From fd0e1bafef06e1d00d157639fbd1d82c12ea94cc Mon Sep 17 00:00:00 2001
From: nawazishkhan1-nk <nawazishkhan1.nk@gmail.com>
Date: Wed, 9 Oct 2024 12:28:42 -0600
Subject: [PATCH] rebase changes

---
 Libs/Particles/ParticleShapeStatistics.cpp |  2 ++
 Studio/Analysis/AnalysisTool.cpp           |  2 +-
 Studio/Data/Session.cpp                    |  2 +-
 Studio/Interface/ShapeWorksStudioApp.cpp   |  4 ++--
 Studio/Optimize/OptimizeTool.h             |  2 +-
 Studio/Optimize/OptimizeTool.ui            | 10 ++++++++++
 6 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/Libs/Particles/ParticleShapeStatistics.cpp b/Libs/Particles/ParticleShapeStatistics.cpp
index 288eae4a44..aa6d8c008b 100644
--- a/Libs/Particles/ParticleShapeStatistics.cpp
+++ b/Libs/Particles/ParticleShapeStatistics.cpp
@@ -694,4 +694,6 @@ Eigen::MatrixXd ParticleShapeStatistics::get_group1_matrix() const { return grou
 //---------------------------------------------------------------------------
 Eigen::MatrixXd ParticleShapeStatistics::get_group2_matrix() const { return group2_matrix_; }
 
+
+
 }  // namespace shapeworks
diff --git a/Studio/Analysis/AnalysisTool.cpp b/Studio/Analysis/AnalysisTool.cpp
index 6119d9cccb..5896cf7187 100644
--- a/Studio/Analysis/AnalysisTool.cpp
+++ b/Studio/Analysis/AnalysisTool.cpp
@@ -869,7 +869,7 @@ void AnalysisTool::store_settings() {
   params.set("network_pvalue_of_interest", ui_->network_pvalue_of_interest->text().toStdString());
   params.set("network_pvalue_threshold", ui_->network_pvalue_threshold->text().toStdString());
 
-  params.set("regression_slope", session->)
+  // params.set("regression_slope", session->)
 
   session_->get_project()->set_parameters(Parameters::ANALYSIS_PARAMS, params);
 }
diff --git a/Studio/Data/Session.cpp b/Studio/Data/Session.cpp
index c79528a74b..36b3d6ba2b 100644
--- a/Studio/Data/Session.cpp
+++ b/Studio/Data/Session.cpp
@@ -837,7 +837,7 @@ void Session::new_plane_point(PickResult result) {
 //---------------------------------------------------------------------------
 QString Session::get_filename() { return filename_; }
 
-QString Session::get_parent_dir()
+// QString Session::get_parent_dir()
 
 //---------------------------------------------------------------------------
 int Session::get_num_shapes() { return shapes_.size(); }
diff --git a/Studio/Interface/ShapeWorksStudioApp.cpp b/Studio/Interface/ShapeWorksStudioApp.cpp
index 7f58d3f812..b312dea14e 100644
--- a/Studio/Interface/ShapeWorksStudioApp.cpp
+++ b/Studio/Interface/ShapeWorksStudioApp.cpp
@@ -1532,8 +1532,8 @@ void ShapeWorksStudioApp::open_project(QString filename) {
   if (optimize_tool_->get_regression_analysis_status())
   {
     // Verify if slope and intercept files exist
-    auto particles_dir = session_->get_filename().dir().absolutePath().toStdString();
-    auto slope_filename = session_->get_filename().toStdString()
+    // auto particles_dir = session_->get_filename().dir().absolutePath().toStdString();
+    // auto slope_filename = session_->get_filename().toStdString();
   }
   analysis_tool_->store_settings();
   update_from_preferences();
diff --git a/Studio/Optimize/OptimizeTool.h b/Studio/Optimize/OptimizeTool.h
index f88e322626..cab850aa3f 100644
--- a/Studio/Optimize/OptimizeTool.h
+++ b/Studio/Optimize/OptimizeTool.h
@@ -39,7 +39,7 @@ Q_OBJECT;
   //! Store params to project
 
   //! Get flag if regression needs to enabled for analysis in Studio
-  inline bool get_regression_analysis_status() { return regression_analysis_status; }
+  inline bool get_regression_analysis_status() { return regression_analysis_status_; }
 
   void store_params();
 
diff --git a/Studio/Optimize/OptimizeTool.ui b/Studio/Optimize/OptimizeTool.ui
index 92fcf61bd6..f741c6c05e 100644
--- a/Studio/Optimize/OptimizeTool.ui
+++ b/Studio/Optimize/OptimizeTool.ui
@@ -881,6 +881,16 @@ QWidget#optimize_panel {
                  </property>
                 </widget>
                </item>
+               <item row="8" column="2">
+                <widget class="QLineEdit" name="geodesic_remesh_percent">
+                 <property name="text">
+                  <string>100</string>
+                 </property>
+                 <property name="alignment">
+                  <set>Qt::AlignCenter</set>
+                 </property>
+                </widget>
+               </item>
                <item row="22" column="2">
                 <widget class="QWidget" name="linear_regression_widget" native="true">
                  <layout class="QGridLayout" name="gridLayout_18">