From 570a239fae3d5aeb818d558019e371cf5e117f6a Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 3 Sep 2019 13:03:54 +0100
Subject: [PATCH] ENH: Support for reading "statistic" xml atlas descriptions
---
fsl/data/atlases.py | 105 ++++++++++++++++++++++++++++++++------------
1 file changed, 77 insertions(+), 28 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 8d5dad9bd..950eeff16 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -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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