Merge branch 'dev' into feat/ci_39

.travis.yml

@@ -1,4 +1,7 @@
 language: python
+
+cache: pip
+
 matrix:
   include:
   - name: Minimal installation 3.9

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Add measure_time context for measuring exection time (#765)
+- Add method to combine legends of multiple matplotlib axes (#782)
+- Functionality plot onto a matplotlib Axes object (#785)
 
 ### Changed
 
@@ -22,6 +24,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Deprecated
 
 - Deprecated instrument adapters. Deprecated post-processing tools in qtt.measurements.post_processing (#777)
+- Deprecated functionality to store system states with h5py (#780)
+- Deprecated methods in qtt.instrument_storage (#783)
+
 ### Fixed
 
 ## \[1.2.3] - 22-3-2021

pytest.ini

@@ -6,11 +6,12 @@ python_functions = test_*
 addopts = --pyargs src/tests/unittests src/tests/integration
 
 # exclude some directories from searching to save time
-norecursedirs = .svn _build tmp* .git docs untitled* deprecated* build dist .cache
+norecursedirs = .svn _build tmp* .git docs untitled* deprecated* build dist .cache *.egg-info __pycache__
 
 # ignore deprecation warnings from external packages
 filterwarnings =
     ignore:.*invalid escape sequence.*:DeprecationWarning
     ignore:.*Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working*:DeprecationWarning
     ignore:.*time.clock has been deprecated in Python 3.3 and will be removed from Python 3.8*:DeprecationWarning
     ignore:.*No module named '_tifffile'*:UserWarning
+	ignore:.*Call to deprecated create function FileDescriptor().*:DeprecationWarning

requirements_lock.txt

@@ -63,7 +63,7 @@ nbformat==5.1.2
 nest-asyncio==1.5.1
 netCDF4==1.5.6
 networkx==2.5
-notebook==6.2.0
+notebook==6.4.1
 numdifftools==0.9.39
 numpy==1.20.1
 opencensus==0.7.12

src/qtt/algorithms/allxy.py

@@ -1,12 +1,14 @@
-from typing import Dict, Any, List, Union, Optional
+from typing import Any, Dict, List, Optional, Union
+
 import numpy as np
-import matplotlib.pyplot as plt
 from lmfit import Model
-
-from qcodes.data.data_set import DataSet
+from matplotlib.axes import Axes
 from qcodes.data.data_array import DataArray
-from qtt.utilities.visualization import plot_vertical_line
+from qcodes.data.data_set import DataSet
+
 from qtt.algorithms.fitting import extract_lmfit_parameters
+from qtt.utilities.visualization import get_axis, plot_vertical_line
+
 
 def generate_allxy_combinations() -> List[Any]:
     """ Generate all combinations of the AllXY sequence from Reed 2013 """
@@ -89,42 +91,43 @@ def fit_allxy(dataset: DataSet, initial_parameters: Optional[np.ndarray] = None)
     return analysis_results
 
 
-def plot_allxy(dataset: DataSet, result: Dict[str, Any], fig: int = 1, plot_initial_estimate: bool = False):
+def plot_allxy(dataset: DataSet, result: Dict[str, Any], fig: Union[int, Axes, None] = 1, plot_initial_estimate: bool = False):
     """ Plot the results of an AllXY fit
 
     Args:
         dataset: Dataset containing the measurement data
         result: Fitting result of fit_allxy
-        int: Figure handle
+        fig: Figure or axis handle. Is passed on to `get_axis`
         plot_initial_guess: If True, then plot the initial estimate of the model
     """
     allxy_data = _default_measurement_array(dataset)
     xy_pairs = generate_allxy_combinations()
     x_data = np.arange(21)
 
-    plt.figure(fig)
-    plt.clf()
+    ax = get_axis(fig)
     fitted_parameters = result['fitted_parameters']
     xfine = np.arange(0, 21, 1e-3)
-    plt.plot(xfine, allxy_model(xfine, *fitted_parameters), 'm', label='fitted allxy', alpha=.5)
+    ax.plot(xfine, allxy_model(xfine, *fitted_parameters), 'm', label='fitted allxy', alpha=.5)
 
-    plt.plot(x_data, allxy_data, '.b', label='allxy data')
+    ax.plot(x_data, allxy_data, '.b', label='allxy data')
 
     if plot_initial_estimate:
         p = [0, 0, .5, 0, 1, 0]
-        plt.plot(xfine, allxy_model(xfine, *p), 'c', label='baseline', alpha=.5)
+        ax.plot(xfine, allxy_model(xfine, *p), 'c', label='baseline', alpha=.5)
 
         initial_params = _estimate_allxy_parameters(allxy_data)
-        plt.plot(xfine, allxy_model(xfine, *initial_params), 'g', label='initial estimate', alpha=.35)
+        ax.plot(xfine, allxy_model(xfine, *initial_params), 'g', label='initial estimate', alpha=.35)
 
         initial_parameters = result['initial_parameters']
-        plt.plot(xfine, allxy_model(xfine, *initial_parameters), ':g', label='initial estimate', alpha=.35)
+        ax.plot(xfine, allxy_model(xfine, *initial_parameters), ':g', label='initial estimate', alpha=.35)
+
+    ax.set_xticks(x_data)
+    ax.set_xticklabels([v[0] + "," + v[1] for v in xy_pairs], rotation='vertical')
 
-    plt.xticks(x_data, [v[0] + "," + v[1] for v in xy_pairs], rotation='vertical')
     vl = plot_vertical_line(4.5)
     vl.set_linestyle(':')
     vl = plot_vertical_line(16.5)
     vl.set_linestyle(':')
-    plt.title('AllXY')
+    ax.set_title('AllXY')
 
-    plt.legend()
+    ax.legend()

src/qtt/algorithms/functions.py

@@ -1,16 +1,18 @@
 """ Mathematical functions and models """
 
+from typing import Union
+
+import matplotlib.pyplot as plt
 import numpy as np
 import scipy
 import scipy.constants
-from typing import Union
-import matplotlib.pyplot as plt
 from lmfit import Model
+from matplotlib.axes import Axes
 
 import qtt.pgeometry
 import qtt.utilities.tools
-from qtt.utilities.visualization import plot_vertical_line
 from qtt.algorithms.generic import subpixelmax
+from qtt.utilities.visualization import get_axis, plot_vertical_line
 
 
 def gaussian(x, mean, std, amplitude=1, offset=0):
@@ -392,26 +394,26 @@ def gauss_ramsey_model(x, amplitude, decay_time, frequency, phase, offset):
     return result_dict['fitted_parameters'], result_dict
 
 
-def plot_gauss_ramsey_fit(x_data, y_data, fit_parameters, fig):
+def plot_gauss_ramsey_fit(x_data, y_data, fit_parameters, fig: Union[int, Axes, None]):
     """ Plot Gauss Ramsey fit
 
     Args:
         x_data: Input array with time variable (in seconds)
         y_data: Input array with signal
         fit_parameters: Result of fit_gauss_ramsey (fitting units in seconds)
+        fig: Figure or axis handle. Is passed to `get_axis`
     """
     test_x = np.linspace(0, np.max(x_data), 200)
     freq_fit = abs(fit_parameters[2] * 1e-6)
     t2star_fit = fit_parameters[1] * 1e6
 
-    plt.figure(fig)
-    plt.clf()
-    plt.plot(x_data * 1e6, y_data, 'o', label='Data')
-    plt.plot(test_x * 1e6, gauss_ramsey(test_x, fit_parameters), label='Fit')
-    plt.title(r'Gauss Ramsey fit: %.2f MHz / $T_2^*$: %.1f $\mu$s' % (freq_fit, t2star_fit))
-    plt.xlabel(r'time ($\mu$s)')
-    plt.ylabel('Spin-up probability')
-    plt.legend()
+    ax = get_axis(fig)
+    ax.plot(x_data * 1e6, y_data, 'o', label='Data')
+    ax.plot(test_x * 1e6, gauss_ramsey(test_x, fit_parameters), label='Fit')
+    ax.set_title(r'Gauss Ramsey fit: %.2f MHz / $T_2^*$: %.1f $\mu$s' % (freq_fit, t2star_fit))
+    ax.set_xlabel(r'time ($\mu$s)')
+    ax.set_ylabel('Spin-up probability')
+    ax.legend()
 
 
 def linear_function(x, a, b):

src/qtt/instrument_storage.py

@@ -1,17 +1,21 @@
 """ Functionality to store instrument data in a configuration file """
-import numpy as np
+import configparser
 import json
 import numbers
-import configparser
+
+import numpy as np
+
 import qtt.utilities.tools
+from qtt.utilities.tools import rdeprecated
 
 
+@rdeprecated(txt='This method will be removed in a future release', expire='Sep 1 2021')
 def save_instrument_configparser(instr, ifile, verbose=1):
     """ Save instrument configuration to configparser structure
 
     Args:
         instr (Instrument): instrument to apply settings to
-        ifile (str): configuration file    
+        ifile (str): configuration file
     """
     jdict = configparser.ConfigParser()
     jdict.read(ifile)
@@ -30,12 +34,13 @@ def save_instrument_configparser(instr, ifile, verbose=1):
         jdict.write(fid)
 
 
+@rdeprecated(txt='This method will be removed in a future release', expire='Sep 1 2021')
 def load_instrument_configparser(instr, ifile, verbose=1):
     """ Load instrument configuration from configparser structure
 
     Args:
         instr (Instrument): instrument to apply settings to
-        ifile (str): configuration file    
+        ifile (str): configuration file
     """
     jdict = configparser.ConfigParser()
     jdict.read(ifile)
@@ -65,6 +70,7 @@ def load_instrument_configparser(instr, ifile, verbose=1):
 
 if __name__ == '__main__':
     import os
+
     from stationV2.tools import V2hardware
     v2hardware = V2hardware(name='v2hardware', server_name=None)
 

src/qtt/measurements/storage.py

@@ -1,12 +1,14 @@
 # %%
-from datetime import datetime
-import os
-import h5py
 import logging
+import os
 import warnings
+from datetime import datetime
 
+import h5py
 import qcodes
+
 import qtt.instrument_drivers.virtual_gates
+from qtt.utilities.tools import rdeprecated
 
 try:
     import hickle
@@ -18,6 +20,7 @@
 # %%
 
 
+@rdeprecated(txt='Method will be removed in a future version', expire='Jun 1 2022')
 def list_states(verbose=1):
     """ List available states of the system
 
@@ -53,6 +56,7 @@ def _get_statefile(statefile=None):
     return statefile
 
 
+@rdeprecated(txt='Method will be removed in a future version', expire='Jun 1 2022')
 def load_state(tag=None, station=None, verbose=1, statefile=None):
     """ Load state of the system from disk
 
@@ -94,6 +98,7 @@ def load_state(tag=None, station=None, verbose=1, statefile=None):
     return obj, virtual_gates
 
 
+@rdeprecated(txt='Method will be removed in a future version', expire='Jun 1 2022')
 def save_state(station, tag=None, overwrite=False, virtual_gates=None, data=None, verbose=1, statefile=None):
     """ Save current state of the system to disk
 
@@ -119,7 +124,7 @@ def save_state(station, tag=None, overwrite=False, virtual_gates=None, data=None
     snapshot = station.snapshot()
     gv = station.gates.allvalues()
 
-    date_string = "{:%Y%m%d-%H%M%S}".format(datetime.now())
+    date_string = f"{datetime.now():%Y%m%d-%H%M%S}"
 
     if verbose >= 2:
         print(date_string)

src/qtt/pgeometry.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 
 pgeometry
@@ -20,25 +19,25 @@
 @author: eendebakpt
 """
 
+import logging
+import math
 # %% Load necessary packages
 import os
+import pickle
+import pkgutil
+import re
+import subprocess
 import sys
 import tempfile
-import math
 import time
 import warnings
-import pickle
-import subprocess
-import re
-import logging
-import pkgutil
 from functools import wraps
 
 import numpy
 import numpy as np
 import scipy.io
-import scipy.ndimage.morphology as morphology
 import scipy.ndimage.filters as filters
+import scipy.ndimage.morphology as morphology
 import shapely.geometry
 
 __version__ = '0.7.0'
@@ -66,9 +65,7 @@ def qtModules(verbose=0):
         import qtpy.QtCore as QtCore
         import qtpy.QtGui as QtGui
         import qtpy.QtWidgets as QtWidgets
-        from qtpy.QtCore import QObject
-        from qtpy.QtCore import Slot
-        from qtpy.QtCore import Signal
+        from qtpy.QtCore import QObject, Signal, Slot
     except ImportError:
         _haveqtpy = False
         warnings.warn('could not import qtpy, not all functionality available')
@@ -123,8 +120,9 @@ def go(self):
     pass
 
 try:
-    import matplotlib.pyplot as plt
     import matplotlib
+    import matplotlib.pyplot as plt
+
     # needed for 3d plot points, do not remove!
     try:
         from mpl_toolkits.mplot3d import Axes3D
@@ -147,9 +145,9 @@ def go(self):
 try:
     import cv2
     _haveOpenCV = True
-except ModuleNotFoundError:
+except (ModuleNotFoundError, ImportError):
     _haveOpenCV = False
-    warnings.warn('could not find OpenCV, not all functionality is available')
+    warnings.warn('could not find or load OpenCV, not all functionality is available')
     pass
 
 # %% Utils
@@ -177,8 +175,9 @@ def memory():
     Returns:
             float: memory usage in mb
     """
-    import psutil
     import os
+
+    import psutil
     process = psutil.Process(os.getpid())
     mem = process.memory_info().rss / (1024. * 1024.)
     return mem
@@ -624,7 +623,7 @@ def RBE2euler(Rbe):
 
 def pg_rotation2H(R):
     """ Convert rotation matrix to homogenous transform matrix """
-    X = np.array(np.eye((R.shape[0] + 1)))
+    X = np.array(np.eye(R.shape[0] + 1))
     X[0:-1, 0:-1] = R
     return X
 
@@ -1547,9 +1546,7 @@ def deprecation(message):
 # %%
 try:
     import PIL
-    from PIL import ImageFont
-    from PIL import Image
-    from PIL import ImageDraw
+    from PIL import Image, ImageDraw, ImageFont
 
     def writeTxt(im, txt, pos=(10, 10), fontsize=25, color=(0, 0, 0), fonttype=None):
         """ Write text on image using PIL """