Python numpy.compress() Examples

def dens_elec_vec(sv, crds, dm):
  """ Compute the electronic density using vectorized oprators """
  from pyscf.nao.m_rsphar_vec import rsphar_vec as rsphar_vec_python

  assert crds.ndim==2  
  assert crds.shape[-1]==3  
  nc = crds.shape[0]
  
  lmax = sv.ao_log.jmx
  for ia,[ra,sp] in enumerate(zip(sv.atom2coord,sv.atom2sp)):
    lngs = cdist(crds, sv.atom2coord[ia:ia+1,:])
    bmask = lngs<sv.ao_log.sp2rcut[sp]
    crds_selec = compress(bmask[:,0], crds, axis=0)
    t1 = timer()
    rsh1 = rsphar_vec_python(crds_selec, lmax)
    t2 = timer(); print(t2-t1); t1 = timer()
        
  return 0 

def test_numpy_compress(self):
        cond = [True, False, True, False, False]
        s = Series([1, -1, 5, 8, 7],
                   index=list('abcde'), name='foo')
        expected = Series(s.values.compress(cond),
                          index=list('ac'), name='foo')
        with tm.assert_produces_warning(FutureWarning, check_stacklevel=False):
            tm.assert_series_equal(np.compress(cond, s), expected)

        with tm.assert_produces_warning(FutureWarning, check_stacklevel=False):
            msg = "the 'axis' parameter is not supported"
            with pytest.raises(ValueError, match=msg):
                np.compress(cond, s, axis=1)

            msg = "the 'out' parameter is not supported"
            with pytest.raises(ValueError, match=msg):
                np.compress(cond, s, out=s) 

def _min_or_max_axis(self, axis, min_or_max):
        N = self.shape[axis]
        if N == 0:
            raise ValueError("zero-size array to reduction operation")
        M = self.shape[1 - axis]

        mat = self.tocsc() if axis == 0 else self.tocsr()
        mat.sum_duplicates()

        major_index, value = mat._minor_reduce(min_or_max)
        not_full = np.diff(mat.indptr)[major_index] < N
        value[not_full] = min_or_max(value[not_full], 0)

        mask = value != 0
        major_index = np.compress(mask, major_index)
        value = np.compress(mask, value)

        from . import coo_matrix
        if axis == 0:
            return coo_matrix((value, (np.zeros(len(value)), major_index)),
                              dtype=self.dtype, shape=(1, M))
        else:
            return coo_matrix((value, (major_index, np.zeros(len(value)))),
                              dtype=self.dtype, shape=(M, 1)) 

def _min_or_max_axis(X, axis, min_or_max):
    N = X.shape[axis]
    if N == 0:
        raise ValueError("zero-size array to reduction operation")
    M = X.shape[1 - axis]
    mat = X.tocsc() if axis == 0 else X.tocsr()
    mat.sum_duplicates()
    major_index, value = _minor_reduce(mat, min_or_max)
    not_full = np.diff(mat.indptr)[major_index] < N
    value[not_full] = min_or_max(value[not_full], 0)
    mask = value != 0
    major_index = np.compress(mask, major_index)
    value = np.compress(mask, value)

    if axis == 0:
        res = sp.coo_matrix((value, (np.zeros(len(value)), major_index)),
                            dtype=X.dtype, shape=(1, M))
    else:
        res = sp.coo_matrix((value, (major_index, np.zeros(len(value)))),
                            dtype=X.dtype, shape=(M, 1))
    return res.A.ravel() 

def test_numpy_compress(self):
        cond = [True, False, True, False, False]
        s = Series([1, -1, 5, 8, 7],
                   index=list('abcde'), name='foo')
        expected = Series(s.values.compress(cond),
                          index=list('ac'), name='foo')
        with tm.assert_produces_warning(FutureWarning, check_stacklevel=False):
            tm.assert_series_equal(np.compress(cond, s), expected)

        with tm.assert_produces_warning(FutureWarning, check_stacklevel=False):
            msg = "the 'axis' parameter is not supported"
            with pytest.raises(ValueError, match=msg):
                np.compress(cond, s, axis=1)

            msg = "the 'out' parameter is not supported"
            with pytest.raises(ValueError, match=msg):
                np.compress(cond, s, out=s) 

def test_small_large(self):
        # test the small and large code paths, current cutoff 400 elements
        for s in [5, 20, 51, 200, 1000]:
            d = np.random.randn(4, s)
            # Randomly set some elements to NaN:
            w = np.random.randint(0, d.size, size=d.size // 5)
            d.ravel()[w] = np.nan
            d[:,0] = 1.  # ensure at least one good value
            # use normal median without nans to compare
            tgt = []
            for x in d:
                nonan = np.compress(~np.isnan(x), x)
                tgt.append(np.median(nonan, overwrite_input=True))

            assert_array_equal(np.nanmedian(d, axis=-1), tgt) 

def test_compress(self):
        arr = [[0, 1, 2, 3, 4],
               [5, 6, 7, 8, 9]]
        tgt = [[5, 6, 7, 8, 9]]
        out = np.compress([0, 1], arr, axis=0)
        assert_equal(out, tgt) 

def _get_default_locs(self, vmin, vmax):
        "Returns the default locations of ticks."

        if self.plot_obj.date_axis_info is None:
            self.plot_obj.date_axis_info = self.finder(vmin, vmax, self.freq)

        locator = self.plot_obj.date_axis_info

        if self.isminor:
            return np.compress(locator['min'], locator['val'])
        return np.compress(locator['maj'], locator['val']) 

def test_compress(self):
        cond = [True, False, True, False, False]
        s = Series([1, -1, 5, 8, 7],
                   index=list('abcde'), name='foo')
        expected = Series(s.values.compress(cond),
                          index=list('ac'), name='foo')
        with tm.assert_produces_warning(FutureWarning):
            result = s.compress(cond)
        tm.assert_series_equal(result, expected) 

def _get_single_element(self, row, col):
        M, N = self.shape
        if (row < 0):
            row += M
        if (col < 0):
            col += N
        if not (0 <= row < M) or not (0 <= col < N):
            raise IndexError("index out of bounds: 0<=%d<%d, 0<=%d<%d" %
                             (row, M, col, N))

        major_index, minor_index = self._swap((row, col))

        start = self.indptr[major_index]
        end = self.indptr[major_index + 1]

        if self.has_sorted_indices:
            # Copies may be made, if dtypes of indices are not identical
            minor_index = self.indices.dtype.type(minor_index)
            minor_indices = self.indices[start:end]
            insert_pos_left = np.searchsorted(
                minor_indices, minor_index, side='left')
            insert_pos_right = insert_pos_left + np.searchsorted(
                minor_indices[insert_pos_left:], minor_index, side='right')
            return self.data[start + insert_pos_left:
                             start + insert_pos_right].sum(dtype=self.dtype)
        else:
            return np.compress(minor_index == self.indices[start:end],
                               self.data[start:end]).sum(dtype=self.dtype) 

def test_small_large(self):
        # test the small and large code paths, current cutoff 400 elements
        for s in [5, 20, 51, 200, 1000]:
            d = np.random.randn(4, s)
            # Randomly set some elements to NaN:
            w = np.random.randint(0, d.size, size=d.size // 5)
            d.ravel()[w] = np.nan
            d[:,0] = 1.  # ensure at least one good value
            # use normal median without nans to compare
            tgt = []
            for x in d:
                nonan = np.compress(~np.isnan(x), x)
                tgt.append(np.median(nonan, overwrite_input=True))

            assert_array_equal(np.nanmedian(d, axis=-1), tgt) 

def test_small_large(self):
        # test the small and large code paths, current cutoff 400 elements
        for s in [5, 20, 51, 200, 1000]:
            d = np.random.randn(4, s)
            # Randomly set some elements to NaN:
            w = np.random.randint(0, d.size, size=d.size // 5)
            d.ravel()[w] = np.nan
            d[:,0] = 1.  # ensure at least one good value
            # use normal median without nans to compare
            tgt = []
            for x in d:
                nonan = np.compress(~np.isnan(x), x)
                tgt.append(np.median(nonan, overwrite_input=True))

            assert_array_equal(np.nanmedian(d, axis=-1), tgt) 

def test_compress(self):
        arr = [[0, 1, 2, 3, 4],
               [5, 6, 7, 8, 9]]
        tgt = [[5, 6, 7, 8, 9]]
        out = np.compress([0, 1], arr, axis=0)
        assert_equal(out, tgt) 

def compress(condition, x, axis=None):
    """
    Return selected slices of an array along given axis.

    It returns the input tensor, but with selected slices along a given axis
    retained. If no axis is provided, the tensor is flattened.
    Corresponds to numpy.compress

    .. versionadded:: 0.7

    Parameters
    ----------
    x
        Input data, tensor variable.
    condition
         1 dimensional array of non-zero and zero values
         corresponding to indices of slices along a selected axis.

    Returns
    -------
    object
        `x` with selected slices.

    """
    indices = theano.tensor.basic.flatnonzero(condition)
    return x.take(indices, axis=axis) 

def test_op(self):
        for axis, cond, shape in zip(self.axis_list, self.cond_list,
                                     self.shape_list):
            cond_var = theano.tensor.ivector()
            data = numpy.random.random(size=shape).astype(theano.config.floatX)
            data_var = theano.tensor.matrix()

            f = theano.function([cond_var, data_var],
                                self.op(cond_var, data_var, axis=axis))

            expected = numpy.compress(cond, data, axis=axis)
            tested = f(cond, data)

            assert tested.shape == expected.shape
            assert numpy.allclose(tested, expected) 

def test_small_large(self):
        # test the small and large code paths, current cutoff 400 elements
        for s in [5, 20, 51, 200, 1000]:
            d = np.random.randn(4, s)
            # Randomly set some elements to NaN:
            w = np.random.randint(0, d.size, size=d.size // 5)
            d.ravel()[w] = np.nan
            d[:,0] = 1.  # ensure at least one good value
            # use normal median without nans to compare
            tgt = []
            for x in d:
                nonan = np.compress(~np.isnan(x), x)
                tgt.append(np.median(nonan, overwrite_input=True))

            assert_array_equal(np.nanmedian(d, axis=-1), tgt) 

def test_compress(self):
        arr = [[0, 1, 2, 3, 4],
               [5, 6, 7, 8, 9]]
        tgt = [[5, 6, 7, 8, 9]]
        out = np.compress([0, 1], arr, axis=0)
        assert_equal(out, tgt) 

def _get_default_locs(self, vmin, vmax):
        "Returns the default locations of ticks."

        if self.plot_obj.date_axis_info is None:
            self.plot_obj.date_axis_info = self.finder(vmin, vmax, self.freq)

        locator = self.plot_obj.date_axis_info

        if self.isminor:
            return np.compress(locator['min'], locator['val'])
        return np.compress(locator['maj'], locator['val']) 

def test_compress(self):
        cond = [True, False, True, False, False]
        s = Series([1, -1, 5, 8, 7],
                   index=list('abcde'), name='foo')
        expected = Series(s.values.compress(cond),
                          index=list('ac'), name='foo')
        tm.assert_series_equal(s.compress(cond), expected) 

def test_numpy_compress(self):
        cond = [True, False, True, False, False]
        s = Series([1, -1, 5, 8, 7],
                   index=list('abcde'), name='foo')
        expected = Series(s.values.compress(cond),
                          index=list('ac'), name='foo')
        tm.assert_series_equal(np.compress(cond, s), expected)

        msg = "the 'axis' parameter is not supported"
        tm.assert_raises_regex(ValueError, msg, np.compress,
                               cond, s, axis=1)

        msg = "the 'out' parameter is not supported"
        tm.assert_raises_regex(ValueError, msg, np.compress,
                               cond, s, out=s) 

def test_compress(self):
    if legacy_opset_pre_ver(9):
      raise unittest.SkipTest(
          "ONNX version {} doesn't support Compress.".format(
              defs.onnx_opset_version()))
    axis = 1
    node_def = helper.make_node("Compress",
                                inputs=['X', 'condition'],
                                outputs=['Y'],
                                axis=axis)
    x = self._get_rnd_float32(shape=[5, 5, 5])
    cond = np.array([1, 0, 1])
    output = run_node(node_def, inputs=[x, cond])
    np.testing.assert_almost_equal(output['Y'], np.compress(cond, x, axis=axis)) 

def test_compress(self):
    if legacy_opset_pre_ver(9):
      raise unittest.SkipTest(
          "ONNX version {} doesn't support Compress.".format(
              defs.onnx_opset_version()))
    axis = 1
    node_def = helper.make_node("Compress",
                                inputs=['X', 'condition'],
                                outputs=['Y'],
                                axis=axis)
    graph_def = helper.make_graph(
        [node_def],
        name="test_unknown_shape",
        inputs=[
            helper.make_tensor_value_info("X", TensorProto.FLOAT,
                                          [None, None, None]),
            helper.make_tensor_value_info("condition", TensorProto.BOOL, [None])
        ],
        outputs=[
            helper.make_tensor_value_info("Y", TensorProto.FLOAT,
                                          [None, None, None])
        ])
    x = self._get_rnd_float32(shape=[5, 5, 5])
    cond = np.array([1, 0, 1])
    tf_rep = onnx_graph_to_tensorflow_rep(graph_def)
    output = tf_rep.run({"X": x, "condition": cond})
    np.testing.assert_almost_equal(output['Y'], np.compress(cond, x, axis=axis)) 

def compress(condition, a, axis=0):
    return np.compress(condition, a, axis)

# only returns a view 

def compress(condition, m, axis=-1):
    return np.compress(condition, m, axis) 

def _set_default_format(self, vmin, vmax):
        "Returns the default ticks spacing."

        if self.plot_obj.date_axis_info is None:
            self.plot_obj.date_axis_info = self.finder(vmin, vmax, self.freq)
        info = self.plot_obj.date_axis_info

        if self.isminor:
            format = np.compress(info['min'] & np.logical_not(info['maj']),
                                 info)
        else:
            format = np.compress(info['maj'], info)
        self.formatdict = dict([(x, f) for (x, _, _, f) in format])
        return self.formatdict 

def test_small_large(self):
        # test the small and large code paths, current cutoff 400 elements
        for s in [5, 20, 51, 200, 1000]:
            d = np.random.randn(4, s)
            # Randomly set some elements to NaN:
            w = np.random.randint(0, d.size, size=d.size // 5)
            d.ravel()[w] = np.nan
            d[:,0] = 1.  # ensure at least one good value
            # use normal median without nans to compare
            tgt = []
            for x in d:
                nonan = np.compress(~np.isnan(x), x)
                tgt.append(np.median(nonan, overwrite_input=True))

            assert_array_equal(np.nanmedian(d, axis=-1), tgt) 

def test_compress(self):
        arr = [[0, 1, 2, 3, 4],
               [5, 6, 7, 8, 9]]
        tgt = [[5, 6, 7, 8, 9]]
        out = np.compress([0, 1], arr, axis=0)
        assert_equal(out, tgt) 

def testCompress(self):

    def run_test(condition, arr, *args, **kwargs):
      for fn1 in self.array_transforms:
        for fn2 in self.array_transforms:
          arg1 = fn1(condition)
          arg2 = fn2(arr)
          self.match(
              array_ops.compress(arg1, arg2, *args, **kwargs),
              np.compress(
                  np.asarray(arg1).astype(np.bool), arg2, *args, **kwargs))

    run_test([True], 5)
    run_test([False], 5)
    run_test([], 5)
    run_test([True, False, True], [1, 2, 3])
    run_test([True, False], [1, 2, 3])
    run_test([False, True], [[1, 2], [3, 4]])
    run_test([1, 0, 1], [1, 2, 3])
    run_test([1, 0], [1, 2, 3])
    run_test([0, 1], [[1, 2], [3, 4]])
    run_test([True], [[1, 2], [3, 4]])
    run_test([False, True], [[1, 2], [3, 4]], axis=1)
    run_test([False, True], [[1, 2], [3, 4]], axis=0)
    run_test([False, True], [[1, 2], [3, 4]], axis=-1)
    run_test([False, True], [[1, 2], [3, 4]], axis=-2) 

def test_small_large(self):
        # test the small and large code paths, current cutoff 400 elements
        for s in [5, 20, 51, 200, 1000]:
            d = np.random.randn(4, s)
            # Randomly set some elements to NaN:
            w = np.random.randint(0, d.size, size=d.size // 5)
            d.ravel()[w] = np.nan
            d[:,0] = 1.  # ensure at least one good value
            # use normal median without nans to compare
            tgt = []
            for x in d:
                nonan = np.compress(~np.isnan(x), x)
                tgt.append(np.median(nonan, overwrite_input=True))

            assert_array_equal(np.nanmedian(d, axis=-1), tgt) 

def test_compress(self):
        arr = [[0, 1, 2, 3, 4],
               [5, 6, 7, 8, 9]]
        tgt = [[5, 6, 7, 8, 9]]
        out = np.compress([0, 1], arr, axis=0)
        assert_equal(out, tgt)