From 486a8d1892d8cdbf9b641bf7991e040efd7fe957 Mon Sep 17 00:00:00 2001
From: Anthony Lombardi <anthony.lombardi@kitware.com>
Date: Thu, 1 Jun 2023 14:00:08 -0400
Subject: [PATCH] ENH: Add Support for loading mesh files

---
 libautoscoper/CMakeLists.txt |  8 +++++++-
 libautoscoper/src/Mesh.cpp   | 24 +++++++++++++++++++++++
 libautoscoper/src/Mesh.hpp   | 17 +++++++++++++++++
 libautoscoper/src/Trial.cpp  | 27 ++++++++++++++++++++++++++
 libautoscoper/src/Trial.hpp  | 37 ++++++++++++++++++++++--------------
 5 files changed, 98 insertions(+), 15 deletions(-)
 create mode 100644 libautoscoper/src/Mesh.cpp
 create mode 100644 libautoscoper/src/Mesh.hpp

diff --git a/libautoscoper/CMakeLists.txt b/libautoscoper/CMakeLists.txt
index e615f044..9db43b73 100644
--- a/libautoscoper/CMakeLists.txt
+++ b/libautoscoper/CMakeLists.txt
@@ -33,7 +33,13 @@ set(libautoscoper_SOURCES
   src/VolumeTransform.cpp
 )
 
-if(Autoscoper_COLLISION_DETECTION) # Add collision detection sources
+if(Autoscoper_COLLISION_DETECTION) # Add collision detection sources/headers
+  list(APPEND libautoscoper_SOURCES
+    src/Mesh.cpp
+  )
+  list(APPEND libautoscoper_HEADERS
+    src/Mesh.hpp
+  )
 endif()
 
 if(Autoscoper_RENDERING_BACKEND STREQUAL "CUDA")
diff --git a/libautoscoper/src/Mesh.cpp b/libautoscoper/src/Mesh.cpp
new file mode 100644
index 00000000..261118b2
--- /dev/null
+++ b/libautoscoper/src/Mesh.cpp
@@ -0,0 +1,24 @@
+#include "Mesh.hpp"
+#include <vtkSTLReader.h>
+#include <vtkSTLWriter.h>
+
+Mesh::Mesh(const std::string& filename) {
+  vtkSTLReader* reader = vtkSTLReader::New();
+  reader->SetFileName(filename.c_str());
+  reader->Update();
+  this->polyData = reader->GetOutput();
+  reader->Delete();
+}
+
+Mesh::Mesh(const Mesh& other) {
+  this->polyData = vtkPolyData::New();
+  this->polyData->DeepCopy(other.polyData);
+}
+
+void Mesh::Write(const std::string& filename) const {
+  vtkSTLWriter* writer = vtkSTLWriter::New();
+  writer->SetFileName(filename.c_str());
+  writer->SetInputData(this->polyData);
+  writer->Write();
+  writer->Delete();
+}
diff --git a/libautoscoper/src/Mesh.hpp b/libautoscoper/src/Mesh.hpp
new file mode 100644
index 00000000..baf98001
--- /dev/null
+++ b/libautoscoper/src/Mesh.hpp
@@ -0,0 +1,17 @@
+#pragma once
+#include <string>
+#include <vtkPolyData.h>
+
+class Mesh {
+public:
+	Mesh(const std::string& filename);
+	Mesh(const Mesh&);
+
+	vtkPolyData* GetPolyData() const { return this->polyData; }
+
+	void Write(const std::string& filename) const;
+
+private:
+
+	vtkPolyData* polyData;
+};
\ No newline at end of file
diff --git a/libautoscoper/src/Trial.cpp b/libautoscoper/src/Trial.cpp
index 651695ee..dde967d2 100644
--- a/libautoscoper/src/Trial.cpp
+++ b/libautoscoper/src/Trial.cpp
@@ -75,6 +75,7 @@ namespace xromm
     std::vector<std::string> volumeFlips;
     std::vector<std::string> renderResolution;
     std::vector<std::string> optimizationOffsets;
+    std::vector<std::string> meshFiles;
 
     std::string line, key, value;
     while (getline(file, line)) {
@@ -114,6 +115,10 @@ namespace xromm
         getline(lineStream, value);
         optimizationOffsets.push_back(value);
       }
+      else if (key.compare("MeshFile") == 0) {
+        getline(lineStream, value);
+        meshFiles.push_back(value);
+      }
     }
 
     // Close the file.
@@ -132,6 +137,9 @@ namespace xromm
     if (volumeFiles.size() != voxelSizes.size()) {
       throw std::runtime_error("You must sepcify a voxels size for each volume.");
     }
+    if (meshFiles.size() != 0 && volumeFiles.size() != meshFiles.size()) {
+      throw std::runtime_error("You must sepcify a mesh file for each volume or none at all.");
+    }
 
     cameras.clear();
     for (unsigned int i = 0; i < mayaCams.size(); ++i) {
@@ -179,6 +187,25 @@ namespace xromm
       }
     }
 
+    // load in mesh files if they exist
+    if (meshFiles.size() > 0) {
+#ifdef Autoscoper_COLLISION_DETECTION
+      meshes.clear();
+      for (unsigned int i = 0; i < meshFiles.size(); ++i) {
+        try {
+          Mesh mesh(meshFiles[i]);
+          meshes.push_back(mesh);
+        }
+        catch (std::exception& e) {
+          std::cerr << e.what() << std::endl;
+        }
+      }
+#else
+      std::cerr << "WARNING: Autoscoper was not compiled with collision detection support.  No mesh files will be loaded." << std::endl;
+#endif // Autoscoper_COLLISION_DETECTION
+    }
+
+
     int maxVideoFrames = 0;
     videos.clear();
     for (unsigned int i = 0; i < camRootDirs.size(); ++i) {
diff --git a/libautoscoper/src/Trial.hpp b/libautoscoper/src/Trial.hpp
index c0e5fb8a..2cb6bb27 100644
--- a/libautoscoper/src/Trial.hpp
+++ b/libautoscoper/src/Trial.hpp
@@ -52,6 +52,11 @@
 #include "Volume.hpp"
 #include "VolumeTransform.hpp"
 
+#ifdef Autoscoper_COLLISION_DETECTION
+#include "Mesh.hpp"
+#endif // Autoscoper_COLLISION_DETECTION
+
+
 namespace xromm
 {
 // The trial class contains all of the state information for an autoscoper run.
@@ -63,28 +68,32 @@ class Trial
 {
 public:
 
-    // Loads a trial file
+  // Loads a trial file
 
-    Trial(const std::string& filename = "");
+  Trial(const std::string& filename = "");
 
-    void save(const std::string& filename);
+  void save(const std::string& filename);
 
-    std::vector<Camera> cameras;
-    std::vector<Video>  videos;
-    std::vector<Volume> volumes;
+  std::vector<Camera> cameras;
+  std::vector<Video>  videos;
+  std::vector<Volume> volumes;
   std::vector<VolumeTransform> volumestransform;
+#ifdef Autoscoper_COLLISION_DETECTION
+  std::vector<Mesh> meshes;
+#endif // Autoscoper_COLLISION_DETECTION
+
 
-    // State information
-    int frame;
-    int num_frames;
+  // State information
+  int frame;
+  int num_frames;
   int current_volume;
   int num_volumes;
 
-    //Controls for the optimization process
-    int guess;
-    double offsets[6];
-    int render_width;
-    int render_height;
+  //Controls for the optimization process
+  int guess;
+  double offsets[6];
+  int render_width;
+  int render_height;
 
   KeyCurve * getXCurve(int volumeID);
   KeyCurve * getYCurve(int volumeID);