Raster Scanning Code

.gitignore

@@ -146,4 +146,6 @@ dmypy.json
 .pytype/
 
 # Cython debug symbols
-cython_debug/
+cython_debug/**/.DS_Store
+
+**/.DS_Store

cleo/base.py

@@ -335,6 +335,11 @@ class CLSimulator(NeoExportable):
     _processing_net_op: NetworkOperation = field(default=None, init=False, repr=False)
     _net_store_name: str = field(default="cleo default", init=False, repr=False)
 
+    @property
+    def registry(self):
+        """Returns the DeviceInteractionRegistry for this simulator."""
+        return registry_for_sim(self)
+
     def inject(
         self, device: InterfaceDevice, *neuron_groups: NeuronGroup, **kwparams: Any
     ) -> CLSimulator:

cleo/imaging/scope.py

@@ -2,20 +2,21 @@
 
 import warnings
 from datetime import datetime
-from typing import Callable
 
 import matplotlib as mpl
 import neo
 import quantities as pq
 from attrs import define, field, fields
-from brian2 import NeuronGroup, Quantity, Unit, meter, mm, ms, np, um
+from brian2 import NeuronGroup, Quantity, Unit, meter, mm, ms, np, um, second
 from jaxtyping import Float, UInt
 from matplotlib.artist import Artist
 from mpl_toolkits.mplot3d import Axes3D
+from numpy import pi
 
 from cleo.base import Recorder
 from cleo.coords import coords_from_ng
 from cleo.imaging.sensors import Sensor
+from cleo.light import Light, GaussianEllipsoid
 from cleo.utilities import (
     analog_signal,
     normalize_coords,
@@ -157,6 +158,11 @@ class Scope(Recorder):
     )
     """relative expression levels of neurons selected from each injection"""
 
+    imaging_light: Light = field(init=False, repr=False, default=None)
+    """raster scanning parameters"""
+
+    _is_scanning: bool = field(default=False, init=False, repr=False)
+
     @property
     def n(self) -> int:
         """Number of imaged ROIs"""
@@ -314,6 +320,8 @@ 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)
+        if self.imaging_light is not None:
+            self.sim.registry.set_img_width(self.imaging_light, self.img_width)
 
     def i_targets_for_neuron_group(self, neuron_group):
         """can handle multiple injections into same ng"""
@@ -451,3 +459,39 @@ def to_neo(self) -> neo.AnalogSignal:
             )
         return signal
         # want ROI coordinates and size in image
+
+    # Method for optional raster scanning
+    def create_imaging_light(self, wavelength=920e-9 * meter, pulse_freq=30):
+        spot_area = pi * self.soma_radius**2
+        img_width_area = pi * (self.img_width / 2) ** 2
+        pulse_width = spot_area / img_width_area * (1 / pulse_freq) * second
+        self.imaging_light = Light(
+            name=f"{self.name}_imlight",
+            light_model=GaussianEllipsoid(),
+            wavelength=wavelength,  # user can pass in wavelength values
+            pulse_freq=pulse_freq,  # user sets pulse freq when creating imaging light
+            pulse_stagger=True,
+            is_scanning=True,
+            pulse_width=pulse_width,
+        )
+        # attach soma_radius for registry use
+        self.imaging_light.soma_radius = self.soma_radius
+        return self.imaging_light
+
+    # turn raster scanning on/off
+    @property
+    def is_scanning(self):
+        return self._is_scanning
+
+    @is_scanning.setter
+    def is_scanning(self, flag: bool):
+        self._is_scanning = flag
+        if self.imaging_light is not None:
+            self.sim.registry.set_is_scanning(self.imaging_light, flag)
+
+    # keep img_width validator and update imaging width
+    @img_width.validator
+    def _update_img_width(self, attr, value):
+        # Make sure create_imaging_light has been called
+        if self.imaging_light is not None:
+            self.sim.registry.set_img_width(self.imaging_light, value)

cleo/light/light.py

@@ -1,4 +1,5 @@
 """Contains Light device and propagation models"""
+
 from __future__ import annotations
 
 import datetime
@@ -14,13 +15,17 @@
     Subgroup,
     np,
 )
+
+from brian2 import ms
+
 from brian2.units import (
     Quantity,
     mm,
     mm2,
     mwatt,
     nmeter,
     um,
+    second,
 )
 from jaxtyping import Float
 from matplotlib import colors
@@ -316,6 +321,42 @@ class Light(Stimulator):
     wavelength: Quantity = field(default=473 * nmeter, kw_only=True)
     """light wavelength with unit (usually nmeter)"""
 
+    _pulse_freq: float = field(default=30, kw_only=True, alias="pulse_freq")
+    _pulse_width: Quantity = field(default=0 * ms, kw_only=True, alias="pulse_width")
+
+    is_scanning: bool = field(default=False, kw_only=True)
+    _pulse_stagger: bool = field(default=False, kw_only=True, alias="pulse_stagger")
+
+    @property
+    def pulse_freq(self):
+        return self._pulse_freq
+
+    @pulse_freq.setter
+    def pulse_freq(self, hz: float):
+        self._pulse_freq = hz
+        if self.sim is not None:
+            registry_for_sim(self.sim).set_pulse_freq(self, hz)
+
+    @property
+    def pulse_width(self):
+        return self._pulse_width
+
+    @pulse_width.setter
+    def pulse_width(self, width: Quantity):
+        self._pulse_width = width
+        if self.sim is not None:
+            registry_for_sim(self.sim).set_pulse_width(self, width)
+
+    @property
+    def pulse_stagger(self):
+        return self._pulse_stagger
+
+    @pulse_stagger.setter
+    def pulse_stagger(self, stagger: bool):
+        self._pulse_stagger = stagger
+        if self.sim is not None:
+            registry_for_sim(self.sim).set_pulse_stagger(self, stagger)
+
     @coords.validator
     def _check_coords(self, attribute, value):
         if len(value.shape) != 2 or value.shape[1] != 3: