From e6b2518ed77a3c75725eaf20393f33e0d4f4eaa4 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Sat, 15 Apr 2017 17:54:19 +0100
Subject: [PATCH] Feat analysis unit tests, and some additions to test utils.
---
tests/__init__.py | 34 ++-
tests/test_featanalysis.py | 491 +++++++++++++++++++++++++++++++++++++
2 files changed, 521 insertions(+), 4 deletions(-)
create mode 100644 tests/test_featanalysis.py
diff --git a/tests/__init__.py b/tests/__init__.py
index 7170e9e75..3b89f3a30 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -15,24 +15,50 @@ import numpy as np
import nibabel as nib
-def testdir():
+def testdir(contents=None):
"""Returnsa context manager which creates and returns a temporary
directory, and then deletes it on exit.
"""
+
+ if contents is not None:
+ contents = [op.join(*c.split('/')) for c in contents]
+ print(contents)
+
class ctx(object):
+
+ def __init__(self, contents):
+ self.contents = contents
+
def __enter__(self):
+
self.testdir = tempfile.mkdtemp()
+
+ if self.contents is not None:
+ contents = [op.join(self.testdir, c) for c in self.contents]
+ make_dummy_files(contents)
+
return self.testdir
def __exit__(self, *a, **kwa):
shutil.rmtree(self.testdir)
- return ctx()
+ return ctx(contents)
+
+def make_dummy_files(paths):
+ """Creates dummy files for all of the given paths. """
+ for p in paths:
+ make_dummy_file(p)
-def make_dummy_file(path):
+def make_dummy_file(path, contents=None):
"""Makes a plain text file. Returns a hash of the file contents. """
- contents = '{}\n'.format(op.basename(path))
+ dirname = op.dirname(path)
+
+ if not op.exists(dirname):
+ os.makedirs(dirname)
+
+ if contents is None:
+ contents = '{}\n'.format(op.basename(path))
with open(path, 'wt') as f:
f.write(contents)
diff --git a/tests/test_featanalysis.py b/tests/test_featanalysis.py
new file mode 100644
index 000000000..c58758c7e
--- /dev/null
+++ b/tests/test_featanalysis.py
@@ -0,0 +1,491 @@
+#!/usr/bin/env python
+#
+# test_featanalysis.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os
+import os.path as op
+import itertools as it
+import glob
+import shutil
+import textwrap
+import collections
+
+import numpy as np
+
+import pytest
+
+import tests
+import fsl.data.featanalysis as featanalysis
+import fsl.data.featdesign as featdesign
+import fsl.data.image as fslimage
+import fsl.utils.path as fslpath
+
+
+def test_isFEATImage():
+ paths = ['analysis.feat/filtered_func_data.nii.gz',
+ 'analysis.feat/filtered_func_data.txt',
+ 'analysis.feat/design.fsf',
+ 'analysis.feat/design.mat',
+ 'analysis.feat/design.con',
+ 'analysis.bleat/filtered_func_data.nii.gz']
+
+ with tests.testdir(paths) as testdir:
+ for p in paths:
+ expected = p == 'analysis.feat/filtered_func_data.nii.gz'
+ assert featanalysis.isFEATImage(op.join(testdir, p)) == expected
+
+
+def test_isFEATDir():
+
+ # We need these files for a directory
+ # to be considered a FEAT directory
+ paths = ['analysis.feat/filtered_func_data.nii.gz',
+ 'analysis.feat/design.fsf',
+ 'analysis.feat/design.mat',
+ 'analysis.feat/design.con']
+
+ with tests.testdir(paths) as testdir:
+ assert featanalysis.isFEATDir(op.join(testdir, 'analysis.feat'))
+
+ # If the directory does not end in .feat,
+ # then it's not a feat directory
+ with tests.testdir([p.replace('feat', 'bleat') for p in paths]) as testdir:
+ assert not featanalysis.isFEATDir(op.join(testdir, 'analysis.bleat'))
+
+ # If the directory doesn't exist, then
+ # it's not a feat directory
+ assert not featanalysis.isFEATDir('nonexistent.feat')
+
+ # If any of the above files are not
+ # present, it is not a FEAT directory
+ perms = it.chain(it.combinations(paths, 1),
+ it.combinations(paths, 2),
+ it.combinations(paths, 3))
+ for p in perms:
+ with tests.testdir(p) as testdir:
+ assert not featanalysis.isFEATDir(
+ op.join(testdir, 'analysis.feat'))
+
+
+def test_hasStats():
+
+ with tests.testdir(['analysis.feat/stats/zstat1.nii.gz']) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ assert featanalysis.hasStats(featdir)
+
+ with tests.testdir(['analysis.feat/stats/zstat1.txt']) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ assert not featanalysis.hasStats(featdir)
+
+
+def test_hasMelodicDir():
+ paths = ['analysis.feat/filtered_func_data.ica/melodic_IC.nii.gz']
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ assert featanalysis.hasMelodicDir(featdir)
+
+
+def test_getAnalysisDir():
+
+ paths = ['analysis.feat/filtered_func_data.nii.gz',
+ 'analysis.feat/design.fsf',
+ 'analysis.feat/design.mat',
+ 'analysis.feat/design.con']
+
+ testpaths = ['analysis.feat/filtered_func_data.nii.gz',
+ 'analysis.feat/stats/zstat1.nii.gz',
+ 'analysis.feat/logs/feat4_post',
+ 'analysis.feat/.ramp.gif']
+
+ with tests.testdir(paths) as testdir:
+ expected = op.join(testdir, 'analysis.feat')
+ for t in testpaths:
+ t = op.join(testdir, t)
+ assert featanalysis.getAnalysisDir(t) == expected
+
+
+def test_getTopLevelAnalysisDir():
+ testcases = [
+ ('analysis.feat/filtered_func_data.ica/melodic_IC.nii.gz', 'analysis.feat'),
+ ('analysis.feat/filtered_func_data.nii.gz', 'analysis.feat'),
+ ('analysis.gfeat/cope1.feat/stats/zstat1.nii.gz', 'analysis.gfeat'),
+ ('filtered_func_data.ica/melodic_mix', 'filtered_func_data.ica'),
+ ('rest.ica/filtered_func_data.ica/melodic_IC.nii.gz', 'rest.ica')
+ ]
+
+ for path, expected in testcases:
+ assert featanalysis.getTopLevelAnalysisDir(path) == expected
+
+
+def test_getReportFile():
+
+ testcases = [(['analysis.feat/report.html'], True),
+ (['analysis.feat/filtered_func_data.nii.gz'], False)]
+
+ for paths, expected in testcases:
+ with tests.testdir(paths) as testdir:
+
+ featdir = op.join(testdir, 'analysis.feat')
+
+ if expected:
+ expected = op.join(featdir, 'report.html')
+ else:
+ expected = None
+
+ assert featanalysis.getReportFile(featdir) == expected
+
+
+def test_loadContrasts():
+ # (design.con contents, expected names, expected vectors)
+ goodtests = [
+ ("""
+ /ContrastName1 c1
+ /ContrastName2 c2
+ /ContrastName3 c3
+ /NumContrasts 3
+ /Matrix
+ 1 0 0
+ 0 1 0
+ 0 0 1
+ """,
+ ['c1', 'c2', 'c3'],
+ [[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
+ ("""
+ /NumContrasts 2
+ /Matrix
+ 1 0 0 0
+ 0 1 0 0
+ """,
+ ['1', '2'],
+ [[1, 0, 0, 0], [0, 1, 0, 0]]),
+ ("""
+ /NumContrasts 1
+ /ContrastName1 My contrast
+ /Matrix
+ 5
+ """,
+ ['My contrast'], [[5]])
+ ]
+ badtests = [
+ """
+ /Matrix
+ 1 0 0
+ 0 1 0
+ """,
+ """
+ /NumContrasts 2
+ /Matrix
+ 1 0
+ 0 1 1
+ """,
+ """
+ /NumContrasts 3
+ /Matrix
+ 1 0 0
+ 0 1 1
+ """,
+ ]
+
+ with pytest.raises(Exception):
+ featanalysis.loadContrasts('no file')
+
+ with tests.testdir() as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ for contents, expnames, expvectors in goodtests:
+ designcon = op.join(featdir, 'design.con')
+ tests.make_dummy_file(designcon, textwrap.dedent(contents).strip())
+
+ result = featanalysis.loadContrasts(featdir)
+ assert result[0] == expnames
+ assert result[1] == expvectors
+
+ for contents in badtests:
+ designcon = op.join(featdir, 'design.con')
+ tests.make_dummy_file(designcon, textwrap.dedent(contents).strip())
+
+ with pytest.raises(Exception):
+ featanalysis.loadContrasts(featdir)
+
+
+def test_loadSettings():
+
+ contents = """
+ set random_setting true
+ any lines that don't start with "set" should be ignored
+ # regardless of whether they are commented or not
+ set fmri(blah) 0.66
+ set something "quoted"
+ set somethingelse 'quotedagain'
+ set fmri_thing(no) none
+ # set comment commented out
+ set athing with spaces in the value
+ """
+
+ expected = collections.OrderedDict((
+ ('random_setting', 'true'),
+ ('blah', '0.66'),
+ ('something', 'quoted'),
+ ('somethingelse', 'quotedagain'),
+ ('fmri_thing(no)', 'none'),
+ ('athing', 'with spaces in the value'),
+ ))
+
+ contents = textwrap.dedent(contents).strip()
+
+ with pytest.raises(Exception):
+ featanalysis.loadSettings('no file')
+
+ with tests.testdir() as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ tests.make_dummy_file(op.join(featdir, 'design.fsf'), contents)
+ result = featanalysis.loadSettings(featdir)
+ assert result == expected
+
+
+def test_loadDesign():
+
+ datadir = op.join(op.dirname(__file__), 'testdata', 'test_feat')
+ featdir = op.join(datadir, '1stlevel_1.feat')
+
+ settings = featanalysis.loadSettings(featdir)
+ design = featanalysis.loadDesign(featdir, settings)
+
+ assert isinstance(design, featdesign.FEATFSFDesign)
+ assert len(design.getEVs()) == 10
+ assert design.getDesign().shape == (45, 10)
+
+
+def test_getThresholds():
+ datadir = op.join(op.dirname(__file__), 'testdata', 'test_feat')
+ featdir = op.join(datadir, '1stlevel_1.feat')
+ settings = featanalysis.loadSettings(featdir)
+
+ thresholds = featanalysis.getThresholds(settings)
+ assert np.isclose(thresholds['p'], 0.05)
+ assert np.isclose(thresholds['z'], 2.3)
+
+
+def test_isFirstLevelAnalysis():
+ datadir = op.join(op.dirname(__file__), 'testdata', 'test_feat')
+ featdirs = ['1stlevel_1.feat', '1stlevel_2.feat', '1stlevel_3.feat',
+ '2ndlevel_1.gfeat', '2ndlevel_2.gfeat']
+
+ for featdir in featdirs:
+
+ expected = featdir.startswith('1')
+ featdir = op.join(datadir, featdir)
+ settings = featanalysis.loadSettings(featdir)
+
+ assert featanalysis.isFirstLevelAnalysis(settings) == expected
+
+
+def test_loadClusterResults():
+ datadir = op.join(op.dirname(__file__), 'testdata', 'test_feat')
+ featdirs = ['1stlevel_1.feat', '1stlevel_2.feat', '1stlevel_3.feat',
+ '2ndlevel_1.gfeat/cope1.feat', '2ndlevel_1.gfeat/cope2.feat',
+ '2ndlevel_2.gfeat/cope1.feat', '2ndlevel_2.gfeat/cope2.feat']
+ ncontrasts = [2, 2, 2, 1, 1, 1, 1]
+ nclusters = [[1, 5], [2, 2], [3, 5], [7], [1], [10], [27]]
+
+ with pytest.raises(Exception):
+ featanalysis.loadClusterResults('notafeatdir')
+
+ for i, featdir in enumerate(featdirs):
+
+ firstlevel = featdir.startswith('1')
+ featdir = op.join(datadir, featdir)
+
+ with tests.testdir() as testdir:
+
+ # For higher level analyses, the
+ # loadClusterResults function peeks
+ # at the FEAT input data file
+ # header, so we have to generate it.
+ newfeatdir = op.join(testdir, 'analysis.feat')
+ shutil.copytree(op.join(datadir, featdir), newfeatdir)
+ featdir = newfeatdir
+
+ if not firstlevel:
+ datafile = op.join(featdir, 'filtered_func_data.nii.gz')
+ data = np.random.randint(1, 10, (91, 109, 91))
+ xform = np.array([[-2, 0, 0, 90],
+ [ 0, 2, 0, -126],
+ [ 0, 0, 2, -72],
+ [ 0, 0, 0, 1]])
+ fslimage.Image(data, xform=xform).save(datafile)
+
+ settings = featanalysis.loadSettings(featdir)
+ for c in range(ncontrasts[i]):
+ clusters = featanalysis.loadClusterResults(
+ featdir, settings, c)
+
+ assert len(clusters) == nclusters[i][c]
+
+ # Test calling the function on a feat dir
+ # which doesn't have any cluster results
+ if i == len(featdirs) - 1:
+ for clustfile in glob.glob(op.join(featdir, 'cluster*txt')):
+ os.remove(clustfile)
+ assert featanalysis.loadClusterResults(
+ featdir, settings, 0) is None
+
+
+def test_getDataFile():
+ paths = ['analysis.feat/filtered_func_data.nii.gz',
+ 'analysis.feat/design.fsf',
+ 'analysis.feat/design.mat',
+ 'analysis.feat/design.con']
+
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ expect = op.join(featdir, 'filtered_func_data.nii.gz')
+
+ assert featanalysis.getDataFile(featdir) == expect
+
+ paths = ['analysis.feat/filtered_func_data.txt',
+ 'analysis.feat/design.fsf',
+ 'analysis.feat/design.mat',
+ 'analysis.feat/design.con']
+
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+
+ with pytest.raises(fslpath.PathError):
+ assert featanalysis.getDataFile(featdir)
+
+
+def test_getMelodicFile():
+ testcases = [
+ (['analysis.feat/filtered_func_data.ica/melodic_IC.nii.gz'], True),
+ (['analysis.feat/filtered_func_data.ica/melodic_IC.txt'], False),
+ ]
+
+ for paths, shouldPass in testcases:
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ icadir = op.join(featdir, 'filtered_func_data.ica')
+ expect = op.join(icadir, 'melodic_IC.nii.gz')
+
+ if shouldPass:
+ assert featanalysis.getMelodicFile(featdir) == expect
+ else:
+ with pytest.raises(fslpath.PathError):
+ featanalysis.getMelodicFile(featdir)
+
+
+
+def test_getResidualFile():
+ testcases = [
+ (['analysis.feat/stats/res4d.nii.gz'], True),
+ (['analysis.feat/stats/res4d.txt'], False),
+ ]
+
+ for paths, shouldPass in testcases:
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+ expect = op.join(featdir, 'stats', 'res4d.nii.gz')
+
+ if shouldPass:
+ assert featanalysis.getResidualFile(featdir) == expect
+ else:
+ with pytest.raises(fslpath.PathError):
+ featanalysis.getResidualFile(featdir)
+
+
+def test_getPEFile():
+ testcases = [
+ (['analysis.feat/stats/pe1.nii.gz',
+ 'analysis.feat/stats/pe2.nii.gz'], True),
+ (['analysis.feat/stats/pe1.nii.gz'], True),
+ (['analysis.feat/stats/pe0.nii.gz'], False),
+ (['analysis.feat/stats/pe1.txt'], False),
+ ]
+
+ for paths, shouldPass in testcases:
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+
+ for pei in range(len(paths)):
+ expect = op.join(
+ featdir, 'stats', 'pe{}.nii.gz'.format(pei + 1))
+
+ if shouldPass:
+ assert featanalysis.getPEFile(featdir, pei) == expect
+ else:
+ with pytest.raises(fslpath.PathError):
+ featanalysis.getPEFile(featdir, pei)
+
+
+def test_getCOPEFile():
+ testcases = [
+ (['analysis.feat/stats/cope1.nii.gz',
+ 'analysis.feat/stats/cope2.nii.gz'], True),
+ (['analysis.feat/stats/cope1.nii.gz'], True),
+ (['analysis.feat/stats/cope0.nii.gz'], False),
+ (['analysis.feat/stats/cope1.txt'], False),
+ ]
+
+ for paths, shouldPass in testcases:
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+
+ for ci in range(len(paths)):
+ expect = op.join(
+ featdir, 'stats', 'cope{}.nii.gz'.format(ci + 1))
+
+ if shouldPass:
+ assert featanalysis.getCOPEFile(featdir, ci) == expect
+ else:
+ with pytest.raises(fslpath.PathError):
+ featanalysis.getCOPEFile(featdir, ci)
+
+
+def test_getZStatFile():
+ testcases = [
+ (['analysis.feat/stats/zstat1.nii.gz',
+ 'analysis.feat/stats/zstat2.nii.gz'], True),
+ (['analysis.feat/stats/zstat1.nii.gz'], True),
+ (['analysis.feat/stats/zstat0.nii.gz'], False),
+ (['analysis.feat/stats/zstat1.txt'], False),
+ ]
+
+ for paths, shouldPass in testcases:
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+
+ for zi in range(len(paths)):
+ expect = op.join(
+ featdir, 'stats', 'zstat{}.nii.gz'.format(zi + 1))
+
+ if shouldPass:
+ assert featanalysis.getZStatFile(featdir, zi) == expect
+ else:
+ with pytest.raises(fslpath.PathError):
+ featanalysis.getZStatFile(featdir, zi)
+
+
+def test_getClusterMaskFile():
+ testcases = [
+ (['analysis.feat/cluster_mask_zstat1.nii.gz',
+ 'analysis.feat/cluster_mask_zstat2.nii.gz'], True),
+ (['analysis.feat/cluster_mask_zstat1.nii.gz'], True),
+ (['analysis.feat/cluster_mask_zstat0.nii.gz'], False),
+ (['analysis.feat/cluster_mask_zstat1.txt'], False),
+ ]
+
+ for paths, shouldPass in testcases:
+ with tests.testdir(paths) as testdir:
+ featdir = op.join(testdir, 'analysis.feat')
+
+ for ci in range(len(paths)):
+ expect = op.join(
+ featdir, 'cluster_mask_zstat{}.nii.gz'.format(ci + 1))
+
+ if shouldPass:
+ assert featanalysis.getClusterMaskFile(featdir, ci) == expect
+ else:
+ with pytest.raises(fslpath.PathError):
+ featanalysis.getClusterMaskFile(featdir, ci)
--
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