From 08d8b4686f4ed94788fa1d72eb3eea6550780720 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 4 Dec 2018 09:29:15 +0000
Subject: [PATCH] TEST: Test utils.guessType
---
tests/__init__.py | 50 ++++++++++++++++
tests/test_fsl_data_utils.py | 107 +++++++++++++++++++++++++++++++++++
2 files changed, 157 insertions(+)
create mode 100644 tests/test_fsl_data_utils.py
diff --git a/tests/__init__.py b/tests/__init__.py
index 06bd6b5b7..2ed387e0b 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -358,6 +358,56 @@ def make_mock_feat_analysis(featdir,
return featdir
+def make_mock_melodic_analysis(basedir, shape4D, ntimepoints, xform=None):
+
+ if xform is None:
+ xform = np.eye(4)
+
+ ncomps = shape4D[-1]
+ halftime = int(np.floor(ntimepoints / 2))
+
+ os.makedirs(basedir)
+
+ make_random_image(op.join(basedir, 'melodic_IC.nii.gz'),
+ dims=shape4D,
+ xform=xform)
+
+ mix = np.random.randint(1, 255, (ntimepoints, ncomps))
+ ftmix = np.random.randint(1, 255, (halftime, ncomps))
+
+ np.savetxt(op.join(basedir, 'melodic_mix'), mix)
+ np.savetxt(op.join(basedir, 'melodic_FTmix'), ftmix)
+
+
+def make_mock_dtifit_analysis(basedir, shape3D, basename='dti', xform=None, tensor=False):
+
+ if xform is None:
+ xform = np.eye(4)
+
+ os.makedirs(basedir)
+
+ shape4D = tuple(shape3D) + (3,)
+
+ def mk(ident, shp):
+ make_random_image(
+ op.join(basedir, '{}_{}.nii.gz'.format(basename, ident)),
+ shp,
+ xform)
+
+ mk('V1', shape4D)
+ mk('V2', shape4D)
+ mk('V3', shape4D)
+ mk('L1', shape3D)
+ mk('L2', shape3D)
+ mk('L3', shape3D)
+ mk('S0', shape3D)
+ mk('MD', shape3D)
+ mk('MO', shape3D)
+ mk('FA', shape3D)
+
+ if tensor:
+ mk('tensor', tuple(shape3D) + (6,))
+
def make_random_mask(filename, shape, xform, premask=None, minones=1):
"""Make a random binary mask image. """
diff --git a/tests/test_fsl_data_utils.py b/tests/test_fsl_data_utils.py
new file mode 100644
index 000000000..3fd02a8f9
--- /dev/null
+++ b/tests/test_fsl_data_utils.py
@@ -0,0 +1,107 @@
+#!/usr/bin/env python
+#
+# test_fsl_data_utils.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import shutil
+import os
+import os.path as op
+
+import fsl.utils.tempdir as tempdir
+import fsl.data.utils as dutils
+
+import fsl.utils.path as fslpath
+import fsl.data.image as fslimage
+import fsl.data.vtk as fslvtk
+import fsl.data.gifti as fslgifti
+import fsl.data.freesurfer as fslfs
+import fsl.data.mghimage as fslmgh
+import fsl.data.featimage as featimage
+import fsl.data.melodicimage as melimage
+import fsl.data.dtifit as dtifit
+import fsl.data.melodicanalysis as melanalysis
+import fsl.data.featanalysis as featanalysis
+
+from . import (touch,
+ make_mock_feat_analysis,
+ make_mock_melodic_analysis,
+ make_mock_dtifit_analysis)
+
+
+def test_guessType():
+
+ def asrt(path, cls):
+ restype, respath = dutils.guessType(path)
+
+ assert restype is cls
+
+ if path.startswith('fsleyes://'):
+ path = path[10:]
+
+ # image path might not have an extension
+
+ try:
+ path = fslimage.addExt(path, mustExist=True)
+ except fslimage.PathError:
+ pass
+
+ assert respath == op.abspath(path)
+
+ with tempdir.tempdir() as td:
+
+ touch('foo.nii')
+ asrt('foo', fslimage.Image)
+ asrt('foo.nii', fslimage.Image)
+ asrt('fsleyes://foo', fslimage.Image)
+ asrt('fsleyes://foo.nii', fslimage.Image)
+ os.remove('foo.nii')
+
+
+ touch('foo.vtk')
+ asrt('foo.vtk', fslvtk.VTKMesh)
+ os.remove('foo.vtk')
+
+ touch('foo.surf.gii')
+ asrt('foo.surf.gii', fslgifti.GiftiMesh)
+ os.remove('foo.surf.gii')
+
+ touch('lh.pial')
+ asrt('lh.pial', fslfs.FreesurferMesh)
+ os.remove('lh.pial')
+
+ touch('foo.mgz')
+ asrt('foo.mgz', fslmgh.MGHImage)
+ os.remove('foo.mgz')
+
+ make_mock_melodic_analysis('filtered_func_data.ica',
+ (10, 10, 10, 10),
+ 20)
+ asrt('filtered_func_data.ica/melodic_IC', melimage.MelodicImage)
+ asrt('filtered_func_data.ica/melodic_IC.nii.gz', melimage.MelodicImage)
+ asrt('filtered_func_data.ica', melimage.MelodicImage)
+ asrt('filtered_func_data.ica/', melimage.MelodicImage)
+ shutil.rmtree('filtered_func_data.ica')
+
+ featdir = op.join(op.dirname(__file__),
+ 'testdata', 'test_feat', '1stlevel_1.feat')
+ make_mock_feat_analysis(featdir,
+ td,
+ (10, 10, 10, 10))
+ asrt('1stlevel_1.feat/filtered_func_data', featimage.FEATImage)
+ asrt('1stlevel_1.feat/filtered_func_data.nii.gz', featimage.FEATImage)
+ asrt('1stlevel_1.feat', featimage.FEATImage)
+
+ make_mock_dtifit_analysis('dti', (10, 10, 10))
+ asrt('dti', dtifit.DTIFitTensor)
+ shutil.rmtree('dti')
+
+ asrt('noexist', None)
+
+ touch('norecognise')
+ asrt('norecognise', None)
+ touch('norecognise.txt')
+ asrt('norecognise.txt', None)
+ os.remove('norecognise')
+ os.remove('norecognise.txt')
--
GitLab