first draft - not working

scilpy/surfaces/surface_operations.py

@@ -5,7 +5,7 @@
 import trimeshpy.vtk_util as vtk_u
 
 
-def apply_transform(mesh, ants_affine, ants_warp=None):
+def apply_transform(mesh, ants_affine, ants_warp=None, inverse=False):
     """
     Apply transformation to a surface
         - Apply linear transformation with affine
@@ -27,6 +27,8 @@ def apply_transform(mesh, ants_affine, ants_warp=None):
     """
     # Affine transformation
     inv_affine = np.linalg.inv(ants_affine)
+        if inverse:
+        linear_transfo = np.linalg.inv(linear_transfo)
 
     # Transform mesh vertices
     mesh.set_vertices(mesh.vertices_affine(inv_affine))

scripts/scil_surface_apply_transform.py

@@ -8,7 +8,7 @@
 Example usage from T1 to b0 using ANTs transforms:
 > ConvertTransformFile 3 output0GenericAffine.mat vtk_transfo.txt --hm
 > scil_surface_apply_transform.py lh_white_lps.vtk affine.txt lh_white_b0.vtk\\
-    --ants_warp warp.nii.gz
+    --in_deformation warp.nii.gz
 
 Important: The input surface needs to be in *T1 world LPS* coordinates
 (aligned over the T1 in MI-Brain).
@@ -30,7 +30,8 @@
 from scilpy.io.utils import (add_overwrite_arg,
                              add_verbose_arg,
                              assert_inputs_exist,
-                             assert_outputs_exist)
+                             assert_outputs_exist,
+                             load_matrix_in_any_format)
 from scilpy.surfaces.surface_operations import apply_transform
 
 
@@ -45,17 +46,20 @@ def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__, epilog=EPILOG,
                                 formatter_class=argparse.RawTextHelpFormatter)
 
-    p.add_argument('in_surface',
+    p.add_argument('in_moving_surface',
                    help='Input surface (.vtk).')
 
-    p.add_argument('ants_affine',
-                   help='Affine transform from ANTs (.txt or .mat).')
-
+    p.add_argument('in_transfo',
+                   help='Path of the file containing the 4x4 \n'
+                        'transformation, matrix (.txt, .npy or .mat).'))
     p.add_argument('out_surface',
                    help='Output surface (.vtk).')
 
-    p.add_argument('--ants_warp',
-                   help='Warp image from ANTs (Nifti image).')
+    g = p.add_argument_group("Transformation options")
+    g.add_argument('--inverse', action='store_true',
+                   help='Apply the inverse linear transformation.')
+    g.add_argument('--in_deformation', metavar='file',
+                   help='Path to the file containing a deformation field.')
 
     add_verbose_arg(p)
     add_overwrite_arg(p)
@@ -68,23 +72,23 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_surface, args.ants_affine],
+    assert_inputs_exist(parser, [args.in_surface, args.in_transfo],
                         args.ants_warp)
     assert_outputs_exist(parser, args, args.out_surface)
 
     # Load mesh
     mesh = load_mesh_from_file(args.in_surface)
 
-    warp_img = None
-    # Load affine
-    affine = np.loadtxt(args.ants_affine)
+    # Load transformation
+    transfo = load_matrix_in_any_format(args.in_transfo)
 
-    # Non linear transformation
-    if args.ants_warp:
-        # Load warp
-        warp_img = nib.load(args.ants_warp)
+    deformation_data = None
+    if args.in_deformation is not None:
+        deformation_data = np.squeeze(nib.load(
+            args.in_deformation).get_fdata(dtype=np.float32))
 
-    mesh = apply_transform(mesh, affine, warp_img)
+    mesh = apply_transform(mesh, transfo, deformation_data,
+                           inverse=args.inverse)
 
     # Save mesh
     mesh.save(args.out_surface)