From b9444d1b532437e3ddec6cf9d33d5288f1435cb5 Mon Sep 17 00:00:00 2001
From: Simone <simone.poncioni@gmail.com>
Date: Mon, 8 Jan 2024 15:16:11 +0100
Subject: [PATCH] adapted for hfe-accurate branch merge

---
 src/pyhexspline/gmsh_mesh_builder.py |  2 +-
 src/pyhexspline/spline_volume.py     |  4 ++++
 standalone.py                        | 14 ++++++++------
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/src/pyhexspline/gmsh_mesh_builder.py b/src/pyhexspline/gmsh_mesh_builder.py
index 01edc38..352172b 100644
--- a/src/pyhexspline/gmsh_mesh_builder.py
+++ b/src/pyhexspline/gmsh_mesh_builder.py
@@ -1170,7 +1170,7 @@ def sort_trab_coords(self, point_tags):
         )  # split every x, y, z coordinate
 
         # sort the sub-arrays in counterclockwise order
-        point_tags_sorted0 = self.sort_ccw(coords_split[0])  # ! HERE
+        point_tags_sorted0 = self.sort_ccw(coords_split[0])
         # for each sub-array point_tags, sort the points with point_tags_sorted0
         point_tags_sorted = [
             point_tags[point_tags_sorted0] for point_tags in point_tags
diff --git a/src/pyhexspline/spline_volume.py b/src/pyhexspline/spline_volume.py
index 14bb631..13dcebf 100644
--- a/src/pyhexspline/spline_volume.py
+++ b/src/pyhexspline/spline_volume.py
@@ -12,10 +12,14 @@
 import SimpleITK as sitk
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from scipy.interpolate import splev, splprep
+import matplotlib
+
 
 LOGGING_NAME = "MESHING"
 # flake8: noqa: E203
 
+matplotlib.use("TkAgg")
+
 
 class OCC_volume:
     def __init__(
diff --git a/standalone.py b/standalone.py
index 4d9f822..a4e3691 100644
--- a/standalone.py
+++ b/standalone.py
@@ -4,13 +4,15 @@
 Date: 09.2022 - Ongoing
 """
 
-import os
 import logging
-from src.pyhexspline.spline_mesher import HexMesh
-import hfe_input_transformer as transformer
+import os
+
 import coloredlogs
 import numpy as np
 
+import hfe_input_transformer as transformer
+from src.pyhexspline.spline_mesher import HexMesh
+
 # flake8: noqa: E501
 
 
@@ -51,9 +53,9 @@ def main():
         "thickness_tol": 5e-1,  # minimum cortical thickness tolerance: 3 * XCTII voxel size
         "phases": 2,  # 1: only external contour, 2: external and internal contour
         "center_square_length_factor": 0.4,  # size ratio of the refinement square: 0 < l_f < 1
-        "n_elms_longitudinal": 4,  # number of elements in the longitudinal direction
-        "n_elms_transverse_trab": 12,  # number of elements in the transverse direction for the trabecular compartment
-        "n_elms_transverse_cort": 3,  # number of elements in the transverse direction for the cortical compartment
+        "n_elms_longitudinal": 3,  # number of elements in the longitudinal direction
+        "n_elms_transverse_trab": 10,  # number of elements in the transverse direction for the trabecular compartment
+        "n_elms_transverse_cort": 4,  # number of elements in the transverse direction for the cortical compartment
         "n_elms_radial": 10,  # number of elements in the radial direction # ! Should be 10 if trab_refinement is True
         "mesh_order": 1,  # set order of the mesh (1: linear, 2: quadratic)
         "ellipsoid_fitting": True,  # True: perform ellipsoid fitting