def prepare_cos_fit_dict(data_dict, keys_in=None, **params):
fit_dicts = OrderedDict()
data_to_proc_dict = hlp_mod.get_data_to_process(data_dict, keys_in)
cp, sp, mospm, mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['cp', 'sp', 'mospm', 'mobjn'], **params)
indep_var_array = hlp_mod.get_param('indep_var_array',
data_dict,
raise_error=False,
**params)
if indep_var_array is None:
indep_var_array = sp[0][mospm[mobjn][0]][0]
plot_params = hlp_mod.get_param('plot_params',
data_dict,
default_value={},
**params)
if 'setlabel' not in plot_params:
plot_params['setlabel'] = 'CosFit'
params_to_print = hlp_mod.get_param('params_to_print',
data_dict,
default_value=None,
**params)
fit_name = hlp_mod.get_param('fit_name',
data_dict,
raise_error=False,
**params)
for keyi, data in data_to_proc_dict.items():
data_fit = hlp_mod.get_msmt_data(data, cp, mobjn)
cos_mod = lmfit.Model(fit_mods.CosFunc)
guess_pars = fit_mods.Cos_guess(model=cos_mod,
t=indep_var_array,
data=data_fit)
guess_pars['amplitude'].vary = True
guess_pars['amplitude'].min = -10
guess_pars['offset'].vary = True
guess_pars['frequency'].vary = True
guess_pars['phase'].vary = True
fit_name_to_set = fit_name
if fit_name_to_set is None:
fit_name_to_set = 'CosFit'
fit_name_to_set += keyi
fit_dicts[fit_name_to_set] = {
'fit_fn': fit_mods.CosFunc,
'fit_xvals': {
't': indep_var_array
},
'fit_yvals': {
'data': data_fit
},
'guess_pars': guess_pars,
'params_to_print': params_to_print,
**plot_params
}
hlp_mod.add_param('fit_dicts',
fit_dicts,
data_dict,
add_param_method='update')
def analyze_ramsey_fit_results(data_dict, keys_in, **params):
# Get from the hdf5 file any parameters specified in
# params_dict and numeric_params.
mobjn = hlp_mod.get_measurement_properties(data_dict,
props_to_extract=['mobjn'],
**params)
params_dict = {}
s = 'Instrument settings.' + mobjn
for trans_name in ['ge', 'ef']:
params_dict[f'{mobjn}.{trans_name}_freq'] = s + f'.{trans_name}_freq'
hlp_mod.get_params_from_hdf_file(data_dict,
params_dict=params_dict,
numeric_params=list(params_dict),
**params)
fit_names = hlp_mod.get_param('fit_names', params, raise_error=True)
artificial_detuning_dict = hlp_mod.get_param('artificial_detuning_dict',
data_dict,
raise_error=True,
**params)
fit_dicts = hlp_mod.get_param('fit_dicts', data_dict, raise_error=True)
for keyi in keys_in:
trans_name = 'ef' if 'f' in keyi else 'ge'
old_qb_freq = hlp_mod.get_param(f'{mobjn}.{trans_name}_freq',
data_dict)
if old_qb_freq != old_qb_freq:
old_qb_freq = 0
hlp_mod.add_param(f'{mobjn}.old_freq',
old_qb_freq,
data_dict,
add_param_method='replace')
for fit_name in fit_names:
key = fit_name + keyi
fit_res = fit_dicts[key]['fit_res']
hlp_mod.add_param(f'{mobjn}.new_freq ' + fit_name,
old_qb_freq + artificial_detuning_dict[mobjn] -
fit_res.best_values['frequency'],
data_dict,
add_param_method='replace')
hlp_mod.add_param(f'{mobjn}.new_freq ' + fit_name + '_stderr',
fit_res.params['frequency'].stderr,
data_dict,
add_param_method='replace')
hlp_mod.add_param(f'{mobjn}.T2_star ' + fit_name,
fit_res.best_values['tau'],
data_dict,
add_param_method='replace')
hlp_mod.add_param(f'{mobjn}.T2_star ' + fit_name + '_stderr',
fit_res.params['tau'].stderr,
data_dict,
add_param_method='replace')
def dump_fit_results(self, entry_point):
"""
Saves the fit results from data_dict['fit_dicts']
:param entry_point: HDF5 file object to save to or a group within
this file
"""
try:
group = entry_point.create_group('Fit Results')
except ValueError:
# If the analysis group already exists.
group = entry_point['Fit Results']
# Iterate over all the fit result dicts as not to overwrite
# old/other analysis
fit_dicts = hlp_mod.get_param('fit_dicts', self.data_dict)
for fr_key, fit_dict in fit_dicts.items():
fit_res = fit_dict['fit_res']
try:
fr_group = group.create_group(fr_key)
except ValueError:
# If the analysis sub group already exists
# (each fr_key should be unique)
# Delete the old group and create a new group
# (overwrite).
del group[fr_key]
fr_group = group.create_group(fr_key)
d = _convert_dict_rec(fit_res)
h5d.write_dict_to_hdf5(d, entry_point=fr_group)
def __init__(self, data_dict, savedir=None, save_processed_data=True,
save_figures=True, filename=None, file_suffix=None,
extension='hdf5', filter_keys=None, add_timestamp=False, **save_figs_params):
opt = np.get_printoptions()
np.set_printoptions(threshold=sys.maxsize)
try:
self.data_dict = data_dict
if filter_keys is None:
filter_keys = []
self.filter_keys = filter_keys + ['fit_dicts', 'plot_dicts', 'axes',
'figures', 'data_files']
if savedir is None:
savedir = hlp_mod.get_param('folders', data_dict)
if savedir is None:
savedir = hlp_mod.get_param(
'timestamps', data_dict, raise_error=True,
error_message='Either folders or timestamps must be '
'in data_dict if save_dir is not '
'specified.')
savedir = a_tools.get_folder(savedir[-1])
else:
savedir = savedir[-1]
self.savedir = savedir
if file_suffix is None:
file_suffix = 'AnalysisResults'
if filename is not None:
filename = filename + f'.{extension}'
else:
filename = self.savedir.split('\\')[-1] + f'_{file_suffix}.{extension}'
if add_timestamp:
filename = '{:%Y%m%d_%H%M%S}--{}'.format(
datetime.datetime.now(), filename)
self.filepath = self.savedir + '\\' + filename
if save_processed_data:
self.save_data_dict()
if save_figures and hlp_mod.get_param('figures', self.data_dict) \
is not None:
self.save_figures(**save_figs_params)
np.set_printoptions(**opt)
except Exception:
np.set_printoptions(**opt)
log.warning("Unhandled error during saving!")
log.warning(traceback.format_exc())
def analyze_rabi_fit_results(data_dict, keys_in, **params):
sp, mospm, mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['sp', 'mospm', 'mobjn'], **params)
physical_swpts = sp[0][mospm[mobjn][0]][0]
fit_dicts = hlp_mod.get_param('fit_dicts', data_dict, raise_error=True)
for keyi in keys_in:
fit_res = fit_dicts['rabi_fit' + keyi]['fit_res']
rabi_amps_dict = extract_rabi_amplitudes(fit_res=fit_res,
sweep_points=physical_swpts)
for k, v in rabi_amps_dict.items():
hlp_mod.add_param(f'{mobjn}.{k}', v, data_dict,
add_param_method='replace')
def prepare_ramsey_fitting(data_dict, keys_in, **params):
fit_names = hlp_mod.get_param('fit_names', params, raise_error=True)
sp, mospm, mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['sp', 'mospm', 'mobjn'], **params)
physical_swpts = sp[0][mospm[mobjn][0]][0]
for i, fit_name in enumerate(fit_names):
fit_mod.prepare_expdamposc_fit_dict(
data_dict,
keys_in=keys_in,
meas_obj_names=mobjn,
fit_name=fit_name,
indep_var_array=physical_swpts,
guess_params={'n': i + 1},
plot_params={
'color': 'r' if i == 0 else 'C4',
'setlabel': 'expFit' if i == 0 else 'gaussFit'
})
def ramsey_analysis(data_dict, keys_in, **params):
data_to_proc_dict = hlp_mod.get_data_to_process(data_dict, keys_in)
keys_in = list(data_to_proc_dict)
prep_fit_dicts = params.pop('prep_fit_dicts', True)
do_fitting = params.pop('do_fitting', True)
prepare_plotting = params.pop('prepare_plotting', True)
do_plotting = params.pop('do_plotting', True)
# prepare fitting
if prep_fit_dicts:
fit_gaussian_decay = hlp_mod.get_param('fit_gaussian_decay',
data_dict,
default_value=True,
**params)
if fit_gaussian_decay:
fit_names = ['exp_decay', 'gauss_decay']
else:
fit_names = ['exp_decay']
params.update({'fit_names': fit_names})
prepare_ramsey_fitting(data_dict, keys_in, **params)
if do_fitting:
getattr(fit_mod, 'run_fitting')(data_dict,
keys_in=list(data_dict['fit_dicts']),
**params)
# calculate new qubit frequecy, extract T2 star
analyze_ramsey_fit_results(data_dict, keys_in, **params)
# prepare plots
if prepare_plotting:
prepare_ramsey_plots(data_dict, data_to_proc_dict, **params)
if do_plotting:
getattr(plot_mod, 'plot')(data_dict,
keys_in=list(data_dict['plot_dicts']),
**params)
def get_rabi_textbox_properties(data_dict, textstr='',
transition='ge', **params):
mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['mobjn'], **params)
# Get from the hdf5 file any parameters specified in
# params_dict and numeric_params.
params_dict = {}
s = 'Instrument settings.' + mobjn
params_dict[f'{mobjn}.{transition}_amp180'] = \
s + f'.{transition}_amp180'
params_dict[f'{mobjn}.{transition}_amp90scale'] = \
s + f'.{transition}_amp90_scale'
hlp_mod.get_params_from_hdf_file(data_dict, params_dict=params_dict,
numeric_params=list(params_dict), **params)
# create textstring
old_pipulse_val = hlp_mod.get_param(f'{mobjn}.{transition}_amp180',
data_dict, default_value=0.0)
# if old_pipulse_val != old_pipulse_val:
# old_pipulse_val = 0
old_pihalfpulse_val = hlp_mod.get_param(f'{mobjn}.{transition}_amp90scale',
data_dict, default_value=0.0)
# if old_pihalfpulse_val != old_pihalfpulse_val:
# old_pihalfpulse_val = 0
old_pihalfpulse_val *= old_pipulse_val
textstr += (' $\pi-Amp$:\n {:.3f} V'.format(
hlp_mod.get_param(f'{mobjn}.piPulse_value', data_dict)) +
'$\pm$ {:.3f} V '.format(
hlp_mod.get_param(f'{mobjn}.piPulse_stderr', data_dict)) +
'\n$\pi/2-Amp$:\n {:.3f} V '.format(
hlp_mod.get_param(f'{mobjn}.piHalfPulse_value', data_dict)) +
' $\pm$ {:.3f} V '.format(
hlp_mod.get_param(f'{mobjn}.piHalfPulse_stderr', data_dict)) +
'\n $\pi-Amp_{old}$ = ' + '{:.3f} V '.format(
old_pipulse_val) +
'\n$\pi/2-Amp_{old}$ = ' + '{:.3f} V '.format(
old_pihalfpulse_val))
hp = -0.135
vp = -0.3
return textstr, hp, vp
def prepare_rabi_plots(data_dict, data_to_proc_dict, **params):
cp, sp, mospm, mobjn = \
hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['cp', 'sp', 'mospm', 'mobjn'],
**params)
physical_swpts = sp[0][mospm[mobjn][0]][0]
# check whether active reset was used
reset_reps = hlp_mod.get_reset_reps_from_data_dict(data_dict)
# prepare raw data plot
if reset_reps != 0:
swpts = deepcopy(physical_swpts)
swpts = np.concatenate([
swpts, hlp_mod.get_cal_sweep_points(
physical_swpts, cp, mobjn)])
swpts = np.repeat(swpts, reset_reps+1)
swpts = np.arange(len(swpts))
plot_mod.prepare_1d_raw_data_plot_dicts(
data_dict, xvals=swpts, **params)
filtered_raw_keys = [k for k in data_dict.keys() if 'filter' in k]
if len(filtered_raw_keys) > 0:
plot_mod.prepare_1d_raw_data_plot_dicts(
data_dict=data_dict, keys_in=filtered_raw_keys,
figure_name='raw_data_filtered', **params)
else:
plot_mod.prepare_1d_raw_data_plot_dicts(data_dict, **params)
plot_dicts = OrderedDict()
# the prepare plot dict functions below also iterate over data_to_proc_dict,
# however the prepare functions add all the data corresponding to keys_in
# to the same figure.
# Here we want a figure for each keyi
for keyi, data in data_to_proc_dict.items():
figure_name = 'Rabi_' + keyi
sp_name = mospm[mobjn][0]
# plot data
plot_mod.prepare_1d_plot_dicts(data_dict=data_dict, keys_in=[keyi],
figure_name=figure_name,
sp_name=sp_name, do_plotting=False,
**params)
if len(cp.states) != 0:
# plot cal states
plot_mod.prepare_cal_states_plot_dicts(data_dict=data_dict,
keys_in=[keyi],
figure_name=figure_name,
sp_name=sp_name,
do_plotting=False,
**params)
if 'fit_dicts' in data_dict:
# plot fits
fit_dicts = data_dict['fit_dicts']
fit_name = 'rabi_fit' + keyi
textstr = ''
plot_mod.prepare_fit_plot_dicts(data_dict=data_dict,
figure_name=figure_name,
fit_names=[fit_name],
do_plotting=False, **params)
fit_res = fit_dicts[fit_name]['fit_res']
piPulse_amp = hlp_mod.get_param(f'{mobjn}.piPulse_value', data_dict,
default_value=0.0)
# pi-pulse marker
plot_dicts['piamp_marker_' + keyi] = {
'fig_id': figure_name,
'plotfn': 'plot_line',
'xvals': np.array([piPulse_amp]),
'yvals': np.array([fit_res.model.func(piPulse_amp,
**fit_res.best_values)]),
'setlabel': '$\pi$ amp',
'color': 'r',
'marker': 'o',
'line_kws': {'markersize': plot_mod.get_default_plot_params(
set_params=False, return_full_rc_params=True).get(
'lines.markersize', 2) + 2},
'linestyle': '',
'legend_ncol': 2,
'legend_bbox_to_anchor': (1.02, -0.2),
'do_legend': True}
# pi-pulse dashed line
plot_dicts['piamp_hline_' + keyi] = {
'fig_id': figure_name,
'plotfn': 'plot_hlines',
'y': np.array([fit_res.model.func(piPulse_amp,
**fit_res.best_values)]),
'xmin': physical_swpts[0],
'xmax': hlp_mod.get_cal_sweep_points(physical_swpts,
cp, mobjn)[-1],
'colors': 'gray'}
piHalfPulse_amp = hlp_mod.get_param(f'{mobjn}.piHalfPulse_value',
data_dict, default_value=0.0)
# piHalf-pulse marker
plot_dicts['pihalfamp_marker_' + keyi] = {
'fig_id': figure_name,
'plotfn': 'plot_line',
'xvals': np.array([piHalfPulse_amp]),
'yvals': np.array([fit_res.model.func(piHalfPulse_amp,
**fit_res.best_values)]),
'setlabel': '$\pi /2$ amp',
'color': 'm',
'marker': 'o',
'line_kws': {'markersize': plot_mod.get_default_plot_params(
set_params=False, return_full_rc_params=True).get(
'lines.markersize', 2) + 2},
'linestyle': '',
'do_legend': True,
'legend_bbox_to_anchor': (1.02, -0.2),#'right',
'legend_ncol': 2}
# piHalf-pulse dashed line
plot_dicts['pihalfamp_hline_' + keyi] = {
'fig_id': figure_name,
'plotfn': 'plot_hlines',
'y': np.array([fit_res.model.func(piHalfPulse_amp,
**fit_res.best_values)]),
'xmin': physical_swpts[0],
'xmax': hlp_mod.get_cal_sweep_points(physical_swpts,
cp, mobjn)[-1],
'colors': 'gray'}
# plot textbox
textstr, _, _ = get_rabi_textbox_properties(
data_dict, textstr, transition='ef' if 'f' in keyi else 'ge',
**params)
plot_dicts['text_msg_' + keyi] = {
'fig_id': figure_name,
'ypos': -0.15,
'xpos': -0.13,
'horizontalalignment': 'left',
'verticalalignment': 'top',
'plotfn': 'plot_text',
'text_string': textstr}
hlp_mod.add_param('plot_dicts', plot_dicts, data_dict,
add_param_method='update')
def prepare_rbleakage_fit_dict(data_dict, keys_in=None, **params):
"""
:param data_dict: OrderedDict containing data to be processed and where
processed data is to be stored
:param keys_in: list of key names or dictionary keys paths in
data_dict for the data to be processed
:param params: keyword args
do_fitting (bool, default: False): whether to perform the fit
guess_params (dict, default: dict()): dict of guess pars for fit
:return: adds fit_dicts to data_dict
"""
fit_dicts = OrderedDict()
data_to_proc_dict = hlp_mod.get_data_to_process(data_dict, keys_in)
cp, sp, mospm, mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['cp', 'sp', 'mospm', 'mobjn'], **params)
indep_var_array = hlp_mod.get_param('indep_var_array',
data_dict,
raise_error=False,
**params)
if indep_var_array is None:
indep_var_array = sp[0][mospm[mobjn][0]][0]
plot_params = hlp_mod.get_param('plot_params',
data_dict,
default_value={},
**params)
if 'setlabel' not in plot_params:
plot_params['setlabel'] = 'RBLeakageFit'
params_to_print = hlp_mod.get_param('params_to_print',
data_dict,
default_value=None,
**params)
fit_name = hlp_mod.get_param('fit_name',
data_dict,
raise_error=False,
**params)
for keyi, data in data_to_proc_dict.items():
data_fit = hlp_mod.get_msmt_data(data, cp, mobjn)
rbleak_mod = lmfit.Model(fit_mods.RandomizedBenchmarkingLeakage)
guess_pars = rbleak_mod.make_params(pu=0.01, pd=0.05, p0=0)
guess_params_new = hlp_mod.get_param('guess_params',
data_dict,
default_value=dict(),
raise_error=False,
**params)
update_fit_guess_pars(guess_params_new, guess_pars)
fit_name_to_set = fit_name
if fit_name_to_set is None:
fit_name_to_set = 'rbleak_fit'
fit_name_to_set += keyi
fit_dicts[fit_name_to_set] = {
'fit_fn': fit_mods.RandomizedBenchmarkingLeakage,
'fit_xvals': {
'numCliff': indep_var_array
},
'fit_yvals': {
'data': data_fit
},
'guess_pars': guess_pars,
'params_to_print': params_to_print,
**plot_params
}
hlp_mod.add_param('fit_dicts',
fit_dicts,
data_dict,
add_param_method='update')
if params.get('do_fitting', False):
run_fitting(data_dict, keys_in=list(fit_dicts), **params)
def save_figures(self, **params):
"""
Saves figures from self.data_dict['figures'].
:param params: keyword arguments
keys_in (list; default 'auto'): list of keys in data_dict['figures']
denoting which figures to save. If "auto", all figures will be
saved.
fmt (str; default: 'png'): figures format
dpi (int; default: 300): figures dpi
tag_tstamp(bool; default: True): whether to add the last timestamp
in data_dict['timestamps'] to the figure title
savebase (str; default: None): base of the figure name
presentation_mode (bool; default: False): whether to save and 'svg
file in addition to the figure
"""
keys_in = params.get('keys_in', 'auto')
fmt = params.get('fmt', 'png')
dpi = params.get('dpi', 300)
tag_tstamp = params.get('tag_tstamp', True)
savebase = params.get('savebase', None)
if savebase is None:
savebase = ''
if tag_tstamp:
timestamps = hlp_mod.get_param(
'timestamps', self.data_dict, raise_error=True,
error_message='"tag_tstamp" == True but "timestamps" not found '
'in data_dict.')
tstag = '_' + timestamps[-1]
else:
tstag = ''
# get figures from data_dict
figs = hlp_mod.get_param('figures', self.data_dict, raise_error=True)
if isinstance(figs, list):
figs_dicts = OrderedDict()
for fig_dict in figs:
figs_dicts.update(fig_dict)
else:
figs_dicts = figs
if keys_in == 'auto' or keys_in is None:
keys_in = list(figs_dicts)
for key in keys_in:
if params.get('presentation_mode', False):
savename = os.path.join(self.savedir, savebase + key + tstag +
'presentation' + '.' + fmt)
figs_dicts[key].savefig(savename, bbox_inches='tight',
format=fmt, dpi=dpi)
savename = os.path.join(self.savedir, savebase + key + tstag +
'presentation' + '.svg')
figs_dicts[key].savefig(savename, bbox_inches='tight',
format='svg')
else:
savename = os.path.join(self.savedir, savebase + key + tstag
+ '.' + fmt)
figs_dicts[key].savefig(savename, bbox_inches='tight',
format=fmt, dpi=dpi)
if params.get('close_figs', True):
plt.close(figs_dicts[key])
def extract_data_hdf(data_dict=None,
timestamps=None,
params_dict=OrderedDict(),
numeric_params=None,
append_data=False,
replace_data=False,
**params):
"""
Extracts the data specified in params_dict and pumeric_params
from each timestamp in timestamps and stores it into data_dict
Args:
data_dict (dict): place where extracted data will be stored, under the
keys of params_dict
timestamps (list): list of timestamps from where to extract data. If
not specified, they will be taken from data_dict, and, if not found
there, from get_timestamps
params_dict (dict): if the form {storing_key: path_to_data}, where
storing_key will be created in data_dict for storing the data
indicated by path_to_data as a parameter name or a
path + parameter name inside an HDF file.
numeric_params (list or tuple): passed to get_params_from_hdf_file, see
docstring there.
append_data (bool): passed to add_measured_data_hdf, see docstring there
replace_data (bool): passed to add_measured_data_hdf, see docstring
there
Keyword args (**params)
passed to get_timestamps and add_measured_data_dict
Returns
data_dict containing the extracted data
"""
if data_dict is None:
data_dict = OrderedDict()
# Add flag that this is an analysis_v3 data_dict. This is used by the
# Saving class.
data_dict['is_data_dict'] = True
if timestamps is None:
timestamps = hlp_mod.get_param('timestamps', data_dict)
if timestamps is None:
get_timestamps(data_dict, **params)
timestamps = hlp_mod.get_param('timestamps', data_dict)
if isinstance(timestamps, str):
timestamps = [timestamps]
hlp_mod.add_param('timestamps',
timestamps,
data_dict,
add_param_method='replace')
data_dict['folders'] = []
for i, timestamp in enumerate(timestamps):
folder = a_tools.get_folder(timestamp)
data_dict['folders'] += [folder]
# extract the data array and add it as data_dict['measured_data'].
add_measured_data_hdf(data_dict, folder, append_data, replace_data)
# extract exp_metadata separately, then call
# combine_metadata_list, then extract all other parameters.
# Otherwise, data_dict['exp_metadata'] is a list and it is unclear
# from where to extract parameters.
hlp_mod.get_params_from_hdf_file(
data_dict,
params_dict={
'exp_metadata': 'Experimental Data.Experimental Metadata'
},
folder=folder,
add_param_method='append')
if len(timestamps) > 1:
# If data_dict['exp_metadata'] is a list, then the following functions
# defines exp_metadata in data_dict as the combined version of the list
# of metadata dicts extracted above for each timestamp
combine_metadata_list(data_dict, **params)
# call get_params_from_hdf_file which gets values for params
# in params_dict and adds them to the dictionary data_dict
params_dict_temp = params_dict
params_dict = OrderedDict({
'exp_metadata.sweep_parameter_names':
'sweep_parameter_names',
'exp_metadata.sweep_parameter_units':
'sweep_parameter_units',
'exp_metadata.value_names':
'value_names',
'exp_metadata.value_units':
'value_units',
'exp_metadata.measurementstrings':
'measurementstring'
})
params_dict.update(params_dict_temp)
hlp_mod.get_params_from_hdf_file(data_dict,
params_dict=params_dict,
numeric_params=numeric_params,
folder=data_dict['folders'][-1],
add_param_method=params.get(
'add_param_method', 'replace'))
# add entries in data_dict for each readout channel and its corresponding
# data array.
add_measured_data_dict(data_dict, **params)
return data_dict
def prepare_joint_residzz_fit_dict(data_dict, keys_in=None, **params):
"""
This function does a joint fit to Ramsey data without and with the other
qubit in the |e> state.
keys_in should have two entries corresponding to two 1d arrays for the
data mentioned above, IN THAT ORDER.
:param data_dict: OrderedDict containing data to be processed and where
processed data is to be stored
:param keys_in: list of key names or dictionary keys paths in
data_dict for the data to be processed
:param params: keyword args
do_fitting (bool, default: False): whether to perform the fit
guess_params (dict, default: dict()): dict of guess pars for fit
:return: adds fit_dicts to data_dict
"""
if len(keys_in) != 2:
raise ValueError('keys_in must have two entries.')
fit_dicts = OrderedDict()
data_to_proc_dict = hlp_mod.get_data_to_process(data_dict, keys_in)
cp, sp, mospm, mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['cp', 'sp', 'mospm', 'mobjn'], **params)
indep_var_array = hlp_mod.get_param('indep_var_array',
data_dict,
raise_error=False,
**params)
if indep_var_array is None:
indep_var_array = sp[0][mospm[mobjn][0]][0]
plot_params = hlp_mod.get_param('plot_params',
data_dict,
default_value={},
**params)
if 'setlabel' not in plot_params:
plot_params['setlabel'] = 'JointResidZZFit'
params_to_print = hlp_mod.get_param('params_to_print',
data_dict,
default_value=None,
**params)
data_wo_pulse = hlp_mod.get_msmt_data(
list(data_to_proc_dict.values())[0], cp, mobjn)
data_w_pulse = hlp_mod.get_msmt_data(
list(data_to_proc_dict.values())[1], cp, mobjn)
residzz_mod = lmfit.Model(fit_mods.ResidZZFuncJoint)
guess_pars = fit_mods.exp_damp_osc_guess(model=residzz_mod,
t=indep_var_array,
data=data_wo_pulse)
guess_pars['alpha'].value = -50e3
guess_pars['alpha'].max = 0
# guess_pars['x'].value = 12e-6*guess_pars['alpha'].value
guess_pars['t11'].value = 12e-6
guess_pars['t11'].min = 0
guess_pars['offset'].value = np.mean(data_wo_pulse)
guess_pars['amplitude1'].value = guess_pars['amplitude'].value
# guess_pars['phase1'].value = guess_pars['phase'].value + np.pi/2
# guess_pars['amplitude'].min = -1
# guess_pars['amplitude1'].min = -1
# guess_pars['amplitude'].max = 1
# guess_pars['amplitude1'].max = 1
for par in guess_pars:
guess_pars[par].vary = True
guess_pars['offset'].vary = False
guess_params_new = hlp_mod.get_param('guess_params',
data_dict,
default_value=dict(),
raise_error=False,
**params)
update_fit_guess_pars(guess_params_new, guess_pars)
fit_name = hlp_mod.get_param('fit_name',
data_dict,
raise_error=False,
**params)
fit_name_to_set = fit_name
if fit_name_to_set is None:
fit_name_to_set = 'residzz_fit'
fit_name_to_set += ','.join(mobjn)
fit_dicts[fit_name] = {
'fit_fn': fit_mods.ResidZZFuncJoint,
'fit_xvals': {
't': indep_var_array
},
'fit_yvals': {
'data': (data_wo_pulse, data_w_pulse)
},
'guess_pars': guess_pars,
'params_to_print': params_to_print,
**plot_params
}
hlp_mod.add_param('fit_dicts',
fit_dicts,
data_dict,
add_param_method='update')
if params.get('do_fitting', False):
run_fitting(data_dict, keys_in=list(fit_dicts), **params)
def prepare_ramsey_plots(data_dict, data_to_proc_dict, **params):
cp, sp, mospm, mobjn = \
hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['cp', 'sp', 'mospm', 'mobjn'],
**params)
physical_swpts = sp[0][mospm[mobjn][0]][0]
# check whether active reset was used
reset_reps = hlp_mod.get_reset_reps_from_data_dict(data_dict)
# prepare raw data plot
if reset_reps != 0:
swpts = deepcopy(physical_swpts)
swpts = np.concatenate(
[swpts,
hlp_mod.get_cal_sweep_points(physical_swpts, cp, mobjn)])
swpts = np.repeat(swpts, reset_reps + 1)
swpts = np.arange(len(swpts))
plot_mod.prepare_1d_raw_data_plot_dicts(data_dict,
xvals=swpts,
**params)
filtered_raw_keys = [k for k in data_dict.keys() if 'filter' in k]
if len(filtered_raw_keys) > 0:
plot_mod.prepare_1d_raw_data_plot_dicts(
data_dict=data_dict,
keys_in=filtered_raw_keys,
figure_name='raw_data_filtered',
**params)
else:
plot_mod.prepare_1d_raw_data_plot_dicts(data_dict, **params)
fit_names = hlp_mod.pop_param('fit_names', params, raise_error=True)
artificial_detuning_dict = hlp_mod.get_param('artificial_detuning_dict',
data_dict,
raise_error=True,
**params)
plot_dicts = OrderedDict()
# the prepare plot dict functions below also iterate over data_to_proc_dict,
# however the prepare functions add all the data corresponding to keys_in
# to the same figure.
# Here we want a figure for each keyi
for keyi, data in data_to_proc_dict.items():
figure_name = 'Ramsey_' + keyi
sp_name = mospm[mobjn][0]
# plot data
plot_mod.prepare_1d_plot_dicts(data_dict=data_dict,
keys_in=[keyi],
figure_name=figure_name,
sp_name=sp_name,
do_plotting=False,
**params)
if len(cp.states) != 0:
# plot cal states
plot_mod.prepare_cal_states_plot_dicts(data_dict=data_dict,
keys_in=[keyi],
figure_name=figure_name,
sp_name=sp_name,
do_plotting=False,
**params)
if 'fit_dicts' in data_dict:
textstr = ''
T2_star_str = ''
for i, fit_name in enumerate(fit_names):
plot_mod.prepare_fit_plot_dicts(data_dict=data_dict,
figure_name=figure_name,
fit_names=[fit_name + keyi],
plot_params={
'legend_bbox_to_anchor':
(1, -0.55),
'legend_ncol':
1
},
do_plotting=False,
**params)
fit_res = data_dict['fit_dicts'][fit_name + keyi]['fit_res']
if i != 0:
textstr += '\n'
textstr += \
('$f_{{qubit \_ new \_ {{{key}}} }}$ = '.format(
key=('exp' if i == 0 else 'gauss')) +
'{:.6f} GHz '.format(hlp_mod.get_param(
f'{mobjn}.new_freq '+fit_name, data_dict)*1e-9) +
'$\pm$ {:.2E} GHz '.format(hlp_mod.get_param(
f'{mobjn}.new_freq ' + fit_name + '_stderr',
data_dict)*1e-9))
T2_star_str += \
('\n$T_{{2,{{{key}}} }}^\star$ = '.format(
key=('exp' if i == 0 else 'gauss')) +
'{:.2f} $\mu$s'.format(
fit_res.params['tau'].value*1e6) +
' $\pm$ {:.2f} $\mu$s'.format(
fit_res.params['tau'].stderr*1e6))
fit_name = 'exp_decay'
fit_res = data_dict['fit_dicts'][fit_name + keyi]['fit_res']
old_qb_freq = hlp_mod.get_param(f'{mobjn}.old_freq', data_dict)
textstr += '\n$f_{qubit \_ old}$ = ' + '{:.6f} GHz '.format(
old_qb_freq * 1e-9)
textstr += ('\n$\Delta f$ = {:.4f} MHz '.format(
(hlp_mod.get_param(f'{mobjn}.new_freq ' + fit_name, data_dict)
- old_qb_freq) * 1e-6) + '$\pm$ {:.2E} MHz'.format(
fit_res.params['frequency'].stderr * 1e-6) +
'\n$f_{Ramsey}$ = ' +
'{:.4f} MHz $\pm$ {:.2E} MHz'.format(
fit_res.params['frequency'].value * 1e-6,
fit_res.params['frequency'].stderr * 1e-6))
textstr += T2_star_str
textstr += '\nartificial detuning = {:.2f} MHz'.format(
artificial_detuning_dict[mobjn] * 1e-6)
plot_dicts['text_msg_' + keyi] = {
'fig_id': figure_name,
'ypos': -0.3,
'xpos': -0.125,
'horizontalalignment': 'left',
'verticalalignment': 'top',
'plotfn': 'plot_text',
'text_string': textstr
}
plot_dicts['half_hline_' + keyi] = {
'fig_id': figure_name,
'plotfn': 'plot_hlines',
'y': 0.5,
'xmin': physical_swpts[0],
'xmax': hlp_mod.get_cal_sweep_points(physical_swpts, cp,
mobjn)[-1],
'colors': 'gray'
}
hlp_mod.add_param('plot_dicts',
plot_dicts,
data_dict,
add_param_method='update')
def add_measured_data_hdf(data_dict,
folder=None,
append_data=False,
replace_data=False,
**params):
"""
Extracts the dataset from the "Experimental Data" data of an HDF file and
stores it in data_dict under "measured_data".
Args:
data_dict (dict): extracted dataset will be stored here under the key
"measured_data"
folder (str): full path to an hdf file
append_data (bool): if True, and "measured_data" exists in data_dict,
the new dataset will be appended
replace_data (bool): if True, and "measured_data" exists in data_dict,
it will be replaced by the new dataset
Keyword args (**params)
passed to helper_functions.py/add_param, see docstring there
Returns
data_dict containing the extracted dataset
"""
if folder is None:
folder = hlp_mod.get_param('folders',
data_dict,
raise_error=True,
**params)
if len(folder) > 0:
folder = folder[-1]
h5mode = hlp_mod.get_param('h5mode',
data_dict,
default_value='r+',
**params)
dtype = hlp_mod.get_param('meas_data_dtype',
data_dict,
default_value=None,
**params)
if dtype is not None:
log.warning(f'Setting Experimental data type: {dtype}')
h5filepath = a_tools.measurement_filename(folder)
data_file = h5py.File(h5filepath, h5mode)
meas_data_array = np.array(data_file['Experimental Data']['Data'],
dtype=dtype).T
if 'measured_data' in data_dict:
if replace_data:
data_dict['measured_data'] = meas_data_array
data_dict['data_replaced'] = True
elif append_data:
if not isinstance(data_dict['measured_data'], list):
data_dict['measured_data'] = [data_dict['measured_data']]
data_dict['measured_data'] += [meas_data_array]
data_dict['data_appended'] = True
else:
raise ValueError(
'Both "append_data" and "replace_data" are False. '
'Unclear how to add "measured_data" to data_dict.')
else:
data_dict['measured_data'] = meas_data_array
return data_dict
def add_measured_data_dict(data_dict, **params):
"""
Adds to the data_dict the acquisition channels with the corresponding data
array taken from "measured_data," which must exist in data_dict.
Args:
data_dict (dict): the measured data dict will be stored here
Keyword args (**params)
passed to helper_functions.py/get_param, helper_functions.py/pop_param,
and helper_functions.py/add_param, see docstrings there
This function expects to find the following parameters:
- exp_metadata must exist in data_dict
- value_names must exist in exp_metadata
- meas_obj_value_names_map must exist in data_dict
Other possible keywargs
- TwoD (bool; default: False) whether the measurement had two
sweep dimensions
- compression_factor (int; default: 1) sequence compression factor
(see Sequence.compress_2D_sweep)
- percentage_done (int; default: 100) for interrupted measurements;
indicates percentage of the total data that was acquired
Returns
data_dict containing the following entries:
- acquisition channels (keys of the meas_obj_value_names_map) with
the corresponding raw data
- sweep points (if not already in data_dict)
"""
metadata = hlp_mod.get_param('exp_metadata', data_dict, raise_error=True)
TwoD = hlp_mod.get_param('TwoD', data_dict, default_value=False, **params)
compression_factor = hlp_mod.get_param('compression_factor',
data_dict,
default_value=1,
**params)
if 'measured_data' in data_dict and 'value_names' in metadata:
value_names = metadata['value_names']
rev_movnm = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['rev_movnm'])
if rev_movnm is not None:
data_key = lambda ro_ch, rev_movnm=rev_movnm: f'{rev_movnm[ro_ch]}.{ro_ch}'
else:
data_key = lambda ro_ch: ro_ch
[
hlp_mod.add_param(data_key(ro_ch), [], data_dict)
for ro_ch in value_names
]
measured_data = data_dict.pop('measured_data')
if not isinstance(measured_data, list):
measured_data = [measured_data]
for meas_data in measured_data:
data = meas_data[-len(value_names):]
if data.shape[0] != len(value_names):
raise ValueError(
'Shape mismatch between data and ro channels.')
mc_points = meas_data[:-len(value_names)]
hsp = np.unique(mc_points[0])
if mc_points.shape[0] > 1:
ssp, counts = np.unique(mc_points[1:], return_counts=True)
if counts[0] != len(hsp):
# ssro data
hsp = np.tile(hsp, counts[0] // len(hsp))
# if needed, decompress the data
# (assumes hsp and ssp are indices)
if compression_factor != 1:
hsp = hsp[:int(len(hsp) / compression_factor)]
ssp = np.arange(len(ssp) * compression_factor)
for i, ro_ch in enumerate(value_names):
if TwoD:
meas_data = np.reshape(data[i], (len(ssp), len(hsp))).T
else:
meas_data = data[i]
hlp_mod.add_param(data_key(ro_ch), [meas_data],
data_dict,
add_param_method='append')
for ro_ch in value_names:
data = hlp_mod.pop_param(data_key(ro_ch), data_dict)
if len(data) == 1:
hlp_mod.add_param(data_key(ro_ch), data[0], data_dict)
else:
hlp_mod.add_param(data_key(ro_ch), np.array(data), data_dict)
# check for and deal with interrupted measurements
perc_done = hlp_mod.get_param('percentage_done',
data_dict,
default_value=100,
**params)
if perc_done < 100 and mc_points.shape[0] > 1:
sp = hlp_mod.get_measurement_properties(data_dict,
props_to_extract=['sp'],
raise_error=False)
if len(sp): # above call returns [] if sp not found
sp_new = sp_mod.SweepPoints([sp.get_sweep_dimension(0)])
sp_new.add_sweep_dimension()
for param_name, props_tup in sp.get_sweep_dimension(1).items():
sp_new.add_sweep_parameter(param_name,
props_tup[0][:len(ssp)],
props_tup[1], props_tup[2])
hlp_mod.add_param('sweep_points', sp_new, data_dict, **params)
else:
log.warning('sweep_points not found. Cannot deal with '
'interrupted measurements.')
else:
raise ValueError('Either "measured_data" was not found in data_dict '
'or "value_names" was not found in metadata. '
'"measured_data" was not added.')
return data_dict
def prepare_residzz_fit_dict(data_dict, keys_in=None, **params):
"""
This function does a fit to Ramsey data with the other
qubit in the |e> state.
:param data_dict: OrderedDict containing data to be processed and where
processed data is to be stored
:param keys_in: list of key names or dictionary keys paths in
data_dict for the data to be processed
:param params: keyword args
do_fitting (bool, default: False): whether to perform the fit
guess_params (dict, default: dict()): dict of guess pars for fit
:return: adds fit_dicts to data_dict
"""
fit_dicts = OrderedDict()
data_to_proc_dict = hlp_mod.get_data_to_process(data_dict, keys_in)
cp, sp, mospm, mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['cp', 'sp', 'mospm', 'mobjn'], **params)
indep_var_array = hlp_mod.get_param('indep_var_array',
data_dict,
raise_error=False,
**params)
if indep_var_array is None:
indep_var_array = sp[0][mospm[mobjn][0]][0]
plot_params = hlp_mod.get_param('plot_params',
data_dict,
default_value={},
**params)
if 'setlabel' not in plot_params:
plot_params['setlabel'] = 'ResidZZFit'
params_to_print = hlp_mod.get_param('params_to_print',
data_dict,
default_value=None,
**params)
fit_name = hlp_mod.get_param('fit_name',
data_dict,
raise_error=False,
**params)
for keyi, data in data_to_proc_dict.items():
data_fit = hlp_mod.get_msmt_data(data, cp, mobjn)
residzz_mod = lmfit.Model(fit_mods.ResidZZFunc)
guess_pars = fit_mods.exp_damp_osc_guess(model=residzz_mod,
t=indep_var_array,
data=data_fit)
guess_pars['alpha'].value = -50e3
guess_pars['x'].value = 12e-6 * guess_pars['alpha'].value
guess_pars['offset'].value = np.mean(data_fit)
# guess_pars['amplitude'].min = -1
# guess_pars['amplitude'].max = 1
guess_params_new = hlp_mod.get_param('guess_params',
data_dict,
default_value=dict(),
raise_error=False,
**params)
update_fit_guess_pars(guess_params_new, guess_pars)
fit_name_to_set = fit_name
if fit_name_to_set is None:
fit_name_to_set = 'residzz_fit'
fit_name_to_set += keyi
fit_dicts[fit_name_to_set] = {
'fit_fn': fit_mods.ResidZZFunc,
'fit_xvals': {
't': indep_var_array
},
'fit_yvals': {
'data': data_fit
},
'guess_pars': guess_pars,
'params_to_print': params_to_print,
**plot_params
}
hlp_mod.add_param('fit_dicts',
fit_dicts,
data_dict,
add_param_method='update')
if params.get('do_fitting', False):
run_fitting(data_dict, keys_in=list(fit_dicts), **params)
def process_pipeline(data_dict,
processing_pipeline=None,
append_pipeline=False,
save_processed_data=True,
save_figures=True,
**params):
"""
Calls all the classes/functions found in processing_pipeline,
which is a list of dictionaries of the form:
[
{'node_name': function_name0, **node_params0},
{'node_name': function_name1, **node_params1},
]
All node functions must exist in the modules specified in the global vaiable
"search_modules" define at the top of this module, and will process the
data corresponding to the keys specified as "keys_in" in the **node_params
of each node.
Each node in the pipeline will put the processed data in the data_dict,
under the key(s)/dictionary key path(s) specified in 'keys_out' in the
the **node_params of each node.
"""
# Add flag that this is an analysis_v3 data_dict. This is used by the
# Saving class.
if 'is_data_dict' not in data_dict:
data_dict['is_data_dict'] = True
if processing_pipeline is None:
processing_pipeline = hlp_mod.get_param('processing_pipeline',
data_dict,
raise_error=True)
elif append_pipeline:
for node_params in processing_pipeline:
hlp_mod.add_param('processing_pipeline', [node_params],
data_dict,
append_value=True)
# Instantiate a ProcessingPipeline instance in case it is an ordinary list
processing_pipeline = ProcessingPipeline(processing_pipeline)
for node_params in processing_pipeline:
try:
node = None
for module in search_modules:
try:
node = getattr(module, node_params["node_name"])
break
except AttributeError:
continue
if node is None:
raise KeyError(f'Node function "{node_params["node_name"]}" '
f'not recognized')
node(data_dict=data_dict, **node_params)
except Exception:
log.warning(
f'Unhandled error during node {node_params["node_name"]}!')
log.warning(traceback.format_exc())
if save_figures and hlp_mod.get_param('figures', data_dict) is None:
log.warning('save_figures is True but there are no figures to save.')
save_figures = False
if save_processed_data or save_figures:
save_mod.Save(data_dict,
save_processed_data=save_processed_data,
save_figures=save_figures,
**params)
def prepare_expdamposc_fit_dict(data_dict, keys_in=None, **params):
"""
This function does a to Ramsey data
:param data_dict: OrderedDict containing data to be processed and where
processed data is to be stored
:param keys_in: list of key names or dictionary keys paths in
data_dict for the data to be processed
:param params: keyword args
do_fitting (bool, default: False): whether to perform the fit
guess_params (dict, default: dict()): dict of guess pars for fit
fit_name
indep_var_array
plot_params
params_to_print
:return: adds fit_dicts to data_dict
"""
fit_dicts = OrderedDict()
data_to_proc_dict = hlp_mod.get_data_to_process(data_dict, keys_in)
cp, sp, mospm, mobjn = hlp_mod.get_measurement_properties(
data_dict, props_to_extract=['cp', 'sp', 'mospm', 'mobjn'], **params)
indep_var_array = hlp_mod.get_param('indep_var_array',
data_dict,
raise_error=False,
**params)
if indep_var_array is None:
indep_var_array = sp[0][mospm[mobjn][0]][0]
plot_params = hlp_mod.get_param('plot_params',
data_dict,
default_value={},
**params)
if 'setlabel' not in plot_params:
plot_params['setlabel'] = 'ExpDampOscFit'
params_to_print = hlp_mod.get_param('params_to_print',
data_dict,
default_value=None,
**params)
fit_name = hlp_mod.get_param('fit_name',
data_dict,
raise_error=False,
**params)
for keyi, data in data_to_proc_dict.items():
data_fit = hlp_mod.get_msmt_data(data, cp, mobjn)
exp_damped_decay_mod = lmfit.Model(fit_mods.ExpDampOscFunc)
guess_pars = fit_mods.exp_damp_osc_guess(model=exp_damped_decay_mod,
data=data_fit,
t=indep_var_array,
n_guess=1)
guess_pars['amplitude'].vary = False
guess_pars['amplitude'].value = 0.5
guess_pars['frequency'].vary = True
guess_pars['tau'].vary = True
guess_pars['phase'].vary = True
guess_pars['n'].vary = False
guess_pars['oscillation_offset'].vary = False
guess_pars['exponential_offset'].vary = True
guess_params_new = hlp_mod.get_param('guess_params',
data_dict,
default_value=dict(),
raise_error=False,
**params)
update_fit_guess_pars(guess_params_new, guess_pars)
fit_name_to_set = fit_name
if fit_name_to_set is None:
fit_name_to_set = 'expdamposc_fit'
fit_name_to_set += keyi
fit_dicts[fit_name_to_set] = {
'fit_fn': fit_mods.ExpDampOscFunc,
'fit_xvals': {
't': indep_var_array
},
'fit_yvals': {
'data': data_fit
},
'guess_pars': guess_pars,
'params_to_print': params_to_print,
'plot_params': plot_params
}
hlp_mod.add_param('fit_dicts',
fit_dicts,
data_dict,
add_param_method='update')
if params.get('do_fitting', False):
run_fitting(data_dict, keys_in=list(fit_dicts), **params)
