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-rw-r--r--Wrappers/Python/ccpi/astra/astra_ops.py6
-rw-r--r--Wrappers/Python/ccpi/astra/astra_processors.py2
-rwxr-xr-xWrappers/Python/ccpi/astra/ops.py132
-rwxr-xr-xWrappers/Python/ccpi/astra/processors.py205
-rwxr-xr-x[-rw-r--r--]Wrappers/Python/ccpi/astra/utils.py (renamed from Wrappers/Python/ccpi/astra/astra_utils.py)0
-rwxr-xr-xWrappers/Python/conda-recipe/meta.yaml2
-rwxr-xr-xWrappers/Python/wip/demo_sophiabeads.py4
-rwxr-xr-xWrappers/Python/wip/simple_demo_astra.py6
-rwxr-xr-xWrappers/Python/wip/simple_mc_demo.py6
9 files changed, 350 insertions, 13 deletions
diff --git a/Wrappers/Python/ccpi/astra/astra_ops.py b/Wrappers/Python/ccpi/astra/astra_ops.py
index 45b8238..cd0ef9e 100644
--- a/Wrappers/Python/ccpi/astra/astra_ops.py
+++ b/Wrappers/Python/ccpi/astra/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/astra_processors.py
index 3de43bf..16c1f78 100644
--- a/Wrappers/Python/ccpi/astra/astra_processors.py
+++ b/Wrappers/Python/ccpi/astra/astra_processors.py
@@ -1,5 +1,5 @@
from ccpi.framework import DataSetProcessor, ImageData, AcquisitionData
-from ccpi.astra.astra_utils import convert_geometry_to_astra
+from ccpi.astra.utils import convert_geometry_to_astra
import astra
diff --git a/Wrappers/Python/ccpi/astra/ops.py b/Wrappers/Python/ccpi/astra/ops.py
new file mode 100755
index 0000000..cd0ef9e
--- /dev/null
+++ b/Wrappers/Python/ccpi/astra/ops.py
@@ -0,0 +1,132 @@
+# -*- coding: utf-8 -*-
+# This work is independent part of the Core Imaging Library developed by
+# Visual Analytics and Imaging System Group of the Science Technology
+# Facilities Council, STFC
+# This program 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.
+#
+# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
+
+from ccpi.optimisation.ops import Operator
+import numpy
+import astra
+from ccpi.framework import AcquisitionData, ImageData, DataContainer
+from ccpi.optimisation.ops import PowerMethodNonsquare
+from ccpi.astra.processors import AstraForwardProjector, AstraBackProjector, \
+ AstraForwardProjectorMC, AstraBackProjectorMC
+
+class AstraProjectorSimple(Operator):
+ """ASTRA projector modified to use DataSet and geometry."""
+ def __init__(self, geomv, geomp, device):
+ super(AstraProjectorSimple, self).__init__()
+
+ # Store volume and sinogram geometries.
+ self.sinogram_geometry = geomp
+ self.volume_geometry = geomv
+
+ self.fp = AstraForwardProjector(volume_geometry=geomv,
+ sinogram_geometry=geomp,
+ proj_id=None,
+ device=device)
+
+ self.bp = AstraBackProjector(volume_geometry=geomv,
+ sinogram_geometry=geomp,
+ proj_id=None,
+ device=device)
+
+ # Initialise empty for singular value.
+ self.s1 = None
+
+ def direct(self, IM):
+ self.fp.set_input(IM)
+ out = self.fp.get_output()
+ return out
+
+ def adjoint(self, DATA):
+ self.bp.set_input(DATA)
+ out = self.bp.get_output()
+ return out
+
+ #def delete(self):
+ # astra.data2d.delete(self.proj_id)
+
+ def get_max_sing_val(self):
+ self.s1, sall, svec = PowerMethodNonsquare(self,10)
+ return self.s1
+
+ def size(self):
+ # Only implemented for 2D
+ return ( (self.sinogram_geometry.angles.size, \
+ self.sinogram_geometry.pixel_num_h), \
+ (self.volume_geometry.voxel_num_x, \
+ self.volume_geometry.voxel_num_y) )
+
+ def create_image_data(self):
+ inputsize = self.size()[1]
+ return DataContainer(numpy.random.randn(inputsize[0],
+ inputsize[1]))
+
+
+class AstraProjectorMC(Operator):
+ """ASTRA Multichannel projector"""
+ def __init__(self, geomv, geomp, device):
+ super(AstraProjectorMC, self).__init__()
+
+ # Store volume and sinogram geometries.
+ self.sinogram_geometry = geomp
+ self.volume_geometry = geomv
+
+ self.fp = AstraForwardProjectorMC(volume_geometry=geomv,
+ sinogram_geometry=geomp,
+ proj_id=None,
+ device=device)
+
+ self.bp = AstraBackProjectorMC(volume_geometry=geomv,
+ sinogram_geometry=geomp,
+ proj_id=None,
+ device=device)
+
+ # Initialise empty for singular value.
+ self.s1 = None
+
+ def direct(self, IM):
+ self.fp.set_input(IM)
+ out = self.fp.get_output()
+ return out
+
+ def adjoint(self, DATA):
+ self.bp.set_input(DATA)
+ out = self.bp.get_output()
+ return out
+
+ #def delete(self):
+ # astra.data2d.delete(self.proj_id)
+
+ def get_max_sing_val(self):
+ if self.s1 is None:
+ self.s1, sall, svec = PowerMethodNonsquare(self,10)
+ return self.s1
+ else:
+ return self.s1
+
+ def size(self):
+ # Only implemented for 2D
+ return ( (self.sinogram_geometry.angles.size, \
+ self.sinogram_geometry.pixel_num_h), \
+ (self.volume_geometry.voxel_num_x, \
+ self.volume_geometry.voxel_num_y) )
+
+ def create_image_data(self):
+ inputsize = self.size()[1]
+ return DataContainer(numpy.random.randn(self.volume_geometry.channels,
+ inputsize[0],
+ inputsize[1]))
+
diff --git a/Wrappers/Python/ccpi/astra/processors.py b/Wrappers/Python/ccpi/astra/processors.py
new file mode 100755
index 0000000..16c1f78
--- /dev/null
+++ b/Wrappers/Python/ccpi/astra/processors.py
@@ -0,0 +1,205 @@
+from ccpi.framework import DataSetProcessor, ImageData, AcquisitionData
+from ccpi.astra.utils import convert_geometry_to_astra
+import astra
+
+
+class AstraForwardProjector(DataSetProcessor):
+ '''AstraForwardProjector
+
+ Forward project ImageData to AcquisitionData using ASTRA proj_id.
+
+ Input: ImageData
+ Parameter: proj_id
+ Output: AcquisitionData
+ '''
+
+ def __init__(self,
+ volume_geometry=None,
+ sinogram_geometry=None,
+ proj_id=None,
+ device='cpu'):
+ kwargs = {
+ 'volume_geometry' : volume_geometry,
+ 'sinogram_geometry' : sinogram_geometry,
+ 'proj_id' : proj_id,
+ 'device' : device
+ }
+
+ #DataSetProcessor.__init__(self, **kwargs)
+ super(AstraForwardProjector, self).__init__(**kwargs)
+
+ self.set_ImageGeometry(volume_geometry)
+ self.set_AcquisitionGeometry(sinogram_geometry)
+
+ # Set up ASTRA Volume and projection geometry, not to be stored in self
+ vol_geom, proj_geom = convert_geometry_to_astra(self.volume_geometry,
+ self.sinogram_geometry)
+
+ # ASTRA projector, to be stored
+ if device == 'cpu':
+ # Note that 'line' only one option
+ if self.sinogram_geometry.geom_type == 'parallel':
+ self.set_projector(astra.create_projector('line', proj_geom, vol_geom) )
+ elif self.sinogram_geometry.geom_type == 'cone':
+ self.set_projector(astra.create_projector('line_fanflat', proj_geom, vol_geom) )
+ else:
+ NotImplemented
+ elif device == 'gpu':
+ self.set_projector(astra.create_projector('cuda', proj_geom, vol_geom) )
+ else:
+ NotImplemented
+
+ def check_input(self, dataset):
+ if dataset.number_of_dimensions == 3 or\
+ dataset.number_of_dimensions == 2:
+ return True
+ else:
+ raise ValueError("Expected input dimensions is 2 or 3, got {0}"\
+ .format(dataset.number_of_dimensions))
+
+ def set_projector(self, proj_id):
+ self.proj_id = proj_id
+
+ def set_ImageGeometry(self, volume_geometry):
+ self.volume_geometry = volume_geometry
+
+ def set_AcquisitionGeometry(self, sinogram_geometry):
+ self.sinogram_geometry = sinogram_geometry
+
+ def process(self):
+ IM = self.get_input()
+ DATA = AcquisitionData(geometry=self.sinogram_geometry)
+ #sinogram_id, DATA = astra.create_sino( IM.as_array(),
+ # self.proj_id)
+ sinogram_id, DATA.array = astra.create_sino(IM.as_array(),
+ self.proj_id)
+ astra.data2d.delete(sinogram_id)
+ #return AcquisitionData(array=DATA, geometry=self.sinogram_geometry)
+ return DATA
+
+class AstraBackProjector(DataSetProcessor):
+ '''AstraBackProjector
+
+ Back project AcquisitionData to ImageData using ASTRA proj_id.
+
+ Input: AcquisitionData
+ Parameter: proj_id
+ Output: ImageData
+ '''
+
+ def __init__(self,
+ volume_geometry=None,
+ sinogram_geometry=None,
+ proj_id=None,
+ device='cpu'):
+ kwargs = {
+ 'volume_geometry' : volume_geometry,
+ 'sinogram_geometry' : sinogram_geometry,
+ 'proj_id' : proj_id,
+ 'device' : device
+ }
+
+ #DataSetProcessor.__init__(self, **kwargs)
+ super(AstraBackProjector, self).__init__(**kwargs)
+
+ self.set_ImageGeometry(volume_geometry)
+ self.set_AcquisitionGeometry(sinogram_geometry)
+
+ # Set up ASTRA Volume and projection geometry, not to be stored in self
+ vol_geom, proj_geom = convert_geometry_to_astra(self.volume_geometry,
+ self.sinogram_geometry)
+
+ # ASTRA projector, to be stored
+ if device == 'cpu':
+ # Note that 'line' only one option
+ if self.sinogram_geometry.geom_type == 'parallel':
+ self.set_projector(astra.create_projector('line', proj_geom, vol_geom) )
+ elif self.sinogram_geometry.geom_type == 'cone':
+ self.set_projector(astra.create_projector('line_fanflat', proj_geom, vol_geom) )
+ else:
+ NotImplemented
+ elif device == 'gpu':
+ self.set_projector(astra.create_projector('cuda', proj_geom, vol_geom) )
+ else:
+ NotImplemented
+
+ def check_input(self, dataset):
+ if dataset.number_of_dimensions == 3 or dataset.number_of_dimensions == 2:
+ return True
+ else:
+ raise ValueError("Expected input dimensions is 2 or 3, got {0}"\
+ .format(dataset.number_of_dimensions))
+
+ def set_projector(self, proj_id):
+ self.proj_id = proj_id
+
+ def set_ImageGeometry(self, volume_geometry):
+ self.volume_geometry = volume_geometry
+
+ def set_AcquisitionGeometry(self, sinogram_geometry):
+ self.sinogram_geometry = sinogram_geometry
+
+ def process(self):
+ DATA = self.get_input()
+ IM = ImageData(geometry=self.volume_geometry)
+ rec_id, IM.array = astra.create_backprojection(DATA.as_array(),
+ self.proj_id)
+ astra.data2d.delete(rec_id)
+ return IM
+
+class AstraForwardProjectorMC(AstraForwardProjector):
+ '''AstraForwardProjector Multi channel
+
+ Forward project ImageData to AcquisitionDataSet using ASTRA proj_id.
+
+ Input: ImageDataSet
+ Parameter: proj_id
+ Output: AcquisitionData
+ '''
+ def check_input(self, dataset):
+ if dataset.number_of_dimensions == 2 or \
+ dataset.number_of_dimensions == 3 or \
+ dataset.number_of_dimensions == 4:
+ return True
+ else:
+ raise ValueError("Expected input dimensions is 2 or 3, got {0}"\
+ .format(dataset.number_of_dimensions))
+ def process(self):
+ IM = self.get_input()
+ #create the output AcquisitionData
+ DATA = AcquisitionData(geometry=self.sinogram_geometry)
+
+ for k in range(DATA.geometry.channels):
+ sinogram_id, DATA.as_array()[k] = astra.create_sino(IM.as_array()[k],
+ self.proj_id)
+ astra.data2d.delete(sinogram_id)
+ return DATA
+
+class AstraBackProjectorMC(AstraBackProjector):
+ '''AstraBackProjector Multi channel
+
+ Back project AcquisitionData to ImageData using ASTRA proj_id.
+
+ Input: AcquisitionData
+ Parameter: proj_id
+ Output: ImageData
+ '''
+ def check_input(self, dataset):
+ if dataset.number_of_dimensions == 2 or \
+ dataset.number_of_dimensions == 3 or \
+ dataset.number_of_dimensions == 4:
+ return True
+ else:
+ raise ValueError("Expected input dimensions is 2 or 3, got {0}"\
+ .format(dataset.number_of_dimensions))
+ def process(self):
+ DATA = self.get_input()
+
+ IM = ImageData(geometry=self.volume_geometry)
+
+ for k in range(IM.geometry.channels):
+ rec_id, IM.as_array()[k] = astra.create_backprojection(
+ DATA.as_array()[k],
+ self.proj_id)
+ astra.data2d.delete(rec_id)
+ return IM \ No newline at end of file
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/demo_sophiabeads.py b/Wrappers/Python/wip/demo_sophiabeads.py
index e3c7f3a..33ce9ec 100755
--- a/Wrappers/Python/wip/demo_sophiabeads.py
+++ b/Wrappers/Python/wip/demo_sophiabeads.py
@@ -3,8 +3,8 @@ 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("C:/Users/mbbssjj2/Documents/SophiaBeads_256_averaged/SophiaBeads_256_averaged.xtekct")
diff --git a/Wrappers/Python/wip/simple_demo_astra.py b/Wrappers/Python/wip/simple_demo_astra.py
index 3365504..26f3ff4 100755
--- a/Wrappers/Python/wip/simple_demo_astra.py
+++ b/Wrappers/Python/wip/simple_demo_astra.py
@@ -2,9 +2,9 @@
#sys.path.append("..")
from ccpi.framework import ImageData , ImageGeometry, AcquisitionGeometry
-from ccpi.reconstruction.algs import FISTA, FBPD, CGLS
-from ccpi.reconstruction.funcs import Norm2sq, Norm1 , TV2D
-from ccpi.astra.astra_ops import AstraProjectorSimple
+from ccpi.optimisation.algs import FISTA, FBPD, CGLS
+from ccpi.optimisation.funcs import Norm2sq, Norm1 , TV2D
+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 f77a678..7369d8f 100755
--- a/Wrappers/Python/wip/simple_mc_demo.py
+++ b/Wrappers/Python/wip/simple_mc_demo.py
@@ -2,9 +2,9 @@
#sys.path.append("..")
from ccpi.framework import ImageData, AcquisitionData, ImageGeometry, AcquisitionGeometry
-from ccpi.reconstruction.algs import FISTA
-from ccpi.reconstruction.funcs import Norm2sq, Norm1
-from ccpi.astra.astra_ops import AstraProjectorMC
+from ccpi.optimisation.algs import FISTA
+from ccpi.optimisation.funcs import Norm2sq, Norm1
+from ccpi.astra.ops import AstraProjectorMC
import numpy
import matplotlib.pyplot as plt
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 08:29:29 +0000