Python numpy.bitwise_or() 使用实例

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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 
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