palmari.processing package#
Subpackages#
- palmari.processing.steps package
- Submodules
- palmari.processing.steps.base module
- palmari.processing.steps.drift_corrector module
- palmari.processing.steps.quot_localizer module
- palmari.processing.steps.quot_tracker module
- palmari.processing.steps.trackpy_tracker module
- palmari.processing.steps.window_percentile module
- Module contents
Submodules#
palmari.processing.edit_pipeline_window module#
palmari.processing.image_pipeline module#
- class palmari.processing.image_pipeline.ImagePipeline(name: str, movie_preprocessors: List[palmari.processing.steps.base.MoviePreProcessor], detector: palmari.processing.steps.base.Detector, localizer: palmari.processing.steps.base.SubpixelLocalizer, loc_processors: List[palmari.processing.steps.base.LocProcessor], tracker: palmari.processing.steps.base.Tracker)[source]#
Bases:
object
- property available_steps#
- exp_params_path(acq: palmari.data_structure.acquisition.Acquisition) str [source]#
- exp_run_df_path(acq: palmari.data_structure.acquisition.Acquisition) str [source]#
- classmethod from_dict(p: Dict)[source]#
Instantiate from a dictionnary. Here’s an example Dictionnary which could be passed as an argument :
{ "name":"my_pipeline", "movie_preprocessors":[ { "MyPreProcessingClass":{"param1":value,"param2":other_value} }, { "WindowPercentileFilter":{} # If the parameter's dict is empty, default parameters will be used } }], "localizer":{ "DefaultLocalizer":{"threshold_factor":1.5} }, "tracker":{ "UnknownClass":{"bla":bla} # If the class is not found, this will raise an exception # Similarly, if the class provided does not inherit Tracker, an exception will be raised } # If some step is not mentioned (e.g. here, there's nothing about localization processing), then # if it's movie_preprocessors, then no movie_preprocessors will be used (same for loc_processors) # it it's localizer or tracker, then the default classes will be used. }
- is_already_localized(acq: palmari.data_structure.acquisition.Acquisition)[source]#
- is_already_tracked(acq: palmari.data_structure.acquisition.Acquisition)[source]#
- loc_processing(mov: dask.array.core.Array, locs: pandas.core.frame.DataFrame, pixel_size: float = 1.0) pandas.core.frame.DataFrame [source]#
- mark_as_localized(acq: palmari.data_structure.acquisition.Acquisition)[source]#
- mark_as_tracked(acq: palmari.data_structure.acquisition.Acquisition)[source]#
- movie_localization(mov: dask.array.core.Array, DT: float, pixel_size: float) pandas.core.frame.DataFrame [source]#
- process(to_process: Union[palmari.data_structure.acquisition.Acquisition, palmari.data_structure.experiment.Experiment], force_reprocess: bool = False)[source]#