[1.3.62] 2026-01-12

- Fixed `Tube::appendTubeSegment()` to correctly add triangles for new segments using proper vertex indices instead of hardcoded values.
- Refactored `readPNGAlpha()` to use RAII patterns for proper resource management and added PNG signature validation.
- Fixed `cart2sphere()` singularity when converting vectors pointing straight up or down (gimbal lock), which caused camera orientation issues.

- The voxel intersection plug-in has been deprecated. Use the collision detection instead.

- All functionality from the voxel intersection plug-in has been incorporated in the collision detection plug-in. This also includes an OpenMP fallback if no GPU is available.

- Added `electron_transport_ratio` (J/Jmax) as optional output primitive data for computing fluorescence quantum yield.

- Added `listShootTypeLabels()` method with three overloads to discover available shoot types: query the currently loaded model (no parameters), query any model by name (string parameter), or query a plant instance by ID (uint parameter).
- Added `resolveTextureFile()` static method for simplified asset path resolution when loading textures and OBJ models.
- Updates to pistachio and walnut model parameters.
- Fixed nitrogen model to track all leaves in the nitrogen map even when no nitrogen is available in the pool.

- Added optional primitive data output for biochemical properties (chlorophyll, carotenoid, etc.) when using nitrogen-based automatic mode.

- Fixed horizontal mirroring in camera output functions: `writePrimitiveDataLabelMap()`, `writeObjectDataLabelMap()`, `writeImageBoundingBoxes()`, `writeImageSegmentationMasks()`, `writeCameraImage()`, and related methods.
- Refactored COCO annotation generation in `writeImageSegmentationMasks_ObjectData()` to ensure 1:1 correspondence between annotations and their attribute values.
- Fixed `runBand()` to validate band labels from the input parameter rather than an internal variable, which caused incorrect error messages when invalid bands were passed.

Author: bnbailey-psl

README.md

@@ -2,7 +2,7 @@
 
 [![YouTube](https://img.shields.io/badge/YouTube-FF0000?style=for-the-badge&logo=youtube&logoColor=white)](https://www.youtube.com/channel/UCUlyE4rKNGokwH5a-TioS0A)
 
-For complete documentation of this software, please consult <a href="https://baileylab.ucdavis.edu/software/helios">https://baileylab.ucdavis.edu/software/helios.
+For complete documentation of this software, please consult <a href="https://plantsimulationlab.github.io/Helios/">https://plantsimulationlab.github.io/Helios/.
 
 Helios is a C++ library for 3D physical simulation of plant and environmental systems. It can generate and manipulate plant and other geometric objects, which can feed into biophysical model plug-ins such as radiation transfer, photosynthesis, and evapotranspiration, among others. 
 

core/include/Context.h

@@ -1,7 +1,7 @@
 /**
  * \file "Context.h" Context header file.
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

core/include/global.h

@@ -1,7 +1,7 @@
 /**
  * \file "global.h" Header file for all global function/object definitions.
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

core/include/helios_vector_types.h

@@ -1,7 +1,7 @@
 /**
  * \file "helios_vector_types.h" Declarations for vector types
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

core/src/Context.cpp

@@ -1,7 +1,7 @@
 /**
  * \file "Context.cpp" Context declarations.
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

core/src/Context_data.cpp

@@ -1,7 +1,7 @@
 /**
  * \file "Context_data.cpp" Context primitive data, object data, and global data declarations.
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

core/src/Context_fileIO.cpp

@@ -1,7 +1,7 @@
 /**
  * \file "Context_fileIO.cpp" Filesystem input/output functions within the Context.
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

core/src/Context_object.cpp

@@ -1,7 +1,7 @@
 /**
  * \file "Context_object.cpp" Context compound object definitions and methods.
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -2093,16 +2093,18 @@ void Tube::appendTubeSegment(const helios::vec3 &node_position, float node_radiu
 
     // add triangles for new segment
 
+    int second_last = node_count - 2;
+    int last = node_count - 1;
     for (int j = 0; j < radial_subdivisions; j++) {
-        vec3 v0 = triangle_vertices.at(1).at(j);
-        vec3 v1 = triangle_vertices.at(1 + 1).at(j + 1);
-        vec3 v2 = triangle_vertices.at(1).at(j + 1);
+        vec3 v0 = triangle_vertices.at(second_last).at(j);
+        vec3 v1 = triangle_vertices.at(last).at(j + 1);
+        vec3 v2 = triangle_vertices.at(second_last).at(j + 1);
 
         UUIDs.push_back(context->addTriangle(v0, v1, v2, node_color));
 
-        v0 = triangle_vertices.at(1).at(j);
-        v1 = triangle_vertices.at(1 + 1).at(j);
-        v2 = triangle_vertices.at(1 + 1).at(j + 1);
+        v0 = triangle_vertices.at(second_last).at(j);
+        v1 = triangle_vertices.at(last).at(j);
+        v2 = triangle_vertices.at(last).at(j + 1);
 
         UUIDs.push_back(context->addTriangle(v0, v1, v2, node_color));
     }
@@ -2628,7 +2630,7 @@ void Cone::scaleLength(float S) {
     float angle = acos_safe(dot);
 
     // only rotate if the cone is not alread aligned with the z axis (i.e., angle is not zero. If zero, the axis of rotation is 0,0,0 and we end up with problems)
-    if (angle != float(0.0)) {
+    if (angle != 0.f) {
         rotate(-1 * angle, ra);
     }
 
@@ -2645,7 +2647,7 @@ void Cone::scaleLength(float S) {
     }
 
     // rotate back
-    if (angle != 0.0) {
+    if (angle != 0.f) {
         rotate(angle, ra);
     }
 
@@ -2672,7 +2674,7 @@ void Cone::scaleGirth(float S) {
     float dot = axis_unit_vector * z_axis;
     float angle = acos_safe(dot);
     // only rotate if the cone is not already aligned with the z axis (i.e., angle is not zero. If zero, the axis of rotation is 0,0,0 and we end up with problems)
-    if (angle != float(0.0)) {
+    if (angle != 0.f) {
         rotate(-1 * angle, ra);
     }
 
@@ -2681,7 +2683,7 @@ void Cone::scaleGirth(float S) {
 
 
     // rotate back
-    if (angle != 0.0) {
+    if (angle != 0.f) {
         rotate(angle, ra);
     }
 

core/src/Context_primitive.cpp

@@ -1,7 +1,7 @@
 /**
  * \file "Context_primitive.cpp" Context primitive type definitions and methods.
  *
- * Copyright (C) 2016-2025 Brian Bailey
+ * Copyright (C) 2016-2026 Brian Bailey
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -1587,14 +1587,7 @@ float Voxel::getVolume() {
 }
 
 vec3 Voxel::getCenter() const {
-    vec3 center;
-    vec3 Y;
-
-    center.x = transform[0] * Y.x + transform[1] * Y.y + transform[2] * Y.z + transform[3];
-    center.y = transform[4] * Y.x + transform[5] * Y.y + transform[6] * Y.z + transform[7];
-    center.z = transform[8] * Y.x + transform[9] * Y.y + transform[10] * Y.z + transform[11];
-
-    return center;
+    return make_vec3(transform[3], transform[7], transform[11]);
 }
 
 vec3 Voxel::getSize() const {