TEST: Unit tests for extract_noise. Needs a couple more.

tests/test_extract_noise.py

+#!/usr/bin/env python
+#
+# test_extract_noise.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import numpy as np
+
+import fsl.utils.tempdir         as tempdir
+import fsl.scripts.extract_noise as extn
+
+
+def test_genComponentIndexList():
+
+    with tempdir.tempdir():
+
+        # sequence of 1-indexed integers/file paths
+        # both potentially containing larger than
+        # the actual number of components
+        icomps  = [1, 5, 28, 12, 42, 54]
+        fcomps1 = [1, 4, 6, 3, 7]
+        fcomps2 = [12, 42, 31, 1, 4, 8]
+
+        with open('comps1.txt', 'wt') as f:
+            f.write(','.join([str(l) for l in fcomps1]))
+        with open('comps2.txt', 'wt') as f:
+            f.write(','.join([str(l) for l in fcomps2]))
+
+        ncomps   = 60
+        comps    = icomps + ['comps1.txt', 'comps2.txt']
+        expcomps = list(sorted(set(icomps + fcomps1 + fcomps2)))
+        expcomps = [c - 1 for c in expcomps]
+
+        assert extn.genComponentIndexList(comps, ncomps) == expcomps
+
+        ncomps   = 40
+        comps    = icomps + ['comps1.txt', 'comps2.txt'] + [0, -1]
+        expcomps = list(sorted(set(icomps + fcomps1 + fcomps2)))
+        expcomps = [c - 1 for c in expcomps if c <= ncomps]
+
+        assert extn.genComponentIndexList(comps, ncomps) == expcomps
+
+
+def test_loadConfoundFiles():
+    with tempdir.tempdir():
+
+        npts  = 50
+        confs = [
+            np.random.randint(1, 100, (50, 10)),
+            np.random.randint(1, 100, (50, 1)),
+            np.random.randint(1, 100, (50, 5)),
+            np.random.randint(1, 100, (40, 10)),
+            np.random.randint(1, 100, (60, 10))]
+
+        expected            = np.empty((50, 36), dtype=np.float64)
+        expected[:,   :]      = np.nan
+        expected[:,   :10]    = confs[0]
+        expected[:,    10:11] = confs[1]
+        expected[:,    11:16] = confs[2]
+        expected[:40,  16:26] = confs[3]
+        expected[:,    26:36] = confs[4][:50, :]
+
+        conffiles = []
+        for i, c in enumerate(confs):
+            fname = 'conf{}.txt'.format(i)
+            conffiles.append(fname)
+            np.savetxt(fname, c)
+
+        result = extn.loadConfoundFiles(conffiles, npts)
+        amask  = ~np.isnan(expected)
+
+        assert np.all(~np.isnan(result) == amask)
+        assert np.all(result[amask]     == expected[amask])
+        assert np.all(result[amask]     == expected[amask])