From 605d531538178fad8ac7624f44d8a8332fdbb6f7 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 5 Sep 2019 16:22:47 +0100
Subject: [PATCH] TEST: update dicom tests
---
tests/test_dicom.py | 154 ++++++++++++++++++++++++++++++++------------
1 file changed, 113 insertions(+), 41 deletions(-)
diff --git a/tests/test_dicom.py b/tests/test_dicom.py
index 70b5117bc..5354e86e2 100644
--- a/tests/test_dicom.py
+++ b/tests/test_dicom.py
@@ -1,14 +1,21 @@
#!/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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