From de5013fcf3f4705b7f8305ea2a0cd99ca4fd1f34 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 5 Dec 2017 14:28:47 +1030
Subject: [PATCH] Small bugfixes in atlasq, which never arose because I assumed
that all atlas files have int type, which they don't. Also atlases handles
spaces in XML specifications
---
fsl/data/atlases.py | 10 +++++-----
fsl/scripts/atlasq.py | 8 ++++----
2 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 6ed038f1a..259b91fdf 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -483,8 +483,8 @@ class AtlasDescription(object):
self.atlasID = atlasID
self.specPath = op.abspath(filename)
- self.name = header.find('name').text
- self.atlasType = header.find('type').text.lower()
+ self.name = header.find('name').text.strip()
+ self.atlasType = header.find('type').text.strip().lower()
# Spelling error in some of the atlas.xml files.
if self.atlasType == 'probabalistic':
@@ -501,8 +501,8 @@ class AtlasDescription(object):
for image in images:
# Every image must also have a summary image
- imagefile = image.find('imagefile') .text
- summaryimagefile = image.find('summaryimagefile').text
+ imagefile = image.find('imagefile') .text.strip()
+ summaryimagefile = image.find('summaryimagefile').text.strip()
# Assuming that the path
# names begin with a slash
@@ -533,7 +533,7 @@ class AtlasDescription(object):
for i, label in enumerate(labels):
- name = label.text
+ name = label.text.strip()
index = int( label.attrib['index'])
x = float(label.attrib['x'])
y = float(label.attrib['y'])
diff --git a/fsl/scripts/atlasq.py b/fsl/scripts/atlasq.py
index 10acf8ff2..486e2c02a 100644
--- a/fsl/scripts/atlasq.py
+++ b/fsl/scripts/atlasq.py
@@ -171,8 +171,8 @@ def queryLongOutput(atlas, sources, types, allLabels, allProps):
label = labels[0]
name = names[ 0]
- if label is None:
- label = np.nan
+ if label is None: label = np.nan
+ else: label = int(label)
fields = ['name', 'index']
values = [name, label]
@@ -304,7 +304,7 @@ def ohi(namespace):
props, labels = zip(*reversed(sorted(zip(props, labels))))
for label, prop in zip(labels, props):
- label = atlasDesc.labels[label].name
+ label = atlasDesc.labels[int(label)].name
labelStrs.append('{:d}% {}'.format(int(round(prop)), label))
if len(labelStrs) == 0: labels = 'No label found!'
@@ -331,7 +331,7 @@ def labelNames(atlas, labels):
for l in labels:
if l is None: names.append('No label')
- else: names.append(atlas.desc.labels[l].name)
+ else: names.append(atlas.desc.labels[int(l)].name)
return names
--
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