ProcessPlans
¶
more info coming…
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class
mosaicpy.processplan.
ProcessPlan
(llsdir, imps=[], t_range=None, c_range=None)¶ A class to store the processing plan for a given data directory and set of Imps
The ProcessPlan is responsible for accepting a data direcory, an ordered list of ImgProcessors, and an optional t_range and c_range for processing. It also creates the self.meta dict, which will hold and pass metadata throughout the processing chain.
Parameters: - llsdir (LLSdir) – instance of LLSdir, the data directory.
- imps (list) – A list of 3 or 4-tuples, where each item contains: 1. (ImgProcessor) The image processor class (uninstantiated) 2. (dict) - The params dict that will be passed to ImgProcessor on instantiation 3. (bool) - Whether the ImgProcessor is active or not 4. (bool, optional) - Whether the ImgProcessor is collapsed in the GUI
- t_range (list) – a list of timepoints to process. Defaults to all timepoints
- c_range (list) – a list of channels to process. Defaults to all channels
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exception
PlanError
¶ hard error if the plan cannot be executed as requested
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exception
PlanWarning
¶ light error, if a plan has ill-advised steps
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exception
ProcessError
(imp, position=None)¶ error occured during processing
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exception
SetupError
(imp, position=None)¶
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exception
TeardownError
(imp, position=None)¶
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execute
()¶ executes the processing plan, iterating over timepoints
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plan
(skip_warnings=False)¶ This actually instantiates the ImgProcessors (but does not run them).
Unless explicitly skipped, it runs check_sanity() to look for potential problems in the plan. Then in instantiates all active image processors, by calling the ImgProcessor.from_llsdir() class method.
It also creates the self.meta object that will be passed through the processing chain.
Raises: self.PlanWarning
– if check_sanity() failsself.PlanError
– if ImgProcessor instantiation fails
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setup_t
(data)¶ Called before all ImgProcs, at every timepoint.
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teardown_t
(data)¶ Called after every ImgProcs, at every timepoint.