Merge branch 'mnt/ignore-dirs-when-finding-tests' into 'master'

MNT: Ignore any candidate tests within output/benchmark/input data directories

See merge request !38

.gitlab-ci.yml

@@ -54,14 +54,6 @@ variables:
     - bash ./.ci/unit_tests.sh
 
 
-test:3.8:
-  image: python:3.8
-  <<: *test_template
-
-test:3.9:
-  image: python:3.9
-  <<: *test_template
-
 test:3.10:
   image: python:3.10
   <<: *test_template
@@ -69,3 +61,11 @@ test:3.10:
 test:3.11:
   image: python:3.11
   <<: *test_template
+
+test:3.12:
+  image: python:3.12
+  <<: *test_template
+
+test:3.13:
+  image: python:3.13
+  <<: *test_template

CHANGELOG.rst

@@ -2,6 +2,17 @@
 =====================
 
 
+0.13.0 (Tuesday 17th December 2024)
+-----------------------------------
+
+
+* Pyfeeds now ignores any tests found within the input data, benchmark data,
+  or output directories, in case any of those are contained within the
+  specified test directories.
+* New `evalImageMaxDiff` evaluation routine, which evaluates an image based
+  on the maximum absolute difference to the benchmark image.
+
+
 0.12.4 (Thursday 18th January 2024)
 -----------------------------------
 

pyfeeds/__init__.py

@@ -5,7 +5,7 @@
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
 
-__version__ = '0.12.4'
+__version__ = '0.13.0'
 """The pyfeeds version number. """
 
 

pyfeeds/evaluate.py

@@ -436,12 +436,25 @@ def evalHeaderRestrictDims(pyf, testfile, benchmark):
 
 def evalImage(pyf, testfile, benchmark):
     """Evaluation routine which compares the data from two NIFTI images.
+    Returns the mean difference between the two images, normalised by
+    the combined data range.
 
     The :func:`cmpArrays` function does the calculation.
     """
     data1  = pyf.imageCache[testfile][1]
     data2  = pyf.imageCache[benchmark][1]
-    return cmpArrays(data1, data2)
+    return cmpArrays(data1, data2, metric='mean')
+
+
+def evalImageMaxDiff(pyf, testfile, benchmark):
+    """Evaluation routine which compares the data from two NIFTI images.
+    Returns the maximum absolute difference between the two images.
+
+    The :func:`cmpArrays` function does the calculation.
+    """
+    data1  = pyf.imageCache[testfile][1]
+    data2  = pyf.imageCache[benchmark][1]
+    return cmpArrays(data1, data2, metric='max')
 
 
 def evalNumericalText(pyf, testfile, benchmark):
@@ -564,10 +577,10 @@ def evalGiftiVertices(pyf, testfile, benchmark):
     return cmpArrays(verts1, verts2)
 
 
-def cmpArrays(arr1, arr2):
+def cmpArrays(arr1, arr2, metric='mean'):
     """Compares the values in the given ``numpy`` arrays.
 
-    Returns the mean difference between the two arrays, normalised
+    Returns the mean or max difference between the two arrays, normalised
     by the combined data range of the two arrays.
     """
 
@@ -607,10 +620,13 @@ def cmpArrays(arr1, arr2):
     if denom == 0:
         return 0
 
-    normdiff = np.abs((arr2 - arr1) / denom)
+    if metric == 'mean':
+        normdiff = np.abs((arr2 - arr1) / denom)
+        # The final error is the mean error across all voxels
+        return normdiff.mean()
 
-    # The final error is the mean error across all voxels
-    return normdiff.mean()
+    elif metric == 'max':
+        return np.max(np.abs(arr2 - arr1))
 
 
 def cmpVectorArrays(arr1, arr2):

pyfeeds/main.py

@@ -62,6 +62,7 @@ upon which sub-command the user has specified:
 
 import os.path as op
 import            os
+import pathlib as pl
 import            sys
 import            logging
 import            fnmatch
@@ -226,10 +227,23 @@ class Pyfeeds:
 
         testDirs = functools.reduce(lambda a, b: a + b, testDirs)
         testDirs = sorted(set(testDirs))
+        testDirs = [op.abspath(td) for td in testDirs]
 
         if len(testDirs) == 0:
             return []
 
+        # Do not consider anything within the
+        # input, benchmark, or output directories
+        def filterOut(dirs, filterDir):
+            if filterDir is None:
+                return dirs
+            fdir = pl.Path(op.abspath(filterDir))
+            return [td for td in dirs if fdir not in pl.Path(td).parents]
+
+        testDirs = filterOut(testDirs, self.outputDir)
+        testDirs = filterOut(testDirs, self.benchmarkDir)
+        testDirs = filterOut(testDirs, self.inputDir)
+
         # Find the deepest directory in
         # the file system which contains
         # all of the detected tests.