diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 66c835e87cfb1d58748b00290b3151f2ca4d53f1..911b6fe9e46bb872e0b90bde9696fc2a00f27b76 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,16 @@
=====================
+0.14.1 (Friday 31st January 2025)
+---------------------------------
+
+* Fixed a few bugs introduced in the previous release.
+* Adjusted the ``evalHeader`` routine - now it compares ``dim`` and ``pixdim``
+ for all valid dimensions by default. The ``alldims`` parameter has been
+ replaced with a ``ndims`` parameter, allowing the number of dimensions to
+ be set (e.g. when you only want to compare the first three dimensions).
+
+
0.14.0 (Friday 31st January 2025)
---------------------------------
diff --git a/pyfeeds/__init__.py b/pyfeeds/__init__.py
index 5f1fb6a2daa90cfc00842fb239e4cefd75635a2a..3171118da15e1bca8eb57632c0f67d37f1f59909 100644
--- a/pyfeeds/__init__.py
+++ b/pyfeeds/__init__.py
@@ -5,7 +5,7 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-__version__ = '0.14.0'
+__version__ = '0.14.1'
"""The pyfeeds version number. """
diff --git a/pyfeeds/common.py b/pyfeeds/common.py
index 33a49f7d807a8d7954cd783993e00d8b9e08f440..3f02e7512bd58bf5b580540109ab25925212413f 100644
--- a/pyfeeds/common.py
+++ b/pyfeeds/common.py
@@ -45,10 +45,10 @@ def tempdir():
prevdir = os.getcwd()
- with tempfile.TemporaryDirectory(delete=True) as td:
+ with tempfile.TemporaryDirectory() as td:
try:
- os.chdir(testdir)
- yield td.name
+ os.chdir(td)
+ yield td
finally:
os.chdir(prevdir)
diff --git a/pyfeeds/evaluate.py b/pyfeeds/evaluate.py
index 3f9bc3c19837ebfc79c6586d9b9d998020cc1578..d7d8e6dc10b153f38999a815c809a1f97be145e9 100644
--- a/pyfeeds/evaluate.py
+++ b/pyfeeds/evaluate.py
@@ -413,22 +413,24 @@ def loadImage(pyf, filename):
return pyf.imageCache[filename]
else:
img = nib.load(filename)
- if isinstance(image, nib.Nifti1Image):
- data = np.asanyarray(image.dataobj)
+ if isinstance(img, nib.Nifti1Image):
+ data = np.asanyarray(img.dataobj)
else:
data = None
return img, data
-def evalHeader(testfile, benchmark, alldims=True, pyf=None):
+def evalHeader(testfile, benchmark, ndims=None, pyf=None):
"""Evaluation routine which compares the header fields of two NIFTI
- images.
+ images. By default the dim/pixdim values for every dimension are compared,
+ but the ``ndims`` argument can be used if you only want to compare the
+ first three dimensions for instance.
Returns 0 if they all match, 1 otherwise.
"""
- img1 = loadImage(testfile)[0]
- img2 = loadImage(benchmark)[0]
+ img1 = loadImage(pyf, testfile)[0]
+ img2 = loadImage(pyf, benchmark)[0]
hdr1 = img1.header
hdr2 = img2.header
fields = ['dim', 'pixdim', 'intent_code',
@@ -437,14 +439,17 @@ def evalHeader(testfile, benchmark, alldims=True, pyf=None):
'qoffset_x', 'qoffset_y', 'qoffset_z',
'srow_x', 'srow_y', 'srow_z']
+ if ndims is None:
+ ndims = max(img1.header['dim'][0],
+ img2.header['dim'][0])
+
for f in fields:
f1 = hdr1[f]
f2 = hdr2[f]
- if (not alldims) and (f in ('dim', 'pixdim')):
- ndim = img1.header['dim'][0]
- f1 = f1[:ndim + 1]
- f2 = f2[:ndim + 1]
+ if f in ('dim', 'pixdim'):
+ f1 = f1[:ndims + 1]
+ f2 = f2[:ndims + 1]
if not np.all(np.isclose(f1, f2)):
return 1
@@ -453,14 +458,8 @@ def evalHeader(testfile, benchmark, alldims=True, pyf=None):
def evalHeaderRestrictDims(testfile, benchmark, pyf=None):
- """Evaluation routine which compares the header fields of two NIFTI
- images. For the `dim` and `pixdim` fields, only the entries which
- are expected to be valid (e.g. `dim1`, `dim2`, and `dim3` for a 3D image)
- are compared.
-
- Returns 0 if they all match, 1 otherwise.
- """
- return evalHeader(testfile, benchmark, alldims=False, pyf=pyf)
+ """Legacy alias for ``evalHeader``. """
+ return evalHeader(testfile, benchmark, pyf=pyf)
def evalImage(testfile, benchmark, pyf=None):
diff --git a/pyfeeds/imagecache.py b/pyfeeds/imagecache.py
index aefca31b1b4cf479d1170892676466dd2d89aae8..c101fc0431409c8aba9fbcf0c4516a2e995f7453 100644
--- a/pyfeeds/imagecache.py
+++ b/pyfeeds/imagecache.py
@@ -77,7 +77,7 @@ class ImageCache:
returned value will be ``None``.
"""
- imagefile = op.realpath(op.abspath(imagefile))
+ imagefile = str(op.realpath(op.abspath(imagefile)))
image = self.__images.get(imagefile, None)
if image is not None:
@@ -108,7 +108,7 @@ class ImageCache:
# it in this way because all keys
# passed to __getitem__ get
# transformed in the same way.
- imagefile = op.realpath(op.abspath(imagefile))
+ imagefile = str(op.realpath(op.abspath(imagefile)))
imagesize = size(image)
self.__images[ imagefile] = image, data
self.__imagesizes[imagefile] = imagesize
diff --git a/pyfeeds/tests/__init__.py b/pyfeeds/tests/__init__.py
index 7feda3307a62c5d69ea0a8dbe7b06bfd32cd5bd6..a3ec65ba2896a33cda076df112c4337553fd4954 100644
--- a/pyfeeds/tests/__init__.py
+++ b/pyfeeds/tests/__init__.py
@@ -9,8 +9,6 @@
import os
import sys
import os.path as op
-import contextlib
-import tempfile
from io import StringIO
@@ -61,17 +59,6 @@ class CaptureStdout(object):
return self.__mock_stderr.read()
-@contextlib.contextmanager
-def tempdir():
- prevdir = os.getcwd()
- with tempfile.TemporaryDirectory() as td:
- try:
- os.chdir(td)
- yield td
- finally:
- os.chdir(prevdir)
-
-
def makepaths(paths):
for path in paths:
dirname = op.dirname(path)
diff --git a/pyfeeds/tests/test_config.py b/pyfeeds/tests/test_config.py
index 647201f4588920104e632034987bbd269b503dcc..02811dc87d5fa16906c0f42db7d2bdf35bb452ef 100644
--- a/pyfeeds/tests/test_config.py
+++ b/pyfeeds/tests/test_config.py
@@ -13,7 +13,7 @@ from unittest import mock
import pyfeeds.main as main
-from pyfeeds.tests import tempdir
+from pyfeeds.common import tempdir
def test_loadPyfeedsConfig():
diff --git a/pyfeeds/tests/test_evaluate.py b/pyfeeds/tests/test_evaluate.py
index 4c9b4a0b82c1c52fcc0ef77b4439f8b29e61aa8a..98ebaf97ffe42675d676dc0a3b632d5328b1d1c2 100644
--- a/pyfeeds/tests/test_evaluate.py
+++ b/pyfeeds/tests/test_evaluate.py
@@ -11,9 +11,10 @@ import os.path as op
import numpy as np
import nibabel as nib
-from . import tempdir, makepaths, maketest, makepyfeeds, CaptureStdout
+from . import makepaths, maketest, makepyfeeds, CaptureStdout
from pyfeeds import testing, evaluate
+from pyfeeds.common import tempdir
def test_evaluateTestAgainstBenchmark():
@@ -79,6 +80,9 @@ def test_evalVectorImage():
assert evaluate.evalVectorImage(fname1, fname1, pyf=pyf) == 0
assert evaluate.evalVectorImage(fname2, fname2, pyf=pyf) == 0
assert evaluate.evalVectorImage(fname1, fname2, pyf=pyf) != 0
+ assert evaluate.evalVectorImage(fname1, fname1) == 0
+ assert evaluate.evalVectorImage(fname2, fname2) == 0
+ assert evaluate.evalVectorImage(fname1, fname2) != 0
def test_evalImage():
@@ -98,3 +102,102 @@ def test_evalImage():
assert evaluate.evalImage(fname1, fname1, pyf=pyf) == 0
assert evaluate.evalImage(fname2, fname2, pyf=pyf) == 0
assert evaluate.evalImage(fname1, fname2, pyf=pyf) != 0
+ assert evaluate.evalImage(fname1, fname1) == 0
+ assert evaluate.evalImage(fname2, fname2) == 0
+ assert evaluate.evalImage(fname1, fname2) != 0
+
+
+def test_evalHeader():
+
+ arr1 = -1 + 2 * np.random.random((10, 10, 10, 10))
+ arr2 = -1 + 2 * np.random.random((10, 10, 10, 10))
+ arr3 = -1 + 2 * np.random.random((10, 10, 10, 20))
+ arr4 = -1 + 2 * np.random.random(( 5, 5, 5, 20))
+
+ with tempdir():
+
+ pyf = makepyfeeds()
+ fname1 = 'image1.nii.gz'
+ fname2 = 'image2.nii.gz'
+ fname3 = 'image3.nii.gz'
+ fname4 = 'image4.nii.gz'
+
+ nib.Nifti1Image(arr1, np.eye(4)).to_filename(fname1)
+ nib.Nifti1Image(arr2, np.eye(4)).to_filename(fname2)
+ nib.Nifti1Image(arr3, np.eye(4)).to_filename(fname3)
+ nib.Nifti1Image(arr4, np.eye(4)).to_filename(fname4)
+
+ assert evaluate.evalHeader(fname1, fname1, pyf=pyf) == 0
+ assert evaluate.evalHeader(fname2, fname2, pyf=pyf) == 0
+ assert evaluate.evalHeader(fname3, fname3, pyf=pyf) == 0
+ assert evaluate.evalHeader(fname4, fname4, pyf=pyf) == 0
+ assert evaluate.evalHeader(fname1, fname1) == 0
+ assert evaluate.evalHeader(fname2, fname2) == 0
+ assert evaluate.evalHeader(fname3, fname3) == 0
+ assert evaluate.evalHeader(fname4, fname4) == 0
+
+ assert evaluate.evalHeader(fname1, fname2) == 0
+ assert evaluate.evalHeader(fname1, fname3) != 0
+ assert evaluate.evalHeader(fname1, fname4) != 0
+ assert evaluate.evalHeader(fname1, fname3, ndims=3) == 0
+ assert evaluate.evalHeader(fname3, fname4) != 0
+ assert evaluate.evalHeader(fname3, fname4, ndims=3) != 0
+
+ assert evaluate.evalHeaderRestrictDims(fname1, fname2, pyf=pyf) == 0
+ assert evaluate.evalHeaderRestrictDims(fname1, fname3, pyf=pyf) != 0
+ assert evaluate.evalHeaderRestrictDims(fname1, fname2) == 0
+ assert evaluate.evalHeaderRestrictDims(fname1, fname3) != 0
+
+
+def test_evalImageMaxDiff():
+
+ arr1 = np.zeros((10, 10, 10))
+ arr2 = np.zeros((10, 10, 10))
+
+ arr1[0, 0, 0] = 100
+
+ with tempdir():
+
+ pyf = makepyfeeds()
+ fname1 = 'image1.nii.gz'
+ fname2 = 'image2.nii.gz'
+ nib.Nifti1Image(arr1, np.eye(4)).to_filename(fname1)
+ nib.Nifti1Image(arr2, np.eye(4)).to_filename(fname2)
+
+ assert evaluate.evalImageMaxDiff(fname1, fname1, pyf=pyf) == 0
+ assert evaluate.evalImageMaxDiff(fname1, fname1) == 0
+ assert evaluate.evalImageMaxDiff(fname1, fname2) == 100
+
+def test_evalNumericalText():
+
+ arr1 = np.random.random(100)
+ arr2 = np.random.random(100) * 4
+
+ with tempdir():
+
+ pyf = makepyfeeds()
+ fname1 = 'data1.txt'
+ fname2 = 'data2.txt'
+ np.savetxt(fname1, arr1)
+ np.savetxt(fname2, arr2)
+
+ assert evaluate.evalNumericalText(fname1, fname1, pyf=pyf) == 0
+ assert evaluate.evalNumericalText(fname1, fname1) == 0
+ assert evaluate.evalNumericalText(fname1, fname2) != 0
+
+def test_evalMD5():
+
+ arr1 = np.random.random(100)
+ arr2 = np.random.random(100) * 4
+
+ with tempdir():
+
+ pyf = makepyfeeds()
+ fname1 = 'data1.txt'
+ fname2 = 'data2.txt'
+ np.savetxt(fname1, arr1)
+ np.savetxt(fname2, arr2)
+
+ assert evaluate.evalMD5(fname1, fname1, pyf=pyf) == 0
+ assert evaluate.evalMD5(fname1, fname1) == 0
+ assert evaluate.evalMD5(fname1, fname2) != 0
diff --git a/pyfeeds/tests/test_hashing.py b/pyfeeds/tests/test_hashing.py
index bb303a706d8ab87068fd45e6270166529b95893f..808cab884b4612e9dab2b67f81e6bfa3941c817f 100644
--- a/pyfeeds/tests/test_hashing.py
+++ b/pyfeeds/tests/test_hashing.py
@@ -13,8 +13,9 @@ import os.path as op
import time
from pyfeeds import hashing, testing
+from pyfeeds.common import tempdir
-from . import CaptureStdout, makepyfeeds, maketest, makepaths, tempdir
+from . import CaptureStdout, makepyfeeds, maketest, makepaths
def test_genHashes():
diff --git a/pyfeeds/tests/test_testing.py b/pyfeeds/tests/test_testing.py
index 3dcadbb17188e8f1f1cc20b41264701ff40c64a8..2761aa07409efdd574b371b62d2d2b3d4388c550 100644
--- a/pyfeeds/tests/test_testing.py
+++ b/pyfeeds/tests/test_testing.py
@@ -10,9 +10,10 @@ import os
import datetime
import os.path as op
-from . import tempdir, makepaths, maketest, makepyfeeds, CaptureStdout
+from . import makepaths, maketest, makepyfeeds, CaptureStdout
from pyfeeds import testing
+from pyfeeds.common import tempdir
def test_findTestDirs():