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Commit 570a239f authored by Paul McCarthy's avatar Paul McCarthy 🚵
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ENH: Support for reading "statistic" xml atlas descriptions

parent 41ad8b85
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fsl/data/atlases.py
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......@@ -36,27 +36,29 @@ load an atlas image, which will be one of the following atlas-specific
:nosignatures:
LabelAtlas
StatisticAtlas
ProbabilisticAtlas
"""
from __future__ import division
import xml.etree.ElementTree as et
import os.path as op
import glob
import bisect
import logging
import xml.etree.ElementTree as et
import os.path as op
import glob
import bisect
import logging
import numpy as np
import numpy as np
import fsl.data.image as fslimage
import fsl.data.constants as constants
from fsl.utils.platform import platform as platform
import fsl.utils.image.resample as resample
import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
import fsl.utils.settings as fslsettings
import fsl.data.image as fslimage
import fsl.data.constants as constants
from fsl.utils.platform import platform
import fsl.utils.image.resample as resample
import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
import fsl.utils.settings as fslsettings
import fsl.utils.deprecated as deprecated
log = logging.getLogger(__name__)
......@@ -322,9 +324,9 @@ class AtlasLabel(object):
========= ================================================================
``name`` Region name
``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.
``AtlasDescription`` that owns it. For statistic/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
......@@ -386,8 +388,13 @@ class AtlasDescription(object):
<atlas>
<header>
<name></name> # Atlas name
<type></type> # 'Probabilistic' or 'Label'
<name></name> # Atlas name
<type></type> # 'Statistic', 'Probabilistic' or 'Label'
<statistic></statistic> # Optional. Type of statistic
<units></units> # Optional. Units of measurement
<precision></precision> # Optional. Decimal precision to report
<upper></upper> # Optional. Upper threshold
<lower></lower> # Optional. Lower threshold
<images>
<imagefile>
</imagefile> # If type is Probabilistic, path
......@@ -412,11 +419,12 @@ class AtlasDescription(object):
</header>
<data>
# 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. For probabilistic atlases,
# it is assumed that the value for each region in the summary
# image(s) are equal to ``index + 1``.
# index - For statistic/probabilistic atlases, index of corresponding
# volume in 4D image file. For label images, the value of
# voxels which are in the corresponding region. For
# statistic/probabilistic atlases, it is assumed that the
# value for each region in the summary image(s) are equal to
# ``index + 1``.
#
#
# x |
......@@ -452,7 +460,18 @@ class AtlasDescription(object):
``specPath`` Path to the atlas XML specification file.
``atlasType`` Atlas type - either *probabilistic* or *label*.
``atlasType`` Atlas type - either *statistic*, *probabilistic* or
*label*.
``statistic`` Type of statistic, for statistic atlases.
``units`` Unit of measurement, for statistic atlases.
``precision`` Reporting precision, for statistic atlases.
``upper`` Upper threshold, for statistic atlases.
``lower`` Lower threshold, for statistic atlases.
``images`` A list of images available for this atlas - usually
:math:`1mm^3` and :math:`2mm^3` images are present.
......@@ -500,6 +519,38 @@ class AtlasDescription(object):
if self.atlasType == 'probabalistic':
self.atlasType = 'probabilistic'
if self.atlasType == 'statistic':
statistic = header.find('statistic')
units = header.find('units')
lower = header.find('lower')
upper = header.find('upper')
precision = header.find('precision')
if statistic is None: statistic = ''
else: statistic = statistic.text.strip()
if units is None: units = ''
else: units = units.text.strip()
if lower is None: lower = 0
else: lower = float(lower.text.strip())
if upper is None: upper = 100
else: upper = float(upper.text.strip())
if precision is None: precision = 2
else: precision = float(precision.text.strip())
self.statistic = statistic
self.units = units
self.lower = lower
self.upper = upper
self.precision = precision
elif self.atlasType == 'probabilistic':
self.statistic = ''
self.units = '%'
self.lower = 5
self.upper = 100
self.precision = 0
images = header.findall('images')
self.images = []
self.summaryImages = []
......@@ -661,7 +712,7 @@ class Atlas(fslimage.Image):
:arg resolution: Desired isotropic resolution in millimetres.
:arg isLabel: Pass in ``True`` for label atlases, ``False`` for
probabilistic atlases.
statistic/probabilistic atlases.
All other arguments are passed to :meth:`.Image.__init__`.
"""
......@@ -708,7 +759,7 @@ class Atlas(fslimage.Image):
"""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.
:meth:`.StatisticAtlas.maskProportions` methods.
:arg mask: A :class:`.Image`
......@@ -738,13 +789,11 @@ class Atlas(fslimage.Image):
return mask
class MaskError(Exception):
"""Exception raised by the :meth:`LabelAtlas.maskLabel` and
:meth:`ProbabilisticAtlas.maskProportions` when a mask is provided which
does not match the atlas space.
"""
pass
class LabelAtlas(Atlas):
......
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