/
workspaceplots.py
4363 lines (3667 loc) · 179 KB
/
workspaceplots.py
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"""
Classes corresponding to plots within a Workspace context.
"""
#***************************************************************************************************
# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
# in this software.
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE file in the root pyGSTi directory.
#***************************************************************************************************
import collections as _collections
import warnings as _warnings
import numpy as _np
import plotly
import plotly.graph_objs as go
import scipy as _scipy
from scipy.stats import chi2 as _chi2
from pygsti.objectivefns.objectivefns import ModelDatasetCircuitsStore as _ModelDatasetCircuitStore
from pygsti.report import colormaps as _colormaps
from pygsti.report import plothelpers as _ph
from pygsti.report.figure import ReportFigure
from pygsti.report.workspace import WorkspacePlot, NotApplicable
from pygsti import algorithms as _alg
from pygsti import baseobjs as _baseobjs
from pygsti.objectivefns import objectivefns as _objfns
from pygsti.circuits.circuit import Circuit as _Circuit
from pygsti.circuits.circuitstructure import PlaquetteGridCircuitStructure as _PlaquetteGridCircuitStructure, \
GermFiducialPairPlaquette as _GermFiducialPairPlaquette
from pygsti.circuits.circuitlist import CircuitList as _CircuitList
from pygsti.data import DataSet as _DataSet
#Plotly v3 changes heirarchy of graph objects
# Do this to avoid deprecation warning is plotly 3+
if int(plotly.__version__.split('.')[0]) >= 3: # Plotly 3+
go_x_axis = go.layout.XAxis
go_y_axis = go.layout.YAxis
go_margin = go.layout.Margin
go_annotation = go.layout.Annotation
else:
go_x_axis = go.XAxis
go_y_axis = go.YAxis
go_margin = go.Margin
go_annotation = go.Annotation
#DEBUG
#import time as _time #DEBUG TIMER
#from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
def _color_boxplot(plt_data, colormap, colorbar=False, box_label_size=0,
prec=0, hover_label_fn=None, hover_labels=None):
"""
Create a color box plot.
Creates a plot.ly heatmap figure composed of colored boxes and
possibly labels.
Parameters
----------
plt_data : numpy array
A 2D array containing the values to be plotted. None values will
show up as white.
colormap : Colormap
The colormap used to determine box color.
colorbar : bool, optional
Whether or not to show the color scale bar.
box_label_size : int, optional
If greater than 0, display static labels on each box with font
size equal to `box_label_size`.
prec : int or {'compact','compacthp'}, optional
Precision for box labels. Allowed values are:
'compact' = round to nearest whole number using at most 3 characters
'compacthp' = show as much precision as possible using at most 3 characters
int >= 0 = fixed precision given by int
int < 0 = number of significant figures given by -int
hover_label_fn : function, optional
A function with signature `f(z,i,j)` where `z ==plt_data[i,j]` which
computes the hover label for the each element of `plt_data`. Cannot
be used with `hover_labels`.
hover_labels : list of lists, optional
Strings specifying the hover labels for each element of `plt_data`.
E.g. `hover_labels[i,j]` is the string for the i-th row (y-value)
and j-th column (x-value) of the plot.
Returns
-------
plotly.Figure
"""
masked_data = _np.ma.array(plt_data, mask=_np.isnan(plt_data))
heatmapArgs = {'z': colormap.normalize(masked_data),
'colorscale': colormap.create_plotly_colorscale(),
'showscale': colorbar, 'hoverinfo': 'none',
'zmin': colormap.hmin, 'zmax': colormap.hmax}
#if xlabels is not None: heatmapArgs['x'] = xlabels
#if ylabels is not None: heatmapArgs['y'] = ylabels
annotations = []
if box_label_size:
# Write values on colored squares
for y in range(plt_data.shape[0]):
for x in range(plt_data.shape[1]):
if _np.isnan(plt_data[y, x]): continue
annotations.append(
dict(
text=_ph._eformat(plt_data[y, x], prec),
x=x, y=y,
xref='x1', yref='y1',
font=dict(size=box_label_size,
color=colormap.besttxtcolor(plt_data[y, x])),
showarrow=False)
)
if hover_label_fn:
assert(not hover_labels), "Cannot specify hover_label_fn and hover_labels!"
hover_labels = []
for y in range(plt_data.shape[0]):
hover_labels.append([hover_label_fn(plt_data[y, x], y, x)
for x in range(plt_data.shape[1])])
if hover_labels:
heatmapArgs['hoverinfo'] = 'text'
heatmapArgs['text'] = hover_labels
trace = go.Heatmap(**heatmapArgs)
#trace = dict(type='heatmapgl', **heatmapArgs)
data = [trace]
xaxis = go_x_axis(
showgrid=False,
zeroline=False,
showline=True,
ticks="",
showticklabels=True,
mirror=True,
linewidth=2,
range=[-0.5, plt_data.shape[1] - 0.5]
)
yaxis = go_y_axis(
showgrid=False,
zeroline=False,
showline=True,
ticks="",
showticklabels=True,
mirror=True,
linewidth=2,
range=[-0.5, plt_data.shape[0] - 0.5]
)
layout = go.Layout(
xaxis=xaxis,
yaxis=yaxis,
annotations=annotations
)
fig = go.Figure(data=data, layout=layout)
return ReportFigure(fig, colormap, plt_data, plt_data=plt_data)
def _nested_color_boxplot(plt_data_list_of_lists, colormap,
colorbar=False, box_label_size=0, prec=0,
hover_label_fn=None):
"""
Creates a "nested" color box plot.
Tiles the plaquettes given by `plt_data_list_of_lists`
onto a single heatmap.
Parameters
----------
plt_data_list_of_lists : list of lists of numpy arrays
A complete square 2D list of lists, such that each element is a
2D numpy array of the same size.
colormap : Colormap
The colormap used to determine box color.
colorbar : bool, optional
Whether or not to show the color scale bar.
box_label_size : int, optional
If greater than 0, display static labels on each box with font
size equal to `box_label_size`.
prec : int or {'compact','compacthp'}, optional
Precision for box labels. Allowed values are:
'compact' = round to nearest whole number using at most 3 characters
'compacthp' = show as much precision as possible using at most 3 characters
int >= 0 = fixed precision given by int
int < 0 = number of significant figures given by -int
hover_label_fn : function, optional
A function with signature `f(z,i,j)` where `z ==plt_data[i,j]` which
computes the hover label for the each element of `plt_data`. Cannot
be used with `hoverLabels`.
Returns
-------
plotly.Figure
"""
#Assemble the single 2D grid to pass to _color_boxplot
# (assume a complete 2D rectangular list of lists, and that
# each element is a numpy array of the same size)
if len(plt_data_list_of_lists) == 0 or len(plt_data_list_of_lists[0]) == 0: return
elRows, elCols = plt_data_list_of_lists[0][0].shape # nE,nr
nRows = len(plt_data_list_of_lists)
nCols = len(plt_data_list_of_lists[0])
data = _np.zeros((elRows * nRows + (nRows - 1), elCols * nCols + (nCols - 1)))
for i in range(1, nRows):
data[(elRows + 1) * i - 1:(elRows + 1) * i, :] = _np.nan
for j in range(1, nCols):
data[:, (elCols + 1) * j - 1:(elCols + 1) * j] = _np.nan
for i in range(nRows):
for j in range(nCols):
data[(elRows + 1) * i:(elRows + 1) * (i + 1) - 1, (elCols + 1)
* j:(elCols + 1) * (j + 1) - 1] = plt_data_list_of_lists[i][j]
xtics = []; ytics = []
for i in range(nRows): ytics.append(float((elRows + 1) * i) - 0.5 + 0.5 * float(elRows))
for j in range(nCols): xtics.append(float((elCols + 1) * j) - 0.5 + 0.5 * float(elCols))
if hover_label_fn:
hoverLabels = []
for _ in range(elRows * nRows + (nRows - 1)):
hoverLabels.append([""] * (elCols * nCols + (nCols - 1)))
for i in range(nRows):
for j in range(nCols):
for ii in range(elRows):
for jj in range(elCols):
hoverLabels[(elRows + 1) * i + ii][(elCols + 1) * j + jj] = \
hover_label_fn(plt_data_list_of_lists[i][j][ii][jj], i, j, ii, jj)
else:
hoverLabels = None
fig = _color_boxplot(data, colormap, colorbar, box_label_size,
prec, None, hoverLabels)
#Layout updates: add tic marks (but not labels - leave that to user)
fig.plotlyfig['layout']['xaxis'].update(tickvals=xtics)
fig.plotlyfig['layout']['yaxis'].update(tickvals=ytics)
return fig
def _summable_color_boxplot(sub_mxs, xlabels, ylabels, xlabel, ylabel,
colormap, colorbar=False, box_labels=True, prec=0, hover_info=True,
sum_up=False, scale=1.0, bgcolor='white'):
"""
A helper function for generating typical nested color box plots used in pyGSTi.
Given the list-of-lists, `sub_mxs`, along with x and y labels for both the "outer"
(i.e. the list-indices), this function will produce a nested color box plot with
the option of summing over the sub-matrix elements (the "inner" axes).
Parameters
----------
sub_mxs : list
A list of lists of 2D numpy.ndarrays. sub_mxs[iy][ix] specifies the matrix of values
or sum (if sum_up == True) displayed in iy-th row and ix-th column of the plot. NaNs
indicate elements should not be displayed.
xlabels : list
Labels for the outer x-axis values.
ylabels : list
Labels for the outer y-axis values.
xlabel : str
Outer x-axis label.
ylabel : str
Outer y-axis label.
colormap : Colormap
The colormap used to determine box color.
colorbar : bool, optional
Whether or not to show the color scale bar.
box_labels : bool, optional
Whether to display static value-labels over each box.
prec : int or {'compact','compacthp'}, optional
Precision for box labels. Allowed values are:
'compact' = round to nearest whole number using at most 3 characters
'compacthp' = show as much precision as possible using at most 3 characters
int >= 0 = fixed precision given by int
int < 0 = number of significant figures given by -int
hover_info : bool or function, optional
If a boolean, indicates whether to include interactive hover labels. If
a function, then must take arguments `(val, i, j, ii, jj)` if
`sum_up == False` or `(val, i, j)` if `sum_up == True` and return a
label string, where `val` is the box value, `j` and `i` index
`xlabels` and `ylabels`, and `ii` and `jj` index the row and column index
of the sub-matrix element the label is for.
sum_up : bool, optional
False displays each matrix element as it's own color box
True sums the elements of each (x,y) matrix and displays
a single color box for the sum.
scale : float, optional
Scaling factor to adjust the size of the final figure.
bgcolor : str, optional
Background color for this plot. Can be common color names, e.g.
`"black"`, or string RGB values, e.g. `"rgb(255,128,0)"`.
Returns
-------
plotly.Figure
"""
nYs = len(sub_mxs)
nXs = len(sub_mxs[0]) if nYs > 0 else 0
nIYs = nIXs = 0
for ix in range(nXs):
for iy in range(nYs):
if sub_mxs[iy][ix] is not None:
nIYs, nIXs = sub_mxs[iy][ix].shape; break
# flip so [0,0] el of original sub_mxs is at *top*-left (FLIP)
sub_mxs = [[_np.flipud(subMx) for subMx in row] for row in sub_mxs]
#inner_ylabels = list(reversed(inner_ylabels))
#FUTURE: to restore "invert" functionality, make PlaquetteGridCircuitStructure invertible
#if invert:
# if sum_up:
# _warnings.warn("Cannot invert a summed-up plot. Ignoring invert=True.")
# else:
# invertedSubMxs = [] # will be indexed as invertedSubMxs[inner-y][inner-x]
# for iny in range(nIYs):
# invertedSubMxs.append([])
# for inx in range(nIXs):
# mx = _np.array([[sub_mxs[iy][ix][iny, inx] for ix in range(nXs)]
# for iy in range(nYs)], 'd')
# invertedSubMxs[-1].append(mx)
#
# # flip the now-inverted mxs to counteract the flip that will occur upon
# # entering _summable_color_boxplot again (with invert=False this time), since we
# # *don't* want the now-inner dimension (the germs) actually flipped (FLIP)
# invertedSubMxs = [[_np.flipud(subMx) for subMx in row] for row in invertedSubMxs]
# ylabels = list(reversed(ylabels))
#
# return _summable_color_boxplot(invertedSubMxs,
# inner_xlabels, inner_ylabels,
# xlabels, ylabels, inner_xlabel, inner_ylabel, xlabel, ylabel,
# colormap, colorbar, box_labels, prec, hover_info,
# sum_up, False, scale, bgcolor)
def val_filter(vals):
"""filter to latex-ify circuits. Later add filter as a possible parameter"""
formatted_vals = []
for val in vals:
if isinstance(val, _Circuit):
if len(val) == 0:
#formatted_vals.append(r"$\{\}$")
formatted_vals.append(r"{}")
else:
#formatted_vals.append( "$" + "\\cdot".join([("\\mathrm{%s}" % el) for el in val]) + "$" )
formatted_vals.append(val.str)
else:
formatted_vals.append(str(val))
return formatted_vals
def sum_up_mx(mx):
""" Sum up `mx` in a NAN-ignoring way """
flat_mx = mx.flatten()
if any([_np.isnan(x) for x in flat_mx]):
if all([_np.isnan(x) for x in flat_mx]):
return _np.nan
# replace NaNs with zeros for purpose of summing (when there's at least one non-NaN)
return sum(_np.nan_to_num(flat_mx))
else:
return sum(flat_mx)
#Setup and create plotting functions
if sum_up:
subMxSums = _np.array([[sum_up_mx(sub_mxs[iy][ix]) for ix in range(nXs)] for iy in range(nYs)], 'd')
if hover_info is True:
def hover_label_fn(val, i, j):
""" Standard hover labels """
if _np.isnan(val): return ""
return "%s: %s<br>%s: %s<br>%g" % \
(xlabel, str(xlabels[j]), ylabel, str(ylabels[i]), val)
elif callable(hover_info):
hover_label_fn = hover_info
else: hover_label_fn = None
boxLabelSize = 8 * scale if box_labels else 0
fig = _color_boxplot(subMxSums, colormap, colorbar, boxLabelSize,
prec, hover_label_fn)
#update tickvals b/c _color_boxplot doesn't do this (unlike _nested_color_boxplot)
if fig is not None:
fig.plotlyfig['layout']['xaxis'].update(tickvals=list(range(nXs)))
fig.plotlyfig['layout']['yaxis'].update(tickvals=list(range(nYs)))
xBoxes = nXs
yBoxes = nYs
else: # not summing up
if hover_info is True:
def hover_label_fn(val, i, j, ii, jj):
""" Standard hover labels """
if _np.isnan(val): return ""
return "%s: %s<br>%s: %s<br>%s: %s<br>%s: %s<br>%g" % \
(xlabel, str(xlabels[j]), ylabel, str(ylabels[i]),
"row", str(ii), "column", str(jj), val)
elif callable(hover_info):
def hover_label_fn(val, i, j, ii, jj):
N = len(sub_mxs[i][j]) # number of rows in submatrix
return hover_info(val, i, j, N - 1 - ii, jj) # FLIP row index
else: hover_label_fn = None
boxLabelSize = 8 if box_labels else 0 # do not scale (OLD: 8*scale)
fig = _nested_color_boxplot(sub_mxs, colormap, colorbar, boxLabelSize,
prec, hover_label_fn)
xBoxes = nXs * (nIXs + 1) - 1
yBoxes = nYs * (nIYs + 1) - 1
#assert(fig is not None), "No data to display!"
if fig is not None: # i.e., if there was data to plot
pfig = fig.plotlyfig
if xlabel: pfig['layout']['xaxis'].update(title=xlabel,
titlefont={'size': 12 * scale, 'color': "black"})
if ylabel: pfig['layout']['yaxis'].update(title=ylabel,
titlefont={'size': 12 * scale, 'color': "black"})
if xlabels:
pfig['layout']['xaxis'].update(tickmode="array",
ticktext=val_filter(xlabels),
tickfont={'size': 10 * scale, 'color': "black"})
if ylabels:
pfig['layout']['yaxis'].update(tickmode="array",
ticktext=val_filter(ylabels),
tickfont={'size': 10 * scale, 'color': "black"})
#Set plot size and margins
lmargin = rmargin = tmargin = bmargin = 20
if xlabel: bmargin += 30
if ylabel: lmargin += 30
if xlabels:
max_xl = max([len(xl) for xl in pfig['layout']['xaxis']['ticktext']])
if max_xl > 0: bmargin += max_xl * 5
if ylabels:
max_yl = max([len(yl) for yl in pfig['layout']['yaxis']['ticktext']])
if max_yl > 0: lmargin += max_yl * 5
if colorbar: rmargin = 100
#make sure there's enough margin for hover tooltips
if 10 * xBoxes < 200: rmargin = max(200 - 10 * xBoxes, rmargin)
if 10 * yBoxes < 200: bmargin = max(200 - 10 * xBoxes, bmargin)
width = lmargin + 10 * xBoxes + rmargin
height = tmargin + 10 * yBoxes + bmargin
width *= scale
height *= scale
lmargin *= scale
rmargin *= scale
tmargin *= scale
bmargin *= scale
pfig['layout'].update(width=width,
height=height,
margin=go_margin(l=lmargin, r=rmargin, b=bmargin, t=tmargin),
plot_bgcolor=bgcolor)
else: # fig is None => use a "No data to display" placeholder figure
trace = go.Heatmap(z=_np.zeros((10, 10), 'd'),
colorscale=[[0, 'white'], [1, 'black']],
showscale=False, zmin=0, zmax=1, hoverinfo='none')
layout = go.Layout(
width=100, height=100,
annotations=[go_annotation(x=5, y=5, text="NO DATA", showarrow=False,
font={'size': 20, 'color': "black"},
xref='x', yref='y')],
xaxis=dict(showline=False, zeroline=False,
showticklabels=False, showgrid=False,
ticks=""),
yaxis=dict(showline=False, zeroline=False,
showticklabels=False, showgrid=False,
ticks="")
)
fig = ReportFigure(go.Figure(data=[trace], layout=layout),
None, "No data!")
return fig
def _create_hover_info_fn(circuit_structure, xvals, yvals, sum_up, addl_hover_submxs):
if sum_up:
def hover_label_fn(val, iy, ix):
""" Standard hover labels """
if _np.isnan(val): return ""
plaq = circuit_structure.plaquette(xvals[ix], yvals[iy], empty_if_missing=True)
txt = plaq.summary_label()
txt += "<br>value: %g" % val
for lbl, addl_subMxs in addl_hover_submxs.items():
txt += "<br>%s: %s" % (lbl, str(addl_subMxs[iy][ix]))
return txt
else:
def hover_label_fn(val, iy, ix, iiy, iix):
""" Standard hover labels """
#Note: in this case, we need to "flip" the iiy index because
# the matrices being plotted are flipped within _summable_color_boxplot(...)
if _np.isnan(val): return ""
plaq = circuit_structure.plaquette(xvals[ix], yvals[iy], empty_if_missing=True)
txt = plaq.element_label(iiy, iix) # note: *row* index = iiy
txt += ("<br>value: %g" % val)
for lbl, addl_subMxs in addl_hover_submxs.items():
txt += "<br>%s: %s" % (lbl, str(addl_subMxs[iy][ix][iiy][iix]))
return txt
return hover_label_fn
def _create_hover_info_fn_circuit_list(circuit_structure, sum_up, addl_hover_submxs):
if sum_up:
pass
else:
if isinstance(circuit_structure, _CircuitList):
def hover_label_fn(val, i):
""" Standard hover labels """
#Note: in this case, we need to "flip" the iiy index because
# the matrices being plotted are flipped within _summable_color_boxplot(...)
if _np.isnan(val): return ""
ckt = circuit_structure[i].copy(editable=True)
ckt.factorize_repetitions_inplace()
txt = ckt.layerstr # note: *row* index = iiy
txt += ("<br>value: %g" % val)
for lbl, addl_subMxs in addl_hover_submxs.items():
txt += "<br>%s: %s" % (lbl, str(addl_subMxs[i]))
return txt
elif isinstance(circuit_structure, list) and all([isinstance(el, _CircuitList) for el in circuit_structure]):
def hover_label_fn(val, i, j):
""" Standard hover labels """
#Note: in this case, we need to "flip" the iiy index because
# the matrices being plotted are flipped within _summable_color_boxplot(...)
if _np.isnan(val): return ""
ckt = circuit_structure[i][j].copy(editable=True)
ckt.factorize_repetitions_inplace()
txt = ckt.layerstr # note: *row* index = iiy
txt += ("<br>value: %g" % val)
for lbl, addl_subMxs in addl_hover_submxs.items():
txt += "<br>%s: %s" % (lbl, str(addl_subMxs[i][j]))
return txt
return hover_label_fn
def _circuit_color_boxplot(circuit_structure, sub_mxs, colormap,
colorbar=False, box_labels=True, prec='compact', hover_info=True,
sum_up=False, invert=False, scale=1.0, bgcolor="white", addl_hover_submxs=None):
"""
A wrapper around :func:`_summable_color_boxplot` for creating color box plots displaying circuits.
Generates a plot from the structure of the circuits as contained in a
`CircuitStructure` object.
Parameters
----------
circuit_structure : CircuitStructure
Specifies a set of circuits along with their structure, e.g. fiducials, germs,
and maximum lengths.
sub_mxs : list
A list of lists of 2D numpy.ndarrays. sub_mxs[iy][ix] specifies the matrix of values
or sum (if sum_up == True) displayed in iy-th row and ix-th column of the plot. NaNs
indicate elements should not be displayed.
colormap : Colormap
The colormap used to determine box color.
colorbar : bool, optional
Whether or not to show the color scale bar.
box_labels : bool, optional
Whether to display static value-labels over each box.
prec : int or {'compact','compacthp'}, optional
Precision for box labels. Allowed values are:
'compact' = round to nearest whole number using at most 3 characters
'compacthp' = show as much precision as possible using at most 3 characters
int >= 0 = fixed precision given by int
int < 0 = number of significant figures given by -int
hover_info : bool, optional
Whether to incude interactive hover labels.
sum_up : bool, optional
False displays each matrix element as it's own color box
True sums the elements of each (x,y) matrix and displays
a single color box for the sum.
invert : bool, optional
If True, invert the nesting order of the nested color box plot
(applicable only when sum_up == False). E.g. use inner_x_labels and
inner_y_labels to label the x and y axes.
scale : float, optional
Scaling factor to adjust the size of the final figure.
bgcolor : str, optional
Background color for this plot. Can be common color names, e.g.
`"black"`, or string RGB values, e.g. `"rgb(255,128,0)"`.
addl_hover_submxs : dict, optional
If not None, a dictionary whose values are lists-of-lists in the same
format as `sub_mxs` which specify additional values to add to the
hover-info of the corresponding boxes. The keys of this dictionary
are used as labels within the hover-info text.
Returns
-------
plotly.Figure
"""
xvals = circuit_structure.used_xs
yvals = circuit_structure.used_ys
if addl_hover_submxs is None:
addl_hover_submxs = {}
# Note: invert == True case not handled yet
assert(invert is False), "`invert=True` is no longer supported."
if hover_info:
hover_info = _create_hover_info_fn(circuit_structure, xvals, yvals, sum_up, addl_hover_submxs)
return _summable_color_boxplot(sub_mxs, circuit_structure.used_xs, circuit_structure.used_ys,
circuit_structure.xlabel, circuit_structure.ylabel, colormap, colorbar,
box_labels, prec, hover_info, sum_up, scale, bgcolor)
def _circuit_color_scatterplot(circuit_structure, sub_mxs, colormap,
colorbar=False, hover_info=True, sum_up=False,
ylabel="", scale=1.0, addl_hover_submxs=None):
"""
Similar to :func:`_circuit_color_boxplot` except a scatter plot is created.
Parameters
----------
circuit_structure : PlaquetteGridCircuitStructure
Specifies a set of circuits along with their outer and inner x,y
structure, e.g. fiducials, germs, and maximum lengths.
sub_mxs : list
A list of lists of 2D numpy.ndarrays. sub_mxs[iy][ix] specifies the matrix of values
or sum (if sum_up == True) displayed in iy-th row and ix-th column of the plot. NaNs
indicate elements should not be displayed.
colormap : Colormap
The colormap used to determine box color.
colorbar : bool, optional
Whether or not to show the color scale bar.
hover_info : bool, optional
Whether to incude interactive hover labels.
sum_up : bool, optional
False displays each matrix element as it's own color box
True sums the elements of each (x,y) matrix and displays
a single color box for the sum.
ylabel : str, optional
The y-axis label to use.
scale : float, optional
Scaling factor to adjust the size of the final figure.
addl_hover_submxs : dict, optional
If not None, a dictionary whose values are lists-of-lists in the same
format as `sub_mxs` which specify additional values to add to the
hover-info of the corresponding boxes. The keys of this dictionary
are used as labels within the hover-info text.
Returns
-------
plotly.Figure
"""
g = circuit_structure
if addl_hover_submxs is None:
addl_hover_submxs = {}
if hover_info:
if isinstance(g, _PlaquetteGridCircuitStructure):
hover_info = _create_hover_info_fn(circuit_structure, g.used_xs, g.used_ys, sum_up, addl_hover_submxs)
elif isinstance(g, _CircuitList) or (isinstance(g, list) and all([isinstance(el, _CircuitList) for el in g])):
hover_info = _create_hover_info_fn_circuit_list(circuit_structure, sum_up, addl_hover_submxs)
xs = []; ys = []; texts = []
gstrs = set() # to eliminate duplicate strings
if isinstance(g, _PlaquetteGridCircuitStructure):
for ix, x in enumerate(g.used_xs):
for iy, y in enumerate(g.used_ys):
plaq = g.plaquette(x, y, empty_if_missing=True)
if sum_up:
if plaq.base not in gstrs:
tot = sum([sub_mxs[iy][ix][iiy][iix] for iiy, iix, _ in plaq])
xs.append(len(plaq.base)) # x-coord is len of *base* string
ys.append(tot)
gstrs.add(plaq.base)
if hover_info:
if callable(hover_info):
texts.append(hover_info(tot, iy, ix))
else:
texts.append(str(tot))
else:
for iiy, iix, opstr in plaq:
if opstr in gstrs: continue # skip duplicates
xs.append(len(opstr))
ys.append(sub_mxs[iy][ix][iiy][iix])
gstrs.add(opstr)
if hover_info:
if callable(hover_info):
texts.append(hover_info(sub_mxs[iy][ix][iiy][iix], iy, ix, iiy, iix))
else:
texts.append(str(sub_mxs[iy][ix][iiy][iix]))
elif isinstance(g, _CircuitList):
for i, ckt in enumerate(g):
if ckt in gstrs:
continue
else:
if sum_up:
pass
#TODO: Implement sum_up behavior mirroring that above.
gstrs.add(ckt)
ys.append(sub_mxs[i])
xs.append(len(ckt))
if hover_info:
if callable(hover_info):
texts.append(hover_info(sub_mxs[i], i))
else:
texts.append(str(sub_mxs[i]))
elif isinstance(g, list) and all([isinstance(el, _CircuitList) for el in g]):
for i, circuit_list in enumerate(g):
for j, ckt in enumerate(circuit_list):
if ckt in gstrs:
continue
else:
if sum_up:
pass
#TODO: Implement sum_up behavior mirroring that above.
gstrs.add(ckt)
ys.append(sub_mxs[i][j])
xs.append(len(ckt))
if hover_info:
if callable(hover_info):
texts.append(hover_info(sub_mxs[i][j], i, j))
else:
texts.append(str(sub_mxs[i][j]))
#This GL version works, but behaves badly, sometimes failing to render...
#trace = go.Scattergl(x=xs, y=ys, mode="markers",
# marker=dict(size=8,
# color=[colormap.interpolate_color(y) for y in ys],
# #colorscale=colormap.create_plotly_colorscale(), #doesn't seem to work properly in GL?
# line=dict(width=1)))
trace = go.Scatter(x=xs, y=ys, mode="markers",
marker=dict(size=8,
color=[colormap.interpolate_color(y) for y in ys],
colorscale=colormap.create_plotly_colorscale(),
line=dict(width=1)))
if hover_info:
trace['hoverinfo'] = 'text'
trace['text'] = texts
else:
trace['hoverinfo'] = 'none'
xaxis = go_x_axis(
title='sequence length',
showline=False,
zeroline=True,
)
yaxis = go_y_axis(
title=ylabel
)
layout = go.Layout(
#title="Sum = %.2f" % sum(ys), #DEBUG
width=400 * scale,
height=400 * scale,
hovermode='closest',
xaxis=xaxis,
yaxis=yaxis,
)
return ReportFigure(go.Figure(data=[trace], layout=layout), colormap,
{'x': xs, 'y': ys})
def _circuit_color_histogram(circuit_structure, sub_mxs, colormap,
ylabel="", scale=1.0):
"""
Similar to :func:`_circuit_color_boxplot` except a histogram is created.
Parameters
----------
circuit_structure : PlaquetteGridCircuitStructure
Specifies a set of circuits along with their outer and inner x,y
structure, e.g. fiducials, germs, and maximum lengths.
sub_mxs : list
A list of lists of 2D numpy.ndarrays. sub_mxs[iy][ix] specifies the matrix of values
or sum (if sum_up == True) displayed in iy-th row and ix-th column of the plot. NaNs
indicate elements should not be displayed.
colormap : Colormap
The colormap used to determine box color.
ylabel : str, optional
The y-axis label to use.
scale : float, optional
Scaling factor to adjust the size of the final figure.
Returns
-------
plotly.Figure
"""
g = circuit_structure
#For all of the fanciness below, this all essentially looks like it just produces
#a flattened list of all of the contents of sub_mxs, so we can still do that with the
#submx structures we get from using CircuitList objects.
ys = [] # artificially add minval so
gstrs = set() # to eliminate duplicate strings
if isinstance(g, _PlaquetteGridCircuitStructure):
for ix, x in enumerate(g.used_xs):
for iy, y in enumerate(g.used_ys):
plaq = g.plaquette(x, y, empty_if_missing=True)
#TODO: if sum_up then need to sum before appending...
for iiy, iix, opstr in plaq:
if opstr in gstrs: continue # skip duplicates
ys.append(sub_mxs[iy][ix][iiy][iix])
gstrs.add(opstr)
elif isinstance(g, _CircuitList):
for i, ckt in enumerate(g):
if ckt in gstrs:
continue
else:
gstrs.add(ckt)
ys.append(sub_mxs[i])
elif isinstance(g, list) and all([isinstance(el, _CircuitList) for el in g]):
for i, circuit_list in enumerate(g):
for j, ckt in enumerate(circuit_list):
if ckt in gstrs:
continue
else:
gstrs.add(ckt)
ys.append(sub_mxs[i][j])
else:
raise ValueError('Can only handle PlaquetteGridCircuitStructure, CircuitList or lists of CircuitList objects at present.')
if len(ys) == 0: ys = [0] # case of no data - dummy so max works below
minval = 0
maxval = max(minval + 1e-3, _np.max(ys)) # don't let minval==maxval
nvals = len(ys)
cumulative = dict(enabled=False)
# marker=dict(color=barcolor),
#barcolor = 'gray'
nbins = 50
binsize = (maxval - minval) / (nbins - 1)
bincenters = _np.linspace(minval, maxval, nbins)
bindelta = (maxval - minval) / (nbins - 1) # spacing between bin centers
trace = go.Histogram(
x=[bincenters[0]] + ys, # artificially add 1 count in lowest bin so plotly anchors histogram properly
autobinx=False,
xbins=dict(
start=minval - binsize / 2.0,
end=maxval + binsize / 2.0,
size=binsize
),
name="count",
marker=dict(
color=[colormap.interpolate_color(t) for t in bincenters],
line=dict(
color='black',
width=1.0,
)
),
cumulative=cumulative,
opacity=1.00,
showlegend=False,
)
dof = colormap.dof if hasattr(colormap, "dof") else 1
line_trace = go.Scatter(
x=bincenters,
y=[nvals * bindelta * _chi2.pdf(xval, dof) for xval in bincenters],
name="expected",
showlegend=False,
line=dict(
color=('rgb(0, 0, 0)'),
width=1) # dash = 'dash') # dash options include 'dash', 'dot', and 'dashdot'
)
hist_values, np_bins = _np.histogram(ys, nbins, range=(minval - binsize / 2.0,
maxval + binsize / 2.0))
if len(hist_values) > 0 and len(hist_values[hist_values > 0]) > 0:
minlog = _np.log10(max(_np.min(hist_values[hist_values > 0]) / 10.0, 1e-3))
maxlog = _np.log10(1.5 * _np.max(hist_values))
else:
minlog, maxlog = -3, 0 # defaults to (1e-3,1) when there's no data
layout = go.Layout(
#title="Sum = %.2f" % sum(ys), #DEBUG
width=500 * scale,
height=350 * scale,
font=dict(size=10),
xaxis=dict(
title=ylabel, # b/c "y-values" are along x-axis in histogram
showline=True
),
yaxis=dict(
type='log',
#tickformat='g',
exponentformat='power',
showline=True,
range=[minlog, maxlog]
),
bargap=0,
bargroupgap=0,
legend=dict(orientation="h")
)
pythonVal = {'histogram values': ys}
return ReportFigure(go.Figure(data=[trace, line_trace], layout=layout),
colormap, pythonVal)
def _opmatrix_color_boxplot(op_matrix, color_min, color_max, mx_basis=None, mx_basis_y=None,
xlabel=None, ylabel=None,
box_labels=False, colorbar=None, prec=0, scale=1.0,
eb_matrix=None, title=None):
"""
Creates a color box plot for visualizing a single matrix.
Parameters
----------
op_matrix : numpy array
The matrix to visualize.
color_min : float
Color scale minimum.
color_max : float
Color scale maximum.
mx_basis : str or Basis, optional
The name abbreviation for the basis or a Basis object. Used to label the
columns & rows (x- and y-ticklabels). Typically in
{"pp","gm","std","qt"}. If you don't want labels, leave as None.
mx_basis_y : str or Basis, optional
Same as `mx_basis` but for just the y-ticklabels, overriding `mx_basis` and
allowing the y-ticklabels to be different.
xlabel : str, optional
X-axis label of the plot.
ylabel : str, optional
Y-axis label of the plot.
box_labels : bool, optional
Whether box labels are displayed.
colorbar : bool optional
Whether to display a color bar to the right of the box plot. If None,
then a colorbar is displayed when `box_labels == False`.
prec : int or {'compact','compacthp'}, optional
Precision for box labels. Only relevant when box_labels == True. Allowed
values are: