From 327d4454658f824f9d6a533761e8771eeb25a980 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 3 Sep 2019 13:05:20 +0100
Subject: [PATCH] ENH: New "binary" flag to LabelAtlas.get
---
fsl/data/atlases.py | 26 +++++++++++++++++---------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 97f779a02..0a5d822f9 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -926,17 +926,20 @@ class LabelAtlas(Atlas):
return values, props
- def get(self, label=None, index=None, value=None, name=None):
- """
- Returns the binary image for given label
+
+ def get(self, label=None, index=None, value=None, name=None, binary=True):
+ """Returns the binary image for the 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
+ :arg label: :class:`AtlasLabel` contained within this atlas
+ :arg index: index of the label
+ :arg value: value of the label
+ :arg name: string of the label
+ :arg binary: If ``True`` (the default), the image will contain 1s in
+ the label region. Otherwise the image will contain the
+ label value.
+ :return: :class:`.Image` with the mask
"""
if ((label is not None) + (index is not None) +
(value is not None) + (name is not None)) != 1:
@@ -945,7 +948,12 @@ class LabelAtlas(Atlas):
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)
+
+ arr = (self.data == label.value).astype(np.int32)
+
+ if not binary:
+ arr[arr > 0] = label.value
+
return fslimage.Image(arr, name=label.name, header=self.header)
--
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