scilus · arnaudbore · Nov 20, 2023 · Oct 25, 2023 · Oct 27, 2023 · Oct 27, 2023
diff --git a/requirements.txt b/requirements.txt
@@ -37,7  37,7 @@ scipy==1.9.*
 six==1.16.*
 spams==2.6.*
 statsmodels==0.13.*
-trimeshpy==0.0.2
 trimeshpy==0.0.3
 vtk==9.2.*
 # Dipy requirements
 h5py>=2.8.0

diff --git a/scilpy/gradients/tests/test_utils.py → ...y/gradients/tests/test_gradients_utils.py b/scilpy/gradients/tests/test_utils.py → ...y/gradients/tests/test_gradients_utils.py
diff --git a/scilpy/io/fetcher.py b/scilpy/io/fetcher.py
@@ -93,7  93,7 @@ def get_testing_files_dict():
              'a2f982b8d84833f5ccfe709b725307d2'],
             'surface_vtk_fib.zip':
             ['1c9KMNFeSkyYDgu3SH_aMf0kduIlpt7cN',
-             '946beb4271b905a2bd69ad2d80136ca9'],
              'bf131869a6722778a234869bf585520a'],
             'tracking.zip':
             ['1QSekZYDoMvv-An6FRMSt_s_qPeB3BHfw',
              '6d88910403fb4d9b79604f11100d8915'],

diff --git a/scilpy/surfaces/tests/test_surfaces_utils.py b/scilpy/surfaces/tests/test_surfaces_utils.py
@@ -0,0  1,17 @@
 import numpy as np
 
 from scilpy.surfaces.utils import (extract_xform)
 from scilpy.tests.arrays import (xform, xform_matrix_ref)
 
 
 def test_convert_freesurfer_into_polydata():
     pass
 
 
 def test_flip_LPS():
     pass
 
 
 def test_extract_xform():
     out = extract_xform(xform)
     assert np.allclose(out, xform_matrix_ref)
diff --git a/scilpy/surfaces/utils.py b/scilpy/surfaces/utils.py
@@ -0,0  1,124 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
 import vtk
 from nibabel.freesurfer.io import read_geometry
 
 
 def convert_freesurfer_into_polydata(surface_to_polydata, xform):
     """
     Convert a freesurfer surface into a polydata surface with vtk.
 
     Parameters
     ----------
     surface_to_vtk: Input a surface from freesurfer.
         The header must not contain any of these suffixes:
         '.vtk', '.vtp', '.fib', '.ply', '.stl', '.xml', '.obj'.
 
     xform: array [float]
         Apply a transformation matrix to the surface to align
         freesurfer surface with T1.
 
     Returns
     -------
     polydata : A polydata surface.
         A polydata is a mesh structure that can hold data arrays
         in points, cells, or in the dataset itself.
     """
     surface = read_geometry(surface_to_polydata)
     points = vtk.vtkPoints()
     triangles = vtk.vtkCellArray()
 
     flip_LPS = [-1, -1, 1]
 
     for vertex in surface[0]:
         id = points.InsertNextPoint((vertex[0:3] xform)*flip_LPS)
 
     for vertex_id in surface[1]:
         triangle = vtk.vtkTriangle()
         triangle.GetPointIds().SetId(0, vertex_id[0])
         triangle.GetPointIds().SetId(1, vertex_id[1])
         triangle.GetPointIds().SetId(2, vertex_id[2])
         triangles.InsertNextCell(triangle)
 
     polydata = vtk.vtkPolyData()
     polydata.SetPoints(points)
     polydata.SetPolys(triangles)
     polydata.Modified()
 
     return polydata
 
 
 def extract_xform(xform):
     """
     Use the log.txt file from mri_info to generate a transformation
     matrix to align the freesurfer surface with the T1.
 
     Parameters
     ----------
     filename : list
         The copy-paste output from mri_info of the surface using:
         mri_info $surface >> log.txt
 
     Returns
     -------
     Matrix : np.array
         a transformation matrix to align the surface with the T1.
     """
 
     raw_xform = []
     for i in xform:
         raw_xform.extend(i.split())
 
     start_read = 0
     for i, value in enumerate(raw_xform):
         if value == 'xform':
             start_read = int(i)
             break
 
     if start_read == 0:
         raise ValueError('No xform in that file...')
 
     matrix = np.eye(4)
     for i in range(3):
         for j in range(4):
             matrix[i, j] = float(raw_xform[13*i   (j*3)   4 2 start_read][:-1])
     return matrix
 
 
 def flip_LPS(polydata):
     """
     Apply a flip to the freesurfer surface of the anteroposterior axis.
 
     Parameters
     ----------
     polydata : polydata surface.
         A surface mesh structure after a transformation in polydata
         surface with vtk.
 
     Returns
     -------
     polydata : polydata surface.
         return the polydata turned over.
     """
     flip_LPS = vtk.vtkMatrix4x4()
     flip_LPS.Identity()
     flip_LPS.SetElement(0, 0, -1)
     flip_LPS.SetElement(1, 1, -1)
 
     # Apply the transforms
     transform = vtk.vtkTransform()
     transform.Concatenate(flip_LPS)
 
     # Apply the transforms
     transform = vtk.vtkTransform()
     transform.Concatenate(flip_LPS)
 
     # Transform the polydata
     transform_polydata = vtk.vtkTransformPolyDataFilter()
     transform_polydata.SetTransform(transform)
     transform_polydata.SetInputData(polydata)
     transform_polydata.Update()
     polydata = transform_polydata.GetOutput()
 
     return polydata
diff --git a/scilpy/tests/arrays.py b/scilpy/tests/arrays.py
@@ -252,3  252,33 @@
 ref_out_labels = copy.deepcopy(ref_in_labels)
 for i in range(1, 8, 2):
     ref_out_labels[ref_out_labels == i] = 0
 
 # mri-info log.txt output file from freesurfer input
 xform = ['Volume information for mni__mask.nii.gz', 'type: nii',
          'dimensions: 193 x 229 x 193',
          'voxel sizes: 1.000000, 1.000000, 1.000000',
          'type: SHORT (4)', 'fov: 193.000', 'dof: 1',
          'xstart: -96.5, xend: 96.5', 'ystart: -114.5, yend: 114.5',
          'zstart: -96.5, zend: 96.5',
          'TR: 0.0 msec, TE: 0.0 msec, TI: 0.0 msec, flip angle: 0.0 degrees',
          'nframes: 1', 'PhEncDir: UNKNOWN', 'FieldStrength: 0.000000',
          'ras xform present',
          'xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000',
          ': x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000',
          ': x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000',
          'Orientation   : RAS', 'Primary Slice Direction: axial',
          '', 'voxel to ras transform:',
          '1.0000   0.0000   0.0000   -96.0000',
          '0.0000   1.0000   0.0000  -132.0000',
          '0.0000   0.0000   1.0000   -78.0000',
          '0.0000   0.0000   0.0000     1.0000',
          '', 'voxel-to-ras determinant 1',
          '', 'ras to voxel transform:',
          '1.0000   0.0000   0.0000    96.0000',
          '0.0000   1.0000   0.0000   132.0000',
          '0.0000   0.0000   1.0000    78.0000',
          '0.0000   0.0000   0.0000     1.0000']
 
 # Reference matrix for xform file
 xform_matrix_ref = np.array(((1, 0, 0, 0.5), (0, 1, 0, -17.5),
                              (0, 0, 1, 18.5), (0, 0, 0, 1)))
diff --git a/scripts/scil_convert_surface.py b/scripts/scil_convert_surface.py
@@ -7,10  7,15 @@
 
 > scil_convert_surface.py surf.vtk converted_surf.ply
 """
-
 import argparse
 import os
 
 from trimeshpy.vtk_util import (load_polydata,
                                 save_polydata)
 
-from trimeshpy.io import load_mesh_from_file
 from scilpy.surfaces.utils import (convert_freesurfer_into_polydata,
                                    extract_xform,
                                    flip_LPS)
 
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist,
@@ -33,19  38,47 @@ def _build_arg_parser():
     p.add_argument('out_surface',
                    help='Output flipped surface (formats supported by VTK).')
 
     p.add_argument('--xform',
                    help='Path of the copy-paste output from mri_info \n'
                         'Using: mri_info $input >> log.txt, \n'
                         'The file log.txt would be this parameter')
 
     p.add_argument('--to_lps', action='store_true',
                    help='Flip for Surface/MI-Brain LPS')
 
     add_overwrite_arg(p)
 
     return p
 
 
 def main():
 
     parser = _build_arg_parser()
     args = parser.parse_args()
 
     assert_inputs_exist(parser, args.in_surface)
     assert_outputs_exist(parser, args, args.out_surface)
 
-    mesh = load_mesh_from_file(args.in_surface)
-    mesh.save(args.out_surface)
     if args.xform:
         with open(args.xform) as f:
             content = f.readlines()
         xform = [x.strip() for x in content]
         xform_matrix = extract_xform(xform)
         xform_translation = xform_matrix[0:3, 3]
     else:
         xform_translation = [0, 0, 0]
 
     if not ((os.path.splitext(args.in_surface)[1])
             in ['.vtk', '.vtp', '.fib', '.ply', '.stl', '.xml', '.obj']):
         polydata = convert_freesurfer_into_polydata(args.in_surface,
                                                     xform_translation)
     else:
         polydata = load_polydata(args.out_surface)
 
     if args.to_lps:
         polydata = flip_LPS(polydata)
 
     save_polydata(polydata, args.out_surface, legacy_vtk_format=True)
 
 
 if __name__ == "__main__":

diff --git a/scripts/tests/test_convert_surface.py b/scripts/tests/test_convert_surface.py
@@ -24,3  24,15 @@ def test_execution_surface_vtk_fib(script_runner):
     ret = script_runner.run('scil_convert_surface.py', in_surf,
                             'rhpialt.ply')
     assert ret.success
 
 
 def test_execution_surface_vtk_xfrom(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_surf = os.path.join(get_home(), 'surface_vtk_fib',
                            'lh.pialt_xform')
     x_form = os.path.join(get_home(), 'surface_vtk_fib',
                           'log.txt')
     ret = script_runner.run('scil_convert_surface.py', in_surf,
                             'lh.pialt_xform.vtk', '--xform', x_form,
                             '--to_lps')
     assert ret.success