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Diffstat (limited to 'samples/python/s018_plugin.py')
| -rw-r--r-- | samples/python/s018_plugin.py | 140 |
1 files changed, 140 insertions, 0 deletions
diff --git a/samples/python/s018_plugin.py b/samples/python/s018_plugin.py new file mode 100644 index 0000000..85b5486 --- /dev/null +++ b/samples/python/s018_plugin.py @@ -0,0 +1,140 @@ +#----------------------------------------------------------------------- +#Copyright 2015 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np +import six + +# Define the plugin class (has to subclass astra.plugin.base) +# Note that usually, these will be defined in a separate package/module +class LandweberPlugin(astra.plugin.base): + """Example of an ASTRA plugin class, implementing a simple 2D Landweber algorithm. + + Options: + + 'Relaxation': relaxation factor (optional) + """ + + # The astra_name variable defines the name to use to + # call the plugin from ASTRA + astra_name = "LANDWEBER-PLUGIN" + + def initialize(self,cfg, Relaxation = 1): + self.W = astra.OpTomo(cfg['ProjectorId']) + self.vid = cfg['ReconstructionDataId'] + self.sid = cfg['ProjectionDataId'] + self.rel = Relaxation + + def run(self, its): + v = astra.data2d.get_shared(self.vid) + s = astra.data2d.get_shared(self.sid) + tv = np.zeros(v.shape, dtype=np.float32) + ts = np.zeros(s.shape, dtype=np.float32) + W = self.W + for i in range(its): + W.FP(v,out=ts) + ts -= s # ts = W*v - s + + W.BP(ts,out=tv) + tv *= self.rel / s.size + + v -= tv # v = v - rel * W'*(W*v-s) / s.size + +if __name__=='__main__': + + vol_geom = astra.create_vol_geom(256, 256) + proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + + # As before, create a sinogram from a phantom + import scipy.io + P = scipy.io.loadmat('phantom.mat')['phantom256'] + proj_id = astra.create_projector('cuda',proj_geom,vol_geom) + + # construct the OpTomo object + W = astra.OpTomo(proj_id) + + sinogram = W * P + sinogram = sinogram.reshape([180, 384]) + + # Register the plugin with ASTRA + # First we import the package that contains the plugin + import s018_plugin + # Then, we register the plugin class with ASTRA + astra.plugin.register(s018_plugin.LandweberPlugin) + + # Get a list of registered plugins + six.print_(astra.plugin.get_registered()) + + # To get help on a registered plugin, use get_help + six.print_(astra.plugin.get_help('LANDWEBER-PLUGIN')) + + # Create data structures + sid = astra.data2d.create('-sino', proj_geom, sinogram) + vid = astra.data2d.create('-vol', vol_geom) + + # Create config using plugin name + cfg = astra.astra_dict('LANDWEBER-PLUGIN') + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + + # Create algorithm object + alg_id = astra.algorithm.create(cfg) + + # Run algorithm for 100 iterations + astra.algorithm.run(alg_id, 100) + + # Get reconstruction + rec = astra.data2d.get(vid) + + # Options for the plugin go in cfg['option'] + cfg = astra.astra_dict('LANDWEBER-PLUGIN') + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['option'] = {} + cfg['option']['Relaxation'] = 1.5 + alg_id_rel = astra.algorithm.create(cfg) + astra.algorithm.run(alg_id_rel, 100) + rec_rel = astra.data2d.get(vid) + + # We can also use OpTomo to call the plugin + rec_op = W.reconstruct('LANDWEBER-PLUGIN', sinogram, 100, extraOptions={'Relaxation':1.5}) + + import pylab as pl + pl.gray() + pl.figure(1) + pl.imshow(rec,vmin=0,vmax=1) + pl.figure(2) + pl.imshow(rec_rel,vmin=0,vmax=1) + pl.figure(3) + pl.imshow(rec_op,vmin=0,vmax=1) + pl.show() + + # Clean up. + astra.projector.delete(proj_id) + astra.algorithm.delete([alg_id, alg_id_rel]) + astra.data2d.delete([vid, sid]) |