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
import numpy as np
import os
from cil.io import TXRMDataReader, TIFFWriter
from cil.processors import TransmissionAbsorptionConverter, Binner
from cil.plugins.tigre import FBP
from cil.utilities.display import show2D, show_geometry
base_dir = os.path.abspath(r"C:\Users\ofn77899\Data\walnut")
data_name = "valnut"
filename = os.path.join(base_dir, data_name,
"valnut_2014-03-21_643_28/tomo-A/valnut_tomo-A.txrm")
is2D = False
data = TXRMDataReader(file_name=filename).read()
if is2D:
data = data.get_slice(vertical='centre')
else:
binner = Binner(roi={
'horizontal': (None, None, 4),
'vertical': (None, None, 4)
})
data = binner(data)
# show_geometry(data.geometry)
data = TransmissionAbsorptionConverter()(data)
data.reorder(order='tigre')
ig = data.geometry.get_ImageGeometry()
#%%
#%%
path = os.path.abspath('/home/edo/scratch/Dataset/')
filename = os.path.join(path, 'CCPi', 'valnut_tomo-A.txrm')
# reader = TXRMDataReader()
# reader.set_up(file_name=filename)
# data = reader.read()
# reader = TXRMDataReader(file_name=filename)
# data = reader.read()
data = TXRMDataReader(file_name=filename).read()
print("read in data type", data.dtype)
#%%
show2D(data, slice_list=('angle', 800), cmap='inferno', origin='upper-right')
#%%
# get central slice
# data2d = data.get_slice(vertical='centre')
# data2d.reorder(order='tigre')
#%%
# Centre of rotation finder
#%%
# neg log
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)
import wget
from cil.io import TXRMDataReader, NEXUSDataReader
from cil.framework import AcquisitionGeometry, ImageGeometry
from cil.plugins.tigre import FBP as tFBP
from cil.plugins.astra.processors import FBP as aFBP
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