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# -*- coding: utf-8 -*-
# CCP in Tomographic Imaging (CCPi) Core Imaging Library (CIL).
# Copyright 2017 UKRI-STFC
# Copyright 2017 University of Manchester
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import unittest
import os
from ccpi.io import NEXUSDataReader
from ccpi.io import NEXUSDataWriter
from ccpi.framework import AcquisitionData, AcquisitionGeometry, ImageData, ImageGeometry
import numpy
class TestNexusReaderWriter(unittest.TestCase):
def setUp(self):
pass
def testwriteImageData(self):
im_size = 5
ig = ImageGeometry(voxel_num_x = im_size,
voxel_num_y = im_size)
im = ig.allocate()
writer = NEXUSDataWriter()
writer.set_up(file_name = os.path.join(os.getcwd(), 'test_nexus_im.nxs'),
data_container = im)
writer.write_file()
self.stestreadImageData()
def testwriteAcquisitionData(self):
im_size = 5
ag2d = AcquisitionGeometry(geom_type = 'parallel',
dimension = '2D',
angles = numpy.array([0, 1]),
pixel_num_h = im_size,
pixel_size_h = 1,
pixel_num_v = im_size,
pixel_size_v = 1)
ad2d = ag2d.allocate()
writer = NEXUSDataWriter()
writer.set_up(file_name = os.path.join(os.getcwd(), 'test_nexus_ad2d.nxs'),
data_container = ad2d)
writer.write_file()
ag3d = AcquisitionGeometry(geom_type = 'cone',
dimension = '3D',
angles = numpy.array([0, 1]),
pixel_num_h = im_size,
pixel_size_h = 1,
pixel_num_v = im_size,
pixel_size_v = 1,
dist_source_center = 1,
dist_center_detector = 1,
channels = im_size)
ad3d = ag3d.allocate()
writer = NEXUSDataWriter()
writer.set_up(file_name = os.path.join(os.getcwd(), 'test_nexus_ad3d.nxs'),
data_container = ad3d)
writer.write_file()
self.stestreadAcquisitionData()
def stestreadImageData(self):
im_size = 5
ig_test = ImageGeometry(voxel_num_x = im_size,
voxel_num_y = im_size)
im_test = ig_test.allocate()
reader = NEXUSDataReader()
reader.set_up(nexus_file = os.path.join(os.getcwd(), 'test_nexus_im.nxs'))
im = reader.load_data()
ig = reader.get_geometry()
numpy.testing.assert_array_equal(im.as_array(), im_test.as_array(), 'Loaded image is not correct')
self.assertEqual(ig.voxel_num_x, ig_test.voxel_num_x, 'ImageGeometry is not correct')
self.assertEqual(ig.voxel_num_y, ig_test.voxel_num_y, 'ImageGeometry is not correct')
def stestreadAcquisitionData(self):
im_size = 5
ag2d_test = AcquisitionGeometry(geom_type = 'parallel',
dimension = '2D',
angles = numpy.array([0, 1]),
pixel_num_h = im_size,
pixel_size_h = 1,
pixel_num_v = im_size,
pixel_size_v = 1)
ad2d_test = ag2d_test.allocate()
reader2d = NEXUSDataReader()
reader2d.set_up(nexus_file = os.path.join(os.getcwd(), 'test_nexus_ad2d.nxs'))
ad2d = reader2d.load_data()
ag2d = reader2d.get_geometry()
numpy.testing.assert_array_equal(ad2d.as_array(), ad2d_test.as_array(), 'Loaded image is not correct')
self.assertEqual(ag2d.geom_type, ag2d_test.geom_type, 'ImageGeometry.geom_type is not correct')
numpy.testing.assert_array_equal(ag2d.angles, ag2d_test.angles, 'ImageGeometry.angles is not correct')
self.assertEqual(ag2d.pixel_num_h, ag2d_test.pixel_num_h, 'ImageGeometry.pixel_num_h is not correct')
self.assertEqual(ag2d.pixel_size_h, ag2d_test.pixel_size_h, 'ImageGeometry.pixel_size_h is not correct')
self.assertEqual(ag2d.pixel_num_v, ag2d_test.pixel_num_v, 'ImageGeometry.pixel_num_v is not correct')
self.assertEqual(ag2d.pixel_size_v, ag2d_test.pixel_size_v, 'ImageGeometry.pixel_size_v is not correct')
ag3d_test = AcquisitionGeometry(geom_type = 'cone',
dimension = '3D',
angles = numpy.array([0, 1]),
pixel_num_h = im_size,
pixel_size_h = 1,
pixel_num_v = im_size,
pixel_size_v = 1,
dist_source_center = 1,
dist_center_detector = 1,
channels = im_size)
ad3d_test = ag3d_test.allocate()
reader3d = NEXUSDataReader()
reader3d.set_up(nexus_file = os.path.join(os.getcwd(), 'test_nexus_ad3d.nxs'))
ad3d = reader3d.load_data()
ag3d = reader3d.get_geometry()
numpy.testing.assert_array_equal(ad3d.as_array(), ad3d_test.as_array(), 'Loaded image is not correct')
numpy.testing.assert_array_equal(ag3d.angles, ag3d_test.angles, 'AcquisitionGeometry.angles is not correct')
self.assertEqual(ag3d.geom_type, ag3d_test.geom_type, 'AcquisitionGeometry.geom_type is not correct')
self.assertEqual(ag3d.dimension, ag3d_test.dimension, 'AcquisitionGeometry.dimension is not correct')
self.assertEqual(ag3d.pixel_num_h, ag3d_test.pixel_num_h, 'AcquisitionGeometry.pixel_num_h is not correct')
self.assertEqual(ag3d.pixel_size_h, ag3d_test.pixel_size_h, 'AcquisitionGeometry.pixel_size_h is not correct')
self.assertEqual(ag3d.pixel_num_v, ag3d_test.pixel_num_v, 'AcquisitionGeometry.pixel_num_v is not correct')
self.assertEqual(ag3d.pixel_size_v, ag3d_test.pixel_size_v, 'AcquisitionGeometry.pixel_size_v is not correct')
self.assertEqual(ag3d.dist_source_center, ag3d_test.dist_source_center, 'AcquisitionGeometry.dist_source_center is not correct')
self.assertEqual(ag3d.dist_center_detector, ag3d_test.dist_center_detector, 'AcquisitionGeometry.dist_center_detector is not correct')
self.assertEqual(ag3d.channels, ag3d_test.channels, 'AcquisitionGeometry.channels is not correct')
def tearDown(self):
os.remove(os.path.join(os.getcwd(), 'test_nexus_im.nxs'))
os.remove(os.path.join(os.getcwd(), 'test_nexus_ad2d.nxs'))
os.remove(os.path.join(os.getcwd(), 'test_nexus_ad3d.nxs'))
if __name__ == '__main__':
unittest.main()
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