Raster Scanning Code

cleo/imaging/scope.py

@@ -11,6 +11,7 @@
 
 from cleo.base import Recorder
 
+from cleo.registry import DeviceInteractionRegistry, registry_for_sim
 from cleo.imaging.sensors import Sensor
 from cleo.coords import coords_from_ng
 from cleo.utilities import normalize_coords, rng
@@ -83,6 +84,10 @@ def target_neurons_in_plane(
 
     return i_targets, noise_focus_factor[i_targets], coords_on_plane[i_targets]
 
+'''
+def fov_change_observation(instance, attribute, value):
+    instance.Registry.update_fov(value)
+'''
 
 @define(eq=False)
 class Scope(Recorder):
@@ -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
 
     @property
     def n(self) -> int:
@@ -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)
 
     def i_targets_for_neuron_group(self, neuron_group):
         """can handle multiple injections into same ng"""

cleo/light/light.py

@@ -294,6 +294,8 @@ class Light(Stimulator):
     wavelength: Quantity = field(default=473 * nmeter, kw_only=True)
     """light wavelength with unit (usually nmeter)"""
 
+    scan_freq : int = field(default=30, kw_only=True)
+
     @coords.validator
     def _check_coords(self, attribute, value):
         if len(value.shape) != 2 or value.shape[1] != 3:

cleo/registry.py

@@ -8,11 +8,15 @@
 
 from attrs import define, field
 from brian2 import NeuronGroup, Subgroup, Synapses
+from brian2 import defaultclock
 from brian2.units.allunits import joule, kgram, meter, meter2, nmeter, second
+from numpy import pi
 
 from cleo.coords import coords_from_ng
 from cleo.utilities import brian_safe_name
 
+import warnings
+
 
 @define(repr=False)
 class DeviceInteractionRegistry:
@@ -46,11 +50,21 @@ class DeviceInteractionRegistry:
     """Set of (light, light-dependent device, neuron group) tuples representing
     previously created connections."""
 
+    raster_fov: int = field(default=500 * 1e-6 * meter, kw_only=True)
+
+    raster_enable: int = field(default=0, kw_only=True)
+
     light_prop_model = """
         T : 1
+        scale : 1
         epsilon : 1
         Ephoton : joule
-        Irr_post = epsilon * T * Irr0_pre : watt/meter**2 (summed)
+        raster_enable : 1
+        scan_period : second
+        raster_dwell_time: second
+        Irr_norm = epsilon * T * Irr0_pre : watt/meter**2 
+        Irr_raster = epsilon * T * Irr0_pre * int(((t + scan_period * (i/N)) % (scan_period)) < (raster_dwell_time * scale * 10)) / (scale * 10): watt/meter**2 
+        Irr_post = Irr_norm * (1 - raster_enable) + Irr_raster * raster_enable : watt/meter**2 (summed)
         phi_post = Irr_post / Ephoton : 1/second/meter**2 (summed)
     """
     """Model used in light propagation synapses"""
@@ -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
+        light_prop_syn.raster_dwell_time = (pi * 10 ** -10 * meter2)/ (pi*(self.raster_fov/2)**2) * second / light.scan_freq
+        light_prop_syn.scale = 1 + (defaultclock.dt > light_prop_syn.raster_dwell_time).astype(int) * (defaultclock.dt / (light_prop_syn.raster_dwell_time) - 1)
+        light_prop_syn.raster_enable = self.raster_enable
         # fmt: off
         # Ephoton = h*c/lambda
         light_prop_syn.Ephoton[i_source, :] = (
@@ -195,6 +213,15 @@ def source_for_light(self, light: "Light") -> Subgroup:
         """Returns the subgroup representing the given light source"""
         i = self.subgroup_idx_for_light[light]
         return self.light_source_ng[i]
+
+    def update_fov(self, new_fov: float):
+        self.raster_enable = 1
+        def custom_warning_format(message, category, filename, lineno, line=None):
+            return f"{category.__name__}: {message}\n"
+        warnings.formatwarning = custom_warning_format
+        if self.raster_fov != new_fov:
+            self.raster_fov = new_fov
+            warnings.warn("Warning: cleo currently supports use of single scanning fov in simulation, the latest update parameter will be used", UserWarning)
 
 
 registries: dict["CLSimulator", DeviceInteractionRegistry] = {}