Merge branch 'master' into cleandemos

9 files changed, 14 insertions, 103 deletions

diff --git a/Wrappers/Python/ccpi/astra/astra_ops.py b/Wrappers/Python/ccpi/astra/ops.py
index 45b8238..cd0ef9e 100644..100755
--- a/Wrappers/Python/ccpi/astra/astra_ops.py
+++ b/Wrappers/Python/ccpi/astra/ops.py
@@ -15,12 +15,12 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-from ccpi.reconstruction.ops import Operator
+from ccpi.optimisation.ops import Operator
 import numpy
 import astra
 from ccpi.framework import AcquisitionData, ImageData, DataContainer
-from ccpi.reconstruction.ops import PowerMethodNonsquare
-from ccpi.astra.astra_processors import AstraForwardProjector, AstraBackProjector, \
+from ccpi.optimisation.ops import PowerMethodNonsquare
+from ccpi.astra.processors import AstraForwardProjector, AstraBackProjector, \
      AstraForwardProjectorMC, AstraBackProjectorMC
 
 class AstraProjectorSimple(Operator):
diff --git a/Wrappers/Python/ccpi/astra/astra_processors.py b/Wrappers/Python/ccpi/astra/processors.py
index fac4551..02c9070 100644
--- a/Wrappers/Python/ccpi/astra/astra_processors.py
+++ b/Wrappers/Python/ccpi/astra/processors.py
@@ -1,5 +1,5 @@
-from ccpi.framework import DataProcessor, ImageData, AcquisitionData
-from ccpi.astra.astra_utils import convert_geometry_to_astra
+from ccpi.framework import DataSetProcessor, ImageData, AcquisitionData
+from ccpi.astra.utils import convert_geometry_to_astra
 import astra
 
 
@@ -202,4 +202,4 @@ class AstraBackProjectorMC(AstraBackProjector):
                     DATA.as_array()[k], 
                     self.proj_id)
             astra.data2d.delete(rec_id)
-        return IM
\ No newline at end of file
+        return IM
diff --git a/Wrappers/Python/ccpi/astra/astra_utils.py b/Wrappers/Python/ccpi/astra/utils.py
index 9f8fe46..9f8fe46 100644..100755
--- a/Wrappers/Python/ccpi/astra/astra_utils.py
+++ b/Wrappers/Python/ccpi/astra/utils.py
diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml
index 12e83e2..ca91ed0 100755
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/Wrappers/Python/conda-recipe/meta.yaml
@@ -19,7 +19,7 @@ requirements:
     - python
     - numpy
     - scipy
-    - ccpi-common
+    - ccpi-framework
     - astra-toolbox
 	
 about:
diff --git a/Wrappers/Python/wip/astra_test.py b/Wrappers/Python/wip/astra_test.py
deleted file mode 100755
index c0a7359..0000000
--- a/Wrappers/Python/wip/astra_test.py
+++ /dev/null
@@ -1,87 +0,0 @@
-# -*- coding: utf-8 -*-

-"""

-Created on Wed Mar  7 15:07:16 2018

-

-@author: ofn77899

-"""

-

-# -----------------------------------------------------------------------

-# Copyright: 2010-2018, imec Vision Lab, University of Antwerp

-#            2013-2018, CWI, Amsterdam

-#

-# Contact: astra@astra-toolbox.com

-# Website: http://www.astra-toolbox.com/

-#

-# This file is part of the ASTRA Toolbox.

-#

-#

-# 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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.

-#

-# -----------------------------------------------------------------------

-

-import astra

-import numpy as np

-

-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))

-

-# For CPU-based algorithms, a "projector" object specifies the projection

-# model used. In this case, we use the "strip" model.

-proj_id = astra.create_projector('strip', proj_geom, vol_geom)

-

-# Create a sinogram from a phantom

-import scipy.io

-P = scipy.io.loadmat('phantom.mat')['phantom256']

-sinogram_id, sinogram = astra.create_sino(P, proj_id)

-

-import pylab

-pylab.gray()

-pylab.figure(1)

-pylab.imshow(P)

-pylab.figure(2)

-pylab.imshow(sinogram)

-

-# Create a data object for the reconstruction

-rec_id = astra.data2d.create('-vol', vol_geom)

-

-# Set up the parameters for a reconstruction algorithm using the CPU

-# The main difference with the configuration of a GPU algorithm is the

-# extra ProjectorId setting.

-cfg = astra.astra_dict('SIRT')

-cfg['ReconstructionDataId'] = rec_id

-cfg['ProjectionDataId'] = sinogram_id

-cfg['ProjectorId'] = proj_id

-

-# Available algorithms:

-# ART, SART, SIRT, CGLS, FBP

-

-

-# Create the algorithm object from the configuration structure

-alg_id = astra.algorithm.create(cfg)

-

-# Run 20 iterations of the algorithm

-# This will have a runtime in the order of 10 seconds.

-astra.algorithm.run(alg_id, 20)

-

-# Get the result

-rec = astra.data2d.get(rec_id)

-pylab.figure(3)

-pylab.imshow(rec)

-pylab.show()

-

-# Clean up.

-astra.algorithm.delete(alg_id)

-astra.data2d.delete(rec_id)

-astra.data2d.delete(sinogram_id)

-astra.projector.delete(proj_id)

diff --git a/Wrappers/Python/wip/demo_sophiabeads.py b/Wrappers/Python/wip/demo_sophiabeads.py
index 8c72964..53a0bf8 100755
--- a/Wrappers/Python/wip/demo_sophiabeads.py
+++ b/Wrappers/Python/wip/demo_sophiabeads.py
@@ -11,8 +11,8 @@ from ccpi.io.reader import XTEKReader
 import numpy as np
 import matplotlib.pyplot as plt
 from ccpi.framework import ImageGeometry, AcquisitionGeometry, AcquisitionData, ImageData
-from ccpi.astra.astra_ops import AstraProjectorSimple
-from ccpi.reconstruction.algs import CGLS
+from ccpi.astra.ops import AstraProjectorSimple
+from ccpi.optimisation.algs import CGLS
 
 # Set up reader object and read the data
 datareader = XTEKReader("REPLACE_THIS_BY_PATH_TO_DATASET/SophiaBeads_256_averaged.xtekct")
diff --git a/Wrappers/Python/wip/desktop.ini b/Wrappers/Python/wip/desktop.ini
deleted file mode 100755
index bb9f3d6..0000000
--- a/Wrappers/Python/wip/desktop.ini
+++ /dev/null
@@ -1,4 +0,0 @@
-[ViewState]

-Mode=

-Vid=

-FolderType=Generic

diff --git a/Wrappers/Python/wip/simple_demo_astra.py b/Wrappers/Python/wip/simple_demo_astra.py
index 369bc99..b4f0c61 100755
--- a/Wrappers/Python/wip/simple_demo_astra.py
+++ b/Wrappers/Python/wip/simple_demo_astra.py
@@ -8,7 +8,8 @@
 from ccpi.framework import ImageData , ImageGeometry, AcquisitionGeometry
 from ccpi.optimisation.algs import FISTA, FBPD, CGLS
 from ccpi.optimisation.funcs import Norm2sq, Norm1, TV2D
-from ccpi.astra.astra_ops import AstraProjectorSimple
+from ccpi.astra.ops import AstraProjectorSimple
+
 import numpy as np
 import matplotlib.pyplot as plt
 
diff --git a/Wrappers/Python/wip/simple_mc_demo.py b/Wrappers/Python/wip/simple_mc_demo.py
index eb69c88..3b78eb3 100755
--- a/Wrappers/Python/wip/simple_mc_demo.py
+++ b/Wrappers/Python/wip/simple_mc_demo.py
@@ -8,7 +8,8 @@
 from ccpi.framework import ImageData, AcquisitionData, ImageGeometry, AcquisitionGeometry
 from ccpi.optimisation.algs import FISTA
 from ccpi.optimisation.funcs import Norm2sq, Norm1
-from ccpi.astra.astra_ops import AstraProjectorMC
+from ccpi.astra.ops import AstraProjectorMC
+
 import numpy
 import matplotlib.pyplot as plt
 
@@ -133,4 +134,4 @@ plt.show()
 
 plt.semilogy(criter1)
 plt.title('Criterion vs iterations, least squares plus 1-norm regu')
-plt.show()
\ No newline at end of file
+plt.show()