And adjust for new as lt import
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commit
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17 changed files with 240 additions and 293 deletions
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@ -17,10 +17,7 @@ from fastapi import Depends
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import numpy as np
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from pydantic import BaseModel
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from labthings_fastapi.thing import Thing
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from labthings_fastapi.dependencies.blocking_portal import BlockingPortal
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from labthings_fastapi.decorators import thing_action
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from labthings_fastapi.descriptors import ThingSetting
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import labthings_fastapi as lt
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from labthings_fastapi.types.numpy import NDArray
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from .camera import RawCameraDependency as Camera
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@ -190,7 +187,7 @@ class SharpnessDataArrays(BaseModel):
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class JPEGSharpnessMonitor:
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def __init__(self, stage: Stage, camera: Camera, portal: BlockingPortal):
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def __init__(self, stage: Stage, camera: Camera, portal: lt.deps.BlockingPortal):
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self.camera = camera
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self.stage = stage
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self.portal = portal
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@ -288,14 +285,14 @@ class JPEGSharpnessMonitor:
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SharpnessMonitorDep = Annotated[JPEGSharpnessMonitor, Depends()]
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class AutofocusThing(Thing):
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class AutofocusThing(lt.Thing):
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"""The Thing concerned with combinations of z axis movements and the camera.
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Actions here involve moving a stage in z, and using the camera to either
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capture images (generally, z-stacking) and measuring the sharpness of the
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field of view to assess focus (autofocus and testing the success of a z-stack)"""
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@thing_action
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@lt.thing_action
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def fast_autofocus(
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self,
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sharpness_monitor: SharpnessMonitorDep,
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@ -325,7 +322,7 @@ class AutofocusThing(Thing):
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# Return all focus data
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return sharpness_monitor.data_dict()
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@thing_action
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@lt.thing_action
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def z_move_and_measure_sharpness(
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self,
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sharpness_monitor: SharpnessMonitorDep,
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@ -351,7 +348,7 @@ class AutofocusThing(Thing):
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sharpness_monitor.focus_rel(current_dz)
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return sharpness_monitor.data_dict()
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@thing_action
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@lt.thing_action
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def looping_autofocus(
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self,
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stage: Stage,
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@ -397,7 +394,7 @@ class AutofocusThing(Thing):
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stage.move_absolute(z=peak_height)
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return heights.tolist(), sizes.tolist()
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stack_images_to_save = ThingSetting(
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stack_images_to_save = lt.ThingSetting(
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initial_value=1,
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model=int,
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description="""The number of images to save in a stack.
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@ -405,7 +402,7 @@ class AutofocusThing(Thing):
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Defaults to 1 unless you need to see either side of focus""",
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)
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stack_min_images_to_test = ThingSetting(
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stack_min_images_to_test = lt.ThingSetting(
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initial_value=9,
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model=int,
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description="""The minimum number of images to capture in a stack.
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@ -419,7 +416,7 @@ class AutofocusThing(Thing):
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""",
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)
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stack_dz = ThingSetting(
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stack_dz = lt.ThingSetting(
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initial_value=50,
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model=int,
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description="""Space in steps between images in a z-stack
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@ -428,7 +425,7 @@ class AutofocusThing(Thing):
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200 for 20x""",
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)
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@thing_action
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@lt.thing_action
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def run_smart_stack(
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self,
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cam: WrappedCamera,
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