# HG changeset patch
# User Dmitriy Morozov <dmitriy@mrzv.org>
# Date 1256323883 25200
# Node ID a172b960aaaa82eaec689193fffb58709ca15f90
# Parent e8b6706cedfc2b317fe92293346fe25e6706a78d
Added draw.py under tools/draw-diagram
diff -r e8b6706cedfc -r a172b960aaaa doc/get-build-install.rst
--- a/doc/get-build-install.rst Fri Oct 23 09:36:55 2009 -0700
+++ b/doc/get-build-install.rst Fri Oct 23 11:51:23 2009 -0700
@@ -54,6 +54,8 @@
:CGAL_: for alpha shapes (version :math:`\geq` 3.4)
:CVXOPT_: for :ref:`circle-valued parametrization <cohomology-parametrization>` using LSQR
+ :PyX_: :sfile:`tools/draw-diagram/draw.py` uses `PyX`_ to
+ produce a PDF of the diagram
:rlog_: used for logging only (not needed by default)
.. :dsrpdb_: for reading PDB files
@@ -64,6 +66,7 @@
.. _Boost: http://www.boost.org
.. _CGAL: http://www.cgal.org
.. _CVXOPT: http://abel.ee.ucla.edu/cvxopt/
+.. _PyX: http://pyx.sourceforge.net/
.. _rlog: http://www.arg0.net/rlog
.. _dsrpdb: http://www.salilab.org/~drussel/pdb/
.. _SYNAPS: http://www-sop.inria.fr/galaad/synaps/
diff -r e8b6706cedfc -r a172b960aaaa tools/draw-diagram/draw.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/draw-diagram/draw.py Fri Oct 23 11:51:23 2009 -0700
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+
+import pd
+from sys import argv, exit
+
+if len(argv) < 2:
+ print "Usage: %s FILENAME [MULTIPLIER=1] [NOISE=0] [RADIUS=.15] [DIMENSIONS=XMIN,YMIN,XMAX,YMAX]" % argv[0]
+ print " MULTIPLIER - multiply coordinates of each point by this quantity"
+ print " NOISE - filter out points below this persistence"
+ print " RADIUS - radius of a point in the persistence diagram"
+ print " DIMENSIONS - dimensions of the persistence diagram"
+ print
+ print " Example: %s torus.dgm 1 0 .05 -1,-1,10,10" % argv[0]
+ exit()
+
+multiplier = float(argv[2]) if len(argv) > 2 else 1
+noise = float(argv[3]) if len(argv) > 3 else 0
+R = float(argv[4]) if len(argv) > 4 else .15
+dimensions = map(float, argv[5].split(',')) if len(argv) > 5 else None
+
+noise_filter = pd.noise_filter(noise)
+amplify_filter = pd.amplify_filter(multiplier)
+
+dgm = pd.PersistenceDiagram(argv[1], lambda x,y: noise_filter(x,y) and amplify_filter(x,y))
+dgm.savePDF(argv[1] + '.', radius = R, dimensions = dimensions)
diff -r e8b6706cedfc -r a172b960aaaa tools/draw-diagram/pd.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/draw-diagram/pd.py Fri Oct 23 11:51:23 2009 -0700
@@ -0,0 +1,113 @@
+#!/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