Commit 605d5315 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

TEST: update dicom tests

parent e58be5f9
#!/usr/bin/env python
#
# test_dicom.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
# These tests require an internet connection, and will only work on linux.
#
import os.path as op
import tarfile
import os.path as op
import os
import functools as ft
import subprocess as sp
import tarfile
import zipfile
import random
import string
import binascii
import contextlib
import urllib.request as request
from unittest import mock
import mock
import pytest
import fsl.data.dicom as fsldcm
......@@ -21,14 +28,35 @@ datadir = op.join(op.dirname(__file__), 'testdata')
pytestmark = pytest.mark.dicomtest
def setup_module():
@contextlib.contextmanager
def install_dcm2niix(version='1.0.20190902'):
filenames = {
'1.0.20190902' : 'v1.0.20190902/dcm2niix_lnx.zip',
'1.0.20190410' : 'v1.0.20190410/dcm2niix_11-Apr-2019_lnx.zip',
'1.0.20181125' : 'v1.0.20181125/dcm2niix_25-Nov-2018_lnx.zip',
'1.0.20171017' : 'v1.0.20171017/dcm2niix_18-Oct-2017_lnx.zip',
}
prefix = 'https://github.com/rordenlab/dcm2niix/releases/download/'
url = prefix + filenames[version]
if not fsldcm.enabled():
raise RuntimeError('dcm2niix is not present - tests cannot be run')
with tempdir.tempdir() as td:
request.urlretrieve(url, 'dcm2niix.zip')
with zipfile.ZipFile('dcm2niix.zip', 'r') as f:
f.extractall('.')
os.chmod(op.join(td, 'dcm2niix'), 0o755)
path = op.pathsep.join((op.abspath('.'), os.environ['PATH']))
with mock.patch.dict('os.environ', {'PATH' : path}):
try:
yield
finally:
fsldcm.installedVersion.invalidate()
def test_disabled():
def test_disabled():
with mock.patch('fsl.data.dicom.enabled', return_value=False):
with pytest.raises(RuntimeError):
fsldcm.scanDir('.')
......@@ -36,20 +64,37 @@ def test_disabled():
fsldcm.loadSeries({})
def test_installedVersion():
tests = [
('1.0.20190902', (1, 0, 2019, 9, 2)),
('1.0.20181125', (1, 0, 2018, 11, 25)),
('1.0.20171017', (1, 0, 2017, 10, 17))]
for version, expect in tests:
fsldcm.installedVersion.invalidate()
with install_dcm2niix(version):
got = fsldcm.installedVersion()
assert got == expect
def test_enabled():
try:
fsldcm.enabled.invalidate()
assert fsldcm.enabled()
fsldcm.enabled.invalidate()
with install_dcm2niix('1.0.20190902'):
fsldcm.installedVersion.invalidate()
assert fsldcm.enabled()
# test dcm2niix not present
with mock.patch('subprocess.check_output',
side_effect=Exception()):
fsldcm.installedVersion.invalidate()
assert not fsldcm.enabled()
# test presence of different versions
tests = [(b'version v2.1.20191212', True),
(b'version v1.0.20190902', True),
(b'version v1.0.20171216', True),
(b'version v1.0.20171215', True),
(b'version v1.0.20171214', False),
......@@ -59,19 +104,19 @@ def test_enabled():
(b'version blurgh', False)]
for verstr, expected in tests:
fsldcm.enabled.invalidate()
fsldcm.installedVersion.invalidate()
with mock.patch('subprocess.check_output', return_value=verstr):
assert fsldcm.enabled() == expected
finally:
fsldcm.enabled.invalidate()
fsldcm.installedVersion.invalidate()
def test_scanDir():
with tempdir.tempdir() as td:
with install_dcm2niix():
series = fsldcm.scanDir(td)
series = fsldcm.scanDir('.')
assert len(series) == 0
datafile = op.join(datadir, 'example_dicom.tbz2')
......@@ -79,42 +124,69 @@ def test_scanDir():
with tarfile.open(datafile) as f:
f.extractall()
series = fsldcm.scanDir(td)
assert len(series) == 3
series = fsldcm.scanDir('.')
assert len(series) == 2
for s in series:
assert (s['PatientName'] == 'MCCARTHY_PAUL' or
s['PatientName'] == 'MCCARTHY_PAUL_2')
def test_sersiesCRC():
RANDOM = object()
tests = [
({'SeriesInstanceUID' : 'hello-world'}, '2983461467'),
({'SeriesInstanceUID' : RANDOM, 'EchoNumber' : 0}, RANDOM),
({'SeriesInstanceUID' : RANDOM, 'EchoNumber' : 1}, RANDOM),
({'SeriesInstanceUID' : RANDOM, 'EchoNumber' : 2}, RANDOM),
({'SeriesInstanceUID' : RANDOM, 'EchoNumber' : 3}, RANDOM),
]
for series, expect in tests:
series = dict(series)
if expect is RANDOM:
expect = ''.join(random.choices(
string.ascii_letters + string.digits, k=30))
series['SeriesInstanceUID'] = expect
expect = str(binascii.crc32(expect.encode()))
echo = series.get('EchoNumber', 0)
if echo > 1:
expect += '.{}'.format(echo)
assert fsldcm.seriesCRC(series) == expect
def test_loadSeries():
with tempdir.tempdir() as td:
# test a pre-CRC and a post-CRC version
for version in ('1.0.20190410', '1.0.20190902'):
datafile = op.join(datadir, 'example_dicom.tbz2')
with install_dcm2niix(version):
with tarfile.open(datafile) as f:
f.extractall()
datafile = op.join(datadir, 'example_dicom.tbz2')
with tarfile.open(datafile) as f:
f.extractall()
series = fsldcm.scanDir(td)
expShape = (512, 512, 1)
explens = [1, 2]
dcmdir = os.getcwd()
series = fsldcm.scanDir(dcmdir)
expShape = (512, 512, 1)
explens = [1, 1]
for s, explen in zip(series, explens):
for s, explen in zip(series, explens):
imgs = fsldcm.loadSeries(s)
imgs = fsldcm.loadSeries(s)
assert len(imgs) == explen
assert len(imgs) == explen
for img in imgs:
for img in imgs:
assert img.dicomDir == td
assert img.shape == expShape
assert img[:].shape == expShape
assert img.getMeta('PatientName') == 'MCCARTHY_PAUL' or \
img.getMeta('PatientName') == 'MCCARTHY_PAUL_2'
assert 'PatientName' in img.metaKeys()
assert 'MCCARTHY_PAUL' in img.metaValues() or \
'MCCARTHY_PAUL_2' in img.metaValues()
assert ('PatientName', 'MCCARTHY_PAUL') in img.metaItems() or \
('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()
assert img.dicomDir == dcmdir
assert img.shape == expShape
assert img[:].shape == expShape
assert img.getMeta('PatientName') == 'MCCARTHY_PAUL' or \
img.getMeta('PatientName') == 'MCCARTHY_PAUL_2'
assert 'PatientName' in img.metaKeys()
assert 'MCCARTHY_PAUL' in img.metaValues() or \
'MCCARTHY_PAUL_2' in img.metaValues()
assert ('PatientName', 'MCCARTHY_PAUL') in img.metaItems() or \
('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()
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