[1.3.39] 2025-07-09

- More minor documentation fixes.

- Implemented some improvements for file path handling on Windows systems to improve robustness.
- Added *= and /= operators for `helios::vec2`, `helios::vec3` and `helios::vec4` vector types.

- Fixed 'haloing' around text.
- Efficiency of changing the visualization type was improved (e.g., via `Visualizer::colorContextPrimitivesByData()` or `Visualizer::colorContextObjectsByData()`), whereby only the color data is changed rather than rebuilding the entire geometry.
- Added `Visualizer::deleteGeometry()` method to delete a geometric element based on its ID.
- The visualizer window can now be freely resized with arbitrary aspect ratio, including making the visualizer window full screen.

- Console now auto-scrolls to the bottom when new text is added.
- Disabled keyboard controls so that rotating the view via keyboard does not conflict.

- There was an unhandled error when the combination of `leaves_per_petiole` and `leaflet_offset` are too large such that there is no more space along the petiole to place leaflets. There was a similar issue with flowers for the parameters `flowers_per_peduncle` and `flower_offset`, potentially resulting in too many flowers per peduncle.
- Fixed a minor issue where the max leaf age was not properly enforced when the plant hits its maximum age and stops growing.

- Changed how the camera image post-processing pipeline works. It now applies global histogram equalization, followed by an optional saturation, brightness, and contrast adjustment.

- Added documentation page.

- Added optional output primitive data to write stomatal conductance model parameters to primitive data.

Author: bnbailey-psl

.clang-format

@@ -30,6 +30,7 @@ BreakConstructorInitializers: AfterColon
 BreakConstructorInitializersBeforeComma: false
 ColumnLimit: 250
 PenaltyBreakString: 1000
+BreakStringLiterals: false
 ConstructorInitializerAllOnOneLineOrOnePerLine: false
 ContinuationIndentWidth: 8
 IncludeCategories: 

core/include/helios_vector_types.h

@@ -748,6 +748,10 @@ namespace helios {
         inline vec2 &operator+=(const vec2 &a) noexcept;
         //! Decrement vec2 vector
         inline vec2 &operator-=(const vec2 &a) noexcept;
+        //! Multiplication assignment operator for vec2 vector
+        inline vec2 &operator*=(float a) noexcept;
+        //! Division assignment operator for vec2 vector
+        inline vec2 &operator/=(float a) noexcept;
         //! Difference of two vec2 vectors noexcept
         constexpr vec2 operator-(const vec2 &a) const noexcept;
         //! Multiply each element by scalar (scalar is multiplied on right: vec2*a)
@@ -814,6 +818,18 @@ namespace helios {
         return *this;
     }
 
+    inline vec2 &vec2::operator*=(float a) noexcept {
+        x *= a;
+        y *= a;
+        return *this;
+    }
+
+    inline vec2 &vec2::operator/=(float a) noexcept {
+        x /= a;
+        y /= a;
+        return *this;
+    }
+
     constexpr vec2 vec2::operator+(const float a) const noexcept {
         return {a + x, a + y};
     }
@@ -924,6 +940,10 @@ namespace helios {
         inline vec3 &operator+=(const vec3 &a) noexcept;
         //! Decrement vec3 vector
         inline vec3 &operator-=(const vec3 &a) noexcept;
+        //! Multiplication assignment operator for vec3 vector
+        inline vec3 &operator*=(float a) noexcept;
+        //! Division assignment operator for vec2 vector
+        inline vec3 &operator/=(float a) noexcept;
         //! Difference of two vec3 vectors
         constexpr vec3 operator-(const vec3 &a) const noexcept;
         //! Multiply each element by scalar (scalar is multiplied on right: vec3*a)
@@ -997,6 +1017,20 @@ namespace helios {
         return *this;
     }
 
+    inline vec3 &vec3::operator*=(float a) noexcept {
+        x *= a;
+        y *= a;
+        z *= a;
+        return *this;
+    }
+
+    inline vec3 &vec3::operator/=(float a) noexcept {
+        x /= a;
+        y /= a;
+        z /= a;
+        return *this;
+    }
+
     constexpr vec3 vec3::operator+(float a) const noexcept {
         return {x + a, y + a, z + a};
     }
@@ -1112,6 +1146,10 @@ namespace helios {
         inline vec4 &operator+=(const vec4 &a) noexcept;
         //! Decrement vec4 vector
         inline vec4 &operator-=(const vec4 &a) noexcept;
+        //! Multiplication assignment operator for vec4 vector
+        inline vec4 &operator*=(float a) noexcept;
+        //! Division assignment operator for vec4 vector
+        inline vec4 &operator/=(float a) noexcept;
         //! Difference of two vec4 vectors
         constexpr vec4 operator-(const vec4 &a) const noexcept;
         //! Multiply each element by scalar (scalar is multiplied on right: vec4*a)
@@ -1182,6 +1220,22 @@ namespace helios {
         return *this;
     }
 
+    inline vec4 &vec4::operator*=(float a) noexcept {
+        x *= a;
+        y *= a;
+        z *= a;
+        w *= a;
+        return *this;
+    }
+
+    inline vec4 &vec4::operator/=(float a) noexcept {
+        x /= a;
+        y /= a;
+        z /= a;
+        w /= a;
+        return *this;
+    }
+
     constexpr vec4 vec4::operator+(float a) const noexcept {
         return {x + a, y + a, z + a, w + a};
     }

core/src/Context_fileIO.cpp

@@ -3936,7 +3936,8 @@ void Context::writeOBJ(const std::string &filename, const std::vector<uint> &UUI
         mtlfilename.append(".mtl");
     } else {
         if (!file_path.empty()) {
-            mtlfilename = file_path + "/" + file_stem + ".mtl";
+            std::filesystem::path mtl_path = std::filesystem::path(file_path) / (file_stem + ".mtl");
+            mtlfilename = mtl_path.string();
         } else {
             mtlfilename = file_stem + ".mtl";
         }
@@ -4119,12 +4120,12 @@ void Context::writeOBJ(const std::string &filename, const std::vector<uint> &UUI
     }
 
     // copy material textures to new directory and edit old file paths
-    std::string texture_dir = std::string(file_path);
+    std::filesystem::path texture_dir = std::filesystem::path(file_path);
     for (auto &material: materials) {
         std::string texture = material.texture;
         if (!texture.empty() && std::filesystem::exists(texture)) {
             auto file = std::filesystem::path(texture).filename();
-            std::filesystem::copy_file(texture, texture_dir + file.string(), std::filesystem::copy_options::overwrite_existing);
+            std::filesystem::copy_file(texture, texture_dir / file, std::filesystem::copy_options::overwrite_existing);
             material.texture = file.string();
         }
     }
@@ -4250,7 +4251,8 @@ void Context::writeOBJ(const std::string &filename, const std::vector<uint> &UUI
 
 
         for (const std::string &label: primitive_dat_fields) {
-            std::string datfilename = file_path + file_stem + "_" + std::string(label) + ".dat";
+            std::filesystem::path dat_path = std::filesystem::path(file_path) / (file_stem + "_" + std::string(label) + ".dat");
+            std::string datfilename = dat_path.string();
             std::ofstream datout(datfilename);
 
             for (int mat = 0; mat < materials.size(); mat++) {

core/src/global.cpp

@@ -2165,14 +2165,15 @@ std::string helios::getFileName(const std::string &filepath) {
 
 std::string helios::getFilePath(const std::string &filepath, bool trailingslash) {
     std::filesystem::path output_path_fs = filepath;
-    std::string output_path = output_path_fs.parent_path().string();
-    if (trailingslash) {
-        if (output_path.find_last_of('/') != output_path.length() - 1) {
-            output_path += "/";
+    std::filesystem::path output_path = output_path_fs.parent_path();
+    std::string out_str = output_path.make_preferred().string();
+    if (trailingslash && !out_str.empty()) {
+        char last = out_str.back();
+        if (last != '/' && last != '\\') {
+            out_str += std::filesystem::path::preferred_separator;
         }
     }
-
-    return output_path;
+    return out_str;
 }
 
 bool helios::validateOutputPath(std::string &output_path, const std::vector<std::string> &allowable_file_extensions) {

core/src/selfTest.cpp

@@ -1171,24 +1171,38 @@ int Context::selfTest(){
 
     std::string filename = "/path/to/.hidden/file/filename";
 
+    std::string expected_path;
+#ifdef _WIN32
+    expected_path = "\\path\\to\\.hidden\\file\\";
+#else
+    expected_path = "/path/to/.hidden/file/";
+#endif
+
+
     std::string ext = getFileExtension(filename);
     std::string name = getFileName(filename);
     std::string stem = getFileStem(filename);
     std::string path = getFilePath(filename,true);
 
-    if( !ext.empty() || name!="filename" || stem!="filename" || path!="/path/to/.hidden/file/" ){
+    if( !ext.empty() || name!="filename" || stem!="filename" || path!=expected_path ){
       std::cerr << "failed: file path parsing functions were not correct." << std::endl;
       error_count++;
     }
 
     filename = ".hidden/path/to/file/filename.ext";
 
+#ifdef _WIN32
+    expected_path = ".hidden\\path\\to\\file";
+#else
+    expected_path = ".hidden/path/to/file";
+#endif
+
     ext = getFileExtension(filename);
     name = getFileName(filename);
     stem = getFileStem(filename);
     path = getFilePath(filename,false);
 
-    if( ext!=".ext" || name!="filename.ext" || stem!="filename" || path!=".hidden/path/to/file" ){
+    if( ext!=".ext" || name!="filename.ext" || stem!="filename" || path!=expected_path ){
       std::cerr << "failed: file path parsing functions were not correct." << std::endl;
       error_count++;
     }

doc/CHANGELOG.md

@@ -2148,7 +2148,7 @@ The radiation model has been re-designed, with the following primary additions:
 ## Plant Architecture
 - Added PlantArchitecture::isPlantDormant().
 - Carbohydrate model updated to take a parameter structure rather than having hard-coded model parameters. Thanks to Ethan Frehner for these updates.
-- Minor refactoring improvements throughtout plant architecture code.
+- Minor refactoring improvements throughout plant architecture code.
 - Error corrected that was causing plants to flower too quickly if starting with closed flowers.
 
 ## Visualizer
@@ -2209,9 +2209,6 @@ The radiation model has been re-designed, with the following primary additions:
 ## Radiation
 - Added specular reflection in synthetic images for collimated and sun sphere sources (still need to implement disk, rectangle, and sphere sources).
 
-Co-authored by: Ethan Frehner <ehfrehner@users.noreply.github.com>
-Co-authored by: Sean Banks <smbanx@users.noreply.github.com>
-
 # [1.3.33] 2025-06-08
 
 ## Context
@@ -2247,9 +2244,6 @@ Co-authored by: Sean Banks <smbanx@users.noreply.github.com>
 ## Project Builder
 - Several updates including changing how canopies are handled, and improving the rig tab. Credit to Sean Banks for this update.
 
-Co-authored by: Ethan Frehner <ehfrehner@users.noreply.github.com>
-Co-authored by: Sean Banks <smbanx@users.noreply.github.com>
-
 # [1.3.34] 2025-06-15
 
 - Added .clang-format file for consistent code formatting across IDEs and agents.
@@ -2401,4 +2395,35 @@ Co-authored by: Sean Banks <smbanx@users.noreply.github.com>
 - Added self-test to check `plantID` assignment.
 
 ## Radiation, Energy Balance, LiDAR, Aerial LiDAR
-- CMake now uses consistent c++ standard for CUDA code based on the standard used for regular c++ code. It also now explicitly sets the c++ standard for Windows CUDA code.
+- CMake now uses consistent c++ standard for CUDA code based on the standard used for regular c++ code. It also now explicitly sets the c++ standard for Windows CUDA code.
+
+# [1.3.39] 2025-07-09
+
+- More minor documentation fixes.
+
+## Context
+- Implemented some improvements for file path handling on Windows systems to improve robustness.
+- Added *= and /= operators for `helios::vec2`, `helios::vec3` and `helios::vec4` vector types.
+
+## Visualizer
+- Fixed 'haloing' around text.
+- Efficiency of changing the visualization type was improved (e.g., via `Visualizer::colorContextPrimitivesByData()` or `Visualizer::colorContextObjectsByData()`), whereby only the color data is changed rather than rebuilding the entire geometry.
+- Added `Visualizer::deleteGeometry()` method to delete a geometric element based on its ID.
+- The visualizer window can now be freely resized with arbitrary aspect ratio, including making the visualizer window full screen.
+
+## Project Builder
+- Console now auto-scrolls to the bottom when new text is added.
+- Disabled keyboard controls so that rotating the view via keyboard does not conflict.
+
+## Plant Architecture
+- There was an unhandled error when the combination of `leaves_per_petiole` and `leaflet_offset` are too large such that there is no more space along the petiole to place leaflets. There was a similar issue with flowers for the parameters `flowers_per_peduncle` and `flower_offset`, potentially resulting in too many flowers per peduncle.
+- Fixed a minor issue where the max leaf age was not properly enforced when the plant hits its maximum age and stops growing.
+
+## Radiation
+- Changed how the camera image post-processing pipeline works. It now applies global histogram equalization, followed by an optional saturation, brightness, and contrast adjustment.
+
+## Leaf Optics
+- Added documentation page.
+
+## Stomatal Conductance
+- Added optional output primitive data to write stomatal conductance model parameters to primitive data.

doc/Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = Helios
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v1.3.38
+PROJECT_NUMBER         = v1.3.39
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -1302,7 +1302,8 @@ HTML_EXTRA_STYLESHEET  = doc/assets/doxygen-awesome-sidebar-only-darkmode-toggle
 HTML_EXTRA_FILES = doc/assets/doxygen-awesome-darkmode-toggle.js \
                      doc/assets/doxygen-awesome-tabs.js \
                         doc/assets/doxygen-awesome-interactive-toc.js \
-                        doc/assets/doxygen-awesome-paragraph-link.js
+                        doc/assets/doxygen-awesome-paragraph-link.js \
+                        doc/assets/navsync-default.js
 
 # The HTML_COLORSTYLE tag can be used to specify if the generated HTML output
 # should be rendered with a dark or light theme.

doc/DoxygenLayout.xml

@@ -23,6 +23,7 @@
       <tab type="user" visible="yes" url="@ref CanopyGeneratorDoc" title="Canopy Generator"/>
       <tab type="user" visible="yes" url="@ref WeberPennDoc" title="Weber-Penn Tree"/>
       <tab type="user" visible="yes" url="@ref PlantHydraulicsDoc" title="Plant Hydraulics Model"/>
+      <tab type="user" visible="yes" url="@ref LeafOpticsDoc" title="Leaf Optics Model"/>
       <tab type="user" visible="yes" url="@ref ProjectBuilderDoc" title="Project Builder"/>
     </tab>
     <tab type="usergroup" visible="yes" url="@ref Tutorials" title="Tutorials" intro="">

doc/UserGuide.dox

@@ -155,6 +155,7 @@
   - \subpage CanopyGeneratorDoc "Canopy Generator: Simple generation of different type of plant and canopy geometries."
   - \subpage PlantArchitectureDoc "Plant Architecture: Flexible procedural plant generation with dynamic growth and phenology."
   - \subpage PlantHydraulicsDoc "Plant Hydraulics: Models the water potentials, water contents, hydraulic conductances, and hydraulic capacitances."
+  - \subpage LeafOpticsDoc "Leaf Optics: Implementation of the PROSPECT-PRO leaf optical model of leaf reflectance and transmittance spectra."
   - \subpage ProjectBuilderDoc "GUI and XML interface for creating and running Helios projects."
 
 */
@@ -1195,17 +1196,17 @@ This will first rotate the patch by 0.25\f$\pi\f$ rad about the x-axis such that
 
  <table>
  <tr><th>Data type</th><th>Enumeration (HeliosDataType)</th></tr>
- <tr><td>\htmlonly<font face="courier" color="green">int</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT "HELIOS_TYPE_INT"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">uint</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_UINT "HELIOS_TYPE_UINT"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">float</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_FLOAT "HELIOS_TYPE_FLOAT"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">double</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_DOUBLE "HELIOS_TYPE_DOUBLE"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">vec2</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_VEC2 "HELIOS_TYPE_VEC2"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">vec3</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_VEC3 "HELIOS_TYPE_VEC3"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">vec4</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_VEC4 "HELIOS_TYPE_VEC4"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">int2</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT2 "HELIOS_TYPE_INT2"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">int3</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT3 "HELIOS_TYPE_INT3"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">int4</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT4 "HELIOS_TYPE_INT4"</td></tr>
- <tr><td>\htmlonly<font face="courier" color="green">std::string</font>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_STRING "HELIOS_TYPE_STRING"</td></tr>	
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">int</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT "HELIOS_TYPE_INT"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">uint</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_UINT "HELIOS_TYPE_UINT"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">float</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_FLOAT "HELIOS_TYPE_FLOAT"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">double</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_DOUBLE "HELIOS_TYPE_DOUBLE"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">vec2</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_VEC2 "HELIOS_TYPE_VEC2"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">vec3</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_VEC3 "HELIOS_TYPE_VEC3"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">vec4</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_VEC4 "HELIOS_TYPE_VEC4"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">int2</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT2 "HELIOS_TYPE_INT2"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">int3</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT3 "HELIOS_TYPE_INT3"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">int4</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_INT4 "HELIOS_TYPE_INT4"</td></tr>
+ <tr><td>\htmlonly<span style="font-family: Courier, monospace; color: green;">std::string</span>\endhtmlonly</td><td>\ref helios::HELIOS_TYPE_STRING "HELIOS_TYPE_STRING"</td></tr>
  </table>
 
  <!--

doc/assets/navsync-default.js

@@ -0,0 +1,15 @@
+/*!
+ * Toggle the navtree sync button twice during page load.
+ * This resets Doxygen's internal sync state so the
+ * navigation pane stays synchronized and the icon shows
+ * the correct status.
+ */
+window.addEventListener('load', function() {
+    var navSync = document.getElementById('nav-sync');
+    if (!navSync) return;
+    try {
+        navSync.click();
+    } catch (e) {
+        /* ignore */
+    }
+});