From 3af1f6110d71c1d279ff6b50401e3c6784afe889 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@gmail.com>
Date: Tue, 14 May 2019 17:17:10 +0100
Subject: [PATCH] ENH: wrote get methods
these return 3D images with the binary or probabilistic mask
in a new image.Image with the name set to the label name
and the same NIFTI header as the atlas
---
fsl/data/atlases.py | 47 +++++++++++++++++++++++++++++++++++++++++--
tests/test_atlases.py | 19 +++++++++++++++--
2 files changed, 62 insertions(+), 4 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index d43a09d95..b28eb952c 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -586,8 +586,8 @@ class AtlasDescription(object):
def find(self, index=None, value=None, name=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 an invalid ``index`` or
+ Exactly one of ``index``, ``value``, or ``name`` may be specified - a
+ ``ValueError`` is raised otherwise. If an invalid ``index``, ``name``, or
``value`` is specified, an ``IndexError`` or ``KeyError`` will be
raised.
@@ -877,6 +877,28 @@ class LabelAtlas(Atlas):
return values, props
+ def get(self, label=None, index=None, value=None, name=None):
+ """
+ Returns the binary image for given label
+
+ Only one of the arguments should be used to define the label
+
+ :arg label: AtlasLabel contained within this atlas
+ :arg index: index of the label
+ :arg value: value of the label
+ :arg name: string of the label
+ :return: image.Image with the mask
+ """
+ if ((label is not None) + (index is not None) +
+ (value is not None) + (name is not None)) != 1:
+ raise ValueError('Only one of label, index, value, or name may be specified')
+ if label is None:
+ label = self.find(index=index, name=name, value=value)
+ elif label not in self.desc.labels:
+ raise ValueError("Unknown label provided")
+ arr = (self.data == label.value).astype(int)
+ return fslimage.Image(arr, name=label.name, header=self.header)
+
class ProbabilisticAtlas(Atlas):
"""A 4D atlas which contains one volume for each region.
@@ -895,6 +917,27 @@ class ProbabilisticAtlas(Atlas):
"""
Atlas.__init__(self, atlasDesc, resolution, False, **kwargs)
+ def get(self, label=None, index=None, value=None, name=None):
+ """
+ Returns the probabilistic image for given label
+
+ Only one of the arguments should be used to define the label
+
+ :arg label: AtlasLabel contained within this atlas
+ :arg index: index of the label
+ :arg value: value of the label
+ :arg name: string of the label
+ :return: image.Image with the probabilistic mask
+ """
+ if ((label is not None) + (index is not None) +
+ (value is not None) + (name is not None)) != 1:
+ raise ValueError('Only one of label, index, value, or name may be specified')
+ if label is None:
+ label = self.find(index=index, value=value, name=name)
+ elif label not in self.desc.labels:
+ raise ValueError("Unknown label provided")
+ arr = self[..., label.index]
+ return fslimage.Image(arr, name=label.name, header=self.header)
def proportions(self, location, *args, **kwargs):
"""Looks up and returns the proportions of of all regions at the given
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index 8f4136b5d..b2dfec113 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -142,8 +142,6 @@ def test_AtlasDescription():
registry.getAtlasDescription('non-existent-atlas')
-
-
def test_add_remove_atlas():
with tests.testdir() as testdir:
@@ -237,6 +235,23 @@ def test_load_atlas():
assert isinstance(lblatlas, atlases.LabelAtlas)
+def test_get():
+
+ reg = atlases.registry
+ reg.rescanAtlases()
+
+ probatlas = reg.loadAtlas('harvardoxford-cortical')
+ lblatlas = reg.loadAtlas('talairach')
+ for atlas in (probatlas, lblatlas):
+ for idx, label in enumerate(atlas.desc.labels[:10]):
+ target = probatlas[..., idx] if atlas is probatlas else lblatlas.data == label.value
+ assert (target == atlas.get(label).data).all()
+ assert label.name == atlas.get(label).name
+ assert (target == atlas.get(index=label.index).data).all()
+ assert (target == atlas.get(value=label.value).data).all()
+ assert (target == atlas.get(name=label.name).data).all()
+
+
def test_find():
reg = atlases.registry
--
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