#!/usr/bin/env python3
import unittest
import os.path
from datetime import datetime
import numpy as np
import tempfile
import argparse
from .context import imagedata
import imagedata.cmdline
import imagedata.readdata
import imagedata.formats
from imagedata.series import Series
from .compare_headers import compare_headers, compare_template_headers, compare_geometry_headers
[docs]class ShouldHaveFailed(Exception):
pass
[docs]class TestDicomTemplate(unittest.TestCase):
[docs] def setUp(self):
parser = argparse.ArgumentParser()
imagedata.cmdline.add_argparse_options(parser)
self.opts = parser.parse_args(['--of', 'dicom'])
self.opts_template = parser.parse_args(['--of', 'dicom',
'--input_options', 'AcceptDuplicateTag=True',
'--template', 'data/dicom/time/time00/'])
self.opts_geometry = parser.parse_args(['--of', 'dicom',
'--input_options', 'AcceptDuplicateTag=True',
'--geometry', 'data/dicom/time/time00/'])
self.opts_tempgeom = parser.parse_args(['--of', 'dicom',
'--input_options', 'AcceptDuplicateTag=True',
'--template', 'data/dicom/time/time00/',
'--geometry', 'data/dicom/time/time00/'])
plugins = imagedata.formats.get_plugins_list()
self.dicom_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'dicom':
self.dicom_plugin = pclass
self.assertIsNotNone(self.dicom_plugin)
# Create a DICOM series with empty header
si0 = Series(os.path.join('data', 'mat', 'time', 'Image_00000.mat'), input_order='time')
self.emptydir = tempfile.TemporaryDirectory()
si00 = Series(si0[0], input_order='none')
si01 = Series(si0[:2], input_order='time')
si00.write(os.path.join(self.emptydir.name, 'empty_header'), formats=['dicom'])
# Provide sensible time tags
for s in range(40):
for t in range(2):
time_str = datetime.utcfromtimestamp(float(t)).strftime("%H%M%S.%f")
si01.setDicomAttribute('AcquisitionTime', time_str, slice=s, tag=t)
si01.write(os.path.join(self.emptydir.name, 'empty_header_time'), formats=['dicom'])
[docs] def tearDown(self):
self.emptydir.cleanup()
self.emptydir = None
# @unittest.skip("skipping test_dicom_template_cmdline")
[docs] def test_dicom_template_cmdline(self):
# Read the DICOM empty header series,
# adding DICOM template
si1 = Series(
os.path.join(self.emptydir.name, 'empty_header'),
'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)
try:
compare_geometry_headers(self, si1, si2)
except 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, 'none', self.opts)
np.testing.assert_array_equal(si2, si3)
compare_template_headers(self, si2, si3)
# @unittest.skip("skipping test_dicom_template_prog")
[docs] def test_dicom_template_prog(self):
# Read the DICOM empty header series,
# adding DICOM template in Series constructor
template = Series(os.path.join('data', 'dicom', 'time', 'time00'))
si1 = Series(
os.path.join(self.emptydir.name, 'empty_header'),
template=template)
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)
# @unittest.skip("skipping test_dicom_geometry_cmdline")
[docs] def test_dicom_geometry_cmdline(self):
# Read the DICOM empty header series,
# adding DICOM geometry
si1 = Series(
os.path.join(self.emptydir.name, 'empty_header'),
'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 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, 'none', self.opts)
np.testing.assert_array_equal(si2, si3)
compare_geometry_headers(self, si2, si2)
# @unittest.skip("skipping test_dicom_geometry_prog")
[docs] def test_dicom_geometry_prog(self):
# Read the DICOM empty header series,
# adding DICOM geometry in Series constructor
geometry = Series(os.path.join('data', 'dicom', 'time', 'time00'))
si1 = Series(
os.path.join(self.emptydir.name, 'empty_header'),
geometry=geometry)
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 AssertionError:
# Excpected to fail
pass
else:
raise ShouldHaveFailed('Template header should differ when joining geometry')
# @unittest.skip("skipping test_dicom_tempgeom_cmdline")
[docs] def test_dicom_tempgeom_cmdline(self):
# Read the DICOM empty header series,
# adding DICOM template
si1 = Series(
os.path.join(self.emptydir.name, 'empty_header'),
'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, 'none', self.opts)
np.testing.assert_array_equal(si2, si3)
compare_headers(self, si2, si3)
# @unittest.skip("skipping test_dicom_tempgeom_prog")
[docs] def test_dicom_tempgeom_prog(self):
# Read the DICOM empty header series,
# adding DICOM template in Series constructor
template = Series(os.path.join('data', 'dicom', 'time', 'time00'))
geometry = Series(os.path.join('data', 'dicom', 'time', 'time00'))
si1 = Series(
os.path.join(self.emptydir.name, 'empty_header'),
template=template,
geometry=geometry)
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)
# @unittest.skip("skipping test_dicom_temp_slice")
[docs] def test_dicom_temp_slice(self):
# Read the DICOM empty header series,
# adding DICOM template in Series constructor
# Then slice the si1 Series
template = Series(os.path.join('data', 'dicom', 'time'), input_order='time')
geometry = Series(os.path.join('data', 'dicom', 'time'), input_order='time')
si1 = Series(
os.path.join(self.emptydir.name, 'empty_header_time'),
input_order='time',
template=template,
geometry=geometry)
si1_0 = si1[0]
si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'))
# Compare constructed series si1_0 to original series si2
self.assertEqual(si1_0.dtype, si2.dtype)
np.testing.assert_array_equal(si1_0, si2)
# Tags do not match, so copy them to enable header comparison.
si1_0.tags = si2.tags
compare_headers(self, si1_0, si2)
if __name__ == '__main__':
unittest.main()