_filter *= np.cos(omega)
elif filter == "hamming":
fourier_filter *= (0.54 + 0.46 * np.cos(omega / 2))
elif filter == "hann":
fourier_filter *= (1 + np.cos(omega / 2)) / 2
elif filter is None:
fourier_filter[:] = 1
else:
raise ValueError("Unknown filter: %s" % filter)
# Apply filter in Fourier domain
projection = fft(img, axis=0) * fourier_filter
radon_filtered = np.real(ifft(projection, axis=0))
# Resize filtered image back to original size
radon_filtered = radon_filtered[:radon_image.shape[0], :]
reconstructed = np.zeros((output_size, output_size))
# Determine the center of the projections (= center of sinogram)
mid_index = radon_image.shape[0] // 2
[X, Y] = np.mgrid[0:output_size, 0:output_size]
xpr = X - int(output_size) // 2
ypr = Y - int(output_size) // 2
# Reconstruct image by interpolation
for i in range(len(theta)):
t = ypr * np.cos(th[i]) - xpr * np.sin(th[i])
x = np.arange(radon_filtered.shape[0]) - mid_index
if interpolation == 'linear':
backprojected = np.interp(t,
x,
radon_filtered[:, i],
left=0,
right=0)
else:
interpolant = interp1d(x,
radon_filtered[:, i],
kind=interpolation,
bounds_error=False,
fill_value=0)
backprojected = interpolant(t)
reconstructed += backprojected
if circle:
radius = output_size // 2
reconstruction_circle = (xpr**2 + ypr**2) <= radius**2
reconstructed[~reconstruction_circle] = 0.
return reconstructed * np.pi / (2 * len(th))
def pad_clip(clip, h, w):
im_h, im_w = clip[0].shape[:2]
pad_h = (0, 0) if h < im_h else ((h - im_h) // 2, (h - im_h + 1) // 2)
pad_w = (0, 0) if w < im_w else ((w - im_w) // 2, (w - im_w + 1) // 2)
return pad(clip, ((0, 0), pad_h, pad_w, (0, 0)), mode='edge')
def nlm(img, t, f, h): #
img = img_as_float(img)
[m, n] = img.shape
img_denoised = np.zeros((m, n))
h = h * h
# Normalization
kernel = np.zeros((2 * f + 1, 2 * f + 1))
for d in range(1, f + 1):
value = 1. / ((2 * d + 1) * (2 * d + 1))
for i in range(-d, d + 1):
for j in range(-d, d + 1):
kernel[f - i, f - j] = kernel[f - i, f - j] + value
kernel = kernel / f
kernel = kernel / sum(sum(kernel))
vkernel = np.reshape(kernel, (2 * f + 1) * (2 * f + 1))
pdimg = util.pad(img, ((f, f)), mode='symmetric') # padding
#Denoising
for i in range(0, m):
for j in range(0, n):
i1 = i + f
j1 = j + f
W1 = pdimg[range(i1 - f, i1 + f + 1), :]
W1 = W1[:, range(j1 - f, j1 + f + 1)]
wmax = 0
average = 0
sweight = 0
rmin = max(i1 - t, f)
rmax = min(i1 + t, m + f - 1)
smin = max(j1 - t, f)
smax = min(j1 + t, n + f - 1)
# Find similarity between neighborhoods W1(center) and W2(surrounding)
for r in range(rmin, rmax + 1):
for s in range(smin, smax + 1):
if ((r == i1) and (s == j1)):
continue
W2 = pdimg[range(r - f, r + f + 1), :]
W2 = W2[:, range(s - f, s + f + 1)]
# Use L2-norm
temp = np.reshape(np.square(W1 - W2),
(2 * f + 1) * (2 * f + 1))
d = np.dot(vkernel, temp)
w = np.exp(-d / h)
if (w > wmax):
wmax = w
sweight = sweight + w
average = average + w * pdimg[r, s]
average = average + wmax * pdimg[i1, j1]
sweight = sweight + wmax # Calculation of the weight
# Compute value of the denoised pixel
if (sweight > 0):
img_denoised[i, j] = average / sweight
else:
img_denoised[i, j] = img[i, j]
return img_denoised
def test_zero_pad_width(self):
arr = np.arange(30)
arr = np.reshape(arr, (6, 5))
for pad_width in (0, (0, 0), ((0, 0), (0, 0))):
assert_array_equal(arr, pad(arr, pad_width, mode='constant'))
def calc_training_patches(self, save=False):
ps = self.conf.patch_size
my_gaze = self.conf.myGaze_fg
scale_factor = self.conf.scale_factor
seen_patches = list()
unseen_patches = list()
selem = morphology.square(5)
print('Getting seen patches')
with progressbar.ProgressBar(maxval=len(self.conf.frameFileNames)) as bar:
for i in range(len(self.conf.frameFileNames)):
bar.update(i)
img = utls.imread(self.conf.frameFileNames[i])
img = (color.rgb2gray(img)*255).astype(np.uint8)
img = median(img, selem=selem) # Uses square of size 3
ci_seen, cj_seen = gaze.gazeCoord2Pixel(
my_gaze[i, 3], my_gaze[i, 4], img.shape[1], img.shape[0])
i_, j_ = self.get_centers_negatives(ci_seen, cj_seen, ps,
self.conf.overlap_ratio,
img.shape)
img_padded = pad(img,((ps,ps),),mode='symmetric')
seen_patch = img_padded[int(ci_seen + ps/2):int(ci_seen + 3*ps/2),int(cj_seen + ps/2):int(cj_seen + 3*ps/2)]
seen_patch_mean = np.mean(seen_patch)
seen_patch_std = np.std(seen_patch)
if(seen_patch_std == 0): seen_patch_std = 1
seen_patch = (seen_patch - seen_patch_mean) / seen_patch_std
seen_patch = rescale(
seen_patch,
scale=scale_factor,
order=1,
mode='reflect',
preserve_range=True)
seen_patches.append((i,
ci_seen,
cj_seen,
seen_patch.ravel()))
for k in range(i_.shape[0]):
unseen_patch = img[int(i_[k]- ps / 2):int(i_[k] + ps / 2), int(
j_[k]- ps / 2):int(j_[k]+ ps / 2)]
unseen_patch_mean = np.mean(unseen_patch)
unseen_patch_std = np.std(unseen_patch)
if(unseen_patch_std == 0): unseen_patch_std = 1
unseen_patch = (unseen_patch - unseen_patch_mean) / unseen_patch_std
unseen_patch = rescale(
unseen_patch,
scale=scale_factor,
order=1,
mode='reflect',
preserve_range=True)
unseen_patches.append((i,
i_[k],
j_[k],
unseen_patch.ravel()))
if(save):
seen_patches_df = pd.DataFrame(seen_patches,
columns=['frame',
'c_i',
'c_j',
'patch'])
unseen_patches_df = pd.DataFrame(unseen_patches,
columns=['frame',
'c_i',
'c_j',
'patch'])
save_path = os.path.join(self.conf.dataOutDir,
'vilar')
if(not os.path.exists(save_path)):
os.mkdir(save_path)
seen_patches_df.to_pickle(os.path.join(save_path,
'vilar_seen_patches_df.p'))
unseen_patches_df.to_pickle(
os.path.join(save_path,
'vilar_unseen_patches_df.p'))
return True
def denoising(noisy_image,
learning_image,
window_shape,
window_step,
sigma,
learning_ratio=0.1,
ksvd_iter=1):
# 1. Form noisy patches.
padded_noisy_image = pad(noisy_image,
pad_width=window_shape,
mode='symmetric')
noisy_patches, noisy_patches_shape = patch_matrix_windows(
padded_noisy_image, window_shape, window_step)
padded_lea_image = pad(learning_image,
pad_width=window_shape,
mode='symmetric')
lea_patches, lea_patches_shape = patch_matrix_windows(
padded_lea_image, window_shape, window_step)
print('Shape of dataset : ' + str(noisy_patches.shape))
# 2. Form explanatory dictionary.
k = int(learning_ratio * lea_patches.shape[1])
indexes = np.random.random_integers(0, lea_patches.shape[1] - 1, k)
basis = lea_patches[:, indexes]
basis /= np.sum(basis.T.dot(basis), axis=-1)
print('Shape of dictionary : ' + str(basis.shape) + '\n')
# 3. Compute K-SVD.
start = timeit.default_timer()
#--------------------------------
basis_final, sparse_final, n_total = k_svd(basis, noisy_patches, sigma,
single_channel_omp, ksvd_iter)
txtHandle = open(r".\dictionary.txt", 'w+')
print('dictionary saving ~')
np.save(r".\TestTemp\dictionary.npy", sparse_final)
np.save(r".\TestTemp\phi.npy", basis_final)
#--------------------------------
stop = timeit.default_timer()
print("Calculation time : " + str(stop - start) + ' seconds.')
# 4. Reconstruct the image.
patches_approx = basis_final.dot(sparse_final)
tx = open(r".\size.txt", "w")
tx.close()
tx = open(r".\size.txt", "a")
tx.write(str(padded_noisy_image.shape))
tx.write(str(noisy_patches_shape))
tx.write(str(window_step))
tx.write(str(patches_approx.shape))
tx.close()
padded_denoised_image = image_reconstruction_windows(
padded_noisy_image.shape, patches_approx, noisy_patches_shape,
window_step)
shrunk_0, shrunk_1 = tuple(
map(sub, padded_denoised_image.shape, window_shape))
denoised_image = np.abs(padded_denoised_image)[window_shape[0]:shrunk_0,
window_shape[1]:shrunk_1]
plt.imshow(Image.fromarray(np.uint8(denoised_image)))
plt.show()
#recover info
return denoised_image, stop - start, n_total
def select_random_augmentation(img):
f = np.random.choice(augmenters)
return f(img)
if __name__ == '__main__':
# TODO parse args
parser = argparse.ArgumentParser()
parser.add_argument('image', help='image name')
parser.add_argument('--pad-size', default=10)
args = parser.parse_args()
images = []
original_img = io.imread(args.image)
padded_img = util.pad(original_img, args.pad_size, 'constant', constant_values=255)
images.append(padded_img)
# iaa.GaussianBlur
blur = iaa.GaussianBlur(sigma=(0, 1.0))
blur_img = blur.augment_image(padded_img)
images.append(blur_img)
# downsample (PIL) LANCZOS
downsample_aug = iaa.Lambda(func_images=downsample_func(0.5))
downsampled = downsample_aug.augment_image(padded_img)
images.append(downsampled)
# downsample + stretch ???
# morphology.closing ???
def reflect_pad(img):
return pad(
resize(img, (101 * 2, 101 * 2), mode='constant', preserve_range=True),
27, 'reflect')
def ARC(kspace, AtA, kernel_size, c, lamda):
'''ARC.'''
sx, sy, ncoils = kspace.shape[:]
kx, ky = kernel_size[:]
# Zero-pad data
px = int(kx / 2)
py = int(ky / 2)
kspace = pad( # pylint: disable=E1102
kspace, ((px, px), (py, py), (0, 0)),
mode='constant')
dummyK = np.zeros((kx, ky, ncoils))
dummyK[int(kx / 2), int(ky / 2), c] = 1
idxy = np.where(dummyK)
res = np.zeros((sx, sy), dtype=kspace.dtype)
MaxListLen = 100 # max number of kernels we'll store for lookup
LIST = np.zeros((kx * ky * ncoils, MaxListLen), dtype=kspace.dtype)
KEY = np.zeros((kx * ky * ncoils, MaxListLen))
count = 0 # current index for the next kernel to store in LIST
for xy in np.ndindex((sx, sy)):
x, y = xy[:]
tmp = kspace[x:x + kx, y:y + ky, :]
pat = np.abs(tmp) > 0
if pat[idxy]:
# If we aquired this k-space sample, use it!
res[x, y] = tmp[idxy].squeeze()
else:
# If we didn't aquire it, let's either look up the
# kernel or compute a new one
key = pat.flatten()
# If we have a matching kernel, the key will exist
# in our array of KEYs. This little loop looks through
# the list to find if we have the kernel already
idx = 0
for nn in range(1, KEY.shape[1] + 1):
if np.sum(key == KEY[:, nn - 1]) == key.size:
idx = nn
break
if idx == 0:
# If we didn't find a matching kernel, compute one.
# We'll only hold MaxListLen kernels in the lookup
# at one time to save on memory and lookup time
count += 1
kernel = calibrate(AtA, kernel_size, ncoils, c, lamda,
pat)[0].flatten()
KEY[:, np.mod(count, MaxListLen)] = key
LIST[:, np.mod(count, MaxListLen)] = kernel
else:
# If we found it, use it!
kernel = LIST[:, idx - 1]
# Apply kernel weights to coil data for interpolation
res[x, y] = np.sum(kernel * tmp.flatten())
return res
def test_check_02(self):
a = pad([1, 2, 3], 4, 'wrap')
b = np.array([3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1])
assert_array_equal(a, b)
def process_study(study_id, in_train_set,
isotropic_volumes_folder, volumes_metadata,
annotations_grouped, out_dir, config):
dimensions, patchsize, scaling, multiple, padding, offcenter, rotation, view = config
isometric_volume = np.load('../data_proc/stage1/{}/{}.npy'.format(isotropic_volumes_folder, study_id))
mean = np.mean(isometric_volume).astype(np.float32)
std = np.std(isometric_volume).astype(np.float32)
resize_factor = np.divide(volumes_metadata['volume_resampled_shape'], volumes_metadata['volume_shape'])
nodules = []
for i, group in enumerate(annotations_grouped):
data = [a['data'] for a in group]
z0 = int(round(resize_factor[0] * min([a['sliceNum'] for a in group])))
z1 = int(round(resize_factor[0] * max([a['sliceNum'] for a in group])) + 1)
y0 = int(round(resize_factor[1] * min([d['y'] for d in data])))
y1 = int(round(resize_factor[1] * max([(d['y'] + d['height']) for d in data])) + 1)
x0 = int(round(resize_factor[2] * min([d['x'] for d in data])))
x1 = int(round(resize_factor[2] * max([(d['x'] + d['width']) for d in data])) + 1)
# add padding to patch if specified
z0 = max(0, int(z0 - ((z1 - z0) * padding / 100)))
z1 = min(isometric_volume.shape[0], int(z1 + ((z1 - z0) * padding / 100)))
y0 = max(0, int(y0 - ((y1 - y0) * padding / 100)))
y1 = min(isometric_volume.shape[1], int(y1 + ((y1 - y0) * padding / 100)))
x0 = max(0, int(x0 - ((x1 - x0) * padding / 100)))
x1 = min(isometric_volume.shape[2], int(x1 + ((x1 - x0) * padding / 100)))
if scaling == 'original':
if (z1 - z0) < patchsize:
z0 -= (patchsize - (z1 - z0)) // 2
z1 += (patchsize - (z1 - z0)) - (patchsize - (z1 - z0)) // 2
if (y1 - y0) < patchsize:
y0 -= (patchsize - (y1 - y0)) // 2
y1 += (patchsize - (y1 - y0)) - (patchsize - (y1 - y0)) // 2
if (x1 - x0) < patchsize:
x0 -= (patchsize - (x1 - x0)) // 2
x1 += (patchsize - (x1 - x0)) - (patchsize - (x1 - x0)) // 2
shape = (z1-z0, y1-y0, x1-x0)
nodule = isometric_volume[z0:z1, y0:y1, x0:x1]
nodules.append(nodule)
if len(nodules) == 0:
return 0, []
if multiple == 'largest':
nodule_sizes_sorted = np.argsort([np.prod(nodule.shape) for nodule in nodules])
nodules = [nodules[nodule_sizes_sorted[-1]]]
if scaling == 'stretch':
nodules = [resize(nodule, [patchsize, patchsize, patchsize],
mode='edge', clip=True, preserve_range=True) for nodule in nodules]
elif scaling == 'original':
nodules_reshaped = []
for nodule in nodules:
pad_width = []
for s in nodule.shape:
if s < patchsize:
pad_width.append(((patchsize - s) // 2, (patchsize - s) - (patchsize - s) // 2))
else:
pad_width.append((0, 0))
crop_width = []
for s in nodule.shape:
if s > patchsize:
crop_width.append(((s - patchsize) // 2, (s - patchsize) - (s - patchsize) // 2))
else:
crop_width.append((0, 0))
nodules_reshaped.append(crop(pad(nodule, pad_width, mode='minimum'), crop_width))
nodules = nodules_reshaped
nodules = [(nodule.astype(np.float32) - mean) / (std + 1e-7) for nodule in nodules]
if offcenter > 0:
offcenter_range = range(-int(patchsize * offcenter / 100), int(patchsize * offcenter / 100))
else:
offcenter_range = [0]
patches = []
if dimensions == '2d':
for nodule in nodules:
for i in offcenter_range:
if view == 'axial':
patches.append(np.expand_dims(nodule[int(round(i + nodule.shape[0] / 2)), :, :], axis=2))
else:
patches.append(np.expand_dims(nodule[int(round(i + nodule.shape[0] / 2)), :, :], axis=2))
patches.append(np.expand_dims(nodule[:, int(round(i + nodule.shape[1] / 2)), :], axis=2))
patches.append(np.expand_dims(nodule[:, :, int(round(i + nodule.shape[2] / 2))], axis=2))
elif dimensions == '3d':
patches = [np.expand_dims(nodule, axis=3) for nodule in nodules]
if in_train_set:
dirname1 = 'train'
else:
dirname1 = 'val'
dirname2 = str(labels.ix[study_id, 'cancer'])
for patch in patches:
out_filepath = os.path.join(out_dir, dirname1, dirname2, '{}.npy'.format(uuid4()))
np.save(out_filepath, patch)
return len(patches), [nodule.shape for nodule in nodules]
def test_check_large_pad(self):
a = np.arange(12)
a = np.reshape(a, (3, 4))
a = pad(a, (10, 12), 'wrap')
b = np.array([[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
],
[
2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
0, 1, 2, 3, 0, 1, 2, 3
],
[
6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7, 4, 5, 6, 7,
4, 5, 6, 7, 4, 5, 6, 7
],
[
10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11, 8,
9, 10, 11, 8, 9, 10, 11, 8, 9, 10, 11
]])
assert_array_equal(a, b)
def test_check_03(self):
a = pad([1, 2, 3], 4, 'reflect')
b = np.array([1, 2, 3, 2, 1, 2, 3, 2, 1, 2, 3])
assert_array_equal(a, b)
def test_check_median_02(self):
a = np.array([[3, 1, 4], [4, 5, 9], [9, 8, 2]])
a = pad(a.T, 1, 'median').T
b = np.array([[5, 4, 5, 4, 5], [3, 3, 1, 4, 3], [5, 4, 5, 9, 5],
[8, 9, 8, 2, 8], [5, 4, 5, 4, 5]])
assert_array_equal(a, b)
def depth_segment():
palm_location_file = "/s/red/a/nobackup/cwc/skeleton/ChaLearn17/frames/palm_location/valid/%03d/K_%05d.npy"
image_root = "/s/red/a/nobackup/cwc/skeleton/ChaLearn17/frames/valid/%03d/K_%05d"
hand_root = "/s/red/a/nobackup/cwc/skeleton/ChaLearn17/frames/hands/individual/valid/%03d/K_%05d"
for video in range(5600,5600):
folder = ((video - 1) / 200) + 1
hand_dir = hand_root % (folder, video)
try:
os.makedirs(hand_dir)
except:
pass
palm_location = np.load(palm_location_file % (folder, video))
depth_images = get_all_frames(image_root % (folder, video))
print folder, video, palm_location.shape, depth_images.shape, hand_dir
image_name = ["%d_right.png", "%d_left.png"]
for frame, (palm, image) in enumerate(zip(palm_location, depth_images)):
for i in range(2):
if np.sum(palm[i]) != -2:
x_start = palm[i, 0] - 50
x_end = x_start + 100
y_start = palm[i, 1] - 50
y_end = y_start + 100
width = [[0, 0], [0, 0]]
#if y_end<=320:
# continue
print frame,
if x_end > 240:
width[0][1] = x_end - 240
x_end = 240
if y_end > 320:
width[1][1] = y_end - 320
y_end = 320
if x_start < 0:
width[0][0] = -x_start
x_start = 0
if y_start < 0:
width[1][0] = -y_start
y_start = 0
palm_depth = image[palm[i, 0], palm[i, 1]]
translate = 0.5 - palm_depth
hand = np.copy(image[x_start:x_end, y_start:y_end]) + translate
hand = pad(hand, width, 'constant', constant_values=1)
palm_depth_max = 0.5 + 0.1
palm_depth_min = 0.5 - 0.2
hand[hand > palm_depth_max] = 1
hand[hand < palm_depth_min] = 1
binary_hand = np.copy(hand)
binary_hand[binary_hand != 1] = 2
labels = measure.label(binary_hand)
palm_label = labels[50, 50]
labels[labels != palm_label] = 0
hand[labels == 0] = 1
else:
hand = np.ones((100, 100))
hand *= 255
hand = hand.astype("uint8")
skimage.io.imsave(os.path.join(hand_dir, image_name[i] % frame), hand)
# plt.show()
print
min_height = np.min(heights)
to_crop_im = [np.ceil((((ims_flat[i].shape[0]-min_height)/2,(ims_flat[i].shape[0]-min_height)/2), ((ims_flat[i].shape[1]-min_width)/2,(ims_flat[i].shape[1]-min_width)/2),(0,0))) for i in range(len(ims_flat))]
ims_crop = [util.crop(ims_flat[i], to_crop_im[i]) for i in range(len(ims_flat))]
preds_my_crop = [util.crop(preds_my_flat[i], to_crop_im[i]) for i in range(len(ims_flat))]
preds_true_crop = [util.crop(preds_true_flat[i], to_crop_im[i]) for i in range(len(ims_flat))]
f_size = ims_crop[0].shape
ims_res = [(transform.resize(ims_crop[i], f_size)*255).astype(np.uint8) for i in range(len(ims_crop))]
preds_my_res = [(transform.resize(preds_my_crop[i], f_size)*255).astype(np.uint8) for i in range(len(ims_crop))]
preds_true_res = [(transform.resize(preds_true_crop[i], f_size)*255).astype(np.uint8) for i in range(len(ims_crop))]
pw = 10
ims_pad = [util.pad(ims_res[i], ((pw,pw),(pw,pw),(0,0)), mode='constant', constant_values=255) for i in range(len(ims_res))]
preds_my_pad = [util.pad(preds_my_res[i], ((pw,pw),(pw,pw),(0,0)), mode='constant', constant_values=255) for i in range(len(ims_res))]
preds_true_pad = [util.pad(preds_true_res[i], ((pw,pw),(pw,pw),(0,0)), mode='constant', constant_values=255) for i in range(len(ims_res))]
all_ = np.concatenate([np.concatenate([ims_pad[i], preds_my_pad[i], preds_true_pad[i]], axis=1) for i in range(len(ims_pad))], axis=0)
all_ = np.split(all_, 2, axis=0)
all_ = np.concatenate(all_,axis=1)
#Write methods on image
header_height = 150
header = np.ones((header_height,all_.shape[1],3)).astype(np.uint8)*255
all_with_header = np.concatenate((header, all_),axis=0)
im_path = os.path.join(out_result_dir, 'all_learning.png')
print('Saving to: ' + im_path)
io.imsave(im_path, all_with_header)
def edge_pad(img):
return pad(
resize(img, (101 * 2, 101 * 2), mode='constant', preserve_range=True),
27, 'edge')
# imsave("./data/mask.png", mask.astype(np.float) )
# exit()
# initialization
image = img_as_float(imread('./data/image.png')[:, :, 0:3])
init_image = image.copy()
init_image[mask, :] = resize(
pyramid_expand(pyramid_reduce(image, 10, multichannel=True),
10,
multichannel=True), image.shape)[mask, :]
true_init = make_patch_collage([image, image, init_image], 3)
w1 = true_init.shape[1]
true_init = make_patch_collage([image, init_image], 2)
w2 = true_init.shape[1]
true_init = pad(true_init,
((0, 0), ((w1 - w2) // 2, (w1 - w2) // 2 + 1), (0, 0)),
mode='edge')
imsave(output_dir + "true_init.png", true_init)
# exit()
# # 3rd party solutions
# im3rdparty = []
# # im3rdparty.append(img_as_float(imread('output/3rdparty/fedorov_means_p15.png')))
# im3rdparty.append(img_as_float(imread('output/3rdparty/fedorov_poisson_p15_lmd001.png')))
# im3rdparty.append(img_as_float(imread('output/3rdparty/crim_p9.png')))
# im3rdparty.append(img_as_float(imread('output/3rdparty/newson.png')))
# im3rdparty.append(img_as_float(imread('output/3rdparty/cntx_att_places2.png')))
# im3rdparty.append(img_as_float(imread('output/3rdparty/ec_places2.png')))
# im3rdparty.append(img_as_float(imread('output/3rdparty/gmcnn_places2.png')))
# imsave(output_dir+"3rdparty/3rdparty.png", make_patch_collage(im3rdparty, len(im3rdparty)) )
# exit()
# Let's look a a single image before padding. # In[ ]: plt.imshow(seis, cmap='gray') # And let's compare it with different padded ones # In[ ]: filter_size = 99 from skimage.util import pad plt.imshow(pad(seis, 7, mode='symmetric', reflect_type='odd'), cmap='gray') # In[ ]: filter_size = 99 from skimage.util import pad plt.imshow(pad(seis, 7, mode='symmetric', reflect_type='even'), cmap='gray') # In[ ]: filter_size = 99 from skimage.util import pad
def createContourFromMask(self, mask, bbox):
"""
It creates the contour (and the corrisponding polygon) from the blob mask.
"""
# NOTE: The mask is expected to be cropped around its bbox (!!) (see the __init__)
self.inner_contours.clear()
# we need to pad the mask to avoid to break the contour that touches the borders
PADDED_SIZE = 4
img_padded = pad(mask, (PADDED_SIZE, PADDED_SIZE),
mode="constant",
constant_values=(0, 0))
contours = measure.find_contours(img_padded, 0.6)
inner_contours = measure.find_contours(img_padded, 0.4)
number_of_contours = len(contours)
threshold = 20 #min number of points in a small hole
if number_of_contours > 1:
# search the longest contour
npoints_max = 0
longest = 0
for i, contour in enumerate(contours):
npoints = contour.shape[0]
if npoints > npoints_max:
npoints_max = npoints
longest = i
npoints_max = 0
inner_longest = 0
for i, contour in enumerate(inner_contours):
npoints = contour.shape[0]
if npoints > npoints_max:
npoints_max = npoints
inner_longest = i
# divide the contours in OUTER contour and INNER contours
for i, contour in enumerate(contours):
if i == longest:
self.contour = np.array(contour)
for i, contour in enumerate(inner_contours):
if i != inner_longest:
if contour.shape[0] > threshold:
coordinates = np.array(contour)
self.inner_contours.append(coordinates)
# adjust the coordinates of the outer contour
# (NOTE THAT THE COORDINATES OF THE BBOX ARE IN THE GLOBAL MAP COORDINATES SYSTEM)
for i in range(self.contour.shape[0]):
ycoor = self.contour[i, 0]
xcoor = self.contour[i, 1]
self.contour[i, 0] = xcoor - PADDED_SIZE + bbox[1]
self.contour[i, 1] = ycoor - PADDED_SIZE + bbox[0]
# adjust coordinates of the INNER contours
for j, contour in enumerate(self.inner_contours):
for i in range(contour.shape[0]):
ycoor = contour[i, 0]
xcoor = contour[i, 1]
self.inner_contours[j][i,
0] = xcoor - PADDED_SIZE + bbox[1]
self.inner_contours[j][i,
1] = ycoor - PADDED_SIZE + bbox[0]
elif number_of_contours == 1:
coords = measure.approximate_polygon(contours[0], tolerance=0.2)
self.contour = np.array(coords)
# adjust the coordinates of the outer contour
# (NOTE THAT THE COORDINATES OF THE BBOX ARE IN THE GLOBAL MAP COORDINATES SYSTEM)
for i in range(self.contour.shape[0]):
ycoor = self.contour[i, 0]
xcoor = self.contour[i, 1]
self.contour[i, 0] = xcoor - PADDED_SIZE + bbox[1]
self.contour[i, 1] = ycoor - PADDED_SIZE + bbox[0]
else:
raise Exception("Empty contour")
#TODO optimize the bbox
self.bbox = bbox
def test_blob_log():
r2 = math.sqrt(2)
img = np.ones((256, 256))
xs, ys = circle(200, 65, 5)
img[xs, ys] = 255
xs, ys = circle(80, 25, 15)
img[xs, ys] = 255
xs, ys = circle(50, 150, 25)
img[xs, ys] = 255
xs, ys = circle(100, 175, 30)
img[xs, ys] = 255
blobs = blob_log(img, min_sigma=5, max_sigma=20, threshold=1)
radius = lambda x: r2 * x[2]
s = sorted(blobs, key=radius)
thresh = 3
b = s[0]
assert abs(b[0] - 200) <= thresh
assert abs(b[1] - 65) <= thresh
assert abs(radius(b) - 5) <= thresh
b = s[1]
assert abs(b[0] - 80) <= thresh
assert abs(b[1] - 25) <= thresh
assert abs(radius(b) - 15) <= thresh
b = s[2]
assert abs(b[0] - 50) <= thresh
assert abs(b[1] - 150) <= thresh
assert abs(radius(b) - 25) <= thresh
b = s[3]
assert abs(b[0] - 100) <= thresh
assert abs(b[1] - 175) <= thresh
assert abs(radius(b) - 30) <= thresh
# Testing log scale
blobs = blob_log(img,
min_sigma=5,
max_sigma=20,
threshold=1,
log_scale=True)
b = s[0]
assert abs(b[0] - 200) <= thresh
assert abs(b[1] - 65) <= thresh
assert abs(radius(b) - 5) <= thresh
b = s[1]
assert abs(b[0] - 80) <= thresh
assert abs(b[1] - 25) <= thresh
assert abs(radius(b) - 15) <= thresh
b = s[2]
assert abs(b[0] - 50) <= thresh
assert abs(b[1] - 150) <= thresh
assert abs(radius(b) - 25) <= thresh
b = s[3]
assert abs(b[0] - 100) <= thresh
assert abs(b[1] - 175) <= thresh
assert abs(radius(b) - 30) <= thresh
# Testing no peaks
img_empty = np.zeros((100, 100))
assert blob_log(img_empty).size == 0
# Testing 3D
r = 6
pad = 10
im3 = ellipsoid(r, r, r)
im3 = util.pad(im3, pad, mode='constant')
blobs = blob_log(im3, min_sigma=3, max_sigma=10)
b = blobs[0]
assert b.shape == (4, )
assert b[0] == r + pad + 1
assert b[1] == r + pad + 1
assert b[2] == r + pad + 1
assert abs(math.sqrt(3) * b[3] - r) < 1
# Testing 3D anisotropic
r = 6
pad = 10
im3 = ellipsoid(r / 2, r, r)
im3 = util.pad(im3, pad, mode='constant')
blobs = blob_log(
im3,
min_sigma=[1, 2, 2],
max_sigma=[5, 10, 10],
)
b = blobs[0]
assert b.shape == (6, )
assert b[0] == r / 2 + pad + 1
assert b[1] == r + pad + 1
assert b[2] == r + pad + 1
assert abs(math.sqrt(3) * b[3] - r / 2) < 1
assert abs(math.sqrt(3) * b[4] - r) < 1
assert abs(math.sqrt(3) * b[5] - r) < 1
# Testing exclude border
# image where blob is 5 px from borders, radius 5
img = np.ones((512, 512))
xs, ys = circle(5, 5, 5)
img[xs, ys] = 255
blobs = blob_log(
img,
min_sigma=1.5,
max_sigma=5,
)
assert blobs.shape[0] == 1
b = blobs[0]
assert b[0] == b[1] == 5, "blob should be 5 px from x and y borders"
blobs = blob_dog(img, min_sigma=1.5, max_sigma=5, exclude_border=5)
msg = "zero blobs should be detected, as only blob is 5 px from border"
assert blobs.shape[0] == 0, msg
def detect_ads(self): #doesn't work for dataset3
def adjust_time(start_stop_time):
(t1, t2) = start_stop_time
if t2 - t1 - 15 > 1:
t2 = t1 + 15
elif t2 - t1 <15:
t2 = t1 + 15
return [t1, t2]
print('Detecting ads for {}...'.format(self.name))
self.arr = self.audio.to_soundarray()[:, 0]
self.blocksize = np.array([self.Fs][0]).reshape(1, ) # np.array(44100).lreshape((-1,1))
self.w = 8 # window size
if self.arr.shape[0] % self.Fs != 0:
# self.arr=audiosegment.from_file(self.source).resample(sample_rate_Hz=48000, sample_width=2, channels=1).to_numpy_array()
padding = int(np.abs((self.arr.shape[0] % self.Fs - self.Fs)))
# self.padding = (padding,0)
self.padding = (padding + self.Fs, self.Fs)
else:
# self.padding = 0
self.padding = (self.Fs, self.Fs)
#padded = util.pad(self.arr, self.padding, mode='constant')
#blocks = util.view_as_blocks(padded, tuple(self.blocksize, ))
blocks = util.view_as_blocks(self.arr, tuple(self.blocksize,))
blocked_dct = np.zeros(blocks.shape[0])
fft_blocks=np.zeros((blocks.shape[0],24000))
'''for i in np.arange(blocks.shape[0]): # - 1):
blocked_dct[i] = np.sum(np.abs(fftpack.fft(blocks[i][11000:12000])))
fft_blocks.append(fftpack.fft(blocks[i])
self.fft=fft_blocks'''
for i in np.arange(blocks.shape[0]): # - 1):
blocked_dct[i] = np.abs(fftpack.dct(blocks[i])[0])
fft_blocks[i]=np.abs(fftpack.fft(blocks[i]))[0:24000]
self.dct = blocked_dct
self.fft=fft_blocks
diff_dct = np.diff(blocked_dct) # ,append=blocked_dct[-2])#,prepend=blocked_dct[1])#,append=blocked_dct[-1])
diff2_dct = np.diff(diff_dct, n=2) # ,append=blocked_dct[-2])#prepend=diff_dct[1])#,append=diff_dct[-1])
x, y = smooth_approx(diff2_dct)
xthreshold, xpeaks, xpeak_idxs = self.get_peaks(y)
shift = 0
diff2_dct_slices = util.view_as_windows(y, window_shape=(self.w,), step=1)
sliced_peaks = np.zeros(diff2_dct_slices.shape[0] + shift)
self.Tmax = sliced_peaks.shape[0]
self.scale = self.Tmax / self.duration
diff2_dct_thresh = np.max(diff2_dct) * .1
for i in np.arange(sliced_peaks.shape[0] - shift):
sliced_peaks[i + shift] = np.max(diff2_dct_slices[i])
if np.abs(sliced_peaks[i]) < diff2_dct_thresh:
sliced_peaks[i] = 0
sliced_peaks = util.pad(sliced_peaks, (self.w, 0), 'symmetric')
threshold, peaks, peak_idxs = self.get_peaks(sliced_peaks)
self.sliced_peaks = sliced_peaks
self.threshold = threshold
'''plt.figure()
plt.plot(x, y, ':')
plt.title('{}: Peaks for smooth_approx(diff2_dct)'.format(self.name))
plt.ylabel('Magnitude of 2nd Order Diff')
plt.xlabel('Time (s)')
plt.plot(np.arange(len(sliced_peaks)), sliced_peaks, '-.')
plt.scatter(peak_idxs, peaks)'''
#thresholded = group_consecutive(np.where(self.sliced_peaks > 0)[0].tolist())
#thresholded = [grp for grp in thresholded if len(grp) >= 15]
idxs = group_consecutive(peak_idxs)
start_stop_times = [[np.min(x), np.max(x)] for x in idxs]
start_stop_times = [adjust_time(x) for x in start_stop_times]
self.ad_times = start_stop_times
return start_stop_times#, start_stop_times_rev # use reversed to make adjustments to intervals if needed