From 8bc789a8c014c9a26bde54939ffcea1393c54027 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Fri, 2 Sep 2016 16:47:42 +0100
Subject: [PATCH] More path tests, and tests for fsl.data.image
---
tests/test_fsl_utils_path.py | 22 ++---
tests/test_image.py | 165 +++++++++++++++++++++++++++++++++--
2 files changed, 168 insertions(+), 19 deletions(-)
diff --git a/tests/test_fsl_utils_path.py b/tests/test_fsl_utils_path.py
index bb6b9cb17..25f945620 100644
--- a/tests/test_fsl_utils_path.py
+++ b/tests/test_fsl_utils_path.py
@@ -10,6 +10,7 @@ import os.path as op
import pytest
import fsl.utils.path as fslpath
+import fsl.data.image as fslimage
def test_addExt_exists_shouldPass(testdir):
@@ -17,9 +18,8 @@ def test_addExt_exists_shouldPass(testdir):
are valid.
"""
- # If we have a .hdr/.img pair, the .img should take precedence
- replacements = {'.hdr' : ['.img', '.img.gz']}
- allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
+ replacements = fslimage.REPLACEMENTS
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
tests = [
('compressed', 'compressed.nii.gz'),
@@ -30,7 +30,7 @@ def test_addExt_exists_shouldPass(testdir):
('img_hdr_pair.hdr', 'img_hdr_pair.hdr'),
('img_hdr_pair.img', 'img_hdr_pair.img'),
('compressed_img_hdr_pair', 'compressed_img_hdr_pair.img.gz'),
- ('compressed_img_hdr_pair.hdr', 'compressed_img_hdr_pair.hdr'),
+ ('compressed_img_hdr_pair.hdr.gz', 'compressed_img_hdr_pair.hdr.gz'),
('compressed_img_hdr_pair.img.gz', 'compressed_img_hdr_pair.img.gz'),
]
@@ -48,9 +48,9 @@ def test_addExt_exists_shouldFail(testdir):
"""Tests the addExt function with inputs that should cause it to raise an
error.
"""
-
- replacements = {'.hdr' : ['.img', '.img.gz']}
- allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
+
+ replacements = fslimage.REPLACEMENTS
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
shouldFail = [
@@ -73,6 +73,8 @@ def test_addExt_exists_shouldFail(testdir):
('ambiguous', [], {'.hdr' : ['.img']}),
('ambiguous', False, {'.hdr' : ['.img.gz']}),
('ambiguous', [], {'.hdr' : ['.img.gz']}),
+ ('ambiguous', False, {'.hdr' : ['.img', '.img.gz', '.nii']}),
+ ('ambiguous', [], {'.hdr' : ['.img', '.img.gz', '.nii']}),
('badpath'),
('badpath.nii.gz'),
@@ -101,7 +103,7 @@ def test_addExt_exists_shouldFail(testdir):
def test_addExt_noExist(testdir):
- allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
# Prefix, output, defaultExt, allowedExts
tests = [
@@ -136,7 +138,7 @@ def test_addExt_noExist(testdir):
def test_removeExt(testdir):
- allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
# If len(test) == 2, allowedExts is set from above
# Otherwise, it is set from the test tuple
@@ -170,7 +172,7 @@ def test_removeExt(testdir):
def test_getExt(testdir):
- allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
# len(test) == 2 -> allowedExts set from above
# Otherwise, allowedExts set from test tuple
diff --git a/tests/test_image.py b/tests/test_image.py
index ff722fc2b..757789f17 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -6,13 +6,16 @@
#
import os.path as op
-import logging
+import pytest
+import glob
import numpy as np
import nibabel as nib
-import fsl.data.image as fslimage
+import fsl.data.constants as constants
+import fsl.data.image as fslimage
+import fsl.utils.path as fslpath
# Need to test:
@@ -25,13 +28,157 @@ import fsl.data.image as fslimage
def test_load(testdir):
assert testdir is not None
+
+ shouldPass = ['compressed',
+ 'compressed.nii.gz',
+ 'uncompressed',
+ 'uncompressed.nii',
+ 'img_hdr_pair',
+ 'img_hdr_pair.img',
+ 'img_hdr_pair.hdr',
+ 'compressed_img_hdr_pair',
+ 'compressed_img_hdr_pair.img.gz',
+ 'compressed_img_hdr_pair.hdr.gz',
+ 'ambiguous.nii',
+ 'ambiguous.hdr',
+ 'ambiguous.img',
+ 'ambiguous.hdr.gz',
+ 'ambiguous.img.gz']
+ shouldRaise = ['notexist',
+ 'notexist.nii.gz',
+ 'ambiguous']
- fslimage.Image(op.join(testdir, 'nifti_formats', 'compressed'))
- fslimage.Image(op.join(testdir, 'nifti_formats', 'compressed.nii.gz'))
- fslimage.Image(op.join(testdir, 'nifti_formats', 'uncompressed'))
- fslimage.Image(op.join(testdir, 'nifti_formats', 'uncompressed.nii'))
- fslimage.Image(op.join(testdir, 'nifti_formats', 'img_hdr_pair'))
- fslimage.Image(op.join(testdir, 'nifti_formats', 'img_hdr_pair.img'))
- fslimage.Image(op.join(testdir, 'nifti_formats', 'img_hdr_pair.hdr'))
+ # Not raising an error means the test passes
+ for fname in shouldPass:
+ fslimage.Image(op.join(testdir, 'nifti_formats', fname))
+
+ # These should raise an error
+ for fname in shouldRaise:
+ with pytest.raises(fslpath.PathError):
+ print fname
+ fslimage.Image(op.join(testdir, 'nifti_formats', fname))
+
+
+
+def test_Image_atts(testdir):
+
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
+
+ # (file, dims, pixdims)
+ tests = [
+ ('MNI152_T1_0.5mm', (364, 436, 364), (0.5, 0.5, 0.5), np.uint8),
+ ('MNI152_T1_1mm', (182, 218, 182), (1.0, 1.0, 1.0), np.int16),
+ ('MNI152_T1_2mm', (91, 109, 91), (2.0, 2.0, 2.0), np.int16),
+ ('MNI152_T1_2mm_4D', (91, 109, 91, 5), (2.0, 2.0, 2.0, 1.0), np.int16),
+ (op.join('nifti2D', 'MNI152_T1_2mm_sliceXY'), (91, 109, 1), (2.0, 2.0, 2.0), np.int16),
+ (op.join('nifti2D', 'MNI152_T1_2mm_sliceXZ'), (91, 1, 91), (2.0, 2.0, 2.0), np.int16),
+ (op.join('nifti2D', 'MNI152_T1_2mm_sliceYZ'), (1, 109, 91), (2.0, 2.0, 2.0), np.int16)]
+
+ for path, dims, pixdims, dtype in tests:
+
+ path = op.abspath(op.join(testdir, path))
+ i = fslimage.Image(path)
+
+ assert tuple(i.shape) == tuple(dims)
+ assert tuple(i.pixdim) == tuple(pixdims)
+ assert tuple(i.nibImage.shape) == tuple(dims)
+ assert tuple(i.nibImage.header.get_zooms()) == tuple(pixdims)
+
+ assert i.dtype == dtype
+ assert i.name == op.basename(path)
+ assert i.dataSource == fslpath.addExt(path, allowedExts, mustExist=True)
+
+
+def test_looksLikeImage():
+
+ # (file, expected)
+ tests = [
+ ('blah', False),
+ ('blah.moo', False),
+ ('blah.nii', True),
+ ('blah.nii.gz', True),
+ ('blah.hdr', True),
+ ('blah.img', True),
+ ('blah.hdr.gz', True),
+ ('blah.img.gz', True),
+ ]
+
+ for path, expected in tests:
+ assert fslimage.looksLikeImage(path) == expected
+
+def test_addExt(testdir):
+ default = fslimage.DEFAULT_EXTENSION
+
+ # (file, mustExist, expected)
+ tests = [
+ ('blah', False, 'blah{}'.format(default)),
+ ('blah.nii', False, 'blah.nii'),
+ ('blah.nii.gz', False, 'blah.nii.gz'),
+ ('blah.img', False, 'blah.img'),
+ ('blah.hdr', False, 'blah.hdr'),
+ ('blah.img.gz', False, 'blah.img.gz'),
+ ('blah.hdr.gz', False, 'blah.hdr.gz'),
+ ('compressed', True, 'compressed.nii.gz'),
+ ('compressed.nii.gz', True, 'compressed.nii.gz'),
+ ('uncompressed', True, 'uncompressed.nii'),
+ ('uncompressed.nii', True, 'uncompressed.nii'),
+ ('img_hdr_pair', True, 'img_hdr_pair.img'),
+ ('img_hdr_pair.hdr', True, 'img_hdr_pair.hdr'),
+ ('img_hdr_pair.img', True, 'img_hdr_pair.img'),
+ ('compressed_img_hdr_pair', True, 'compressed_img_hdr_pair.img.gz'),
+ ('compressed_img_hdr_pair.img.gz', True, 'compressed_img_hdr_pair.img.gz'),
+ ('compressed_img_hdr_pair.hdr.gz', True, 'compressed_img_hdr_pair.hdr.gz'),
+ ('ambiguous.nii', True, 'ambiguous.nii'),
+ ('ambiguous.nii.gz', True, 'ambiguous.nii.gz'),
+ ('ambiguous.img', True, 'ambiguous.img'),
+ ('ambiguous.hdr', True, 'ambiguous.hdr'),
+ ('ambiguous.img.gz', True, 'ambiguous.img.gz'),
+ ('ambiguous.hdr.gz', True, 'ambiguous.hdr.gz')]
+
+ for path, mustExist, expected in tests:
+ if mustExist:
+ path = op.join(testdir, 'nifti_formats', path)
+ expected = op.join(testdir, 'nifti_formats', expected)
+
+ assert fslimage.addExt(path, mustExist) == expected
+
+ with pytest.raises(fslimage.PathError):
+ path = op.join(testdir, 'nifti_formats', 'ambiguous')
+ fslimage.addExt(path, mustExist=True)
+
+
+def test_Image_orientation(testdir):
+
+ neuro = op.join(testdir, 'dtifit', 'neuro', 'dti_FA')
+ radio = op.join(testdir, 'dtifit', 'radio', 'dti_FA')
+
+ neuro = fslimage.Image(neuro)
+ radio = fslimage.Image(radio)
+
+ assert neuro.isNeurological()
+ assert not radio.isNeurological()
+
+ # Both images should have the
+ # same orientation in the
+ # world coordinate system
+ assert neuro.getOrientation(0, np.eye(4)) == constants.ORIENT_L2R
+ assert neuro.getOrientation(1, np.eye(4)) == constants.ORIENT_P2A
+ assert neuro.getOrientation(2, np.eye(4)) == constants.ORIENT_I2S
+ assert radio.getOrientation(0, np.eye(4)) == constants.ORIENT_L2R
+ assert radio.getOrientation(1, np.eye(4)) == constants.ORIENT_P2A
+ assert radio.getOrientation(2, np.eye(4)) == constants.ORIENT_I2S
+
+ # The radio image should be
+ # l/r flipped in the voxel
+ # coordinate system
+ assert neuro.getOrientation(0, neuro.worldToVoxMat) == constants.ORIENT_L2R
+ assert neuro.getOrientation(1, neuro.worldToVoxMat) == constants.ORIENT_P2A
+ assert neuro.getOrientation(2, neuro.worldToVoxMat) == constants.ORIENT_I2S
+
+ assert radio.getOrientation(0, radio.worldToVoxMat) == constants.ORIENT_R2L
+ assert radio.getOrientation(1, radio.worldToVoxMat) == constants.ORIENT_P2A
+ assert radio.getOrientation(2, radio.worldToVoxMat) == constants.ORIENT_I2S
+
+
--
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