add --json option and associated logic

closes #6 (closed)

tests/avscale/feedsRun

+#!/usr/bin/env fslpython
+
+# test avscale with different input affines
+
+
+import sys
+import os
+
+import fsl.utils.run as run
+
+import numpy as np
+
+
+PI    = np.pi
+PION2 = np.pi / 2
+
+
+# Each test has the form (input-affine, expected-output)
+# where expected-output comprises:
+#   - scales
+#   - translations
+#   - rotations
+#   - skews
+#   - L/R orientation (preserved or swapped)
+tests = [
+
+    ([[1, 0, 0, 0],
+      [0, 1, 0, 0],
+      [0, 0, 1, 0],
+      [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, 0, 0), (0, 0, 0), 'preserved']),
+    ([[2, 0, 0, 0],
+      [0, 2, 0, 0],
+      [0, 0, 2, 0],
+      [0, 0, 0, 1]], [(2, 2, 2), (0, 0, 0), (0, 0, 0), (0, 0, 0), 'preserved']),
+    ([[-2, 0, 0, 0],
+      [ 0, 2, 0, 0],
+      [ 0, 0, 2, 0],
+      [ 0, 0, 0, 1]], [(2, 2, 2), (0, 0, 0), (0, 0, PI), (0, 0, 0), 'swapped']),
+    ([[0, 0, 1, 0],
+      [0, 1, 0, 0],
+      [1, 0, 0, 0],
+      [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, -PION2, 0), (0, 0, 0), 'swapped']),
+    ([[ 0,  0, -1, 0],
+      [ 0, -1,  0, 0],
+      [-1,  0,  0, 0],
+      [ 0,  0,  0, 1]], [(1, 1, 1), (0, 0, 0), (-PI, PION2, 0), (0, 0, 0), 'preserved']),
+    ([[0, 1, 0, 0],
+      [1, 0, 0, 0],
+      [0, 0, 1, 0],
+      [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (0, 0, PION2), (0, 0, 0), 'swapped']),
+    ([[1, 0, 0, 0],
+      [0, 0, 1, 0],
+      [0, 1, 0, 0],
+      [0, 0, 0, 1]], [(1, 1, 1), (0, 0, 0), (PION2, 0, 0), (0, 0, 0), 'swapped']),
+    ([[-2, 0, 0,  90],
+      [ 0, 2, 0, -126],
+      [ 0, 0, 2, -72],
+      [ 0, 0, 0,  1]], [(2, 2, 2), (90, -126, -72), (0, 0, PI), (0, 0, 0), 'swapped']),
+
+]
+
+def read_avscale_output(output):
+    lines = output.split('\n')
+    # scales
+    # translations
+    # rotations
+    # skews
+    # l/r orientation (preserved or swapped)
+    scales       = [l for l in lines if l.startswith('Scales ')]        [0]
+    translations = [l for l in lines if l.startswith('Translations ')]  [0]
+    rotations    = [l for l in lines if l.startswith('Rotation Angles')][0]
+    skews        = [l for l in lines if l.startswith('Skews ')]         [0]
+    orient       = [l for l in lines if l.startswith('Left-Right ')]    [0]
+
+    scales       = [float(s) for s in scales      .split()[-3:]]
+    translations = [float(s) for s in translations.split()[-3:]]
+    rotations    = [float(s) for s in rotations   .split()[-3:]]
+    skews        = [float(s) for s in skews       .split()[-3:]]
+    orient       = orient.split()[-1]
+
+    return {
+        'scales'       : np.array(scales),
+        'translations' : np.array(translations),
+        'rotations'    : np.array(rotations),
+        'skews'        : np.array(skews),
+        'orient'       : orient.lower(),
+    }
+
+
+def test_avscale():
+
+    for affine, expected in tests:
+        affine = np.array(affine)
+        np.savetxt('affine.mat', affine, '%0.6f')
+        print(affine)
+        output = run.runfsl('avscale --allparams affine.mat')
+        output = read_avscale_output(output)
+
+        scales, translations, rotations, skews, orient = expected
+
+        try:
+            assert np.all(np.isclose(scales,       output['scales']))
+            assert np.all(np.isclose(translations, output['translations']))
+            assert np.all(np.isclose(rotations,    output['rotations']))
+            assert np.all(np.isclose(skews,        output['skews']))
+            assert                   orient     == output['orient']
+        except AssertionError:
+            print(affine)
+            print(output)
+            raise
+
+
+if __name__ == '__main__':
+    if len(sys.argv) > 1:
+        os.chdir(sys.argv[1])
+    test_avscale()