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-rw-r--r--src/Python/ccpi/reconstruction/AstraDevice.py36
-rw-r--r--src/Python/ccpi/reconstruction/DeviceModel.py7
-rw-r--r--src/Python/ccpi/reconstruction/FISTAReconstructor.py33
-rw-r--r--src/Python/test/test_reconstructor.py67
4 files changed, 84 insertions, 59 deletions
diff --git a/src/Python/ccpi/reconstruction/AstraDevice.py b/src/Python/ccpi/reconstruction/AstraDevice.py
index d854183..ba174b3 100644
--- a/src/Python/ccpi/reconstruction/AstraDevice.py
+++ b/src/Python/ccpi/reconstruction/AstraDevice.py
@@ -1,5 +1,5 @@
import astra
-from DeviceModel import DeviceModel
+from ccpi.reconstruction.DeviceModel import DeviceModel
class AstraDevice(DeviceModel):
'''Concrete class for Astra Device'''
@@ -9,6 +9,9 @@ class AstraDevice(DeviceModel):
data_aquisition_geometry,
reconstructed_volume_geometry):
+ super(AstraDevice, self).__init__(device_type,
+ data_aquisition_geometry,
+ reconstructed_volume_geometry)
self.proj_geom = astra.creators.create_proj_geom(
device_type,
@@ -17,7 +20,6 @@ class AstraDevice(DeviceModel):
self.acquisition_data_geometry['cameraX'],
self.acquisition_data_geometry['cameraY'],
self.acquisition_data_geometry['angles'],
- angles_rad
)
self.vol_geom = astra.creators.create_vol_geom(
@@ -48,19 +50,27 @@ Uses Astra-toolbox
self.vol_geom)
astra.matlab.data3d('delete', idx)
return volume
-
def createReducedDevice(self):
- return AstraDevice(self.proj_geom['type'],
- {'detectorSpacingX' : self.proj_geom['DetectorSpacingX'] ,
- 'detectorSpacingY' : self.proj_geom['DetectorSpacingY'] ,
- 'cameraX' : self.proj_geom['DetectorColCount'] ,
- 'cameraY' : 1 ,
- 'angles' : self.proj_geom['ProjectionAngles'] } ,
- {
- 'X' : self.vol_geom['GridColCount'],
- 'Y' : self.vol_geom['GridRowCount']
- 'Z' : 1} )
+ proj_geom = astra.creators.create_proj_geom(
+ device_type,
+ self.acquisition_data_geometry['detectorSpacingX'],
+ self.acquisition_data_geometry['detectorSpacingX'],
+ self.acquisition_data_geometry['cameraX'],
+ 1,
+ self.acquisition_data_geometry['angles'],
+ )
+ vol_geom = astra.creators.create_vol_geom(
+ self.reconstructed_volume_geometry['X'],
+ self.reconstructed_volume_geometry['Y'],
+ 1
+ )
+ return AstraDevice(proj_geom['type'] ,
+ proj_geom,
+ vol_geom)
+
+
+
if __name__=="main":
a = AstraDevice()
diff --git a/src/Python/ccpi/reconstruction/DeviceModel.py b/src/Python/ccpi/reconstruction/DeviceModel.py
index 1717321..6214437 100644
--- a/src/Python/ccpi/reconstruction/DeviceModel.py
+++ b/src/Python/ccpi/reconstruction/DeviceModel.py
@@ -44,7 +44,7 @@ reconstructed_volume_geometry: tuple (dimX,dimY,dimZ)
'Z': reconstructed_volume_geometry[2] }
@abstractmethod
- def doFowardProject(self, volume):
+ def doForwardProject(self, volume):
'''Forward projects the volume according to the device geometry'''
return NotImplemented
@@ -53,5 +53,10 @@ reconstructed_volume_geometry: tuple (dimX,dimY,dimZ)
def doBackwardProject(self, projections):
'''Backward projects the projections according to the device geometry'''
return NotImplemented
+
+ @abstractmethod
+ def createReducedDevice(self):
+ '''Create a Device to do forward/backward projections on 2D slices'''
+ return NotImplemented
diff --git a/src/Python/ccpi/reconstruction/FISTAReconstructor.py b/src/Python/ccpi/reconstruction/FISTAReconstructor.py
index 1e464a1..d2eefc0 100644
--- a/src/Python/ccpi/reconstruction/FISTAReconstructor.py
+++ b/src/Python/ccpi/reconstruction/FISTAReconstructor.py
@@ -27,7 +27,7 @@ import numpy
from enum import Enum
import astra
-from ccpi.reconstruction.AstraDevice import AstraDevice
+#from ccpi.reconstruction.AstraDevice import AstraDevice
@@ -74,7 +74,10 @@ class FISTAReconstructor():
# 3. "A novel tomographic reconstruction method based on the robust
# Student's t function for suppressing data outliers" D. Kazantsev et.al.
# D. Kazantsev, 2016-17
- def __init__(self, projector_geometry, output_geometry, input_sinogram,
+ def __init__(self, projector_geometry,
+ output_geometry,
+ input_sinogram,
+ device,
**kwargs):
# handle parmeters:
# obligatory parameters
@@ -87,16 +90,10 @@ class FISTAReconstructor():
self.pars['number_of_angles'] = nangles
self.pars['SlicesZ'] = sliceZ
self.pars['output_volume'] = None
-
+ self.pars['device'] = device
- device = createAstraDevice(projector_geometry, output_geometry)
- self.setParameter(device_model=device)
- proj_geomT = projector_geometry.copy();
- proj_geomT['DetectorRowCount'] = 1;
- vol_geomT = output_geometry.copy();
- vol_geomT['GridSliceCount'] = 1;
- reduced_device = createAstraDevice(proj_geomT, vol_geomT)
+ reduced_device = device.createReducedDevice()
self.setParameter(reduced_device_model=reduced_device)
self.use_device = True
@@ -187,21 +184,7 @@ class FISTAReconstructor():
self.pars['initialize'] = False
- def createAstraDevice(self, projector_geometry, output_geometry):
- '''TODO remove'''
-
- device = AstraDevice(DeviceModel.PARALLEL3D,
- {'detectorSpacingX' : projector_geometry['DetectorSpacingX'] ,
- 'detectorSpacingY' : projector_geometry['DetectorSpacingY'] ,
- 'cameraX' : projector_geometry['DetectorColCount'] ,
- 'cameraY' : projector_geometry['DetectorRowCount'] ,
- 'angles' : projector_geometry['ProjectionAngles'] } ,
- {
- 'X' : output_geometry['GridColCount'],
- 'Y' : output_geometry['GridRowCount']
- 'Z' : output_geometry['GridSliceCount']} )
- return device
-
+
def setParameter(self, **kwargs):
'''set named parameter for the reconstructor engine
diff --git a/src/Python/test/test_reconstructor.py b/src/Python/test/test_reconstructor.py
index 3342301..343b9bb 100644
--- a/src/Python/test/test_reconstructor.py
+++ b/src/Python/test/test_reconstructor.py
@@ -12,6 +12,9 @@ import numpy
from ccpi.reconstruction.FISTAReconstructor import FISTAReconstructor
import astra
import matplotlib.pyplot as plt
+from ccpi.imaging.Regularizer import Regularizer
+from ccpi.reconstruction.AstraDevice import AstraDevice
+from ccpi.reconstruction.DeviceModel import DeviceModel
def RMSE(signal1, signal2):
'''RMSE Root Mean Squared Error'''
@@ -22,7 +25,23 @@ def RMSE(signal1, signal2):
return err
else:
raise Exception('Input signals must have the same shape')
-
+
+def createAstraDevice(projector_geometry, output_geometry):
+ '''TODO remove'''
+
+ device = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
+ [projector_geometry['DetectorSpacingX'] ,
+ projector_geometry['DetectorSpacingY'] ,
+ projector_geometry['DetectorColCount'] ,
+ projector_geometry['DetectorRowCount'] ,
+ projector_geometry['ProjectionAngles']
+ ],
+ [
+ output_geometry['GridColCount'],
+ output_geometry['GridRowCount'],
+ output_geometry['GridSliceCount'] ] )
+ return device
+
filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5'
nx = h5py.File(filename, "r")
#getEntry(nx, '/')
@@ -65,23 +84,23 @@ vol_geom = astra.creators.create_vol_geom( image_size_x,
## First pass the arguments to the FISTAReconstructor and test the
## Lipschitz constant
-fistaRecon = FISTAReconstructor(proj_geom,
- vol_geom,
- Sino3D ,
- weights=Weights3D)
-
-print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-fistaRecon.setParameter(number_of_iterations = 12)
-fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-fistaRecon.setParameter(ring_alpha = 21)
-fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-
-reg = Regularizer(Regularizer.Algorithm.LLT_model)
-reg.setParameter(regularization_parameter=25,
- time_step=0.0003,
- tolerance_constant=0.0001,
- number_of_iterations=300)
-fistaRecon.setParameter(regularizer = reg)
+##fistaRecon = FISTAReconstructor(proj_geom,
+## vol_geom,
+## Sino3D ,
+## weights=Weights3D)
+##
+##print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
+##fistaRecon.setParameter(number_of_iterations = 12)
+##fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
+##fistaRecon.setParameter(ring_alpha = 21)
+##fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
+##
+##reg = Regularizer(Regularizer.Algorithm.LLT_model)
+##reg.setParameter(regularization_parameter=25,
+## time_step=0.0003,
+## tolerance_constant=0.0001,
+## number_of_iterations=300)
+##fistaRecon.setParameter(regularizer=reg)
## Ordered subset
if False:
@@ -294,16 +313,24 @@ if False:
## fprintf('%s %i %s %s %f \n', 'Iteration Number:', i, '|', 'Objective:', objective(i));
## end
else:
+
+ # create a device for forward/backprojection
+ astradevice = createAstraDevice(proj_geom, vol_geom)
fistaRecon = FISTAReconstructor(proj_geom,
vol_geom,
Sino3D ,
- weights=Weights3D)
+ device = astradevice,
+ weights=Weights3D
+ )
print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
- fistaRecon.setParameter(number_of_iterations = 12)
+ fistaRecon.setParameter(number_of_iterations = 3)
fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
fistaRecon.setParameter(ring_alpha = 21)
fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
+
+
+
fistaRecon.prepareForIteration()
X = fistaRecon.iterate(numpy.load("X.npy"))
numpy.save("X_out.npy", X)
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-04 06:38:57 +0000