Merge branch 'rel/3.6.3' into 'v3.6'

Version 3.6.3

See merge request fsl/fslpy!303

CHANGELOG.rst

@@ -3,6 +3,19 @@ order.
 
 
 
+3.6.3 (Wednesday 28th July 2021)
+--------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* When creating an ``Image`` object with ``loadData=False``, the ``calcRange``
+  argument is ignored, as it would otherwise cause the data to be loaded
+  (!301).
+
+
 3.6.2 (Wednesday 23rd June 2021)
 --------------------------------
 

fsl/data/image.py

@@ -1042,7 +1042,8 @@ class Image(Nifti):
                          calculated immediately (vi a call to
                          :meth:`calcRange`). Otherwise, the image range is
                          incrementally updated as more data is read from memory
-                         or disk.
+                         or disk. If ``loadData=False``, ``calcRange`` is also
+                         set to ``False``.
 
         :arg threaded:   If ``True``, the :class:`.ImageWrapper` will use a
                          separate thread for data range calculation. Defaults
@@ -1065,8 +1066,11 @@ class Image(Nifti):
         nibImage = None
         saved    = False
 
-        if loadData:
-            threaded = False
+        # disable threaded access if loadData is True
+        threaded = threaded and (not loadData)
+
+        # don't calcRange if not loading data
+        calcRange = calcRange and loadData
 
         # Take a copy of the header if one has
         # been provided

fsl/data/imagewrapper.py

@@ -388,6 +388,14 @@ class ImageWrapper(notifier.Notifier):
             self.__data = np.asanyarray(self.__image.dataobj)
 
 
+    @property
+    def dataIsLoaded(self):
+        """Return true if the image data has been loaded into memory, ``False``
+        otherwise.
+        """
+        return self.__data is not None
+
+
     def __getData(self, sliceobj, isTuple=False):
         """Retrieves the image data at the location specified by ``sliceobj``.
 

fsl/data/melodicanalysis.py

@@ -133,10 +133,18 @@ def getDataFile(meldir):
     if topDir is None:
         return None
 
-    dataFile = op.join(topDir, 'filtered_func_data')
-
+    # People often rename filtered_func_data.nii.gz
+    # to something like filtered_func_data_clean.nii.gz,
+    # because that is the recommended approach when
+    # performing ICA-based denoising). So we try both.
+    candidates = ['filtered_func_data', 'filtered_func_data_clean']
+
+    for candidate in candidates:
+        dataFile = op.join(topDir, candidate)
         try:                       return fslimage.addExt(dataFile)
-    except fslimage.PathError: return None
+        except fslimage.PathError: continue
+
+    return None
 
 
 def getMeanFile(meldir):

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.6.2'
+__version__ = '3.6.3'
 """Current version number, as a string. """
 
 

tests/test_image_advanced.py

@@ -321,3 +321,26 @@ def _test_image_calcRange(threaded):
     if threaded:
         img.getImageWrapper().getTaskThread().waitUntilIdle()
     assert img.dataRange == (0, 1)
+
+
+# sanity check - make sure data is not loaded
+# when loadData is False (fsl/fslpy#374)
+def test_Image_loadData():
+    with tests.testdir() as testdir:
+        filename = 'image.nii.gz'
+
+        # Data range grows with volume
+        data  = np.zeros((50, 50, 50, 50))
+        for vol in range(data.shape[-1]):
+            data[..., vol] = vol
+
+        fslimage.Image(data).save(filename)
+
+        img = fslimage.Image(filename, loadData=False)
+        assert not img.getImageWrapper().dataIsLoaded
+
+        img = fslimage.Image(filename, loadData=False, calcRange=False)
+        assert not img.getImageWrapper().dataIsLoaded
+
+        img = fslimage.Image(filename, loadData=False, calcRange=True)
+        assert not img.getImageWrapper().dataIsLoaded

tests/test_melodicanalysis.py

@@ -129,6 +129,12 @@ def test_getDataFile():
                    'analysis.feat/filtered_func_data.nii.gz'],
                   'analysis.feat/filtfunc.ica',
                   'analysis.feat/filtered_func_data.nii.gz'),
+                 (['analysis.feat/filtfunc.ica/melodic_IC.nii.gz',
+                   'analysis.feat/filtfunc.ica/melodic_mix',
+                   'analysis.feat/filtfunc.ica/melodic_FTmix',
+                   'analysis.feat/filtered_func_data_clean.nii.gz'],
+                  'analysis.feat/filtfunc.ica',
+                  'analysis.feat/filtered_func_data_clean.nii.gz'),
                  (['no/analysis/dirs/here/melodic_IC.nii.gz'],
                    'no/analysis/dirs/here/',
                    None),
@@ -137,7 +143,6 @@ def test_getDataFile():
                    'analysis.feat/analysis.ica/melodic_FTmix'],
                    'analysis.feat/analysis.ica',
                    None),
-
     ]
 
     for paths, meldir, expected in testcases: