Implement manual deep copy for C3DData instead of relying on ezc3d's shallow copy constructor

[Copilot]

ezc3d::c3d stores Header, Parameters, and Data as shared_ptr internally, and Frame similarly stores Points, Analogs, Rotations as shared_ptr. The copy constructor only copies the pointers, so the previous deepCopy() via std::make_shared<ezc3d::c3d>(*data_) produced a shallow copy where mutations to the copy would affect the original.

Replaced with a manual recursive reconstruction:

• Point/Analog registration — calls c3d::point(name) and c3d::analog(name) to initialize the POINT/ANALOG configuration consistently in the new object
• Frame-level deep copy — rebuilds each frame from scratch:
  • Points: copies x, y, z, residual, cameraMask per point
  • Analogs: copies each subframe's channel data values
  • Rotations: copies all 4×4 matrix elements + reliability via Rotation::set()
• Parameter groups — copies non-auto-managed groups (FORCE_PLATFORM, TRIAL, custom metadata) via c3d::parameter(); POINT/ANALOG groups are skipped since they're already initialized by the registration step

// Before: shallow — src and copy share the same internal data
return C3DData{std::make_shared<ezc3d::c3d>(*data_), source_};

// After: fully independent copy
auto dst = std::make_shared<ezc3d::c3d>();
for (const auto& name : src.pointNames()) { dst->point(name); }
for (const auto& name : src.channelNames()) { dst->analog(name); }
// ... rebuild each frame element by element ...
return C3DData{std::move(dst), source_};

---

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Cpp-Linter Report ⚠️

Some files did not pass the configured checks!

clang-format (v19.1.1) reports: 2 file(s) not formatted

• misc/c3d/include/inviwo/c3d/processors/c3dtransformpoints.h
• misc/c3d/src/processors/c3dtodataframe.cpp

clang-tidy (v19.1.1) reports: 37 concern(s)

• misc/c3d/include/inviwo/c3d/c3dmodule.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/c3dmodule.h:36:26: warning: [cppcoreguidelines-avoid-non-const-global-variables]

  variable 'C3DModule' is non-const and globally accessible, consider making it const

     36 | class IVW_MODULE_C3D_API C3DModule : public InviwoModule {
        |                          ^

• misc/c3d/include/inviwo/c3d/datastructures/c3ddata.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/datastructures/c3ddatatraits.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/io/c3dreader.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/io/c3dreader.h:46:26: warning: [cppcoreguidelines-avoid-non-const-global-variables]

  variable 'C3DReader' is non-const and globally accessible, consider making it const

     46 | class IVW_MODULE_C3D_API C3DReader : public DataReaderType<ezc3d::c3d> {
        |                          ^

• misc/c3d/include/inviwo/c3d/ports/c3dport.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/processors/c3daveragedpositions.h:32:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     32 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/processors/c3daveragedpositions.h:45:26: warning: [cppcoreguidelines-avoid-non-const-global-variables]

  variable 'C3DAveragedPositions' is non-const and globally accessible, consider making it const

     45 | class IVW_MODULE_C3D_API C3DAveragedPositions : public Processor {
        |                          ^

• misc/c3d/include/inviwo/c3d/processors/c3dsource.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/processors/c3dsource.h:39:26: warning: [cppcoreguidelines-avoid-non-const-global-variables]

  variable 'C3DSource' is non-const and globally accessible, consider making it const

     39 | class IVW_MODULE_C3D_API C3DSource : public DataSource<ezc3d::c3d, C3DDataOutport> {
        |                          ^

• misc/c3d/include/inviwo/c3d/processors/c3dtodataframe.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/processors/c3dtodataframe.h:49:26: warning: [cppcoreguidelines-avoid-non-const-global-variables]

  variable 'C3DToDataFrame' is non-const and globally accessible, consider making it const

     49 | class IVW_MODULE_C3D_API C3DToDataFrame : public Processor {
        |                          ^

• misc/c3d/include/inviwo/c3d/processors/c3dtomesh.h:31:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     31 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/processors/c3dtomesh.h:59:26: warning: [cppcoreguidelines-avoid-non-const-global-variables]

  variable 'C3DToMesh' is non-const and globally accessible, consider making it const

     59 | class IVW_MODULE_C3D_API C3DToMesh : public Processor {
        |                          ^

• misc/c3d/include/inviwo/c3d/processors/c3dtransformpoints.h:32:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmoduledefine.h' file not found

     32 | #include <inviwo/c3d/c3dmoduledefine.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/include/inviwo/c3d/processors/c3dtransformpoints.h:50:26: warning: [cppcoreguidelines-avoid-non-const-global-variables]

  variable 'C3DTransformPoints' is non-const and globally accessible, consider making it const

     50 | class IVW_MODULE_C3D_API C3DTransformPoints : public Processor {
        |                          ^

• misc/c3d/src/c3dmodule.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/c3dmodule.h' file not found

     30 | #include <inviwo/c3d/c3dmodule.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/datastructures/c3ddata.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/datastructures/c3ddata.h' file not found

     30 | #include <inviwo/c3d/datastructures/c3ddata.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/datastructures/c3ddata.cpp:39:35: warning: [misc-use-internal-linkage]

  function 'copyPoints' can be made static or moved into an anonymous namespace to enforce internal linkage

     39 | ezc3d::DataNS::Points3dNS::Points copyPoints(const ezc3d::DataNS::Frame& srcFrame) {
        |                                   ^         
        |                                             static 

• misc/c3d/src/datastructures/c3ddata.cpp:51:35: warning: [misc-use-internal-linkage]

  function 'copyAnalogs' can be made static or moved into an anonymous namespace to enforce internal linkage

     51 | ezc3d::DataNS::AnalogsNS::Analogs copyAnalogs(const ezc3d::DataNS::Frame& srcFrame) {
        |                                   ^          
        |                                              static 

• misc/c3d/src/datastructures/c3ddata.cpp:66:38: warning: [misc-use-internal-linkage]

  function 'copyRotations' can be made static or moved into an anonymous namespace to enforce internal linkage

     66 | ezc3d::DataNS::RotationNS::Rotations copyRotations(const ezc3d::DataNS::Frame& srcFrame) {
        |                                      ^            
        |                                                   static 

• misc/c3d/src/datastructures/c3ddata.cpp:84:6: warning: [misc-use-internal-linkage]

  function 'copyAnalogs' can be made static or moved into an anonymous namespace to enforce internal linkage

     84 | void copyAnalogs(const ezc3d::DataNS::Frame& srcFrame, ezc3d::DataNS::Frame& dstFrame) {
        |      ^
        | static 

• misc/c3d/src/datastructures/c3ddata.cpp:91:6: warning: [misc-use-internal-linkage]

  function 'copyRotations' can be made static or moved into an anonymous namespace to enforce internal linkage

     91 | void copyRotations(const ezc3d::DataNS::Frame& srcFrame, ezc3d::DataNS::Frame& dstFrame) {
        |      ^
        | static 

• misc/c3d/src/datastructures/c3ddata.cpp:98:6: warning: [misc-use-internal-linkage]

  function 'copyPoints' can be made static or moved into an anonymous namespace to enforce internal linkage

     98 | void copyPoints(const ezc3d::DataNS::Frame& srcFrame, ezc3d::DataNS::Frame& dstFrame) {
        |      ^
        | static 

• misc/c3d/src/datastructures/c3ddata.cpp:105:29: warning: [misc-use-internal-linkage]

  function 'copy' can be made static or moved into an anonymous namespace to enforce internal linkage

    105 | std::shared_ptr<ezc3d::c3d> copy(const ezc3d::c3d& src) {
        |                             ^   
        |                                 static 

• misc/c3d/src/datastructures/c3ddatatraits.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/datastructures/c3ddatatraits.h' file not found

     30 | #include <inviwo/c3d/datastructures/c3ddatatraits.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/io/c3dreader.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/io/c3dreader.h' file not found

     30 | #include <inviwo/c3d/io/c3dreader.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/ports/c3dport.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/ports/c3dport.h' file not found

     30 | #include <inviwo/c3d/ports/c3dport.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/processors/c3daveragedpositions.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/processors/c3daveragedpositions.h' file not found

     30 | #include <inviwo/c3d/processors/c3daveragedpositions.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/processors/c3dsource.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/processors/c3dsource.h' file not found

     30 | #include <inviwo/c3d/processors/c3dsource.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/processors/c3dtodataframe.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/processors/c3dtodataframe.h' file not found

     30 | #include <inviwo/c3d/processors/c3dtodataframe.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/processors/c3dtomesh.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/processors/c3dtomesh.h' file not found

     30 | #include <inviwo/c3d/processors/c3dtomesh.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/processors/c3dtransformpoints.cpp:30:10: error: [clang-diagnostic-error]

  'inviwo/c3d/processors/c3dtransformpoints.h' file not found

     30 | #include <inviwo/c3d/processors/c3dtransformpoints.h>
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

• misc/c3d/src/processors/c3dtransformpoints.cpp:77:7: warning: [misc-use-internal-linkage]

  function 'basisEstimation' can be made static or moved into an anonymous namespace to enforce internal linkage

     77 | dmat4 basisEstimation(dvec3 a, dvec3 b, dvec3 c, dvec3 d) {
        |       ^              
        |                      static 

• misc/c3d/src/processors/c3dtransformpoints.cpp:77:23: warning: [bugprone-easily-swappable-parameters]

  4 adjacent parameters of 'basisEstimation' of similar type ('int') are easily swapped by mistake

     77 | dmat4 basisEstimation(dvec3 a, dvec3 b, dvec3 c, dvec3 d) {
        |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtransformpoints.cpp:77:29: note: the first parameter in the range is 'a'
     77 | dmat4 basisEstimation(dvec3 a, dvec3 b, dvec3 c, dvec3 d) {
        |                             ^
  /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtransformpoints.cpp:77:56: note: the last parameter in the range is 'd'
     77 | dmat4 basisEstimation(dvec3 a, dvec3 b, dvec3 c, dvec3 d) {
        |                                                        ^

• misc/c3d/src/processors/c3dtransformpoints.cpp:85:7: warning: [misc-use-internal-linkage]

  function 'toGLM' can be made static or moved into an anonymous namespace to enforce internal linkage

     85 | dvec3 toGLM(const ezc3d::DataNS::Points3dNS::Point& p) { return dvec3{p.x(), p.y(), p.z()}; }
        |       ^    
        |            static 

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