def test_writeImageData(self):
im_size = 5
ig = ImageGeometry(voxel_num_x=im_size, voxel_num_y=im_size)
im = ig.allocate('random', seed=9)
writer = NEXUSDataWriter()
writer.set_up(file_name=os.path.join(self.data_dir,
'test_nexus_im.nxs'),
data=im)
writer.write()
self.readImageDataAndTest()
def test_writeImageData_compressed(self):
im_size = 5
ig = ImageGeometry(voxel_num_x=im_size, voxel_num_y=im_size)
im = ig.allocate('random', seed=9)
writer = NEXUSDataWriter()
writer.set_up(file_name=os.path.join(self.data_dir,
'test_nexus_im.nxs'),
data=im,
compression=16)
writer.write()
self.assertTrue(writer.dtype == numpy.uint16)
self.assertTrue(writer.compression == 16)
self.readImageDataAndTest(atol=1e-4)
voxel_size_y=voxel_size_h,
voxel_size_z=data.geometry.pixel_size_v / mag)
print('done set up astra op')
fbpalg = FBP(ig2d,data2d.geometry)
fbpalg.set_input(data2d)
recfbp = fbpalg.get_output()
plt.figure()
plt.imshow(recfbp.as_array())
plt.gray()
plt.colorbar()
writer = NEXUSDataWriter()
cwd = os.getcwd()
writer.set_up(data_container = recfbp,
file_name = os.path.join(cwd,'walnut_slice512.nxs'))
writer.write_file()
shuffle = data.subset(dimensions=['vertical','angle','horizontal'])
shuffle.log(out=shuffle)
shuffle *= -1
fbp3d = FBP(ig3d, shuffle.geometry)
fbp3d.set_input(shuffle)
vol = fbp3d.get_output()
plt.figure()
plt.imshow(vol.subset(vertical=512).as_array())
def test_writeAcquisitionData(self):
writer = NEXUSDataWriter()
writer.set_up(file_name=os.path.join(self.data_dir,
'test_nexus_ad2d.nxs'),
data=self.ad2d)
writer.write()
writer = NEXUSDataWriter()
writer.set_up(file_name=os.path.join(self.data_dir,
'test_nexus_ad3d.nxs'),
data=self.ad3d)
writer.write()
self.readAcquisitionDataAndTest()
'vertical': (None, None, 4)
})
data = binner(data)
# show_geometry(data.geometry)
data = TransmissionAbsorptionConverter()(data)
data.reorder(order='tigre')
ig = data.geometry.get_ImageGeometry()
fbp = FBP(ig, data.geometry)
recon = fbp(data)
from cil.io import NEXUSDataWriter
writer = NEXUSDataWriter()
writer.set_up(data=recon, file_name=os.path.abspath('noce.nxs'))
writer.write()
# show2D([data, recon], fix_range=(-0.01,0.06))
from ccpi.viewer import viewer2D, viewer3D
from ccpi.viewer.utils.conversion import Converter
import vtk
from functools import partial
v = viewer3D()
def clipping_plane(v, interactor, event):
if interactor.GetKeyCode() == "c":
planew = vtk.vtkImplicitPlaneWidget()