def band_plot(log_likelihood, x_min, x_max, y_min, y_max, n_sigma=1, steps=20, **kwargs): r"""This is an alias for `likelihood_contour` which is present for backward compatibility.""" warnings.warn("The `band_plot` function has been replaced " "by `likelihood_contour` (or " "`likelihood_contour_data` in conjunction with `contour`) " "and might be removed in the future. " "Please update your code.", FutureWarning) valid_args = inspect.signature(likelihood_contour_data).parameters.keys() data_kwargs = {k:v for k,v in kwargs.items() if k in valid_args} if 'pre_calculated_z' not in kwargs: contour_kwargs = likelihood_contour_data(log_likelihood, x_min, x_max, y_min, y_max, n_sigma, steps, **data_kwargs) else: contour_kwargs = {} nx, ny = kwargs['pre_calculated_z'].shape _x = np.linspace(x_min, x_max, nx) _y = np.linspace(y_min, y_max, ny) x, y = np.meshgrid(_x, _y) contour_kwargs['x'] = x contour_kwargs['y'] = y contour_kwargs['z'] = kwargs['pre_calculated_z'] if isinstance(n_sigma, Number): contour_kwargs['levels'] = [delta_chi2(n_sigma, dof=2)] else: contour_kwargs['levels'] = [delta_chi2(n, dof=2) for n in n_sigma] valid_args = inspect.signature(contour).parameters.keys() contour_kwargs.update({k:v for k,v in kwargs.items() if k in valid_args}) contour(**contour_kwargs) return contour_kwargs['x'], contour_kwargs['y'], contour_kwargs['z']
def likelihood_contour_data(log_likelihood, x_min, x_max, y_min, y_max, n_sigma=1, steps=20, threads=1, pool=None): r"""Generate data required to plot coloured confidence contours (or bands) given a log likelihood function. Parameters: - `log_likelihood`: function returning the logarithm of the likelihood. Can e.g. be the method of the same name of a FastFit instance. - `x_min`, `x_max`, `y_min`, `y_max`: data boundaries - `n_sigma`: plot confidence level corresponding to this number of standard deviations. Either a number (defaults to 1) or a tuple to plot several contours. - `steps`: number of grid steps in each dimension (total computing time is this number squared times the computing time of one `log_likelihood` call!) - `threads`: number of threads, defaults to 1. If greater than one, computation of z values will be done in parallel. - `pool`: an instance of `multiprocessing.Pool` (or a compatible implementation, e.g. from `multiprocess` or `schwimmbad`). Overrides the `threads` argument. """ _x = np.linspace(x_min, x_max, steps) _y = np.linspace(y_min, y_max, steps) x, y = np.meshgrid(_x, _y) if threads == 1: @np.vectorize def chi2_vect(x, y): # needed for evaluation on meshgrid return -2 * log_likelihood([x, y]) z = chi2_vect(x, y) else: xy = np.array([x, y]).reshape(2, steps**2).T pool = pool or Pool(threads) try: z = -2 * np.array(pool.map(log_likelihood, xy)).reshape( (steps, steps)) except PicklingError: pool.close() raise PicklingError( "When using more than 1 thread, the " "log_likelihood function must be picklable; " "in particular, you cannot use lambda expressions.") pool.close() pool.join() z = z - np.min(z) # subtract the best fit point (on the grid) # get the correct values for 2D confidence/credibility contours for n sigma if isinstance(n_sigma, Number): levels = [delta_chi2(n_sigma, dof=2)] else: levels = [delta_chi2(n, dof=2) for n in n_sigma] return {'x': x, 'y': y, 'z': z, 'levels': levels}
def band_plot(log_likelihood, x_min, x_max, y_min, y_max, n_sigma=1, steps=20, **kwargs): r"""This is an alias for `likelihood_contour` which is present for backward compatibility.""" warnings.warn("The `band_plot` function has been replaced " "by `likelihood_contour` (or " "`likelihood_contour_data` in conjunction with `contour`) " "and might be removed in the future. " "Please update your code.", FutureWarning) valid_args = inspect.signature(likelihood_contour_data).parameters.keys() data_kwargs = {k:v for k,v in kwargs.items() if k in valid_args} if 'pre_calculated_z' not in kwargs: contour_kwargs = likelihood_contour_data(log_likelihood, x_min, x_max, y_min, y_max, n_sigma, steps, **data_kwargs) else: contour_kwargs = {} nx, ny = kwargs['pre_calculated_z'].shape _x = np.linspace(x_min, x_max, nx) _y = np.linspace(y_min, y_max, ny) x, y = np.meshgrid(_x, _y) contour_kwargs['x'] = x contour_kwargs['y'] = y contour_kwargs['z'] = kwargs['pre_calculated_z'] if isinstance(n_sigma, Number): contour_kwargs['levels'] = [delta_chi2(n_sigma, dof=2)] else: contour_kwargs['levels'] = [delta_chi2(n, dof=2) for n in n_sigma] valid_args = inspect.signature(contour).parameters.keys() contour_kwargs.update({k:v for k,v in kwargs.items() if k in valid_args}) contour(**contour_kwargs) return contour_kwargs['x'], contour_kwargs['y'], contour_kwargs['z']
def likelihood_contour_data(log_likelihood, x_min, x_max, y_min, y_max, n_sigma=1, steps=20, threads=1, pool=None): r"""Generate data required to plot coloured confidence contours (or bands) given a log likelihood function. Parameters: - `log_likelihood`: function returning the logarithm of the likelihood. Can e.g. be the method of the same name of a FastFit instance. - `x_min`, `x_max`, `y_min`, `y_max`: data boundaries - `n_sigma`: plot confidence level corresponding to this number of standard deviations. Either a number (defaults to 1) or a tuple to plot several contours. - `steps`: number of grid steps in each dimension (total computing time is this number squared times the computing time of one `log_likelihood` call!) - `threads`: number of threads, defaults to 1. If greater than one, computation of z values will be done in parallel. - `pool`: an instance of `multiprocessing.Pool` (or a compatible implementation, e.g. from `multiprocess` or `schwimmbad`). Overrides the `threads` argument. """ _x = np.linspace(x_min, x_max, steps) _y = np.linspace(y_min, y_max, steps) x, y = np.meshgrid(_x, _y) if threads == 1: @np.vectorize def chi2_vect(x, y): # needed for evaluation on meshgrid return -2*log_likelihood([x,y]) z = chi2_vect(x, y) else: xy = np.array([x, y]).reshape(2, steps**2).T pool = pool or Pool(threads) try: z = -2*np.array(pool.map(log_likelihood, xy )).reshape((steps, steps)) except PicklingError: pool.close() raise PicklingError("When using more than 1 thread, the " "log_likelihood function must be picklable; " "in particular, you cannot use lambda expressions.") pool.close() pool.join() z = z - np.min(z) # subtract the best fit point (on the grid) # get the correct values for 2D confidence/credibility contours for n sigma if isinstance(n_sigma, Number): levels = [delta_chi2(n_sigma, dof=2)] else: levels = [delta_chi2(n, dof=2) for n in n_sigma] return {'x': x, 'y': y, 'z': z, 'levels': levels}
def plot(fin, fout, x0=None): ''' Read data from file and plot it in flavio-style ''' f = open(fin, 'rt') _x = [] _y = [] for l in f.readlines(): ls = l.split('\t') _x.append(float(ls[1])) _y.append(float(ls[2])) f.close() stepx = float('Inf') stepy = float('Inf') minx = min(_x) miny = min(_y) maxx = max(_x) maxy = max(_y) for i in range(0, len(_x)): if _x[i] != minx: stepx = min(stepx, _x[i] - minx) for i in range(0, len(_y)): if _y[i] != miny: stepy = min(stepy, _y[i] - miny) x, y = np.meshgrid(np.arange(minx, maxx, stepx), np.arange(miny, maxy, stepy)) shape1, shape2 = x.shape f = open(fin, 'rt') i = 0 zbs = np.zeros(x.shape) zDMs = np.zeros(x.shape) zACP = np.zeros(x.shape) zglob = np.zeros(x.shape) for l in f.readlines(): i1 = i % shape1 i2 = i // shape1 i += 1 ls = l.split('\t') zbs[i1, i2] = float(ls[-4]) zACP[i1, i2] = float(ls[-2]) zDMs[i1, i2] = float(ls[-3]) zglob[i1, i2] = float(ls[-1]) f.close() zbs = zbs - np.min(zbs) zDMs = zDMs - np.min(zDMs) zACP = zACP - np.min(zACP) zglob = zglob - np.min(zglob) levels = [delta_chi2(n, dof=2) for n in (1, 2)] plotbs = { 'x': x, 'y': y, 'z': zbs, 'levels': levels, 'interpolation_factor': 5, 'col': 0, 'label': r'$b \to s \mu^+ \mu^-$' } plotDMs = { 'x': x, 'y': y, 'z': zDMs, 'levels': levels, 'interpolation_factor': 5, 'col': 1, 'label': r'$\Delta B_s$' } plotACP = { 'x': x, 'y': y, 'z': zACP, 'levels': levels, 'interpolation_factor': 5, 'col': 2, 'label': r'$A_{CP}^{\mathrm{mix}}$' } plotglob = { 'x': x, 'y': y, 'z': zglob, 'levels': levels, 'interpolation_factor': 5, 'col': 3, 'label': 'Global' } fig = texfig.figure() #fig = plt.figure() plt.xlim([-0.15, 0.15]) plt.ylim([-0.15, 0.15]) flavio.plots.contour(**plotbs) flavio.plots.contour(**plotDMs) flavio.plots.contour(**plotACP) flavio.plots.contour(**plotglob) plt.axhline(0, c='k', lw=0.2) plt.axvline(0, c='k', lw=0.2) if x0 is not None: plt.plot(x0[0], x0[1], marker='x', c='k') plt.xlabel(r'$\mathrm{Re}\ y^{QL}_{32} y^{QL*}_{22}$') plt.ylabel(r'$\mathrm{Im}\ y^{QL}_{32} y^{QL*}_{22}$') #plt.xlabel(r'$\mathrm{Re}\ \lambda^Q_{23}$') #plt.ylabel(r'$\mathrm{Im}\ \lambda^Q_{23}$') plt.legend(loc=2, bbox_to_anchor=(1.05, 1)) texfig.savefig(fout)