def diff_pkl2chomp ( files , savedir ) :
#grab files, skip directories
if os.path.isdir (files):
fdir = files + '/'
dlist = os.listdir(fdir)
frames = []
for f in dlist:
if f.endswith('npy') and not os.path.isdir(fdir+f):
frames.append(f)
else:
frames = [ files ]
fdir = files.rpartition('/')[0].rpartition('/')[0]+'/'
#savedir = '/home/kellys/RBC_Deriv_120125_r01/'
#print 'attempting chomp runs..'
frames.sort(key=natural_key)
for frame in frames:
savename = frame.rstrip('npy') + 'cub'
#CB.png2chomp(fdir + frame)
arr = numpy.load(fdir+frame)
w = numpy.where(arr==True)
newarr = numpy.vstack( (w[0],w[1])).T
CB.array2chomp(newarr,fdir+savename)
CB.run_chomp(fdir + savename, savedir+savename)
"/sciclone/home04/jberwald/data10/wyss/data/Cells_Jesse/Old/frames/old_50125/" "fft_frames/bandpass/smooth_r0708/"
)
# grab files, skip directories
if os.path.isdir(files):
fdir = files + "/"
dlist = os.listdir(fdir)
frames = []
for f in dlist:
if f.endswith("npy") and not os.path.isdir(fdir + f):
frames.append(f)
else:
frames = [files]
fdir = files.rpartition("/")[0].rpartition("/")[0] + "/"
# savedir = '/home/kellys/RBC_Deriv_120125_r01/'
# savedir = '/home/kellys/RBC_Deriv_110125_r01/'
savedir = files + "betti/" #'/home/kellys/RBC_Deriv_120125_r005/'
print "attempting chomp runs.."
for frame in frames:
filename = frame.rstrip("npy") + "cub"
savename = frame.rstrip("npy") + "cbetti"
# CB.png2chomp(fdir + frame)
arr = numpy.load(fdir + frame)
w = numpy.where(arr == True)
# w2 = numpy.where(w[2] == 0)[0]
newarr = numpy.vstack((w[0], w[1])).T
CB.array2chomp(newarr, fdir + filename)
CB.run_chomp(fdir + filename, fdir + savename)
print "finished.."
# vol = find_volume( test_voxel )
# pts = subdivide( test_voxel )
# print "voxel\n", test_voxel
# print "voxel vol", vol
# print ""
# print "sub voxel\n", pts
# print "vol", find_volume( pts )
# print ""
# dx = np.absolute( pts[1][0]-pts[0][0] )
# print "dx", dx
# scaled = pts * 1./dx
# print "scaled\n", scaled
pts, scalars, dx, dy, dz = run()
pts[:,:-1] *= 1./dx
# pts[:,0] *= 1./dx
# pts[:,1] *= 1./dy
# pts[:,2] *= 1./dz
uniq_scalars = np.unique( scalars )
colors_idx = [ np.where( pts[:,-1] == s )[0]
for s in uniq_scalars ]
cubset = [ np.array( pts[ colors_idx[i], :-1 ], dtype=np.uint )
for i,s in enumerate( uniq_scalars ) ]
fname = 'cylinder'
for i,s in enumerate( uniq_scalars ):
cb.array2chomp( cubset[i], fname+str(s)+'.cub' )