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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: d5fcdde67471bfee017155e49d79be32
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/configuration.doctree b/.doctrees/configuration.doctree
diff --git a/.doctrees/contributing.doctree b/.doctrees/contributing.doctree
diff --git a/.doctrees/cortical_sanity.doctree b/.doctrees/cortical_sanity.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/getting_started.doctree b/.doctrees/getting_started.doctree
diff --git a/.doctrees/gmsh_mesh_builder.doctree b/.doctrees/gmsh_mesh_builder.doctree
diff --git a/.doctrees/hr_pqct_meshing.doctree b/.doctrees/hr_pqct_meshing.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/installation.doctree b/.doctrees/installation.doctree
diff --git a/.doctrees/quad_refinement.doctree b/.doctrees/quad_refinement.doctree
diff --git a/.doctrees/spline_mesher.doctree b/.doctrees/spline_mesher.doctree
diff --git a/.doctrees/spline_volume.doctree b/.doctrees/spline_volume.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/_modules/cortical_sanity.html b/_modules/cortical_sanity.html
diff --git a/_modules/gmsh_mesh_builder.html b/_modules/gmsh_mesh_builder.html
diff --git a/_modules/index.html b/_modules/index.html
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+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; PyHexSpline 0.2.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
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+            PyHexSpline
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+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
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+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../getting_started.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../hr_pqct_meshing.html">HR-pQCT Structured Hexahedral Meshing</a></li>
+</ul>
+
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+      <li class="breadcrumb-item active">Overview: module code</li>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="cortical_sanity.html">cortical_sanity</a></li>
+<li><a href="gmsh_mesh_builder.html">gmsh_mesh_builder</a></li>
+<li><a href="quad_refinement.html">quad_refinement</a></li>
+<li><a href="spline_mesher.html">spline_mesher</a></li>
+<li><a href="spline_volume.html">spline_volume</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
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+  <hr/>
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+  <div role="contentinfo">
+    <p>&#169; Copyright 2023, Simone Poncioni.</p>
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diff --git a/_modules/quad_refinement.html b/_modules/quad_refinement.html
diff --git a/_modules/spline_mesher.html b/_modules/spline_mesher.html
diff --git a/_modules/spline_volume.html b/_modules/spline_volume.html
diff --git a/_sources/configuration.rst.txt b/_sources/configuration.rst.txt
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+Configuration
+=============
+
+This section provides the configuration settings for the spline-mesher project.
+
+Image Settings
+--------------
+
+The following settings are used to configure the image paths and filenames:
+
+- **img_basefilename**: Base filename for the images. For example `"C0001234"`.
+- **img_basepath**: Base path for the images. Default is the current working directory concatenated with `"/01_AIM"`.
+- **meshpath**: Path where the mesh files are stored. Default is the current working directory concatenated with `"/03_MESH"`.
+- **outputpath**: Path where the output files are stored. Default is the current working directory concatenated with `"/04_OUTPUT"`.
+
+Meshing Settings
+----------------
+
+The following settings are used to configure the meshing process:
+
+- **aspect**: Aspect ratio of the plots. Default is `100`.
+- **_slice**: Slice of the image to be plotted. Default is `1`.
+- **undersampling**: Undersampling factor of the image. Default is `1`.
+- **slicing_coefficient**: Using every nth slice of the image for the spline reconstruction. Default is `20`.
+- **inside_val**: Threshold value for the inside of the mask. Default is `0`.
+- **outside_val**: Threshold value for the outside of the mask. Default is `1`.
+- **lower_thresh**: Lower threshold for the mask. Default is `0.0`.
+- **upper_thresh**: Upper threshold for the mask. Default is `0.9`.
+- **s**: Smoothing factor of the spline. Default is `500`.
+- **k**: Degree of the spline. Default is `3`.
+- **interp_points**: Number of points to interpolate the spline. Default is `1000`.
+- **dp_simplification_outer**: Ramer-Douglas-Peucker simplification factor for the periosteal contour. Default is `5`.
+- **dp_simplification_inner**: Ramer-Douglas-Peucker simplification factor for the endosteal contour. Default is `5`.
+- **thickness_tol**: Minimum cortical thickness tolerance. Default is `1`.
+- **phases**: Number of phases for contouring. Default is `2` (1: only external contour, 2: external and internal contour).
+- **center_square_length_factor**: Size ratio of the refinement square. Default is `0.4`.
+- **mesh_order**: Element order for the mesh. Default is `1` (1: linear, 2: quadratic, >2: higher order, not tested).
+- **n_elms_longitudinal**: Number of elements in the longitudinal direction. Default is `3`.
+- **n_elms_transverse_trab**: Number of elements in the transverse direction for the trabecular compartment. Default is `15`.
+- **n_elms_transverse_cort**: Number of elements in the transverse direction for the cortical compartment. Default is `3`.
+- **n_elms_radial**: Number of elements in the radial direction. Default is `20`.
+  - Note: Should be `10` if `trab_refinement` is `True`.
+- **ellipsoid_fitting**: Perform ellipsoid fitting in the inner trabecular compartment. Default is `True`.
+- **show_plots**: Show plots during construction. Default is `False`.
+- **show_gmsh**: Show GMSH GUI. Default is `False`.
+- **write_mesh**: Write mesh to file. Default is `True`.
+- **trab_refinement**: Refine trabecular mesh at the center. Default is `False`.
+  - Note: Should be set to `False` if `ellipsoid_fitting` is `True`.
+- **mesh_analysis**: Perform mesh analysis (plot JAC det in GMSH GUI). Default is `True`.
diff --git a/_sources/contributing.rst.txt b/_sources/contributing.rst.txt
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+Contributing
+------------
+
+Contributions are what make the open source community such an amazing
+place to learn, inspire, and create. Any contributions you make are
+**greatly appreciated**.
+
+If you have a suggestion that would make this better, please fork the
+repo and create a pull request. You can also simply open an issue with
+the tag “enhancement”. Don’t forget to give the project a star! Thanks
+again!
+
+1. Fork the Project
+2. Create your Feature Branch
+   (``git checkout -b feature/AmazingFeature``)
+3. Commit your Changes (``git commit -m 'Add some AmazingFeature'``)
+4. Push to the Branch (``git push origin feature/AmazingFeature``)
+5. Open a Pull Request
diff --git a/_sources/cortical_sanity.rst.txt b/_sources/cortical_sanity.rst.txt
@@ -0,0 +1,7 @@
+cortical\_sanity module
+=======================
+
+.. automodule:: cortical_sanity
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/getting_started.rst.txt b/_sources/getting_started.rst.txt
@@ -0,0 +1,9 @@
+Getting Started
+===============
+
+.. toctree::
+   :maxdepth: 2
+
+   installation
+   configuration
+   contributing
diff --git a/_sources/gmsh_mesh_builder.rst.txt b/_sources/gmsh_mesh_builder.rst.txt
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+gmsh\_mesh\_builder module
+==========================
+
+.. automodule:: gmsh_mesh_builder
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/hr_pqct_meshing.rst.txt b/_sources/hr_pqct_meshing.rst.txt
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+HR-pQCT Structured Hexahedral Meshing
+=====================================
+
+.. toctree::
+   :maxdepth: 4
+
+   cortical_sanity
+   gmsh_mesh_builder
+   spline_volume
+   spline_mesher
+   quad_refinement
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -0,0 +1,22 @@
+.. spline-mesher documentation master file, created by
+   sphinx-quickstart on Sun Mar  5 23:08:13 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to PyHexSpline's documentation!
+=========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   getting_started
+   hr_pqct_meshing
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt
@@ -0,0 +1,25 @@
+Installation
+============
+
+1. Clone the repo
+
+   .. code:: sh
+
+      git clone https://github.com/simoneponcioni/spline-mesher.git
+
+2. Install dependencies
+
+   .. code:: sh
+
+      conda create -n meshenv python=3.9 --file requirements.txt
+      conda activate meshenv
+      python setup.py build_ext --inplace
+      python setup.py install
+
+3. For developers: install the package in editable mode and install
+   requirements for testing
+
+   .. code:: sh
+
+      pip install -e .
+      pip install -r requirements-dev.txt
diff --git a/_sources/quad_refinement.rst.txt b/_sources/quad_refinement.rst.txt
@@ -0,0 +1,7 @@
+quad_refinement module
+======================
+
+.. automodule:: quad_refinement
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/spline_mesher.rst.txt b/_sources/spline_mesher.rst.txt
@@ -0,0 +1,7 @@
+spline_mesher module
+=======================
+
+.. automodule:: spline_mesher
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/spline_volume.rst.txt b/_sources/spline_volume.rst.txt
@@ -0,0 +1,7 @@
+spline_volume module
+=======================
+
+.. automodule:: spline_volume
+   :members:
+   :undoc-members:
+   :show-inheritance: