Python numpy 模块，logical_xor() 实例源码

def calculate_plane_histogram(plane, doseplane, dosegridpoints,
                              maxdose, dd, id, structure, hist):
    """Calculate the DVH for the given plane in the structure."""
    contours = [[x[0:2] for x in c['data']] for c in plane]

    # If there is no dose for the current plane, go to the next plane
    if not len(doseplane):
        return (np.arange(0, maxdose), 0)

    # Create a zero valued bool grid
    grid = np.zeros((dd['rows'], dd['columns']), dtype=np.uint8)

    # Calculate the histogram for each contour in the plane
    # and boolean xor to remove holes
    for i, contour in enumerate(contours):
        m = get_contour_mask(dd, id, dosegridpoints, contour)
        grid = np.logical_xor(m.astype(np.uint8), grid).astype(np.bool)

    hist, vol = calculate_contour_dvh(
        grid, doseplane, maxdose, dd, id, structure)
    return (hist, vol)

def _gene_signature(self,wm,size,key):
        '''????????????????????????'''
        wm = cv2.resize(wm,(size,size))        
        wU,_,wV = np.linalg.svd(np.mat(wm))


        sumU = np.sum(np.array(wU),axis=0)
        sumV = np.sum(np.array(wV),axis=0)

        sumU_mid = np.median(sumU)
        sumV_mid = np.median(sumV)

        sumU=np.array([1 if sumU[i] >sumU_mid else 0 for i in range(len(sumU)) ])
        sumV=np.array([1 if sumV[i] >sumV_mid else 0 for i in range(len(sumV)) ])

        uv_xor=np.logical_xor(sumU,sumV)

        np.random.seed(key)
        seq=np.random.randint(2,size=len(uv_xor))

        signature = np.logical_xor(uv_xor, seq)

        sqrts = int(np.sqrt(size))
        return np.array(signature,dtype=np.int8).reshape((sqrts,sqrts))

def _gene_signature(self,wm,key):
        '''????????????????????????'''
        wm = cv2.resize(wm,(256,256))        
        wU,_,wV = np.linalg.svd(np.mat(wm))


        sumU = np.sum(np.array(wU),axis=0)
        sumV = np.sum(np.array(wV),axis=0)

        sumU_mid = np.median(sumU)
        sumV_mid = np.median(sumV)

        sumU=np.array([1 if sumU[i] >sumU_mid else 0 for i in range(len(sumU)) ])
        sumV=np.array([1 if sumV[i] >sumV_mid else 0 for i in range(len(sumV)) ])

        uv_xor=np.logical_xor(sumU,sumV)

        np.random.seed(key)
        seq=np.random.randint(2,size=len(uv_xor))

        signature = np.logical_xor(uv_xor, seq)
        return np.array(signature,dtype=np.int8)

def _gene_signature(self,wU,wV,key):
        '''????????????????????????'''
        sumU = np.sum(wU,axis=0)
        sumV = np.sum(wV,axis=0)

        sumU_mid = np.median(sumU)
        sumV_mid = np.median(sumV)

        sumU=np.array([1 if sumU[i] >sumU_mid else 0 for i in range(len(sumU)) ])
        sumV=np.array([1 if sumV[i] >sumV_mid else 0 for i in range(len(sumV)) ])

        uv_xor=np.logical_xor(sumU,sumV)

        np.random.seed(key)
        seq=np.random.randint(2,size=len(uv_xor))

        signature = np.logical_xor(uv_xor, seq)
        return np.array(signature,dtype=np.int8)

def test_truth_table_logical(self):
        # 2, 3 and 4 serves as true values
        input1 = [0, 0, 3, 2]
        input2 = [0, 4, 0, 2]

        typecodes = (np.typecodes['AllFloat']
                     + np.typecodes['AllInteger']
                     + '?')     # boolean
        for dtype in map(np.dtype, typecodes):
            arg1 = np.asarray(input1, dtype=dtype)
            arg2 = np.asarray(input2, dtype=dtype)

            # OR
            out = [False, True, True, True]
            for func in (np.logical_or, np.maximum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # AND
            out = [False, False, False, True]
            for func in (np.logical_and, np.minimum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # XOR
            out = [False, True, True, False]
            for func in (np.logical_xor, np.not_equal):
                assert_equal(func(arg1, arg2).astype(bool), out)

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)

def calculate_plane_histogram(plane, doseplane, dosegridpoints, maxdose, dd,
                              id, structure, hist):
    """Calculate the DVH for the given plane in the structure."""
    contours = [[x[0:2] for x in c['data']] for c in plane]

    # Create a zero valued bool grid
    grid = np.zeros((dd['rows'], dd['columns']), dtype=np.uint8)

    # Calculate the dose plane mask for each contour in the plane
    # and boolean xor to remove holes
    for i, contour in enumerate(contours):
        m = get_contour_mask(dd, id, dosegridpoints, contour)
        grid = np.logical_xor(m.astype(np.uint8), grid).astype(np.bool)

    hist, vol = calculate_contour_dvh(grid, doseplane, maxdose, dd, id,
                                      structure)
    return (hist, vol)

def test_truth_table_logical(self):
        # 2, 3 and 4 serves as true values
        input1 = [0, 0, 3, 2]
        input2 = [0, 4, 0, 2]

        typecodes = (np.typecodes['AllFloat']
                     + np.typecodes['AllInteger']
                     + '?')     # boolean
        for dtype in map(np.dtype, typecodes):
            arg1 = np.asarray(input1, dtype=dtype)
            arg2 = np.asarray(input2, dtype=dtype)

            # OR
            out = [False, True, True, True]
            for func in (np.logical_or, np.maximum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # AND
            out = [False, False, False, True]
            for func in (np.logical_and, np.minimum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # XOR
            out = [False, True, True, False]
            for func in (np.logical_xor, np.not_equal):
                assert_equal(func(arg1, arg2).astype(bool), out)

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)

def test_truth_table_logical(self):
        # 2, 3 and 4 serves as true values
        input1 = [0, 0, 3, 2]
        input2 = [0, 4, 0, 2]

        typecodes = (np.typecodes['AllFloat']
                     + np.typecodes['AllInteger']
                     + '?')     # boolean
        for dtype in map(np.dtype, typecodes):
            arg1 = np.asarray(input1, dtype=dtype)
            arg2 = np.asarray(input2, dtype=dtype)

            # OR
            out = [False, True, True, True]
            for func in (np.logical_or, np.maximum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # AND
            out = [False, False, False, True]
            for func in (np.logical_and, np.minimum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # XOR
            out = [False, True, True, False]
            for func in (np.logical_xor, np.not_equal):
                assert_equal(func(arg1, arg2).astype(bool), out)

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)

def data_cleaning(file_path):
    data = pd.read_csv(file_path, index_col=False)
    data.drop(['Street', 'Utilities', 'Condition2', 'RoofMatl', 'Alley',
               'GarageYrBlt', 'GarageCond', 'PoolQC', 'MiscFeature'],
              axis=1, inplace=True)
    # marked as NA in BsmtExposure and not NA in other Bsmt Attributes
    data.loc[np.logical_xor(data['BsmtCond'].isnull(), data['BsmtExposure'].isnull()), 'BsmtExposure'] = 'No'
    # LotFrontage's N/A is assigned zero, will it cause problem?
    data.fillna(value={'MasVnrType': 'None', 'MasVnrArea': 0, 'BsmtQual': 'NoBsmt', 'BsmtCond': 'NoBsmt',
                       'BsmtExposure': 'NoBsmt', 'BsmtFinType1': 'NoBsmt', 'BsmtFinType2': 'NoBsmt',
                       'Electrical': 'SBrkr', 'FireplaceQu': 'NoFP', 'GarageType': 'Noga',
                       'GarageFinish': 'Noga', 'GarageQual': 'Noga', 'Fence': 'NoFence', 'LotFrontage': 0},
                inplace=True)
    data.loc[:, 'YrSold'] = 2016 - data.loc[:, 'YrSold']
    data.loc[data.loc[:, 'PoolArea'] != 0, 'PoolArea'] = 1
    data.loc[:, 'Porch'] = np.sum(data.loc[:, ['EnclosedPorch', '3SsnPorch', 'ScreenPorch']], axis=1)
    data.drop(['EnclosedPorch', '3SsnPorch', 'ScreenPorch'], axis=1, inplace=True)
    data.replace({'BsmtFullBath': {3: 2},
                  'LotShape': {'IR3': 'IR2'}},
                 inplace=True)
    data.columns
    # examine columns containing NA value
    print(data)
    print(data.columns[np.sum(data.isnull(), axis=0) != 0])

def test_truth_table_logical(self):
        # 2, 3 and 4 serves as true values
        input1 = [0, 0, 3, 2]
        input2 = [0, 4, 0, 2]

        typecodes = (np.typecodes['AllFloat']
                     + np.typecodes['AllInteger']
                     + '?')     # boolean
        for dtype in map(np.dtype, typecodes):
            arg1 = np.asarray(input1, dtype=dtype)
            arg2 = np.asarray(input2, dtype=dtype)

            # OR
            out = [False, True, True, True]
            for func in (np.logical_or, np.maximum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # AND
            out = [False, False, False, True]
            for func in (np.logical_and, np.minimum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # XOR
            out = [False, True, True, False]
            for func in (np.logical_xor, np.not_equal):
                assert_equal(func(arg1, arg2).astype(bool), out)

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)

def m_menu(self):
        """Runs the Mathmatically defined sculpture menu item."""
        sin, cos = np.sin, np.cos
        res = raw_input("Enter a functional definition of a volume (x**2+y**2+z**2 < 1) \n")
        self.user_text = res
        self.volume_data = self.bool_ops()
        self.create_iso_surface(.7)

        while True:

            res = raw_input("Enter another functional definition of a volume (x**2+y**2+z**2 < 1) \n")
            self.user_text = res
            self.sec_volume_data = self.bool_ops()
            self.create_iso_surface(.7, second=True)
            res = raw_input("Enter a boolean operation to do with the previous solid (a = and, o = or, n = not, x = xor):\n")
            if res == "a":
                self.sec_volume_data = 0+ np.logical_and(my_sculpture.volume_data, my_sculpture.bool_ops())
            elif res == "o":
                self.sec_volume_data = 0+ np.logical_or(my_sculpture.volume_data, my_sculpture.bool_ops())
            elif res == "n":
                self.sec_volume_data = 0+ np.logical_not(my_sculpture.volume_data, my_sculpture.bool_ops())
            elif res == "x":
                self.sec_volume_data = 0+ np.logical_xor(my_sculpture.volume_data, my_sculpture.bool_ops())
            self.create_iso_surface(.7, second=True)

def test_truth_table_logical(self):
        # 2, 3 and 4 serves as true values
        input1 = [0, 0, 3, 2]
        input2 = [0, 4, 0, 2]

        typecodes = (np.typecodes['AllFloat']
                     + np.typecodes['AllInteger']
                     + '?')     # boolean
        for dtype in map(np.dtype, typecodes):
            arg1 = np.asarray(input1, dtype=dtype)
            arg2 = np.asarray(input2, dtype=dtype)

            # OR
            out = [False, True, True, True]
            for func in (np.logical_or, np.maximum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # AND
            out = [False, False, False, True]
            for func in (np.logical_and, np.minimum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # XOR
            out = [False, True, True, False]
            for func in (np.logical_xor, np.not_equal):
                assert_equal(func(arg1, arg2).astype(bool), out)

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)

def test_truth_table_logical(self):
        # 2, 3 and 4 serves as true values
        input1 = [0, 0, 3, 2]
        input2 = [0, 4, 0, 2]

        typecodes = (np.typecodes['AllFloat']
                     + np.typecodes['AllInteger']
                     + '?')     # boolean
        for dtype in map(np.dtype, typecodes):
            arg1 = np.asarray(input1, dtype=dtype)
            arg2 = np.asarray(input2, dtype=dtype)

            # OR
            out = [False, True, True, True]
            for func in (np.logical_or, np.maximum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # AND
            out = [False, False, False, True]
            for func in (np.logical_and, np.minimum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # XOR
            out = [False, True, True, False]
            for func in (np.logical_xor, np.not_equal):
                assert_equal(func(arg1, arg2).astype(bool), out)

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)

def selectShell(ref_coords, coords, R, sw):
    """
    Return indices of the particles within the spherical shell of
    inner radius (R-sw) and outer radius R, ie the shell.

    Parameters
    ----------
    ref_coords : array_like (n_atoms, n_dim)
        Reference atoms positions
    coords : array_like (n_atoms, n_dim)
        atoms positions
    R : float
        distance to any atoms

    Returns
    -------
    array
        particle indices within shell
    """
    if R < sw:
        raise RuntimeError("selection radius smaller then shell width")
    body_query = get_selection(coords, ref_coords, R=R)
    core_query = get_selection(coords, ref_coords, R=R - sw)
    query = np.logical_xor(body_query, core_query)
    return np.where(query)

def test_truth_table_logical(self):
        # 2, 3 and 4 serves as true values
        input1 = [0, 0, 3, 2]
        input2 = [0, 4, 0, 2]

        typecodes = (np.typecodes['AllFloat']
                     + np.typecodes['AllInteger']
                     + '?')     # boolean
        for dtype in map(np.dtype, typecodes):
            arg1 = np.asarray(input1, dtype=dtype)
            arg2 = np.asarray(input2, dtype=dtype)

            # OR
            out = [False, True, True, True]
            for func in (np.logical_or, np.maximum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # AND
            out = [False, False, False, True]
            for func in (np.logical_and, np.minimum):
                assert_equal(func(arg1, arg2).astype(bool), out)
            # XOR
            out = [False, True, True, False]
            for func in (np.logical_xor, np.not_equal):
                assert_equal(func(arg1, arg2).astype(bool), out)

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)

def encodeMask(M):
        """
        Encode binary mask M using run-length encoding.
        :param   M (bool 2D array)  : binary mask to encode
        :return: R (object RLE)     : run-length encoding of binary mask
        """
        [h, w] = M.shape
        M = M.flatten(order='F')
        N = len(M)
        counts_list = []
        pos = 0
        # counts
        counts_list.append(1)
        diffs = np.logical_xor(M[0:N-1], M[1:N])
        for diff in diffs:
            if diff:
                pos +=1
                counts_list.append(1)
            else:
                counts_list[pos] += 1
        # if array starts from 1. start with 0 counts for 0
        if M[0] == 1:
            counts_list = [0] + counts_list
        return {'size':      [h, w],
               'counts':    counts_list ,
               }

def _gene_signature(wm,size,key):
        '''
            ????????????????????????
            wm   : ????
            size ??????????
            key  ????????
        '''
        wm = cv2.resize(wm,(size,size))        
        wU,_,wV = np.linalg.svd(np.mat(wm))

        sumU = np.sum(np.array(wU),axis=0)
        sumV = np.sum(np.array(wV),axis=0)

        sumU_mid = np.median(sumU)
        sumV_mid = np.median(sumV)

        sumU=np.array([1 if sumU[i] >sumU_mid else 0 for i in range(len(sumU)) ])
        sumV=np.array([1 if sumV[i] >sumV_mid else 0 for i in range(len(sumV)) ])

        uv_xor=np.logical_xor(sumU,sumV)

        np.random.seed(key)
        seq=np.random.randint(2,size=len(uv_xor))

        signature = np.logical_xor(uv_xor, seq)

        sqrts = int(np.sqrt(size))
        return np.array(signature,dtype=np.int8).reshape((sqrts,sqrts))

def test_logical_and_or_xor(self):
        assert_array_equal(self.t | self.t, self.t)
        assert_array_equal(self.f | self.f, self.f)
        assert_array_equal(self.t | self.f, self.t)
        assert_array_equal(self.f | self.t, self.t)
        np.logical_or(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.t)
        assert_array_equal(self.t & self.t, self.t)
        assert_array_equal(self.f & self.f, self.f)
        assert_array_equal(self.t & self.f, self.f)
        assert_array_equal(self.f & self.t, self.f)
        np.logical_and(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.t)
        assert_array_equal(self.t ^ self.t, self.f)
        assert_array_equal(self.f ^ self.f, self.f)
        assert_array_equal(self.t ^ self.f, self.t)
        assert_array_equal(self.f ^ self.t, self.t)
        np.logical_xor(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.f)

        assert_array_equal(self.nm & self.t, self.nm)
        assert_array_equal(self.im & self.f, False)
        assert_array_equal(self.nm & True, self.nm)
        assert_array_equal(self.im & False, self.f)
        assert_array_equal(self.nm | self.t, self.t)
        assert_array_equal(self.im | self.f, self.im)
        assert_array_equal(self.nm | True, self.t)
        assert_array_equal(self.im | False, self.im)
        assert_array_equal(self.nm ^ self.t, self.im)
        assert_array_equal(self.im ^ self.f, self.im)
        assert_array_equal(self.nm ^ True, self.im)
        assert_array_equal(self.im ^ False, self.im)

def encodeMask(M):
        """
        Encode binary mask M using run-length encoding.
        :param   M (bool 2D array)  : binary mask to encode
        :return: R (object RLE)     : run-length encoding of binary mask
        """
        [h, w] = M.shape
        M = M.flatten(order='F')
        N = len(M)
        counts_list = []
        pos = 0
        # counts
        counts_list.append(1)
        diffs = np.logical_xor(M[0:N-1], M[1:N])
        for diff in diffs:
            if diff:
                pos +=1
                counts_list.append(1)
            else:
                counts_list[pos] += 1
        # if array starts from 1. start with 0 counts for 0
        if M[0] == 1:
            counts_list = [0] + counts_list
        return {'size':      [h, w],
               'counts':    counts_list ,
               }

def xor_(a: Bool = True, b: Bool = False) -> Bool:
    return np.logical_xor(a, b)

def count_matrices(data, start_state=None, threshold=None, display=False):
    num_clusters = 2
    if threshold is None:
        clust = clusterer(data)
        state = clust.fit_predict(data.reshape(-1, 1)).reshape(data.shape)
    else:
        logger.debug("Cluster data based on threshold = {}".format(threshold))
        state = data > threshold

    init_state  = state[:,:,0]
    final_state = state[:,:,1]
    switched    = np.logical_xor(init_state, final_state)

    init_state_frac = [np.mean(init_state == ct) for ct in range(num_clusters)]
    for ct, fraction in enumerate(init_state_frac):
        logger.debug("Initial fraction of state %d: %f" %(ct, fraction))

    if start_state is not None and start_state in range(num_clusters):
        start_stt = start_state
    else:
        start_stt = np.argmax(init_state_frac)
    logger.debug("Start state set to state: {}".format(start_stt))
    logger.debug("Switched state is state: {}".format(1-start_stt))

    # This array contains a 2x2 count_matrix for each coordinate tuple
    count_mat = np.zeros((init_state.shape[0], 2, 2))

    # count_mat      = np.zeros((2,2), dtype=np.int)
    count_mat[:,0,0] = np.logical_and(init_state == 0, np.logical_not(switched)).sum(axis=-1)
    count_mat[:,0,1] = np.logical_and(init_state == 0, switched).sum(axis=-1)
    count_mat[:,1,0] = np.logical_and(init_state == 1, switched).sum(axis=-1)
    count_mat[:,1,1] = np.logical_and(init_state == 1, np.logical_not(switched)).sum(axis=-1)

    return count_mat, start_stt

def count_matrices_ber(data, start_state=None, threshold=None, display=None):
    num_clusters = 2
    if threshold is None:
        clust = clusterer(data)
        state = clust.fit_predict(data.reshape(-1, 1)).reshape((-1,2))
    else:
        logger.debug("Cluster data based on threshold = {}".format(threshold))
        state = data > threshold
        state = state.reshape((-1,2))

    init_state  = state[:,0]
    final_state = state[:,1]
    switched    = np.logical_xor(init_state, final_state)

    init_state_frac = [np.mean(init_state == ct) for ct in range(num_clusters)]
    for ct, fraction in enumerate(init_state_frac):
        logger.debug("Initial fraction of state %d: %f" %(ct, fraction))

    if start_state is not None and start_state in range(num_clusters):
        start_stt = start_state
    else:
        start_stt = np.argmax(init_state_frac)
    logger.debug("Start state set to state: {}".format(start_stt))
    logger.debug("Switched state is state: {}".format(1-start_stt))

    # This array contains a 2x2 count_matrix for each coordinate tuple
    count_mat = np.zeros((2, 2))

    # count_mat      = np.zeros((2,2), dtype=np.int)
    count_mat[0,0] = np.logical_and(init_state == 0, np.logical_not(switched)).sum()
    count_mat[0,1] = np.logical_and(init_state == 0, switched).sum()
    count_mat[1,0] = np.logical_and(init_state == 1, switched).sum()
    count_mat[1,1] = np.logical_and(init_state == 1, np.logical_not(switched)).sum()

    return count_mat, start_stt

def encodeMask(M):
    """
    Encode binary mask M using run-length encoding.
    :param   M (bool 2D array)  : binary mask to encode
    :return: R (object RLE)     : run-length encoding of binary mask
    """
    [h, w] = M.shape
    M = M.flatten(order='F')
    N = len(M)
    counts_list = []
    pos = 0
    # counts
    counts_list.append(1)
    diffs = np.logical_xor(M[0:N - 1], M[1:N])
    for diff in diffs:
        if diff:
            pos += 1
            counts_list.append(1)
        else:
            counts_list[pos] += 1
    # if array starts from 1. start with 0 counts for 0
    if M[0] == 1:
        counts_list = [0] + counts_list
    return {'size': [h, w],
            'counts': counts_list,
            }

def encodeMask(M):
        """
        Encode binary mask M using run-length encoding.
        :param   M (bool 2D array)  : binary mask to encode
        :return: R (object RLE)     : run-length encoding of binary mask
        """
        [h, w] = M.shape
        M = M.flatten(order='F')
        N = len(M)
        counts_list = []
        pos = 0
        # counts
        counts_list.append(1)
        diffs = np.logical_xor(M[0:N-1], M[1:N])
        for diff in diffs:
            if diff:
                pos +=1
                counts_list.append(1)
            else:
                counts_list[pos] += 1
        # if array starts from 1. start with 0 counts for 0
        if M[0] == 1:
            counts_list = [0] + counts_list
        return {'size':      [h, w],
               'counts':    counts_list ,
               }

def encodeMask(M):
    """
    Encode binary mask M using run-length encoding.
    :param   M (bool 2D array)  : binary mask to encode
    :return: R (object RLE)     : run-length encoding of binary mask
    """
    [h, w] = M.shape
    M = M.flatten(order='F')
    N = len(M)
    counts_list = []
    pos = 0
    # counts
    counts_list.append(1)
    diffs = np.logical_xor(M[0:N - 1], M[1:N])
    for diff in diffs:
        if diff:
            pos += 1
            counts_list.append(1)
        else:
            counts_list[pos] += 1
    # if array starts from 1. start with 0 counts for 0
    if M[0] == 1:
        counts_list = [0] + counts_list
    return {'size': [h, w],
            'counts': counts_list,
            }

def encodeMask(M):
        """
        Encode binary mask M using run-length encoding.
        :param   M (bool 2D array)  : binary mask to encode
        :return: R (object RLE)     : run-length encoding of binary mask
        """
        [h, w] = M.shape
        M = M.flatten(order='F')
        N = len(M)
        counts_list = []
        pos = 0
        # counts
        counts_list.append(1)
        diffs = np.logical_xor(M[0:N-1], M[1:N])
        for diff in diffs:
            if diff:
                pos +=1
                counts_list.append(1)
            else:
                counts_list[pos] += 1
        # if array starts from 1. start with 0 counts for 0
        if M[0] == 1:
            counts_list = [0] + counts_list
        return {'size':      [h, w],
               'counts':    counts_list ,
               }

def compute_accuracy(scores, labels):
    is_pos = (labels != 0)
    is_neg = np.logical_not(is_pos)
    num_pos = np.sum(is_pos)
    num_neg = np.sum(is_neg)
    num_all = num_pos + num_neg

    is_correct = np.logical_xor(scores < 0, is_pos)
    accuracy_all = np.sum(is_correct) / num_all
    accuracy_pos = np.sum(is_correct[is_pos]) / (num_pos + 1)
    accuracy_neg = np.sum(is_correct[is_neg]) / num_neg
    return accuracy_all, accuracy_pos, accuracy_neg

def test_logical_and_or_xor(self):
        assert_array_equal(self.t | self.t, self.t)
        assert_array_equal(self.f | self.f, self.f)
        assert_array_equal(self.t | self.f, self.t)
        assert_array_equal(self.f | self.t, self.t)
        np.logical_or(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.t)
        assert_array_equal(self.t & self.t, self.t)
        assert_array_equal(self.f & self.f, self.f)
        assert_array_equal(self.t & self.f, self.f)
        assert_array_equal(self.f & self.t, self.f)
        np.logical_and(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.t)
        assert_array_equal(self.t ^ self.t, self.f)
        assert_array_equal(self.f ^ self.f, self.f)
        assert_array_equal(self.t ^ self.f, self.t)
        assert_array_equal(self.f ^ self.t, self.t)
        np.logical_xor(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.f)

        assert_array_equal(self.nm & self.t, self.nm)
        assert_array_equal(self.im & self.f, False)
        assert_array_equal(self.nm & True, self.nm)
        assert_array_equal(self.im & False, self.f)
        assert_array_equal(self.nm | self.t, self.t)
        assert_array_equal(self.im | self.f, self.im)
        assert_array_equal(self.nm | True, self.t)
        assert_array_equal(self.im | False, self.im)
        assert_array_equal(self.nm ^ self.t, self.im)
        assert_array_equal(self.im ^ self.f, self.im)
        assert_array_equal(self.nm ^ True, self.im)
        assert_array_equal(self.im ^ False, self.im)

def calcAnomaly(self, actual, predicted):
    """
    Calculates the anomaly of two SDRs

    Uses the equation presented on the wiki: 
    https://github.com/numenta/nupic/wiki/Anomaly-Score-Memo

    To put this in terms of the temporal pooler:
      A is the actual input array at a given timestep
      P is the predicted array that was produced from the previous timestep(s)
      [A - (A && P)] / [A]
    Rephrasing as questions:
      What bits are on in A that are not on in P?
      How does that compare to total on bits in A?

    Outputs 0 is there's no difference between P and A.
    Outputs 1 if P and A are totally distinct.

    Not a perfect metric - it doesn't credit proximity
    Next step: combine with a metric for a spatial pooler
    """
    combined = numpy.logical_and(actual, predicted)
    delta = numpy.logical_xor(actual,combined)
    delta_score = sum(delta)
    actual_score = float(sum(actual))
    return delta_score / actual_score

def points_in_polys(points, polys, polyy=None):
    """
    :param points: Numpy array of Nx2 points
    :param polys: Numpy array of N polygons of degree M represented
    by Mx2 points (NxMx2) for each point, see if respective poly
    contains it. Returns array of True/False
    """

    result = np.zeros((points.shape[0],), dtype=bool)
    if isinstance(points, np.ma.masked_array):
        points = points.data
    if isinstance(polys, np.ma.masked_array):
        polys = polys.data
    if polyy is not None and isinstance(polyy, np.ma.masked_array):
        polyy = polyy.data
    pointsx = points[:, 0]
    pointsy = points[:, 1]
    v1x = v1y = v2x = v2y = -1
    for i in range(0, polys.shape[1]):
        if polyy is not None:
            v1x = polys[:, i - 1]
            v1y = polyy[:, i - 1]
            v2x = polys[:, i]
            v2y = polyy[:, i]
        else:
            v1x = polys[:, i - 1, 0]
            v1y = polys[:, i - 1, 1]
            v2x = polys[:, i, 0]
            v2y = polys[:, i, 1]
        test1 = (v2y > pointsy) != (v1y > pointsy)
        test2 = np.zeros(points.shape[0], dtype=bool)
        m = np.where(test1 == 1)[0]
        test2[m] = pointsx[m] < \
            (v1x[m] - v2x[m]) * (pointsy[m] - v2y[m]) / \
            (v1y[m] - v2y[m]) + v2x[m]
        np.logical_and(test1, test2, test1)
        np.logical_xor(result, test1, result)
    return result

def gold(bits, idx):
    """Generate the idx-th Gold code of length 2^bits - 1.

    Parameters
    ----------
    bits : int
        Length of LFSR. The length of the gold code will be
        :math:`2^{\\mathtt{bits}} - 1`.
    idx : int
        Index of the code to generate within the set of gold codes, where
        :math:`0 \\le \\mathtt{idx} < 2^{\\mathtt{bits}} + 1`.
    """
    bits = int(bits)
    if bits not in TAPS:
        raise ValueError('Preferred pairs for %d bits unknown.' % bits)
    seed = np.ones(bits, dtype=bool)

    seq1 = lfsr(TAPS[bits][0], seed)
    seq2 = lfsr(TAPS[bits][1], seed)

    if idx == 0:
        return seq1
    elif idx == 1:
        return seq2
    else:
        return np.logical_xor(seq1, np.roll(seq2, -idx + 2))

def test_logical_and_or_xor(self):
        assert_array_equal(self.t | self.t, self.t)
        assert_array_equal(self.f | self.f, self.f)
        assert_array_equal(self.t | self.f, self.t)
        assert_array_equal(self.f | self.t, self.t)
        np.logical_or(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.t)
        assert_array_equal(self.t & self.t, self.t)
        assert_array_equal(self.f & self.f, self.f)
        assert_array_equal(self.t & self.f, self.f)
        assert_array_equal(self.f & self.t, self.f)
        np.logical_and(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.t)
        assert_array_equal(self.t ^ self.t, self.f)
        assert_array_equal(self.f ^ self.f, self.f)
        assert_array_equal(self.t ^ self.f, self.t)
        assert_array_equal(self.f ^ self.t, self.t)
        np.logical_xor(self.t, self.t, out=self.o)
        assert_array_equal(self.o, self.f)

        assert_array_equal(self.nm & self.t, self.nm)
        assert_array_equal(self.im & self.f, False)
        assert_array_equal(self.nm & True, self.nm)
        assert_array_equal(self.im & False, self.f)
        assert_array_equal(self.nm | self.t, self.t)
        assert_array_equal(self.im | self.f, self.im)
        assert_array_equal(self.nm | True, self.t)
        assert_array_equal(self.im | False, self.im)
        assert_array_equal(self.nm ^ self.t, self.im)
        assert_array_equal(self.im ^ self.f, self.im)
        assert_array_equal(self.nm ^ True, self.im)
        assert_array_equal(self.im ^ False, self.im)

def read_train(file_path):
    data = pd.read_csv(file_path, index_col=False)

    data.drop(['Street', 'Utilities', 'Condition2', 'RoofMatl', 'Alley',
               'GarageYrBlt', 'GarageCond', 'PoolQC', 'MiscFeature'],
              axis=1, inplace=True)

    # marked as NA in BsmtExposure and not NA in other Bsmt Attributes
    data.loc[np.logical_xor(data['BsmtCond'].isnull(), data['BsmtExposure'].isnull()), 'BsmtExposure'] = 'No'

    # LotFrontage's N/A is assigned zero, will it cause problem?
    data.fillna(value={'MasVnrType': 'None', 'MasVnrArea': 0, 'BsmtQual': 'NoBsmt', 'BsmtCond': 'NoBsmt',
                       'BsmtExposure': 'NoBsmt', 'BsmtFinType1': 'NoBsmt', 'BsmtFinType2': 'NoBsmt',
                       'Electrical': 'SBrkr', 'FireplaceQu': 'NoFP', 'GarageType': 'Noga',
                       'GarageFinish': 'Noga', 'GarageQual': 'Noga', 'Fence': 'NoFence', 'LotFrontage': 0},
                inplace=True)

    data.loc[:, 'YrSold'] = 2016 - data.loc[:, 'YrSold']

    data.loc[data.loc[:, 'PoolArea'] != 0, 'PoolArea'] = 1

    data.loc[:, 'Porch'] = np.sum(data.loc[:, ['EnclosedPorch', '3SsnPorch', 'ScreenPorch']], axis=1)
    data.drop(['EnclosedPorch', '3SsnPorch', 'ScreenPorch'], axis=1, inplace=True)

    data.replace({'BsmtFullBath': {3: 2}, 'LotShape': {'IR3': 'IR2'}}, inplace=True)

    return data

def data_cleaning(file_path):
    data = pd.read_csv(file_path, index_col=False)
    data.drop(['Street', 'Utilities', 'Condition2', 'RoofMatl', 'Alley',
               'GarageYrBlt', 'GarageCond', 'PoolQC', 'MiscFeature'],
              axis=1, inplace=True)
    # marked as NA in BsmtExposure and not NA in other Bsmt Attributes
    data.loc[np.logical_xor(data['BsmtCond'].isnull(), data['BsmtExposure'].isnull()), 'BsmtExposure'] = 'No'
    # LotFrontage's N/A is assigned zero, will it cause problem?
    data.fillna(value={'MasVnrType': 'None', 'MasVnrArea': 0, 'BsmtQual': 'NoBsmt', 'BsmtCond': 'NoBsmt',
                       'BsmtExposure': 'NoBsmt', 'BsmtFinType1': 'NoBsmt', 'BsmtFinType2': 'NoBsmt',
                       'Electrical': 'SBrkr', 'FireplaceQu': 'NoFP', 'GarageType': 'Noga',
                       'GarageFinish': 'Noga', 'GarageQual': 'Noga', 'Fence': 'NoFence', 'LotFrontage': 0},
                inplace=True)
    data.loc[:, 'YrSold'] = 2016 - data.loc[:, 'YrSold']
    data.loc[:, 'YearBuilt'] = 2016 - data.loc[:, 'YearBuilt']
    data.loc[:, 'YearRemodAdd'] = 2016 - data.loc[:, 'YearRemodAdd']
    data.loc[data.loc[:, 'PoolArea'] != 0, 'PoolArea'] = 'Y'
    data.loc[data.loc[:, 'PoolArea'] == 0, 'PoolArea'] = 'N'
    data.loc[:, 'Porch'] = np.sum(data.loc[:, ['EnclosedPorch', '3SsnPorch', 'ScreenPorch']], axis=1)
    data.drop(['EnclosedPorch', '3SsnPorch', 'ScreenPorch'], axis=1, inplace=True)
    data.replace({'BsmtFullBath': {3: 2},
                  'LotShape': {'IR3': 'IR2'}},
                 inplace=True)
    return data
    # data.columns
    # examine columns containing NA value
    # print(data)
    # print(data.columns[np.sum(data.isnull(), axis=0) != 0])