From 18b6d25f7e4f0943b3592f3bb4f6ca5ed9c285d3 Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Fri, 19 Jun 2015 22:28:06 +0200
Subject: Add support for Python algorithm plugins
---
samples/python/s018_plugin.py | 138 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 138 insertions(+)
create mode 100644 samples/python/s018_plugin.py
(limited to 'samples/python')
diff --git a/samples/python/s018_plugin.py b/samples/python/s018_plugin.py
new file mode 100644
index 0000000..6677930
--- /dev/null
+++ b/samples/python/s018_plugin.py
@@ -0,0 +1,138 @@
+#-----------------------------------------------------------------------
+#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 SIRTPlugin(astra.plugin.base):
+ """Example of an ASTRA plugin class, implementing a simple 2D SIRT algorithm.
+
+ Optional options:
+
+ 'rel_factor': relaxation factor
+ """
+ required_options=[]
+ optional_options=['rel_factor']
+
+ def initialize(self,cfg):
+ self.W = astra.OpTomo(cfg['ProjectorId'])
+ self.vid = cfg['ReconstructionDataId']
+ self.sid = cfg['ProjectionDataId']
+ try:
+ self.rel = cfg['option']['rel_factor']
+ except KeyError:
+ self.rel = 1
+
+ def run(self, its):
+ v = astra.data2d.get_shared(self.vid)
+ s = astra.data2d.get_shared(self.sid)
+ W = self.W
+ for i in range(its):
+ v[:] += self.rel*(W.T*(s - (W*v).reshape(s.shape))).reshape(v.shape)/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
+ # A default set of plugins to load can be defined in:
+ # - /etc/astra-toolbox/plugins.txt
+ # - [ASTRA_INSTALL_PATH]/python/astra/plugins.txt
+ # - [USER_HOME_PATH]/.astra-toolbox/plugins.txt
+ # - [ASTRA_PLUGIN_PATH environment variable]/plugins.txt
+ # In these files, create a separate line for each plugin with:
+ # [PLUGIN_ASTRA_NAME] [FULL_PLUGIN_CLASS]
+ #
+ # So in this case, it would be a line:
+ # SIRT-PLUGIN s018_plugin.SIRTPlugin
+ #
+ astra.plugin.register('SIRT-PLUGIN','s018_plugin.SIRTPlugin')
+
+ # To get help on a registered plugin, use get_help
+ six.print_(astra.plugin.get_help('SIRT-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('SIRT-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('SIRT-PLUGIN')
+ cfg['ProjectorId'] = proj_id
+ cfg['ProjectionDataId'] = sid
+ cfg['ReconstructionDataId'] = vid
+ cfg['option'] = {}
+ cfg['option']['rel_factor'] = 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('SIRT-PLUGIN', sinogram, 100, extraOptions={'rel_factor':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])
--
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