TEST: test fslcreatehd with xml input

unit_tests/avwutils/fslcreatehd/feedsRun

 #!/usr/bin/env fslpython
 
 import os
+import os.path as op
 import sys
 import subprocess as sp
 
@@ -8,6 +9,9 @@ import numpy   as np
 import nibabel as nib
 
 
+THISDIR = op.dirname(__file__)
+
+
 # 2=char, 4=short, 8=int, 16=float, 64=double
 DTYPE_MAPPING = {
     2  : np.uint8,
@@ -17,6 +21,11 @@ DTYPE_MAPPING = {
     64 : np.float64
 }
 
+MNI152_2MM_AFFINE = np.array([[-2, 0, 0,   90],
+                              [ 0, 2, 0, -126],
+                              [ 0, 0, 2,  -72],
+                              [ 0, 0, 0,   1]])
+
 
 def validate_result(imgfile, expshape, exppixdim, exporigin, expdtype):
 
@@ -83,6 +92,13 @@ def test_new_file():
         args    = list(test.split())
         imgfile = 'image.nii.gz'
 
+        try:
+            os.remove(imgfile)
+        except:
+            pass
+
+        print(['fslcreatehd'] + args + [imgfile])
+
         sp.run(['fslcreatehd'] + args + [imgfile])
 
         args      = [float(a) for a in args]
@@ -175,9 +191,72 @@ def test_existing_file():
             os.remove(imgfile)
 
 
+def test_new_file_xml():
+    xmlfile = op.join(THISDIR, 'mni2mm.xml')
+    sp.run(['fslcreatehd', xmlfile, 'mni.nii.gz'])
+    img = nib.load('mni.nii.gz')
+
+    assert img.shape                   == (91, 109, 91)
+    assert img.header.get_zooms()[:3]  == (2.0, 2.0, 2.0)
+    assert img.header['intent_code']   == 10
+    assert img.header['intent_p1']     == 20
+    assert img.header['intent_p2']     == 30
+    assert img.header['intent_p3']     == 40
+
+
+def test_existing_file_xml_same_shape():
+    xmlfile = op.join(THISDIR, 'mni2mm.xml')
+    img = create_image((91, 109, 91), (3, 3, 3), (5, 5, 5), np.float32)
+    img.to_filename('image.nii.gz')
+
+    sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
+
+    result = nib.load('image.nii.gz')
+
+    assert result.shape                  == (91, 109, 91)
+    assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+
+    # bug in FSL<=6.0.4 caused intent codes to not be set
+    assert result.header['intent_code']  == 10
+    assert result.header['intent_p1']    == 20
+    assert result.header['intent_p2']    == 30
+    assert result.header['intent_p3']    == 40
+    assert np.all(result.affine          == MNI152_2MM_AFFINE)
+
+    # data should be preserved
+    assert np.all(result.get_fdata()     == img.get_fdata())
+
+
+def test_existing_file_xml_different_shape():
+
+    xmlfile = op.join(THISDIR, 'mni2mm.xml')
+    img = create_image((20, 20, 20), (3, 3, 3), (5, 5, 5), np.float32)
+
+    img.to_filename('image.nii.gz')
+
+    sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
+
+    result = nib.load('image.nii.gz')
+
+    assert result.shape                  == (91, 109, 91)
+    assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
+    assert result.header['intent_code']  == 10
+    assert result.header['intent_p1']    == 20
+    assert result.header['intent_p2']    == 30
+    assert result.header['intent_p3']    == 40
+    assert np.all(result.affine          == MNI152_2MM_AFFINE)
+
+    # data should be cleared
+    assert np.all(result.get_fdata()     == 0)
+
+
 def main():
     test_new_file()
     test_existing_file()
+    test_new_file_xml()
+    test_existing_file_xml_same_shape()
+    test_existing_file_xml_different_shape()
+
 
 if __name__ == '__main__':
     sys.exit(main())

unit_tests/avwutils/fslcreatehd/mni2mm.xml

+<nifti_image
+  image_offset = '352'
+  ndim = '3'
+  nx = '91'
+  ny = '109'
+  nz = '91'
+  nt = '1'
+  dx = '2'
+  dy = '2'
+  dz = '2'
+  dt = '1'
+  datatype = '4'
+  nvox = '902629'
+  nbyper = '2'
+  scl_slope = '1'
+  scl_inter = '0'
+  intent_code = '10'
+  intent_p1 = '20'
+  intent_p2 = '30'
+  intent_p3 = '40'
+  intent_name = ''
+  toffset = '0'
+  xyz_units = '2'
+  time_units = '8'
+  freq_dim = '0'
+  phase_dim = '0'
+  slice_dim = '0'
+  descrip = 'FSL5.0'
+  aux_file = ''
+  qform_code = '4'
+  qfac = '-1'
+  quatern_b = '0'
+  quatern_c = '1'
+  quatern_d = '0'
+  qoffset_x = '90'
+  qoffset_y = '-126'
+  qoffset_z = '-72'
+  sform_code = '4'
+  sto_xyz_matrix = '-2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1'
+  slice_code = '0'
+  slice_start = '0'
+  scl_end = '0'
+  scl_duration = '0'
+/>