Raster Scanning Code #55
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| @@ -146,6 +151,7 @@ class Scope(Recorder): | |||
| factory=list, repr=False, init=False | |||
| ) | |||
| """relative expression levels of neurons selected from each injection""" | |||
| Registry: DeviceInteractionRegistry = None | |||
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Are you sure we need to store the registry when we can just do registry_for_sim(self.sim)?
| @@ -291,6 +297,8 @@ def connect_to_neuron_group(self, neuron_group: NeuronGroup, **kwparams) -> None | |||
| self.sigma_per_injct.append(sigma_noise) | |||
| self.focus_coords_per_injct.append(focus_coords) | |||
| self.rho_rel_per_injct.append(rho_rel) | |||
| self.Registry = registry_for_sim(self.sim) | |||
| self.Registry.update_fov(self.img_width) | |||
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would this need to be updated on every injection? Also, it can't be right that there's a single update_fov for the whole registry, since this should vary for each light device
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the Scope should optionally have an imaging_light object, and the img_width and scan_freq would be updated specific to that light
| @@ -46,11 +50,21 @@ class DeviceInteractionRegistry: | |||
| """Set of (light, light-dependent device, neuron group) tuples representing | |||
| previously created connections.""" | |||
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| raster_fov: int = field(default=500 * 1e-6 * meter, kw_only=True) | |||
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| raster_enable: int = field(default=0, kw_only=True) | |||
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again, these would be at the level of individual lights, not the whole registry
| @@ -294,6 +294,8 @@ class Light(Stimulator): | |||
| wavelength: Quantity = field(default=473 * nmeter, kw_only=True) | |||
| """light wavelength with unit (usually nmeter)""" | |||
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| scan_freq : int = field(default=30, kw_only=True) | |||
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I'd create a subclass RasterScanningLight to hide the scan_freq details from the typical Light object
| @@ -104,6 +118,10 @@ def connect_light_to_ldd_for_ng( | |||
| i_source = self.subgroup_idx_for_light[light] | |||
| light_prop_syn.epsilon[i_source, :] = epsilon | |||
| light_prop_syn.T[i_source, :] = light.transmittance(coords_from_ng(ng)).ravel() | |||
| light_prop_syn.scan_period = second / light.scan_freq | |||
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I'd put these in a separate function that you call both here (on injection) and when you change the params on the scope/imaging light (setter functions). like update_raster_scan_params(scope) or something like that
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like you've already done with update_fov but can include these other variables too
Uploaded the code for raster scanning.
Since there's only one registry for simulation, the flag might not work at this moment