Python numpy.put() Examples

def __init__(self, action_set, x = None, **kwargs):

        self.built = False

        #setup the optimizer here:
        self._optimizer = SolverFactory('cbc')
        self._results = None

        #todo: Alex fill out these functions
        ## todo: check what each of these does in CPLEX.
        self._set_mip_time_limit = lambda mip, time_limit: True #_set_mip_time_limit(self, mip, time_limit)
        self._set_mip_node_limit = lambda mip, node_limit: True #_set_mip_node_limit(self, mip, node_limit)
        ## todo: not sure what to put for this. let's talk about what the cplex display flag does.
        self._set_mip_display = lambda mip, display_flag: True #_set_mip_display(self, mip, display)

        self._apriori_infeasible = False

        super().__init__(action_set = action_set, x = x, **kwargs)


    #### building MIP #### 

def merge( self, inmodel=None ):
        """
        Rescue profiles and info records from input model into result model.
        """
        r = self.result.clone()
        m = inmodel or self.model
        i1, i2 = r.compareAtoms( m )

        mask1 = N.zeros( len( r ), N.int )
        N.put( mask1, i1, 1 )

        r.atoms.update( m.atoms, mask=mask1 )
        r.fileName = m.fileName
        r.source = m.source
        
        return r 

def put(a, ind, v, mode='wrap'):
    """Replaces specified elements of an array with given values.

    Args:
        a (cupy.ndarray): Target array.
        ind (array-like): Target indices, interpreted as integers.
        v (array-like): Values to place in `a` at target indices.
            If `v` is shorter than `ind` it will be repeated as necessary.
        mode (str): How out-of-bounds indices will behave. Its value must be
            either `'raise'`, `'wrap'` or `'clip'`. Otherwise,
            :class:`TypeError` is raised.

    .. note::
        Default `mode` is set to `'wrap'` to avoid unintended performance drop.
        If you need NumPy's behavior, please pass `mode='raise'` manually.

    .. seealso:: :func:`numpy.put`
    """
    a.put(ind, v, mode=mode) 

def get_onehot_arr(place, dim, put_value=1.):
    """
    get a `dim` dimensional one-hot vector, with `place`-th entry being `put_value` and dtype being np.float32
    e.g.:
        >>> get_onehot_arr(3, 5, 1.3)
        np.ndarray([0, 0, 0, 1.3, 0], dtype=np.float32)
    :param place: the place to put a non-zero value
    :param dim: the length of the vector
    :param put_value: the value to be put
    :return: a `dim` dimensional one-hot vector, with `place`-th entry being `put_value` and dtype being np.float32
    """
    if place >= dim or place < 0:
        print("Invalid input: place = {}, dim = {}".format(place, dim))
    ans = np.zeros(dim, dtype=np.float32)
    np.put(ans, place, put_value)
    return ans 

def _transform_gradients(self, g):
        """
        Transform the gradients by multiplying the gradient factor for each
        constraint to it.
        """
        #py3 fix
        #[np.put(g, i, c.gradfactor(self.param_array[i], g[i])) for c, i in self.constraints.iteritems() if c != __fixed__]
        [np.put(g, i, c.gradfactor(self.param_array[i], g[i])) for c, i in self.constraints.items() if c != __fixed__]
        if self._has_fixes(): return g[self._fixes_]
        return g

    #def _transform_gradients_non_natural(self, g):
    #    """
    #    Transform the gradients by multiplying the gradient factor for each
    #    constraint to it, using the theta transformed natural gradient.
    #    """
    #    #py3 fix
    #    #[np.put(g, i, c.gradfactor_non_natural(self.param_array[i], g[i])) for c, i in self.constraints.iteritems() if c != __fixed__]
    #    [np.put(g, i, c.gradfactor_non_natural(self.param_array[i], g[i])) for c, i in self.constraints.items() if c != __fixed__]
    #    if self._has_fixes(): return g[self._fixes_]
    #    return g 

def readCuts(myfile):
	cuts = open(myfile).readlines()
	haps = np.zeros((len(cuts), m))
	totalPSVs = 0
	for idx, psvs in enumerate(cuts):
		psvs=psvs.strip().split()
		psvs = map(int, psvs)
		for psv in psvs:
			psvPositions.append(psv)
		np.put(haps[idx], psvs, [1])		
		totalPSVs += len(psvs)
	# get rid of positions where there are two PSVs at one stop
	# not sure why this happens, will Have to fix with mark
	# confirmed as a bug, a fix is in the works
	# hack to skip it for now
	toRm = list(np.where( (haps.sum(axis = 0) > 1) )[0])
	for pos in toRm:
		print("mulitple PSVs in one spot!")
		psvPositions.remove(pos)

	return(haps) 

def _inverse_permutation(p):
    """inverse permutation p"""
    n = p.size
    s = np.zeros(n, dtype=np.int32)
    i = np.arange(n, dtype=np.int32)
    np.put(s, p, i)  # s[p] = i
    return s 

def to_one_hot(self, X):
        one_hot = np.zeros((len(X), NO_LABEL))
        for i in range(len(X)):
            np.put(one_hot[i, :], X[i], 1)

        return one_hot 

def place(arr, mask, vals):
    """Change elements of an array based on conditional and input values.

    This function uses the first N elements of `vals`, where N is the number
    of true values in `mask`.

    Args:
        arr (cupy.ndarray): Array to put data into.
        mask (array-like): Boolean mask array. Must have the same size as `a`.
        vals (array-like): Values to put into `a`. Only the first
            N elements are used, where N is the number of True values in
            `mask`. If `vals` is smaller than N, it will be repeated, and if
            elements of `a` are to be masked, this sequence must be non-empty.

    Examples
    --------
    >>> arr = np.arange(6).reshape(2, 3)
    >>> np.place(arr, arr>2, [44, 55])
    >>> arr
    array([[ 0,  1,  2],
           [44, 55, 44]])

    .. warning::

        This function may synchronize the device.

    .. seealso:: :func:`numpy.place`
    """
    # TODO(niboshi): Avoid nonzero which may synchronize the device.
    mask = cupy.asarray(mask)
    if arr.size != mask.size:
        raise ValueError('Mask and data must be the same size.')
    vals = cupy.asarray(vals)

    mask_indices = mask.ravel().nonzero()[0]  # may synchronize
    if mask_indices.size == 0:
        return
    if vals.size == 0:
        raise ValueError('Cannot insert from an empty array.')
    arr.put(mask_indices, vals, mode='wrap') 

def __sf(self, X):
        """Internal function to calculate for Smoothing Factors of data points
        Repeated n_iter_ of times in randomized mode.
        """
        dis_ = np.zeros(shape=(X.shape[0],))
        card_ = np.zeros(shape=(X.shape[0],))
        # perform one process with the original input order
        itr_res = self.__dis(X)
        np.put(card_, X.shape[0] - sum([i > 0. for i in itr_res]),
               np.where(itr_res > 0.))

        # create a copy of random state to preserve original state for
        # future fits (if any)
        random_state = np.random.RandomState(
            seed=self.random_state_.get_state()[1][0])
        indices = np.arange(X.shape[0])
        for _ in range(self.n_iter_):
            ind_ = indices
            random_state.shuffle(ind_)
            _x = X[indices]
            # get dissimilarity of this iteration and restore original order
            itr_res = self.__dis(_x)[np.argsort(ind_)]
            current_card = X.shape[0] - sum([i > 0. for i in itr_res])
            # compare with previous iteration to get the maximal dissimilarity
            for i, j in enumerate(itr_res):
                if j > dis_[i]:
                    dis_[i] = j
                    card_[i] = current_card
            # Increase random state seed by one to reorder input next iteration
            random_state.seed(random_state.get_state()[1][0] + 1)

        return np.multiply(dis_, card_) 

def _inverse_permutation(p):
    """inverse permutation p"""
    n = p.size
    s = np.zeros(n, dtype=np.int32)
    i = np.arange(n, dtype=np.int32)
    np.put(s, p, i)  # s[p] = i
    return s 

def diag(s, leg, dtype=None, labels=None):
    """Returns a square, diagonal matrix of entries `s`.

    The resulting matrix has legs ``(leg, leg.conj())`` and charge 0.

    Parameters
    ----------
    s : scalar | 1D array
        The entries to put on the diagonal. If scalar, all diagonal entries are the same.
    leg : :class:`LegCharge`
        The first leg of the resulting matrix.
    dtype : None | type
        The data type to be used for the result. By default, use dtype of `s`.
    labels : list of {str | None}
        Labels associated to each leg, ``None`` for non-named labels.

    Returns
    -------
    diagonal : :class:`Array`
        A square matrix with diagonal entries `s`.

    See also
    --------
    Array.scale_axis : similar as ``tensordot(diag(s), ...)``, but faster.
    """
    s = np.asarray(s, dtype)
    scalar = (s.ndim == 0)
    if not scalar and len(s) != leg.ind_len:
        raise ValueError("len(s)={0:d} not equal to leg.ind_len={1:d}".format(len(s), leg.ind_len))
    res = Array((leg, leg.conj()), s.dtype, labels=labels)  # default charge is 0
    # qdata = [[0, 0], [1, 1], ....]
    res._qdata = np.arange(leg.block_number, dtype=np.intp)[:, np.newaxis] * np.ones(2, np.intp)
    # ``res._qdata_sorted = True`` was already set
    if scalar:
        res._data = [np.diag(s * np.ones(size, dtype=s.dtype)) for size in leg.get_block_sizes()]
    else:
        res._data = [np.diag(s[leg.get_slice(qi)]) for qi in range(leg.block_number)]
    return res 

def patchAround( self, atom, size ):
        """
        patchAround( int_atom, int_nAtoms ) -> mask for self.model
        Create single patch of given size around given atom
        """
        dist = self.__distances( atom )
        order = N.argsort( dist )

        r = N.zeros( len( self.model ), 'i' )
        N.put( r, order[:size], 1 )

        return r 

def modelMask( self ):
        """
        Create a mask for parent Polymer, marking every position covered by
        this feature.
        @return:
        @rtype: N.array of int or bool
        """
        r = N.zeros( len( self.model ) )
        N.put( r, self.map, 1 )
        return r 

def optimizer_array(self):
        """
        Array for the optimizer to work on.
        This array always lives in the space for the optimizer.
        Thus, it is untransformed, going from Transformations.

        Setting this array, will make sure the transformed parameters for this model
        will be set accordingly. It has to be set with an array, retrieved from
        this method, as e.g. fixing will resize the array.

        The optimizer should only interfere with this array, such that transformations
        are secured.
        """
        if self.__dict__.get('_optimizer_copy_', None) is None or self.size != self._optimizer_copy_.size:
            self._optimizer_copy_ = np.empty(self.size)

        if not self._optimizer_copy_transformed:
            self._optimizer_copy_.flat = self.param_array.flat
            #py3 fix
            #[np.put(self._optimizer_copy_, ind, c.finv(self.param_array[ind])) for c, ind in self.constraints.iteritems() if c != __fixed__]
            [np.put(self._optimizer_copy_, ind, c.finv(self.param_array[ind])) for c, ind in self.constraints.items() if c != __fixed__]
            self._optimizer_copy_transformed = True

        if self._has_fixes():# or self._has_ties()):
            self._ensure_fixes()
            return self._optimizer_copy_[self._fixes_]
        return self._optimizer_copy_ 

def optimizer_array(self, p):
        """
        Make sure the optimizer copy does not get touched, thus, we only want to
        set the values *inside* not the array itself.

        Also we want to update param_array in here.
        """
        f = None
        if self.has_parent() and self.constraints[__fixed__].size != 0:
            f = np.ones(self.size).astype(bool)
            f[self.constraints[__fixed__]] = FIXED
        elif self._has_fixes():
            f = self._fixes_
        if f is None:
            self.param_array.flat = p
            [np.put(self.param_array, ind, c.f(self.param_array.flat[ind]))
             #py3 fix
             #for c, ind in self.constraints.iteritems() if c != __fixed__]
             for c, ind in self.constraints.items() if c != __fixed__]
        else:
            self.param_array.flat[f] = p
            [np.put(self.param_array, ind[f[ind]], c.f(self.param_array.flat[ind[f[ind]]]))
             #py3 fix
             #for c, ind in self.constraints.iteritems() if c != __fixed__]
             for c, ind in self.constraints.items() if c != __fixed__]
        #self._highest_parent_.tie.propagate_val()

        self._optimizer_copy_transformed = False
        self.trigger_update() 

def unique_encode(self, cls_targets):
        batch_size, _, _ = cls_targets.size()
        target_mask = (cls_targets >= 0) * (cls_targets != self.ignore_label)
        cls_targets = [cls_targets[idx].masked_select(target_mask[idx]) for idx in np.arange(batch_size)]

        # unique_cls = [np.unique(label.numpy(), return_counts=True) for label in cls_targets]
        unique_cls = [np.unique(label.numpy()) for label in cls_targets]

        encode = np.zeros((batch_size, self.num_classes), dtype=np.uint8)

        for idx in np.arange(batch_size):
            np.put(encode[idx], unique_cls[idx], 1)

        return torch.from_numpy(encode).float() 

def setdiag0(K):
    """Set the diagonal entries of a square matrix to 0
    """
    n = K.shape[0]
    numpy.put(K, numpy.arange(n) * (n + 1), 0.0) 

def store_data(self) -> None:
        if self.lpv:
            state = self.vehicle.state.copy()
            interval = []
            for x_t in self.lpv.change_coordinates(self.lpv.x_i_t, back=True, interval=True):
                # lateral state to full state
                np.put(state, [1, 2, 4, 5], x_t)
                # full state to absolute coordinates
                interval.append(state.squeeze(-1).copy())
            self.interval_trajectory.append(interval)
        self.trajectory.append(copy.deepcopy(self.vehicle.state)) 

def shift2(arr,num):
    arr=np.roll(arr,num)
    if num < 0:
         np.put(arr,range(len(arr)+num,len(arr)),np.nan)
    elif num > 0:
         np.put(arr,range(num),np.nan)
    return arr
    
#parameters: string 'inpath' which is the path of the .csv dataset
#returns: the dataset in a numpy array 

def qdrdist_matrix_indices(self, ntraf):
        """ This function gives the indices that can be used in the lon/lat-vectors """
        # The indices will be n*(n-1)/2 long
        # Only works for n >= 2, which is logical...
        # This is faster than np.triu_indices :)
        tmp_range = np.arange(ntraf - 1, dtype=np.int32)
        ind1 = np.repeat(tmp_range, (tmp_range + 1)[::-1])
        ind2 = np.ones(ind1.shape[0], dtype=np.int32)
        inds = np.cumsum(tmp_range[1:][::-1] + 1)
        np.put(ind2, inds, np.arange(ntraf * -1 + 3, 1))
        ind2 = np.cumsum(ind2, out=ind2)
        return ind1, ind2 

def _inverse_permutation(p):
    """inverse permutation p"""
    n = p.size
    s = np.zeros(n, dtype=np.int32)
    i = np.arange(n, dtype=np.int32)
    np.put(s, p, i)  # s[p] = i
    return s 

def test_tf_keras_iris_explainer(tf_keras_iris_explainer, use_kdtree, k):
    X_train, model, cf = tf_keras_iris_explainer

    # instance to be explained
    x = X_train[0].reshape(1, -1)
    pred_class = np.argmax(model.predict(x))
    not_pred_class = np.argmin(model.predict(x))

    # test fit
    cf.fit(X_train)
    if use_kdtree:  # k-d trees
        assert len(cf.kdtrees) == cf.classes  # each class has a k-d tree
        n_by_class = 0
        for c in range(cf.classes):
            n_by_class += cf.X_by_class[c].shape[0]
        assert n_by_class == X_train.shape[0]  # all training instances are stored in the trees
        assert cf.kdtrees[pred_class].query(x, k=1)[0] == 0.  # nearest distance to own class equals 0
        assert cf.score(x, not_pred_class, pred_class) == 0.  # test score fn
    else:  # encoder
        assert len(list(cf.class_proto.keys())) == cf.classes
        assert [True for _ in range(cf.classes)] == [v.shape == (1, 2) for _, v in cf.class_proto.items()]
        n_by_class = 0
        for c in range(cf.classes):
            n_by_class += cf.class_enc[c].shape[0]
        assert n_by_class == X_train.shape[0]  # all training instances encoded

    # test explanation
    explanation = cf.explain(x, k=k)
    assert cf.id_proto != pred_class
    assert np.argmax(model.predict(explanation.cf['X'])) == explanation.cf['class']
    assert explanation.cf['grads_num'].shape == explanation.cf['grads_graph'].shape == x.shape
    assert explanation.meta.keys() == DEFAULT_META_CFP.keys()
    assert explanation.data.keys() == DEFAULT_DATA_CFP.keys()

    # test gradient shapes
    y = np.zeros((1, cf.classes))
    np.put(y, pred_class, 1)
    cf.predict = cf.predict.predict  # make model black box
    grads = cf.get_gradients(x, y, x.shape[1:])
    assert grads.shape == x.shape 

def test_remove_noise():
    # Create process object
    tmp = ConvertEK60(ek60_raw_path)
    tmp.raw2nc()
    e_data = Process(tmp.nc_path)
    freq, npings, nrange = [100000], 2, 100
    ping_index = np.arange(npings)
    range_bin = np.arange(nrange)
    # Test noise rsemoval on upside-down parabola
    data = np.ones(nrange)
    # Insert noise points
    np.put(data, 30, -30)
    np.put(data, 60, -30)
    # Add more pings
    data = np.array([data] * npings)
    # Make DataArray
    Sv = xr.DataArray([data], coords=[('frequency', freq),
                                      ('ping_time', ping_index),
                                      ('range_bin', range_bin)])
    Sv.name = "Sv"
    ds = Sv.to_dataset()
    e_data.Sv = ds
    # Create range, and seawater_absorption needed for noise_removal
    e_data.sample_thickness = xr.DataArray([0.1], coords=[('frequency', freq)])
    e_data._range = e_data.sample_thickness * \
        xr.DataArray([np.arange(nrange)], coords=[('frequency', freq),
                                                  ('range_bin', np.arange(nrange))])

    e_data._seawater_absorption = xr.DataArray([0.1], coords=[('frequency', freq)])
    # Run noise removal
    e_data.remove_noise()
    # Test if noise points are are nan
    assert np.isnan(e_data.Sv_clean.Sv[0][0][30])
    assert np.isnan(e_data.Sv_clean.Sv[0][0][60])

    # delete created nc file
    os.remove(tmp.nc_path) 

def _next_observation(self):
        frame = np.zeros((5, LOOKBACK_WINDOW_SIZE + 1))

        # Get the stock data points for the last 5 days and scale to between 0-1
        np.put(frame, [0, 4], [
            self.df.loc[self.current_step: self.current_step +
                        LOOKBACK_WINDOW_SIZE, 'Open'].values / MAX_SHARE_PRICE,
            self.df.loc[self.current_step: self.current_step +
                        LOOKBACK_WINDOW_SIZE, 'High'].values / MAX_SHARE_PRICE,
            self.df.loc[self.current_step: self.current_step +
                        LOOKBACK_WINDOW_SIZE, 'Low'].values / MAX_SHARE_PRICE,
            self.df.loc[self.current_step: self.current_step +
                        LOOKBACK_WINDOW_SIZE, 'Close'].values / MAX_SHARE_PRICE,
            self.df.loc[self.current_step: self.current_step +
                        LOOKBACK_WINDOW_SIZE, 'Volume'].values / MAX_NUM_SHARES,
        ])

        # Append additional data and scale each value to between 0-1
        obs = np.append(frame, [
            [self.balance / MAX_ACCOUNT_BALANCE],
            [self.max_net_worth / MAX_ACCOUNT_BALANCE],
            [self.shares_held / MAX_NUM_SHARES],
            [self.cost_basis / MAX_SHARE_PRICE],
            [self.total_sales_value / (MAX_NUM_SHARES * MAX_SHARE_PRICE)],
        ], axis=1)

        return obs 

def _call_lim(self, fz, z, f):
        err = np.zeros_like(fz)
        final_step = np.zeros_like(fz)
        index = np.zeros_like(fz, dtype=int)
        k = np.flatnonzero(np.isnan(fz))
        if k.size > 0:
            fz = np.where(np.isnan(fz), 0, fz)
            lim_fz, info1 = self._lim(f, z.flat[k])
            np.put(fz, k, lim_fz)
            if self.full_output:
                np.put(final_step, k, info1.final_step)
                np.put(index, k, info1.index)
                np.put(err, k, info1.error_estimate)
        return fz, self.info(err, final_step, index) 

def _remap_factors(entity_mapping, entity_factors, num_entities, num_factors):
        shape = (num_entities, num_factors)
        entity_id = np.repeat(entity_mapping.loc[:, 1].values, num_factors, axis=0).astype(np.int64)
        factor_id = entity_factors['col2'].values.astype(np.int64)
        entity_factors_idx = np.ravel_multi_index((entity_id, factor_id), dims=shape)
        entity_factors_new = np.zeros(shape)
        np.put(entity_factors_new, entity_factors_idx, entity_factors['col3'].values)
        return entity_factors_new 

def setUpClass(cls):
        # simple ERxN graph
        n = 15
        p = 0.5
        cls.A = np.zeros((n, n))
        nedge = int(round(n * n * p))
        np.put(
            cls.A,
            np.random.choice(np.arange(0, n * n), size=nedge, replace=False),
            np.random.normal(size=nedge),
        ) 

def setup_class(cls):
        # simple ERxN graph
        n = 15
        p = 0.5
        cls.A = np.zeros((n, n))
        nedge = int(round(n * n * p))
        np.put(
            cls.A,
            np.random.choice(np.arange(0, n * n), size=nedge, replace=False),
            np.random.normal(size=nedge),
        ) 

def setUpClass(cls):
        # simple ERxN graph
        n = 15
        p = 0.5
        cls.A = np.zeros((n, n))
        nedge = int(round(n * n * p))
        np.put(
            cls.A,
            np.random.choice(np.arange(0, n * n), size=nedge, replace=False),
            np.random.normal(size=nedge),
        )