#!/usr/bin/env python3
import unittest
import os.path
import tempfile
import numpy as np
import argparse
# from .context import imagedata
import src.imagedata.cmdline as cmdline
import src.imagedata.formats as formats
from src.imagedata.series import Series
from .compare_headers import compare_headers, compare_template_headers, compare_geometry_headers
[docs]
class ShouldHaveFailed(Exception):
pass
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class TestItkTemplate(unittest.TestCase):
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def setUp(self):
parser = argparse.ArgumentParser()
cmdline.add_argparse_options(parser)
self.opts_template = parser.parse_args(['--of', 'itk',
'--template', 'data/dicom/time/time00/'])
self.opts_geometry = parser.parse_args(['--of', 'itk',
'--geometry', 'data/dicom/time/time00/'])
self.opts_tempgeom = parser.parse_args(['--of', 'itk',
'--template', 'data/dicom/time/time00/',
'--geometry', 'data/dicom/time/time00/'])
plugins = formats.get_plugins_list()
self.dicom_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'itk':
self.itk_plugin = pclass
self.assertIsNotNone(self.itk_plugin)
self.template = Series(os.path.join('data', 'dicom', 'time', 'time00'))
self.geometry = Series(os.path.join('data', 'dicom', 'time', 'time00'))
self.geometry.spacing = (3, 2, 1)
# @unittest.skip("skipping test_itk_template_cmdline")
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def test_itk_template_cmdline(self):
# Read the ITK series, adding DICOM template
si1 = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
'none',
self.opts_template)
# Read the original DICOM series
si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'))
# Compare constructed series si1 to original series si2
self.assertEqual(si1.dtype, si2.dtype)
np.testing.assert_array_equal(si1, si2)
compare_template_headers(self, si1, si2)
# Write constructed series si1 to disk,
# then re-read and compare to original si2
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['dicom'])
si3 = Series(d)
# np.testing.assert_array_equal(si2, si3)
compare_template_headers(self, si2, si3)
# @unittest.skip("skipping test_itk_template_prog")
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def test_itk_template_prog(self):
# Read the ITK series, adding DICOM template
# adding DICOM template in Series constructor
si1 = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
template=self.template)
# Compare constructed series si1 to original series
self.assertEqual(si1.dtype, self.template.dtype)
np.testing.assert_array_equal(si1, self.template)
compare_template_headers(self, si1, self.template)
# @unittest.skip("skipping test_itk_geometry_cmdline")
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def test_itk_geometry_cmdline(self):
# Read the ITK series, adding DICOM geometry
si1 = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
'none',
self.opts_geometry)
# Read the original DICOM series
si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'))
# Compare constructed series si1 to original series si2
self.assertEqual(si1.dtype, si2.dtype)
np.testing.assert_array_equal(si1, si2)
compare_geometry_headers(self, si1, si2)
try:
compare_template_headers(self, si1, si2)
except (ValueError, AssertionError):
# Expected to fail
pass
else:
raise ShouldHaveFailed('Template header should differ when joining geometry')
# Write constructed series si1 to disk,
# then re-read and compare to original si2
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['dicom'])
si3 = Series(d)
np.testing.assert_array_equal(si2, si3)
compare_geometry_headers(self, si2, si2)
# @unittest.skip("skipping test_itk_geometry_prog")
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def test_itk_geometry_prog(self):
# Read the ITK series,
# adding DICOM geometry in Series constructor
si1 = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
geometry=self.geometry)
# Compare constructed series si1 to original series
self.assertEqual(si1.dtype, self.geometry.dtype)
np.testing.assert_array_equal(si1, self.geometry)
compare_geometry_headers(self, si1, self.geometry)
try:
compare_template_headers(self, si1, self.geometry)
except (ValueError, AssertionError):
# Excpected to fail
pass
else:
raise ShouldHaveFailed('Template header should differ when joining geometry')
# @unittest.skip("skipping test_itk_tempgeom_cmdline")
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def test_itk_tempgeom_cmdline(self):
# Read the ITK series, adding DICOM template and geometry
si1 = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
'none',
self.opts_tempgeom)
# Read the original DICOM series
si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'))
# Compare constructed series si1 to original series si2
self.assertEqual(si1.dtype, si2.dtype)
np.testing.assert_array_equal(si1, si2)
compare_headers(self, si1, si2)
# Write constructed series si1 to disk,
# then re-read and compare to original si2
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['dicom'])
si3 = Series(d)
np.testing.assert_array_equal(si2, si3)
compare_headers(self, si2, si3)
# @unittest.skip("skipping test_itk_tempgeom_prog")
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def test_itk_tempgeom_prog(self):
# Read the ITK series,
# adding DICOM template in Series constructor
si1 = Series(
os.path.join('data', 'itk', 'time', 'Image_00000.mha'),
template=self.template,
geometry=self.geometry)
# Compare constructed series si1 to original series
self.assertEqual(si1.dtype, self.template.dtype)
np.testing.assert_array_equal(si1, self.template)
compare_geometry_headers(self, si1, self.geometry)
compare_template_headers(self, si1, self.template)
if __name__ == '__main__':
unittest.main()