From dd37b51c088894fa9436762ba428204b96cd3137 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:37:05 +0000
Subject: [PATCH 1/8] BF:: copy+paste typo
---
pyfeeds/evaluate.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyfeeds/evaluate.py b/pyfeeds/evaluate.py
index 3f9bc3c..287a060 100644
--- a/pyfeeds/evaluate.py
+++ b/pyfeeds/evaluate.py
@@ -413,8 +413,8 @@ 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
--
GitLab
From 4708e507ab1ebdb1476680ce75ea77f2cc9f822c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:37:17 +0000
Subject: [PATCH 2/8] MNT: Accept pathlib.Path, normalise to string for image
cache keys. All other eval routines should already be compatible
---
pyfeeds/imagecache.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyfeeds/imagecache.py b/pyfeeds/imagecache.py
index aefca31..c101fc0 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
--
GitLab
From 80c380c802b1b031badb8e25037d58ab11ab0a75 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:38:02 +0000
Subject: [PATCH 3/8] RF: Adjust evalHeader so it compares all valid
dimensions. Replace alldims arg with ndims for comparing 3D
---
pyfeeds/evaluate.py | 27 +++++++++++++--------------
1 file changed, 13 insertions(+), 14 deletions(-)
diff --git a/pyfeeds/evaluate.py b/pyfeeds/evaluate.py
index 287a060..e4eb575 100644
--- a/pyfeeds/evaluate.py
+++ b/pyfeeds/evaluate.py
@@ -420,9 +420,11 @@ def loadImage(pyf, filename):
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.
"""
@@ -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):
--
GitLab
From c4c97158cfce152b644a0f78d906949d8f1140b1 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:42:08 +0000
Subject: [PATCH 4/8] BF: Not passing pyfeeds object to loadImage
---
pyfeeds/evaluate.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyfeeds/evaluate.py b/pyfeeds/evaluate.py
index e4eb575..d7d8e6d 100644
--- a/pyfeeds/evaluate.py
+++ b/pyfeeds/evaluate.py
@@ -429,8 +429,8 @@ def evalHeader(testfile, benchmark, ndims=None, pyf=None):
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',
--
GitLab
From 596657c7a74cce30b2855a78de7e5c212158a682 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:46:10 +0000
Subject: [PATCH 5/8] BF: Typos/mistakes in tempdir routine
---
pyfeeds/common.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/pyfeeds/common.py b/pyfeeds/common.py
index 33a49f7..3f02e75 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)
--
GitLab
From bb5d2df9b3975dbfe9d5a46c8264af4adc353e16 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:53:19 +0000
Subject: [PATCH 6/8] TEST: Tests are useful it turns out. Use
pyfeeds.common.tempdir instead of pyfeeds.tests.tempdir
---
pyfeeds/tests/__init__.py | 13 ----
pyfeeds/tests/test_config.py | 2 +-
pyfeeds/tests/test_evaluate.py | 105 ++++++++++++++++++++++++++++++++-
pyfeeds/tests/test_hashing.py | 3 +-
pyfeeds/tests/test_testing.py | 3 +-
5 files changed, 109 insertions(+), 17 deletions(-)
diff --git a/pyfeeds/tests/__init__.py b/pyfeeds/tests/__init__.py
index 7feda33..a3ec65b 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 647201f..02811dc 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 4c9b4a0..98ebaf9 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 bb303a7..808cab8 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 3dcadbb..2761aa0 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():
--
GitLab
From 477f1738ba8c13f9e0d269fc180a64bcef7783b9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:55:12 +0000
Subject: [PATCH 7/8] DOC: Changelog
---
CHANGELOG.rst | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 66c835e..911b6fe 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)
---------------------------------
--
GitLab
From 1f1b86ea085b8f611bb253888289159d3ece51d2 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 12:55:22 +0000
Subject: [PATCH 8/8] MNT: Version
---
pyfeeds/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyfeeds/__init__.py b/pyfeeds/__init__.py
index 5f1fb6a..3171118 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. """
--
GitLab