From 5d9b31eea0a255a3c1d9a35aa817be3fe434a7a8 Mon Sep 17 00:00:00 2001
From: Guillaume Cerutti <guillaume.cerutti@inria.fr>
Date: Thu, 28 Mar 2024 12:19:56 +0100
Subject: [PATCH] add cgal image building function
---
CMakeLists.txt | 14 +++++-----
cpp/CMakeLists.txt | 3 +++
cpp/CgalLabelledImage.cpp | 26 +++++++++++++++++++
cpp/CgalLabelledImage.h | 8 ++++++
.../labelled_tetrahedral_mesh.py | 9 ++++++-
wrp/LabelledTetrahedralMeshWrapper.cpp | 3 +++
6 files changed, 54 insertions(+), 9 deletions(-)
create mode 100644 cpp/CgalLabelledImage.cpp
create mode 100644 cpp/CgalLabelledImage.h
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4148520..8567691 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,14 +22,12 @@ find_package(Eigen3 3.3 REQUIRED NO_MODULE)
# make cache variables for install destinations
include(GNUInstallDirs)
-if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
- if (DEFINED ENV{CONDA_PREFIX})
- set(CMAKE_INSTALL_LIBDIR "lib")
- set(CMAKE_INSTALL_PREFIX "$ENV{CONDA_PREFIX}")
- else()
- set(CMAKE_INSTALL_PREFIX "${CMAKE_SOURCE_DIR}/install")
- endif()
-endif(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+if (DEFINED ENV{CONDA_PREFIX})
+ set(CMAKE_INSTALL_LIBDIR "lib")
+ set(CMAKE_INSTALL_PREFIX "$ENV{CONDA_PREFIX}")
+else()
+ set(CMAKE_INSTALL_PREFIX "${CMAKE_SOURCE_DIR}/install")
+endif()
add_subdirectory(cpp)
add_subdirectory(wrp)
diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
index 8c0ddac..80a241c 100644
--- a/cpp/CMakeLists.txt
+++ b/cpp/CMakeLists.txt
@@ -1,9 +1,12 @@
project(_cpp)
add_library(_cpp SHARED
+ CgalLabelledImage.h
LabelledTetrahedralMesh.h
+ CgalLabelledImage.cpp
LabelledTetrahedralMesh.cpp
)
target_link_libraries(_cpp PUBLIC Eigen3::Eigen)
+target_link_libraries(_cpp PUBLIC CGAL::CGAL)
install(TARGETS _cpp DESTINATION "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
\ No newline at end of file
diff --git a/cpp/CgalLabelledImage.cpp b/cpp/CgalLabelledImage.cpp
new file mode 100644
index 0000000..aa7dd2b
--- /dev/null
+++ b/cpp/CgalLabelledImage.cpp
@@ -0,0 +1,26 @@
+#include <iostream>
+
+#include "CgalLabelledImage.h"
+
+
+int buildCgalImage(Eigen::Array<unsigned short, Eigen::Dynamic, 1> image_array, Eigen::Array<int, 3, 1> shape, Eigen::Array<double, 3, 1> voxelsize)
+{
+ _image* image = _createImage(
+ shape(0), shape(1), shape(2), 1,
+ voxelsize(0), voxelsize(1), voxelsize(2), 2,
+ WK_FIXED, SGN_UNSIGNED
+ );
+
+ auto it = image_array.begin();
+ for (int x=0; x<shape(0); x++) {
+ for (int y=0; y<shape(1); y++) {
+ for (int z=0; z<shape(2); z++) {
+ CGAL::IMAGEIO::static_evaluate<unsigned short>(image, x, y, z) = *it;
+ ++it;
+ }
+ }
+ }
+ CGAL::Image_3 cgal_image(image);
+
+ return 0;
+}
diff --git a/cpp/CgalLabelledImage.h b/cpp/CgalLabelledImage.h
new file mode 100644
index 0000000..8a8200d
--- /dev/null
+++ b/cpp/CgalLabelledImage.h
@@ -0,0 +1,8 @@
+#pragma once
+
+#include <CGAL/Image_3.h>
+
+#include <Eigen/Dense>
+
+
+int buildCgalImage(Eigen::Array<unsigned short, Eigen::Dynamic, 1> image_array, Eigen::Array<int, 3, 1> shape, Eigen::Array<double, 3, 1> voxelsize={1.0, 1.0, 1.0});
\ No newline at end of file
diff --git a/src/pybind_example/labelled_tetrahedral_mesh.py b/src/pybind_example/labelled_tetrahedral_mesh.py
index 7014b32..ce7b8b7 100644
--- a/src/pybind_example/labelled_tetrahedral_mesh.py
+++ b/src/pybind_example/labelled_tetrahedral_mesh.py
@@ -1 +1,8 @@
-from ._wrp import LabelledTetrahedralMesh, make_tetrahedron
\ No newline at end of file
+import numpy as np
+
+from ._wrp import LabelledTetrahedralMesh, make_tetrahedron
+from ._wrp import build_cgal_image as _build_cgal_image
+
+
+def build_cgal_image(img: np.ndarray) -> bool:
+ return _build_cgal_image(img.ravel().astype(np.uint16), img.shape, [1., 1., 1.])
diff --git a/wrp/LabelledTetrahedralMeshWrapper.cpp b/wrp/LabelledTetrahedralMeshWrapper.cpp
index 8fcc884..6c9a1a6 100644
--- a/wrp/LabelledTetrahedralMeshWrapper.cpp
+++ b/wrp/LabelledTetrahedralMeshWrapper.cpp
@@ -2,6 +2,7 @@
#include <pybind11/stl.h> // This header is needed to work with STL containers like std::vector
#include <pybind11/eigen.h>
+#include "CgalLabelledImage.h"
#include "LabelledTetrahedralMesh.h"
namespace py = pybind11;
@@ -16,4 +17,6 @@ PYBIND11_MODULE(_wrp, m) {
.def("add_tetra", &LabelledTetrahedralMesh::addTetra, py::arg("tetra"), py::arg("label"));
m.def("make_tetrahedron", &makeTetrahedron);
+
+ m.def("build_cgal_image", &buildCgalImage, py::arg("image_array"), py::arg("shape"), py::arg("voxelsize"));
}
\ No newline at end of file
--
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