diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 4d37542fbbbc65888f48418c5c5e5e20384c5bba..31b62178cd2d711fae19645e813e666be314e467 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -29,6 +29,17 @@ Removed
* Many deprecated items removed.
+Fixed
+^^^^^
+
+
+* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
+ class.
+* Make sure that FEAT ``Cluster`` objects (created by the
+ :func:`.loadClusterResults` function) contain ``p`` and ``logp`` attributes,
+ even when cluster thresholding was not used.
+
+
1.13.0 (Thursday 22nd November 2018)
------------------------------------
@@ -36,9 +47,9 @@ Removed
Added
^^^^^
-* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Matrin
+* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
Craig).
-* New :func:`.fileOrText` decorator for use in wrapper functions (Matrin
+* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
Craig).
diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index 246722b576e47abb5acf9de89cc714c952e1d421..7c38eb7773465fa79cc952e4038c38451e7e3b97 100644
--- a/fsl/data/featanalysis.py
+++ b/fsl/data/featanalysis.py
@@ -385,6 +385,12 @@ def loadClusterResults(featdir, settings, contrast):
setattr(self, attrName, val)
+ # if cluster thresholding was not used,
+ # the cluster table will not contain
+ # P valuse.
+ if not hasattr(self, 'p'): self.p = 1.0
+ if not hasattr(self, 'logp'): self.logp = 0.0
+
# This dict provides a mapping between
# Cluster object attribute names, and
# the corresponding column name in the
diff --git a/fsl/data/featdesign.py b/fsl/data/featdesign.py
index 68e7e398ed6d066c506f0365482e07daeb1d21f9..633b712b4b04f9de986ae096612987e6814a00a8 100644
--- a/fsl/data/featdesign.py
+++ b/fsl/data/featdesign.py
@@ -219,6 +219,59 @@ class FEATFSFDesign(object):
return design
+class VoxelwiseEVMixin(object):
+ """Mixin class for voxelwise EVs.
+
+ ``VoxelwiseEVMixin`` instances contain the following attributes:
+
+ ============ ======================================================
+ ``filename`` Path to the image file containing the data for this EV
+ ``image`` Reference to the :class:`.Image` object
+ ============ ======================================================
+ """
+
+ def __init__(self, filename):
+ """Create a ``VoxelwiseEVMixin``.
+
+ :arg filename: Path to the file containing the data for this
+ ``VoxelwiseEV``.
+ """
+ if op.exists(filename):
+ self.__filename = filename
+ else:
+ log.warning('Voxelwise EV file does not '
+ 'exist: {}'.format(filename))
+ self.__filename = None
+
+ self.__image = None
+
+
+ def __del__(self):
+ """Clears any reference to the voxelwise EV image. """
+ self.__image = None
+
+
+ @property
+ def filename(self):
+ """Returns the path to the image file containing the data for this EV.
+ """
+ return self.__filename
+
+
+ @property
+ def image(self):
+ """Returns the :class:`.Image` containing the voxelwise EV data. """
+
+ if self.__filename is None:
+ return None
+
+ if self.__image is not None:
+ return self.__image
+
+ self.__image = fslimage.Image(self.__filename, mmap=False)
+ return self.__image
+
+
class EV(object):
"""Class representing an explanatory variable in a FEAT design matrix.
@@ -276,7 +329,7 @@ class BasisFunctionEV(NormalEV):
pass
-class VoxelwiseEV(NormalEV):
+class VoxelwiseEV(NormalEV, VoxelwiseEVMixin):
"""Class representing an EV with different values for each voxel in the
analysis.
@@ -308,34 +361,7 @@ class VoxelwiseEV(NormalEV):
``VoxelwiseEV``.
"""
NormalEV.__init__(self, realIdx, origIdx, title)
-
- if op.exists(filename):
- self.filename = filename
- else:
- log.warning('Voxelwise EV file does not '
- 'exist: {}'.format(filename))
- self.filename = None
-
- self.__image = None
-
-
- def __del__(self):
- """Clears any reference to the voxelwise EV image. """
- self.__image = None
-
-
- @property
- def image(self):
- """Returns the :class:`.Image` containing the voxelwise EV data. """
-
- if self.filename is None:
- return None
-
- if self.__image is not None:
- return self.__image
-
- self.__image = fslimage.Image(self.filename, mmap=False)
- return self.__image
+ VoxelwiseEVMixin.__init__(self, filename)
class ConfoundEV(EV):
@@ -386,7 +412,7 @@ class MotionParameterEV(EV):
self.motionIndex = motionIndex
-class VoxelwiseConfoundEV(EV):
+class VoxelwiseConfoundEV(EV, VoxelwiseEVMixin):
"""Class representing a voxelwise confound EV.
``VoxelwiseConfoundEV`` instances contain the following attributes (in
@@ -396,6 +422,7 @@ class VoxelwiseConfoundEV(EV):
``voxIndex`` Index of this ``VoxelwiseConfoundEV`` (starting from 0) in
relation to all other voxelwise confound EVs.
``filename`` Path to the image file containing the data for this EV
+ ``image`` Reference to the :class:`.Image` object
============ ==========================================================
"""
def __init__(self, index, voxIndex, title, filename):
@@ -407,17 +434,13 @@ class VoxelwiseConfoundEV(EV):
``VoxelwiseConfoundEV`` in relation to all other
voxelwise confound EVs.
:arg title: Name of this ``VoxelwiseConfoundEV``.
+ :arg filename: Path to the file containing the data for this
+ ``VoxelwiseConfoundEV``.
"""
EV.__init__(self, index, title)
+ VoxelwiseEVMixin.__init__(self, filename)
self.voxIndex = voxIndex
- if op.exists(filename):
- self.filename = filename
- else:
- log.warning('Voxelwise confound EV file does '
- 'not exist: {}'.format(filename))
- self.filename = None
-
def getFirstLevelEVs(featDir, settings, designMat):
"""Derives the EVs for the given first level FEAT analysis.
diff --git a/tests/test_featdesign.py b/tests/test_featdesign.py
index b10aa23091954d0dd4b840d0c11132d3427bd8ab..dd821127e925bf37a15f17fab5f40d40b5268a26 100644
--- a/tests/test_featdesign.py
+++ b/tests/test_featdesign.py
@@ -109,8 +109,9 @@ import numpy as np
import pytest
import tests
-import fsl.data.featdesign as featdesign
-import fsl.data.featanalysis as featanalysis
+from fsl.utils.tempdir import tempdir
+import fsl.data.featdesign as featdesign
+import fsl.data.featanalysis as featanalysis
datadir = op.join(op.dirname(__file__), 'testdata', 'test_feat')
@@ -397,3 +398,17 @@ def test_loadDesignMat():
with pytest.raises(Exception):
featdesign.loadDesignMat(badfile)
+
+
+def test_VoxelwiseEVs():
+ with tempdir():
+ img = tests.make_random_image('image.nii.gz', (10, 10, 10, 10))
+
+ ev1 = featdesign.VoxelwiseEV( 0, 0, 'ev1', 'image.nii.gz')
+ ev2 = featdesign.VoxelwiseConfoundEV(0, 0, 'ev2', 'image.nii.gz')
+
+ for xyz in tests.random_voxels((10, 10, 10), 10):
+ x, y, z = map(int, xyz)
+ exp = img.dataobj[x, y, z, :]
+ assert np.all(ev1.image[x, y, z, :] == exp)
+ assert np.all(ev2.image[x, y, z, :] == exp)