Merge branch 'bf/nb5' into 'master'

BF: get_data() raises error in nibabel >=5

See merge request !32

CHANGELOG.rst

@@ -2,8 +2,15 @@
 =====================
 
 
-0.11.0 (Tuesday 7th February 2023
----------------------------------
+0.11.1 (Thursday 2nd March 2023)
+--------------------------------
+
+
+* Update uses of the deprecated `nibabel.Nifti1Image.get_data` function.
+
+
+0.11.0 (Tuesday 7th February 2023)
+----------------------------------
 
 
 * Environment variables and tildes (``~``) can now be used in the pyfeeds

pyfeeds/__init__.py

@@ -5,7 +5,7 @@
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
 
-__version__ = '0.11.0'
+__version__ = '0.11.1'
 """The pyfeeds version number. """
 
 

pyfeeds/evaluate.py

@@ -441,8 +441,8 @@ def evalImage(pyf, testfile, benchmark):
 
     img1  = pyf.imageCache[testfile]
     img2  = pyf.imageCache[benchmark]
-    data1 = img1.get_data()
-    data2 = img2.get_data()
+    data1 = img1.get_fdata()
+    data2 = img2.get_fdata()
 
     return cmpArrays(data1, data2)
 
@@ -483,8 +483,8 @@ def evalVectorImage(pyf, testfile, benchmark):
     img1  = pyf.imageCache[testfile]
     img2  = pyf.imageCache[benchmark]
 
-    data1 = img1.get_data().reshape(-1, 3).T
-    data2 = img2.get_data().reshape(-1, 3).T
+    data1 = img1.get_fdata().reshape(-1, 3).T
+    data2 = img2.get_fdata().reshape(-1, 3).T
 
     # Calculate the length of each vector,
     # discard vectors of length 0, and
@@ -567,10 +567,10 @@ def evalPolarCoordinateImageGroup(pyf, testfiles, benchmarks):
         raise ValueError('Wrong number of files: {} <-> {}'
                          ''.format(testfiles, benchmarks))
 
-    testtheta  = pyf.imageCache[testtheta[ 0]].get_data()
-    testphi    = pyf.imageCache[testphi[   0]].get_data()
-    benchtheta = pyf.imageCache[benchtheta[0]].get_data()
-    benchphi   = pyf.imageCache[benchphi[  0]].get_data()
+    testtheta  = pyf.imageCache[testtheta[ 0]].get_fdata()
+    testphi    = pyf.imageCache[testphi[   0]].get_fdata()
+    benchtheta = pyf.imageCache[benchtheta[0]].get_fdata()
+    benchphi   = pyf.imageCache[benchphi[  0]].get_fdata()
 
     if any((testphi   .shape != testtheta.shape,
             benchtheta.shape != testtheta.shape,

pyfeeds/hashing.py

@@ -143,14 +143,14 @@ def loadHashes(hashFile):
     Hash files may be in one of two formats:
 
       - Format 2: A three-column text file where each row contains information
-        about one test, with each column containing:
-         - The test name
-         - a hash calculated on the contents of the test directory, and
-         - a hash calculated on the test input data
+        about one test, with columns corresponding to:
+         - Test names
+         - Hashes calculated on the contents of the test directories, and
+         - Hashes calculated on the test input data
         This format is produced by pyfeeds versions 0.11 and newer.
 
       - Format 1: A two-column text file where each row contains hashes for
-        one test, with each column containing:
+        one test, with columns corresponding to:
          - a hash calculated on the contents of the test directory, and
          - a hash calculated on the test input data
         This format was produced by pyfeeds versions 0.10 and older.