def register_astra_geometry(proj_fix, proj_mov, geom_fix, geom_mov, subsamp=1):
"""
Compute a rigid transformation that makes sure that two reconstruction volumes are alligned.
Args:
proj_fix : projection data of the fixed volume
proj_mov : projection data of the fixed volume
geom_fix : projection data of the fixed volume
geom_mov : projection data of the fixed volume
Returns:
geom : geometry for the second reconstruction volume
"""
print('Computing a rigid tranformation between two datasets.')
# Find maximum vol size:
sz = numpy.array([proj_fix.shape, proj_mov.shape]).max(0)
sz += 10 # for safety...
vol1 = numpy.zeros(sz, dtype='float32')
vol2 = numpy.zeros(sz, dtype='float32')
projector.settings.bounds = [0, 10]
projector.settings.subsets = 10
projector.settings['mode'] = 'sequential'
projector.FDK(proj_fix, vol1, geom_fix)
projector.SIRT(proj_fix, vol1, geom_fix, iterations=5)
projector.FDK(proj_mov, vol2, geom_mov)
projector.SIRT(proj_mov, vol2, geom_mov, iterations=5)
display.slice(vol1, title='Fixed volume preview')
display.slice(vol1, title='Moving volume preview')
# Find transformation between two volumes:
R, T = register_volumes(vol1,
vol2,
subsamp=subsamp,
use_moments=True,
use_CG=True)
return R, T
flat = data.read_stack(path, 'io00', sample=binn)
proj = data.read_stack(path, 'scan_', sample=binn, skip=binn)
geom = data.read_flexraylog(path, sample=binn)
#%% Prepro:
flat = (flat - dark).mean(1)
proj = (proj - dark) / flat[:, None, :]
proj = -numpy.log(proj).astype('float32')
display.slice(proj, dim=1, title='Projection')
#%% FDK Recon
vol = projector.init_volume(proj)
projector.FDK(proj, vol, geom)
display.slice(vol, bounds=[], title='FDK')
#%% SIRT with additional options
vol = projector.init_volume(proj)
projector.settings.bounds = [0, 10]
projector.settings.subsets = 10
projector.settings.sorting = 'equidistant'
projector.SIRT(proj, vol, geom, iterations=5)
display.slice(vol, title='SIRT')
projector.backproject(proj, vol_rec, geom) display.slice(vol_rec, title = 'Backprojection') #%% Filtered back-project # Make volume: vol_rec = numpy.zeros_like(vol) # Use FDK: projector.FDK(proj, vol_rec, geom) display.slice(vol_rec, title = 'FDK') #%% Simple SIRT: vol_rec = numpy.zeros_like(vol) projector.SIRT(proj, vol_rec, geom, iterations = 20) display.slice(vol_rec, title = 'SIRT') #%% SIRT with subsets and non-negativity: # Settings: projector.settings.update_residual = True projector.settings.bounds = [0, 2] projector.settings.subsets = 10 projector.settings.sorting = 'equidistant' # Reonstruction: vol_rec = numpy.zeros_like(vol) projector.SIRT(proj, vol_rec, geom, iterations = 20) display.slice(vol_rec, title = 'SIRT')
proj_a = numpy.zeros([128, 32, 128], dtype = 'float32') proj_b = numpy.zeros([128, 32, 128], dtype = 'float32') # Define a simple projection geometry: geom_a = geometry.circular(src2obj = 100, det2obj = 100, det_pixel = 0.01, ang_range = [0, 360]) geom_b = geom_a.copy() geom_b['axs_roll'] = 90 # Create phantom and project into proj: vol = phantom.random_spheroids([128, 128, 128], geom_a, number = 10) display.slice(vol, title = 'Phantom') # Forward project: projector.forwardproject(proj_a, vol, geom_a) projector.forwardproject(proj_b, vol, geom_b) display.slice(proj_a, dim = 1, title = 'Proj A') display.slice(proj_b, dim = 1, title = 'Proj B') #%% Single-dataset SIRT: vol_rec = numpy.zeros_like(vol) projector.SIRT(proj_a, vol_rec, geom_a, iterations = 20) display.slice(vol_rec, bounds = [0, 1], title = 'SIRT') #%% Multi-dataset SIRT: vol_rec = numpy.zeros_like(vol) projector.SIRT([proj_a, proj_b], vol_rec, [geom_a, geom_b], iterations = 20) display.slice(vol_rec, bounds = [0, 1], title = 'Multi-data SIRT')