Python numpy.column_stack() Examples

def _evaluate(self, x, out, *args, **kwargs):

        # variable names for convenient access
        x1 = x[:, 0]
        x2 = x[:, 1]
        y = x[:, 2]

        # first objectives
        f1 = x1 * anp.sqrt(16 + anp.square(y)) + x2 * anp.sqrt((1 + anp.square(y)))

        # measure which are needed for the second objective
        sigma_ac = 20 * anp.sqrt(16 + anp.square(y)) / (y * x1)
        sigma_bc = 80 * anp.sqrt(1 + anp.square(y)) / (y * x2)

        # take the max
        f2 = anp.max(anp.column_stack((sigma_ac, sigma_bc)), axis=1)

        # define a constraint
        g1 = f2 - self.Smax

        out["F"] = anp.column_stack([f1, f2])
        out["G"] = g1 

def store_transition(self, s, a, r, s_):
        if not hasattr(self, 'memory_counter'):
            self.memory_counter = 0
        #print(s,s_.size)
        s=s.reshape(-1)
        s_=s_.reshape(-1)
        transition = np.hstack((s, [a, r], s_))
        #transition = np.column_stack((s, [a, r], s_))
        #transition = np.concatenate((s, [a, r], s_), axis=1)
        #transition = scipy.sparse.hstack([s, [a, r], s_]).toarray()

        # replace the old memory with new memory
        index = self.memory_counter % self.memory_size
        self.memory[index, :] = transition

        self.memory_counter += 1 

def _positional_to_optimal(self, K):
        k, l = self.k, self.l

        suffix = np.full((len(K), self.l), 0.0)
        X = np.column_stack([K, suffix])
        X[:, self.k + self.l - 1] = 0.35

        for i in range(self.k + self.l - 2, self.k - 1, -1):
            m = X[:, i + 1:k + l]
            val = m.sum(axis=1) / m.shape[1]
            X[:, i] = 0.35 ** ((0.02 + 1.96 * val) ** -1)

        ret = X * (2 * (np.arange(self.n_var) + 1))
        return ret


# ---------------------------------------------------------------------------------------------------------
# TRANSFORMATIONS
# --------------------------------------------------------------------------------------------------------- 

def _do(self, problem, X, **kwargs):

        # get the X of parents and count the matings
        _, n_matings, n_var = X.shape

        # start point of crossover
        r = np.row_stack([np.random.permutation(n_var - 1) + 1 for _ in range(n_matings)])[:, :self.n_points]
        r.sort(axis=1)
        r = np.column_stack([r, np.full(n_matings, n_var)])

        # the mask do to the crossover
        M = np.full((n_matings, n_var), False)

        # create for each individual the crossover range
        for i in range(n_matings):

            j = 0
            while j < r.shape[1] - 1:
                a, b = r[i, j], r[i, j + 1]
                M[i, a:b] = True
                j += 2

        _X = crossover_mask(X, M)

        return _X 

def geometric_mean_var(z):
    for row in np.eye(z.shape[1]):
        if not np.any(np.all(row == z, axis=1)):
            z = np.row_stack([z, row])
    n_points, n_dim = z.shape

    D = vectorized_cdist(z, z)
    np.fill_diagonal(D, np.inf)

    k = n_dim - 1
    I = D.argsort(axis=1)[:, :k]

    first = np.column_stack([np.arange(n_points) for _ in range(k)])

    val = gmean(D[first, I], axis=1)

    return val.var() 

def mean_mean(z):
    for row in np.eye(z.shape[1]):
        if not np.any(np.all(row == z, axis=1)):
            z = np.row_stack([z, row])
    n_points, n_dim = z.shape

    D = vectorized_cdist(z, z)
    np.fill_diagonal(D, np.inf)

    k = n_dim - 1
    I = D.argsort(axis=1)[:, :k]

    first = np.column_stack([np.arange(n_points) for _ in range(k)])

    val = np.mean(D[first, I], axis=1)

    return val.mean() 

def map_onto_unit_simplex(rnd, method):
    n_points, n_dim = rnd.shape

    if method == "sum":
        ret = rnd / rnd.sum(axis=1)[:, None]

    elif method == "kraemer":
        M = sys.maxsize

        rnd *= M
        rnd = rnd[:, :n_dim - 1]
        rnd = np.column_stack([np.zeros(n_points), rnd, np.full(n_points, M)])

        rnd = np.sort(rnd, axis=1)

        ret = np.full((n_points, n_dim), np.nan)
        for i in range(1, n_dim + 1):
            ret[:, i - 1] = rnd[:, i] - rnd[:, i - 1]
        ret /= M

    else:
        raise Exception("Invalid unit simplex mapping!")

    return ret 

def _evaluate(self, x, out, *args, **kwargs):

        f1 = x[:, 0]
        c = np.sum(x[:, 1:], axis=1)
        g = 1.0 + 9.0 * c / (self.n_var - 1)
        f2 = g * (1 - np.power(f1 * 1.0 / g, 0.5) - (f1 * 1.0 / g) * np.sin(10 * np.pi * f1))

        out["F"] = np.column_stack([f1, f2])

        if "dF" in out:
            dF = np.zeros([x.shape[0], self.n_obj, self.n_var], dtype=np.float)

            dF[:, 0, 0], dF[:, 0, 1:] = 1, 0
            dF[:, 1, 0] = -0.5 * np.sqrt(g / x[:, 0]) - np.sin(10 * np.pi * x[:, 0]) - 10 * np.pi * x[:, 0] * np.cos(
                10 * np.pi * x[:, 0])
            dF[:, 1, 1:] = (9 / (self.n_var - 1)) * (1 - 0.5 * np.sqrt(x[:, 0] / g))[:, None]
            out["dF"] = dF 

def SaveYML(w_um, RefInd, filename, references='', comments=''):
    
    header = np.empty(9, dtype=object)
    header[0] = '# this file is part of refractiveindex.info database'
    header[1] = '# refractiveindex.info database is in the public domain'
    header[2] = '# copyright and related rights waived via CC0 1.0'
    header[3] = ''
    header[4] = 'REFERENCES:' + references
    header[5] = 'COMMENTS:' + comments
    header[6] = 'DATA:'
    header[7] = '  - type: tabulated nk'
    header[8] = '    data: |'
    
    export = np.column_stack((w_um, np.real(RefInd), np.imag(RefInd)))
    np.savetxt(filename, export, fmt='%4.2f %#.4g %#.4g', delimiter=' ', header='\n'.join(header), comments='',newline='\n        ')
    return

###############################################################################

## Wavelengths to sample ## 

def SaveYML(w_um, RefInd, filename, references='', comments=''):
    
    header = np.empty(9, dtype=object)
    header[0] = '# this file is part of refractiveindex.info database'
    header[1] = '# refractiveindex.info database is in the public domain'
    header[2] = '# copyright and related rights waived via CC0 1.0'
    header[3] = ''
    header[4] = 'REFERENCES:' + references
    header[5] = 'COMMENTS:' + comments
    header[6] = 'DATA:'
    header[7] = '  - type: tabulated nk'
    header[8] = '    data: |'
    
    export = np.column_stack((w_um, np.real(RefInd), np.imag(RefInd)))
    np.savetxt(filename, export, fmt='%4.2f %#.4g %#.3e', delimiter=' ', header='\n'.join(header), comments='',newline='\n        ')
    return

###############################################################################

## Wavelengths to sample ## 

def SaveYML(w_um, RefInd, filename, references='', comments=''):
    
    header = np.empty(9, dtype=object)
    header[0] = '# this file is part of refractiveindex.info database'
    header[1] = '# refractiveindex.info database is in the public domain'
    header[2] = '# copyright and related rights waived via CC0 1.0'
    header[3] = ''
    header[4] = 'REFERENCES:' + references
    header[5] = 'COMMENTS:' + comments
    header[6] = 'DATA:'
    header[7] = '  - type: tabulated nk'
    header[8] = '    data: |'
    
    export = np.column_stack((w_um, np.real(RefInd), np.imag(RefInd)))
    np.savetxt(filename, export, fmt='%4.3f %#.4g %#.3e', delimiter=' ', header='\n'.join(header), comments='',newline='\n        ')
    return

###############################################################################

## Wavelengths to sample ## 

def SaveYML(w_um, RefInd, filename, references='', comments=''):
    
    header = np.empty(9, dtype=object)
    header[0] = '# this file is part of refractiveindex.info database'
    header[1] = '# refractiveindex.info database is in the public domain'
    header[2] = '# copyright and related rights waived via CC0 1.0'
    header[3] = ''
    header[4] = 'REFERENCES:' + references
    header[5] = 'COMMENTS:' + comments
    header[6] = 'DATA:'
    header[7] = '  - type: tabulated nk'
    header[8] = '    data: |'
    
    export = np.column_stack((w_um, np.real(RefInd), np.imag(RefInd)))
    np.savetxt(filename, export, fmt='%4.2f %#.4g %#.4g', delimiter=' ', header='\n'.join(header), comments='',newline='\n        ')
    return

###############################################################################

## Wavelengths to sample ## 

def fit(self, magnitude, time, dt_bins, dm_bins):
        def delta_calc(idx):
            t0 = time[idx]
            m0 = magnitude[idx]
            deltat = time[idx + 1 :] - t0
            deltam = magnitude[idx + 1 :] - m0

            deltat[np.where(deltat < 0)] *= -1
            deltam[np.where(deltat < 0)] *= -1

            return np.column_stack((deltat, deltam))

        lc_len = len(time)
        n_vals = int(0.5 * lc_len * (lc_len - 1))

        deltas = np.vstack(tuple(delta_calc(idx) for idx in range(lc_len - 1)))

        deltat = deltas[:, 0]
        deltam = deltas[:, 1]

        bins = [dt_bins, dm_bins]
        counts = np.histogram2d(deltat, deltam, bins=bins, normed=False)[0]
        result = np.fix(255.0 * counts / n_vals + 0.999).astype(int)

        return {"DMDT": result} 

def calc_axon_contribution(self, axons):
        xyret = np.column_stack((self.grid.xret.ravel(),
                                 self.grid.yret.ravel()))
        # Only include axon segments that are < `max_d2` from the soma. These
        # axon segments will have `sensitivity` > `self.min_ax_sensitivity`:
        max_d2 = -2.0 * self.axlambda ** 2 * np.log(self.min_ax_sensitivity)
        axon_contrib = []
        for xy, bundle in zip(xyret, axons):
            idx = np.argmin((bundle[:, 0] - xy[0]) ** 2 +
                            (bundle[:, 1] - xy[1]) ** 2)
            # Cut off the part of the fiber that goes beyond the soma:
            axon = np.flipud(bundle[0: idx + 1, :])
            # Add the exact location of the soma:
            axon = np.insert(axon, 0, xy, axis=0)
            # For every axon segment, calculate distance from soma by
            # summing up the individual distances between neighboring axon
            # segments (by "walking along the axon"):
            d2 = np.cumsum(np.diff(axon[:, 0], axis=0) ** 2 +
                           np.diff(axon[:, 1], axis=0) ** 2)
            idx_d2 = d2 < max_d2
            sensitivity = np.exp(-d2[idx_d2] / (2.0 * self.axlambda ** 2))
            idx_d2 = np.insert(idx_d2, 0, False)
            contrib = np.column_stack((axon[idx_d2, :], sensitivity))
            axon_contrib.append(contrib)
        return axon_contrib 

def test_AxonMapModel_calc_axon_contribution(engine):
    model = AxonMapModel(xystep=2, engine=engine, n_axons=10,
                         xrange=(-20, 20), yrange=(-15, 15),
                         axons_range=(-30, 30))
    model.build()
    xyret = np.column_stack((model.spatial.grid.xret.ravel(),
                             model.spatial.grid.yret.ravel()))
    bundles = model.spatial.grow_axon_bundles()
    axons = model.spatial.find_closest_axon(bundles)
    contrib = model.spatial.calc_axon_contribution(axons)

    # Check lambda math:
    for ax, xy in zip(contrib, xyret):
        axon = np.insert(ax, 0, list(xy) + [0], axis=0)
        d2 = np.cumsum(np.diff(axon[:, 0], axis=0) ** 2 +
                       np.diff(axon[:, 1], axis=0) ** 2)
        sensitivity = np.exp(-d2 / (2.0 * model.spatial.axlambda ** 2))
        npt.assert_almost_equal(sensitivity, ax[:, 2]) 

def store_transition(self, s, a, r, s_):
        if not hasattr(self, 'memory_counter'):
            self.memory_counter = 0
        #print(s,s_.size)
        s=s.reshape(-1)
        s_=s_.reshape(-1)
        transition = np.hstack((s, [a, r], s_))
        #transition = np.column_stack((s, [a, r], s_))
        #transition = np.concatenate((s, [a, r], s_), axis=1)
        #transition = scipy.sparse.hstack([s, [a, r], s_]).toarray()

        # replace the old memory with new memory
        index = self.memory_counter % self.memory_size
        self.memory[index, :] = transition

        self.memory_counter += 1 

def store_transition(self, s, a, r, s_):
        if not hasattr(self, 'memory_counter'):
            self.memory_counter = 0
        #print(s,s_.size)
        s=s.reshape(-1)
        s_=s_.reshape(-1)
        transition = np.hstack((s, [a, r], s_))
        #transition = np.column_stack((s, [a, r], s_))
        #transition = np.concatenate((s, [a, r], s_), axis=1)
        #transition = scipy.sparse.hstack([s, [a, r], s_]).toarray()

        # replace the old memory with new memory
        index = self.memory_counter % self.memory_size
        self.memory[index, :] = transition

        self.memory_counter += 1 

def store_transition(self, s, a, r, s_):
        self.lo.acquire()

        s=s.reshape(-1)
        s_=s_.reshape(-1)
        transition = np.hstack((s, [a, r], s_))
        #transition = np.column_stack((s, [a, r], s_))
        #transition = np.concatenate((s, [a, r], s_), axis=1)
        #transition = scipy.sparse.hstack([s, [a, r], s_]).toarray()

        # replace the old memory with new memory
        index = self.memory_counter % self.memory_size
        self.memory[index, :] = transition

        self.memory_counter += 1
        self.lo.release()
        # print(index) 

def store_transition(self, s, a, r, s_):
        if not hasattr(self, 'memory_counter'):
            self.memory_counter = 0
        #print(s,s_.size)
        s=s.reshape(-1)
        s_=s_.reshape(-1)
        transition = np.hstack((s, [a, r], s_))
        #transition = np.column_stack((s, [a, r], s_))
        #transition = np.concatenate((s, [a, r], s_), axis=1)
        #transition = scipy.sparse.hstack([s, [a, r], s_]).toarray()

        # replace the old memory with new memory
        index = self.memory_counter % self.memory_size
        self.memory[index, :] = transition

        self.memory_counter += 1 

def SaveYML(w_um, RefInd, filename, references='', comments=''):
    
    header = np.empty(9, dtype=object)
    header[0] = '# this file is part of refractiveindex.info database'
    header[1] = '# refractiveindex.info database is in the public domain'
    header[2] = '# copyright and related rights waived via CC0 1.0'
    header[3] = ''
    header[4] = 'REFERENCES:' + references
    header[5] = 'COMMENTS:' + comments
    header[6] = 'DATA:'
    header[7] = '  - type: tabulated nk'
    header[8] = '    data: |'
    
    export = np.column_stack((w_um, np.real(RefInd), np.imag(RefInd)))
    np.savetxt(filename, export, fmt='%4.2f %#.4g %#.3e', delimiter=' ', header='\n'.join(header), comments='',newline='\n        ')
    return

###############################################################################

## Wavelengths to sample ## 

def update(self, labels, preds):
        """Updates the internal evaluation result.

        Parameters
        ----------
        labels : list of `NDArray`
            The labels of the data.

        preds : list of `NDArray`
            Predicted values.
        """
        mx.metric.check_label_shapes(labels, preds)

        for label, pred in zip(labels, preds):
            label = label.asnumpy()
            pred = pred.asnumpy()
            pred = np.column_stack((1 - pred, pred))

            label = label.ravel()
            num_examples = pred.shape[0]
            assert label.shape[0] == num_examples, (label.shape[0], num_examples)
            prob = pred[np.arange(num_examples, dtype=np.int64), np.int64(label)]
            self.sum_metric += (-np.log(prob + self.eps)).sum()
            self.num_inst += num_examples 

def plot(algorithm):
        pop = algorithm.pop
        sc = Scatter(title=algorithm.n_gen)
        sc.add(curve(algorithm.problem), plot_type="line", color="black")
        sc.add(np.column_stack([pop.get("X"), pop.get("F")]), color="red")
        sc.do() 

def plot(algorithm):
        pop = algorithm.pop
        sc = Scatter(title=algorithm.n_gen)
        sc.add(curve(algorithm.problem), plot_type="line", color="black")
        sc.add(np.column_stack([pop.get("X"), pop.get("F")]), color="red")
        sc.do() 

def plot(algorithm):
        pop = algorithm.pop
        sc = Scatter(title=algorithm.n_gen)
        sc.add(curve(algorithm.problem), plot_type="line", color="black")
        sc.add(np.column_stack([pop.get("X"), pop.get("F")]), color="red")
        sc.do() 

def test_no_pareto_front_given(self):
        class ZDT1NoPF(ZDT):
            def _evaluate(self, x, out, *args, **kwargs):
                f1 = x[:, 0]
                g = 1 + 9.0 / (self.n_var - 1) * np.sum(x[:, 1:], axis=1)
                f2 = g * (1 - np.power((f1 / g), 0.5))
                out["F"] = np.column_stack([f1, f2])

        algorithm = NSGA2(pop_size=100, eliminate_duplicates=True)
        minimize(ZDT1NoPF(), algorithm, ('n_gen', 20), seed=1, verbose=True) 

def test_no_feasible_solution_found(self):
        class MyProblem(Problem):

            def __init__(self):
                super().__init__(n_var=2,
                                 n_obj=1,
                                 n_constr=36,
                                 xl=np.array([0, 0]),
                                 xu=np.array([100, 100]))

            def _evaluate(self, x, out, *args, **kwargs):
                f1 = x[:, 0] + x[:, 1]
                out["F"] = np.column_stack([f1])
                out["G"] = np.ones(len(x))

        res = minimize(MyProblem(),
                       NSGA2(),
                       ("n_gen", 10),
                       seed=1)

        self.assertEqual(res.X, None)
        self.assertEqual(res.F, None)
        self.assertEqual(res.G, None)

        res = minimize(MyProblem(),
                       NSGA2(),
                       ("n_gen", 10),
                       seed=1,
                       verbose=True,
                       return_least_infeasible=True,
                       save_history=True)

        self.assertAlmostEqual(res.CV[0], 1.0) 

def save_shapefile(cdsdata, path, template):
    """
    Accepts bokeh ColumnDataSource data and saves it as a shapefile,
    using an existing template to determine the required schema.
    """
    collection = fiona.open(template)
    arrays = [np.column_stack([xs, ys]) for xs, ys in zip(cdsdata['xs'], cdsdata['ys'])]
    polys = gv.Polygons(arrays, crs=ccrs.GOOGLE_MERCATOR)
    projected = gv.operation.project_path(polys, projection=ccrs.PlateCarree())
    data = [list(map(tuple, arr)) for arr in projected.split(datatype='array')]
    shape_data = list(collection.items())[0][1]
    shape_data['geometry']['coordinates'] = data
    with fiona.open(path, 'w', collection.driver, collection.schema, collection.crs) as c:
        c.write(shape_data) 

def load_annotations(self, img_names):
        y = [np.column_stack(self.get_class_bbox(img))
             for img
             in img_names[self.img_idx]]

        return np.array(y) 

def t1(x, n):
        ret = []
        for i in range(0, n - 1):
            aux = _reduction_weighted_sum_uniform(x[:, i + 1:])
            ret.append(_transformation_param_dependent(x[:, i], aux))
        return np.column_stack(ret) 

def t3(x, m, n, k):
        gap = k // (m - 1)
        t = [_reduction_non_sep(x[:, (m - 1) * gap: (m * gap)], gap) for m in range(1, m)]
        t.append(_reduction_non_sep(x[:, k:], n - k))
        return np.column_stack(t)