class TestTXRMDataReader(unittest.TestCase):
def setUp(self):
print ("has_astra",has_astra)
print ("has_wget",has_wget)
print ("has_olefile",has_olefile)
print ("has_dxchange",has_dxchange)
print ("has_file",has_file)
if has_file:
self.reader = TXRMDataReader()
angle_unit = AcquisitionGeometry.RADIAN
self.reader.set_up(file_name=filename,
angle_unit=angle_unit)
data = self.reader.read()
if data.geometry is None:
raise AssertionError("WTF")
# Choose the number of voxels to reconstruct onto as number of detector pixels
N = data.geometry.pixel_num_h
# Geometric magnification
mag = (np.abs(data.geometry.dist_center_detector) + \
np.abs(data.geometry.dist_source_center)) / \
np.abs(data.geometry.dist_source_center)
# Voxel size is detector pixel size divided by mag
voxel_size_h = data.geometry.pixel_size_h / mag
voxel_size_v = data.geometry.pixel_size_v / mag
self.mag = mag
self.N = N
self.voxel_size_h = voxel_size_h
self.voxel_size_v = voxel_size_v
self.data = data
def tearDown(self):
pass
def test_run_test(self):
print("run test Zeiss Reader")
self.assertTrue(True)
@unittest.skipIf(True, 'skip test by default')
def test_not_run_test(self):
print("run test Zeiss Reader")
self.assertTrue(True)
@unittest.skipIf(not has_prerequisites, "Prerequisites not met")
def test_read_and_reconstruct_2D(self):
print (type(self.data))
# get central slice
data2d = self.data.subset(vertical='centre')
# d512 = self.data.subset(vertical=512)
# data2d.fill(d512.as_array())
# neg log
data2d.log(out=data2d)
data2d *= -1
ig2d = data2d.geometry.get_ImageGeometry()
# Construct the appropriate ImageGeometry
ig2d = ImageGeometry(voxel_num_x=self.N,
voxel_num_y=self.N,
voxel_size_x=self.voxel_size_h,
voxel_size_y=self.voxel_size_h)
if data2d.geometry is None:
raise AssertionError('What? None?')
fbpalg = FDK(ig2d,data2d.geometry)
fbpalg.set_input(data2d)
recfbp = fbpalg.get_output()
wget.download('https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/walnut_slice512.nxs',
out=data_dir)
fname = os.path.join(data_dir, 'walnut_slice512.nxs')
reader = NEXUSDataReader()
reader.set_up(file_name=fname)
gt = reader.read()
qm = mse(gt, recfbp)
print ("MSE" , qm )
np.testing.assert_almost_equal(qm, 0, decimal=3)
fname = os.path.join(data_dir, 'walnut_slice512.nxs')
os.remove(fname)
from cil.utilities.display import show2D
from cil.processors import CentreOfRotationCorrector
from cil.utilities.quality_measures import *
filename = os.path.abspath('/home/edo/scratch/Dataset/CCPi/valnut_tomo-A.txrm')
data_dir = os.getcwd()
# show2D(gt)
#%%
reader = TXRMDataReader()
angle_unit = AcquisitionGeometry.RADIAN
filename = os.path.abspath('/home/edo/scratch/Dataset/CCPi/valnut_tomo-A.txrm')
reader.set_up(file_name=filename, angle_unit=angle_unit)
data = reader.read()
if data.geometry is None:
raise AssertionError("The reader should set the geometry!!")
# angles = data.geometry.angles * -1
# data.geometry.set_angles(angles)
#%%
show2D(data, slice_list=('vertical', 600))
#%%
# get central slice
data2d = [data.get_slice(vertical='centre')]
data2d.append(data2d[0].copy())
data2d[0].reorder(order='tigre')
data2d[1].reorder(order='astra')
#%%