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)