Remove autorecentre
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jaknapper
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4 changed files with 0 additions and 160 deletions
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@ -2,7 +2,6 @@
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"things": {
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"/camera/": "openflexure_microscope_server.things.camera.picamera:StreamingPiCamera2",
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"/stage/": "openflexure_microscope_server.things.stage.sangaboard:SangaboardThing",
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"/auto_recentre_stage/": "openflexure_microscope_server.things.auto_recentre_stage:RecentringThing",
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"/autofocus/": "openflexure_microscope_server.things.autofocus:AutofocusThing",
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"/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
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"/system/": "openflexure_microscope_server.things.system:OpenFlexureSystem",
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@ -2,7 +2,6 @@
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"things": {
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"/camera/": "openflexure_microscope_server.things.camera.simulation:SimulatedCamera",
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"/stage/": "openflexure_microscope_server.things.stage.dummy:DummyStage",
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"/auto_recentre_stage/": "openflexure_microscope_server.things.auto_recentre_stage:RecentringThing",
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"/autofocus/": "openflexure_microscope_server.things.autofocus:AutofocusThing",
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"/camera_stage_mapping/": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
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"/system/": "openflexure_microscope_server.things.system:OpenFlexureSystem",
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@ -1,145 +0,0 @@
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"""Provide functionality for automatically recentring the Stage."""
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import numpy as np
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import logging
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import labthings_fastapi as lt
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from .stage import StageDependency as StageDep
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from openflexure_microscope_server.things.autofocus import AutofocusThing
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from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
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CSMDep = lt.deps.direct_thing_client_dependency(
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CameraStageMapper, "/camera_stage_mapping/"
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)
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AutofocusDep = lt.deps.direct_thing_client_dependency(AutofocusThing, "/autofocus/")
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class RecentringThing(lt.Thing):
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"""A Thing for recentring the stage by monitoring parasitic z motion of the stage.
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As the stage moves over a sphere-cap there is parasitic motion in z during xy
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movement. The highest z position is the centre of motion.
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"""
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@lt.thing_action
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def recentre(
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self,
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autofocus: AutofocusDep,
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stage: StageDep,
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max_steps=15,
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lateral_distance=5000,
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):
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"""Recentre the stage, based on the focal plane.
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Autofocuses at multiple points around the sample to
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find the overall maximum (or minimum) height, which
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corresponds to the centre of the stage. This exploits the
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fact that the OpenFlexure stage moves in an arc, i.e. its
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height will vary with X and Y. The point where the variation
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of Z with X and Y motion is smallest is the centre of its
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XY travel. This routine moves in X and Y, monitoring the
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Z value of the focal plane, and attempts to find the point
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where Z does not vary with X and Y, which is where it stops.
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max_steps: The maximum number of moves in x or y before
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aborting due to a poorly positioned stage or hard to focus
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sample
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lateral_distance: The xy distance between areas to check.
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Below 3000 becomes less reliable, as focus shouldn't shift
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much between these sites, making the procedure more sensitive
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to noise or a failed autofocus.
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"""
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max_steps = 20
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dx = lateral_distance
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centre = list(stage.position.values())
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# A list of all the positions we've focused
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focused_pos = [[], []]
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autofocus.looping_autofocus()
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for direction in [0, 1]:
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# Start off with the current position, and moving in the positive direction
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focused_pos[direction] = [list(stage.position.values())]
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moves = +1
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stage.move_absolute(x=centre[0], y=centre[1], z=centre[2])
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steps = 0
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all_heights = []
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# We'll run this for x, then y
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while True:
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# If we're moving in the positive direction, we want the highest point
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# Otherwise, we want the lowest
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if moves > 0:
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starting_point = np.max(
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np.array(focused_pos[direction])[:, direction]
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)
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else:
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starting_point = np.min(
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np.array(focused_pos[direction])[:, direction]
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)
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# Next location is an extra move in the direction we want
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destination = centre
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destination[direction] = starting_point + moves * dx
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stage.move_absolute(
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x=int(destination[0]), y=int(destination[1]), z=destination[2]
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)
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autofocus.looping_autofocus(autofocus, stage)
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position = list(stage.position.values())
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focused_pos[direction].append(position)
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logging.info(focused_pos)
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steps += 1
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if steps > max_steps:
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logging.warning(
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"Couldn't find a suitable position. Roughly centre the stage and check your sample is suitable for autofocus"
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)
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break
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if len(focused_pos[direction]) > 4:
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all_heights = [x[2] for x in focused_pos[direction]]
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direction_index = [x[direction] for x in focused_pos[direction]]
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sorted_all_heights = [
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x for y, x in sorted(zip(direction_index, all_heights))
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]
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sorted_lateral = sorted(direction_index)
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quad_fit = np.polyfit(sorted_lateral, sorted_all_heights, 2)
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quad_fit_func = np.poly1d(quad_fit)
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turning = quad_fit_func.deriv()
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turning_loc = -turning[0] / (turning[1])
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logging.warning(sorted_all_heights)
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if (
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np.argmax(sorted_all_heights) != 0
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and np.argmax(sorted_all_heights) != len(all_heights) - 1
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):
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logging.info(
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f"Breaking because the highest point is at {np.argmax(sorted_all_heights)} in the list"
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)
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break
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if turning_loc < np.min(sorted_lateral):
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moves = -1
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elif turning_loc > np.max(sorted_lateral):
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moves = 1
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# Centre value is replaced by the maximum value recorded in that axis
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centre[direction] = focused_pos[direction][np.argmax(all_heights)][
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direction
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]
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stage.move_absolute(x=centre[0], y=centre[1], z=centre[2])
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autofocus.looping_autofocus()
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logging.info(f"Centre of ROM is at {centre, stage.position['z']} \n")
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return focused_pos
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@ -76,19 +76,6 @@
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@finished="updatePosition"
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@error="modalError"
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/>
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<action-button
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thing="auto_recentre_stage"
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action="recentre"
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submit-label="Re-centre Stage"
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:can-terminate="true"
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:requires-confirmation="true"
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:modal-progress="true"
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:confirmation-message="
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'The stage will now move, and autofocus will be used to find the centre of motion. This requires a sample to be visible in the microscope. OK to proceed?'
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"
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@finished="updatePosition"
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@error="modalError"
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/>
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</div>
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</li>
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