def testLoadProjection(self):
xtekReader = XTEKReader(self.filename)
pixels = xtekReader.loadProjection()
self.assertEqual(pixels.shape, (63, 500, 500), "projections shape doesn't match")
def testLoad(self):
xtekReader = XTEKReader(self.filename)
self.assertEqual(xtekReader.geometry.pixel_num_h, 500, "Detector pixel X size is not correct")
self.assertEqual(xtekReader.geometry.pixel_num_v, 500, "Detector pixel Y size is not correct")
self.assertEqual(xtekReader.geometry.dist_source_center, -80.6392412185669, "Distance from source to center is not correct")
self.assertEqual(xtekReader.geometry.dist_center_detector, (1007.006 - 80.6392412185669), "Distance from center to detector is not correct")
def testReadAngles(self):
xtekReader = XTEKReader(self.filename)
angles = xtekReader.readAngles()
self.assertEqual(angles.shape, (63,), "Angles doesn't match")
self.assertAlmostEqual(angles[46], -085.717, 3, "46th Angles doesn't match")
# https://zenodo.org/record/16474
# The filename with full path to the .xtekct file should be given as string
# input to XTEKReader to load in the data.
# Do all imports
from ccpi.io.reader import XTEKReader
import numpy as np
import matplotlib.pyplot as plt
from ccpi.framework import ImageGeometry, AcquisitionData, ImageData
from ccpi.astra.ops import AstraProjector3DSimple
from ccpi.optimisation.algs import CGLS
import numpy
# Set up reader object and read the data
datareader = XTEKReader("REPLACE_THIS_BY_PATH_TO_DATASET/SophiaBeads_256_averaged.xtekct")
data = datareader.get_acquisition_data()
# Crop data and fix dimension labels
data = AcquisitionData(data.array[:,:,901:1101],
geometry=data.geometry,
dimension_labels=['angle','horizontal','vertical'])
data.geometry.pixel_num_v = 200
# Scale and negative-log transform
data.array = -np.log(data.as_array()/60000.0)
# Apply centering correction by zero padding, amount found manually
cor_pad = 30
data_pad = np.zeros((data.shape[0],data.shape[1]+cor_pad,data.shape[2]))
data_pad[:,cor_pad:,:] = data.array