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add extra materials related to lewiner mc algorithm
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Almar Klein
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# -*- coding: utf-8 -*-
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# Copyright (C) 2012, Almar Klein
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""" Create lookup tables for the marching cubes algorithm, by parsing
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the file "LookUpTable.h". This prints a text to the stdout wich
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can then be copied to luts.py.
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The luts are tuples of shape and base64 encoded bytes.
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"""
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import numpy as np
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import sys
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import base64
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# Get base64 encode/decode functions
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PY3 = sys.version_info[0] == 3
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if PY3:
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base64encode = base64.encodebytes
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base64decode = base64.decodebytes
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else:
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base64encode = base64.encodestring
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base64decode = base64.decodestring
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def create_luts(fname):
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# Get the lines in the C header file
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text = open(fname,'rb').read().decode('utf-8')
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lines1 = [line.rstrip() for line in text.splitlines()]
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# Init lines for Python
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lines2 = []
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# Get classic table
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more_lines, ii = get_table(lines1, 'static const char casesClassic', 0)
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lines2.extend(more_lines)
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# Get cases table
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more_lines, ii = get_table(lines1, 'static const char cases', 0)
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lines2.extend(more_lines)
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# Get tiling tables
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ii = 0
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for casenr in range(99):
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# Get table
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more_lines, ii = get_table(lines1, 'static const char tiling', ii+1)
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if ii < 0:
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break
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else:
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lines2.extend(more_lines)
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# Get test tables
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ii = 0
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for casenr in range(99):
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# Get table
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more_lines, ii = get_table(lines1, 'static const char test', ii+1)
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if ii < 0:
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break
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else:
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lines2.extend(more_lines)
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# Get subconfig tables
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ii = 0
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for casenr in range(99):
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# Get table
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more_lines, ii = get_table(lines1, 'static const char subconfig', ii+1)
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if ii < 0:
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break
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else:
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lines2.extend(more_lines)
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return '\n'.join(lines2)
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def get_table(lines1, needle, i):
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# Try to find the start
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ii = search_line(lines1, needle, i)
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if ii < 0:
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return [], -1
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# Init result
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lines2 = []
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# Get size and name
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front, dummu, back = lines1[ii].partition('[')
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name = front.split(' ')[-1].upper()
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size = int(back.split(']',1)[0])
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cdes = lines1[ii].rstrip(' {=')
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# Write name
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lines2.append('%s = np.array([' % name)
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# Get elements
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for i in range(ii+1, ii+1+9999999):
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line1 = lines1[i]
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front, dummy, back = line1.partition('*/')
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if not back:
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front, back = back, front
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line2 = ' '
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line2 += back.strip().replace('{', '[').replace('}',']').replace(';','')
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line2 += front.replace('/*',' #').rstrip()
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lines2.append(line2)
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if line1.endswith('};'):
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break
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# Close and return
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lines2.append(" , 'int8')")
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lines2.append('')
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#return lines2, ii+size
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# Execute code and get array as base64 text
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code = '\n'.join(lines2)
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code = code.split('=',1)[1]
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array = eval(code)
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array64 = base64encode(array.tostring()).decode('utf-8')
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# Reverse: bytes = base64decode(text.encode('utf-8'))
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text = '%s = %s, """\n%s"""' % (name, str(array.shape), array64)
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# Build actual lines
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lines2 = []
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#lines2.append( '# %s -> %s %s' % (cdes, str(array.dtype), str(array.shape)) )
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lines2.append( '#' + cdes)
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lines2.append(text)
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lines2.append('')
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return lines2, ii+size
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def search_line(lines, refline, start=0):
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for i, line in enumerate(lines[start:]):
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if line.startswith(refline):
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return i + start
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return -1
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def getLutNames(prefix):
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aa = []
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for a in dir(luts):
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if a.startswith(prefix): aa.append(a)
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def sortkey(x):
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fullnr = x.split(prefix)[1]
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nr, us, subnr = fullnr.partition('_')
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if len(nr) == 1:
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nr = '0'+nr
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return nr + us + subnr
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return [a for a in sorted(aa, key=sortkey)]
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if __name__ == '__main__':
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import os
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fname = os.path.join(os.getcwd(), 'LookUpTable.h')
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if True:
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with open(os.path.join(os.getcwd(), 'mcluts.py'), 'w') as f:
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f.write('# -*- coding: utf-8 -*-\n')
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f.write('# Copyright (C) 2012, Almar Klein\n# Copyright (C) 2002, Thomas Lewiner\n\n')
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f.write('# This file was auto-generated from LookUpTable.h by createluts.py.\n\n')
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f.write(create_luts(fname))
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else:
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for prefix in ['TILING', 'TEST']:
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tmp = ['luts.'+a for a in getLutNames(prefix)]
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print(', '.join(tmp))
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print('')
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for name in getLutNames(prefix):
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print('self.%s = Lut(%s)' % (name, name))
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print('')
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for name in getLutNames(prefix):
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print('cdef Lut %s' % name)
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print('')
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print('')
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@@ -0,0 +1,64 @@
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"""
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Script to show the results of the two marching cubes algorithms on different
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data.
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"""
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import time
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import numpy as np
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import visvis as vv
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from skimage.measure import marching_cubes, marching_cubes_lewiner
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# Create test volume
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SELECT = 1
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if SELECT == 1:
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# Medical data
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vol = vv.volread('stent')
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isovalue = 800
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elif SELECT == 2:
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# Blocky data
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vol = vv.aVolume(20, 128) # Different every time
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isovalue = 0.2
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elif SELECT == 3:
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# Generate two donuts
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n = 48
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a, b = 2.5/n, -1.25
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isovalue = 0.0
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#
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vol = np.empty((n,n,n), 'float32')
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for iz in range(vol.shape[0]):
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for iy in range(vol.shape[1]):
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for ix in range(vol.shape[2]):
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z, y, x = float(iz)*a+b, float(iy)*a+b, float(ix)*a+b
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vol[iz,iy,ix] = ( (
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(8*x)**2 + (8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) * ( (8*x)**2 +
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(8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) - 64 * ( (8*x)**2 + (8*y-2)**2 )
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) * ( ( (8*x)**2 + ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2 + 16 - 1.85*1.85 )
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* ( (8*x)**2 + ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2 + 16 - 1.85*1.85 ) -
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64 * ( ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2
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) ) + 1025
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# Uncommenting the line below will yield different results for classic MC
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#vol = -vol
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# Get surface meshes
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t0 = time.time()
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vertices1, faces1, *_ = marching_cubes_lewiner(vol, isovalue, use_classic=False)
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print('finding surface lewiner took %1.0f ms' % (1000*(time.time()-t0)) )
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t0 = time.time()
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vertices2, faces2, *_ = marching_cubes(vol, isovalue)
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print('finding surface classic took %1.0f ms' % (1000*(time.time()-t0)) )
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# Show
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vv.figure(1); vv.clf()
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a1 = vv.subplot(121); vv.mesh(np.fliplr(vertices1), faces1)
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a2 = vv.subplot(122); vv.mesh(np.fliplr(vertices2), faces2)
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a1.camera = a2.camera
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vv.use().Run()
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