Unit tests for melodicanalysis module. Made indexed 4D test a bit smaller/faster

tests/test_image_advanced.py

@@ -71,7 +71,7 @@ def _test_image_indexed_read4D(threaded):
 
         # Data range grows with volume
         nvols = 50
-        data  = np.zeros((100, 100, 100, nvols))
+        data  = np.zeros((50, 50, 50, nvols))
         for vol in range(nvols):
             data[..., vol] = vol
         
@@ -88,7 +88,7 @@ def _test_image_indexed_read4D(threaded):
         # 4D (e.g. voxel time course)
         # 
         # n.b. This is SUPER SLOW!!
-        voxels = tests.random_voxels((100, 100, 100), 5)
+        voxels = tests.random_voxels((50, 50, 50), 5)
         for i, xyz in enumerate(voxels):
             
             x, y, z = [int(v) for v in xyz]

tests/test_melodicanalysis.py

+#!/usr/bin/env python
+#
+# test_melodicanalysis.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import              os
+import os.path   as op
+import itertools as it
+
+import numpy     as np
+import pytest
+
+import tests
+import fsl.utils.path           as fslpath
+import fsl.data.melodicanalysis as mela
+
+
+def test_isMelodicImage():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix',
+             'analysis.blica/melodic_IC.nii.gz']
+
+    with tests.testdir(paths) as testdir:
+        for p in paths:
+            expected = p == 'analysis.ica/melodic_IC.nii.gz'
+            assert mela.isMelodicImage(op.join(testdir, p)) == expected
+
+
+def test_isMelodicDir():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        assert mela.isMelodicDir(meldir)
+
+    # Directory must end in .ica
+    with tests.testdir([p.replace('.ica', '.blob') for p in paths]) as testdir:
+        meldir = op.join(testdir, 'analysis.blob')
+        assert not mela.isMelodicDir(meldir)
+
+    # Directory must exist!
+    assert not mela.isMelodicDir('non-existent.ica')
+
+    # Directory must contain all of the above files
+    perms = it.chain(it.combinations(paths, 1),
+                     it.combinations(paths, 2))
+    for p in perms:
+        with tests.testdir(p) as testdir:
+            meldir = op.join(testdir, 'analysis.ica')
+            assert not mela.isMelodicDir(meldir)
+
+
+def test_getAnalysisDir():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    testpaths = ['analysis.ica/melodic_IC.nii.gz',
+                 'analysis.ica/log.txt',
+                 'analysis.ica/stats/thresh_zstat1.nii.gz',
+                 'analysis.ica/report/00index.html']
+
+    with tests.testdir(paths) as testdir:
+        expected = op.join(testdir, 'analysis.ica')
+        for tp in testpaths:
+            assert mela.getAnalysisDir(op.join(testdir, tp)) == expected
+
+
+def test_getTopLevelAnalysisDir():
+    testpaths = [
+        ('REST.ica/filtered_func_data.ica/melodic_IC.nii.gz', 'REST.ica'),
+        ('REST.ica/filtered_func_data.ica/melodic_mix',       'REST.ica'),
+        ('analysis.gica/groupmelodic.ica/melodic_IC.nii.gz',  'analysis.gica'),
+        ('analysis.feat/filtered_func_data.ica/melodic_mix',  'analysis.feat')]
+
+    for tp, expected in testpaths:
+        assert mela.getTopLevelAnalysisDir(tp) == expected
+
+
+def test_getDataFile():
+    
+    testcases = [(['analysis.ica/filtfunc.ica/melodic_IC.nii.gz',
+                   'analysis.ica/filtfunc.ica/melodic_mix',
+                   'analysis.ica/filtfunc.ica/melodic_FTmix',
+                   'analysis.ica/filtered_func_data.nii.gz'],
+                  'analysis.ica/filtfunc.ica',
+                  'analysis.ica/filtered_func_data.nii.gz'),
+                 (['analysis.feat/filtfunc.ica/melodic_IC.nii.gz',
+                   'analysis.feat/filtfunc.ica/melodic_mix',
+                   'analysis.feat/filtfunc.ica/melodic_FTmix',
+                   'analysis.feat/filtered_func_data.nii.gz'],
+                  'analysis.feat/filtfunc.ica',
+                  'analysis.feat/filtered_func_data.nii.gz')]
+
+    for paths, meldir, expected in testcases:
+        with tests.testdir(paths) as testdir:
+            meldir   = op.join(testdir, meldir)
+            expected = op.join(testdir, expected)
+            assert mela.getDataFile(meldir) == expected
+
+ 
+def test_getMeanFile():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix',
+             'analysis.ica/mean.nii.gz']
+
+    with tests.testdir(paths) as testdir:
+        meldir   = op.join(testdir, 'analysis.ica')
+        expected = op.join(testdir, 'analysis.ica/mean.nii.gz')
+        
+        assert mela.getMeanFile(meldir) == expected
+        
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix',
+             'analysis.ica/mean.txt']
+
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        with pytest.raises(fslpath.PathError):
+            mela.getMeanFile(meldir)
+
+
+def test_getICFile():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir   = op.join(testdir, 'analysis.ica')
+        expected = op.join(testdir, 'analysis.ica/melodic_IC.nii.gz')
+        assert mela.getICFile(meldir) == expected
+        
+    paths = ['analysis.ica/melodic_IC.txt',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        with pytest.raises(fslpath.PathError):
+            mela.getICFile(meldir) 
+    
+
+def test_getMixFile():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir   = op.join(testdir, 'analysis.ica')
+        expected = op.join(testdir, 'analysis.ica/melodic_mix')
+        assert mela.getMixFile(meldir) == expected
+        
+    paths = ['analysis.ica/melodic_IC.ni.gz',
+             'analysis.ica/melodic_FTmix']
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        assert mela.getMixFile(meldir) is None
+
+def test_getFTMixFile():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir   = op.join(testdir, 'analysis.ica')
+        expected = op.join(testdir, 'analysis.ica/melodic_FTmix')
+        assert mela.getFTMixFile(meldir) == expected
+        
+    paths = ['analysis.ica/melodic_IC.ni.gz',
+             'analysis.ica/melodic_mix']
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        assert mela.getFTMixFile(meldir) is None 
+
+def test_getReportFile():
+    paths = ['analysis.ica/filtfunc.ica/melodic_IC.nii.gz',
+             'analysis.ica/filtfunc.ica/melodic_mix',
+             'analysis.ica/filtfunc.ica/melodic_FTmix',
+             'analysis.ica/report.html']
+
+    with tests.testdir(paths) as testdir:
+        meldir   = op.join(testdir, 'analysis.ica/filtfunc.ica')
+        expected = op.join(testdir, 'analysis.ica/report.html')
+        assert op.abspath(mela.getReportFile(meldir)) == expected
+        
+    paths = ['analysis.ica/filtfunc.ica/melodic_IC.ni.gz',
+             'analysis.ica/filtfunc.ica/melodic_mix',
+             'analysis.ica/filtfunc.ica/melodic_FTmix']
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        assert mela.getReportFile(meldir) is None 
+
+
+def test_getNumComponents():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        icfile = op.join(meldir,  'melodic_IC.nii.gz')
+
+        tests.make_random_image(icfile, (10, 10, 10, 17))
+
+        assert mela.getNumComponents(meldir) == 17
+
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        with pytest.raises(Exception):
+            mela.getNumComponents(meldir)
+
+
+def test_getComponentTimeSeries():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir  = op.join(testdir, 'analysis.ica')
+        mixfile = op.join(meldir,  'melodic_mix')
+
+        data = np.zeros((40, 20))
+        for i in range(20):
+            data[:, i] = np.arange(i, i + 40)
+
+        np.savetxt(mixfile, data)
+        assert np.all(mela.getComponentTimeSeries(meldir) == data)
+
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        with pytest.raises(Exception):
+            mela.getComponentTimeSeries(meldir)
+
+
+def test_getComponentPowerSpectra():
+    paths = ['analysis.ica/melodic_IC.nii.gz',
+             'analysis.ica/melodic_mix',
+             'analysis.ica/melodic_FTmix']
+
+    with tests.testdir(paths) as testdir:
+        meldir    = op.join(testdir, 'analysis.ica')
+        ftmixfile = op.join(meldir,  'melodic_FTmix')
+
+        data = np.zeros((40, 20))
+        for i in range(20):
+            data[:, i] = np.arange(i, i + 40)
+
+        np.savetxt(ftmixfile, data)
+        assert np.all(mela.getComponentPowerSpectra(meldir) == data)
+
+    with tests.testdir(paths) as testdir:
+        meldir = op.join(testdir, 'analysis.ica')
+        with pytest.raises(Exception):
+            mela.getComponentPowerSpectra(meldir)