unit test for fslcomplex

Specifically testing that fslcomplex correctly sets orientation information on the output file[s].

Note that this test will fail until newimage!26 (merged) is merged and released

unit_tests/avwutils/fslcomplex/feedsRun

@@ -20,39 +20,52 @@ def sprun(cmd):
     sp.run(shlex.split(cmd), check=True)
 
 
+def imtest(path):
+    try:
+        addExt(path)
+        return True
+    except Exception:
+        return False
+
+
 # radio=[True|False] -> whether or not
 # to add a flip on the affine X axis
 def create_test_input_data(radio):
 
-    real  = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
-    imag  = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
-    comp  = real + imag * 1j
-    abso  = np.abs(comp)
-    phase = np.arctan2(comp.imag, comp.real)
+    real   = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
+    imag   = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
+    comp   = real + imag * 1j
+    abso   = np.abs(comp)
+    phase  = np.arctan2(comp.imag, comp.real)
+    comp4d = np.concatenate((comp.reshape(10, 10, 10, 1),
+                             comp.reshape(10, 10, 10, 1)), 3)
 
-    affine        = np.diag([3, 3, 3, 0])
+    affine        = np.diag([3, 3, 3, 1])
     affine[:3, 3] = [10, 20, 30]
 
     if radio:
         affine[0, 0] *= -1
 
-    real  = nib.Nifti1Image(real,  affine)
-    imag  = nib.Nifti1Image(imag,  affine)
-    comp  = nib.Nifti1Image(comp,  affine)
-    abso  = nib.Nifti1Image(abso,  affine)
-    phase = nib.Nifti1Image(phase, affine)
+    real   = nib.Nifti1Image(real,   affine)
+    imag   = nib.Nifti1Image(imag,   affine)
+    comp   = nib.Nifti1Image(comp,   affine)
+    comp4d = nib.Nifti1Image(comp4d, affine)
+    abso   = nib.Nifti1Image(abso,   affine)
+    phase  = nib.Nifti1Image(phase,  affine)
 
-    real .set_qform(*real .get_sform(coded=True))
-    imag .set_qform(*comp .get_sform(coded=True))
-    comp .set_qform(*comp .get_sform(coded=True))
-    abso .set_qform(*abso .get_sform(coded=True))
-    phase.set_qform(*phase.get_sform(coded=True))
+    real  .set_qform(*real  .get_sform(coded=True))
+    imag  .set_qform(*comp  .get_sform(coded=True))
+    comp  .set_qform(*comp  .get_sform(coded=True))
+    comp4d.set_qform(*comp4d.get_sform(coded=True))
+    abso  .set_qform(*abso  .get_sform(coded=True))
+    phase .set_qform(*phase .get_sform(coded=True))
 
-    real .to_filename('real_in.nii.gz')
-    imag .to_filename('imag_in.nii.gz')
-    comp .to_filename('complex_in.nii.gz')
-    abso .to_filename('abs_in.nii.gz')
-    phase.to_filename('phase_in.nii.gz')
+    real  .to_filename('real_in.nii.gz')
+    imag  .to_filename('imag_in.nii.gz')
+    comp  .to_filename('complex_in.nii.gz')
+    comp4d.to_filename('complex4d_in.nii.gz')
+    abso  .to_filename('abs_in.nii.gz')
+    phase .to_filename('phase_in.nii.gz')
 
 
 def compare_images(file1, file2):
@@ -73,42 +86,41 @@ def test_fslcomplex_call(args, infiles, outfiles, radio):
         create_test_input_data(radio)
         sprun(f'fslcomplex {args} {infiles} {outfiles}')
         for outfile in outfiles.split(' '):
+
+            if not imtest(outfile):
+                continue
+
             prefix = outfile.split('_')[0]
             infile = f'{prefix}_in'
-            print(f'Comparing {outfile} against {infile} [prefix {prefix}]')
+
+            print(f'Comparing {outfile} against {infile}')
+
             compare_images(infile, outfile)
 
 
 if __name__ == '__main__':
     tests = [
-        ('-realabs',       'complex_in',      'abs_out',           False),
-        ('-realabs',       'complex_in',      'abs_out',           True),
-        ('-realphase',     'complex_in',      'phase_out',         False),
-        ('-realphase',     'complex_in',      'phase_out',         True),
-        ('-realpolar',     'complex_in',      'abs_out phase_out', False),
-        ('-realpolar',     'complex_in',      'abs_out phase_out', True),
-        ('-realcartesian', 'complex_in',      'real_out imag_out', False),
-        ('-realcartesian', 'complex_in',      'real_out imag_out', True),
-        ('-complex',       'real_in imag_in', 'complex_out',       False),
-        ('-complex',       'real_in imag_in', 'complex_out',       True),
-        ('-complexpolar',  'abs_in phase_in', 'complex_out',       False),
-        ('-complexpolar',  'abs_in phase_in', 'complex_out',       True),
-        # ('-complexsplit',  [], [], False), # ??
-        # ('-complexmerge',  [], [], False), # ??
-        # ('-copyonly',      [], [], False), # ??
-        # ('-complexsplit',  [], [], True), # ??
-        # ('-complexmerge',  [], [], True), # ??
-        # ('-copyonly',      [], [], True), # ??
+        ('-realabs',       'complex_in',            'abs_out'),
+        ('-realphase',     'complex_in',            'phase_out'),
+        ('-realpolar',     'complex_in',            'abs_out phase_out'),
+        ('-realcartesian', 'complex_in',            'real_out imag_out'),
+        ('-complex',       'real_in imag_in',       'complex_out'),
+        ('-complexpolar',  'abs_in phase_in',       'complex_out'),
+        ('-copyonly',      'complex_in',            'complex_out'),
+        ('-complexsplit',  'complex4d_in',          'complex_out 0 0'),
+        ('-complexsplit',  'complex4d_in',          'complex_out 1 1'),
+        ('-complexmerge',  'complex_in complex_in', 'complex4d_out'),
     ]
 
     result = 0
-    for args, infiles, outfiles, radio in tests:
-        try:
-            test_fslcomplex_call(args, infiles, outfiles, radio)
-            print(f'\nTest fslcomplex {args} {infiles} {outfiles} PASSED')
-        except Exception as e:
-            print(f'\nTest fslcomplex {args} {infiles} {outfiles} FAILED')
-            traceback.print_exc()
-            result = 1
+    for radio in [True, False]:
+        for args, infiles, outfiles in tests:
+            try:
+                test_fslcomplex_call(args, infiles, outfiles, radio)
+                print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] PASSED')
+            except Exception as e:
+                print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] FAILED')
+                traceback.print_exc()
+                result = 1
 
     sys.exit(result)