Issues in distmatrix.py (master) - Issues in master - hugobuddel/orange3 - Measure and Improve Code Quality continuously with Scrutinizer

Issues (4082)

Orange/misc/distmatrix.py (9 issues)

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import numpy as np
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from Orange.util import deprecated


class DistMatrix(np.ndarray):
    """
    Distance matrix. Extends ``numpy.ndarray``.

    .. attribute:: row_items

        Items corresponding to matrix rows.

    .. attribute:: col_items

        Items corresponding to matrix columns.

    .. attribute:: axis

        If axis=1 we calculate distances between rows,
        if axis=0 we calculate distances between columns.
    """
    def __new__(cls, data, row_items=None, col_items=None, axis=1):
        """Construct a new distance matrix containing the given data.

        :param data: Distance matrix
        :type data: numpy array
        :param row_items: Items in matrix rows
        :type row_items: `Orange.data.Table` or `Orange.data.Instance`
        :param col_items: Items in matrix columns
        :type col_items: `Orange.data.Table` or `Orange.data.Instance`
        :param axis: The axis along which the distances are calculated
        :type axis: int

        """
        obj = np.asarray(data).view(cls)
        obj.row_items = row_items
        obj.col_items = col_items
        obj.axis = axis
        return obj

    def __array_finalize__(self, obj):
        """See http://docs.scipy.org/doc/numpy/user/basics.subclassing.html"""
        if obj is None: return
        self.row_items = getattr(obj, 'row_items', None)
class Foo:
    def __init__(self, x=None):
        self.x = x
        self.col_items = getattr(obj, 'col_items', None)
class Foo:
    def __init__(self, x=None):
        self.x = x
        self.axis = getattr(obj, 'axis', 1)
class Foo:
    def __init__(self, x=None):
        self.x = x

    def __array_wrap__(self, out_arr, context=None):
        if out_arr.ndim == 0:  # a single scalar
            return out_arr.item()
        return np.ndarray.__array_wrap__(self, out_arr, context)

    """
    __reduce__() and __setstate__() ensure DistMatrix is picklable.
    """

    def __reduce__(self):
        state = super().__reduce__()
        newstate = state[2] + (self.row_items, self.col_items, self.axis)
        return state[0], state[1], newstate

    def __setstate__(self, state):
        self.row_items = state[-3]
class Foo:
    def __init__(self, x=None):
        self.x = x
        self.col_items = state[-2]
class Foo:
    def __init__(self, x=None):
        self.x = x
        self.axis = state[-1]
class Foo:
    def __init__(self, x=None):
        self.x = x
        super().__setstate__(state[0:-3])

    @property
    @deprecated
    def dim(self):
        """Returns the single dimension of the symmetric square matrix."""
        return self.shape[0]

    @property
    @deprecated
    def X(self):
        return self

    @property
    def flat(self):
        return self[np.triu_indices(self.shape[0], 1)]

    def get_KNN(self, i, k):

        """Return k columns with the lowest value in the i-th row.

        :param i: i-th row
        :type i: int
        :param k: number of neighbors
        :type k: int
        """
        idxs = np.argsort(self[i, :])[:]
        return self[:, idxs]

    def invert(self, typ):
        """Invert values in the distance matrix.

        :param type: 0 (-X), 1 (1 - X), 2 (max - X), 3 (1 / X)
        :type type: int
        """
        if typ == 0:
            return -self
        elif typ == 1:
            return 1.-self
        elif typ == 2:
            return 1./self
        else:
            raise ValueError('Unknown option for typ of matrix inversion.')

    def submatrix(self, row_items, col_items=None):
        """Return a submatrix of self, describing only distances between items"""
        if not col_items:
            col_items = row_items
        obj = self[np.ix_(row_items, col_items)]
        if obj.row_items:
            obj.row_items = self.row_items[row_items]
        if obj.col_items:
            obj.col_items = self.col_items[col_items]
        return obj


1			import numpy as np
			0 ignored issues – show Configuration introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `numpy` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
2			from Orange.util import deprecated
3
4
5			class DistMatrix(np.ndarray):
6			"""
7			Distance matrix. Extends ``numpy.ndarray``.
8
9			.. attribute:: row_items
10
11			Items corresponding to matrix rows.
12
13			.. attribute:: col_items
14
15			Items corresponding to matrix columns.
16
17			.. attribute:: axis
18
19			If axis=1 we calculate distances between rows,
20			if axis=0 we calculate distances between columns.
21			"""
22			def __new__(cls, data, row_items=None, col_items=None, axis=1):
23			"""Construct a new distance matrix containing the given data.
24
25			:param data: Distance matrix
26			:type data: numpy array
27			:param row_items: Items in matrix rows
28			:type row_items: `Orange.data.Table` or `Orange.data.Instance`
29			:param col_items: Items in matrix columns
30			:type col_items: `Orange.data.Table` or `Orange.data.Instance`
31			:param axis: The axis along which the distances are calculated
32			:type axis: int
33
34			"""
35			obj = np.asarray(data).view(cls)
36			obj.row_items = row_items
37			obj.col_items = col_items
38			obj.axis = axis
39			return obj
40
41			def __array_finalize__(self, obj):
42			"""See http://docs.scipy.org/doc/numpy/user/basics.subclassing.html"""
43			if obj is None: return
44			self.row_items = getattr(obj, 'row_items', None)
			0 ignored issues – show Coding Style introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `row_items` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
45			self.col_items = getattr(obj, 'col_items', None)
			0 ignored issues – show Coding Style introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `col_items` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
46			self.axis = getattr(obj, 'axis', 1)
			0 ignored issues – show Coding Style introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `axis` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
47
48			def __array_wrap__(self, out_arr, context=None):
49			if out_arr.ndim == 0: # a single scalar
50			return out_arr.item()
51			return np.ndarray.__array_wrap__(self, out_arr, context)
52
53			"""
54			__reduce__() and __setstate__() ensure DistMatrix is picklable.
55			"""
			0 ignored issues – show Unused Code introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this This string statement has no effect and could be removed. Loading history...
56			def __reduce__(self):
57			state = super().__reduce__()
58			newstate = state[2] + (self.row_items, self.col_items, self.axis)
59			return state[0], state[1], newstate
60
61			def __setstate__(self, state):
62			self.row_items = state[-3]
			0 ignored issues – show Coding Style introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `row_items` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
63			self.col_items = state[-2]
			0 ignored issues – show Coding Style introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `col_items` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
64			self.axis = state[-1]
			0 ignored issues – show Coding Style introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `axis` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
65			super().__setstate__(state[0:-3])
66
67			@property
68			@deprecated
69			def dim(self):
70			"""Returns the single dimension of the symmetric square matrix."""
71			return self.shape[0]
72
73			@property
74			@deprecated
75			def X(self):
76			return self
77
78			@property
79			def flat(self):
80			return self[np.triu_indices(self.shape[0], 1)]
81
82			def get_KNN(self, i, k):
			0 ignored issues – show Unused Code introduced 2015-12-02 09:15 UTC by Report Bug Copy Issue Report Show Similar Issues like this The argument `k` seems to be unused. Loading history...
83			"""Return k columns with the lowest value in the i-th row.
84
85			:param i: i-th row
86			:type i: int
87			:param k: number of neighbors
88			:type k: int
89			"""
90			idxs = np.argsort(self[i, :])[:]
91			return self[:, idxs]
92
93			def invert(self, typ):
94			"""Invert values in the distance matrix.
95
96			:param type: 0 (-X), 1 (1 - X), 2 (max - X), 3 (1 / X)
97			:type type: int
98			"""
99			if typ == 0:
100			return -self
101			elif typ == 1:
102			return 1.-self
103			elif typ == 2:
104			return 1./self
105			else:
106			raise ValueError('Unknown option for typ of matrix inversion.')
107
108			def submatrix(self, row_items, col_items=None):
109			"""Return a submatrix of self, describing only distances between items"""
110			if not col_items:
111			col_items = row_items
112			obj = self[np.ix_(row_items, col_items)]
113			if obj.row_items:
114			obj.row_items = self.row_items[row_items]
115			if obj.col_items:
116			obj.col_items = self.col_items[col_items]
117			return obj
118

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Issues (4082)

Orange/misc/distmatrix.py (9 issues)

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Introduced By

1. Missing Dependencies

2. Missing init.py files

hugobuddel / orange3

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Issues (4082)

Orange/misc/distmatrix.py (9 issues)

Labels

Severity

Introduced By

1. Missing Dependencies

2. Missing __init__.py files

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2. Missing init.py files