TEST: unit test for convertwarp, make fslcreatehd test save output to output dir

unit_tests/avwutils/fslcreatehd/feedsRun

@@ -9,7 +9,7 @@ import numpy   as np
 import nibabel as nib
 
 
-THISDIR = op.dirname(__file__)
+THISDIR = op.dirname(op.abspath(__file__))
 
 
 # 2=char, 4=short, 8=int, 16=float, 64=double
@@ -251,6 +251,9 @@ def test_existing_file_xml_different_shape():
 
 
 def main():
+    outdir = sys.argv[1]
+    os.chdir(outdir)
+
     test_new_file()
     test_existing_file()
     test_new_file_xml()

unit_tests/fugue/convertwarp/feedsRun

+#!/usr/bin/env fslpython
+
+
+import os
+import sys
+import os.path as op
+import subprocess as sp
+
+import numpy as np
+import nibabel as nib
+
+from fsl.data.image import Image
+from fsl.utils.image.resample import resampleToPixdims
+
+
+THISDIR = op.dirname(op.abspath(__file__))
+SRC     = op.join(THISDIR, 'src.nii.gz')
+REF     = op.join(THISDIR, 'ref.nii.gz')
+AFF     = op.join(THISDIR, 'src2ref.mat')
+
+
+def register_test_images():
+
+    # use fnirt to register src to ref
+    # (images are small, won't take long)
+    sp.call(f'fnirt --in={SRC} --ref={REF} --aff={AFF} '
+            '--cout=cout --fout=fout'.split())
+
+    # check that fnirt set the
+    # displacement field affine
+    # correctly
+    ref  = Image(REF)
+    fout = Image('fout')
+    assert fout.sameSpace(ref)
+
+
+def test_convertwarp_sets_affine_correctly():
+    # We're assuming that register_test_images
+    # has already been called
+
+    # convert coefficient field to displacement field
+    sp.call(f'convertwarp  --ref={REF} --warp1=cout --out=disp'.split())
+
+    # check that result is in same space as reference
+    ref  = Image(REF)
+    disp = Image('disp')
+    assert disp.sameSpace(ref)
+
+    # repeat the above test, but with a
+    # reference image of different resolution
+    refrs, refxform = resampleToPixdims(ref, np.array(ref.pixdim) / 2)
+    refrs = Image(refrs, xformr=refxform)
+    refrs.save('refrs')
+    sp.call(f'convertwarp  --ref=refrs --warp1=cout --out=disprs'.split())
+
+    # check that result is in same
+    # space as the resampled reference
+    disp = Image('disprs')
+    assert disp.sameSpace(refrs)
+
+
+def main():
+    outdir = sys.argv[1]
+    os.chdir(outdir)
+    register_test_images()
+    test_convertwarp_sets_affine_correctly()
+
+
+if __name__ == '__main__':
+    main()

unit_tests/fugue/convertwarp/src2ref.mat

+1.130654884  -0.02090760163  0.05273442572  -0.523881946  
+0.01777234539  0.9990179929  0.2039857328  5.806280637  
+-0.003319001082  -0.2740303429  1.071017063  0.4915523243  
+0  0  0  1