Merge pull request #30 from Neuroinflab/dev/27_fsaverage_to_mesh

forward solver refactor to allow arbitrary coefficient mfem solving

extras/draw_cross_section_nifty.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 import pylab as pb
-
+from nibabel.affines import apply_affine
 
 def create_meshgrid_from_affine(affine, data):
     x, y, z, comp = data.shape
@@ -21,10 +21,10 @@ def create_meshgrid_from_affine(affine, data):
 
 
 def main():
-    parser = argparse.ArgumentParser(description="Draw crossection nifty files")
+    parser = argparse.ArgumentParser(description="Draw crossection nifty files, works well only with no skew or rotation, rectilinear affine")
     parser.add_argument("files", nargs='+', type=str, help="nifty files")
-    parser.add_argument("-x", type=int, help="Slice at X coordinate (in voxels)", default=130)
-    parser.add_argument("-y", type=int, help="Slice at Y coordinate (in voxels)", default=118)
+    parser.add_argument("-x", type=int, help="Slice at X coordinate (in meters)", default=0)
+    parser.add_argument("-y", type=int, help="Slice at Y coordinate (in meters)", default=0)
 
     args = parser.parse_args()
 
@@ -36,6 +36,12 @@ def main():
         name = os.path.basename(file)
         correction = nibabel.load(file)
         vol_data = correction.get_fdata()
+
+        inv_affine = np.linalg.inv(correction.affine)
+
+        x_vox, y_vox, z_vox = apply_affine(inv_affine, [args.x, args.y, 0])
+        slice_of_interest = np.s_[int(x_vox), int(y_vox), :]
+
         meshgrid = create_meshgrid_from_affine(correction.affine, vol_data) / 1000 # mm to meters
         data_slice = vol_data[slice_of_interest]
         data_x = meshgrid[slice_of_interest]

src/kesi/mfem_solver/forward_solver.py

@@ -46,11 +46,7 @@ def __init__(self, meshfile, conductivities, boundary_value=0, additional_refine
         self.solution_interpolated = None
         self.interpolator = interpolator
 
-    def solve(self, xyz, csd):
-        """
-        saves solution into self.solution as MFEM gridfunction and self.solution_interpolated for sampling at any point
-        """
-        coeff = csd_distribution_coefficient(xyz, csd)
+    def solve_coeff(self, coeff):
         solution = mfem_solve_mesh(csd_coefficient=coeff,
                                    mesh=self.mesh,
                                    boundary_potential=self.boundary_value,
@@ -64,6 +60,14 @@ def solve(self, xyz, csd):
         self.solution_interpolated = self.interpolator(verts_triangulation, sol)
         return solution
 
+    def solve(self, xyz, csd):
+        """
+        saves solution into self.solution as MFEM gridfunction and self.solution_interpolated for sampling at any point
+        """
+        coeff = csd_distribution_coefficient(xyz, csd)
+        return self.solve_coeff(coeff)
+
+
     def sample_solution_probe(self, x, y, z):
         return self.solution_interpolated([x, y, z])[0]