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- Changed all instances of `id` to `track_id` in emitter structures and related functions for consistency. - Introduced `filter_by_state` function to filter emitters based on their state (monomer or dimer). - Updated simulation functions to accept optional starting conditions, allowing for continued simulations from a specified state. - Added utility functions for extracting and converting emitters to diffusing emitters. - Enhanced test cases to validate changes in emitter identification and filtering logic.
…asic simulation, pattern types, photophysics, and localization uncertainty. Update the image generation function to remove frame integration parameter and adjust processing logic accordingly. Introduce new utility functions for extracting final states in interaction diffusion simulations. Refactor relevant code sections to enhance clarity and maintainability.
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