Some testing of atlases module

tests/test_atlases.py

+#!/usr/bin/env python
+#
+# test_atlases.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import            os
+import os.path as op
+import            shutil
+import            tempfile
+import numpy   as np
+
+import pytest
+
+import fsl.data.atlases as atlases
+import fsl.data.image   as fslimage
+
+
+def setup_module():
+    if os.environ.get('FSLDIR', None) is None:
+        raise Exception('FSLDIR is not set - atlas tests cannot be run')
+
+
+def test_registry():
+    registry = atlases.registry
+    registry.rescanAtlases()
+    
+    assert len(registry.listAtlases()) > 0
+    assert registry.hasAtlas('harvardoxford-cortical')
+
+    adesc = registry.getAtlasDescription('harvardoxford-cortical')
+    
+    assert isinstance(adesc, atlases.AtlasDescription)
+
+
+    with pytest.raises(Exception):
+        registry.getAtlasDescription('non-existent-atlas')
+
+
+def test_AtlasDescription():
+    registry = atlases.registry
+    registry.rescanAtlases()
+
+    tal  = registry.getAtlasDescription('talairach')
+    cort = registry.getAtlasDescription('harvardoxford-cortical') 
+
+
+    assert tal.atlasID == 'talairach'
+    assert tal.name    == 'Talairach Daemon Labels'
+    assert tal.specPath
+    assert tal.atlasType == 'label'
+    nimages = len(tal.images)
+    assert nimages                >  0
+    assert len(tal.summaryImages) >  0
+    assert len(tal.pixdims)       == nimages
+    assert len(tal.xforms)        == nimages
+    assert len(tal.labels)        >  0
+
+    for lbl in tal.labels:
+        lbl.name
+        lbl.index
+        lbl.x
+        lbl.y
+        lbl.z
+    
+    assert cort.atlasID == 'harvardoxford-cortical'
+    assert cort.name    == 'Harvard-Oxford Cortical Structural Atlas'
+    assert cort.specPath
+    assert cort.atlasType == 'probabilistic'
+    nimages = len(cort.images)
+    assert nimages                 >  0
+    assert len(cort.summaryImages) >  0
+    assert len(cort.pixdims)       == nimages
+    assert len(cort.xforms)        == nimages
+    assert len(cort.labels)        >  0
+
+    for lbl in cort.labels:
+        lbl.name
+        lbl.index
+        lbl.x
+        lbl.y
+        lbl.z 
+
+    with pytest.raises(Exception):
+        registry.getAtlasDescription('non-existent-atlas')
+
+
+
+dummy_atlas_desc = """<?xml version="1.0" encoding="ISO-8859-1"?>
+<atlas version="1.0">
+  <header>
+    <name>My Little Atlas</name>
+    <shortname>MLA</shortname>
+    <type>Label</type>
+    <images>
+      <imagefile>/MLA/MyLittleAtlas</imagefile>
+       <summaryimagefile>/MLA/MyLittleAtlas</summaryimagefile>
+    </images>
+  </header>
+  <data>
+    <label index="1" x="5" y="5" z="5">First little region</label>
+    <label index="2" x="6" y="6" z="6">Second little region</label>
+  </data>
+</atlas>
+"""
+
+
+def test_add_remove_atlas():
+
+    testdir    = tempfile.mkdtemp()
+    mladir     = op.join(testdir, 'MLA')
+    mlaxmlfile = op.join(testdir, 'MLA.xml')
+    mlaimgfile = op.join(testdir, 'MLA', 'MyLittleAtlas.nii.gz')
+ 
+    def _make_dummy_atlas():
+
+        data = np.zeros((10, 10, 10))
+        data[5, 5, 5] = 1
+        data[6, 6, 6] = 2
+
+        img = fslimage.Image(data, xform=np.eye(4))
+
+        os.makedirs(mladir)
+        img.save(mlaimgfile)
+
+        with open(mlaxmlfile, 'wt') as f:
+            f.write(dummy_atlas_desc)
+
+    added   = [False]
+    removed = [False]
+    reg     = atlases.registry
+
+    def atlas_added(r, topic, val):
+        assert topic == 'add'
+        assert r is reg
+        assert val.atlasID == 'mla'
+        added[0] = True
+        
+    def atlas_removed(r, topic, val):
+        assert r is reg
+        assert topic == 'remove'
+        assert val.atlasID == 'mla'
+        removed[0] = True 
+    
+    try:
+        _make_dummy_atlas()
+
+        reg.register('added',   atlas_added,   topic='add')
+        reg.register('removed', atlas_removed, topic='remove')
+
+        # add an atlas with an ID that is taken
+        with pytest.raises(Exception):
+            reg.addAtlas(mlaxmlfile, atlasID='harvardoxford-cortical')
+
+        reg.addAtlas(mlaxmlfile)
+
+        assert added[0]
+
+        assert reg.hasAtlas('mla')
+
+        reg.removeAtlas('mla')
+
+        assert removed[0]
+        
+
+    finally:
+        shutil.rmtree(testdir)