[1.3.12] 2024-06-03

*utilities/create_project.sh script* - syntheticannotation plug-in was missing from this script, which also caused run_samples.sh to fail to run its self-test. *Context* - Added Context::cleanDeletedUUIDs() to delete UUIDs from a vector when the corresponding primitive does not exist. This is useful, for example, to update UUID vectors when deleting some primitives, such as after calling cropDomain(). - Added fix for edge case in getFileExtension() to consider case where the filename starts with a '.' and had no extension. - Performance improvements when adding geometry with textures. Existence of the texture file is now only checked when a new texture is added. - Performance improvements when loading geometry with textures from XML file. The solid fraction is not re-calculated if it was previously written to the XML file being read. *Radiation* - In-place version of RadiationModel::scaleSpectrum() was not actually added in the last commit. - Added a check to make sure that the radiation camera position and 'lookat' coordinates are not the same. - Added a check in RadiationModel::writeNormCameraImage() to throw an error if the camera data does not exist. This check was there for RadiationModel::writeCameraImage(), but was missing in RadiationModel::writeNormCameraImage() which could cause an uncaught error. - Added support for periodic boundary conditions with depth images. - Changed previous version of RadiationModel::writeDepthImage() to RadiationModel::writeDepthImageData() (writes ASCII files with depth image data). - Added new RadiationModel::writeDepthImage(), which writes a JPEG version of (normalized) depth images. - Removed previously deprecated version of RadiationModel::addRadiationCamera(). Use versions that take a CameraProperties struct instead. - Behavior of twosided_flag = 0 was changed for direct sources. Previously, primitives could receive direct radiation from the back side when twosided_flag = 0, but now they cannot. - twosided_flag = 2 was not implemented correctly and was not working in most cases. - Added case for twosided_flag = 3 to make the primitive completely invisible to any radiation. - Added ability to visualize radiation sources by adding their geometry to the Context. See RadiationModel::enableLightModelVisualization(). - Added ability to visualize radiation cameras by adding their geometry to the Context. See RadiationModel::enableCameraModelVisualization().
PlantSimulationLab · Jun 3, 2024 · dcc0b5f · dcc0b5f
1 parent 7345c95
commit dcc0b5f
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diff --git a/core/include/Context.h b/core/include/Context.h
@@ -2282,6 +2282,24 @@ class Context{
 
     //!Get all primitive UUIDs currently in the Context
     std::vector<uint> getAllUUIDs() const;
+
+    //! Delete UUIDs from vector if primitives no longer exist (1D vector)
+    /**
+     * \param[inout] UUIDs Vector of primitive UUIDs. UUIDs for primitives that do not exist will be deleted from the vector.
+     */
+    void cleanDeletedUUIDs( std::vector<uint> &UUIDs ) const;
+
+    //! Delete UUIDs from vector if primitives no longer exist (2D vector)
+    /**
+     * \param[inout] UUIDs Vector of primitive UUIDs. UUIDs for primitives that do not exist will be deleted from the vector.
+     */
+    void cleanDeletedUUIDs( std::vector<std::vector<uint>> &UUIDs ) const;
+
+    //! Delete UUIDs from vector if primitives no longer exist (3D vector)
+    /**
+     * \param[inout] UUIDs Vector of primitive UUIDs. UUIDs for primitives that do not exist will be deleted from the vector.
+     */
+    void cleanDeletedUUIDs( std::vector<std::vector<std::vector<uint>>> &UUIDs ) const;
 
     //-------- Primitive Data Methods ---------- //
 

diff --git a/core/src/Context.cpp b/core/src/Context.cpp
@@ -52,6 +52,16 @@ std::minstd_rand0* Context::getRandomGenerator(){
 
 void Context::addTexture( const char* texture_file ){
     if( textures.find(texture_file)==textures.end() ){//texture has not already been added
+
+        //texture must have type PNG or JPEG
+        std::string fn = texture_file;
+        std::string ext = getFileExtension(fn);
+        if( ext != ".png" && ext != ".PNG" && ext != ".jpg" && ext != ".jpeg" && ext != ".JPG" && ext != ".JPEG" ){
+            helios_runtime_error("ERROR (Context::addTexture): Texture file " + fn + " is not PNG or JPEG format.");
+        }else if( !doesTextureFileExist(texture_file) ){
+            helios_runtime_error("ERROR (Context::addTexture): Texture file " + std::string(texture_file) + " does not exist.");
+        }
+
         Texture text( texture_file );
         textures[ texture_file ] = text;
     }
@@ -1189,15 +1199,6 @@ uint Context::addPatch( const vec3& center, const vec2& size, const SphericalCoo
 
 uint Context::addPatch( const vec3& center, const vec2& size, const SphericalCoord& rotation, const char* texture_file ){
 
-    //texture must have type PNG or JPEG
-    std::string fn = texture_file;
-    std::string ext = getFileExtension(fn);
-    if( ext != ".png" && ext != ".PNG" && ext != ".jpg" && ext != ".jpeg" && ext != ".JPG" && ext != ".JPEG" ){
-        helios_runtime_error("ERROR (Context::addPatch): Texture file " + fn + " is not PNG or JPEG format.");
-    }else if( !doesTextureFileExist(texture_file) ){
-        helios_runtime_error("ERROR (Context::addPatch): Texture file " + std::string(texture_file) + " does not exist.");
-    }
-
     addTexture( texture_file );
 
     auto* patch_new = (new Patch( texture_file, textures.at(texture_file).getSolidFraction(), 0, currentUUID ));
@@ -1226,15 +1227,6 @@ uint Context::addPatch( const vec3& center, const vec2& size, const SphericalCoo
 
 uint Context::addPatch( const vec3& center, const vec2& size, const SphericalCoord& rotation, const char* texture_file, const helios::vec2& uv_center, const helios::vec2& uv_size ){
 
-    //texture must have type PNG or JPEG
-    std::string fn = texture_file;
-    std::string ext = getFileExtension(fn);
-    if( ext != ".png" && ext != ".PNG" && ext != ".jpg" && ext != ".jpeg" && ext != ".JPG" && ext != ".JPEG" ){
-        helios_runtime_error("ERROR (Context::addPatch): Texture file " + fn + " is not PNG or JPEG format.");
-    }else if( !doesTextureFileExist(texture_file) ){
-        helios_runtime_error("ERROR (Context::addPatch): Texture file " + std::string(texture_file) + " does not exist.");
-    }
-
     if( size.x==0 || size.y==0 ){
         helios_runtime_error("ERROR (Context::addPatch): Size of patch must be greater than 0.");
     }
@@ -1300,15 +1292,6 @@ uint Context::addTriangle( const vec3& vertex0, const vec3& vertex1, const vec3&
 
 uint Context::addTriangle( const helios::vec3& vertex0, const helios::vec3& vertex1, const helios::vec3& vertex2, const char* texture_file, const helios::vec2& uv0, const helios::vec2& uv1, const helios::vec2& uv2 ){
 
-    //texture must have type PNG or JPEG
-    std::string fn = texture_file;
-    std::string ext = getFileExtension(fn);
-    if( ext != ".png" && ext != ".PNG" && ext != ".jpg" && ext != ".jpeg" && ext != ".JPG" && ext != ".JPEG" ){
-        helios_runtime_error("ERROR (Context::addTriangle): Texture file " + fn + " is not PNG or JPEG format.");
-    }else if( !doesTextureFileExist(texture_file) ){
-        helios_runtime_error("ERROR (Context::addTriangle): Texture file " + std::string(texture_file) + " does not exist.");
-    }
-
     addTexture( texture_file );
 
     std::vector<helios::vec2> uv;
@@ -1684,6 +1667,36 @@ std::vector<uint> Context::getAllUUIDs() const{
     return UUIDs;
 }
 
+void Context::cleanDeletedUUIDs( std::vector<uint> &UUIDs ) const {
+    for (int i = UUIDs.size() - 1; i >= 0; i--) {
+        if (!doesPrimitiveExist(UUIDs.at(i))) {
+            UUIDs.erase(UUIDs.begin() + i);
+        }
+    }
+}
+
+void Context::cleanDeletedUUIDs( std::vector<std::vector<uint>> &UUIDs ) const{
+    for( int j=UUIDs.size()-1; j>=0; j-- ){
+        for( int i=UUIDs.at(j).size()-1; i>=0; i-- ){
+            if( !doesPrimitiveExist(UUIDs.at(j).at(i)) ){
+                UUIDs.at(j).erase( UUIDs.at(j).begin()+i );
+            }
+        }
+    }
+}
+
+void Context::cleanDeletedUUIDs( std::vector<std::vector<std::vector<uint>>> &UUIDs ) const{
+    for( int k=UUIDs.size()-1; k>=0; k-- ) {
+        for (int j = UUIDs.at(k).size() - 1; j >= 0; j--) {
+            for (int i = UUIDs.at(k).at(j).size() - 1; i >= 0; i--) {
+                if (!doesPrimitiveExist(UUIDs.at(k).at(j).at(i))) {
+                    UUIDs.at(k).at(j).erase(UUIDs.at(k).at(j).begin() + i);
+                }
+            }
+        }
+    }
+}
+
 void Context::addTimeseriesData(const char* label, float value, const Date &date, const Time &time ){
 
     //floating point value corresponding to date and time
@@ -3993,15 +4006,6 @@ uint Context::addTileObject(const vec3 &center, const vec2 &size, const Spherica
 
 uint Context::addTileObject(const vec3 &center, const vec2 &size, const SphericalCoord &rotation, const int2 &subdiv, const char* texturefile ){
 
-    //texture must have type PNG or JPEG
-    std::string fn = texturefile;
-    std::string ext = getFileExtension(fn);
-    if( ext != ".png" && ext != ".PNG" && ext != ".jpg" && ext != ".jpeg" && ext != ".JPG" && ext != ".JPEG" ){
-        helios_runtime_error("ERROR (Context::addTileObject): Texture file " + fn + " is not PNG or JPEG format.");
-    }else if( !doesTextureFileExist(texturefile) ){
-        helios_runtime_error("ERROR (Context::addTileObject): Texture file " + std::string(texturefile) + " does not exist.");
-    }
-
     if( size.x==0 || size.y==0 ){
         helios_runtime_error("ERROR (addTileObject): Size of tile must be greater than 0.");
     }
@@ -5253,15 +5257,6 @@ std::vector<uint> Context::addTile(const vec3 &center, const vec2 &size, const S
 
 std::vector<uint> Context::addTile(const vec3 &center, const vec2 &size, const SphericalCoord &rotation, const int2 &subdiv, const char* texturefile ){
 
-    //texture must have type PNG or JPEG
-    std::string fn = texturefile;
-    std::string ext = getFileExtension(fn);
-    if( ext != ".png" && ext != ".PNG" && ext != ".jpg" && ext != ".jpeg" && ext != ".JPG" && ext != ".JPEG" ){
-        helios_runtime_error("ERROR (Context::addTile): Texture file " + fn + " is not PNG or JPEG format.");
-    }else if( !doesTextureFileExist(texturefile) ){
-        helios_runtime_error("ERROR (Context::addTile): Texture file " + std::string(texturefile) + " does not exist.");
-    }
-
     std::vector<uint> UUID;
 
     vec2 subsize;
@@ -5278,10 +5273,13 @@ std::vector<uint> Context::addTile(const vec3 &center, const vec2 &size, const S
 
     addTexture( texturefile );
     std::vector<std::vector<bool> > alpha;
-    int2 sz;
+    int2 sz = textures.at(texturefile).getSize();
     if( textures.at(texturefile).hasTransparencyChannel() ){
         alpha = *textures.at(texturefile).getTransparencyData();
-        sz = textures.at(texturefile).getSize();
+    }
+
+    if( subdiv.x>=sz.x || subdiv.y>=sz.y ){
+        helios_runtime_error("ERROR (Context::addTile): The resolution of the texture image '" + std::string(texturefile) + "' is lower than the number of tile subdivisions. Increase resolution of the texture image.");
     }
 
     for( uint j=0; j<subdiv.y; j++ ){

diff --git a/core/src/Context_fileIO.cpp b/core/src/Context_fileIO.cpp
@@ -1339,7 +1339,7 @@ std::vector<uint> Context::loadXML( const char* filename, bool quiet ){
     }
 
     // * Patch Solid Fraction * //
-    float solid_fraction = 1;
+    float solid_fraction = -1;
     if( XMLparser::parse_solid_fraction(p,solid_fraction)==2 ){
       helios_runtime_error("ERROR (Context::loadXML): Solid fraction given in 'patch' block contains invalid data.");
     }
@@ -1356,20 +1356,20 @@ std::vector<uint> Context::loadXML( const char* filename, bool quiet ){
     }
 
     // * Add the Patch * //
-    if( strcmp(texture_file.c_str(),"none")==0 ){
+    if( strcmp(texture_file.c_str(),"none")==0 ){  //no texture file was given
       ID=addPatch( make_vec3(0,0,0), make_vec2(1,1), make_SphericalCoord(0,0), color );
-    }else{
+    }else{ //has a texture file
       std::string texture_file_copy;
-      if( solid_fraction!=1.f ){
+      if( solid_fraction<1.f && solid_fraction>=0.f ){ //solid fraction was given in the XML, and is not equal to 1.0
         texture_file_copy = texture_file;
-        texture_file = "lib/images/solid.jpg"; //load dummy solid texture
+        texture_file = "lib/images/solid.jpg"; //load dummy solid texture to avoid re-calculating the solid fraction
       }
-      if( uv.empty() ){
+      if( uv.empty() ){ //custom (u,v) coordinates were not given
         ID=addPatch( make_vec3(0,0,0), make_vec2(1,1), make_SphericalCoord(0,0), texture_file.c_str() );
       }else{
         ID=addPatch( make_vec3(0,0,0), make_vec2(1,1), make_SphericalCoord(0,0), texture_file.c_str(), 0.5*(uv.at(2)+uv.at(0)), uv.at(2)-uv.at(0) );
       }
-      if( solid_fraction!=1.f ) {
+      if( solid_fraction<1.f && solid_fraction>=0.f ) { //replace dummy texture and set the solid fraction
         getPrimitivePointer_private(ID)->setTextureFile(texture_file_copy.c_str());
         addTexture(texture_file_copy.c_str());
         getPrimitivePointer_private(ID)->setSolidFraction(solid_fraction);
@@ -1422,7 +1422,7 @@ std::vector<uint> Context::loadXML( const char* filename, bool quiet ){
     }
 
     // * Triangle Solid Fraction * //
-    float solid_fraction = 1;
+    float solid_fraction = -1;
     if( XMLparser::parse_solid_fraction(tri,solid_fraction)==2 ){
       helios_runtime_error("ERROR (Context::loadXML): Solid fraction given in 'triangle' block contains invalid data.");
     }
@@ -1449,12 +1449,12 @@ std::vector<uint> Context::loadXML( const char* filename, bool quiet ){
       ID = addTriangle( vert_pos.at(0), vert_pos.at(1), vert_pos.at(2), color );
     }else{
       std::string texture_file_copy;
-      if( solid_fraction!=1.f ){
+      if( solid_fraction<1.f && solid_fraction>=0.f ){ //solid fraction was given in the XML, and is not equal to 1.0
         texture_file_copy = texture_file;
-        texture_file = "lib/images/solid.jpg"; //load dummy solid texture
+        texture_file = "lib/images/solid.jpg"; //load dummy solid texture to avoid re-calculating the solid fraction
       }
       ID = addTriangle( vert_pos.at(0), vert_pos.at(1), vert_pos.at(2), texture_file.c_str(), uv.at(0), uv.at(1), uv.at(2) );
-      if( solid_fraction!=1.f ) {
+      if( solid_fraction<1.f && solid_fraction>=0.f ) {
         getPrimitivePointer_private(ID)->setTextureFile(texture_file_copy.c_str());
         addTexture(texture_file_copy.c_str());
         getPrimitivePointer_private(ID)->setSolidFraction(solid_fraction);

diff --git a/core/src/global.cpp b/core/src/global.cpp
@@ -2820,8 +2820,12 @@ std::string helios::getFileExtension( const std::string &filepath ){
     return "";
   }
 
+  //edge case when filepath starts with '.' and there is no file extension (e.g., './myfile')
+  if( filepath.find_last_of('.')==0 ){
+    ext = "";
+
   //edge case when file is in a hidden directory AND there is no file extension (return empty string)
-  if( filepath.find_last_of('/')<filepath.size() && filepath.at(filepath.find_last_of('.')-1)=='/' ){
+  }else if( filepath.find_last_of('/')<filepath.size() && filepath.at(filepath.find_last_of('.')-1)=='/' ){
     ext = "";
   }
 

diff --git a/doc/CHANGELOG b/doc/CHANGELOG
@@ -1639,4 +1639,29 @@ The radiation model has been re-designed, with the following primary additions:
 - ColorCalibration::addColorboard() was changed to accept everything that is needed to fully define the colorboard. Accordingly, ColorCalibration::setColorboardReflectivity() was removed.
 - Argument order of ColorCalibration::addDefaultColorboard() was changed to be consistent with ColorCalibration::addColorboard() and typical Helios convention.
 - Added method to output optional primitive data (reflectivity and transmissivity values).
-- Updated calibrated_CREE6500K_Basler-acA2500-20gc_spectral_response_[*] spectra in the camera library to be properly normalized.
+- Updated calibrated_CREE6500K_Basler-acA2500-20gc_spectral_response_[*] spectra in the camera library to be properly normalized.
+
+[1.3.12] 2024-06-03
+
+*utilities/create_project.sh script*
+- syntheticannotation plug-in was missing from this script, which also caused run_samples.sh to fail to run its self-test.
+
+*Context*
+- Added Context::cleanDeletedUUIDs() to delete UUIDs from a vector when the corresponding primitive does not exist. This is useful, for example, to update UUID vectors when deleting some primitives, such as after calling cropDomain().
+- Added fix for edge case in getFileExtension() to consider case where the filename starts with a '.' and had no extension.
+- Performance improvements when adding geometry with textures. Existence of the texture file is now only checked when a new texture is added.
+- Performance improvements when loading geometry with textures from XML file. The solid fraction is not re-calculated if it was previously written to the XML file being read.
+
+*Radiation*
+- In-place version of RadiationModel::scaleSpectrum() was not actually added in the last commit.
+- Added a check to make sure that the radiation camera position and 'lookat' coordinates are not the same.
+- Added a check in RadiationModel::writeNormCameraImage() to throw an error if the camera data does not exist. This check was there for RadiationModel::writeCameraImage(), but was missing in RadiationModel::writeNormCameraImage() which could cause an uncaught error.
+- Added support for periodic boundary conditions with depth images.
+- Changed previous version of RadiationModel::writeDepthImage() to RadiationModel::writeDepthImageData() (writes ASCII files with depth image data).
+- Added new RadiationModel::writeDepthImage(), which writes a JPEG version of (normalized) depth images.
+- Removed previously deprecated version of RadiationModel::addRadiationCamera(). Use versions that take a CameraProperties struct instead.
+- Behavior of twosided_flag = 0 was changed for direct sources. Previously, primitives could receive direct radiation from the back side when twosided_flag = 0, but now they cannot.
+- twosided_flag = 2 was not implemented correctly and was not working in most cases.
+- Added case for twosided_flag = 3 to make the primitive completely invisible to any radiation.
+- Added ability to visualize radiation sources by adding their geometry to the Context. See RadiationModel::enableLightModelVisualization().
+- Added ability to visualize radiation cameras by adding their geometry to the Context. See RadiationModel::enableCameraModelVisualization().
diff --git a/doc/UserGuide.dox b/doc/UserGuide.dox
@@ -1,4 +1,4 @@
-/*! \mainpage Helios Documentation v1.3.11
+/*! \mainpage Helios Documentation v1.3.12
 
   <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;v1.3.11</span>
+   <div id="projectname"><span id="projectnumber">&#160;v1.3.12</span>
    </div>
   </td>
  </tr>