[1.3.23] 2024-11-19

*Context* - Still some lingering issues with Context::addTubeObject() in which tube creation could fail. *Visualizer* - Added warning in Visualizer::buildContextGeometry() if there is existing Context geometry already in the Visualizer that may have needed to be cleared. - When calling Visualizer::clearGeometry(), the colorbar range was not being reset, which could cause unexpected behavior. - Changed default lighting intensity to be brighter in order to better match the default behavior of 3rd party renderers such as Blender. - Added method Visualizer::setLightIntensityFactor() to allow users to adjust the intensity of the lighting in the scene. *Plant Architecture* - Some updates to bean, cowpea, and apple model parameters and assets. - Changed PlantArchitecture::buildPlantCanopyFromLibrary() to accept an optional argument specifying the germination rate. - Fixed error in which fruit could potentially become disconnected from their peducle over time. - Fixed error that was causing flowers not to open. - Added optional phenological parameter 'max_leaf_lifespan' to allow leaves to die based on age, which is especially important for evergreen plants. - Updates to carbohydrate model. Credit to Ethan Frehner *Photosynthesis* - Error corrected that could cause an incorrect temperature response depending on how model parameters are set. Thanks to Kyle Rizzo for this fix. - Added methods to disable output messages. *Stomatal Conductance* - Added methods to disable output messages. *Canopy Generator* - Error fixed when parsing XML files for strawberry canopies. Thanks to Heesup Yun for the fix. *Radiation* - Error corrected in the camera model related to the field of view and aspect ratio. Thanks to Peng Wei for this fix. Co-authored-by: Heesup Yun <[email protected]> Co-authored-by: Kyle Rizzo <[email protected]> Co-authored-by: Peng Wei <[email protected]> Co-authored-by: Ethan Frehner <[email protected]>
PlantSimulationLab · Nov 19, 2024 · 3f7de8a · 3f7de8a
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diff --git a/core/src/Context.cpp b/core/src/Context.cpp
@@ -3607,7 +3607,7 @@ void Tube::appendTubeSegment( const helios::vec3 &node_position, float node_radi
 
     for (int i = 0; i < node_count; i++) { // Looping over tube segments
         if (radius.at(i) < 0) {
-            helios_runtime_error("ERROR (Context::appendTubeSegment): Radius of tube must be positive.");
+            helios_runtime_error("ERROR (Context::addTubeObject): Radius of tube must be positive.");
         }
 
         if (i == 0) {
@@ -3628,10 +3628,18 @@ void Tube::appendTubeSegment( const helios::vec3 &node_position, float node_radi
             // Calculate radial direction using parallel transport
             vec3 rotation_axis = cross(previous_axial_vector, axial_vector);
             if (rotation_axis.magnitude() > 1e-6) {
-                float angle = acos(previous_axial_vector * axial_vector);
-                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, vec3(0.0f, 0.0f, 0.0f), rotation_axis, angle);
+                float angle = acos(std::clamp(previous_axial_vector * axial_vector, -1.0f, 1.0f));
+                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, nullorigin, rotation_axis, angle);
+            } else {
+                // Handle the case of nearly parallel vectors
+                // Ensure previous_radial_dir remains orthogonal to axial_vector
+                previous_radial_dir = cross(axial_vector, previous_radial_dir);
+                if (previous_radial_dir.magnitude() < 1e-6) {
+                    // If still degenerate, choose another orthogonal direction
+                    previous_radial_dir = cross(axial_vector, vec3(1.0f, 0.0f, 0.0f));
+                }
+                previous_radial_dir.normalize();
             }
-            previous_radial_dir.normalize();
         }
 
         previous_axial_vector = axial_vector;
@@ -3719,7 +3727,7 @@ void Tube::appendTubeSegment(const helios::vec3 &node_position, float node_radiu
 
     for (int i = 0; i < node_count; i++) { // Looping over tube segments
         if (radius.at(i) < 0) {
-            helios_runtime_error("ERROR (Context::appendTubeSegment): Radius of tube must be positive.");
+            helios_runtime_error("ERROR (Context::addTubeObject): Radius of tube must be positive.");
         }
 
         if (i == 0) {
@@ -3740,10 +3748,18 @@ void Tube::appendTubeSegment(const helios::vec3 &node_position, float node_radiu
             // Calculate radial direction using parallel transport
             vec3 rotation_axis = cross(previous_axial_vector, axial_vector);
             if (rotation_axis.magnitude() > 1e-6) {
-                float angle = acos(previous_axial_vector * axial_vector);
-                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, vec3(0.0f, 0.0f, 0.0f), rotation_axis, angle);
+                float angle = acos(std::clamp(previous_axial_vector * axial_vector, -1.0f, 1.0f));
+                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, nullorigin, rotation_axis, angle);
+            } else {
+                // Handle the case of nearly parallel vectors
+                // Ensure previous_radial_dir remains orthogonal to axial_vector
+                previous_radial_dir = cross(axial_vector, previous_radial_dir);
+                if (previous_radial_dir.magnitude() < 1e-6) {
+                    // If still degenerate, choose another orthogonal direction
+                    previous_radial_dir = cross(axial_vector, vec3(1.0f, 0.0f, 0.0f));
+                }
+                previous_radial_dir.normalize();
             }
-            previous_radial_dir.normalize();
         }
 
         previous_axial_vector = axial_vector;
@@ -4773,10 +4789,18 @@ uint Context::addTubeObject(uint radial_subdivisions, const std::vector<vec3> &n
             // Calculate radial direction using parallel transport
             vec3 rotation_axis = cross(previous_axial_vector, axial_vector);
             if (rotation_axis.magnitude() > 1e-6) {
-                float angle = acos(previous_axial_vector * axial_vector);
-                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, vec3(0.0f, 0.0f, 0.0f), rotation_axis, angle);
+                float angle = acos(std::clamp(previous_axial_vector * axial_vector, -1.0f, 1.0f));
+                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, nullorigin, rotation_axis, angle);
+            } else {
+                // Handle the case of nearly parallel vectors
+                // Ensure previous_radial_dir remains orthogonal to axial_vector
+                previous_radial_dir = cross(axial_vector, previous_radial_dir);
+                if (previous_radial_dir.magnitude() < 1e-6) {
+                    // If still degenerate, choose another orthogonal direction
+                    previous_radial_dir = cross(axial_vector, vec3(1.0f, 0.0f, 0.0f));
+                }
+                previous_radial_dir.normalize();
             }
-            previous_radial_dir.normalize();
         }
 
         previous_axial_vector = axial_vector;
@@ -4895,10 +4919,18 @@ uint Context::addTubeObject(uint radial_subdivisions, const std::vector<vec3> &n
             // Calculate radial direction using parallel transport
             vec3 rotation_axis = cross(previous_axial_vector, axial_vector);
             if (rotation_axis.magnitude() > 1e-6) {
-                float angle = acos(previous_axial_vector * axial_vector);
-                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, vec3(0.0f, 0.0f, 0.0f), rotation_axis, angle);
+                float angle = acos(std::clamp(previous_axial_vector * axial_vector, -1.0f, 1.0f));
+                previous_radial_dir = rotatePointAboutLine(previous_radial_dir, nullorigin, rotation_axis, angle);
+            } else {
+                // Handle the case of nearly parallel vectors
+                // Ensure previous_radial_dir remains orthogonal to axial_vector
+                previous_radial_dir = cross(axial_vector, previous_radial_dir);
+                if (previous_radial_dir.magnitude() < 1e-6) {
+                    // If still degenerate, choose another orthogonal direction
+                    previous_radial_dir = cross(axial_vector, vec3(1.0f, 0.0f, 0.0f));
+                }
+                previous_radial_dir.normalize();
             }
-            previous_radial_dir.normalize();
         }
 
         previous_axial_vector = axial_vector;

diff --git a/doc/CHANGELOG b/doc/CHANGELOG
@@ -1934,4 +1934,36 @@ The radiation model has been re-designed, with the following primary additions:
 - UTC offset variable changed from int to float type.
 
 *Visualizer*
-- Visualizer::printWindow() now creates the output directory if it does not already exist.
+- Visualizer::printWindow() now creates the output directory if it does not already exist.
+
+[1.3.23] 2024-11-19
+
+*Context*
+- Still some lingering issues with Context::addTubeObject() in which tube creation could fail.
+
+*Visualizer*
+- Added warning in Visualizer::buildContextGeometry() if there is existing Context geometry already in the Visualizer that may have needed to be cleared.
+- When calling Visualizer::clearGeometry(), the colorbar range was not being reset, which could cause unexpected behavior.
+- Changed default lighting intensity to be brighter in order to better match the default behavior of 3rd party renderers such as Blender.
+- Added method Visualizer::setLightIntensityFactor() to allow users to adjust the intensity of the lighting in the scene.
+
+*Plant Architecture*
+- Some updates to bean, cowpea, and apple model parameters and assets.
+- Changed PlantArchitecture::buildPlantCanopyFromLibrary() to accept an optional argument specifying the germination rate.
+- Fixed error in which fruit could potentially become disconnected from their peducle over time.
+- Fixed error that was causing flowers not to open.
+- Added optional phenological parameter 'max_leaf_lifespan' to allow leaves to die based on age, which is especially important for evergreen plants.
+- Updates to carbohydrate model. Credit to Ethan Frehner
+
+*Photosynthesis*
+- Error corrected that could cause an incorrect temperature response depending on how model parameters are set. Thanks to Kyle Rizzo for this fix.
+- Added methods to disable output messages.
+
+*Stomatal Conductance*
+- Added methods to disable output messages.
+
+*Canopy Generator*
+- Error fixed when parsing XML files for strawberry canopies. Thanks to Heesup Yun for the fix.
+
+*Radiation*
+- Error corrected in the camera model related to the field of view and aspect ratio. Thanks to Peng Wei for this fix.
diff --git a/doc/UserGuide.dox b/doc/UserGuide.dox
@@ -1,4 +1,4 @@
-/*! \mainpage Helios Documentation v1.3.22
+/*! \mainpage Helios Documentation v1.3.23
 
   <p> <br> </p>
 

diff --git a/doc/header.html b/doc/header.html
@@ -40,7 +40,7 @@
  <tr id="projectrow">
   <td id="projectlogo"><img alt="Logo" src="Helios_logo_small.png"/></td>
   <td id="projectalign">
-   <div id="projectname"><span id="projectnumber">&#160;v1.3.22</span>
+   <div id="projectname"><span id="projectnumber">&#160;v1.3.23</span>
    </div>
   </td>
  </tr>