Made storing negative simplices in StaticPersistence parameter-based, so that DynamicPersistence works again
#!/usr/bin/python
# Author: Dmitriy Morozov <morozov@cs.duke.edu>
# (2004-2008) Department of Computer Science, Duke University
import pyx, string, sys, math
class PersistenceDiagram:
def drawAxes(self,c,radius,spacing = 1, dimensions = None):
if not dimensions:
xmax = math.ceil(max(self.xmax,1) + radius + 1)
xmin = math.floor(min(self.xmin,-1) - radius - 1)
ymax = math.ceil(max(self.ymax,1) + radius + 1)
ymin = math.floor(min(self.ymin,-1) - radius - 1)
else:
xmin,ymin,xmax,ymax = dimensions
minmax = min([xmax, ymax])
maxmin = max([xmin, ymin])
for i in xrange(int(math.floor(xmin)),int(math.ceil(xmax)), spacing):
c.stroke(pyx.path.line(i,ymin,i,ymax), [pyx.style.linestyle.dashed, pyx.color.gray(0.5)])
for j in xrange(int(math.floor(ymin)),int(math.ceil(ymax)), spacing):
c.stroke(pyx.path.line(xmin,j,xmax,j), [pyx.style.linestyle.dashed, pyx.color.gray(0.5)])
c.stroke(pyx.path.line(xmin,0,xmax,0), [pyx.deco.earrow.normal])
c.stroke(pyx.path.line(0,ymin,0,ymax), [pyx.deco.earrow.normal])
c.stroke(pyx.path.line(maxmin,maxmin,minmax,minmax))
def drawCanvas(self, c, points, color = 'red', filled = 1, radius = 0.15):
for p in points:
self.drawPoint(c,p,color,filled,radius)
def drawPoint(self,c,p, color = 'red', filled = 1, radius = 0.15):
if color == 'red':
options = [pyx.color.rgb.red]
elif color == 'blue':
options = [pyx.color.rgb.blue]
elif color == 'green':
options = [pyx.color.rgb.green]
else:
options = []
if filled:
draw = c.fill
else:
draw = c.stroke
xmax = max(self.xmax,1)
xmin = min(self.xmin,-1)
ymax = max(self.ymax,1)
ymin = min(self.ymin,-1)
x,y = p
if abs(x) == float('inf') or abs(y) == float('inf'): radius = radius * 2
if x == float('inf'): x = xmax + 1
if x == float('-inf'): x = xmin - 1
if y == float('inf'): y = ymax + 1
if y == float('-inf'): y = ymin -1
draw(pyx.path.circle(x,y,radius), options)
def savePDF(self, filename, color = 'red', filled = 1, radius = 0.15, axes = 1, dimensions = None):
for d in self.points.keys():
c = pyx.canvas.canvas()
self.drawAxes(c, radius, axes, dimensions)
self.drawCanvas(c, self.points[d], color, filled, radius)
c.writePDFfile(filename + str(d))
def add(self, d, p, filter):
x,y = p
p = filter(x,y)
if not p: return
x,y = p
if d not in self.points.keys():
self.points[d] = []
self.points[d] += [(x,y)]
if abs(x) != float('inf'):
self.xmax = max(x,self.xmax)
self.xmin = min(x,self.xmin)
if abs(y) != float('inf'):
self.ymax = max(y,self.ymax)
self.ymin = min(y,self.ymin)
def load(self,filename, filter):
self.xmax = self.ymax = 0
self.xmin = self.ymin = 0
f = file(filename, 'r')
for line in f:
if line.strip().startswith('#'): continue
dim,xstr,ystr = string.split(line)
self.add(dim, (float(xstr),float(ystr)), filter)
def __init__(self, filename, filter = lambda x,y: (x,y)):
self.points = {}
self.load(filename, filter)
def noise_filter(epsilon):
def noise(x,y):
if y - x <= epsilon: return None
return (x,y)
return noise
def amplify_filter(x_mult, y_mult = None):
if not y_mult: y_mult = x_mult
def amplify(x,y):
return (x_mult*x, y_mult*y)
return amplify