Merge branch 'master' into feature/update_examples_for_paper

Author: thangleiter

filter_functions/__init__.py

@@ -22,11 +22,10 @@
 
 from . import analytic, basis, numeric, pulse_sequence, superoperator, util
 from .basis import Basis
-
+from .gradient import infidelity_derivative
 from .numeric import error_transfer_matrix, infidelity
 from .pulse_sequence import PulseSequence, concatenate, concatenate_periodic, extend, remap
 from .superoperator import liouville_representation
-from .gradient import infidelity_derivative
 
 __all__ = ['Basis', 'PulseSequence', 'analytic', 'basis', 'concatenate', 'concatenate_periodic',
            'error_transfer_matrix', 'extend', 'infidelity', 'liouville_representation', 'numeric',

filter_functions/plotting.py

@@ -54,8 +54,8 @@
 from numpy import ndarray
 
 from . import numeric, util
-from .types import (Axes, Coefficients, Colormap, Figure, FigureAxes,
-                    FigureAxesLegend, FigureGrid, Grid, Operator, State)
+from .types import (Axes, Coefficients, Colormap, Figure, FigureAxes, FigureAxesLegend, FigureGrid,
+                    Grid, Operator, State)
 
 __all__ = ['plot_cumulant_function', 'plot_infidelity_convergence', 'plot_filter_function',
            'plot_pulse_correlation_filter_function', 'plot_pulse_train']
@@ -68,6 +68,24 @@
     qt = mock.Mock()
 
 
+def _make_str_tex_compatible(s: str) -> str:
+    """Escape incompatible characters in strings passed to TeX."""
+    if not plt.rcParams['text.usetex']:
+        return s
+
+    s = str(s)
+    incompatible = ('_',)
+    for char in incompatible:
+        locs = [i for i, c in enumerate(s) if c == char]
+        # Loop backwards so as not to change locs when modifying s
+        for loc in locs[::-1]:
+            # Check if math environment, if not add escape character
+            if not s.count('$', loc) % 2:
+                s = s[:loc] + '\\' + s[loc:]
+
+    return s
+
+
 def get_bloch_vector(states: Sequence[State]) -> ndarray:
     r"""
     Get the Bloch vector from quantum states.
@@ -247,6 +265,7 @@ def plot_pulse_train(
         c_oper_identifiers: Optional[Sequence[int]] = None,
         fig: Optional[Figure] = None,
         axes: Optional[Axes] = None,
+        cycler: Optional['cycler.Cycler'] = None,
         plot_kw: Optional[dict] = {},
         subplot_kw: Optional[dict] = None,
         gridspec_kw: Optional[dict] = None,
@@ -267,6 +286,9 @@ def plot_pulse_train(
         A matplotlib figure instance to plot in
     axes: matplotlib axes, optional
         A matplotlib axes instance to use for plotting.
+    cycler: cycler.Cycler, optional
+        A Cycler instance used to set the style cycle if multiple lines
+        are to be drawn
     plot_kw: dict, optional
         Dictionary with keyword arguments passed to the plot function
     subplot_kw: dict, optional
@@ -307,10 +329,14 @@ def plot_pulse_train(
     elif fig is None and axes is not None:
         fig = axes.figure
 
+    if cycler is not None:
+        axes.set_prop_cycle(cycler)
+
     handles = []
     for i, c_coeffs in enumerate(pulse.c_coeffs[tuple(c_oper_inds), ...]):
         coeffs = np.insert(c_coeffs, 0, c_coeffs[0])
-        handles += axes.step(pulse.t, coeffs, label=c_oper_identifiers[i], **plot_kw)
+        handles += axes.step(pulse.t, coeffs,
+                             label=_make_str_tex_compatible(c_oper_identifiers[i]), **plot_kw)
 
     axes.set_xlim(pulse.t[0], pulse.tau)
     axes.set_xlabel(r'$t$ / a.u.')
@@ -330,6 +356,7 @@ def plot_filter_function(
         xscale: str = 'log',
         yscale: str = 'linear',
         omega_in_units_of_tau: bool = True,
+        cycler: Optional['cycler.Cycler'] = None,
         plot_kw: dict = {},
         subplot_kw: Optional[dict] = None,
         gridspec_kw: Optional[dict] = None,
@@ -363,6 +390,9 @@ def plot_filter_function(
         y-axis scaling. One of ('linear', 'log').
     omega_in_units_of_tau: bool, optional
         Plot :math:`\omega\tau` or just :math:`\omega` on x-axis.
+    cycler: cycler.Cycler, optional
+        A Cycler instance used to set the style cycle if multiple lines
+        are to be drawn
     plot_kw: dict, optional
         Dictionary with keyword arguments passed to the plot function
     subplot_kw: dict, optional
@@ -409,6 +439,9 @@ def plot_filter_function(
     elif fig is None and axes is not None:
         fig = axes.figure
 
+    if cycler is not None:
+        axes.set_prop_cycle(cycler)
+
     if omega_in_units_of_tau:
         tau = np.ptp(pulse.t)
         z = omega*tau
@@ -423,7 +456,8 @@ def plot_filter_function(
     handles = []
     for i, ind in enumerate(n_oper_inds):
         handles += axes.plot(z, filter_function[ind],
-                             label=n_oper_identifiers[i], **plot_kw)
+                             label=_make_str_tex_compatible(n_oper_identifiers[i]),
+                             **plot_kw)
 
     # Set the axis scales
     axes.set_xscale(xscale)
@@ -452,6 +486,7 @@ def plot_pulse_correlation_filter_function(
         xscale: str = 'log',
         yscale: str = 'linear',
         omega_in_units_of_tau: bool = True,
+        cycler: Optional['cycler.Cycler'] = None,
         plot_kw: dict = {},
         subplot_kw: Optional[dict] = None,
         gridspec_kw: Optional[dict] = None,
@@ -483,6 +518,9 @@ def plot_pulse_correlation_filter_function(
         y-axis scaling. One of ('linear', 'log').
     omega_in_units_of_tau: bool, optional
         Plot :math:`\omega\tau` or just :math:`\omega` on x-axis.
+    cycler: cycler.Cycler, optional
+        A Cycler instance used to set the style cycle if multiple lines
+        are to be drawn in one subplot. Used for all subplots.
     plot_kw: dict, optional
         Dictionary with keyword arguments passed to the plot function
     subplot_kw: dict, optional
@@ -546,10 +584,13 @@ def plot_pulse_correlation_filter_function(
     dashed_line = lines.Line2D([], [], color='gray', linestyle='--')
     for i in range(n):
         for j in range(n):
+            if cycler is not None:
+                axes[i, j].set_prop_cycle(cycler)
+
             handles = []
             for k, ind in enumerate(n_oper_inds):
                 handles += axes[i, j].plot(z, F_pc[i, j, ind].real,
-                                           label=n_oper_identifiers[k],
+                                           label=_make_str_tex_compatible(n_oper_identifiers[k]),
                                            **plot_kw)
                 if i != j:
                     axes[i, j].plot(z, F_pc[i, j, ind].imag, linestyle='--',
@@ -566,7 +607,8 @@ def plot_pulse_correlation_filter_function(
 
             if i == 0 and j == n-1:
                 handles += [transparent_line, solid_line, dashed_line]
-                labels = n_oper_identifiers.tolist() + ['', r'$Re$', r'$Im$']
+                labels = ([_make_str_tex_compatible(n) for n in n_oper_identifiers]
+                          + ['', r'$Re$', r'$Im$'])
                 legend = axes[i, j].legend(handles=handles, labels=labels,
                                            bbox_to_anchor=(1.05, 1), loc=2,
                                            borderaxespad=0., frameon=False)
@@ -628,11 +670,12 @@ def plot_cumulant_function(
         omega: Optional[Coefficients] = None,
         cumulant_function: Optional[ndarray] = None,
         n_oper_identifiers: Optional[Sequence[int]] = None,
-        basis_labels: Optional[Sequence[str]] = None,
         colorscale: str = 'linear',
         linthresh: Optional[float] = None,
-        cbar_label: str = 'Cumulant Function',
+        basis_labels: Optional[Sequence[str]] = None,
         basis_labelsize: Optional[int] = None,
+        cbar_label: str = 'Cumulant Function',
+        cbar_labelsize: Optional[int] = None,
         fig: Optional[Figure] = None,
         grid: Optional[Grid] = None,
         cmap: Optional[Colormap] = None,
@@ -669,18 +712,20 @@ def plot_cumulant_function(
         The identifiers of the noise operators for which the cumulant
         function should be plotted. All identifiers can be accessed via
         ``pulse.n_oper_identifiers``. Defaults to all.
-    basis_labels: array_like (str), optional
-        Labels for the elements of the cumulant function (the basis
-        elements).
     colorscale: str, optional
         The scale of the color code ('linear' or 'log' (default))
     linthresh: float, optional
         The threshold below which the colorscale will be linear (only
         for 'log') colorscale
-    cbar_label: str, optional
-        The label for the colorbar. Default: 'Cumulant Function'.
+    basis_labels: array_like (str), optional
+        Labels for the elements of the cumulant function (the basis
+        elements).
     basis_labelsize: int, optional
         The size in points for the basis labels.
+    cbar_label: str, optional
+        The label for the colorbar. Default: 'Cumulant Function'.
+    cbar_labelsize: int, optional
+        The size in points for the colorbar label.
     fig: matplotlib figure, optional
         A matplotlib figure instance to plot in
     grid: matplotlib ImageGrid, optional
@@ -752,6 +797,8 @@ def plot_cumulant_function(
         if len(basis_labels) != K.shape[-1]:
             raise ValueError('Invalid number of basis_labels given')
 
+        basis_labels = [_make_str_tex_compatible(bl) for bl in basis_labels]
+
     if grid is None:
         aspect_ratio = 2/3
         n_rows = int(np.round(np.sqrt(aspect_ratio*len(n_oper_inds))))
@@ -799,6 +846,7 @@ def plot_cumulant_function(
     imshow_kw.setdefault('norm', norm)
 
     basis_labelsize = basis_labelsize or 8
+    cbar_labelsize = cbar_labelsize or plt.rcParams['axes.labelsize']
 
     # Draw the images
     for i, n_oper_identifier in enumerate(n_oper_identifiers):
@@ -818,6 +866,6 @@ def plot_cumulant_function(
     cbar_kw = cbar_kw or {}
     cbar_kw.setdefault('orientation', 'vertical')
     cbar = fig.colorbar(im, cax=grid.cbar_axes[0], **cbar_kw)
-    cbar.set_label(cbar_label)
+    cbar.set_label(_make_str_tex_compatible(cbar_label), fontsize=cbar_labelsize)
 
     return fig, grid

filter_functions/pulse_sequence.py

@@ -49,7 +49,7 @@
 from numpy import linalg as nla
 from numpy import ndarray
 
-from . import numeric, util, gradient
+from . import gradient, numeric, util
 from .basis import Basis, equivalent_pauli_basis_elements, remap_pauli_basis_elements
 from .superoperator import liouville_representation
 from .types import Coefficients, Hamiltonian, Operator, PulseMapping
@@ -2250,7 +2250,8 @@ def extend(
             raise ValueError(f'Expected additional noise operators to have dimensions {(d, d)}, ' +
                              f'not {add_n_opers.shape[1:]}.')
         if any(n_oper_id in n_oper_identifiers for n_oper_id in add_n_oper_id):
-            raise ValueError('Found duplicate noise operator identifiers')
+            identifiers = set(n_oper_identifiers).intersection(add_n_oper_id)
+            raise ValueError(f'Found duplicate noise operator identifiers: {identifiers}')
 
         n_opers.extend(add_n_opers)
         n_coeffs.extend(add_n_coeffs)

tests/gradient_testutil.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 import filter_functions as ff
 
 sigma_x = np.asarray([[0, 1], [1, 0]]) / 2

tests/test_extras.py

@@ -40,8 +40,9 @@ class MissingExtrasTest(testutil.TestCase):
         'fancy_progressbar' in os.environ.get('INSTALL_EXTRAS', all_extras),
         reason='Skipping tests for missing fancy progressbar extra in build with requests')  # noqa
     def test_fancy_progressbar_not_available(self):
-        from filter_functions import util
         from tqdm import tqdm
+
+        from filter_functions import util
         self.assertEqual(util._NOTEBOOK_NAME, '')
         self.assertIs(tqdm, util._tqdm)
 

tests/test_gradient.py

@@ -26,7 +26,6 @@
 import tests.gradient_testutil as grad_util
 from tests import testutil
 
-
 np.random.seed(0)
 initial_pulse = np.random.rand(grad_util.n_time_steps)
 initial_pulse = np.expand_dims(initial_pulse, 0)

tests/test_plotting.py

@@ -22,6 +22,7 @@
 This module tests the plotting functionality of the package.
 """
 import string
+from copy import copy
 from random import sample
 
 import numpy as np
@@ -38,6 +39,7 @@
                                reason='Skipping plotting tests for build without matplotlib')
 if plotting is not None:
     import matplotlib.pyplot as plt
+    from matplotlib import cycler
 
 simple_pulse = testutil.rand_pulse_sequence(2, 1, 1, 1, btype='Pauli')
 complicated_pulse = testutil.rand_pulse_sequence(2, 100, 3, 3)
@@ -67,6 +69,10 @@ def test_plot_pulse_train(self):
                                                  c_oper_identifiers,
                                                  fig=fig, axes=ax)
 
+        # Test cycler arg
+        cycle = cycler(color=['r', 'g', 'b'])
+        fig, ax, leg = plotting.plot_pulse_train(simple_pulse, cycler=cycle)
+
         # invalid identifier
         with self.assertRaises(ValueError):
             plotting.plot_pulse_train(complicated_pulse,
@@ -113,6 +119,10 @@ def test_plot_filter_function(self):
             fig=fig, axes=ax, omega_in_units_of_tau=False
         )
 
+        # Test cycler arg
+        cycle = cycler(color=['r', 'g', 'b'])
+        fig, ax, leg = plotting.plot_filter_function(simple_pulse, cycler=cycle)
+
         # invalid identifier
         with self.assertRaises(ValueError):
             plotting.plot_filter_function(complicated_pulse,
@@ -177,6 +187,11 @@ def test_plot_pulse_correlation_filter_function(self):
             omega_in_units_of_tau=False
         )
 
+        # Test cycler arg
+        cycle = cycler(color=['r', 'g', 'b'])
+        fig, ax, leg = plotting.plot_pulse_correlation_filter_function(concatenated_simple_pulse,
+                                                                       cycler=cycle)
+
         # invalid identifiers
         with self.assertRaises(ValueError):
             plotting.plot_pulse_correlation_filter_function(
@@ -299,6 +314,17 @@ def spectrum(omega):
         fig, ax = plotting.plot_infidelity_convergence(n, infids)
 
 
+class LaTeXRenderingTest(testutil.TestCase):
+
+    def test_plot_filter_function(self):
+        pulse = copy(simple_pulse)
+        pulse.c_oper_identifiers = np.array([f'B_{i}' for i in range(len(pulse.c_opers))])
+        pulse.n_oper_identifiers = np.array([f'B_{i}' for i in range(len(pulse.n_opers))])
+        with plt.rc_context(rc={'text.usetex': True}):
+            _ = plotting.plot_pulse_train(pulse)
+            _ = plotting.plot_filter_function(pulse)
+
+
 @pytest.mark.skipif(
     qutip is None,
     reason='Skipping bloch sphere visualization tests for build without qutip')