#!/usr/bin/env python3
# script copied from https://github.com/fengwangPhysics/matplotlib-chord-diagram/blob/master/README.md
# source data manually edited via https://docs.google.com/spreadsheets/d/1JN9S_A5ICPQOvgyVbWJSFJiw-5gO2vF-4AeYuWl-lbs/edit#gid=0
# chord diagram
import matplotlib.pyplot as plt
from matplotlib.path import Path
import matplotlib.patches as patches
import numpy as np
LW = 0.3
def polar2xy(r, theta):
return np.array([r*np.cos(theta), r*np.sin(theta)])
def hex2rgb(c):
return tuple(int(c[i:i+2], 16)/256.0 for i in (1, 3 ,5))
def IdeogramArc(start=0, end=60, radius=1.0, width=0.2, ax=None, color=(1,0,0)):
# start, end should be in [0, 360)
if start > end:
start, end = end, start
start *= np.pi/180.
end *= np.pi/180.
# optimal distance to the control points
# https://stackoverflow.com/questions/1734745/how-to-create-circle-with-b%C3%A9zier-curves
opt = 4./3. * np.tan((end-start)/ 4.) * radius
inner = radius*(1-width)
verts = [
polar2xy(radius, start),
polar2xy(radius, start) + polar2xy(opt, start+0.5*np.pi),
polar2xy(radius, end) + polar2xy(opt, end-0.5*np.pi),
polar2xy(radius, end),
polar2xy(inner, end),
polar2xy(inner, end) + polar2xy(opt*(1-width), end-0.5*np.pi),
polar2xy(inner, start) + polar2xy(opt*(1-width), start+0.5*np.pi),
polar2xy(inner, start),
polar2xy(radius, start),
]
codes = [Path.MOVETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.LINETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CLOSEPOLY,
]
if ax == None:
return verts, codes
else:
path = Path(verts, codes)
patch = patches.PathPatch(path, facecolor=color+(0.5,), edgecolor=color+(0.4,), lw=LW)
ax.add_patch(patch)
def ChordArc(start1=0, end1=60, start2=180, end2=240, radius=1.0, chordwidth=0.7, ax=None, color=(1,0,0)):
# start, end should be in [0, 360)
if start1 > end1:
start1, end1 = end1, start1
if start2 > end2:
start2, end2 = end2, start2
start1 *= np.pi/180.
end1 *= np.pi/180.
start2 *= np.pi/180.
end2 *= np.pi/180.
opt1 = 4./3. * np.tan((end1-start1)/ 4.) * radius
opt2 = 4./3. * np.tan((end2-start2)/ 4.) * radius
rchord = radius * (1-chordwidth)
verts = [
polar2xy(radius, start1),
polar2xy(radius, start1) + polar2xy(opt1, start1+0.5*np.pi),
polar2xy(radius, end1) + polar2xy(opt1, end1-0.5*np.pi),
polar2xy(radius, end1),
polar2xy(rchord, end1),
polar2xy(rchord, start2),
polar2xy(radius, start2),
polar2xy(radius, start2) + polar2xy(opt2, start2+0.5*np.pi),
polar2xy(radius, end2) + polar2xy(opt2, end2-0.5*np.pi),
polar2xy(radius, end2),
polar2xy(rchord, end2),
polar2xy(rchord, start1),
polar2xy(radius, start1),
]
codes = [Path.MOVETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
]
if ax == None:
return verts, codes
else:
path = Path(verts, codes)
patch = patches.PathPatch(path, facecolor=color+(0.5,), edgecolor=color+(0.4,), lw=LW)
ax.add_patch(patch)
def selfChordArc(start=0, end=60, radius=1.0, chordwidth=0.7, ax=None, color=(1,0,0)):
# start, end should be in [0, 360)
if start > end:
start, end = end, start
start *= np.pi/180.
end *= np.pi/180.
opt = 4./3. * np.tan((end-start)/ 4.) * radius
rchord = radius * (1-chordwidth)
verts = [
polar2xy(radius, start),
polar2xy(radius, start) + polar2xy(opt, start+0.5*np.pi),
polar2xy(radius, end) + polar2xy(opt, end-0.5*np.pi),
polar2xy(radius, end),
polar2xy(rchord, end),
polar2xy(rchord, start),
polar2xy(radius, start),
]
codes = [Path.MOVETO,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
Path.CURVE4,
]
if ax == None:
return verts, codes
else:
path = Path(verts, codes)
patch = patches.PathPatch(path, facecolor=color+(0.5,), edgecolor=color+(0.4,), lw=LW)
ax.add_patch(patch)
def chordDiagram(X, ax, colors=None, width=0.1, pad=2, chordwidth=0.7):
"""Plot a chord diagram
Parameters
----------
X :
flux data, X[i, j] is the flux from i to j
ax :
matplotlib `axes` to show the plot
colors : optional
user defined colors in rgb format. Use function hex2rgb() to convert hex color to rgb color. Default: d3.js category10
width : optional
width/thickness of the ideogram arc
pad : optional
gap pad between two neighboring ideogram arcs, unit: degree, default: 2 degree
chordwidth : optional
position of the control points for the chords, controlling the shape of the chords
"""
# X[i, j]: i -> j
x = X.sum(axis = 1) # sum over rows
ax.set_xlim(-1.1, 1.1)
ax.set_ylim(-1.1, 1.1)
if colors is None:
# use d3.js category10 https://github.com/d3/d3-3.x-api-reference/blob/master/Ordinal-Scales.md#category10
colors = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd',
'#8c564b', '#e377c2', '#7f7f7f', '#bcbd22', '#17becf', '#c49c94']
if len(x) > len(colors):
print('x is too large! Use x smaller than 11')
colors = [hex2rgb(colors[i]) for i in range(len(x))]
# find position for each start and end
y = x/np.sum(x).astype(float) * (360 - pad*len(x))
pos = {}
arc = []
nodePos = []
start = 0
for i in range(len(x)):
end = start + y[i]
arc.append((start, end))
angle = 0.5*(start+end)
#print(start, end, angle)
if -30 <= angle <= 210:
angle -= 90
else:
angle -= 270
nodePos.append(tuple(polar2xy(1.1, 0.5*(start+end)*np.pi/180.)) + (angle,))
z = (X[i, :]/x[i].astype(float)) * (end - start)
ids = np.argsort(z)
z0 = start
for j in ids:
pos[(i, j)] = (z0, z0+z[j])
z0 += z[j]
start = end + pad
for i in range(len(x)):
start, end = arc[i]
IdeogramArc(start=start, end=end, radius=1.0, ax=ax, color=colors[i], width=width)
start, end = pos[(i,i)]
selfChordArc(start, end, radius=1.-width, color=colors[i], chordwidth=chordwidth*0.7, ax=ax)
for j in range(i):
color = colors[i]
if X[i, j] > X[j, i]:
color = colors[j]
start1, end1 = pos[(i,j)]
start2, end2 = pos[(j,i)]
ChordArc(start1, end1, start2, end2,
radius=1.-width, color=colors[i], chordwidth=chordwidth, ax=ax)
#print(nodePos)
return nodePos
##################################
if __name__ == "__main__":
fig = plt.figure(figsize=(6,6))
flux = np.array([
[ 0, 1, 0, 0], #OS Sum:2 ; Centos, Ubuntu
[ 0, 0, 0, 0], #Plays
[ 0, 0, 0, 1], # Cluster: Sum5; Generic, M3, Monarch, SHPC, ACCS
[ 0, 0, 1, 2] #Cloud Sum3: AWS,Nimbus,Nectar
])
from numpy import genfromtxt
flux = genfromtxt('Chord_Diagramm - Sheet1.csv', delimiter=',')
ax = plt.axes([0,0,1,1])
#nodePos = chordDiagram(flux, ax, colors=[hex2rgb(x) for x in ['#666666', '#66ff66', '#ff6666', '#6666ff']])
nodePos = chordDiagram(flux, ax)
ax.axis('off')
prop = dict(fontsize=16*0.8, ha='center', va='center')
nodes = ['OS_Centos76','OS_Centos8','OS_Ubuntu1804','PLY_NFSSQL','PLY_MGMT','PLY_Login','PLY_Compute','C_Generic','C_M3','C_Monarch']
#nodes = ['M3_MONARCH','SHPC','Ubuntu','Centos7','Centos8','Tested','Security','Nectar','?AWS?','DGX@Baremetal','ML@M3','CVL@UWA','CVL_SW','CVL_Desktop','Strudel','/usr/local']
for i in range(len(nodes)):
ax.text(nodePos[i][0], nodePos[i][1], nodes[i], rotation=nodePos[i][2], **prop)
plt.savefig("Chord_Diagramm.png", dpi=600,transparent=False,bbox_inches='tight', pad_inches=0.02)
plt.show(pad_inches=0.02)