Add automatic calibration #293
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…to config and tests, also refactor optimizers
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mschwoer
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Aug 8, 2024
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| optimization_manager_config = { | ||
| "ms1_error": self.config["search_initial"]["initial_ms1_tolerance"], | ||
| "ms2_error": self.config["search_initial"]["initial_ms2_tolerance"], | ||
| "rt_error": self.config["search_initial"]["initial_rt_tolerance"], | ||
| "mobility_error": self.config["search_initial"][ | ||
| "initial_mobility_tolerance" | ||
| ], | ||
| "column_type": "library", | ||
| "num_candidates": self.config["search_initial"]["initial_num_candidates"], | ||
| "classifier_version": -1, | ||
| "fwhm_rt": self.config["optimization_manager"]["fwhm_rt"], | ||
| "fwhm_mobility": self.config["optimization_manager"]["fwhm_mobility"], | ||
| "score_cutoff": self.config["optimization_manager"]["score_cutoff"], | ||
| } | ||
| self._optimization_manager = manager.OptimizationManager( | ||
| self.config["optimization_manager"], | ||
| optimization_manager_config, |
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this seems to me like OptimizationManager-specific logic that is outside of OptimizationManager :-)
suggestion:
pass the self.config to the OptimizationManager and do this mapping during initialization. Also, I suggest separating between constant values (probable fwhm_rt does not change?) and dynamic values (e.g. classifier_version)
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Yes, that is true. I'll change it.
I think everything in the optimization manager should change – fwhm_rt for instance is updated during calibration.
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