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init

master
Stephen Mardson McQuay 10 years ago
commit
961b3b7b26
19 changed files with 560 additions and 0 deletions
  1. +1
    -0
      .hgignore
  2. +2
    -0
      .setup
  3. +43
    -0
      bin/driver-random.py
  4. +45
    -0
      bin/driver-structured.py
  5. +16
    -0
      bin/generate_qhull.pl
  6. BIN
      data/mesh.shelve
  7. +11
    -0
      data/qhull_input.txt
  8. +106
    -0
      lib/baker.py
  9. +77
    -0
      lib/grid.py
  10. +4
    -0
      lib/smcqhull.py
  11. +12
    -0
      lib/tools.py
  12. +75
    -0
      test/baker.test.py
  13. +33
    -0
      test/qhull.test.py
  14. +29
    -0
      test/utest.py
  15. +26
    -0
      tools/mkpoints.py
  16. +22
    -0
      tools/multi/forktest.py
  17. +12
    -0
      tools/multi/pool.py
  18. +24
    -0
      tools/multi/smp.py
  19. +22
    -0
      tools/multi/threadtest.py

+ 1
- 0
.hgignore View File

@@ -0,0 +1 @@
\.pyc$

+ 2
- 0
.setup View File

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export PATH=~/src/baker/bin:~/src/baker/test:$PATH
export PYTHONPATH=~/src/baker/lib

+ 43
- 0
bin/driver-random.py View File

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#!/usr/bin/python

import sys
from optparse import OptionParser

import numpy as np
import scipy.spatial

from grid import simple_random_grid, exact_func
import baker

def rms(errors):
r = 0.0
for i in errors:
r += np.power(i, 2)
r = np.sqrt(r / len(errors))
return r

if __name__ == '__main__':
parser = OptionParser()
parser.add_option("-o", "--output-file", dest="output", type='str', default = '/tmp/for_qhull.txt', help = "qhull output file")
parser.add_option("-e", "--extra-points", dest="extra", type='int', default = 3, help = "how many extra points")
parser.add_option("-s", "--source-total", dest="source_total", type='int', default = 100, help = "total number of source points")
parser.add_option("-d", "--destination-total",dest="destination_total",type='int', default = 100, help = "total number of destination points")
parser.add_option("-v", "--verbose", action = 'store_true', default = False, help = "verbosity")

(options, args) = parser.parse_args()
print >> sys.stderr, options

mesh_source = simple_random_grid(options.source_total)
tree = scipy.spatial.KDTree(mesh_source.points)
mesh_dest = simple_random_grid(options.destination_total)

open(options.output, 'w').write(mesh_source.for_qhull())
print >> sys.stderr, "wrote output to %s" % options.output

errors = []
for x in mesh_dest.points:
(final, exact) = baker.run_baker(x, mesh_source, tree, options.extra, options.verbose)
cur_error = np.abs(final - exact)
errors.append(cur_error)

print rms(errors)

+ 45
- 0
bin/driver-structured.py View File

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#!/usr/bin/python

import sys
from optparse import OptionParser

import numpy as np
import scipy.spatial

from grid import simple_rect_grid, exact_func
import baker
from tools import rms


if __name__ == '__main__':
parser = OptionParser()
parser.add_option("-e", "--extra-points", dest="extra", type='int', default = 3, help = "how many extra points")
parser.add_option("-s", "--source-density", dest="source", type='int', default = 11, help = "resolution of source mesh")
parser.add_option("-d", "--dest-density", dest="dest", type='int', default = 11, help = "resolution of dest mesh")
parser.add_option("-t", "--random-total", dest="random_total", type='int', default = 100, help = "total number of random points")
parser.add_option("-r", "--random-dest", action = 'store_true', default = False, help = "verbosity")
parser.add_option("-v", "--verbose", action = 'store_true', default = False, help = "verbosity")

(options, args) = parser.parse_args()
print >> sys.stderr, options

mesh_source = simple_rect_grid(options.source, options.source)
tree = scipy.spatial.KDTree(mesh_source.points)

mesh_dest = simple_rect_grid(options.dest, options.dest)

if options.random_dest:
x = []
for i in xrange(options.random_total):
rx = np.random.rand() * 2 - 1
ry = np.random.rand() * 2 - 1
x.append([rx, ry])
mesh_dest.points = np.array(x)

errors = []
for x in mesh_dest.points:
(final, exact) = baker.run_baker(x, mesh_source, tree, options.extra, options.verbose)
cur_error = np.abs(final - exact)
errors.append(cur_error)

print rms(errors)

+ 16
- 0
bin/generate_qhull.pl View File

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#!/usr/bin/perl

use strict;
use warnings;

my $output_filename = $ARGV[0] or die "no args";
my $tmp_grid_file = "$output_filename.grid.txt";

system("grid.py > $tmp_grid_file");


system("cat $tmp_grid_file | qdelaunay GD2 s > $output_filename.txt\n" );
system("cat $tmp_grid_file | qdelaunay GD2 s Qt > ${output_filename}_qt.txt\n");
system("cat $tmp_grid_file | qdelaunay GD2 s QJ > ${output_filename}_qj.txt\n");

unlink($tmp_grid_file);

BIN
data/mesh.shelve View File


+ 11
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data/qhull_input.txt View File

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2
9
-1.0000 -1.0000
-1.0000 0.0000
-1.0000 1.0000
0.0000 -1.0000
0.0000 0.0000
0.0000 1.0000
1.0000 -1.0000
1.0000 0.0000
1.0000 1.0000

+ 106
- 0
lib/baker.py View File

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from grid import exact_func
import numpy as np
import sys

def get_phis(X, r):
"""
The get_phis function is used to get barycentric coordonites for a point on a triangle.

X -- the destination point (2D)
X = [0,0]
r -- the three points that make up the triangle (2D)
r = [[-1, -1], [0, 2], [1, -1]]

this will return [0.333, 0.333, 0.333]
"""

# baker: eq 7
A = np.array([
[1, 1, 1 ],
[r[0][0], r[1][0], r[2][0]],
[r[0][1], r[1][1], r[2][1]],
])
b = np.array([1, X[0], X[1]])
try:
phi = np.linalg.solve(A,b)
except:
print >> sys.stderr, "warning: calculation of phis yielded a linearly dependant system"
phi = np.dot(np.linalg.pinv(A), b)

return phi

def qlinear(X, r, q):
"""
this calculates the linear portion of q from X to r

X = destination point
r = simplex points
q = CFD quantities of interest at the simplex points
"""

phis = get_phis(X, r)
qlin = sum([q_i * phi_i for q_i, phi_i in zip(q[:len(phis)], phis)])
return qlin

def run_baker(X, g, tree, extra_points = 3, verbose = False):
"""
This is the main function to call to get an interpolation to X from the tree

X -- the destination point (2D)
X = [0,0]

g -- the grid object

tree -- the kdtree search object (built from the g mesh)
"""

(dist, indicies) = tree.query(X, 3 + extra_points)

nn = [g.points[i] for i in indicies]
nq = [g.q[i] for i in indicies]

phi = get_phis(X, nn[:3])
qlin = nq[0] * phi[0] + nq[1] * phi[1] + nq[2] * phi[2]

error_term = 0.0

if extra_points != 0:
B = [] # baker eq 9
w = [] # baker eq 11

for index in indicies[3:]:
(phi1,phi2,phi3) = get_phis(g.points[index], nn)
B.append([phi1 * phi2, phi2*phi3, phi3*phi1])

w.append(g.q[index] - qlinear(g.points[index], nn, nq))

B = np.array(B)
w = np.array(w)

A = np.dot(B.T, B)
b = np.dot(B.T, w)

# baker solve eq 10
try:
(a, b, c) = np.linalg.solve(A,b)
except:
print >> sys.stderr, "warning: linear calculation went bad, resorting to np.linalg.pinv"
(a, b, c) = np.dot(np.linalg.pinv(A), b)

error_term = a * phi[0] * phi[1]\
+ b * phi[1] * phi[2]\
+ c * phi[2] * phi[0]

exact = exact_func(X[0], X[1])
q_final = qlin + error_term

if verbose:
print "current point : %s" % X
print "exact : %0.4f" % exact
print "qlin : %0.4f" % qlin
print "qlinerr : %0.4f" % np.abs(exact - qlin)
print "q_final : %0.4f" % q_final
print "q_final_err : %0.4f" % np.abs(exact - q_final)
print

return (q_final, exact)

+ 77
- 0
lib/grid.py View File

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#!/usr/bin/python

import sys
import numpy as np
import scipy.spatial

def exact_func(x, y):
return np.power((np.sin(x * np.pi) * np.cos(y * np.pi)), 2)
return np.sin(x * np.pi) * np.cos(y * np.pi)


class grid(object):
def __init__(self, points, q):
self.points = np.array(points)
self.q = np.array(q)

def __str__(self):
r = ''
assert( len(self.points) == len(self.q) )
for i in xrange(len(self.points)):
r += "%r: %0.4f\n" % ( self.points[i], self.q[i] )
return r

class simple_rect_grid(grid):
def __init__(self, xres = 5, yres = 5):
xmin = -1.0
xmax = 1.0
xspan = xmax - xmin
xdel = xspan / float(xres - 1)

ymin = -1.0
ymay = 1.0
yspan = ymay - ymin
ydel = yspan / float(yres - 1)


self.points = []
self.q = []
for x in xrange(xres):
cur_x = xmin + (x * xdel)
for y in xrange(yres):
cur_y = ymin + (y * ydel)
self.points.append([cur_x, cur_y])
self.q.append(exact_func(cur_x, cur_y))
self.points = np.array(self.points)
self.q = np.array(self.q)


def for_qhull(self):
r = '2\n'
r += '%d\n' % len(self.points)
for p in self.points:
r += "%f %f\n" % (p[0], p[1])
return r


class simple_random_grid(simple_rect_grid):
def __init__(self, num_points = 10):
self.points = []
self.q = []

r = np.random

for i in xrange(num_points):
cur_x = r.rand()
cur_y = r.rand()

self.points.append([cur_x, cur_y])
self.q.append(exact_func(cur_x, cur_y))

self.points = np.array(self.points)
self.q = np.array(self.q)


if __name__ == '__main__':
g = simple_random_grid(100)
print g.for_qhull()

+ 4
- 0
lib/smcqhull.py View File

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#!/usr/bin/python

if __name__ == '__main__':
print "hello world"

+ 12
- 0
lib/tools.py View File

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import numpy as np


def rms(errors):
"""
root mean square calculation
"""
r = 0.0
for i in errors:
r += np.power(i, 2)
r = np.sqrt(r / len(errors))
return r

+ 75
- 0
test/baker.test.py View File

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#!/usr/bin/python

import unittest
import baker

import numpy as np
import scipy.spatial

class TestSequenceFunctions(unittest.TestCase):
def setUp(self):
self.l = [[-1, 1], [-1, 0], [-1, 1], [0, -1], [0, 0], [0, 1], [1, -1], [1, 0], [1, 1]]
self.approx_fmt = "%0.6f"

def testGetPhis(self):

X = [0,0]
r = [[-1, -1], [0, 2], [1, -1]]

result = baker.get_phis(X, r)
result = [self.approx_fmt % i for i in result]

right_answer = [self.approx_fmt % i for i in [1/3.0, 1/3.0, 1/3.0]]

for a,b in zip(result, right_answer):
self.assertEqual(a,b)

def testGetPhis2(self):

X = [0.5,0.25]
r = [[0, 0], [1, 0], [1, 1]]

result = baker.get_phis(X, r)

right_answer = [0.5, 0.25, 0.25]

for a,b in zip(result, right_answer):
self.assertEqual(a,b)

def testQlinear(self):
X = [0.5, 0.25]
r = [[0, 0], [1, 0], [1, 1]]
q = [1, 0, 0]

result = baker.qlinear(X, r, q)

right_answer = 0.5

self.assertEqual(result, right_answer)

def testRunBaker(self):
X = [0.5, 0.25]

all_points = [
[ 0, 0], # 0
[ 1, 0], # 1
[ 1, 1], # 2
[ 0, 1], # 3
[ 1,-1], # 4
[ 0,-1], # 5
[-1, 1], # 6
[-1, 0], # 7
[-1,-1], # 8
]
q = [1, 0, 0, 0, 0, 0, 0, 0, 0]

tree = scipy.spatial.KDTree(all_points)
baker.run_baker(X,
result = 3
right_answer = 5

self.assertEqual(result, right_answer)

if __name__ == '__main__':
suite = unittest.TestLoader().loadTestsFromTestCase(TestSequenceFunctions)
unittest.TextTestRunner(verbosity=2).run(suite)

+ 33
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test/qhull.test.py View File

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#!/usr/bin/python

import delaunay
import subprocess

QFILE = '/tmp/forQhull.txt'

l = [[-1, 1], [-1, 0], [-1, 1], [0, -1], [0, 0], [0, 1], [1, -1], [1, 0], [1, 1]]

qdelauney_file = open(QFILE, 'w')

qdelauney_file.write("%d\n" % len(l[0]))
qdelauney_file.write("%d\n" % len(l))
for i in l:
qdelauney_file.write("%0.3f %0.3f\n" % (i[0], i[1]))

dt = delaunay.Triangulation(l)
print dt.indices

answer = [
[4,1,3],
[1,5,0],
[5,1,4],
[7,3,6],
[7,4,3],
[7,5,4],
[5,7,8],
]

print answer == dt.indices
print dt.indices

print "now run /usr/bin/qdelaunay Qt i < %s" % QFILE

+ 29
- 0
test/utest.py View File

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#!/usr/bin/python


import random
import unittest
import delaunay

class TestSequenceFunctions(unittest.TestCase):
def setUp(self):
self.l = [[-1, 1], [-1, 0], [-1, 1], [0, -1], [0, 0], [0, 1], [1, -1], [1, 0], [1, 1]]


def testQhull(self):
dt = delaunay.Triangulation(self.l)
answer = [
[4,1,3],
[1,5,0],
[5,1,4],
[7,3,6],
[7,4,3],
[7,5,4],
[5,7,8],
]

self.assertEqual(dt.indices, answer)

if __name__ == '__main__':
suite = unittest.TestLoader().loadTestsFromTestCase(TestSequenceFunctions)
unittest.TextTestRunner(verbosity=5).run(suite)

+ 26
- 0
tools/mkpoints.py View File

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#!/usr/bin/python

import sqlite3
import sys, os
import numpy as np

output_file = 'points.db'

if os.path.exists(output_file):
print "found old db, erasing"
os.unlink(output_file)

create = 'CREATE TABLE points (point_id integer primary key, x float, y float)'

sqconn = sqlite3.connect(output_file)
sqc = sqconn.cursor()
sqc.execute(create)

for i in xrange(int(1e6)):
rx = np.random.rand() * 2 - 1
ry = np.random.rand() * 2 - 1
sqc.execute('INSERT INTO points VALUES (NULL, ?, ?)', (rx, ry))


sqconn.commit()
sqconn.close()

+ 22
- 0
tools/multi/forktest.py View File

@@ -0,0 +1,22 @@
#!/usr/bin/python

import os
import time

def work():
j = 0.0
for i in xrange(10000000):
j = j + j/2.0



pid = os.fork()
if pid != 0:
print "i spawned %d and am working" % pid
work()
else:
print "i am spawn, and am working"
work()
os._exit(0)

print "parent done"

+ 12
- 0
tools/multi/pool.py View File

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#!/usr/bin/python

from multiprocessing import Pool

def f(x):
return x*x

if __name__ == '__main__':
pool = Pool(processes = 4)
result = pool.apply_async(f, (10,))
print result.get()
print pool.map(f, range(10))

+ 24
- 0
tools/multi/smp.py View File

@@ -0,0 +1,24 @@
#!/usr/bin/python

from multiprocessing import Process, Lock

def f(l, i, d):
d['a'] = 'shutup'
print 'hello world', i, d
j = 0.0
for i in xrange(1000000):
j = j + j/2.0

if __name__ == '__main__':
lock = Lock()

d = {'a': 1, 'b': 2}

ps = []
for num in range(2):
ps.append(Process(target=f, args=(lock, num, d)))

for p in ps: p.start()
for p in ps: p.join()

print d

+ 22
- 0
tools/multi/threadtest.py View File

@@ -0,0 +1,22 @@
#!/usr/bin/python

import thread, time

def work():
j = 0.0
for i in xrange(10000000):
j = j + j/2.0

def child(tid):
print "%d start" % tid
work()
print "%d stop" % tid

def parent():
i = 0
while True:
i += 1
thread.start_new(child, (i,))
if raw_input() == 'q': break

parent()

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