Changes to the sensors.py file in the LightDependentGECI class returned the GECI class to the previous version found on the main github as well.#67
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Made changes to the code to get the parameter values from the Dictionaries dictionaries instead of from having to read json files each time.
made changes to the dictionary
Made changes to the LightDependentGECI code to make sure that the LightDependentGECI objects can be created and used
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tests should go in tests/imaging/test_sensors.py
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I see, this is more of an interactive script for testing parameters...this would go better in an if __name__ == 'main': block at the bottom. Or maybe in notebooks?
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this should go in docs/tutorials
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If these all have the same variables, this would be way more readable as a CSV
| """Defines ``exc_factor``""" | ||
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| model: str | ||
| model: str = field(default="exc_factor = 1 : 1", init=False) |
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no need to put this here, since this is defined in NullExcitationModel
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and LightExcitation is where you'd put your Hill function. Looks like you had it then removed it again?
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| """Uses a Hill equation to convert from Ca2+ to ΔF/F, as in Song et al., 2021""" |
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Most of this stuff should be defined on LightExcitation, not on LightDependentGECI. This keeps the parameter sets for each part of the model nice and separate. Look at DynamicCalcium or DoubExpCalBindingActivation for examples
| if callable(super_post_init): | ||
| super_post_init() | ||
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| def fluorescence(self, GECI_str, brightness, wavelength): |
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this looks like a testing sort of function? If the interface is clunky enough we need code like this to test it, we need to revise the interface. But I don't think so...look at tests/test_sensors.py and you'll see it should be as simple as instantiating it (e.g., geci = gcamp7f(), then injecting it.
| print(f"ng.dFF is: {ng.dFF}") | ||
| return ng.dFF | ||
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| def LightDependentParams(GECI_str) -> dict: |
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we definitely don't want this function: the structure for what params a LightDependentGECI needs is already captured by the class and the model attributes. Look at geci() and you'll see the machinery is already in place to simply load from a bunch of keyword parameters (including the LightExcitation model), which you could load from a CSV using pandas
| k = params['k'] | ||
| return {'A' : A, 'baseline' : baseline, 'k' : k, 'n' : n, 'ec50' : ec50}, params_w | ||
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| def light_dependent_geci(name: str, doub_exp_conv: bool, pre_existing_cal: bool, bind_act_model: bool, x, w, Ca_rest=50 * nmolar, |
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No, again, just use the geci() function I already made
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In general, it seems like you're trying to reinvent the wheel. I already had the structure in place to make this easy. |
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sensors.py