diff options
Diffstat (limited to 'Wrappers')
| -rw-r--r-- | Wrappers/Python/ccpi/astra/astra_processors.py | 143 | ||||
| -rw-r--r-- | Wrappers/Python/ccpi/framework.py | 30 | ||||
| -rw-r--r-- | Wrappers/Python/ccpi/reconstruction/astra_ops.py | 48 | ||||
| -rw-r--r-- | Wrappers/Python/test/simple_mc_demo.py | 71 |
4 files changed, 267 insertions, 25 deletions
diff --git a/Wrappers/Python/ccpi/astra/astra_processors.py b/Wrappers/Python/ccpi/astra/astra_processors.py index 91612b1..650e11b 100644 --- a/Wrappers/Python/ccpi/astra/astra_processors.py +++ b/Wrappers/Python/ccpi/astra/astra_processors.py @@ -1,6 +1,7 @@ from ccpi.framework import DataSetProcessor, DataSet, VolumeData, SinogramData from ccpi.astra.astra_utils import convert_geometry_to_astra import astra +import numpy class AstraForwardProjector(DataSetProcessor): @@ -127,4 +128,146 @@ class AstraBackProjector(DataSetProcessor): DATA = self.getInput() rec_id, IM = astra.create_backprojection(DATA.as_array(), self.proj_id) astra.data2d.delete(rec_id) + return VolumeData(IM,geometry=self.volume_geometry) + +class AstraForwardProjectorMC(DataSetProcessor): + '''AstraForwardProjector + + Forward project VolumeDataSet to SinogramDataSet using ASTRA proj_id. + + Input: VolumeDataSet + Parameter: proj_id + Output: SinogramDataSet + ''' + + 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(AstraForwardProjectorMC, self).__init__(**kwargs) + + self.setVolumeGeometry(volume_geometry) + self.setSinogramGeometry(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' is only for parallel (2D) and only one option + self.setProjector(astra.create_projector('line', proj_geom, vol_geom) ) + elif device == 'gpu': + self.setProjector(astra.create_projector('cuda', proj_geom, vol_geom) ) + else: + NotImplemented + + def checkInput(self, dataset): + if dataset.number_of_dimensions == 3 or dataset.number_of_dimensions == 2: + return True + else: + return True + #raise ValueError("Expected input dimensions is 2 or 3, got {0}"\ + # .format(dataset.number_of_dimensions)) + + def setProjector(self, proj_id): + self.proj_id = proj_id + + def setVolumeGeometry(self, volume_geometry): + self.volume_geometry = volume_geometry + + def setSinogramGeometry(self, sinogram_geometry): + self.sinogram_geometry = sinogram_geometry + + def process(self): + IM = self.getInput() + DATA = numpy.zeros((self.sinogram_geometry.angles.size, + self.sinogram_geometry.pixel_num_h, + 1, + self.sinogram_geometry.channels), + 'float32') + for k in range(self.sinogram_geometry.channels): + sinogram_id, DATA[:,:,0,k] = astra.create_sino(IM.as_array()[:,:,0,k], + self.proj_id) + astra.data2d.delete(sinogram_id) + return SinogramData(DATA,geometry=self.sinogram_geometry) + +class AstraBackProjectorMC(DataSetProcessor): + '''AstraBackProjector + + Back project SinogramDataSet to VolumeDataSet using ASTRA proj_id. + + Input: SinogramDataSet + Parameter: proj_id + Output: VolumeDataSet + ''' + + 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(AstraBackProjectorMC, self).__init__(**kwargs) + + self.setVolumeGeometry(volume_geometry) + self.setSinogramGeometry(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' is only for parallel (2D) and only one option + self.setProjector(astra.create_projector('line', proj_geom, vol_geom) ) + elif device == 'gpu': + self.setProjector(astra.create_projector('cuda', proj_geom, vol_geom) ) + else: + NotImplemented + + def checkInput(self, dataset): + if dataset.number_of_dimensions == 3 or dataset.number_of_dimensions == 2: + return True + else: + return True + #raise ValueError("Expected input dimensions is 2 or 3, got {0}"\ + # .format(dataset.number_of_dimensions)) + + def setProjector(self, proj_id): + self.proj_id = proj_id + + def setVolumeGeometry(self, volume_geometry): + self.volume_geometry = volume_geometry + + def setSinogramGeometry(self, sinogram_geometry): + self.sinogram_geometry = sinogram_geometry + + def process(self): + DATA = self.getInput() + IM = numpy.zeros((self.volume_geometry.voxel_num_x, + self.volume_geometry.voxel_num_y, + 1, + self.volume_geometry.channels), + 'float32') + for k in range(self.volume_geometry.channels): + rec_id, IM[:,:,0,k] = astra.create_backprojection(DATA.as_array()[:,:,0,k], + self.proj_id) + astra.data2d.delete(rec_id) return VolumeData(IM,geometry=self.volume_geometry)
\ No newline at end of file diff --git a/Wrappers/Python/ccpi/framework.py b/Wrappers/Python/ccpi/framework.py index 5ac17ee..5ee8279 100644 --- a/Wrappers/Python/ccpi/framework.py +++ b/Wrappers/Python/ccpi/framework.py @@ -428,20 +428,20 @@ class VolumeData(DataSet): if type(array) == DataSet: # if the array is a DataSet get the info from there - if not ( array.number_of_dimensions == 2 or \ - array.number_of_dimensions == 3 ): - raise ValueError('Number of dimensions are not 2 or 3: {0}'\ - .format(array.number_of_dimensions)) + #if not ( array.number_of_dimensions == 2 or \ + # array.number_of_dimensions == 3 ): + # raise ValueError('Number of dimensions are not 2 or 3: {0}'\ + # .format(array.number_of_dimensions)) #DataSet.__init__(self, array.as_array(), deep_copy, # array.dimension_labels, **kwargs) super(VolumeData, self).__init__(array.as_array(), deep_copy, array.dimension_labels, **kwargs) elif type(array) == numpy.ndarray: - if not ( array.ndim == 3 or array.ndim == 2 ): - raise ValueError( - 'Number of dimensions are not 3 or 2 : {0}'\ - .format(array.ndim)) + #if not ( array.ndim == 3 or array.ndim == 2 ): + # raise ValueError( + # 'Number of dimensions are not 3 or 2 : {0}'\ + # .format(array.ndim)) if dimension_labels is None: if array.ndim == 3: @@ -476,17 +476,17 @@ class SinogramData(DataSet): if type(array) == DataSet: # if the array is a DataSet get the info from there - if not ( array.number_of_dimensions == 2 or \ - array.number_of_dimensions == 3 ): - raise ValueError('Number of dimensions are not 2 or 3: {0}'\ - .format(array.number_of_dimensions)) + #if not ( array.number_of_dimensions == 2 or \ + # array.number_of_dimensions == 3 ): + # raise ValueError('Number of dimensions are not 2 or 3: {0}'\ + # .format(array.number_of_dimensions)) DataSet.__init__(self, array.as_array(), deep_copy, array.dimension_labels, **kwargs) elif type(array) == numpy.ndarray: - if not ( array.ndim == 3 or array.ndim == 2 ): - raise ValueError('Number of dimensions are != 3: {0}'\ - .format(array.ndim)) + #if not ( array.ndim == 3 or array.ndim == 2 ): + # raise ValueError('Number of dimensions are != 3: {0}'\ + # .format(array.ndim)) if dimension_labels is None: if array.ndim == 3: dimension_labels = ['angle' , diff --git a/Wrappers/Python/ccpi/reconstruction/astra_ops.py b/Wrappers/Python/ccpi/reconstruction/astra_ops.py index 6af7af7..cf138b4 100644 --- a/Wrappers/Python/ccpi/reconstruction/astra_ops.py +++ b/Wrappers/Python/ccpi/reconstruction/astra_ops.py @@ -19,7 +19,7 @@ from ccpi.reconstruction.ops import Operator import numpy from ccpi.framework import SinogramData, VolumeData from ccpi.reconstruction.ops import PowerMethodNonsquare -from ccpi.astra.astra_processors import AstraForwardProjector, AstraBackProjector +from ccpi.astra.astra_processors import * class AstraProjectorSimple(Operator): """ASTRA projector modified to use DataSet and geometry.""" @@ -66,6 +66,52 @@ class AstraProjectorSimple(Operator): self.sinogram_geometry.pixel_num_h), \ (self.volume_geometry.voxel_num_x, \ self.volume_geometry.voxel_num_y) ) + +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.setInput(IM) + out = self.fp.getOutput() + return out + + def adjoint(self, DATA): + self.bp.setInput(DATA) + out = self.bp.getOutput() + 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) ) class AstraProjector(Operator): diff --git a/Wrappers/Python/test/simple_mc_demo.py b/Wrappers/Python/test/simple_mc_demo.py index ca6a89e..1888740 100644 --- a/Wrappers/Python/test/simple_mc_demo.py +++ b/Wrappers/Python/test/simple_mc_demo.py @@ -21,23 +21,76 @@ N = 128 numchannels = 3 -x = np.zeros((N,N,numchannels)) +x = np.zeros((N,N,1,numchannels)) -x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),0] = 1.0 -x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),0] = 2.0 +x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),:,0] = 1.0 +x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),:,0] = 2.0 -x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),1] = 0.7 -x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),1] = 1.2 +x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),:,1] = 0.7 +x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),:,1] = 1.2 -x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),2] = 1.5 -x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),2] = 2.2 +x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),:,2] = 1.5 +x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),:,2] = 2.2 f, axarr = plt.subplots(1,numchannels) for k in numpy.arange(3): - axarr[k].imshow(x[:,:,k],vmin=0,vmax=2.5) + axarr[k].imshow(x[:,:,0,k],vmin=0,vmax=2.5) plt.show() vg = VolumeGeometry(N,N,None, 1,1,None,channels=numchannels) -Phantom = VolumeData(x,geometry=vg)
\ No newline at end of file +Phantom = VolumeData(x,geometry=vg) + +# Set up measurement geometry +angles_num = 20; # angles number + +if test_case==1: + angles = np.linspace(0,np.pi,angles_num,endpoint=False) +elif test_case==2: + angles = np.linspace(0,2*np.pi,angles_num,endpoint=False) +else: + NotImplemented + +det_w = 1.0 +det_num = N +SourceOrig = 200 +OrigDetec = 0 + +# Parallelbeam geometry test +if test_case==1: + pg = SinogramGeometry('parallel', + '2D', + angles, + det_num, + det_w, + channels=numchannels) +elif test_case==2: + pg = SinogramGeometry('cone', + '2D', + angles, + det_num, + det_w, + dist_source_center=SourceOrig, + dist_center_detector=OrigDetec, + channels=numchannels) + +# ASTRA operator using volume and sinogram geometries +Aop = AstraProjectorMC(vg, pg, 'gpu') + + +# Try forward and backprojection +b = Aop.direct(Phantom) + +fb, axarrb = plt.subplots(1,numchannels) +for k in numpy.arange(3): + axarrb[k].imshow(b.as_array()[:,:,0,k],vmin=0,vmax=250) +plt.show() + +out2 = Aop.adjoint(b) + +fo, axarro = plt.subplots(1,numchannels) +for k in range(3): + axarro[k].imshow(out2.as_array()[:,:,0,k],vmin=0,vmax=3500) +plt.show() + |