Commit 1fadbdf8 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

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
parent 6caf7778
......@@ -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'])
......
......@@ -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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