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Commit 2263243c authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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Label atlas image values no longer need to match the index of the label 

into the AtlasDescription.labels list.
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with 82 additions and 40 deletions
fsl/data/atlases.py
+ 82
− 40
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......@@ -314,17 +314,18 @@ class AtlasLabel(object):
An ``AtlasLabel`` instance contains the following attributes:
========= ==============================================================
========= ================================================================
``name`` Region name
``index`` For probabilistic atlases, the volume index into the 4D atlas
image that corresponds to this region. For label atlases, the
value of voxels that are in this region. For summary images of
probabilistic atlases, add 1 to this value to get the
corresponding voxel values.
``index`` The index of this label into the list of all labels in the
``AtlasDescription`` that owns it. For probabilistic atlases,
this is also the index into the 4D atlas image of the volume
that corresponds to this region.
``value`` For label atlases and summary images, the value of voxels that
are in this region.
``x`` X coordinate of the region in world space
``y`` Y coordinate of the region in world space
``z`` Z coordinate of the region in world space
========= ==============================================================
========= ================================================================
.. note:: The ``x``, ``y`` and ``z`` label coordinates are pre-calculated
centre-of-gravity coordinates, as listed in the atlas xml file.
......@@ -333,9 +334,10 @@ class AtlasLabel(object):
XML file (typically MNI152 space).
"""
def __init__(self, name, index, x, y, z):
def __init__(self, name, index, value, x, y, z):
self.name = name
self.index = index
self.value = value
self.x = x
self.y = y
self.z = z
......@@ -383,8 +385,11 @@ class AtlasDescription(object):
# as relative to the location of this
# XML file.
<summaryimagefile> # Path to 3D summary file, with each
</summaryimagefile> # region having value (index + 1)
<summaryimagefile> # Path to 3D label summary file,
</summaryimagefile> # Every <image> must be accompanied
# by a <summaryimage> - for label
# atlases, they will typically refer
# to the same image file.
</images>
... # More images - generally both
......@@ -395,7 +400,10 @@ class AtlasDescription(object):
# index - For probabilistic atlases, index of corresponding volume in
# 4D image file. For label images, the value of voxels which
# are in the corresponding region.
# are in the corresponding region. For probabilistic atlases,
# it is assumed that the value for each region in the summary
# image(s) are equal to ``index + 1``.
#
#
# x |
# y |- XYZ *voxel* coordinates into the first image of the <images>
......@@ -487,6 +495,8 @@ class AtlasDescription(object):
atlasDir = op.dirname(self.specPath)
for image in images:
# Every image must also have a summary image
imagefile = image.find('imagefile') .text
summaryimagefile = image.find('summaryimagefile').text
......@@ -505,6 +515,11 @@ class AtlasDescription(object):
labels = data.findall('label')
self.labels = []
# Refs to AtlasLabel objects
# indexed by their value.
# Used by the find method.
self.__labelsByValue = {}
# The xyz coordinates for each label are in terms
# of the voxel space of the first images element
# in the header. For convenience, we're going to
......@@ -519,11 +534,26 @@ class AtlasDescription(object):
x = float(label.attrib['x'])
y = float(label.attrib['y'])
z = float(label.attrib['z'])
al = AtlasLabel(name, index, x, y, z)
# For label images, the index field
# contains the region value
if self.atlasType == 'label':
value = index
index = i
# For probablistic images, the index
# field specifies the volume in the
# 4D atlas corresponding to the region.
# It is assumed that the summary value
# for each region is index + 1
else:
value = index + 1
al = AtlasLabel(name, index, value, x, y, z)
coords[i] = (x, y, z)
self.labels.append(al)
self.__labelsByValue[value] = al
# Load the appropriate transformation matrix
# and transform all those voxel coordinates
......@@ -536,6 +566,20 @@ class AtlasDescription(object):
label.x, label.y, label.z = coords[i]
def find(self, index=None, value=None):
"""Find an :class:`.AtlasLabel` either by ``index``, or by ``value``.
Exactly one of ``index`` or ``value`` may be specified - a
``ValueError`` is raised otherwise.
"""
if (index is None and value is None) or \
(index is not None and value is not None):
raise ValueError('Only one of index or value may be specified')
if index is not None: return self.labels[ index]
else: return self.__labelsByValue[value]
def __eq__(self, other):
"""Compares the ``atlasID`` of this ``AtlasDescription`` with another.
"""
......@@ -605,6 +649,13 @@ class Atlas(fslimage.Image):
self.desc = atlasDesc
def find(self, *args, **kwargs):
"""Find an ``AtlasLabel`` - see the :meth:`AtlasDescription.find`
method.
"""
return self.desc.find(*args, **kwargs)
class MaskError(Exception):
"""Exception raised by the :meth:`LabelAtlas.maskLabel` and
:meth:`ProbabilisticAtlas.maskProportions` when a mask is provided which
......@@ -671,9 +722,8 @@ class LabelAtlas(Atlas):
:returns: The label at the given coordinates, or ``None`` if the
coordinates are out of bounds.
.. note:: If this is a summary image of a probabilistic atlas, you need
to subtract one from the result to get the region volume
index into the probabilistic atlas.
.. note:: Use the :meth:`find` method to retrieve the ``AtlasLabel``
associated with each returned value.
"""
if not voxel:
......@@ -703,15 +753,13 @@ class LabelAtlas(Atlas):
:returns: A tuple containing:
- A sequence of all labels which are present in the mask
- A sequence of all values which are present in the mask
- A sequence containing the proportion, within the mask,
of each present label. The proportions are returned as
of each present value. The proportions are returned as
values between 0 and 100.
.. note:: If this is a summary image of a probabilistic atlas, you need
to subtract one from the returned label values to get the
corresponding region volume indices into the probabilistic
atlas.
.. note:: Use the :meth:`find` method to retrieve the ``AtlasLabel``
associated with each returned value.
"""
# Make sure that the mask has the same
......@@ -726,44 +774,36 @@ class LabelAtlas(Atlas):
# Extract the labels that are in
# Extract the values that are in
# the mask, and their corresponding
# mask weights
boolmask = mask > 0
vals = self[boolmask]
weights = mask[boolmask]
weightsum = weights.sum()
gotLabels = np.unique(vals)
labels = []
gotValues = np.unique(vals)
values = []
props = []
# Only consider labels that
# this atlas is aware of
for label in self.desc.labels:
# For probabilistic images, the label index
# is the index of the volume corresponding
# to the region. We need to add 1 to this
# to get its value in the summary image.
if self.desc.atlasType == 'label': label = label.index
else: label = label.index + 1
if label in gotLabels:
if label.value in gotValues:
# Figure out the number of all voxels
# in the mask with this label, weighted
# in the mask with this value, weighted
# by the mask.
prop = weights[vals == label].sum()
prop = weights[vals == label.value].sum()
# Normalise it to be a proportion
# of all voxels in the mask. We
# multiply by 100 because the FSL
# probabilistic atlases store their
# probabilities as percentages.
labels.append(label)
values.append(label.value)
props .append(100 * prop / weightsum)
return labels, props
return values, props
class ProbabilisticAtlas(Atlas):
......@@ -839,11 +879,13 @@ class ProbabilisticAtlas(Atlas):
loc[2] >= self.shape[2]:
return []
# We only return labels for this atlas
props = self[loc[0], loc[1], loc[2], :]
props = [props[l.index] for l in self.desc.labels]
return props
# We only return labels for this atlas -
# the underlying image may have more
# volumes than this atlas has labels.
return [props[l.index] for l in self.desc.labels]
def maskProportions(self, mask):
......
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