Improve signals #24
Improve signals #24
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- signal_exists checks if the given string is a key in all_signals - behavior_exists similarly for behaviors - remove signal_scales. they're not used - no longer need integers to index signals/behaviors
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Pull Request Overview
This PR improves signal and behavior handling in the PhysiCell codebase by refactoring the core API design and consolidating repetitive necrotic cell detection logic.
- Refactors signal and behavior dictionaries to use modern C++ patterns with function objects and improved API design
- Replaces repetitive necrotic cell detection code with a centralized
is_necrotic()method - Updates function names and return types for better consistency and type safety
Reviewed Changes
Copilot reviewed 11 out of 12 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| sample_projects/celltypes3/custom_modules/custom.cpp | Replace necrotic phase checks with is_necrotic() method calls |
| sample_projects/cancer_immune/custom_modules/cancer_immune_3D.cpp | Replace necrotic phase checks with is_necrotic() method calls |
| modules/PhysiCell_various_outputs.cpp | Replace necrotic phase checks and fix loop variable type |
| modules/PhysiCell_pathology.cpp | Replace multiple necrotic phase checks with is_necrotic() method calls |
| modules/PhysiCell_geometry.cpp | Update function calls from find_behavior_index to behavior_exists |
| core/PhysiCell_signal_behavior.h | Major API refactor with new Signal/Behavior structs and function signatures |
| core/PhysiCell_rules.cpp | Update function calls and fix output stream usage |
| core/PhysiCell_phenotype.h | Add const version of current_phase() method |
| core/PhysiCell_phenotype.cpp | Implement const version of current_phase() method |
| core/PhysiCell_cell.h | Add is_necrotic() method declaration |
| core/PhysiCell_cell.cpp | Implement is_necrotic() method with centralized logic |
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Pull Request Overview
This PR refactors the PhysiCell signal and behavior system to improve code organization and maintainability by replacing manual necrotic state checks with a centralized is_necrotic() method and modernizing the signal/behavior dictionary implementation.
- Replaces repetitive necrotic phase code checks with a new
Cell::is_necrotic()method - Modernizes the signal/behavior dictionary system using function objects and improved APIs
- Updates function calls to use new behavior/signal existence checking methods
Reviewed Changes
Copilot reviewed 11 out of 12 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| sample_projects/celltypes3/custom_modules/custom.cpp | Uses new is_necrotic() method in coloring functions |
| sample_projects/cancer_immune/custom_modules/cancer_immune_3D.cpp | Uses new is_necrotic() method in coloring function |
| modules/PhysiCell_various_outputs.cpp | Uses new is_necrotic() method and fixes loop variable type |
| modules/PhysiCell_pathology.cpp | Uses new is_necrotic() method across multiple coloring functions |
| modules/PhysiCell_geometry.cpp | Updates to use new behavior existence checking API |
| core/PhysiCell_signal_behavior.h | Complete refactor of signal/behavior system with modern C++ features |
| core/PhysiCell_rules.cpp | Updates to use new signal/behavior existence checking methods and fixes output stream |
| core/PhysiCell_phenotype.h | Adds const version of current_phase() method |
| core/PhysiCell_phenotype.cpp | Implements const version of current_phase() method |
| core/PhysiCell_cell.h | Declares new is_necrotic() method |
| core/PhysiCell_cell.cpp | Implements new is_necrotic() method |
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core/PhysiCell_phenotype.cpp
Outdated
| const Phase& Cycle::current_phase() const | ||
| { | ||
| return const_cast<Cycle*>(this)->current_phase(); |
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Using const_cast to remove constness and call the non-const version is an anti-pattern. Instead, implement the const version properly by directly accessing the data member, or refactor the non-const version to call the const version."
| const Phase& Cycle::current_phase() const | |
| { | |
| return const_cast<Cycle*>(this)->current_phase(); | |
| return data.current_phase(); |
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