Implement manual deep copy for C3DData instead of relying on ezc3d's shallow copy constructor by Copilot · Pull Request #277 · inviwo/modules

Copilot · 2026-03-17T13:42:24Z

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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github-actions · 2026-03-18T16:06:53Z

Cpp-Linter Report ⚠️

Some files did not pass the configured checks!

clang-tidy (v19.1.1) reports: 3 concern(s)

misc/c3d/include/inviwo/c3d/c3dmodule.h:36:26: warning: [cppcoreguidelines-special-member-functions]

class 'C3DModule' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator
```
   36 | class IVW_MODULE_C3D_API C3DModule : public InviwoModule {
      |                          ^
```

misc/c3d/src/processors/c3dpointalignment.cpp:62:53: warning: [modernize-return-braced-init-list]

avoid repeating the return type from the declaration; use a braced initializer list instead

   62 | glm::dvec3 toGLM(const Eigen::Vector3d& v) { return glm::dvec3(v(0), v(1), v(2)); }
      |                                                     ^~~~~~~~~~~                ~
      |                                                     {                          }

misc/c3d/src/processors/c3dtodataframe.cpp:72:22: warning: [readability-function-cognitive-complexity]

function 'process' has cognitive complexity of 38 (threshold 25)

   72 | void C3DToDataFrame::process() {
      |                      ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:88:9: note: +1, including nesting penalty of 0, nesting level increased to 1
   88 |         for (size_t f = 0; f < nbFrames; ++f) {
      |         ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:90:48: note: +2, including nesting penalty of 1, nesting level increased to 2
   90 |             timeValues[f] = (frameRate > 0.0f) ? static_cast<float>(f) / frameRate : 0.0f;
      |                                                ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:96:9: note: +1, including nesting penalty of 0, nesting level increased to 1
   96 |         for (size_t p = 0; p < nbPoints; ++p) {
      |         ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:103:13: note: +2, including nesting penalty of 1, nesting level increased to 2
  103 |             if (includeResiduals_) {
      |             ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:107:13: note: +2, including nesting penalty of 1, nesting level increased to 2
  107 |             for (size_t f = 0; f < nbFrames; ++f) {
      |             ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:112:17: note: +3, including nesting penalty of 2, nesting level increased to 3
  112 |                 if (includeResiduals_) {
      |                 ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:120:13: note: +2, including nesting penalty of 1, nesting level increased to 2
  120 |             if (includeResiduals_) {
      |             ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:137:9: note: +1, including nesting penalty of 0, nesting level increased to 1
  137 |         if (nbAnalogs > 0 && nbAnalogByFrame > 0) {
      |         ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:137:27: note: +1
  137 |         if (nbAnalogs > 0 && nbAnalogByFrame > 0) {
      |                           ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:147:36: note: +2, including nesting penalty of 1, nesting level increased to 2
  147 |                 (frameRate > 0.0f) ? frameRate * static_cast<float>(nbSubframes) : 0.0f;
      |                                    ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:149:13: note: +2, including nesting penalty of 1, nesting level increased to 2
  149 |             for (size_t f = 0; f < nbFrames; ++f) {
      |             ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:150:17: note: +3, including nesting penalty of 2, nesting level increased to 3
  150 |                 for (size_t sf = 0; sf < nbSubframes; ++sf) {
      |                 ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:155:45: note: +4, including nesting penalty of 3, nesting level increased to 4
  155 |                         (analogRate > 0.0f) ? static_cast<float>(idx) / analogRate : 0.0f;
      |                                             ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:164:13: note: +2, including nesting penalty of 1, nesting level increased to 2
  164 |             for (size_t ch = 0; ch < nbAnalogs; ++ch) {
      |             ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:167:17: note: +3, including nesting penalty of 2, nesting level increased to 3
  167 |                 for (size_t f = 0; f < nbFrames; ++f) {
      |                 ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:169:21: note: +4, including nesting penalty of 3, nesting level increased to 4
  169 |                     for (size_t sf = 0; sf < nbSubframes; ++sf) {
      |                     ^
/home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:176:48: note: +3, including nesting penalty of 2, nesting level increased to 3
  176 |                     (ch < channelNames.size()) ? channelNames[ch] : fmt::format("Channel_{}", ch);
      |                                                ^

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Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com>

Replace #include <ezc3d/ezc3d.h> in c3ddata.h with a forward declaration of ezc3d::c3d, following the DICOM module pattern. Move DataTraits info() implementation to c3ddatatraits.cpp to keep the external library confined to .cpp files only. Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com>

…rame extraction Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com>

Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com>

Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com> Agent-Logs-Url: https://github.com/inviwo/modules/sessions/802536ca-88dd-4e2a-939e-942170ddc40e

…py() Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com> Agent-Logs-Url: https://github.com/inviwo/modules/sessions/bf174c8c-18ac-496c-ba0d-bf3876b29763

martinfalk

Looks reasonable

.github/presets/common.json

martinfalk · 2026-03-26T16:02:46Z

misc/c3d/src/processors/c3daveragedpositions.cpp

+    "Motion Tracking",                  // Category
+    CodeState::Experimental,            // Code state
+    Tags::CPU | Tag{"C3D"},             // Tags
+    R"(<Explanation of how to use the processor.>)"_unindentHelp,


misc/c3d/src/processors/c3dpointalignment.cpp

github-actions

Cpp-linter Review

Used clang-tidy v19.1.1

Click here for the full clang-tidy patch

diff --git a/misc/c3d/src/processors/c3dpointalignment.cpp b/misc/c3d/src/processors/c3dpointalignment.cpp
index 675f3d3..2bb3669 100644
--- a/misc/c3d/src/processors/c3dpointalignment.cpp
+++ b/misc/c3d/src/processors/c3dpointalignment.cpp
@@ -62 +62 @@ glm::dmat4 toGLM(const Eigen::Matrix3d& R, const Eigen::Vector3d& t) {
-glm::dvec3 toGLM(const Eigen::Vector3d& v) { return glm::dvec3(v(0), v(1), v(2)); }
+glm::dvec3 toGLM(const Eigen::Vector3d& v) { return {v(0), v(1), v(2)}; }

Have any feedback or feature suggestions? Share it here.

github-actions · 2026-03-26T18:23:45Z

misc/c3d/include/inviwo/c3d/c3dmodule.h

+
+namespace inviwo {
+
+class IVW_MODULE_C3D_API C3DModule : public InviwoModule {


clang-tidy diagnostic

misc/c3d/include/inviwo/c3d/c3dmodule.h:36:26: warning: [cppcoreguidelines-special-member-functions]

class 'C3DModule' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator

36 | class IVW_MODULE_C3D_API C3DModule : public InviwoModule { | ^

github-actions · 2026-03-26T18:23:45Z

misc/c3d/src/processors/c3dpointalignment.cpp

+    return M;
+}
+
+glm::dvec3 toGLM(const Eigen::Vector3d& v) { return glm::dvec3(v(0), v(1), v(2)); }


clang-tidy diagnostics

avoid repeating the return type from the declaration; use a braced initializer list instead [modernize-return-braced-init-list]

Suggested change

glm::dvec3 toGLM(const Eigen::Vector3d& v) { return glm::dvec3(v(0), v(1), v(2)); }

glm::dvec3 toGLM(const Eigen::Vector3d& v) { return {v(0), v(1), v(2)}; }

github-actions · 2026-03-26T18:23:45Z

misc/c3d/src/processors/c3dtodataframe.cpp

+    addProperties(includeResiduals_);
+}
+
+void C3DToDataFrame::process() {


clang-tidy diagnostic

misc/c3d/src/processors/c3dtodataframe.cpp:72:22: warning: [readability-function-cognitive-complexity]

function 'process' has cognitive complexity of 38 (threshold 25)

72 | void C3DToDataFrame::process() { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:88:9: note: +1, including nesting penalty of 0, nesting level increased to 1 88 | for (size_t f = 0; f < nbFrames; ++f) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:90:48: note: +2, including nesting penalty of 1, nesting level increased to 2 90 | timeValues[f] = (frameRate > 0.0f) ? static_cast<float>(f) / frameRate : 0.0f; | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:96:9: note: +1, including nesting penalty of 0, nesting level increased to 1 96 | for (size_t p = 0; p < nbPoints; ++p) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:103:13: note: +2, including nesting penalty of 1, nesting level increased to 2 103 | if (includeResiduals_) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:107:13: note: +2, including nesting penalty of 1, nesting level increased to 2 107 | for (size_t f = 0; f < nbFrames; ++f) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:112:17: note: +3, including nesting penalty of 2, nesting level increased to 3 112 | if (includeResiduals_) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:120:13: note: +2, including nesting penalty of 1, nesting level increased to 2 120 | if (includeResiduals_) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:137:9: note: +1, including nesting penalty of 0, nesting level increased to 1 137 | if (nbAnalogs > 0 && nbAnalogByFrame > 0) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:137:27: note: +1 137 | if (nbAnalogs > 0 && nbAnalogByFrame > 0) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:147:36: note: +2, including nesting penalty of 1, nesting level increased to 2 147 | (frameRate > 0.0f) ? frameRate * static_cast<float>(nbSubframes) : 0.0f; | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:149:13: note: +2, including nesting penalty of 1, nesting level increased to 2 149 | for (size_t f = 0; f < nbFrames; ++f) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:150:17: note: +3, including nesting penalty of 2, nesting level increased to 3 150 | for (size_t sf = 0; sf < nbSubframes; ++sf) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:155:45: note: +4, including nesting penalty of 3, nesting level increased to 4 155 | (analogRate > 0.0f) ? static_cast<float>(idx) / analogRate : 0.0f; | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:164:13: note: +2, including nesting penalty of 1, nesting level increased to 2 164 | for (size_t ch = 0; ch < nbAnalogs; ++ch) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:167:17: note: +3, including nesting penalty of 2, nesting level increased to 3 167 | for (size_t f = 0; f < nbFrames; ++f) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:169:21: note: +4, including nesting penalty of 3, nesting level increased to 4 169 | for (size_t sf = 0; sf < nbSubframes; ++sf) { | ^ /home/runner/work/modules/modules/inviwo/misc/c3d/src/processors/c3dtodataframe.cpp:176:48: note: +3, including nesting penalty of 2, nesting level increased to 3 176 | (ch < channelNames.size()) ? channelNames[ch] : fmt::format("Channel_{}", ch); | ^

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Copilot AI changed the title ~~[WIP] Add Inviwo module for loading C3D files~~ Add C3D module for loading biomechanics motion capture files via ezc3d Mar 17, 2026

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Copilot AI changed the title ~~Add C3D module for loading biomechanics motion capture files via ezc3d~~ Hide ezc3d include from public headers using forward declaration Mar 18, 2026

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Copilot AI changed the title ~~Hide ezc3d include from public headers using forward declaration~~ Hide ezc3d include from public C3D module headers Mar 18, 2026

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Copilot AI changed the title ~~Hide ezc3d include from public C3D module headers~~ Change C3DToMesh frame property to MinMaxProperty for multi-frame extraction Mar 18, 2026

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Copilot AI changed the title ~~Change C3DToMesh frame property to MinMaxProperty for multi-frame extraction~~ Add MinMaxProperty frame range and picking support to C3DToMesh Mar 18, 2026

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Copilot AI and others added 5 commits March 19, 2026 11:20

Add C3D module with ezc3d reader, DataFrame and Mesh processors

6dcabfc

Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com>

Change C3DToMesh frame property to IntSizeTMinMaxProperty for multi-f…

a3022ba

…rame extraction Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com>

Add picking support to C3DToMesh processor for hover tooltips

b6bebcb

Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com>

C3D: added BnL

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petersteneteg force-pushed the copilot/add-c3d-file-loader-module branch from 9aa36b1 to 6e92b97 Compare March 19, 2026 10:20

Copilot started work on behalf of petersteneteg March 21, 2026 18:50 View session

Add deepCopy() method to C3DData for independent copies of ezc3d data

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Copilot AI changed the title ~~Add MinMaxProperty frame range and picking support to C3DToMesh~~ Add picking support and deep copy to C3D module Mar 21, 2026

Copilot finished work on behalf of petersteneteg March 21, 2026 18:58

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Implement manual recursive deep copy of ezc3d::c3d in C3DData::deepCo…

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…py() Co-authored-by: petersteneteg <3638222+petersteneteg@users.noreply.github.com> Agent-Logs-Url: https://github.com/inviwo/modules/sessions/bf174c8c-18ac-496c-ba0d-bf3876b29763

Copilot AI changed the title ~~Add picking support and deep copy to C3D module~~ Implement manual deep copy for C3DData instead of relying on ezc3d's shallow copy constructor Mar 21, 2026

Copilot finished work on behalf of petersteneteg March 21, 2026 19:18

petersteneteg added 7 commits March 24, 2026 08:31

C3D: added transformations and average

b47b5d2

C3D: picking fix

56d6505

C3D: Adds PointAlignement

896eb40

C3D: alignment fixes

8628715

GHA: build C3D module

7c155f8

GHA: vcpkg fix

1087450

GHA: missing vcpkg feature

d0d29bb

petersteneteg marked this pull request as ready for review March 26, 2026 12:29

petersteneteg requested a review from martinfalk March 26, 2026 12:29

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C3D: review fixes

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petersteneteg merged commit a329142 into master Mar 27, 2026
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petersteneteg deleted the copilot/add-c3d-file-loader-module branch March 27, 2026 06:58

github-actions bot pushed a commit to inviwo/regression that referenced this pull request Mar 27, 2026

Remove regression reports for MERGED PR inviwo/modules#277

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Implement manual deep copy for C3DData instead of relying on ezc3d's shallow copy constructor#277

Implement manual deep copy for C3DData instead of relying on ezc3d's shallow copy constructor#277
petersteneteg merged 15 commits intomasterfrom
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		namespace inviwo {

		class IVW_MODULE_C3D_API C3DModule : public InviwoModule {

	glm::dvec3 toGLM(const Eigen::Vector3d& v) { return glm::dvec3(v(0), v(1), v(2)); }
	glm::dvec3 toGLM(const Eigen::Vector3d& v) { return {v(0), v(1), v(2)}; }

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