Rename surface scripts

scilpy/surfaces/surface_operations.py

@@ -0,0 +1,82 @@
+# -*- coding: utf-8 -*-
+
+import numpy as np
+from scipy.ndimage import map_coordinates
+import trimeshpy.vtk_util as vtk_u
+
+
+def apply_transform(mesh, ants_affine, ants_warp=None):
+    """
+    Apply transformation to a surface
+        - Apply linear transformation with affine
+        - Apply non linear transformation with ants_warp
+
+    Parameters
+    ----------
+    mesh: trimeshpy - Triangle Mesh VTK class
+        Moving surface
+    ants_affine: numpy.ndarray
+        Transformation matrix to be applied
+    ants_warp: nib.Nifti1Image
+        Warp image from ANTs
+
+    Returns
+    -------
+    mesh: trimeshpy - Triangle Mesh VTK class
+        Surface moved
+    """
+    # Affine transformation
+    inv_affine = np.linalg.inv(ants_affine)
+
+    # Transform mesh vertices
+    mesh.set_vertices(mesh.vertices_affine(inv_affine))
+
+    # Flip triangle face, if needed
+    if mesh.is_transformation_flip(inv_affine):
+        mesh.set_triangles(mesh.triangles_face_flip())
+
+    if ants_warp is not None:
+        warp_img = np.squeeze(ants_warp.get_fdata(dtype=np.float32))
+
+        # Get vertices translation in voxel space, from the warp image
+        vts_vox = vtk_u.vtk_to_vox(mesh.get_vertices(), warp_img)
+        tx = map_coordinates(warp_img[..., 0], vts_vox.T, order=1)
+        ty = map_coordinates(warp_img[..., 1], vts_vox.T, order=1)
+        tz = map_coordinates(warp_img[..., 2], vts_vox.T, order=1)
+
+        # Apply vertices translation in world coordinates
+        mesh.set_vertices(mesh.get_vertices() + np.array([tx, ty, tz]).T)
+
+    return mesh
+
+
+def flip(mesh, axes):
+    """
+    Apply flip to a surface
+
+    Parameters
+    ----------
+    mesh: trimeshpy - Triangle Mesh VTK class
+        Moving surface
+    axes: list
+        Axes (or normal orientation) you want to flip
+
+    Returns
+    -------
+    mesh: trimeshpy - Triangle Mesh VTK class
+        Surface flipped
+    """
+    # Flip axes
+    flip = (-1 if 'x' in axes else 1,
+            -1 if 'y' in axes else 1,
+            -1 if 'z' in axes else 1)
+    tris, vts = mesh.flip_triangle_and_vertices(flip)
+    mesh.set_vertices(vts)
+    mesh.set_triangles(tris)
+
+    # Reverse surface orientation
+    if 'n' in axes:
+        tris = mesh.triangles_face_flip()
+        mesh.set_triangles(tris)
+
+    return mesh

scilpy/surfaces/tests/test_surface_operations.py

@@ -0,0 +1,10 @@
+# -*- coding: utf-8 -*-
+
+def test_surface_apply_transfo():
+    # toDO
+    pass
+
+
+def test_surface_flip():
+    # toDo
+    pass

scripts/legacy/scil_apply_transform_to_surface.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_surface_apply_transform import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_surface_apply_transform.py. Please change
+your existing pipelines accordingly.
+
+"""
+
+
+@deprecate_script("scil_apply_transform_to_surface.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_convert_surface.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_surface_convert import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_surface_convert.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_convert_surface.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_flip_surface.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_surface_flip import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_surface_flip.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_flip_surface.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_smooth_surface.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_surface_smooth import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_surface_smooth.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_smooth_surface.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/scil_apply_transform_to_surface.py → scripts/scil_surface_apply_transform.py

@@ -7,11 +7,12 @@
 
 Best usage with ANTs from T1 to b0:
 > ConvertTransformFile 3 output0GenericAffine.mat vtk_transfo.txt --hm
-> scil_transform_surface.py lh_white_lps.vtk affine.txt lh_white_b0.vtk\\
+> scil_surface_apply_transform.py lh_white_lps.vtk affine.txt lh_white_b0.vtk\\
     --ants_warp warp.nii.gz
 
 The input surface needs to be in *T1 world LPS* coordinates
 (aligned over the T1 in MI-Brain).
+The script will use the linear affine first and then the warp image from ANTs.
 The resulting surface should be aligned *b0 world LPS* coordinates
 (aligned over the b0 in MI-Brain).
 """
@@ -20,13 +21,12 @@
 
 import nibabel as nib
 import numpy as np
-from scipy.ndimage import map_coordinates
 from trimeshpy.io import load_mesh_from_file
-import trimeshpy.vtk_util as vtk_u
 
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
+from scilpy.surfaces.surface_operations import apply_transform
 
 
 EPILOG = """
@@ -67,32 +67,16 @@ def main():
     # Load mesh
     mesh = load_mesh_from_file(args.in_surface)
 
-    # Affine transformation
-    if args.ants_affine:
-        # Load affine
-        affine = np.loadtxt(args.ants_affine)
-        inv_affine = np.linalg.inv(affine)
-
-        # Transform mesh vertices
-        mesh.set_vertices(mesh.vertices_affine(inv_affine))
-
-        # Flip triangle face, if needed
-        if mesh.is_transformation_flip(inv_affine):
-            mesh.set_triangles(mesh.triangles_face_flip())
+    warp_img = None
+    # Load affine
+    affine = np.loadtxt(args.ants_affine)
 
+    # Non linear transformation
     if args.ants_warp:
         # Load warp
         warp_img = nib.load(args.ants_warp)
-        warp = np.squeeze(warp_img.get_fdata(dtype=np.float32))
-
-        # Get vertices translation in voxel space, from the warp image
-        vts_vox = vtk_u.vtk_to_vox(mesh.get_vertices(), warp_img)
-        tx = map_coordinates(warp[..., 0], vts_vox.T, order=1)
-        ty = map_coordinates(warp[..., 1], vts_vox.T, order=1)
-        tz = map_coordinates(warp[..., 2], vts_vox.T, order=1)
 
-        # Apply vertices translation in world coordinates
-        mesh.set_vertices(mesh.get_vertices() + np.array([tx, ty, tz]).T)
+    mesh = apply_transform(mesh, affine, warp_img)
 
     # Save mesh
     mesh.save(args.out_surface)

scripts/scil_convert_surface.py → scripts/scil_surface_convert.py

@@ -5,7 +5,7 @@
 Script to convert a surface (FreeSurfer or VTK supported).
     ".vtk", ".vtp", ".ply", ".stl", ".xml", ".obj"
 
-> scil_convert_surface.py surf.vtk converted_surf.ply
+> scil_surface_convert.py surf.vtk converted_surf.ply
 """
 import argparse
 import os

scripts/scil_flip_surface.py → scripts/scil_surface_flip.py

@@ -10,7 +10,7 @@
 Best usage for FreeSurfer to LPS vtk (for MI-Brain):
 !!! important FreeSurfer surfaces must be in their respective folder !!!
 > mris_convert --to-scanner lh.white lh.white.vtk
-> scil_flip_surface.py lh.white.vtk lh_white_lps.vtk x y
+> scil_surface_flip.py lh.white.vtk lh_white_lps.vtk x y
 """
 
 import argparse
@@ -20,6 +20,7 @@
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
+from scilpy.surfaces.surface_operations import flip
 
 EPILOG = """
 References:
@@ -57,19 +58,7 @@ def main():
     # Load mesh
     mesh = load_mesh_from_file(args.in_surface)
 
-    # Flip axes
-    flip = (-1 if 'x' in args.axes else 1,
-            -1 if 'y' in args.axes else 1,
-            -1 if 'z' in args.axes else 1)
-    tris, vts = mesh.flip_triangle_and_vertices(flip)
-    mesh.set_vertices(vts)
-    mesh.set_triangles(tris)
-
-    # Reverse surface orientation
-    if 'n' in args.axes:
-        tris = mesh.triangles_face_flip()
-        mesh.set_triangles(tris)
-
+    mesh = flip(mesh, args.axes)
     # Save
     mesh.save(args.out_surface)
 

scripts/tests/test_apply_transform_to_surface.py → scripts/tests/test_surface_apply_transform.py

@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_apply_transform_to_surface.py', '--help')
+    ret = script_runner.run('scil_surface_apply_transform.py', '--help')
     assert ret.success
 
 
@@ -23,6 +23,6 @@ def test_execution_surface_vtk_fib(script_runner):
                            'lhpialt.vtk')
     in_aff = os.path.join(get_home(), 'surface_vtk_fib',
                           'affine.txt')
-    ret = script_runner.run('scil_apply_transform_to_surface.py', in_surf,
+    ret = script_runner.run('scil_surface_apply_transform.py', in_surf,
                             in_aff, 'lhpialt_lin.vtk')
     assert ret.success

scripts/tests/test_flip_surface.py → scripts/tests/test_surface_flip.py

@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_flip_surface.py', '--help')
+    ret = script_runner.run('scil_surface_flip.py', '--help')
     assert ret.success
 
 
@@ -23,6 +23,6 @@ def test_execution_surface_vtk_fib(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_surf = os.path.join(get_home(), 'surface_vtk_fib',
                            'lhpialt.vtk')
-    ret = script_runner.run('scil_flip_surface.py', in_surf, 'rhpialt.vtk',
+    ret = script_runner.run('scil_surface_flip.py', in_surf, 'rhpialt.vtk',
                             'x')
     assert ret.success

scripts/tests/test_smooth_surface.py → scripts/tests/test_surface_smooth.py

@@ -13,14 +13,14 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_smooth_surface.py', '--help')
+    ret = script_runner.run('scil_surface_smooth.py', '--help')
     assert ret.success
 
 
 def test_execution_surface_vtk_fib(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_surf = os.path.join(get_home(), 'surface_vtk_fib',
                            'lhpialt.vtk')
-    ret = script_runner.run('scil_smooth_surface.py', in_surf,
+    ret = script_runner.run('scil_surface_smooth.py', in_surf,
                             'lhpialt_smooth.vtk', '-n', '5', '-s', '1')
     assert ret.success