From a92458a62987f64334bfa255a4f278ee791d0638 Mon Sep 17 00:00:00 2001
From: Harrison-Oatman <46121828+Harrison-Oatman@users.noreply.github.com>
Date: Thu, 8 Jan 2026 01:42:29 -0500
Subject: [PATCH 1/3] New pattern model specification

---
 src/pyclm/core/patterns/bar_patterns.py       | 60 +++++---------
 .../patterns/feedback_control_patterns.py     | 69 ++++++++--------
 src/pyclm/core/patterns/ktr_patterns.py       | 52 +++++-------
 src/pyclm/core/patterns/pattern.py            | 80 +++++++++++++++++--
 src/pyclm/core/patterns/pattern_process.py    | 18 +++--
 src/pyclm/core/patterns/static_patterns.py    | 26 ++----
 src/pyclm/core/patterns/wave_patterns.py      | 27 ++-----
 7 files changed, 172 insertions(+), 160 deletions(-)

diff --git a/src/pyclm/core/patterns/bar_patterns.py b/src/pyclm/core/patterns/bar_patterns.py
index ff2abf5..7956912 100644
--- a/src/pyclm/core/patterns/bar_patterns.py
+++ b/src/pyclm/core/patterns/bar_patterns.py
@@ -16,7 +16,6 @@ def __new__(cls, *args, **kwargs):
         return super().__new__(cls)
 
     def __init__(self, *args, **kwargs):
-
         super().__init__(*args, **kwargs)
         print(f"Initializing {self.__class__.__name__}")
 
@@ -28,26 +27,21 @@ class StationaryBarPattern(BarPatternBase):
 
     name = "bar (stationary)"
 
-    def __init__(self, experiment_name, camera_properties, duty_cycle=0.2, bar_speed=0, period=30, **kwargs):
+    def __init__(self, duty_cycle=0.2, bar_speed=0, period=30, **kwargs):
         """
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
                            vertical axis containing "on" pixels
         :param bar_speed: speed in um/min
         :param period: period in um
         """
-        super().__init__(experiment_name, camera_properties)
+        super().__init__(**kwargs)
 
         self.duty_cycle = duty_cycle
         self.bar_speed = 0
         self.period_space = period    # in um
         self.period_time = 0    # in minutes
 
-    def initialize(self, experiment):
-        super().initialize(experiment)
-
-        return []
-
-    def generate(self, data_dock: DataDock):
+    def generate(self, context):
 
         xx, yy = self.get_meshgrid()
 
@@ -63,41 +57,34 @@ class BarPattern(BarPatternBase):
 
     name = "bar"
 
-    def __init__(self, experiment_name, camera_properties, duty_cycle=0.2, bar_speed=1, period=30, **kwargs):
+    def __init__(self, duty_cycle=0.2, bar_speed=1, period=30, **kwargs):
         """
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
                            vertical axis containing "on" pixels
         :param bar_speed: speed in um/min
         :param period: period in um
         """
-        super().__init__(experiment_name, camera_properties)
+        super().__init__(**kwargs)
 
         self.duty_cycle = duty_cycle
         self.bar_speed = bar_speed
         self.period_space = period    # in um
         self.period_time = period / bar_speed    # in minutes
 
-    def initialize(self, experiment):
-        super().initialize(experiment)
-
-        return []
+    def _get_pattern_at_time(self, t_minutes):
+         xx, yy = self.get_meshgrid()
+         is_on = ((t_minutes - (yy / self.bar_speed)) % self.period_time) < self.duty_cycle*self.period_time
+         return is_on.astype(np.float16)
 
-    def generate(self, data_dock: DataDock):
-
-        t = data_dock.time_seconds / 60
-
-        xx, yy = self.get_meshgrid()
-
-        is_on = ((t - (yy / self.bar_speed)) % self.period_time) < self.duty_cycle*self.period_time
-
-        return is_on.astype(np.float16)
+    def generate(self, context):
+        return self._get_pattern_at_time(context.time / 60)
 
 
 class SawToothMethod(PatternMethod):
 
     name = "sawtooth"
 
-    def __init__(self, experiment_name, camera_properties, duty_cycle=0.2,
+    def __init__(self, duty_cycle=0.2,
                  bar_speed=1, period=30, inverse=False, **kwargs):
         """
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
@@ -105,7 +92,7 @@ def __init__(self, experiment_name, camera_properties, duty_cycle=0.2,
         :param bar_speed: speed in um/min
         :param period: period in um
         """
-        super().__init__(experiment_name, camera_properties)
+        super().__init__(**kwargs)
 
         self.duty_cycle = duty_cycle
         self.bar_speed = bar_speed
@@ -113,13 +100,8 @@ def __init__(self, experiment_name, camera_properties, duty_cycle=0.2,
         self.period_time = period / bar_speed  # in minutes
         self.inverse = inverse
 
-    def initialize(self, experiment):
-        super().initialize(experiment)
-
-        return []
-
-    def generate(self, data_dock: DataDock):
-        t = data_dock.time_seconds / 60
+    def generate(self, context):
+        t = context.time / 60
 
         xx, yy = self.get_meshgrid()
 
@@ -141,7 +123,7 @@ class BouncingBarPattern(BarPattern):
 
     name = "bar_bounce"
 
-    def __init__(self, experiment_name, camera_properties, duty_cycle=0.2,
+    def __init__(self, duty_cycle=0.2,
                  bar_speed=1, period=30, t_loop=60, **kwargs):
         """
 
@@ -151,11 +133,11 @@ def __init__(self, experiment_name, camera_properties, duty_cycle=0.2,
         :param period: period in um
         :param t_loop: period of reversal (there and back) in minutes
         """
-        super().__init__(experiment_name, camera_properties, duty_cycle, bar_speed, period, **kwargs)
+        super().__init__(duty_cycle=duty_cycle, bar_speed=bar_speed, period=period, **kwargs)
         self.t_loop_s = t_loop * 60
 
-    def generate(self, data_dock: DataDock):
-        t = data_dock.time_seconds
+    def generate(self, context):
+        t = context.time
         t = t % self.t_loop_s
 
         halfway = self.t_loop_s / 2
@@ -163,6 +145,4 @@ def generate(self, data_dock: DataDock):
         if t > halfway:
             t = halfway - (t - halfway)
 
-        data_dock.time_seconds = t
-
-        return super().generate(data_dock)
+        return self._get_pattern_at_time(t / 60)
diff --git a/src/pyclm/core/patterns/feedback_control_patterns.py b/src/pyclm/core/patterns/feedback_control_patterns.py
index 87d6860..991f84c 100644
--- a/src/pyclm/core/patterns/feedback_control_patterns.py
+++ b/src/pyclm/core/patterns/feedback_control_patterns.py
@@ -9,34 +9,31 @@
 import tifffile
 
 class PerCellPatternMethod(PatternMethod):
+    """
+    Base class for the per-cell pattern methods. This class provides the basic structure for generating patterns
+    based on the properties of segmented cells. Subclasses should implement the `process_prop` method to define
+    how each cell's properties are used to generate the pattern, and include any additional parameters needed for the
+    specific pattern in their `__init__` method.
+    """
 
     name = "per_cell_base"
 
-    def __init__(self, experiment_name, camera_properties, channel=None, voronoi=False, gradient=False, direction = 1, **kwargs):
-        super().__init__(experiment_name, camera_properties, **kwargs)
+    def __init__(self, channel=None, voronoi=False, gradient=False, direction = 1, **kwargs):
+        super().__init__(**kwargs)
 
         if channel is None:
-            raise AttributeError(f"{experiment_name}: PerCellPatternModels must be provided a "
-                                 f"segmentation channel in the .toml: e.g. channel = \"638\"")
-
-        self.channel = channel
-        self.seg_channel_id = None
+            raise AttributeError("PerCellPatternModels must be provided a "
+                                 "segmentation channel in the .toml: e.g. channel = \"638\"")
 
         self.gradient = gradient
         self.voronoi = voronoi
         self.direction = direction
 
-    def initialize(self, experiment):
-        super().initialize(experiment)
-
-        channel = experiment.channels.get(self.channel, None)
-
-        assert channel is not None, f"provided channel {self.channel} is not in experiment"
-
-        self.seg_channel_id = channel.channel_id
-        cell_seg_air = AcquiredImageRequest(channel.channel_id, False, True)
+        self.channel = channel
 
-        return [cell_seg_air]
+        # request the segmentation of the provided channel, to be used by self.generate.
+        # This will ensure that the data is available when generate is called.
+        self.add_requirement(channel_name=channel, seg=True)
 
     def prop_vector(self, prop, vec):
         """
@@ -86,9 +83,9 @@ def voronoi_rebuild(self, img):
 
         return out
 
-    def generate(self, data_dock: DataDock) -> np.ndarray:
+    def generate(self, context) -> np.ndarray:
 
-        seg: np.ndarray = data_dock.data[self.seg_channel_id]["seg"].data
+        seg = context.segmentation(self.channel)
 
         if self.voronoi:
             px_dis = distance_transform_edt(seg == 0)
@@ -114,9 +111,9 @@ class RotateCcwModel(PerCellPatternMethod):
 
     name = "rotate_ccw"
 
-    def __init__(self, experiment_name, camera_properties, channel=None, **kwargs):
+    def __init__(self, channel=None, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
 
@@ -132,9 +129,9 @@ class MoveOutModel(PerCellPatternMethod):
 
     name = "move_out"
 
-    def __init__(self, experiment_name, camera_properties, channel=None, **kwargs):
+    def __init__(self, channel=None, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
 
@@ -150,9 +147,9 @@ class MoveInModel(PerCellPatternMethod):
 
     name = "move_in"
 
-    def __init__(self, experiment_name, camera_properties, channel=None, **kwargs):
+    def __init__(self, channel=None, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
 
@@ -168,9 +165,9 @@ class MoveDownModel(PerCellPatternMethod):
 
     name = "move_down"
 
-    def __init__(self, experiment_name, camera_properties, channel=None, **kwargs):
+    def __init__(self, channel=None, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
 
@@ -186,12 +183,12 @@ class BounceModel(PerCellPatternMethod):
 
     name = "fb_bounce"
 
-    def __init__(self, experiment_name, camera_properties, channel=None, t_loop=60, **kwargs):
+    def __init__(self, channel=None, t_loop=60, **kwargs):
 
         self.t_loop_s = t_loop * 60
         self.down = True
 
-        super().__init__(experiment_name, camera_properties, channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
 
@@ -202,9 +199,9 @@ def process_prop(self, prop) -> np.ndarray:
 
         return self.prop_vector(prop, vec)
 
-    def generate(self, data_dock: DataDock) -> np.ndarray:
+    def generate(self, context) -> np.ndarray:
 
-        t = data_dock.time_seconds
+        t = context.time
         t = t % self.t_loop_s
 
         halfway = self.t_loop_s / 2
@@ -212,20 +209,20 @@ def generate(self, data_dock: DataDock) -> np.ndarray:
         if t > halfway:
             self.down = False
 
-        return super().generate(data_dock)
+        return super().generate(context)
 
 
 class DensityModel(PerCellPatternMethod):
 
     name = "density_gradient"
 
-    def __init__(self, experiment_name, camera_properties, channel=None, **kwargs):
+    def __init__(self, channel=None, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
-    def generate(self, data_dock: DataDock) -> np.ndarray:
+    def generate(self, context) -> np.ndarray:
 
-        seg: np.ndarray = data_dock.data[self.seg_channel_id]["seg"].data
+        seg = context.segmentation(self.channel)
 
         if self.voronoi:
             px_dis = distance_transform_edt(seg == 0)
diff --git a/src/pyclm/core/patterns/ktr_patterns.py b/src/pyclm/core/patterns/ktr_patterns.py
index 231c714..adbf359 100644
--- a/src/pyclm/core/patterns/ktr_patterns.py
+++ b/src/pyclm/core/patterns/ktr_patterns.py
@@ -9,35 +9,23 @@ class NucleusControlMethod(PatternMethod):
 
     name = "nucleus_control_base"
 
-    def __init__(self, experiment_name, camera_properties, nuc_channel=None, **kwargs):
-        super().__init__(experiment_name, camera_properties, **kwargs)
+    def __init__(self, channel=None, **kwargs):
+        super().__init__(**kwargs)
 
-        if nuc_channel is None:
-            raise AttributeError(f"{experiment_name}: PerCellPatternModels must be provided a "
-                                 f"segmentation channel in the .toml: e.g. nuc_channel = \"545\"")
+        if channel is None:
+            raise AttributeError("NucleusControlMethod must be provided a "
+                                 "segmentation channel in the .toml: e.g. nuc_channel = \"545\"")
 
-        self.nuc_channel = nuc_channel
-        self.seg_channel_id = None
-
-    def initialize(self, experiment):
-        super().initialize(experiment)
-
-        channel = experiment.channels.get(self.nuc_channel, None)
-
-        assert channel is not None, f"provided channel {self.nuc_channel} is not in experiment"
-
-        self.seg_channel_id = channel.channel_id
-        cell_seg_air = AcquiredImageRequest(channel.channel_id, True, True)
-
-        return [cell_seg_air]
+        self.channel = channel
+        self.add_requirement(channel, raw=True, seg=True)
 
     def process_prop(self, prop):
         return prop.image
 
-    def generate(self, data_dock: DataDock) -> np.ndarray:
+    def generate(self, context) -> np.ndarray:
 
-        seg: np.ndarray = data_dock.data[self.seg_channel_id]["seg"].data
-        raw: np.ndarray = data_dock.data[self.seg_channel_id]["raw"].data
+        seg = context.segmentation(self.channel)
+        raw = context.raw(self.channel)
 
         h, w = self.pattern_shape
 
@@ -57,9 +45,9 @@ class BinaryNucleusClampModel(NucleusControlMethod):
 
     name = "binary_nucleus_clamp"
 
-    def __init__(self, experiment_name, camera_properties, nuc_channel, clamp_target, **kwargs):
+    def __init__(self, channel, clamp_target, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, nuc_channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
         self.clamp_target = clamp_target
 
@@ -74,10 +62,10 @@ class CenteredImageModel(NucleusControlMethod):
 
     name = "centered_image"
 
-    def __init__(self, experiment_name, camera_properties, nuc_channel="545", tif_path=None,
+    def __init__(self, channel="545", tif_path=None,
                  min_intensity=2000, max_intensity=5000, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, nuc_channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
         self.img = tifffile.imread(tif_path)
         self.min_intensity = min_intensity
@@ -135,27 +123,27 @@ def process_prop(self, prop):
 
         return prop.image
 
-    def generate(self, data_dock: DataDock) -> np.ndarray:
+    def generate(self, context) -> np.ndarray:
 
         if self.target_image is None:
             self.make_target_image()
 
-        return super().generate(data_dock)
+        return super().generate(context)
 
 
 class GlobalCycleModel(NucleusControlMethod):
 
     name = "global_cycle"
 
-    def __init__(self, experiment_name, camera_properties, nuc_channel, period_m=10, **kwargs):
+    def __init__(self, channel, period_m=10, **kwargs):
 
-        super().__init__(experiment_name, camera_properties, nuc_channel, **kwargs)
+        super().__init__(channel=channel, **kwargs)
 
         self.period_s = period_m * 60
 
-    def generate(self, data_dock: DataDock) -> np.ndarray:
+    def generate(self, context) -> np.ndarray:
 
-        t = data_dock.time_seconds
+        t = context.time
 
         is_on = ((t // self.period_s) % 2) == 0
 
diff --git a/src/pyclm/core/patterns/pattern.py b/src/pyclm/core/patterns/pattern.py
index 8bf586b..76628c0 100644
--- a/src/pyclm/core/patterns/pattern.py
+++ b/src/pyclm/core/patterns/pattern.py
@@ -1,7 +1,7 @@
 from ..experiments import Experiment
 from ..datatypes import AcquisitionData, SegmentationData
 import logging
-from typing import NamedTuple, Union
+from typing import NamedTuple, Union, Any
 from uuid import uuid4, UUID
 from collections import defaultdict
 from pathlib import Path
@@ -75,24 +75,85 @@ def check_complete(self):
         return len(self.get_awaiting()) == 0
 
 
+class PatternContext:
+    def __init__(self, data_dock: DataDock, experiment: Experiment):
+        self._dock = data_dock
+        self._experiment = experiment
+        self._channel_map = {name: ch.channel_id for name, ch in experiment.channels.items()}
+
+    @property
+    def time(self) -> float:
+        return self._dock.time_seconds
+
+    def _get_channel_id(self, channel_name: str) -> UUID:
+        if channel_name not in self._channel_map:
+            raise ValueError(f"Channel '{channel_name}' not found in experiment.")
+        return self._channel_map[channel_name]
+
+    def raw(self, channel_name: str) -> np.ndarray:
+        """Get raw image for a channel."""
+        cid = self._get_channel_id(channel_name)
+        if cid not in self._dock.data or "raw" not in self._dock.data[cid]:
+             raise ValueError(f"Raw data for channel '{channel_name}' was not requested.")
+        data = self._dock.data[cid]["raw"]
+        return data.data if data else None
+
+    def segmentation(self, channel_name: str) -> np.ndarray:
+        """Get segmentation mask for a channel."""
+        cid = self._get_channel_id(channel_name)
+        if cid not in self._dock.data or "seg" not in self._dock.data[cid]:
+             raise ValueError(f"Segmentation data for channel '{channel_name}' was not requested.")
+        data = self._dock.data[cid]["seg"]
+        return data.data if data else None
+
+
+
 class PatternMethod:
 
     name = "base"
 
-    def __init__(self, experiment_name, camera_properties: CameraProperties, **kwargs):
-        self.experiment = experiment_name
+    def __init__(self, experiment_name=None, camera_properties: CameraProperties=None, **kwargs):
+        # Support legacy init where these are passed
+        self.experiment_name = experiment_name
+        self.camera_properties = camera_properties
+        if camera_properties:
+            self.pixel_size_um = camera_properties.pixel_size_um
+            self.pattern_shape = (camera_properties.roi.height, camera_properties.roi.width)
+        else:
+            self.pixel_size_um = 1.0
+            self.pattern_shape = (100, 100) # Default placeholders
+        
+        self.binning = 1
+        self._requirements_list = [] # List of (channel_name, raw, seg)
+        self._experiment_ref = None
+
+    def configure_system(self, experiment_name: str, camera_properties: CameraProperties, experiment: Experiment):
+        """Called by the system to inject dependencies."""
+        self.experiment_name = experiment_name
         self.camera_properties = camera_properties
         self.pixel_size_um = camera_properties.pixel_size_um
         self.pattern_shape = (camera_properties.roi.height, camera_properties.roi.width)
-        self.binning = 1
+        self._experiment_ref = experiment
+
+    def add_requirement(self, channel_name: str, raw: bool = False, seg: bool = False):
+        """Declarative way to add requirements."""
+        self._requirements_list.append((channel_name, raw, seg))
 
     def initialize(self, experiment: Experiment) -> list[AcquiredImageRequest]:
+        
+        # If user used add_requirement, process them
+        reqs = []
+        for name, needs_raw, needs_seg in self._requirements_list:
+            ch = experiment.channels.get(name)
+            if ch:
+                reqs.append(AcquiredImageRequest(ch.channel_id, needs_raw, needs_seg))
+            else:
+                logger.warning(f"Pattern {self.name} requested unknown channel {name}")
 
         binning = experiment.stimulation.binning
-
         self.update_binning(binning)
-
-        return []
+        
+        return reqs
 
     def get_meshgrid(self) -> tuple[np.ndarray, np.ndarray]:
         h, w = self.pattern_shape
@@ -104,7 +165,10 @@ def get_meshgrid(self) -> tuple[np.ndarray, np.ndarray]:
 
         return xx, yy
 
-    def generate(self, data_dock: DataDock) -> np.ndarray:
+    def generate(self, data_dock: Union[DataDock, PatternContext]) -> np.ndarray:
+        # If passed PatternContext, user is using new API.
+        # But if user implemented old generate(self, data_dock: DataDock), we need to support that.
+        # This method is called by the system.
         raise NotImplementedError
 
     def update_binning(self, binning: int):
diff --git a/src/pyclm/core/patterns/pattern_process.py b/src/pyclm/core/patterns/pattern_process.py
index 4570558..585fab8 100644
--- a/src/pyclm/core/patterns/pattern_process.py
+++ b/src/pyclm/core/patterns/pattern_process.py
@@ -6,7 +6,7 @@
 from ..datatypes import CameraPattern, AcquisitionData, SegmentationData
 from ..experiments import Experiment
 from ..messages import Message
-from .pattern import PatternReview, PatternMethod, PatternMethodReturnsSLM, DataDock, AcquiredImageRequest, CameraProperties
+from .pattern import PatternReview, PatternMethod, PatternMethodReturnsSLM, DataDock, AcquiredImageRequest, CameraProperties, PatternContext
 from .bar_patterns import BouncingBarPattern, BarPatternBase, SawToothMethod
 from .static_patterns import CirclePattern, FullOnPattern
 from .feedback_control_patterns import RotateCcwModel, MoveInModel, MoveDownModel, MoveOutModel, BounceModel
@@ -97,15 +97,21 @@ def run_model(self, experiment_name, dockname):
 
         assert isinstance(model, PatternMethod), f"self.models[{'experiment_name'}] is not a PatternMethod"
 
-        if isinstance(model, PatternMethodReturnsSLM):
-            slm_pattern = model.generate(data_dock)
+        # Create context wrapper
+
+        # We assume _experiment_ref is available. If not, we might crash, which is acceptable for alpha breakage.
+        # Ideally, we ensure configure_system is called.
+        if model._experiment_ref is None:
+             raise RuntimeError(f"Model {model.name} for {experiment_name} was not properly configured with an experiment reference.")
+        
+        context = PatternContext(data_dock, model._experiment_ref)
 
+        if isinstance(model, PatternMethodReturnsSLM):
+            slm_pattern = model.generate(context)
             self.slm.put(CameraPattern(experiment_name, slm_pattern, slm_coords=True))
 
         else:
-
-            pattern = model.generate(data_dock)
-
+            pattern = model.generate(context)
             self.slm.put(CameraPattern(experiment_name, pattern, slm_coords=False, binning=model.binning))
 
     def dock_string(self, experiment_name, t):
diff --git a/src/pyclm/core/patterns/static_patterns.py b/src/pyclm/core/patterns/static_patterns.py
index c62283e..4d1bb11 100644
--- a/src/pyclm/core/patterns/static_patterns.py
+++ b/src/pyclm/core/patterns/static_patterns.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from .pattern import PatternMethod, DataDock
+from .pattern import PatternMethod
 
 
 class CirclePattern(PatternMethod):
@@ -10,18 +10,12 @@ class CirclePattern(PatternMethod):
 
     name = "circle"
 
-    def __init__(self, experiment_name, camera_properties, rad=1, **kwargs):
-        super().__init__(experiment_name, camera_properties)
+    def __init__(self, rad=1, **kwargs):
+        super().__init__(**kwargs)
 
         self.rad = rad
 
-    def initialize(self, experiment):
-
-        super().initialize(experiment)
-
-        return []
-
-    def generate(self, data_dock: DataDock):
+    def generate(self, context):
 
         h, w = self.pattern_shape
 
@@ -32,8 +26,6 @@ def generate(self, data_dock: DataDock):
 
         print(h, w)
 
-        # pattern = np.ones((int(h), int(w)), dtype=np.float16)
-
         return (((xx - center_x)**2 + (yy - center_y)**2) < (self.rad**2)).astype(np.float16)
 
 
@@ -44,14 +36,10 @@ class FullOnPattern(PatternMethod):
 
     name = "full_on"
 
-    def __init__(self, experiment_name, camera_properties, **kwargs):
-        super().__init__(experiment_name, camera_properties)
-
-    def initialize(self, experiment):
-        super().initialize(experiment)
-        return []
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
 
-    def generate(self, data_dock: DataDock):
+    def generate(self, context):
 
         h, w = self.pattern_shape
         pattern = np.ones((int(h), int(w)), dtype=np.float16)
diff --git a/src/pyclm/core/patterns/wave_patterns.py b/src/pyclm/core/patterns/wave_patterns.py
index 907af88..d96dccf 100644
--- a/src/pyclm/core/patterns/wave_patterns.py
+++ b/src/pyclm/core/patterns/wave_patterns.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from .pattern import DataDock, PatternMethod
+from .pattern import PatternMethod
 
 
 class WavePatternBase(PatternMethod):
@@ -16,7 +16,6 @@ def __new__(cls, *args, **kwargs):
         return super().__new__(cls)
 
     def __init__(self, *args, **kwargs):
-
         super().__init__(*args, **kwargs)
         print(f"Initializing {self.__class__.__name__}")
 
@@ -27,26 +26,21 @@ class StationaryWavePattern(WavePatternBase):
 
     name = "wave (stationary)"
 
-    def __init__(self, experiment_name, camera_properties, duty_cycle=0.2, wave_speed=0, period=30, **kwargs):
+    def __init__(self, duty_cycle=0.2, wave_speed=0, period=30, **kwargs):
         """
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
                            vertical axis containing "on" pixels
         :param wave_speed: speed in um/min
         :param period: period in um
         """
-        super().__init__(experiment_name, camera_properties)
+        super().__init__(**kwargs)
 
         self.duty_cycle = duty_cycle
         self.wave_speed = 0
         self.period_space = period    # in um
         self.period_time = 0    # in minutes
 
-    def initialize(self, experiment):
-        super().initialize(experiment)
-
-        return []
-
-    def generate(self, data_dock: DataDock):
+    def generate(self, context):
 
         xx, yy = self.get_meshgrid()
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
@@ -64,7 +58,7 @@ class WavePattern(WavePatternBase):
 
     name = "wave"
 
-    def __init__(self, experiment_name, camera_properties, duty_cycle=0.2, wave_speed=1, period=30, direction = 1, **kwargs):
+    def __init__(self, duty_cycle=0.2, wave_speed=1, period=30, direction = 1, **kwargs):
         """
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
                            radial axis containing "on" pixels
@@ -72,7 +66,7 @@ def __init__(self, experiment_name, camera_properties, duty_cycle=0.2, wave_spee
         :param period: period in um
         :param direction: movement in/out relative to the center. 1 is out; -1 is in 
         """
-        super().__init__(experiment_name, camera_properties)
+        super().__init__(**kwargs)
 
         self.duty_cycle = duty_cycle
         self.wave_speed = wave_speed
@@ -80,14 +74,9 @@ def __init__(self, experiment_name, camera_properties, duty_cycle=0.2, wave_spee
         self.period_time = period / wave_speed    # in minutes
         self.direction = direction
 
-    def initialize(self, experiment):
-        super().initialize(experiment)
-
-        return []
-
-    def generate(self, data_dock: DataDock):
+    def generate(self, context):
 
-        t = data_dock.time_seconds / 60
+        t = context.time / 60
 
         xx, yy = self.get_meshgrid()
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2

From 22f60a4504b92e0f3142cb0c1af6d20be621efda Mon Sep 17 00:00:00 2001
From: Harrison-Oatman <46121828+Harrison-Oatman@users.noreply.github.com>
Date: Thu, 8 Jan 2026 02:25:11 -0500
Subject: [PATCH 2/3] Fix imports

---
 pyproject.toml             |  1 +
 src/pyclm/core/__init__.py |  1 -
 tests/test_import_pyclm.py |  4 ++++
 uv.lock                    | 19 +++++++++++++++++++
 4 files changed, 24 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_import_pyclm.py

diff --git a/pyproject.toml b/pyproject.toml
index 40972bc..6543e95 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,6 +11,7 @@ dependencies = [
     "h5py>=3.14.0",
     "natsort>=8.4.0",
     "notebook>=7.5.1",
+    "opencv-python>=4.12.0.88",
     "pandas-stubs==2.3.2.250827",
     "pymmcore-plus==0.13.7",
     "pymmcore==11.2.1.71.0",
diff --git a/src/pyclm/core/__init__.py b/src/pyclm/core/__init__.py
index 6f2ad93..0678b0f 100644
--- a/src/pyclm/core/__init__.py
+++ b/src/pyclm/core/__init__.py
@@ -3,7 +3,6 @@
 Import modules that may be used in creating custom pattern and segmentation methods
 """
 
-from ..directories import experiment_from_toml, schedule_from_directory
 from .experiments import ExperimentSchedule
 from .manager import Manager, MicroscopeOutbox, SLMBuffer
 from .microscope import MicroscopeProcess
diff --git a/tests/test_import_pyclm.py b/tests/test_import_pyclm.py
new file mode 100644
index 0000000..e5c10fb
--- /dev/null
+++ b/tests/test_import_pyclm.py
@@ -0,0 +1,4 @@
+def test_import_pyclm():
+    import pyclm
+
+    assert True
diff --git a/uv.lock b/uv.lock
index c14e604..15478dc 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1479,6 +1479,23 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/67/0e/35082d13c09c02c011cf21570543d202ad929d961c02a147493cb0c2bdf5/numpy-2.2.6-cp313-cp313t-win_amd64.whl", hash = "sha256:6031dd6dfecc0cf9f668681a37648373bddd6421fff6c66ec1624eed0180ee06", size = 12771374, upload-time = "2025-05-17T21:43:35.479Z" },
 ]
 
+[[package]]
+name = "opencv-python"
+version = "4.12.0.88"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "numpy" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/ac/71/25c98e634b6bdeca4727c7f6d6927b056080668c5008ad3c8fc9e7f8f6ec/opencv-python-4.12.0.88.tar.gz", hash = "sha256:8b738389cede219405f6f3880b851efa3415ccd674752219377353f017d2994d", size = 95373294, upload-time = "2025-07-07T09:20:52.389Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/85/68/3da40142e7c21e9b1d4e7ddd6c58738feb013203e6e4b803d62cdd9eb96b/opencv_python-4.12.0.88-cp37-abi3-macosx_13_0_arm64.whl", hash = "sha256:f9a1f08883257b95a5764bf517a32d75aec325319c8ed0f89739a57fae9e92a5", size = 37877727, upload-time = "2025-07-07T09:13:31.47Z" },
+    { url = "https://files.pythonhosted.org/packages/33/7c/042abe49f58d6ee7e1028eefc3334d98ca69b030e3b567fe245a2b28ea6f/opencv_python-4.12.0.88-cp37-abi3-macosx_13_0_x86_64.whl", hash = "sha256:812eb116ad2b4de43ee116fcd8991c3a687f099ada0b04e68f64899c09448e81", size = 57326471, upload-time = "2025-07-07T09:13:41.26Z" },
+    { url = "https://files.pythonhosted.org/packages/62/3a/440bd64736cf8116f01f3b7f9f2e111afb2e02beb2ccc08a6458114a6b5d/opencv_python-4.12.0.88-cp37-abi3-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:51fd981c7df6af3e8f70b1556696b05224c4e6b6777bdd2a46b3d4fb09de1a92", size = 45887139, upload-time = "2025-07-07T09:13:50.761Z" },
+    { url = "https://files.pythonhosted.org/packages/68/1f/795e7f4aa2eacc59afa4fb61a2e35e510d06414dd5a802b51a012d691b37/opencv_python-4.12.0.88-cp37-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:092c16da4c5a163a818f120c22c5e4a2f96e0db4f24e659c701f1fe629a690f9", size = 67041680, upload-time = "2025-07-07T09:14:01.995Z" },
+    { url = "https://files.pythonhosted.org/packages/02/96/213fea371d3cb2f1d537612a105792aa0a6659fb2665b22cad709a75bd94/opencv_python-4.12.0.88-cp37-abi3-win32.whl", hash = "sha256:ff554d3f725b39878ac6a2e1fa232ec509c36130927afc18a1719ebf4fbf4357", size = 30284131, upload-time = "2025-07-07T09:14:08.819Z" },
+    { url = "https://files.pythonhosted.org/packages/fa/80/eb88edc2e2b11cd2dd2e56f1c80b5784d11d6e6b7f04a1145df64df40065/opencv_python-4.12.0.88-cp37-abi3-win_amd64.whl", hash = "sha256:d98edb20aa932fd8ebd276a72627dad9dc097695b3d435a4257557bbb49a79d2", size = 39000307, upload-time = "2025-07-07T09:14:16.641Z" },
+]
+
 [[package]]
 name = "overrides"
 version = "7.7.0"
@@ -1794,6 +1811,7 @@ dependencies = [
     { name = "h5py" },
     { name = "natsort" },
     { name = "notebook" },
+    { name = "opencv-python" },
     { name = "pandas-stubs" },
     { name = "pymmcore" },
     { name = "pymmcore-plus" },
@@ -1834,6 +1852,7 @@ requires-dist = [
     { name = "h5py", specifier = ">=3.14.0" },
     { name = "natsort", specifier = ">=8.4.0" },
     { name = "notebook", specifier = ">=7.5.1" },
+    { name = "opencv-python", specifier = ">=4.12.0.88" },
     { name = "pandas-stubs", specifier = "==2.3.2.250827" },
     { name = "pymmcore", specifier = "==11.2.1.71.0" },
     { name = "pymmcore-plus", specifier = "==0.13.7" },

From 9a3d9d72ff8f518fd83b32fd35f95b5c06c06fdc Mon Sep 17 00:00:00 2001
From: Harrison-Oatman <46121828+Harrison-Oatman@users.noreply.github.com>
Date: Thu, 8 Jan 2026 02:25:35 -0500
Subject: [PATCH 3/3] Major pattern method API rework

---
 src/pyclm/core/patterns/bar_patterns.py       |  44 ++++---
 .../patterns/feedback_control_patterns.py     |  60 ++++-----
 src/pyclm/core/patterns/ktr_patterns.py       |  47 +++----
 src/pyclm/core/patterns/pattern.py            | 120 +++++++++++-------
 src/pyclm/core/patterns/pattern_process.py    | 112 +++++++++-------
 src/pyclm/core/patterns/static_patterns.py    |  10 +-
 src/pyclm/core/patterns/wave_patterns.py      |  26 ++--
 7 files changed, 235 insertions(+), 184 deletions(-)

diff --git a/src/pyclm/core/patterns/bar_patterns.py b/src/pyclm/core/patterns/bar_patterns.py
index 7956912..bfd736e 100644
--- a/src/pyclm/core/patterns/bar_patterns.py
+++ b/src/pyclm/core/patterns/bar_patterns.py
@@ -7,6 +7,7 @@ class BarPatternBase(PatternMethod):
     """
     Creates a BarPattern or StationaryBarPattern depending on the requested barspeed
     """
+
     def __new__(cls, *args, **kwargs):
         if cls is BarPatternBase:  # Check if the base class is being instantiated
             if kwargs.get("bar_speed") != 0:
@@ -38,12 +39,11 @@ def __init__(self, duty_cycle=0.2, bar_speed=0, period=30, **kwargs):
 
         self.duty_cycle = duty_cycle
         self.bar_speed = 0
-        self.period_space = period    # in um
-        self.period_time = 0    # in minutes
+        self.period_space = period  # in um
+        self.period_time = 0  # in minutes
 
     def generate(self, context):
-
-        xx, yy = self.get_meshgrid()
+        _xx, yy = self.get_meshgrid()
 
         is_on = ((yy / self.period_space) % 1.0) < self.duty_cycle
 
@@ -68,24 +68,24 @@ def __init__(self, duty_cycle=0.2, bar_speed=1, period=30, **kwargs):
 
         self.duty_cycle = duty_cycle
         self.bar_speed = bar_speed
-        self.period_space = period    # in um
-        self.period_time = period / bar_speed    # in minutes
+        self.period_space = period  # in um
+        self.period_time = period / bar_speed  # in minutes
 
     def _get_pattern_at_time(self, t_minutes):
-         xx, yy = self.get_meshgrid()
-         is_on = ((t_minutes - (yy / self.bar_speed)) % self.period_time) < self.duty_cycle*self.period_time
-         return is_on.astype(np.float16)
+        _xx, yy = self.get_meshgrid()
+        is_on = (
+            (t_minutes - (yy / self.bar_speed)) % self.period_time
+        ) < self.duty_cycle * self.period_time
+        return is_on.astype(np.float16)
 
     def generate(self, context):
         return self._get_pattern_at_time(context.time / 60)
 
 
 class SawToothMethod(PatternMethod):
-
     name = "sawtooth"
 
-    def __init__(self, duty_cycle=0.2,
-                 bar_speed=1, period=30, inverse=False, **kwargs):
+    def __init__(self, duty_cycle=0.2, bar_speed=1, period=30, inverse=False, **kwargs):
         """
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
                            vertical axis containing "on" pixels
@@ -103,16 +103,20 @@ def __init__(self, duty_cycle=0.2,
     def generate(self, context):
         t = context.time / 60
 
-        xx, yy = self.get_meshgrid()
+        _xx, yy = self.get_meshgrid()
 
-        is_on = ((t - (yy / self.bar_speed)) % self.period_time) < self.duty_cycle * self.period_time
+        is_on = (
+            (t - (yy / self.bar_speed)) % self.period_time
+        ) < self.duty_cycle * self.period_time
 
-        val = ((t - (yy / self.bar_speed)) % self.period_time) / (self.duty_cycle * self.period_time)
+        val = ((t - (yy / self.bar_speed)) % self.period_time) / (
+            self.duty_cycle * self.period_time
+        )
 
         if not self.inverse:
             val = 1 - val
 
-        pattern_out = (is_on*val).astype(np.float16)
+        pattern_out = (is_on * val).astype(np.float16)
 
         print(np.min(pattern_out), np.max(pattern_out))
 
@@ -120,11 +124,9 @@ def generate(self, context):
 
 
 class BouncingBarPattern(BarPattern):
-
     name = "bar_bounce"
 
-    def __init__(self, duty_cycle=0.2,
-                 bar_speed=1, period=30, t_loop=60, **kwargs):
+    def __init__(self, duty_cycle=0.2, bar_speed=1, period=30, t_loop=60, **kwargs):
         """
 
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
@@ -133,7 +135,9 @@ def __init__(self, duty_cycle=0.2,
         :param period: period in um
         :param t_loop: period of reversal (there and back) in minutes
         """
-        super().__init__(duty_cycle=duty_cycle, bar_speed=bar_speed, period=period, **kwargs)
+        super().__init__(
+            duty_cycle=duty_cycle, bar_speed=bar_speed, period=period, **kwargs
+        )
         self.t_loop_s = t_loop * 60
 
     def generate(self, context):
diff --git a/src/pyclm/core/patterns/feedback_control_patterns.py b/src/pyclm/core/patterns/feedback_control_patterns.py
index 991f84c..3b15dc4 100644
--- a/src/pyclm/core/patterns/feedback_control_patterns.py
+++ b/src/pyclm/core/patterns/feedback_control_patterns.py
@@ -1,12 +1,12 @@
 import numpy as np
-
-from .pattern import PatternMethod, AcquiredImageRequest, DataDock
-from skimage.measure import regionprops, regionprops_table, label
+import tifffile
+from scipy.ndimage import distance_transform_edt
 from scipy.spatial import KDTree
 from scipy.stats import gaussian_kde
-from scipy.ndimage import distance_transform_edt
+from skimage.measure import label, regionprops, regionprops_table
+
+from .pattern import AcquiredImageRequest, DataDock, PatternMethod
 
-import tifffile
 
 class PerCellPatternMethod(PatternMethod):
     """
@@ -18,12 +18,16 @@ class PerCellPatternMethod(PatternMethod):
 
     name = "per_cell_base"
 
-    def __init__(self, channel=None, voronoi=False, gradient=False, direction = 1, **kwargs):
+    def __init__(
+        self, channel=None, voronoi=False, gradient=False, direction=1, **kwargs
+    ):
         super().__init__(**kwargs)
 
         if channel is None:
-            raise AttributeError("PerCellPatternModels must be provided a "
-                                 "segmentation channel in the .toml: e.g. channel = \"638\"")
+            raise AttributeError(
+                "PerCellPatternModels must be provided a "
+                'segmentation channel in the .toml: e.g. channel = "638"'
+            )
 
         self.gradient = gradient
         self.voronoi = voronoi
@@ -59,11 +63,9 @@ def prop_vector(self, prop, vec):
         return out
 
     def process_prop(self, prop) -> np.ndarray:
-
         return prop.image
 
     def voronoi_rebuild(self, img):
-
         props_table = regionprops_table(img, properties=["centroid"])
 
         pts = np.stack([props_table["centroid-0"], props_table["centroid-1"]], axis=-1)
@@ -84,7 +86,6 @@ def voronoi_rebuild(self, img):
         return out
 
     def generate(self, context) -> np.ndarray:
-
         seg = context.segmentation(self.channel)
 
         if self.voronoi:
@@ -100,7 +101,9 @@ def generate(self, context) -> np.ndarray:
         for prop in regionprops(seg):
             cell_stim = self.process_prop(prop)
 
-            new_img[prop.bbox[0]:prop.bbox[2], prop.bbox[1]:prop.bbox[3]] += cell_stim
+            new_img[prop.bbox[0] : prop.bbox[2], prop.bbox[1] : prop.bbox[3]] += (
+                cell_stim
+            )
 
         new_img_clamped = np.clip(new_img, 0, 1).astype(np.float16)
 
@@ -108,15 +111,12 @@ def generate(self, context) -> np.ndarray:
 
 
 class RotateCcwModel(PerCellPatternMethod):
-
     name = "rotate_ccw"
 
     def __init__(self, channel=None, **kwargs):
-
         super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
-
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
         prop_centroid = prop.centroid
 
@@ -126,15 +126,12 @@ def process_prop(self, prop) -> np.ndarray:
 
 
 class MoveOutModel(PerCellPatternMethod):
-
     name = "move_out"
 
     def __init__(self, channel=None, **kwargs):
-
         super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
-
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
         prop_centroid = prop.centroid
 
@@ -144,15 +141,12 @@ def process_prop(self, prop) -> np.ndarray:
 
 
 class MoveInModel(PerCellPatternMethod):
-
     name = "move_in"
 
     def __init__(self, channel=None, **kwargs):
-
         super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
-
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
         prop_centroid = prop.centroid
 
@@ -162,15 +156,12 @@ def process_prop(self, prop) -> np.ndarray:
 
 
 class MoveDownModel(PerCellPatternMethod):
-
     name = "move_down"
 
     def __init__(self, channel=None, **kwargs):
-
         super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
-
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
         prop_centroid = prop.centroid
 
@@ -180,18 +171,15 @@ def process_prop(self, prop) -> np.ndarray:
 
 
 class BounceModel(PerCellPatternMethod):
-
     name = "fb_bounce"
 
     def __init__(self, channel=None, t_loop=60, **kwargs):
-
         self.t_loop_s = t_loop * 60
         self.down = True
 
         super().__init__(channel=channel, **kwargs)
 
     def process_prop(self, prop) -> np.ndarray:
-
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
         prop_centroid = prop.centroid
 
@@ -200,7 +188,6 @@ def process_prop(self, prop) -> np.ndarray:
         return self.prop_vector(prop, vec)
 
     def generate(self, context) -> np.ndarray:
-
         t = context.time
         t = t % self.t_loop_s
 
@@ -213,15 +200,12 @@ def generate(self, context) -> np.ndarray:
 
 
 class DensityModel(PerCellPatternMethod):
-
     name = "density_gradient"
 
     def __init__(self, channel=None, **kwargs):
-
         super().__init__(channel=channel, **kwargs)
 
     def generate(self, context) -> np.ndarray:
-
         seg = context.segmentation(self.channel)
 
         if self.voronoi:
@@ -229,14 +213,14 @@ def generate(self, context) -> np.ndarray:
             seg = self.voronoi_rebuild(seg)
 
             seg = seg * (px_dis < 50)
-        
+
         h, w = self.pattern_shape
 
         new_img = np.zeros((int(h), int(w)), dtype=np.float16)
-        
+
         density = generate_density(seg)
 
-        if (self.direction == -1):
+        if self.direction == -1:
             dy, dx = np.gradient(density)
         else:
             dy, dx = np.negative(np.gradient(density))
@@ -250,9 +234,11 @@ def generate(self, context) -> np.ndarray:
             vec = (np.sin(vec), np.cos(vec))
 
             cell_stim = self.prop_vector(prop, vec)
-            
-            new_img[prop.bbox[0]:prop.bbox[2], prop.bbox[1]:prop.bbox[3]] += cell_stim
+
+            new_img[prop.bbox[0] : prop.bbox[2], prop.bbox[1] : prop.bbox[3]] += (
+                cell_stim
+            )
 
         new_img_clamped = np.clip(new_img, 0, 1).astype(np.float16)
 
-        return new_img_clamped
\ No newline at end of file
+        return new_img_clamped
diff --git a/src/pyclm/core/patterns/ktr_patterns.py b/src/pyclm/core/patterns/ktr_patterns.py
index adbf359..ef8e0b9 100644
--- a/src/pyclm/core/patterns/ktr_patterns.py
+++ b/src/pyclm/core/patterns/ktr_patterns.py
@@ -1,20 +1,21 @@
 import numpy as np
-
-from .pattern import PatternMethod, AcquiredImageRequest, DataDock
-from skimage.measure import regionprops
 import tifffile
+from skimage.measure import regionprops
 
+from .pattern import AcquiredImageRequest, DataDock, PatternMethod
 
-class NucleusControlMethod(PatternMethod):
 
+class NucleusControlMethod(PatternMethod):
     name = "nucleus_control_base"
 
     def __init__(self, channel=None, **kwargs):
         super().__init__(**kwargs)
 
         if channel is None:
-            raise AttributeError("NucleusControlMethod must be provided a "
-                                 "segmentation channel in the .toml: e.g. nuc_channel = \"545\"")
+            raise AttributeError(
+                "NucleusControlMethod must be provided a "
+                'segmentation channel in the .toml: e.g. nuc_channel = "545"'
+            )
 
         self.channel = channel
         self.add_requirement(channel, raw=True, seg=True)
@@ -23,7 +24,6 @@ def process_prop(self, prop):
         return prop.image
 
     def generate(self, context) -> np.ndarray:
-
         seg = context.segmentation(self.channel)
         raw = context.raw(self.channel)
 
@@ -34,7 +34,9 @@ def generate(self, context) -> np.ndarray:
         for prop in regionprops(seg, intensity_image=raw):
             cell_stim = self.process_prop(prop)
 
-            new_img[prop.bbox[0]:prop.bbox[2], prop.bbox[1]:prop.bbox[3]] += cell_stim
+            new_img[prop.bbox[0] : prop.bbox[2], prop.bbox[1] : prop.bbox[3]] += (
+                cell_stim
+            )
 
         new_img_clamped = np.clip(new_img, 0, 1).astype(np.float16)
 
@@ -42,11 +44,9 @@ def generate(self, context) -> np.ndarray:
 
 
 class BinaryNucleusClampModel(NucleusControlMethod):
-
     name = "binary_nucleus_clamp"
 
     def __init__(self, channel, clamp_target, **kwargs):
-
         super().__init__(channel=channel, **kwargs)
 
         self.clamp_target = clamp_target
@@ -59,12 +59,16 @@ def process_prop(self, prop):
 
 
 class CenteredImageModel(NucleusControlMethod):
-
     name = "centered_image"
 
-    def __init__(self, channel="545", tif_path=None,
-                 min_intensity=2000, max_intensity=5000, **kwargs):
-
+    def __init__(
+        self,
+        channel="545",
+        tif_path=None,
+        min_intensity=2000,
+        max_intensity=5000,
+        **kwargs,
+    ):
         super().__init__(channel=channel, **kwargs)
 
         self.img = tifffile.imread(tif_path)
@@ -77,7 +81,6 @@ def __init__(self, channel="545", tif_path=None,
     # def
 
     def make_target_image(self):
-
         img = self.img
 
         h, w = self.pattern_shape
@@ -90,7 +93,9 @@ def make_target_image(self):
         padding_w_left = (w - img.shape[1]) // 2
         padding_w_right = w - (padding_w_left + img.shape[1])
 
-        padded_img = np.pad(img, ((padding_h_up, padding_h_down), (padding_w_left, padding_w_right)))
+        padded_img = np.pad(
+            img, ((padding_h_up, padding_h_down), (padding_w_left, padding_w_right))
+        )
         padded_img = np.array(padded_img, dtype=np.float16)
 
         max_v = np.max(img)
@@ -99,14 +104,15 @@ def make_target_image(self):
         padded_img = (padded_img - min_v) / (max_v - min_v)
         padded_img = np.clip(padded_img, 0, 1)
 
-        padded_img = (padded_img * (self.max_intensity - self.min_intensity)) + self.min_intensity
+        padded_img = (
+            padded_img * (self.max_intensity - self.min_intensity)
+        ) + self.min_intensity
 
         print(padded_img.shape)
 
         self.target_image = padded_img
 
     def get_target_intensity(self, prop):
-
         y, x = prop.centroid
 
         y = round(y)
@@ -115,7 +121,6 @@ def get_target_intensity(self, prop):
         return self.target_image[y, x]
 
     def process_prop(self, prop):
-
         target = self.get_target_intensity(prop)
 
         if prop.intensity_mean > target:
@@ -124,7 +129,6 @@ def process_prop(self, prop):
         return prop.image
 
     def generate(self, context) -> np.ndarray:
-
         if self.target_image is None:
             self.make_target_image()
 
@@ -132,17 +136,14 @@ def generate(self, context) -> np.ndarray:
 
 
 class GlobalCycleModel(NucleusControlMethod):
-
     name = "global_cycle"
 
     def __init__(self, channel, period_m=10, **kwargs):
-
         super().__init__(channel=channel, **kwargs)
 
         self.period_s = period_m * 60
 
     def generate(self, context) -> np.ndarray:
-
         t = context.time
 
         is_on = ((t // self.period_s) % 2) == 0
diff --git a/src/pyclm/core/patterns/pattern.py b/src/pyclm/core/patterns/pattern.py
index 76628c0..a5a840e 100644
--- a/src/pyclm/core/patterns/pattern.py
+++ b/src/pyclm/core/patterns/pattern.py
@@ -1,25 +1,39 @@
-from ..experiments import Experiment
-from ..datatypes import AcquisitionData, SegmentationData
 import logging
-from typing import NamedTuple, Union, Any
-from uuid import uuid4, UUID
 from collections import defaultdict
 from pathlib import Path
-from h5py import File
+from typing import Any, NamedTuple, Union
+from uuid import UUID, uuid4
+
 import numpy as np
+from h5py import File
 from natsort import natsorted
 
+from ..datatypes import AcquisitionData, SegmentationData
+from ..experiments import Experiment
+
 logger = logging.getLogger(__name__)
 
-ROI = NamedTuple("ROI", [("x_offset", int), ("y_offset", int), ("width", int), ("height", int)])
-CameraProperties = NamedTuple("CameraProperties", [("roi", ROI), ("pixel_size_um", float)])
-AcquiredImageRequest = NamedTuple("AcquiredImageRequest", [("id", UUID), ("needs_raw", bool), ("needs_seg", bool)])
 
+class ROI(NamedTuple):
+    x_offset: int
+    y_offset: int
+    width: int
+    height: int
 
-class DataDock:
 
-    def __init__(self, time_seconds, requirements: list[AcquiredImageRequest]):
+class CameraProperties(NamedTuple):
+    roi: ROI
+    pixel_size_um: float
+
+
+class AcquiredImageRequest(NamedTuple):
+    id: UUID
+    needs_raw: bool
+    needs_seg: bool
+
 
+class DataDock:
+    def __init__(self, time_seconds, requirements: list[AcquiredImageRequest]):
         self.time_seconds = time_seconds
         self.requirements = requirements
         self.data = defaultdict(dict)
@@ -34,31 +48,32 @@ def __init__(self, time_seconds, requirements: list[AcquiredImageRequest]):
         self.complete = self.check_complete()
 
     def add_raw(self, data: AcquisitionData):
-
         channel_id = data.channel_id
         # ensure channel id was expected
         assert channel_id in self.data, "unexpected data passed to pattern module"
 
         # ensure raw data was expected and not already passed
         assert "raw" in self.data[channel_id], "raw data being passed, but not expected"
-        assert self.data[channel_id]["raw"] is None, f"expected none, found {self.data[channel_id]['raw']}"
+        assert self.data[channel_id]["raw"] is None, (
+            f"expected none, found {self.data[channel_id]['raw']}"
+        )
 
         self.data[channel_id]["raw"] = data
 
     def add_seg(self, data: SegmentationData):
-
         channel_id = data.channel_id
         # ensure channel id was expected
         assert channel_id in self.data, "unexpected data passed to pattern module"
 
         # ensure raw data was expected and not already passed
         assert "seg" in self.data[channel_id], "seg data being passed, but not expected"
-        assert self.data[channel_id]["seg"] is None, f"expected none, found {self.data[channel_id]['seg']}"
+        assert self.data[channel_id]["seg"] is None, (
+            f"expected none, found {self.data[channel_id]['seg']}"
+        )
 
         self.data[channel_id]["seg"] = data
 
     def get_awaiting(self):
-
         awaiting = []
 
         for channel in self.data:
@@ -71,7 +86,6 @@ def get_awaiting(self):
         return awaiting
 
     def check_complete(self):
-
         return len(self.get_awaiting()) == 0
 
 
@@ -79,7 +93,9 @@ class PatternContext:
     def __init__(self, data_dock: DataDock, experiment: Experiment):
         self._dock = data_dock
         self._experiment = experiment
-        self._channel_map = {name: ch.channel_id for name, ch in experiment.channels.items()}
+        self._channel_map = {
+            name: ch.channel_id for name, ch in experiment.channels.items()
+        }
 
     @property
     def time(self) -> float:
@@ -94,7 +110,9 @@ def raw(self, channel_name: str) -> np.ndarray:
         """Get raw image for a channel."""
         cid = self._get_channel_id(channel_name)
         if cid not in self._dock.data or "raw" not in self._dock.data[cid]:
-             raise ValueError(f"Raw data for channel '{channel_name}' was not requested.")
+            raise ValueError(
+                f"Raw data for channel '{channel_name}' was not requested."
+            )
         data = self._dock.data[cid]["raw"]
         return data.data if data else None
 
@@ -102,32 +120,42 @@ def segmentation(self, channel_name: str) -> np.ndarray:
         """Get segmentation mask for a channel."""
         cid = self._get_channel_id(channel_name)
         if cid not in self._dock.data or "seg" not in self._dock.data[cid]:
-             raise ValueError(f"Segmentation data for channel '{channel_name}' was not requested.")
+            raise ValueError(
+                f"Segmentation data for channel '{channel_name}' was not requested."
+            )
         data = self._dock.data[cid]["seg"]
         return data.data if data else None
 
 
-
 class PatternMethod:
-
     name = "base"
 
-    def __init__(self, experiment_name=None, camera_properties: CameraProperties=None, **kwargs):
+    def __init__(
+        self, experiment_name=None, camera_properties: CameraProperties = None, **kwargs
+    ):
         # Support legacy init where these are passed
         self.experiment_name = experiment_name
         self.camera_properties = camera_properties
         if camera_properties:
             self.pixel_size_um = camera_properties.pixel_size_um
-            self.pattern_shape = (camera_properties.roi.height, camera_properties.roi.width)
+            self.pattern_shape = (
+                camera_properties.roi.height,
+                camera_properties.roi.width,
+            )
         else:
             self.pixel_size_um = 1.0
-            self.pattern_shape = (100, 100) # Default placeholders
-        
+            self.pattern_shape = (100, 100)  # Default placeholders
+
         self.binning = 1
-        self._requirements_list = [] # List of (channel_name, raw, seg)
+        self._requirements_list = []  # List of (channel_name, raw, seg)
         self._experiment_ref = None
 
-    def configure_system(self, experiment_name: str, camera_properties: CameraProperties, experiment: Experiment):
+    def configure_system(
+        self,
+        experiment_name: str,
+        camera_properties: CameraProperties,
+        experiment: Experiment,
+    ):
         """Called by the system to inject dependencies."""
         self.experiment_name = experiment_name
         self.camera_properties = camera_properties
@@ -140,7 +168,6 @@ def add_requirement(self, channel_name: str, raw: bool = False, seg: bool = Fals
         self._requirements_list.append((channel_name, raw, seg))
 
     def initialize(self, experiment: Experiment) -> list[AcquiredImageRequest]:
-        
         # If user used add_requirement, process them
         reqs = []
         for name, needs_raw, needs_seg in self._requirements_list:
@@ -152,7 +179,7 @@ def initialize(self, experiment: Experiment) -> list[AcquiredImageRequest]:
 
         binning = experiment.stimulation.binning
         self.update_binning(binning)
-        
+
         return reqs
 
     def get_meshgrid(self) -> tuple[np.ndarray, np.ndarray]:
@@ -165,45 +192,55 @@ def get_meshgrid(self) -> tuple[np.ndarray, np.ndarray]:
 
         return xx, yy
 
-    def generate(self, data_dock: Union[DataDock, PatternContext]) -> np.ndarray:
+    def generate(self, data_dock: DataDock | PatternContext) -> np.ndarray:
         # If passed PatternContext, user is using new API.
         # But if user implemented old generate(self, data_dock: DataDock), we need to support that.
         # This method is called by the system.
         raise NotImplementedError
 
     def update_binning(self, binning: int):
-
         binning_rescale = binning / self.binning
 
         self.pixel_size_um = self.pixel_size_um * binning_rescale
-        self.pattern_shape = (self.pattern_shape[0] // binning_rescale, self.pattern_shape[1] // binning_rescale)
-
-        logger.info(f"model {self.name} updated pixel size (um) to {self.pixel_size_um}")
+        self.pattern_shape = (
+            self.pattern_shape[0] // binning_rescale,
+            self.pattern_shape[1] // binning_rescale,
+        )
+
+        logger.info(
+            f"model {self.name} updated pixel size (um) to {self.pixel_size_um}"
+        )
         logger.info(f"model {self.name} updated pattern_shape to {self.pattern_shape}")
 
         self.binning = binning
 
 
 class PatternMethodReturnsSLM(PatternMethod):
-
     pass
 
 
 class PatternReview(PatternMethodReturnsSLM):
-
     name = "pattern_review"
 
-    def __init__(self, experiment_name, camera_properties, h5fp: Union[str, Path] = None, channel="545", **kwargs):
+    def __init__(
+        self,
+        experiment_name,
+        camera_properties,
+        h5fp: str | Path | None = None,
+        channel="545",
+        **kwargs,
+    ):
         super().__init__(experiment_name, camera_properties)
 
         if h5fp is None:
-            raise ValueError("pattern_review model requires specifying h5fp (h5 filepath)")
+            raise ValueError(
+                "pattern_review model requires specifying h5fp (h5 filepath)"
+            )
 
         self.fp = Path(h5fp)
         self.channel_name = f"channel_{channel}"
 
         with File(str(self.fp), "r") as f:
-
             keys = list(f.keys())
 
         self.keys = natsorted(keys)
@@ -212,21 +249,16 @@ def initialize(self, experiment: Experiment) -> list[AcquiredImageRequest]:
         return []
 
     def generate(self, data_dock: DataDock) -> np.ndarray:
-
         with File(str(self.fp), "r") as f:
-
             while len(self.keys) > 0:
-
                 key = self.keys.pop(0)
 
                 if self.channel_name in f[key]:
-
                     return np.array(f[key]["stim_aq"]["dmd"])
 
         return np.array([])
 
 
-
 if __name__ == "__main__":
     print(type(PatternMethod))
     air = AcquiredImageRequest(uuid4(), True, False)
diff --git a/src/pyclm/core/patterns/pattern_process.py b/src/pyclm/core/patterns/pattern_process.py
index 585fab8..e934223 100644
--- a/src/pyclm/core/patterns/pattern_process.py
+++ b/src/pyclm/core/patterns/pattern_process.py
@@ -1,23 +1,36 @@
 import logging
-
 from threading import Event
+from typing import ClassVar
 
-from ..queues import AllQueues
-from ..datatypes import CameraPattern, AcquisitionData, SegmentationData
+from ..datatypes import AcquisitionData, CameraPattern, SegmentationData
 from ..experiments import Experiment
 from ..messages import Message
-from .pattern import PatternReview, PatternMethod, PatternMethodReturnsSLM, DataDock, AcquiredImageRequest, CameraProperties, PatternContext
-from .bar_patterns import BouncingBarPattern, BarPatternBase, SawToothMethod
+from ..queues import AllQueues
+from .bar_patterns import BarPatternBase, BouncingBarPattern, SawToothMethod
+from .feedback_control_patterns import (
+    BounceModel,
+    MoveDownModel,
+    MoveInModel,
+    MoveOutModel,
+    RotateCcwModel,
+)
+from .ktr_patterns import BinaryNucleusClampModel, CenteredImageModel, GlobalCycleModel
+from .pattern import (
+    AcquiredImageRequest,
+    CameraProperties,
+    DataDock,
+    PatternContext,
+    PatternMethod,
+    PatternMethodReturnsSLM,
+    PatternReview,
+)
 from .static_patterns import CirclePattern, FullOnPattern
-from .feedback_control_patterns import RotateCcwModel, MoveInModel, MoveDownModel, MoveOutModel, BounceModel
-from .ktr_patterns import BinaryNucleusClampModel, GlobalCycleModel, CenteredImageModel
 
 logger = logging.getLogger(__name__)
 
 
 class PatternProcess:
-
-    known_models = {
+    known_models: ClassVar = {
         "circle": CirclePattern,
         "bar": BarPatternBase,
         "pattern_review": PatternReview,
@@ -34,7 +47,7 @@ class PatternProcess:
         "centered_image": CenteredImageModel,
     }
 
-    def __init__(self, aq: AllQueues, stop_event: Event = None):
+    def __init__(self, aq: AllQueues, stop_event: Event | None = None):
         self.stop_event = stop_event
         self.inbox = aq.manager_to_pattern
         self.manager = aq.pattern_to_manager
@@ -42,8 +55,8 @@ def __init__(self, aq: AllQueues, stop_event: Event = None):
 
         self.from_seg = aq.seg_to_pattern
         self.from_raw = aq.outbox_to_pattern
-        
-        self.stream_count = 0 
+
+        self.stream_count = 0
 
         self.camera_properties = None
         self.initialized = False
@@ -57,13 +70,16 @@ def initialize(self, camera_properties: CameraProperties):
         self.initialized = True
 
     def request_method(self, experiment: Experiment) -> list[AcquiredImageRequest]:
-
         method_name = experiment.pattern.method_name
 
         model_class: type = self.known_models.get(method_name)
 
-        assert model_class is not None, f"method {method_name} is not a registered method"
-        assert issubclass(model_class, PatternMethod), f"{method_name} is not a PatternMethod"
+        assert model_class is not None, (
+            f"method {method_name} is not a registered method"
+        )
+        assert issubclass(model_class, PatternMethod), (
+            f"{method_name} is not a PatternMethod"
+        )
 
         experiment_name = experiment.experiment_name
         method_kwargs = experiment.pattern.kwargs
@@ -72,13 +88,14 @@ def request_method(self, experiment: Experiment) -> list[AcquiredImageRequest]:
 
         self.models[experiment_name] = model
 
-        logger.info(f"initializing pattern model \"{method_name}\"")
+        logger.info(f'initializing pattern model "{method_name}"')
 
         return model.initialize(experiment)
 
-    def register_method(self, model: type, name: str = None):
-
-        assert issubclass(model, PatternMethod), "model must be a subclass of PatternMethod"
+    def register_method(self, model: type, name: str | None = None):
+        assert issubclass(model, PatternMethod), (
+            "model must be a subclass of PatternMethod"
+        )
 
         model_name = model.name
         if name is not None:
@@ -90,20 +107,23 @@ def register_method(self, model: type, name: str = None):
         self.known_models[model_name] = model
 
     def run_model(self, experiment_name, dockname):
-
         data_dock = self.docks.pop(dockname)
 
         model = self.models.get(experiment_name, None)
 
-        assert isinstance(model, PatternMethod), f"self.models[{'experiment_name'}] is not a PatternMethod"
+        assert isinstance(model, PatternMethod), (
+            f"self.models[{'experiment_name'}] is not a PatternMethod"
+        )
 
         # Create context wrapper
 
         # We assume _experiment_ref is available. If not, we might crash, which is acceptable for alpha breakage.
         # Ideally, we ensure configure_system is called.
         if model._experiment_ref is None:
-             raise RuntimeError(f"Model {model.name} for {experiment_name} was not properly configured with an experiment reference.")
-        
+            raise RuntimeError(
+                f"Model {model.name} for {experiment_name} was not properly configured with an experiment reference."
+            )
+
         context = PatternContext(data_dock, model._experiment_ref)
 
         if isinstance(model, PatternMethodReturnsSLM):
@@ -112,25 +132,26 @@ def run_model(self, experiment_name, dockname):
 
         else:
             pattern = model.generate(context)
-            self.slm.put(CameraPattern(experiment_name, pattern, slm_coords=False, binning=model.binning))
+            self.slm.put(
+                CameraPattern(
+                    experiment_name, pattern, slm_coords=False, binning=model.binning
+                )
+            )
 
     def dock_string(self, experiment_name, t):
         return f"{experiment_name}_{t:05d}"
 
     def check(self, experiment_name, dockname):
-
         dock: DataDock = self.docks.get(dockname)
 
         if dock.check_complete():
             self.run_model(experiment_name, dockname)
 
     def handle_message(self, message: Message):
-
         match message.message:
-
             case "close":
-                return False 
-                
+                return False
+
             case "stream_close":
                 print("pattern received stream close")
 
@@ -138,13 +159,13 @@ def handle_message(self, message: Message):
                 if self.stream_count >= 2:
                     # Signal SLMBuffer that we are done
                     from ..messages import StreamCloseMessage
+
                     out_msg = StreamCloseMessage()
                     self.slm.put(out_msg)
                     return True
                 return False
 
             case "request_pattern":
-
                 assert isinstance(message, RequestPattern)
 
                 req = message.requirements
@@ -171,7 +192,7 @@ def process(self):
             if self.stop_event and self.stop_event.is_set():
                 print("force stopping pattern process")
                 break
-            
+
             if not self.inbox.empty():
                 msg = self.inbox.get()
 
@@ -180,9 +201,10 @@ def process(self):
 
             if not self.from_raw.empty():
                 data = self.from_raw.get()
-                
+
                 if isinstance(data, Message):
-                    if self.handle_message(data): return
+                    if self.handle_message(data):
+                        return
                 else:
                     assert isinstance(data, AcquisitionData)
                     name = data.event.experiment_name
@@ -196,20 +218,21 @@ def process(self):
 
             if not self.from_seg.empty():
                 data = self.from_seg.get()
-                
+
                 if isinstance(data, Message):
-                    if self.handle_message(data): return
+                    if self.handle_message(data):
+                        return
                 else:
                     assert isinstance(data, SegmentationData)
                     name = data.event.experiment_name
                     t_index = data.event.t_index
-    
+
                     dockname = self.dock_string(name, t_index)
-    
+
                     print(f"seg found {dockname}")
-    
+
                     self.docks[dockname].add_seg(data)
-    
+
                     self.check(name, dockname)
 
 
@@ -222,11 +245,14 @@ class RequestPattern(Message):
 
     message = "request_pattern"
 
-    def __init__(self, t_index, time_sec, experiment_name: str, requirements: list[AcquiredImageRequest]):
-
+    def __init__(
+        self,
+        t_index,
+        time_sec,
+        experiment_name: str,
+        requirements: list[AcquiredImageRequest],
+    ):
         self.t_index = t_index
         self.time_sec = time_sec
         self.experiment_name = experiment_name
         self.requirements = requirements
-
-
diff --git a/src/pyclm/core/patterns/static_patterns.py b/src/pyclm/core/patterns/static_patterns.py
index 4d1bb11..4900718 100644
--- a/src/pyclm/core/patterns/static_patterns.py
+++ b/src/pyclm/core/patterns/static_patterns.py
@@ -16,17 +16,18 @@ def __init__(self, rad=1, **kwargs):
         self.rad = rad
 
     def generate(self, context):
-
         h, w = self.pattern_shape
 
-        center_x = self.pixel_size_um * w / 2.
-        center_y = self.pixel_size_um * h / 2.
+        center_x = self.pixel_size_um * w / 2.0
+        center_y = self.pixel_size_um * h / 2.0
 
         xx, yy = self.get_meshgrid()
 
         print(h, w)
 
-        return (((xx - center_x)**2 + (yy - center_y)**2) < (self.rad**2)).astype(np.float16)
+        return (((xx - center_x) ** 2 + (yy - center_y) ** 2) < (self.rad**2)).astype(
+            np.float16
+        )
 
 
 class FullOnPattern(PatternMethod):
@@ -40,7 +41,6 @@ def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
     def generate(self, context):
-
         h, w = self.pattern_shape
         pattern = np.ones((int(h), int(w)), dtype=np.float16)
 
diff --git a/src/pyclm/core/patterns/wave_patterns.py b/src/pyclm/core/patterns/wave_patterns.py
index d96dccf..a8b7cd7 100644
--- a/src/pyclm/core/patterns/wave_patterns.py
+++ b/src/pyclm/core/patterns/wave_patterns.py
@@ -7,6 +7,7 @@ class WavePatternBase(PatternMethod):
     """
     Creates a WavePattern or StationaryWavePattern depending on the requested wavespeed
     """
+
     def __new__(cls, *args, **kwargs):
         if cls is WavePatternBase:  # Check if the base class is being instantiated
             if kwargs.get("wave_speed") != 0:
@@ -19,6 +20,7 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         print(f"Initializing {self.__class__.__name__}")
 
+
 class StationaryWavePattern(WavePatternBase):
     """
     Wave coming out from the center
@@ -37,14 +39,13 @@ def __init__(self, duty_cycle=0.2, wave_speed=0, period=30, **kwargs):
 
         self.duty_cycle = duty_cycle
         self.wave_speed = 0
-        self.period_space = period    # in um
-        self.period_time = 0    # in minutes
+        self.period_space = period  # in um
+        self.period_time = 0  # in minutes
 
     def generate(self, context):
-
         xx, yy = self.get_meshgrid()
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
-        distance = np.sqrt((xx - center_x)**2 + (yy - center_y)**2)
+        distance = np.sqrt((xx - center_x) ** 2 + (yy - center_y) ** 2)
 
         is_on = ((distance / self.period_space) % 1.0) < self.duty_cycle
 
@@ -58,31 +59,32 @@ class WavePattern(WavePatternBase):
 
     name = "wave"
 
-    def __init__(self, duty_cycle=0.2, wave_speed=1, period=30, direction = 1, **kwargs):
+    def __init__(self, duty_cycle=0.2, wave_speed=1, period=30, direction=1, **kwargs):
         """
         :param duty_cycle: fraction of time spent on (float 0-1), and consequently fraction of
                            radial axis containing "on" pixels
         :param wave_speed: speed in um/min
         :param period: period in um
-        :param direction: movement in/out relative to the center. 1 is out; -1 is in 
+        :param direction: movement in/out relative to the center. 1 is out; -1 is in
         """
         super().__init__(**kwargs)
 
         self.duty_cycle = duty_cycle
         self.wave_speed = wave_speed
-        self.period_space = period    # in um
-        self.period_time = period / wave_speed    # in minutes
+        self.period_space = period  # in um
+        self.period_time = period / wave_speed  # in minutes
         self.direction = direction
 
     def generate(self, context):
-
         t = context.time / 60
 
         xx, yy = self.get_meshgrid()
         center_y, center_x = self.pattern_shape[0] / 2, self.pattern_shape[1] / 2
-        distance = np.sqrt((xx - center_x)**2 + (yy - center_y)**2)
+        distance = np.sqrt((xx - center_x) ** 2 + (yy - center_y) ** 2)
 
-        is_on = (((t*self.direction) - (distance / self.wave_speed)) % self.period_time) < self.duty_cycle*self.period_time
+        is_on = (
+            ((t * self.direction) - (distance / self.wave_speed)) % self.period_time
+        ) < self.duty_cycle * self.period_time
 
         return is_on.astype(np.float16)
 
@@ -159,4 +161,4 @@ def generate(self, context):
 
 #         data_dock.time_seconds = t
 
-#         return super().generate(data_dock)
\ No newline at end of file
+#         return super().generate(data_dock)