def shepp3d(sz=512):
import tomopy.misc
import tomobox
vol = tomobox.volume(tomopy.misc.phantom.shepp3d(sz))
vol.meta.history.add_record('SheppLogan phantom is generated', sz)
return vol
projections.reconstruct._initialize_astra()
#%%
import pdm
segmenter = pdm.pdm()
# initialise pdm object
segmenter.rho_method = 'quadratic'
segmenter.proj_geom = projections.reconstruct.proj_geom
segmenter.vol_geom = projections.reconstruct.vol_geom
segmenter.projections = projections.data._data
tau_initial = [0.0, 0.00001, 0.0001]
rho_initial = [0.00001, 0000.1, 0.001, 0.01]
segmenter.rho_fixed = numpy.array([False, False, False, False],
dtype=numpy.bool)
segmenter.tau_fixed = numpy.array([False, False, False], dtype=numpy.bool)
#
#%% Run PDM
start = time.time()
[S, rho_opt, tau_opt] = segmenter.run(volume, projections.meta.theta,
rho_initial, tau_initial)
end = time.time()
print(end - start)
#%%
v = tw.volume(S)
#%%
v.io.save(path='', fname='seg', fmt='tiff')
# -*- coding: utf-8 -*- """ Test of the reconstructor. """ #%% Test IO import tomobox import reconstruction import simulate #%% Create aphantom: #phantom = simulate.phantom.shepp3d([10, 256, 256]) phantom = simulate.phantom.checkers([10, 256, 256]) vol = tomobox.volume(array=phantom, img_pixel=[0.1, 0.1, 0.1], block_sizeGB=3) vol.display.slice() #%% Forward project: proj = tomobox.projections(block_sizeGB=3) proj.data.zeros([20, 100, 256]) proj.meta.geometry.init(100, 100, [0.1, 0.1], theta_n=100) recon = reconstruction.reconstruct(proj, vol) recon.forwardproject() proj.display.slice() #%% Test Back-projector: vol.data.zeros() #recon._projections_to_swap()
b.io.read_flexray('/export/scratch3/kostenko/Fast_Data/rijksmuseum/tiling/al_dummy_vertical_tile_1/')
b.process.flat_field()
b.process.log()
b.display.slice(dim = 1)
b.data.switch_to_swap(keep_data=True, swap_path = '/export/scratch3/kostenko/Fast_Data/swap', swap_name = 'swap_0')
b.data.switch_to_swap(keep_data=True, swap_path = '/export/scratch3/kostenko/Fast_Data/swap', swap_name = 'swap_1')
#%% QC:
a.meta.geometry.report()
b.meta.geometry.report()
#%% Test
import reconstruction
pix = a.meta.geometry.img_pixel[1]
volume = tomobox.volume([500,401,400], pix)
recon = reconstruction.reconstruct([a, b], volume)
#%%
recon.FDK()
volume.display.slice()
volume.display.slice(dim = 0)
prj.io.read_flexray('/export/scratch3/kostenko/Fast_Data/naturalis/oct2017_femora_trinil/whale_ear_1/')
# Process:
prj.process.flat_field()
prj.process.log()
prj.display.slice(dim = 1)
#energy, spec = numpy.loadtxt('/export/scratch3/kostenko/Fast_Data/rijksmuseum/dummy/spectrum.txt')
#prj.process.equivalent_thickness(energy, spec, 'Bone, Compact (ICRU)', 1.6)
prj.meta.geometry.report()
#%%
shape = numpy.array([1500,1900,1900]) // bine
img_pixel = numpy.array([0.03, 0.03, 0.03]) * bine
volume = tomobox.volume(shape = shape, img_pixel = img_pixel)
recon = reconstruction.reconstruct(prj, volume)
recon.FDK()
volume.data.cast_uint8()
volume.io.write_data('/export/scratch3/kostenko/Fast_Data/naturalis/oct2017_femora_trinil/whale_ear_1/'+ 'FDK')
volume.display.slice()
#%% Release:
volume.release()
prj.release()
#energy, spec = numpy.loadtxt('/export/scratch3/kostenko/Fast_Data/rijksmuseum/dummy/spectrum.txt')
#index = [5,]
index = numpy.arange(0, 8)
path = '/export/scratch3/kostenko/Fast_Data/naturalis/oct2017_femora_trinil/femora_i/'
for ii in index:
prj = tomobox.projections(block_sizeGB=4, swap=False)
#prj.data.switch_to_swap(swap_path = '/export/scratch1/kostenko/tomobox_swap', swap_name = 'swap')
prj.io.options['binning'] = 1
prj.io.options['index_step'] = 1
img_pixel = numpy.ones(3) * 0.045 * prj.io.options['binning']
shape = numpy.array([1550, 1450, 1900], 'uint32') // prj.io.binning
volume = tomobox.volume(shape=shape, img_pixel=img_pixel, block_sizeGB=4)
# Read data:
prj.io.read_flexray(path + 'femora_i_tile_%u' % ii)
# Process:
prj.process.flat_field()
prj.process.log()
# Reconstruct:
prj.meta.geometry.vol_trans[0] = 0
prj.meta.geometry.vol_trans[2] = -10
recon = reconstruction.reconstruct(prj, volume)