Layout overhaul #214

boothby · 2021-12-07T16:14:02Z

Normalizes node sizes across the board
Makes yield plots easier to read
Adds qubit-line plots

~~needs a little more documentation~~

boothby · 2021-12-07T17:18:51Z

~~Caught a mistake; will patch later. For now, have a preview.~~

A giant run of sample images:

import dwave_networkx as dnx
import networkx as nx
from minorminer import find_embedding
import random
import gc
from matplotlib import pyplot as plt
import os
from itertools import chain
os.system("rm yield*.png")
for dpi in (100,):
    for i,(m, t) in enumerate([(2, 1), (2, 4), (2,8), (4,4), (4,8), (8,6), (6,8), (15,4), (15,8), (2, 2), (2, 1), (4, 1), (8, 1)]):
        z = dnx.zephyr_graph(m,t,coordinates=True)
        z.remove_nodes_from(random.sample([*z], len(z)//10))
        z.remove_edges_from(random.sample([*z.edges], len(z.edges)//10))
        emb = {}
        hits = set()
        for _ in range(10):
            emb_ = find_embedding(nx.complete_graph(8), z.subgraph(z.nodes - hits), tries=1, max_no_improvement=1, chainlength_patience=0)
            for c in emb_.values():
                hits.update(c)
                emb[len(emb)] = c
            if not emb_: break
        fig, ax = plt.subplots(2, 2, figsize=(20,20), dpi=dpi)
        dnx.draw_zephyr(z, node_color = range(len(z)), ax=ax[0][0])
        dnx.draw_zephyr(z, node_color = range(len(z)), edge_color=range(len(z.edges)), ax=ax[0][1], line_plot=True)
        dnx.draw_zephyr_embedding(z, emb, ax=ax[1][0], line_plot=True)
        dnx.draw_zephyr_yield(z, fault_shape='o', ax=ax[1][1], line_plot=True)
        fig.tight_layout()
        plt.savefig(f'yield{i}z{dpi}.png', bbox_inches='tight')
        plt.close()
        gc.collect()
    for i,(m,crosses) in enumerate([(2,0), (2, 1), (4,0), (6,1), (8,0), (16,1)]):
        z = dnx.pegasus_graph(m,coordinates=True)
        z.remove_nodes_from(random.sample([*z], len(z)//10))
        z.remove_edges_from(random.sample([*z.edges], len(z.edges)//10))
        emb = {}
        hits = set()
        for _ in range(10):
            emb_ = find_embedding(nx.complete_graph(8), z.subgraph(z.nodes - hits), tries=1, max_no_improvement=1, chainlength_patience=0)
            for c in emb_.values():
                hits.update(c)
                emb[len(emb)] = c
            if not emb_: break
        fig, ax = plt.subplots(2, 2, figsize=(20,20), dpi=dpi)
        dnx.draw_pegasus(z, ax=ax[0][0], crosses=crosses)
        dnx.draw_pegasus(z, ax=ax[0][1], crosses=not crosses, line_plot=True)
        dnx.draw_pegasus_embedding(z, emb, ax=ax[1][0], crosses=crosses, line_plot=True)
        dnx.draw_pegasus_yield(z, fault_shape='o', ax=ax[1][1], crosses=crosses)
        fig.tight_layout()
        plt.savefig(f'yield{i}p{dpi}.png', bbox_inches='tight')
        plt.close()
        gc.collect()
    for i,(m, n, t) in enumerate([(2, 2, 2), (2,2,4), (2,2,8), (4,4,8), (4,4,4), (8,4,8), (8,8,4), (16,16,4), (16, 16,8)]):
        z = dnx.chimera_graph(m,n,t,coordinates=True)
        z.remove_nodes_from(random.sample([*z], len(z)//10))
        z.remove_edges_from(random.sample([*z.edges], len(z.edges)//10))
        emb = {}
        hits = set()
        for _ in range(1):
            emb_ = find_embedding(nx.complete_graph(8), z.subgraph(z.nodes - hits), tries=1, max_no_improvement=1, chainlength_patience=0)
            for c in emb_.values():
                hits.update(c)
                emb[len(emb)] = c
            if not emb_: break
        fig, ax = plt.subplots(2, 2, figsize=(20*n/m,20), dpi=dpi)
        dnx.draw_chimera(z, ax=ax[0][0])
        dnx.draw_chimera(z, ax=ax[0][1], line_plot=True)
        dnx.draw_chimera_embedding(z, emb, ax=ax[1][0], line_plot=False)
        dnx.draw_chimera_yield(z, fault_shape='o', ax=ax[1][1], line_plot=False)
        fig.tight_layout()
        plt.savefig(f'yield{i}c{dpi}.png', bbox_inches='tight')
        plt.close()
        gc.collect()

codecov-commenter · 2021-12-10T18:50:20Z

Codecov Report

Merging #214 (25b0adc) into main (4ade84b) will decrease coverage by 5.21%.
The diff coverage is 5.85%.

@@            Coverage Diff             @@
##             main     #214      +/-   ##
==========================================
- Coverage   74.42%   69.20%   -5.22%     
==========================================
  Files          29       29              
  Lines        2045     2205     +160     
==========================================
+ Hits         1522     1526       +4     
- Misses        523      679     +156

Impacted Files	Coverage Δ
dwave_networkx/drawing/qubit_layout.py	`4.63% <3.22%> (-0.41%)`	⬇️
dwave_networkx/drawing/zephyr_layout.py	`15.71% <7.69%> (-4.66%)`	⬇️
dwave_networkx/drawing/chimera_layout.py	`11.82% <8.10%> (-2.84%)`	⬇️
dwave_networkx/drawing/pegasus_layout.py	`13.63% <8.92%> (-3.76%)`	⬇️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4ade84b...25b0adc. Read the comment docs.

JoelPasvolsky

Some comments from a first scan: if I have time, I'd like to try using the new functionality a bit and then returning to this.
Lovely addition!

dwave_networkx/drawing/chimera_layout.py

dwave_networkx/drawing/qubit_layout.py

dwave_networkx/drawing/zephyr_layout.py

dwave_networkx/drawing/chimera_layout.py

dwave_networkx/drawing/qubit_layout.py

JoelPasvolsky

Will you be adding the https://github.com/dwavesystems/dwave-networkx/blob/main/dwave_networkx/drawing/qubit_layout.py functions to RST files (see comment below on __all__ = ['draw_qubit_graph'])? If so, I'll render those docstrings and see how they look too.

JoelPasvolsky · 2022-01-17T21:58:32Z

dwave_networkx/drawing/chimera_layout.py

@@ -51,6 +51,13 @@ def chimera_layout(G, scale=1., center=None, dim=2):
        Number of dimensions. When dim > 2, all extra dimensions are
        set to 0.

+    plot_kwargs : None or dict (default None)
+        A dict of keyword arguments to be used in a plotting function (see
+        :func:`networkx.draw` and :func:`draw_lineplot`), to scale node and edge


":func:networkx.draw" --> to create a linked object this needs to be :func:~networkx.drawing.nx_pylab.draw

Same in many other spots.

JoelPasvolsky · 2022-01-17T22:11:25Z

dwave_networkx/drawing/chimera_layout.py

+        A dict of keyword arguments to be used in a plotting function (see
+        :func:`networkx.draw` and :func:`draw_lineplot`), to scale node and edge
+        sizes appropriately to the graph `G`.  Optional keys in ``plot_kwargs``
+        are set to default values by the :func:`normalize_size_and_aspect`


":func:normalize_size_and_aspect" --> two issues:

Needs to be something like :func:~dwave_networkx.drawing.qubit_layout.normalize_size_and_aspect

You can only link to this function once you add it to an RST file so it's rendered to the docs.

dwave_networkx/drawing/chimera_layout.py

JoelPasvolsky · 2022-01-17T22:16:30Z

dwave_networkx/drawing/chimera_layout.py

@@ -131,6 +138,13 @@ def chimera_node_placer_2d(m, n, t, scale=1., center=None, dim=2):
        Number of dimensions. When dim > 2, all extra dimensions are
        set to 0.

+    plot_kwargs : None or dict (default None)


Same comments as in def chimera_layout() above

JoelPasvolsky · 2022-01-17T22:19:38Z

dwave_networkx/drawing/chimera_layout.py

+        where two qubits overlap.  In this drawing style, the interpretation of
+        the ``width`` and ``node_size`` parameters (provided in ``kwargs``)
+        determine the area of the circles and line widths respectively.  See
+        :func:`dwave_networkx.qubit_layout.draw_lineplot` for more information.


Prefixing with a tilde (~) will be shorter, it might need a .drawing. before the func name, and it needs to be rendered in the docs first.

Also appears in funcs below.

JoelPasvolsky · 2022-01-17T22:21:16Z

dwave_networkx/drawing/pegasus_layout.py

@@ -58,6 +58,13 @@ def pegasus_layout(G, scale=1., center=None, dim=2, crosses=False):
        rather than L configuration. Ignored if G is defined with
        ``nice_coordinates=True``.

+    plot_kwargs : None or dict (default None)


Same comments as in def chimera_layout() above

JoelPasvolsky · 2022-01-17T22:21:44Z

dwave_networkx/drawing/pegasus_layout.py

@@ -120,6 +129,13 @@ def pegasus_node_placer_2d(G, scale=1., center=None, dim=2, crosses=False):
        If True, :math:`K_{4,4}` subgraphs are shown in a cross
        rather than L configuration.

+    plot_kwargs : None or dict (default None)


Same comments as in def chimera_layout() above

JoelPasvolsky · 2022-01-17T22:24:55Z

dwave_networkx/drawing/qubit_layout.py

@@ -23,13 +23,16 @@
 from networkx import draw

 from dwave_networkx.drawing.distinguishable_colors import distinguishable_color_map
+from itertools import repeat, chain
+
+from numbers import Number

 __all__ = ['draw_qubit_graph']


What about funcs draw_embedding, draw_yield, normalize_size_and_aspect, draw_lineplot? Shouldn't these be added? And added to the appropriate RST file?

JoelPasvolsky · 2022-01-17T22:26:17Z

dwave_networkx/drawing/zephyr_layout.py

@@ -52,6 +52,13 @@ def zephyr_layout(G, scale=1., center=None, dim=2):
        Number of dimensions. When dim > 2, all extra dimensions are
        set to 0.

+    plot_kwargs : None or dict (default None)


Same as above comments on func pathnames

dwave_networkx/drawing/qubit_layout.py

)

JoelPasvolsky

I still have two functions remaining that I'll do right after this but I'm submitting these proposed updates now because (1) I want to submit a separate comment on what looks like a bug and (2) I have a lot of work that would be lost if this review hits a snag

JoelPasvolsky · 2023-01-30T23:51:13Z

docs/reference/drawing.rst

+
+Generic Plotting Functions
+--------------------------
+


Suggested change

.. Caution::

The following semi-public methods are intended to be used by public

functions such as :func:`.draw_chimera()`, not directly by the user.

We do something similar for such functions in dimod here

JoelPasvolsky · 2023-01-31T15:10:09Z

dwave_networkx/drawing/qubit_layout.py

+    """Draws the graph G with line segments representing nodes.
+
+    This function is meant to be a drop-in replacement for :func:`networkx.drawing.nx_pylab.draw`
+    where nodes are associated with line segments (specified as 2x2 matrices
+    [[x0, y0], [x1, y1]]).  This function makes significant assumptions about
+    the edges of the graph G, that hold when G is a Chimera, Pegasus, or Zephyr
+    graph and the line segments are provided by :func:`chimera_layout`,
+    :func:`pegasus_layout` and :func:`zephyr_layout` respectively.  These graphs
+    have three classes of edges:
+
+        * internal edges between qubits whose line segments are perpendicular
+            and intersect at a point, drawn as a circle located at the point of
+            intersection,
+        * external edges between qubits whose line segments are colinear, drawn
+            as a line segment between the nearest endpoints, and
+        * odd edges between parallel qubits whose line segments are parallel and
+          overlap in a perpendicular projection, drawn as a line segment between
+          the midpoints of the respective perpendicular projections.


Suggested change

"""Draws the graph G with line segments representing nodes.

This function is meant to be a drop-in replacement for :func:`networkx.drawing.nx_pylab.draw`

where nodes are associated with line segments (specified as 2x2 matrices

[[x0, y0], [x1, y1]]). This function makes significant assumptions about

the edges of the graph G, that hold when G is a Chimera, Pegasus, or Zephyr

graph and the line segments are provided by :func:`chimera_layout`,

:func:`pegasus_layout` and :func:`zephyr_layout` respectively. These graphs

have three classes of edges:

* internal edges between qubits whose line segments are perpendicular

and intersect at a point, drawn as a circle located at the point of

intersection,

* external edges between qubits whose line segments are colinear, drawn

as a line segment between the nearest endpoints, and

* odd edges between parallel qubits whose line segments are parallel and

overlap in a perpendicular projection, drawn as a line segment between

the midpoints of the respective perpendicular projections.

"""Draws the given graph with line segments representing nodes.

This function is meant to be a drop-in replacement for the NetworkX

:func:`~networkx.drawing.nx_pylab.draw` function, where nodes are associated

with line segments specified as 2x2 matrices ``[[x0, y0], [x1, y1]]``.

The function makes significant assumptions about the edges of graph ``G``,

which hold when ``G`` is a Chimera, Pegasus, or Zephyr graph and the line

segments are generated by :func:`.chimera_layout`, :func:`.pegasus_layout`

and :func:`.zephyr_layout` functions respectively. These graphs have three

classes of edges:

* Internal edges between qubits whose line segments are perpendicular

and intersect at a point, drawn as a circle located at the point of

intersection.

* External edges between qubits whose line segments are colinear, drawn

as a line segment between the nearest endpoints.

* Odd edges between parallel qubits whose line segments are parallel and

overlap in a perpendicular projection, drawn as a line segment between

the midpoints of the respective perpendicular projections.

Fixes the formatting problem with the bullets, separates the intro content into sections and formats the non-simple text

JoelPasvolsky · 2023-01-31T15:13:16Z

dwave_networkx/drawing/qubit_layout.py

+        A graph constructed by :func:`chimera_layout`, :func:`pegasus_layout`,
+        or :func:`zephyr_layout`.


Suggested change

A graph constructed by :func:`chimera_layout`, :func:`pegasus_layout`,

or :func:`zephyr_layout`.

A graph constructed by :func:`.chimera_layout`, :func:`.pegasus_layout`,

or :func:.`zephyr_layout`.

JoelPasvolsky · 2023-01-31T15:13:44Z

dwave_networkx/drawing/qubit_layout.py

-        unused_node_color = [unused_color for v in nodelist]
-        unused_edge_color = [unused_color for v in edgelist]
+    layout : dict
+        A dictionary with nodes as keys and 2x2 matrices [[x0, y0], [x1, y1]]


Suggested change

A dictionary with nodes as keys and 2x2 matrices [[x0, y0], [x1, y1]]

A dictionary with nodes as keys and 2x2 matrices ``[[x0, y0], [x1, y1]]``

JoelPasvolsky · 2023-01-31T15:15:36Z

dwave_networkx/drawing/qubit_layout.py

+        representing the line segments of nodes.
+
+    ax : matplotlib.Axis
+        The matplotlib Axis object to draw the graph on.


Suggested change

The matplotlib Axis object to draw the graph on.

The `Matplotlib <https://matplotlib.org/>`_ Axis object to draw the graph on.

JoelPasvolsky · 2023-01-31T20:03:48Z

dwave_networkx/drawing/qubit_layout.py

+        A magic number used to scale node circles -- ignored and replaced with
+        the number 50 when `kwargs["line_plot"]` is True.


Suggested change

A magic number used to scale node circles -- ignored and replaced with

the number 50 when `kwargs["line_plot"]` is True.

A magic number used to scale node circles; ignored and replaced with

the number 50 when ``kwargs["line_plot"]`` is ``True``.

JoelPasvolsky · 2023-01-31T20:12:52Z

dwave_networkx/drawing/qubit_layout.py

@@ -442,22 +487,35 @@ def draw_yield(G, layout, perfect_graph, unused_color=(0.9,0.9,0.9,1.0),
    perfect_graph : NetworkX graph


Parameters G and perfect_graph need end-of-sentence periods.
Parameter layoutshould be updated to, "...perfect_graph. Should be of the form {node: coordinate, ...}``. Coordinates are ..."

JoelPasvolsky · 2023-01-31T20:15:34Z

dwave_networkx/drawing/qubit_layout.py

+        A color to represent nodes absent from the graph G, and edges absent
+        from the graph G which are not incident to faulty nodes. 


Suggested change

A color to represent nodes absent from the graph G, and edges absent

from the graph G which are not incident to faulty nodes.

A color to represent nodes absent from the graph ``G``, and edges absent

from the graph ``G`` which are not incident to faulty nodes.

JoelPasvolsky · 2023-01-31T21:13:34Z

dwave_networkx/drawing/qubit_layout.py

+        If line_plot is True, then qubits are drawn as line segments, and edges
+        are drawn either as line segments between qubits, or as circles where
+        two qubits overlap.  In this drawing style, the interpretation the width
+        and node_size parameters (provided in kwargs) determines the area of the
+        circles, and line widths, respectively.  Qubit line segments are given
+        twice the width of edges.  Layout should be a dict of the form
+        {node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes
+        are associated with endpoints of n-dimensional line segments.


Suggested change

If line_plot is True, then qubits are drawn as line segments, and edges

are drawn either as line segments between qubits, or as circles where

two qubits overlap. In this drawing style, the interpretation the width

and node_size parameters (provided in kwargs) determines the area of the

circles, and line widths, respectively. Qubit line segments are given

twice the width of edges. Layout should be a dict of the form

{node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes

are associated with endpoints of n-dimensional line segments.

If ``line_plot`` is ``True``, qubits are drawn as line segments and edges

are drawn as either line segments between qubits or circles where

two qubits overlap. In this drawing style, the interpretation the ``width``

and ``node_size`` parameters (provided in ``kwargs``) determines the area of the

circles, and line widths, respectively. Qubit line segments are given

twice the width of edges. Layout should be a dict of the form

``{node: ((x0, y0), (y0, x0)), ...}``; instead of coordinates, the nodes

are associated with endpoints of n-dimensional line segments.

JoelPasvolsky · 2023-01-31T21:19:11Z

dwave_networkx/drawing/qubit_layout.py

+        twice the width of edges.  Layout should be a dict of the form
+        {node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes
+        are associated with endpoints of n-dimensional line segments.
+
    kwargs : optional keywords
       See networkx.draw_networkx() for a description of optional keywords,
       with the exception of the `pos` parameter which is not used by this


Suggested change

with the exception of the `pos` parameter which is not used by this

with the exception of the ``pos`` parameter which is not used by this

function. If ``linear_biases`` or ``quadratic_biases`` are provided,

any provided ``node_color`` or ``edge_color`` arguments are ignored.

Examples

--------

This example illustrates how functions such as :func:`.draw_pegasus` can make use of this internal function.

.. code-block:: python

import dwave_networkx as dnx

import matplotlib.pyplot as plt

from dwave_networkx.drawing.qubit_layout import draw_yield

G = dnx.chimera_graph(1)

layout = dnx.chimera_layout(G)

draw_yield(G.subgraph([0, 4, 5, 6, 7]), layout, G, unused_color="green", fault_color="red")

"""

This one will need a minor edit for indent spaces and cleaning up the three lines below after being committed.

JoelPasvolsky · 2023-01-31T21:30:45Z

dwave_networkx/drawing/qubit_layout.py

@@ -424,9 +469,9 @@ def unoverlapped_embedding(G, emb, interaction_edges):


 def draw_yield(G, layout, perfect_graph, unused_color=(0.9,0.9,0.9,1.0),


@boothby, I'm seeing something weird with this function though it might be because I'm using it directly rather than through the public functions as intended, where it might not affect anything. The following code snippet,

import dwave_networkx as dnx import matplotlib.pyplot as plt from dwave_networkx.drawing.qubit_layout import draw_yield G = dnx.chimera_graph(1) layout = dnx.chimera_layout(G) draw_yield(G.subgraph([0, 4, 5, 6, 7]), layout, G, unused_color="green", fault_color="red")

generates the nodes with/without faults correctly but the edges are offset from the nodes:

I'm not reproducing that on my end (matplotlib 3.4.1, networkx 2.4). Can you try the public interface?

Okay, I finally managed to reproduce it through the public interface:

It does not happen for matplotlib 3.4.1, networkx 2.4; it happens if you upgrade to matplotlib 3.6.3 (dwave-netwokx doesn't set a version requirement for Matplotlib so users might have more recent versions)

We need to add draw_chimera_yield and draw_pegasus_yield to the docs, currently there's only draw_zephyr_yield

import dwave_networkx as dnx import matplotlib.pyplot as plt G = dnx.chimera_graph(1) fig, ax = plt.subplots(figsize=(10, 5)) dnx.draw_chimera_yield(G.subgraph([0, 4, 5, 6, 7]), unused_color="green", fault_color="red", ax=ax) plt.show()

Shows up once you zoom in as:

JoelPasvolsky · 2023-01-31T21:53:17Z

@boothby, what about updating the requirement on networkx to a minimum of version 2.8.6 to apply this fix there too?

I'm hitting it on the NetworkX draw() function here:

>>> from dwave_networkx.drawing.qubit_layout import draw_embedding
>>> draw_embedding(G, layout, {0:[0, 4, 5]})
...
File ~\pyenv\ocean_repos\dwave_networkx_3_10_2\lib\site-packages\networkx\drawing\nx_pylab.py:117, in draw(G, pos, ax, **kwds)
    115 cf.set_facecolor('w')
    116 if ax is None:
--> 117     if cf._axstack() is None:
    118         ax = cf.add_axes((0, 0, 1, 1))
    119     else:

TypeError: '_AxesStack' object is not callable

JoelPasvolsky

Okay, these are great functionality additions.
There are still a few small changes (mostly formatting and an example) I'd like but because they're not on code lines directly updated in this PR it's messy to propose them here---I can submit a followup PR to you once this is merged.

JoelPasvolsky · 2023-01-31T22:07:31Z

dwave_networkx/drawing/qubit_layout.py

+        twice the width of edges.  Layout should be a dict of the form
+        {node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes
+        are associated with endpoints of n-dimensional line segments.
+


Suggested change

kwargs : optional keywords

See :func:`networkx.draw_networkx` for a description of optional keywords,

with the exception of the ``pos`` parameter which is not used by this

function. If ``linear_biases`` or ``quadratic_biases`` are provided,

any provided ``node_color`` or ``edge_color`` arguments are ignored.

Examples

--------

This example illustrates how functions such as :func:`.draw_pegasus` can make use of this internal function.

.. code-block:: python

import dwave_networkx as dnx

import matplotlib.pyplot as plt

from dwave_networkx.drawing.qubit_layout import draw_embedding

G = dnx.chimera_graph(1)

layout = dnx.chimera_layout(G)

draw_embedding(G, layout, {0:[0, 4, 5], 1: [1, 6], 2: [2, 6], 3: [3, 7]})

"""

This one will need the deletion of lines 272-277 after committing.

JoelPasvolsky · 2023-01-31T22:11:06Z

dwave_networkx/drawing/qubit_layout.py

+    line_plot : boolean (optional, default False)
+        If line_plot is True, then qubits are drawn as line segments, and edges
+        are drawn either as line segments between qubits, or as circles where
+        two qubits overlap.  In this drawing style, the interpretation the width
+        and node_size parameters (provided in kwargs) determines the area of the
+        circles, and line widths, respectively.  Qubit line segments are given
+        twice the width of edges.  Layout should be a dict of the form
+        {node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes
+        are associated with endpoints of n-dimensional line segments.


Suggested change

line_plot : boolean (optional, default False)

If line_plot is True, then qubits are drawn as line segments, and edges

are drawn either as line segments between qubits, or as circles where

two qubits overlap. In this drawing style, the interpretation the width

and node_size parameters (provided in kwargs) determines the area of the

circles, and line widths, respectively. Qubit line segments are given

twice the width of edges. Layout should be a dict of the form

{node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes

are associated with endpoints of n-dimensional line segments.

line_plot : boolean (optional, default False)

If ``line_plot`` is ``True``, qubits are drawn as line segments and edges

are drawn as either line segments between qubits or circles where

two qubits overlap. In this drawing style, the interpretation of the ``width``

and ``node_size`` parameters (provided in ``kwargs``) determines the area of the

circles, and line widths, respectively. Qubit line segments are given

twice the width of edges. Layout should be a dict of the form

``{node: ((x0, y0), (y0, x0)), ...}``; instead of coordinates, the nodes

are associated with endpoints of n-dimensional line segments.

JoelPasvolsky · 2023-01-31T22:14:06Z

dwave_networkx/drawing/qubit_layout.py

+        If line_plot is True, then qubits are drawn as line segments, and edges
+        are drawn either as line segments between qubits, or as circles where
+        two qubits overlap.  In this drawing style, the interpretation the width
+        and node_size parameters (provided in kwargs) determines the area of the
+        circles, and line widths, respectively.  Qubit line segments are given
+        twice the width of edges.  Layout should be a dict of the form
+        {node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes
+        are associated with endpoints of n-dimensional line segments.


Suggested change

If line_plot is True, then qubits are drawn as line segments, and edges

are drawn either as line segments between qubits, or as circles where

two qubits overlap. In this drawing style, the interpretation the width

and node_size parameters (provided in kwargs) determines the area of the

circles, and line widths, respectively. Qubit line segments are given

twice the width of edges. Layout should be a dict of the form

{node: ((x0, y0), (y0, x0)), ...} -- instead of coordinates, the nodes

are associated with endpoints of n-dimensional line segments.

If ``line_plot`` is ``True``, qubits are drawn as line segments and edges

are drawn as either line segments between qubits or circles where

two qubits overlap. In this drawing style, the interpretation of the ``width``

and ``node_size`` parameters (provided in ``kwargs``) determines the area of the

circles, and line widths, respectively. Qubit line segments are given

twice the width of edges. Layout should be a dict of the form

``{node: ((x0, y0), (y0, x0)), ...}``; instead of coordinates, the nodes

are associated with endpoints of n-dimensional line segments.

boothby force-pushed the layout_overhaul branch 4 times, most recently from 9288684 to 96f586a Compare December 8, 2021 17:14

arcondello mentioned this pull request Dec 8, 2021

Test with python 3.10 #215

Merged

boothby force-pushed the layout_overhaul branch 2 times, most recently from 070454a to f110c95 Compare December 10, 2021 18:45

arcondello requested review from arcondello and JoelPasvolsky December 10, 2021 18:50

JoelPasvolsky reviewed Dec 13, 2021

View reviewed changes

dwave_networkx/drawing/chimera_layout.py Outdated Show resolved Hide resolved

JoelPasvolsky reviewed Dec 13, 2021

View reviewed changes

dwave_networkx/drawing/qubit_layout.py Outdated Show resolved Hide resolved

JoelPasvolsky reviewed Jan 17, 2022

View reviewed changes

boothby added 6 commits January 25, 2023 13:54

normalized Chimera, Pegasus and Zephyr layouts to unit square

5a2317f

added sensible size defaults to Chimera, Pegasus and Zephyr plots

d3afdb3

reworked yield_plot to be more readable

52e2903

added line_plot option

758958e

review

49a1862

doc review; improved references and added generic plotting docs

553581c

boothby force-pushed the layout_overhaul branch from 25b0adc to 553581c Compare January 25, 2023 22:09

JoelPasvolsky reviewed Jan 27, 2023

View reviewed changes

dwave_networkx/drawing/qubit_layout.py Outdated Show resolved Hide resolved

JoelPasvolsky reviewed Jan 27, 2023

View reviewed changes

dwave_networkx/drawing/qubit_layout.py Show resolved Hide resolved

dwave_networkx/drawing/qubit_layout.py Show resolved Hide resolved

resolved incompatibility with matplotlib 3.6 (see networkx/networkx#5937

aba5e46

)

JoelPasvolsky reviewed Jan 31, 2023

View reviewed changes

JoelPasvolsky mentioned this pull request Mar 15, 2023

Fix typos and styling. #226

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Layout overhaul #214

Layout overhaul #214

boothby commented Dec 7, 2021 •

edited

Loading

boothby commented Dec 7, 2021 •

edited

Loading

codecov-commenter commented Dec 10, 2021 •

edited

Loading

JoelPasvolsky left a comment

JoelPasvolsky left a comment

JoelPasvolsky Jan 17, 2022

JoelPasvolsky Jan 17, 2022

JoelPasvolsky Jan 17, 2022

JoelPasvolsky Jan 17, 2022

JoelPasvolsky Jan 17, 2022

JoelPasvolsky Jan 17, 2022

JoelPasvolsky Jan 17, 2022

JoelPasvolsky Jan 17, 2022

JoelPasvolsky left a comment

JoelPasvolsky Jan 30, 2023 •

edited

Loading

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

boothby Feb 1, 2023

JoelPasvolsky Feb 1, 2023 •

edited

Loading

JoelPasvolsky commented Jan 31, 2023

JoelPasvolsky left a comment

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

JoelPasvolsky Jan 31, 2023

+.. Caution::
+   The following semi-public methods are intended to be used by public
+   functions such as :func:`.draw_chimera()`, not directly by the user.

		A graph constructed by :func:`chimera_layout`, :func:`pegasus_layout`,
		or :func:`zephyr_layout`.

	A dictionary with nodes as keys and 2x2 matrices [[x0, y0], [x1, y1]]
	A dictionary with nodes as keys and 2x2 matrices ``[[x0, y0], [x1, y1]]``

	The matplotlib Axis object to draw the graph on.
	The `Matplotlib <https://matplotlib.org/>`_ Axis object to draw the graph on.

		A magic number used to scale node circles -- ignored and replaced with
		the number 50 when `kwargs["line_plot"]` is True.

		@@ -442,22 +487,35 @@ def draw_yield(G, layout, perfect_graph, unused_color=(0.9,0.9,0.9,1.0),
		perfect_graph : NetworkX graph

		A color to represent nodes absent from the graph G, and edges absent
		from the graph G which are not incident to faulty nodes.

-       with the exception of the `pos` parameter which is not used by this
+       with the exception of the ``pos`` parameter which is not used by this
+       function. If ``linear_biases`` or ``quadratic_biases`` are provided,
+       any provided ``node_color`` or ``edge_color`` arguments are ignored.
+       Examples
+       --------
+       This example illustrates how functions such as :func:`.draw_pegasus` can make use of this internal function.
+       .. code-block:: python
+           import dwave_networkx as dnx
+           import matplotlib.pyplot as plt
+           from dwave_networkx.drawing.qubit_layout import draw_yield
+           G = dnx.chimera_graph(1)
+           layout = dnx.chimera_layout(G)
+           draw_yield(G.subgraph([0, 4, 5, 6, 7]), layout, G, unused_color="green", fault_color="red")
+   """

		@@ -424,9 +469,9 @@ def unoverlapped_embedding(G, emb, interaction_edges):


		def draw_yield(G, layout, perfect_graph, unused_color=(0.9,0.9,0.9,1.0),


		Generic Plotting Functions
		--------------------------

Layout overhaul #214

Are you sure you want to change the base?

Layout overhaul #214

Conversation

boothby commented Dec 7, 2021 • edited Loading

boothby commented Dec 7, 2021 • edited Loading

codecov-commenter commented Dec 10, 2021 • edited Loading

Codecov Report

JoelPasvolsky left a comment

Choose a reason for hiding this comment

JoelPasvolsky left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

JoelPasvolsky left a comment

Choose a reason for hiding this comment

JoelPasvolsky Jan 30, 2023 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

JoelPasvolsky Feb 1, 2023 • edited Loading

Choose a reason for hiding this comment

JoelPasvolsky commented Jan 31, 2023

JoelPasvolsky left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

boothby commented Dec 7, 2021 •

edited

Loading

boothby commented Dec 7, 2021 •

edited

Loading

codecov-commenter commented Dec 10, 2021 •

edited

Loading

JoelPasvolsky Jan 30, 2023 •

edited

Loading

JoelPasvolsky Feb 1, 2023 •

edited

Loading