From b91eae219f77db7a65a743f4201b06243721e251 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 23 Nov 2018 12:22:39 +0000
Subject: [PATCH] BF: VoxelwiseConfoundEV was missing image attribute.
Refactored so that VoxelwiseEV and VoxelwiseConfoundEV classes share a common
base class.
---
fsl/data/featdesign.py | 97 ++++++++++++++++++++++++++----------------
1 file changed, 60 insertions(+), 37 deletions(-)
diff --git a/fsl/data/featdesign.py b/fsl/data/featdesign.py
index 68e7e398e..633b712b4 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.
--
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