def setupCCPiGeometries(ig, ag, counter):
Phantom_ccpi = ig.allocate(dimension_labels=[
ImageGeometry.HORIZONTAL_X, ImageGeometry.HORIZONTAL_Y,
ImageGeometry.VERTICAL
])
voxel_per_pixel = 1
angles = ag.angles
geoms = pbalg.pb_setup_geometry_from_image(Phantom_ccpi.as_array(), angles,
voxel_per_pixel)
pg = AcquisitionGeometry(
'parallel',
'3D',
angles,
geoms['n_h'],
1.0,
geoms['n_v'],
1.0 #2D in 3D is a slice 1 pixel thick
)
center_of_rotation = Phantom_ccpi.get_dimension_size('horizontal_x') / 2
#ad = AcquisitionData(geometry=pg,dimension_labels=['angle','vertical','horizontal'])
ad = pg.allocate(dimension_labels=[
AcquisitionGeometry.ANGLE, AcquisitionGeometry.VERTICAL,
AcquisitionGeometry.HORIZONTAL
])
geoms_i = pbalg.pb_setup_geometry_from_acquisition(ad.as_array(), angles,
center_of_rotation,
voxel_per_pixel)
counter += 1
if counter < 4:
print(geoms, geoms_i)
if (not (geoms_i == geoms)):
print("not equal and {} {} {}".format(counter,
geoms['output_volume_z'],
geoms_i['output_volume_z']))
X = max(geoms['output_volume_x'], geoms_i['output_volume_x'])
Y = max(geoms['output_volume_y'], geoms_i['output_volume_y'])
Z = max(geoms['output_volume_z'], geoms_i['output_volume_z'])
return setupCCPiGeometries(X, Y, Z, angles, counter)
else:
print("happy now {} {} {}".format(counter,
geoms['output_volume_z'],
geoms_i['output_volume_z']))
return geoms
else:
return geoms_i
def setupCCPiGeometries(voxel_num_x, voxel_num_y, voxel_num_z, angles, counter):
vg = ImageGeometry(voxel_num_x=voxel_num_x,voxel_num_y=voxel_num_y, voxel_num_z=voxel_num_z)
Phantom_ccpi = ImageData(geometry=vg,
dimension_labels=['horizontal_x','horizontal_y','vertical'])
#.subset(['horizontal_x','horizontal_y','vertical'])
# ask the ccpi code what dimensions it would like
voxel_per_pixel = 1
geoms = pbalg.pb_setup_geometry_from_image(Phantom_ccpi.as_array(),
angles,
voxel_per_pixel )
pg = AcquisitionGeometry('parallel',
'3D',
angles,
geoms['n_h'], 1.0,
geoms['n_v'], 1.0 #2D in 3D is a slice 1 pixel thick
)
center_of_rotation = Phantom_ccpi.get_dimension_size('horizontal_x') / 2
ad = AcquisitionData(geometry=pg,dimension_labels=['angle','vertical','horizontal'])
geoms_i = pbalg.pb_setup_geometry_from_acquisition(ad.as_array(),
angles,
center_of_rotation,
voxel_per_pixel )
counter+=1
if counter < 4:
if (not ( geoms_i == geoms )):
print ("not equal and {0}".format(counter))
X = max(geoms['output_volume_x'], geoms_i['output_volume_x'])
Y = max(geoms['output_volume_y'], geoms_i['output_volume_y'])
Z = max(geoms['output_volume_z'], geoms_i['output_volume_z'])
return setupCCPiGeometries(X,Y,Z,angles, counter)
else:
return geoms
else:
return geoms_i
def process(self, out=None):
projections = self.get_input()
w = projections.get_dimension_size('horizontal')
delta = w - 2 * self.center_of_rotation
padded_width = int(numpy.ceil(abs(delta)) + w)
delta_pix = padded_width - w
voxel_per_pixel = 1
geom = pbalg.pb_setup_geometry_from_acquisition(
projections.as_array(), self.acquisition_geometry.angles,
self.center_of_rotation, voxel_per_pixel)
padded_geometry = self.acquisition_geometry.clone()
padded_geometry.pixel_num_h = geom['n_h']
padded_geometry.pixel_num_v = geom['n_v']
delta_pix_h = padded_geometry.pixel_num_h - self.acquisition_geometry.pixel_num_h
delta_pix_v = padded_geometry.pixel_num_v - self.acquisition_geometry.pixel_num_v
if delta_pix_h == 0:
delta_pix_h = delta_pix
padded_geometry.pixel_num_h = padded_width
#initialize a new AcquisitionData with values close to 0
out = AcquisitionData(geometry=padded_geometry)
out = out + self.pad_value
#pad in the horizontal-vertical plane -> slice on angles
if delta > 0:
#pad left of middle
command = "out.array["
for i in range(out.number_of_dimensions):
if out.dimension_labels[i] == 'horizontal':
value = '{0}:{1}'.format(delta_pix_h, delta_pix_h + w)
command = command + str(value)
else:
if out.dimension_labels[i] == 'vertical':
value = '{0}:'.format(delta_pix_v)
command = command + str(value)
else:
command = command + ":"
if i < out.number_of_dimensions - 1:
command = command + ','
command = command + '] = projections.array'
#print (command)
else:
#pad right of middle
command = "out.array["
for i in range(out.number_of_dimensions):
if out.dimension_labels[i] == 'horizontal':
value = '{0}:{1}'.format(0, w)
command = command + str(value)
else:
if out.dimension_labels[i] == 'vertical':
value = '{0}:'.format(delta_pix_v)
command = command + str(value)
else:
command = command + ":"
if i < out.number_of_dimensions - 1:
command = command + ','
command = command + '] = projections.array'
#print (command)
#cleaned = eval(command)
exec(command)
return out