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Example 1
def labelcolormap(N=256):
def bitget(byteval, idx):
return ((byteval & (1 << idx)) != 0)
cmap = np.zeros((N, 3))
for i in range(0, N):
id = i
r, g, b = 0, 0, 0
for j in range(0, 8):
r = np.bitwise_or(r, (bitget(id, 0) << 7-j))
g = np.bitwise_or(g, (bitget(id, 1) << 7-j))
b = np.bitwise_or(b, (bitget(id, 2) << 7-j))
id = (id >> 3)
cmap[i, 0] = r
cmap[i, 1] = g
cmap[i, 2] = b
cmap = cmap.astype(np.float32) / 255
return cmap Example 2
def loadDepthMap(self,filename):
"""
Read a depth-map
:param filename: file name to load
:return: image data of depth image
"""
img = Image.open(filename)
# top 8 bits of depth are packed into green channel and lower 8 bits into blue
assert len(img.getbands()) == 3
r, g, b = img.split()
r = np.asarray(r, np.int32)
g = np.asarray(g, np.int32)
b = np.asarray(b, np.int32)
dpt = np.bitwise_or(np.left_shift(g, 8), b)
imgdata = np.asarray(dpt, np.float32)
return imgdata Example 3
def label_colormap(N=256):
def bitget(byteval, idx):
return ((byteval & (1 << idx)) != 0)
cmap = np.zeros((N, 3))
for i in range(0, N):
id = i
r, g, b = 0, 0, 0
for j in range(0, 8):
r = np.bitwise_or(r, (bitget(id, 0) << 7-j))
g = np.bitwise_or(g, (bitget(id, 1) << 7-j))
b = np.bitwise_or(b, (bitget(id, 2) << 7-j))
id = (id >> 3)
cmap[i, 0] = r
cmap[i, 1] = g
cmap[i, 2] = b
cmap = cmap.astype(np.float32) / 255
return cmap Example 4
def test_NotImplemented_not_returned(self):
# See gh-5964 and gh-2091. Some of these functions are not operator
# related and were fixed for other reasons in the past.
binary_funcs = [
np.power, np.add, np.subtract, np.multiply, np.divide,
np.true_divide, np.floor_divide, np.bitwise_and, np.bitwise_or,
np.bitwise_xor, np.left_shift, np.right_shift, np.fmax,
np.fmin, np.fmod, np.hypot, np.logaddexp, np.logaddexp2,
np.logical_and, np.logical_or, np.logical_xor, np.maximum,
np.minimum, np.mod
]
# These functions still return NotImplemented. Will be fixed in
# future.
# bad = [np.greater, np.greater_equal, np.less, np.less_equal, np.not_equal]
a = np.array('1')
b = 1
for f in binary_funcs:
assert_raises(TypeError, f, a, b) Example 5
def test_NotImplemented_not_returned(self):
# See gh-5964 and gh-2091. Some of these functions are not operator
# related and were fixed for other reasons in the past.
binary_funcs = [
np.power, np.add, np.subtract, np.multiply, np.divide,
np.true_divide, np.floor_divide, np.bitwise_and, np.bitwise_or,
np.bitwise_xor, np.left_shift, np.right_shift, np.fmax,
np.fmin, np.fmod, np.hypot, np.logaddexp, np.logaddexp2,
np.logical_and, np.logical_or, np.logical_xor, np.maximum,
np.minimum, np.mod
]
# These functions still return NotImplemented. Will be fixed in
# future.
# bad = [np.greater, np.greater_equal, np.less, np.less_equal, np.not_equal]
a = np.array('1')
b = 1
for f in binary_funcs:
assert_raises(TypeError, f, a, b) Example 6
def loadDepthMap(self, filename):
"""
Read a depth-map
:param filename: file name to load
:return: image data of depth image
"""
img = Image.open(filename)
# top 8 bits of depth are packed into green channel and lower 8 bits into blue
assert len(img.getbands()) == 3
r, g, b = img.split()
r = np.asarray(r, np.int32)
g = np.asarray(g, np.int32)
b = np.asarray(b, np.int32)
dpt = np.bitwise_or(np.left_shift(g, 8), b)
imgdata = np.asarray(dpt, np.float32)
return imgdata Example 7
def test_NotImplemented_not_returned(self):
# See gh-5964 and gh-2091. Some of these functions are not operator
# related and were fixed for other reasons in the past.
binary_funcs = [
np.power, np.add, np.subtract, np.multiply, np.divide,
np.true_divide, np.floor_divide, np.bitwise_and, np.bitwise_or,
np.bitwise_xor, np.left_shift, np.right_shift, np.fmax,
np.fmin, np.fmod, np.hypot, np.logaddexp, np.logaddexp2,
np.logical_and, np.logical_or, np.logical_xor, np.maximum,
np.minimum, np.mod
]
# These functions still return NotImplemented. Will be fixed in
# future.
# bad = [np.greater, np.greater_equal, np.less, np.less_equal, np.not_equal]
a = np.array('1')
b = 1
for f in binary_funcs:
assert_raises(TypeError, f, a, b) Example 8
def labelcolormap(N=256):
cmap = np.zeros((N, 3))
for i in range(0, N):
id = i
r, g, b = 0, 0, 0
for j in range(0, 8):
r = np.bitwise_or(r, (bitget(id, 0) << 7-j))
g = np.bitwise_or(g, (bitget(id, 1) << 7-j))
b = np.bitwise_or(b, (bitget(id, 2) << 7-j))
id = (id >> 3)
cmap[i, 0] = r
cmap[i, 1] = g
cmap[i, 2] = b
cmap = cmap.astype(np.float32) / 255
return cmap
# -----------------------------------------------------------------------------
# Evaluation
# ----------------------------------------------------------------------------- Example 9
def test_values(self):
for dt in self.bitwise_types:
zeros = np.array([0], dtype=dt)
ones = np.array([-1], dtype=dt)
msg = "dt = '%s'" % dt.char
assert_equal(np.bitwise_not(zeros), ones, err_msg=msg)
assert_equal(np.bitwise_not(ones), zeros, err_msg=msg)
assert_equal(np.bitwise_or(zeros, zeros), zeros, err_msg=msg)
assert_equal(np.bitwise_or(zeros, ones), ones, err_msg=msg)
assert_equal(np.bitwise_or(ones, zeros), ones, err_msg=msg)
assert_equal(np.bitwise_or(ones, ones), ones, err_msg=msg)
assert_equal(np.bitwise_xor(zeros, zeros), zeros, err_msg=msg)
assert_equal(np.bitwise_xor(zeros, ones), ones, err_msg=msg)
assert_equal(np.bitwise_xor(ones, zeros), ones, err_msg=msg)
assert_equal(np.bitwise_xor(ones, ones), zeros, err_msg=msg)
assert_equal(np.bitwise_and(zeros, zeros), zeros, err_msg=msg)
assert_equal(np.bitwise_and(zeros, ones), zeros, err_msg=msg)
assert_equal(np.bitwise_and(ones, zeros), zeros, err_msg=msg)
assert_equal(np.bitwise_and(ones, ones), ones, err_msg=msg) Example 10
def set_ufunc(self, scalar_op):
# This is probably a speed up of the implementation
if isinstance(scalar_op, theano.scalar.basic.Add):
self.ufunc = numpy.add
elif isinstance(scalar_op, theano.scalar.basic.Mul):
self.ufunc = numpy.multiply
elif isinstance(scalar_op, theano.scalar.basic.Maximum):
self.ufunc = numpy.maximum
elif isinstance(scalar_op, theano.scalar.basic.Minimum):
self.ufunc = numpy.minimum
elif isinstance(scalar_op, theano.scalar.basic.AND):
self.ufunc = numpy.bitwise_and
elif isinstance(scalar_op, theano.scalar.basic.OR):
self.ufunc = numpy.bitwise_or
elif isinstance(scalar_op, theano.scalar.basic.XOR):
self.ufunc = numpy.bitwise_xor
else:
self.ufunc = numpy.frompyfunc(scalar_op.impl, 2, 1) Example 11
def test_NotImplemented_not_returned(self):
# See gh-5964 and gh-2091. Some of these functions are not operator
# related and were fixed for other reasons in the past.
binary_funcs = [
np.power, np.add, np.subtract, np.multiply, np.divide,
np.true_divide, np.floor_divide, np.bitwise_and, np.bitwise_or,
np.bitwise_xor, np.left_shift, np.right_shift, np.fmax,
np.fmin, np.fmod, np.hypot, np.logaddexp, np.logaddexp2,
np.logical_and, np.logical_or, np.logical_xor, np.maximum,
np.minimum, np.mod
]
# These functions still return NotImplemented. Will be fixed in
# future.
# bad = [np.greater, np.greater_equal, np.less, np.less_equal, np.not_equal]
a = np.array('1')
b = 1
for f in binary_funcs:
assert_raises(TypeError, f, a, b) Example 12
def test_truth_table_bitwise(self):
arg1 = [False, False, True, True]
arg2 = [False, True, False, True]
out = [False, True, True, True]
assert_equal(np.bitwise_or(arg1, arg2), out)
out = [False, False, False, True]
assert_equal(np.bitwise_and(arg1, arg2), out)
out = [False, True, True, False]
assert_equal(np.bitwise_xor(arg1, arg2), out) Example 13
def test_NotImplemented_not_returned(self):
# See gh-5964 and gh-2091. Some of these functions are not operator
# related and were fixed for other reasons in the past.
binary_funcs = [
np.power, np.add, np.subtract, np.multiply, np.divide,
np.true_divide, np.floor_divide, np.bitwise_and, np.bitwise_or,
np.bitwise_xor, np.left_shift, np.right_shift, np.fmax,
np.fmin, np.fmod, np.hypot, np.logaddexp, np.logaddexp2,
np.logical_and, np.logical_or, np.logical_xor, np.maximum,
np.minimum, np.mod
]
# These functions still return NotImplemented. Will be fixed in
# future.
# bad = [np.greater, np.greater_equal, np.less, np.less_equal, np.not_equal]
a = np.array('1')
b = 1
for f in binary_funcs:
assert_raises(TypeError, f, a, b) Example 14
def __or__(self, other):
return bitwise_or(self, other) Example 15
def __ior__(self, other):
return bitwise_or(self, other, self) Example 16
def __ror__(self, other):
return bitwise_or(other, self) Example 17
def label_colormap(N=256):
cmap = np.zeros((N, 3))
for i in six.moves.range(0, N):
id = i
r, g, b = 0, 0, 0
for j in six.moves.range(0, 8):
r = np.bitwise_or(r, (bitget(id, 0) << 7 - j))
g = np.bitwise_or(g, (bitget(id, 1) << 7 - j))
b = np.bitwise_or(b, (bitget(id, 2) << 7 - j))
id = (id >> 3)
cmap[i, 0] = r
cmap[i, 1] = g
cmap[i, 2] = b
cmap = cmap.astype(np.float32) / 255
return cmap Example 18
def create_binary_wf_data(wf, sync_mkr=0, samp_mkr=0, vertical_resolution=12):
"""Given numpy arrays of waveform and marker data convert to binary format.
Assumes waveform data is np.float in range -1 to 1 and marker data can be cast to bool
Binary format is waveform in MSB and and markers in LSB
waveform sync_mkr samp_mkr
15 downto 4/2 1 0
"""
#cast the waveform to integers
if not((vertical_resolution == 12) or (vertical_resolution == 14)):
raise ValueError("vertical resolution must be 12 or 14 bits")
#convert waveform to integers
scale_factor = 2**(vertical_resolution-1)
bin_data = np.int16((scale_factor-1)*np.array(wf))
#clip if necessary
if np.max(bin_data) > scale_factor-1 or np.min(bin_data) < -scale_factor:
warnings.warn("Clipping waveform. Max value: {:d} Min value: {:d}. Scale factor: {:d}.".format(np.max(bin_data), np.min(bin_data),scale_factor))
bin_data = np.clip(bin_data, -scale_factor, scale_factor-1)
# bin_data = bin_data.byteswap()
#shift up to the MSB
bin_data = np.left_shift(bin_data, 4 if vertical_resolution == 12 else 2)
#add in the marker bits
bin_data = np.bitwise_or(bin_data, np.bitwise_or(np.left_shift(np.bitwise_and(sync_mkr, 0x1), 1), np.bitwise_and(samp_mkr, 0x1)))
return bin_data Example 19
def get_mask_overlap(mask1, mask2):
intersect = np.bitwise_and(mask1, mask2).sum()
union = np.bitwise_or(mask1, mask2).sum()
return 1.0 * intersect / union Example 20
def _find_DoG_extrema(self, DoG):
# TODO: sample ?
ext = []
for octave in DoG:
_, rows, cols = octave.shape
# assert octave.shape = (<layers>(=s+2), <rows>, <columns>)
##########################
# time ?
##########################
peeled = [octave[ind1, ind2, ind3] for ind1, ind2, ind3 in
product(*[[slice(1, -1), slice(2, None), slice(None, -2)]]*3)]
center_block = peeled[0] # octave[1:-1,1:-1,1:-1], the center part
neighbor_blocks = peeled[1:] # neighbors in 26 directions in 3-D DoG space with offset 1
is_extreme = \
np.bitwise_or(center_block > (np.max(neighbor_blocks, axis=0)),
center_block < (np.min(neighbor_blocks, axis=0)))
# assert is_extreme.shape = (s, rows-2, columns-2)
ext_coord = np.array(
list(product(*[range(1, i-1) for i in octave.shape]))).reshape([x-2 for x in octave.shape]+[-1])
assert ext_coord.shape[:-1] == is_extreme.shape
ext_coord = ext_coord[is_extreme].astype(np.float)
print("%d key point candidates found" % ext_coord.shape[0])
# assert ext_coord.shape = (<number of key points>, 3)
ext_coord /= [1, rows, cols] # convert row, col coord to relative
ext_coord[:, 0] = get_sigma_by_layer(ext_coord[:, 0])
ext.extend(list(ext_coord))
# filters
# for layer, row, col in ext_coord:
# nb = octave[layer-1:layer+2, row-1:row+2, col-1:col+2] # 3x3x3 neighbor
# x_hat, d_x_hat = self._fit_extremum(nb)
# if
# TODO: if x[i] > 0.5, do it recursivey
# print(x_hat, d_x_hat)
return ext Example 21
def test_truth_table_bitwise(self):
arg1 = [False, False, True, True]
arg2 = [False, True, False, True]
out = [False, True, True, True]
assert_equal(np.bitwise_or(arg1, arg2), out)
out = [False, False, False, True]
assert_equal(np.bitwise_and(arg1, arg2), out)
out = [False, True, True, False]
assert_equal(np.bitwise_xor(arg1, arg2), out) Example 22
def test_NotImplemented_not_returned(self):
# See gh-5964 and gh-2091. Some of these functions are not operator
# related and were fixed for other reasons in the past.
binary_funcs = [
np.power, np.add, np.subtract, np.multiply, np.divide,
np.true_divide, np.floor_divide, np.bitwise_and, np.bitwise_or,
np.bitwise_xor, np.left_shift, np.right_shift, np.fmax,
np.fmin, np.fmod, np.hypot, np.logaddexp, np.logaddexp2,
np.logical_and, np.logical_or, np.logical_xor, np.maximum,
np.minimum, np.mod
]
# These functions still return NotImplemented. Will be fixed in
# future.
# bad = [np.greater, np.greater_equal, np.less, np.less_equal, np.not_equal]
a = np.array('1')
b = 1
for f in binary_funcs:
assert_raises(TypeError, f, a, b) Example 23
def __ior__(self, other):
np.bitwise_or(self, other, out=self)
return self Example 24
def spread_bitsv(ival, level):
res = np.zeros_like(ival, dtype='int64')
for i in range(level):
ares = np.bitwise_and(ival, 1<<i) << (i*2)
np.bitwise_or(res, ares, res)
return res Example 25
def get_keyv(iarr, level):
i1, i2, i3 = (v.astype("int64") for v in iarr)
i1 = spread_bitsv(i1, level)
i2 = spread_bitsv(i2, level) << 1
i3 = spread_bitsv(i3, level) << 2
np.bitwise_or(i1, i2, i1)
np.bitwise_or(i1, i3, i1)
return i1 Example 26
def pwdist_jaccard(self, seq1idx, seq2idx):
"""Compute the Jaccard-Needham dissimilarity
between two boolean 1-D arrays.
Returns:
distance value (double)
"""
u = self[seq1idx]
v = self[seq2idx]
dist = (np.double(np.bitwise_and((u != v),
np.bitwise_or(u != 0, v != 0)).sum()) /
np.double(np.bitwise_or(u != 0, v != 0).sum()))
return dist Example 27
def loadNYU(self, path):
img = Image.open(path)
if len(img.getbands()) != 3:
raise ValueError('NYU input should be with 3 channel')
r, g, b = img.split()
r = np.asarray(r,np.int32)
g = np.asarray(g,np.int32)
b = np.asarray(b,np.int32)
dpt = np.bitwise_or(np.left_shift(g,8),b)
self.dmData = np.asarray(dpt, np.float32)
return self.dmData Example 28
def test_truth_table_bitwise(self):
arg1 = [False, False, True, True]
arg2 = [False, True, False, True]
out = [False, True, True, True]
assert_equal(np.bitwise_or(arg1, arg2), out)
out = [False, False, False, True]
assert_equal(np.bitwise_and(arg1, arg2), out)
out = [False, True, True, False]
assert_equal(np.bitwise_xor(arg1, arg2), out) Example 29
def test_truth_table_bitwise(self):
arg1 = [False, False, True, True]
arg2 = [False, True, False, True]
out = [False, True, True, True]
assert_equal(np.bitwise_or(arg1, arg2), out)
out = [False, False, False, True]
assert_equal(np.bitwise_and(arg1, arg2), out)
out = [False, True, True, False]
assert_equal(np.bitwise_xor(arg1, arg2), out) Example 30
def test_truth_table_bitwise(self):
arg1 = [False, False, True, True]
arg2 = [False, True, False, True]
out = [False, True, True, True]
assert_equal(np.bitwise_or(arg1, arg2), out)
out = [False, False, False, True]
assert_equal(np.bitwise_and(arg1, arg2), out)
out = [False, True, True, False]
assert_equal(np.bitwise_xor(arg1, arg2), out) Example 31
def combine_depth_frames(frame1, frame2):
frame2[frame2 > 2046] = 0
return numpy.bitwise_or(frame1, frame2) Example 32
def test_truth_table_bitwise(self):
arg1 = [False, False, True, True]
arg2 = [False, True, False, True]
out = [False, True, True, True]
assert_equal(np.bitwise_or(arg1, arg2), out)
out = [False, False, False, True]
assert_equal(np.bitwise_and(arg1, arg2), out)
out = [False, True, True, False]
assert_equal(np.bitwise_xor(arg1, arg2), out) Example 33
def test_types(self):
for dt in self.bitwise_types:
zeros = np.array([0], dtype=dt)
ones = np.array([-1], dtype=dt)
msg = "dt = '%s'" % dt.char
assert_(np.bitwise_not(zeros).dtype == dt, msg)
assert_(np.bitwise_or(zeros, zeros).dtype == dt, msg)
assert_(np.bitwise_xor(zeros, zeros).dtype == dt, msg)
assert_(np.bitwise_and(zeros, zeros).dtype == dt, msg) Example 34
def test_identity(self):
assert_(np.bitwise_or.identity == 0, 'bitwise_or')
assert_(np.bitwise_xor.identity == 0, 'bitwise_xor')
assert_(np.bitwise_and.identity == -1, 'bitwise_and') Example 35
def test_reduction(self):
binary_funcs = (np.bitwise_or, np.bitwise_xor, np.bitwise_and)
for dt in self.bitwise_types:
zeros = np.array([0], dtype=dt)
ones = np.array([-1], dtype=dt)
for f in binary_funcs:
msg = "dt: '%s', f: '%s'" % (dt, f)
assert_equal(f.reduce(zeros), zeros, err_msg=msg)
assert_equal(f.reduce(ones), ones, err_msg=msg)
# Test empty reduction, no object dtype
for dt in self.bitwise_types[:-1]:
# No object array types
empty = np.array([], dtype=dt)
for f in binary_funcs:
msg = "dt: '%s', f: '%s'" % (dt, f)
tgt = np.array(f.identity, dtype=dt)
res = f.reduce(empty)
assert_equal(res, tgt, err_msg=msg)
assert_(res.dtype == tgt.dtype, msg)
# Empty object arrays use the identity. Note that the types may
# differ, the actual type used is determined by the assign_identity
# function and is not the same as the type returned by the identity
# method.
for f in binary_funcs:
msg = "dt: '%s'" % (f,)
empty = np.array([], dtype=object)
tgt = f.identity
res = f.reduce(empty)
assert_equal(res, tgt, err_msg=msg)
# Non-empty object arrays do not use the identity
for f in binary_funcs:
msg = "dt: '%s'" % (f,)
btype = np.array([True], dtype=object)
assert_(type(f.reduce(btype)) is bool, msg) Example 36
def activate_network(self, num_activations=1):
"""Activates the Markov Network
Parameters
----------
num_activations: int (default: 1)
The number of times the Markov Network should be activated
Returns
-------
None
"""
original_input_values = np.copy(self.states[:self.num_input_states])
for _ in range(num_activations):
for markov_gate, mg_input_ids, mg_output_ids in zip(self.markov_gates, self.markov_gate_input_ids, self.markov_gate_output_ids):
# Determine the input values for this Markov Gate
mg_input_values = self.states[mg_input_ids]
mg_input_index = int(''.join([str(int(val)) for val in mg_input_values]), base=2)
# Determine the corresponding output values for this Markov Gate
roll = np.random.uniform()
mg_output_index = np.where(markov_gate[mg_input_index, :] >= roll)[0][0]
mg_output_values = np.array(list(np.binary_repr(mg_output_index, width=len(mg_output_ids))), dtype=np.uint8)
self.states[mg_output_ids] = np.bitwise_or(self.states[mg_output_ids], mg_output_values)
self.states[:self.num_input_states] = original_input_values Example 37
def mask(self,image):
"""Uses the image passed as parameter as alpha mask."""
if npy:
aux1 = numpy.bitwise_and(self.pixels,0xffffff)
aux2 = numpy.bitwise_and(image.pixels,0xff000000)
self.pixels = numpy.bitwise_or(aux1,aux2)
return
for i in range(self.width):
for j in range(self.height):
n = self.get(i,j)
m = image.get(i,j)
new = ((m & 0xff000000) << 24) | (n & 0xffffff)
self.set(i,j,new) Example 38
def test_truth_table_bitwise(self):
arg1 = [False, False, True, True]
arg2 = [False, True, False, True]
out = [False, True, True, True]
assert_equal(np.bitwise_or(arg1, arg2), out)
out = [False, False, False, True]
assert_equal(np.bitwise_and(arg1, arg2), out)
out = [False, True, True, False]
assert_equal(np.bitwise_xor(arg1, arg2), out) Example 39
def _get_voc_color_map(n=256):
color_map = np.zeros((n, 3))
for i in xrange(n):
r = b = g = 0
cid = i
for j in xrange(0, 8):
r = np.bitwise_or(r, np.left_shift(np.unpackbits(np.array([cid], dtype=np.uint8))[-1], 7-j))
g = np.bitwise_or(g, np.left_shift(np.unpackbits(np.array([cid], dtype=np.uint8))[-2], 7-j))
b = np.bitwise_or(b, np.left_shift(np.unpackbits(np.array([cid], dtype=np.uint8))[-3], 7-j))
cid = np.right_shift(cid, 3)
color_map[i][0] = r
color_map[i][1] = g
color_map[i][2] = b
return color_map Example 40
def seperate_lungs(image):
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers(image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, 1)
sobel_filtered_dy = ndimage.sobel(image, 0)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(3,3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct)
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
##structure = np.ones((BINARY_CLOSING_SIZE,BINARY_CLOSING_SIZE)) # 5 is not enough, 7 is
structure = morphology.disk(BINARY_CLOSING_SIZE) # better , 5 seems sufficient, we use 7 for safety/just in case
lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=structure, iterations=3) #, iterations=3) # was structure=np.ones((5,5))
### NOTE if no iterattions, i.e. default 1 we get holes within lungs for the disk(5) and perhaps more
#Apply the lungfilter (note the filtered areas being assigned -2000 HU)
segmented = np.where(lungfilter == 1, image, -2000*np.ones((512, 512))) ### was -2000
return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed Example 41
def seperate_lungs_3d(image):
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers_3d(image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, axis=2)
sobel_filtered_dy = ndimage.sobel(image, axis=1)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(1,3,3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
blackhat_struct = blackhat_struct[np.newaxis,:,:]
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct) # very long time
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
##structure = np.ones((BINARY_CLOSING_SIZE,BINARY_CLOSING_SIZE)) # 5 is not enough, 7 is
structure = morphology.disk(BINARY_CLOSING_SIZE) # better , 5 seems sufficient, we use 7 for safety/just in case
structure = structure[np.newaxis,:,:]
lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=structure, iterations=3) #, iterations=3) # was structure=np.ones((5,5))
### NOTE if no iterattions, i.e. default 1 we get holes within lungs for the disk(5) and perhaps more
#Apply the lungfilter (note the filtered areas being assigned -2000 HU)
segmented = np.where(lungfilter == 1, image, -2000*np.ones(marker_internal.shape))
return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed Example 42
def get_segmented_lungs(image):
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers(image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, 1)
sobel_filtered_dy = ndimage.sobel(image, 0)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(3,3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
#blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 14) # <- retains more of the area, 12 works well. Changed to 14, 12 still excluded some parts.
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct)
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=np.ones((5,5)), iterations=3)
#Apply the lungfilter (note the filtered areas being assigned threshold_min HU)
segmented = np.where(lungfilter == 1, image, threshold_min*np.ones(image.shape))
#return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed
return segmented Example 43
def get_segmented_lungs(image):
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers(image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, 1)
sobel_filtered_dy = ndimage.sobel(image, 0)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(3,3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
#blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 14) # <- retains more of the area, 12 works well. Changed to 14, 12 still excluded some parts.
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct)
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=np.ones((5,5)), iterations=3)
#Apply the lungfilter (note the filtered areas being assigned threshold_min HU)
segmented = np.where(lungfilter == 1, image, threshold_min*np.ones(image.shape))
#return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed
return segmented Example 44
def get_segmented_lungs(image):
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers(image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, 1)
sobel_filtered_dy = ndimage.sobel(image, 0)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(3,3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
#blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 14) # <- retains more of the area, 12 works well. Changed to 14, 12 still excluded some parts.
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct)
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=np.ones((5,5)), iterations=3)
#Apply the lungfilter (note the filtered areas being assigned threshold_min HU)
segmented = np.where(lungfilter == 1, image, threshold_min*np.ones(image.shape))
#return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed
return segmented Example 45
def get_segmented_lungs(image):
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers(image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, 1)
sobel_filtered_dy = ndimage.sobel(image, 0)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(3,3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
#blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 14) # <- retains more of the area, 12 works well. Changed to 14, 12 still excluded some parts.
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct)
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=np.ones((5,5)), iterations=3)
#Apply the lungfilter (note the filtered areas being assigned threshold_min HU)
segmented = np.where(lungfilter == 1, image, threshold_min*np.ones(image.shape))
#return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed
return segmented 