working on the containing simplex problem. the get containing simplex function works, if the point is in the domain. I am trying to force the domain to contain the point (placing points along perimiter of the mesh). I am not doing that right, but have to run
--HG-- rename : bin/qhull-029.txt => data/qhull-029.txt rename : bin/qhull-029.txt.gv => data/qhull-029.txt.gv
This commit is contained in:
Stephen Mardson McQuay
parent
cfcd1e15a2
commit
3dcc10ea0e
@ -3,6 +3,7 @@
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import sys
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from grid.DDD import random_grid
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from baker import get_phis_3D, run_baker_3D
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from baker.tools import logging as log
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from baker.tools import exact_func_3D, smberror, improved_answer
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try:
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total_points = int(sys.argv[1])
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@ -10,7 +11,7 @@ except:
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total_points = 20
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print total_points
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log.info(total_points)
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g = random_grid(total_points)
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open('/tmp/for_qhull.txt', 'w').write(g.for_qhull())
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@ -7,16 +7,19 @@ from baker.tools import exact_func, smberror, improved_answer
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from glob import glob
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from os import remove
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import numpy as np
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FILE_PREFIX='/tmp/qhull-'
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for g in glob('%s*' % FILE_PREFIX):
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remove(g)
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try:
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total_points = int(sys.argv[1])
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total_tries = int(sys.argv[2])
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total_points = int(sys.argv[1])
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random_points = int(sys.argv[2])
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total_tries = int(sys.argv[3])
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except:
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print "usage: app.py total_points total_tries"
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print "usage: app.py [total points in random grid] [number of random points to attempt] [total attempts]"
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sys.exit(1)
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@ -25,18 +28,19 @@ print "total points", total_points
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d = {True: 0, False: 0}
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for i in xrange(total_tries):
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for cur_try in xrange(total_tries):
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g = random_grid(total_points)
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open('%s%0.3d.txt' % (FILE_PREFIX, cur_try), 'w').write(g.for_qhull())
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open('%s%0.3d.txt' % (FILE_PREFIX, i), 'w').write(g.for_qhull())
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for i in xrange(random_points):
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X = [np.random.rand(), np.random.rand()]
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exact = exact_func(X)
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X = [0.3, 0.3]
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exact = exact_func(X)
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try:
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answer = g.run_baker(X)
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d[improved_answer(answer, exact)] += 1
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except smberror as e:
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print e
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print d
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try:
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answer = g.run_baker(X)
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d[improved_answer(answer, exact)] += 1
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except smberror as e:
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print e
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print d
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print d
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@ -24,9 +24,8 @@ q = [exact_func(i) for i in verts]
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g = grid(verts,q)
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X = [0.3, 0.3]
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X = [0.13206472640187261, 0.98644929172054607]
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g.get_containing_simplex(X)
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exact = exact_func(X)
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try:
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502
data/qhull-000.txt
Normal file
502
data/qhull-000.txt
Normal file
@ -0,0 +1,502 @@
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2
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500
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|
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|
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
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||||
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|
||||
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|
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|
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
||||
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|
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|
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|
||||
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|
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
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0.139690 0.576022
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0.623300 0.284221
|
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0.874903 0.308943
|
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0.050968 0.315062
|
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0.415732 0.861086
|
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0.269109 0.632107
|
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0.915507 0.504078
|
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0.263057 0.955175
|
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0.080084 0.384505
|
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0.825620 0.145982
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0.696184 0.599655
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0.041665 0.753284
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0.935032 0.058134
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0.919558 0.320587
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0.996719 0.935324
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0.034179 0.175121
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0.853912 0.697859
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||||
0.237573 0.737667
|
||||
0.267024 0.466481
|
||||
0.752191 0.412488
|
||||
0.573358 0.776042
|
||||
0.117738 0.008809
|
||||
0.391351 0.799168
|
||||
0.351743 0.448648
|
||||
0.662856 0.038363
|
||||
0.155716 0.234058
|
||||
0.138554 0.485890
|
||||
0.172528 0.261335
|
||||
0.667910 0.841149
|
||||
0.704714 0.702788
|
||||
0.326822 0.296431
|
||||
0.165563 0.696065
|
||||
0.535877 0.037066
|
||||
0.790105 0.399294
|
||||
0.863059 0.179309
|
||||
0.946292 0.349932
|
||||
0.190070 0.030322
|
||||
0.548990 0.765724
|
||||
0.189105 0.326289
|
||||
0.593151 0.625304
|
||||
0.080545 0.071429
|
||||
0.609873 0.315857
|
||||
0.065005 0.557161
|
||||
0.172772 0.854238
|
||||
0.236891 0.340104
|
||||
0.243522 0.490912
|
||||
0.521110 0.131008
|
||||
0.265345 0.106485
|
||||
0.556598 0.480571
|
||||
0.583463 0.318790
|
||||
0.422577 0.524559
|
||||
0.047355 0.832263
|
||||
0.015258 0.359675
|
||||
0.087080 0.749055
|
||||
0.586842 0.711002
|
||||
0.500708 0.511499
|
||||
0.906278 0.753350
|
||||
0.191065 0.742964
|
||||
0.850002 0.747699
|
||||
0.810984 0.958665
|
||||
0.745445 0.101771
|
||||
0.812433 0.356154
|
||||
0.349673 0.482697
|
||||
0.309605 0.448379
|
||||
0.906286 0.305023
|
||||
0.871195 0.236735
|
||||
0.880085 0.619723
|
||||
0.252215 0.218488
|
||||
0.501502 0.938435
|
||||
0.571883 0.839314
|
||||
0.491132 0.508797
|
||||
0.613232 0.418147
|
||||
0.838755 0.849814
|
||||
0.319751 0.694594
|
||||
0.102121 0.280414
|
||||
0.493146 0.520976
|
||||
0.080032 0.935737
|
||||
0.978841 0.426193
|
||||
0.572612 0.929880
|
||||
0.562613 0.788561
|
||||
0.162098 0.497810
|
||||
0.187087 0.439069
|
||||
0.080479 0.414313
|
||||
0.900542 0.203189
|
||||
0.746217 0.777058
|
||||
0.733827 0.872460
|
||||
0.735957 0.728743
|
||||
0.129533 0.625628
|
||||
0.579763 0.036779
|
||||
0.481897 0.045606
|
||||
0.909063 0.879236
|
||||
0.415542 0.769329
|
||||
0.550507 0.500253
|
||||
0.726148 0.975612
|
||||
0.000193 0.603004
|
||||
0.487489 0.695720
|
||||
0.954665 0.714453
|
||||
0.362283 0.292757
|
||||
0.948384 0.300804
|
||||
0.395100 0.822704
|
||||
0.135503 0.304895
|
||||
0.592481 0.260597
|
||||
0.021018 0.757291
|
||||
0.592562 0.782326
|
||||
0.138078 0.735031
|
||||
0.638480 0.457732
|
||||
0.587009 0.255635
|
||||
0.355952 0.747673
|
||||
0.721680 0.346664
|
||||
0.302100 0.822532
|
||||
0.451586 0.424316
|
||||
0.795754 0.368634
|
||||
0.074531 0.085938
|
||||
0.171169 0.610738
|
||||
0.169327 0.627517
|
||||
0.170210 0.139028
|
||||
0.716423 0.333147
|
||||
0.757550 0.343675
|
||||
0.547498 0.134499
|
||||
0.797433 0.285402
|
||||
0.056388 0.965889
|
||||
0.876258 0.041214
|
||||
0.940046 0.599479
|
||||
0.414035 0.393592
|
||||
0.240744 0.965824
|
||||
0.848756 0.776561
|
||||
0.699504 0.236643
|
||||
0.378730 0.003658
|
||||
0.659677 0.101798
|
||||
0.855023 0.541043
|
||||
0.206409 0.835201
|
||||
0.864257 0.742651
|
||||
0.507091 0.737711
|
||||
0.278080 0.176298
|
||||
0.439871 0.586918
|
||||
0.325005 0.662985
|
||||
0.898581 0.664883
|
||||
0.973856 0.807850
|
||||
0.767325 0.718386
|
||||
0.616289 0.183717
|
||||
0.002939 0.230201
|
||||
0.925781 0.241950
|
||||
0.500550 0.574635
|
||||
0.622247 0.624035
|
||||
0.260977 0.344729
|
||||
0.644911 0.765267
|
||||
0.253137 0.819781
|
||||
0.241926 0.709515
|
||||
0.359244 0.740632
|
||||
0.109408 0.105881
|
||||
0.306583 0.231504
|
||||
0.197410 0.586292
|
||||
0.066206 0.518310
|
||||
0.375724 0.151438
|
||||
0.459500 0.107776
|
||||
0.088232 0.245200
|
||||
0.558558 0.076231
|
||||
@ -1,4 +1,5 @@
|
||||
from baker import *
|
||||
from baker.tools import logging as log
|
||||
import numpy as np
|
||||
import sys
|
||||
|
||||
@ -30,7 +31,7 @@ def get_phis(X, R):
|
||||
phi = np.linalg.solve(A,b)
|
||||
except np.linalg.LinAlgError as e:
|
||||
msg = "warning: get_phis: calculation of phis yielded a linearly dependant system (%s)" % e
|
||||
# TODO: log this -- > print >> sys.stderr, msg
|
||||
log.error(msg)
|
||||
raise smberror(msg)
|
||||
phi = np.dot(np.linalg.pinv(A), b)
|
||||
|
||||
@ -136,7 +137,7 @@ def get_error_quadratic(phi, R, S):
|
||||
+ b * phi[1] * phi[2]\
|
||||
+ c * phi[2] * phi[0]
|
||||
|
||||
return error_term, a, b, c
|
||||
return error_term
|
||||
|
||||
def get_error_cubic(phi, R, S):
|
||||
B = [] # baker eq 9
|
||||
@ -181,7 +182,7 @@ def get_error_cubic(phi, R, S):
|
||||
+ f * phi[2] * phi[1] * phi[1]\
|
||||
+ g * phi[0] * phi[1] * phi[2]\
|
||||
|
||||
return error_term, a, b, c
|
||||
return error_term
|
||||
|
||||
|
||||
def run_baker(X, R, S, order=2):
|
||||
@ -195,37 +196,29 @@ def run_baker(X, R, S, order=2):
|
||||
S = extra points
|
||||
"""
|
||||
|
||||
answer = {
|
||||
'qlin': None,
|
||||
'error': None,
|
||||
'final': None,
|
||||
}
|
||||
# calculate values only for the simplex triangle
|
||||
phi, qlin = qlinear(X, R)
|
||||
|
||||
if len(S.points) == 0:
|
||||
answer = {
|
||||
'a': None,
|
||||
'b': None,
|
||||
'c': None,
|
||||
'qlin': qlin,
|
||||
'error': None,
|
||||
'final': None,
|
||||
}
|
||||
if order == 1:
|
||||
answer['qlin'] = qlin
|
||||
return answer
|
||||
|
||||
if order == 2:
|
||||
error_term, a, b, c = get_error_quadratic(phi, R, S)
|
||||
elif order == 2:
|
||||
error_term = get_error_quadratic(phi, R, S)
|
||||
elif order == 3:
|
||||
error_term, a, b, c = get_error_cubic(phi, R, S)
|
||||
error_term = get_error_cubic(phi, R, S)
|
||||
else:
|
||||
raise smberror('unacceptable order for baker method')
|
||||
|
||||
q_final = qlin + error_term
|
||||
|
||||
answer = {
|
||||
'a': a,
|
||||
'b': b,
|
||||
'c': c,
|
||||
'qlin': qlin,
|
||||
'error': error_term,
|
||||
'final': q_final,
|
||||
}
|
||||
answer['qlin' ] = qlin
|
||||
answer['error'] = error_term
|
||||
answer['final'] = q_final
|
||||
|
||||
return answer
|
||||
|
||||
@ -243,14 +236,6 @@ def run_baker_3D(X, R, S):
|
||||
# calculate values only for the triangle
|
||||
phi, qlin = qlinear_3D(X, R)
|
||||
|
||||
if [i for i in phi if i <= 0.0]:
|
||||
s = "this is not a containing simplex:\n"
|
||||
s += " X: %s\n" % X
|
||||
s += " R: %s\n" % R
|
||||
s += " phi: %s, sum(%0.4e)\n" % (phi, sum(phi))
|
||||
print >> sys.stderr, s
|
||||
raise smberror("not containing simplex")
|
||||
|
||||
if len(S.points) == 0:
|
||||
answer = {
|
||||
'a': None,
|
||||
|
||||
@ -1,5 +1,15 @@
|
||||
import os
|
||||
import logging
|
||||
|
||||
logging.basicConfig(
|
||||
level = logging.DEBUG,
|
||||
format = '%(asctime)s %(levelname)s %(message)s',
|
||||
filename = os.path.join(os.sep, 'tmp', 'baker.lol'),
|
||||
)
|
||||
|
||||
import numpy as np
|
||||
|
||||
|
||||
class smberror(Exception):
|
||||
"""
|
||||
this is a silly little exception subclass
|
||||
|
||||
@ -61,6 +61,15 @@ class random_grid(rect_grid):
|
||||
q = []
|
||||
|
||||
r = np.random
|
||||
appx_side_res = int(np.sqrt(num_points))
|
||||
delta = 1.0 / float(appx_side_res)
|
||||
for x in xrange(appx_side_res):
|
||||
cur_x = x * delta
|
||||
for y in xrange(appx_side_res):
|
||||
cur_y = y * delta
|
||||
new_point = [cur_x, cur_y]
|
||||
points.append(new_point)
|
||||
q.append(exact_func(new_point))
|
||||
|
||||
for i in xrange(num_points):
|
||||
cur_x = r.rand()
|
||||
|
||||
@ -6,7 +6,7 @@ import numpy as np
|
||||
import scipy.spatial
|
||||
|
||||
from baker import run_baker
|
||||
from baker.tools import exact_func, smberror
|
||||
from baker.tools import exact_func, smberror, logging
|
||||
from simplex import face, contains
|
||||
from smcqdelaunay import *
|
||||
|
||||
@ -42,7 +42,7 @@ class grid(object):
|
||||
self.tree = scipy.spatial.KDTree(self.points)
|
||||
self.faces = {}
|
||||
self.facets_for_point = defaultdict(list)
|
||||
|
||||
self.counter = 0
|
||||
|
||||
def create_mesh(self, indicies):
|
||||
p = [self.points[i] for i in indicies]
|
||||
@ -50,7 +50,45 @@ class grid(object):
|
||||
return grid(p, q)
|
||||
|
||||
def get_containing_simplex(self, X):
|
||||
pass
|
||||
if not self.faces:
|
||||
logging.debug('get_containing_simplex: setting up connectivity')
|
||||
self.construct_connectivity()
|
||||
|
||||
# get closest point
|
||||
(dist, indicies) = self.tree.query(X, 2)
|
||||
closest_point = indicies[0]
|
||||
|
||||
logging.debug('counter: %d' % self.counter)
|
||||
self.counter += 1
|
||||
logging.debug('X: %s' % X)
|
||||
logging.debug('point index: %d' % closest_point)
|
||||
logging.debug('actual point %s' % self.points[closest_point])
|
||||
logging.debug('distance = %0.4f' % dist[0])
|
||||
|
||||
simplex = None
|
||||
checked_facets = []
|
||||
facets_to_check = self.facets_for_point[closest_point]
|
||||
|
||||
attempts = 0
|
||||
while not simplex:
|
||||
logging.debug('attempt: %d' % attempts)
|
||||
attempts += 1
|
||||
if attempts > 10:
|
||||
raise smberror("probably recursing to many times")
|
||||
cur_facet = facets_to_check.pop()
|
||||
checked_facets.append(cur_facet)
|
||||
facets_to_check.extend([i for i in cur_facet.neighbors if i not in checked_facets])
|
||||
|
||||
if cur_facet.contains(X, self):
|
||||
simplex = cur_facet
|
||||
|
||||
if not simplex:
|
||||
raise AssertionError('no containing simplex found')
|
||||
|
||||
R = self.create_mesh(simplex.verts)
|
||||
|
||||
logging.debug('this must be R: %s' % R)
|
||||
return R
|
||||
|
||||
|
||||
def get_simplex_and_nearest_points(self, X, extra_points = 3, simplex_size = 3):
|
||||
@ -64,9 +102,8 @@ class grid(object):
|
||||
"""
|
||||
(dist, indicies) = self.tree.query(X, simplex_size + extra_points)
|
||||
|
||||
|
||||
# get the containing simplex
|
||||
r_mesh = self.create_mesh(indicies[:simplex_size])
|
||||
# r_mesh = self.create_mesh(indicies[:simplex_size])
|
||||
r_mesh = self.get_containing_simplex(X)
|
||||
# and some extra points
|
||||
s_mesh = self.create_mesh(indicies[simplex_size:])
|
||||
|
||||
@ -103,7 +140,7 @@ class grid(object):
|
||||
if not simplex:
|
||||
raise AssertionError('no containing simplex found')
|
||||
|
||||
R = self.create_mesh(simplex.verts)
|
||||
R = get_containing_simplex(X)# self.create_mesh(simplex.verts)
|
||||
|
||||
|
||||
s = []
|
||||
@ -136,6 +173,7 @@ class grid(object):
|
||||
|
||||
this is part of the __init__ for a rect_grid, but can be called from any grid object
|
||||
"""
|
||||
logging.debug('calling construct_connectivity')
|
||||
qdelaunay_string = get_qdelaunay_dump_str(self)
|
||||
facet_to_facets = []
|
||||
for matcher in grid.facet_re.finditer(qdelaunay_string):
|
||||
|
||||
Loading…
Reference in New Issue
Block a user