From 72da9475f6b4f8c1e9b0fb906e6482e98fae9dec Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 1 Nov 2017 09:44:22 +0000
Subject: [PATCH] Resample methods explicitly raises an error when num dims is
wrong. Cleaned up related code in atlas classes
---
fsl/data/atlases.py | 59 +++++++++++++++++++++++++++++----------------
fsl/data/image.py | 6 ++++-
2 files changed, 43 insertions(+), 22 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 59122134f..6ed038f1a 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -675,6 +675,42 @@ class Atlas(fslimage.Image):
return self.desc.find(*args, **kwargs)
+ def prepareMask(self, mask):
+ """Makes sure that the given mask has the same resolution as this
+ atlas, so it can be used for querying. Used by the
+ :meth:`.LabelAtlas.maskLabels` and
+ :meth:`.ProbabilisticAtlas.maskProportions` methods.
+
+ :arg mask: A :class:`.Image`
+
+ :returns: A ``numpy`` array containing the resampled mask data.
+
+ :raises: A :exc:`MaskError` if the mask is not in the same space as
+ this atlas, or does not have three dimensions.
+ """
+
+ # Make sure that the mask has the same
+ # number of voxels as the atlas image.
+ # Use nearest neighbour interpolation
+ # for resampling, as it is most likely
+ # that the mask is binary.
+ try:
+ mask, xform = mask.resample(self.shape[:3],
+ dtype=np.float32,
+ order=0)
+
+ except ValueError:
+ raise MaskError('Mask has wrong number of dimensions')
+
+ # TODO allow non-aligned mask - as long as it overlaps
+ # in world coordinates, it should be allowed
+ if not fslimage.Image(mask, xform=xform).sameSpace(self):
+ raise MaskError('Mask is not in the same space as atlas')
+
+ return mask
+
+
+
class MaskError(Exception):
"""Exception raised by the :meth:`LabelAtlas.maskLabel` and
:meth:`ProbabilisticAtlas.maskProportions` when a mask is provided which
@@ -781,23 +817,10 @@ class LabelAtlas(Atlas):
associated with each returned value.
"""
- # Make sure that the mask has the same
- # number of voxels as the atlas image.
- # Use nearest neighbour interpolation
- # for resampling, as it is most likely
- # that the mask is binary.
- mask, xform = mask.resample(self.shape[:3], dtype=np.float32, order=0)
-
- if not fslimage.Image(mask, xform=xform).sameSpace(self):
- raise MaskError('Mask is not in the same space as atlas')
-
- # TODO allow non-aligned mask - as long as it overlaps
- # in world coordinates, it should be allowed
-
-
# Extract the values that are in
# the mask, and their corresponding
# mask weights
+ mask = self.prepareMask(mask)
boolmask = mask > 0
vals = self[boolmask]
weights = mask[boolmask]
@@ -924,13 +947,7 @@ class ProbabilisticAtlas(Atlas):
props = []
- # Make sure that the mask has the same
- # number of voxels as the atlas image
- mask, xform = mask.resample(self.shape[:3], dtype=np.float32, order=0)
-
- if not fslimage.Image(mask, xform=xform).sameSpace(self):
- raise MaskError('Mask is not in the same space as atlas')
-
+ mask = self.prepareMask(mask)
boolmask = mask > 0
weights = mask[boolmask]
weightsum = weights.sum()
diff --git a/fsl/data/image.py b/fsl/data/image.py
index b1c93c087..3b3e87041 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1149,7 +1149,8 @@ class Image(Nifti):
:arg sliceobj: Slice into this ``Image``. If ``None``, the whole
image is resampled, and it is assumed that it has the
- same number of dimensions as ``shape``.
+ same number of dimensions as ``shape``. A
+ :exc:`ValueError` is raised if this is not the case.
:arg dtype: ``numpy`` data type of the resampled data. If ``None``,
the :meth:`dtype` of this ``Image`` is used.
@@ -1184,6 +1185,9 @@ class Image(Nifti):
oldShape = np.array(data.shape, dtype=np.float)
newShape = np.array(newShape, dtype=np.float)
+ if len(oldShape) != len(newShape):
+ raise ValueError('Shapes don\'t match')
+
if not np.all(np.isclose(oldShape, newShape)):
ratio = oldShape / newShape
--
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