Completes all necessary movements along a single axis
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Chish36
Julian Stirling
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commit
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1 changed files with 188 additions and 0 deletions
188
src/openflexure_microscope_server/things/stage_measure.py
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src/openflexure_microscope_server/things/stage_measure.py
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import numpy as np
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import logging
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import cv2
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import json
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from PIL import Image
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import time
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from typing import Annotated, Any, Callable, Dict, List, Mapping, NamedTuple, Optional, Sequence, Tuple
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from scipy.optimize import curve_fit
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from camera_stage_mapping import camera_stage_tracker
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from camera_stage_mapping import fft_image_tracking
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from dataclasses import dataclass, field
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from labthings_fastapi.thing import Thing
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from labthings_fastapi.dependencies.thing import direct_thing_client_dependency
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from labthings_fastapi.dependencies.invocation import CancelHook, InvocationLogger, InvocationCancelledError
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from labthings_fastapi.decorators import thing_action, thing_property
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from .stage import StageDependency as StageDep
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from labthings_sangaboard import SangaboardThing
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from labthings_picamera2.thing import StreamingPiCamera2
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from labthings_fastapi.types.numpy import NDArray, denumpify, DenumpifyingDict
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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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StageDep = direct_thing_client_dependency(SangaboardThing, "/stage/")
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CamDep = direct_thing_client_dependency(StreamingPiCamera2, "/camera/")
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CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
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AutofocusDep = direct_thing_client_dependency(AutofocusThing, "/autofocus/")
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def dict_generate(dict_steps, stream_resolution, dir, factor = 1):
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'''
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Creates a single dictionary of step sizes
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'''
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dict = {
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'x':(dict_steps/100) * stream_resolution[0] * factor * dir,
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'y':(dict_steps/100) * stream_resolution[1] * factor * dir
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}
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return dict
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def steps_generate(small_step, z_perc, big_step, dir, stream_resolution):
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'''
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Creates all required dictionaries of all necessary step sizes.
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'''
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step_sizes_big = dict_generate(big_step, stream_resolution, dir)
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step_sizes_small = dict_generate(small_step, stream_resolution, dir)
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minimum_offset_small = dict_generate(small_step, stream_resolution, dir, factor = 0.8)
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z_steps = dict_generate(z_perc, stream_resolution, dir)
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minimum_offset_z = dict_generate(z_perc, stream_resolution, dir, factor = 0.8)
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return step_sizes_small, minimum_offset_small, z_steps, minimum_offset_z, step_sizes_big
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class RangeofMotionThing(Thing):
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def rom_axis(
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self,
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autofocus: AutofocusDep,
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stage: StageDep,
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cam: CamDep,
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csm: CSMDep,
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cancel: CancelHook,
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logger: InvocationLogger,
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axis: str,
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direction: int
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):
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"""
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Measure the range of motion in a single axis and direction.
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"""
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try:
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# Generate required dictionaries for step sizes and minimum offsets
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stream_resolution = cam.stream_resolution
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step_sizes_small, minimum_offset_small, z_steps, minimum_offset_z, step_sizes_big = steps_generate(20, 50, 200, direction, stream_resolution=stream_resolution)
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delta = {
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'x':0,
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'y':0
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}
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logger.info(f"Using the follwing steps: {step_sizes_small, minimum_offset_small, z_steps, minimum_offset_z, step_sizes_big}")
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focus_data = autofocus.looping_autofocus(dz = 1000)
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starting_position = list(stage.position.values())
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logger.info("Moving the stage in 4 medium sized steps.")
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# Medium sized steps
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for loop in range(4):
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image1 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
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if axis == 'x':
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csm.move_in_image_coordinates(x = z_steps['x'], y = 0)
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else:
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csm.move_in_image_coordinates(x = 0, y = z_steps['y'])
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focus_data = autofocus.looping_autofocus(dz = 800)
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image2 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
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offset = [x * 1 for x in fft_image_tracking.displacement_between_images(image_0 = image1, image_1 = image2, sigma=10, fractional_threshold=0.1, pad=True)] # Units is pixels
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delta['x'] = int(offset[1])
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delta['y'] = int(offset[0])
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logger.info(f"Offset measured as {delta[axis]}")
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# 1 big step followed by 3 small steps
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while np.abs(delta[axis]) > minimum_offset_small[axis]:
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if axis == 'x':
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csm.move_in_image_coordinates(x = step_sizes_big['x'], y = 0)
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else:
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csm.move_in_image_coordinates(x = 0, y = step_sizes_big['y'])
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for loop in range(3):
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image1 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
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if axis == 'x':
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csm.move_in_image_coordinates(x = step_sizes_small['x'], y = 0)
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else:
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csm.move_in_image_coordinates(x = 0, y = step_sizes_small['y'])
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focus_data = autofocus.looping_autofocus(dz = 800)
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image2 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
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offset = [x * 1 for x in fft_image_tracking.displacement_between_images(image_0 = image1, image_1 = image2, sigma=10, fractional_threshold=0.1, pad=True)] # Units is pixels
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delta['x'] = int(offset[1])
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delta['y'] = int(offset[0])
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logger.info(f"Offset measured as {delta[axis]}")
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if np.abs(delta[axis]) < minimum_offset_small[axis]: # this means the edge has been found
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logger.info(f"Edge has been found.")
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break
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# Motion detection
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logger.info(f"Running motion detection")
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displacements = np.array([1,2,4,8,16,32,64,128,256,512,1024]) # Array of increasing step sizes
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motion_minimum = 20 # minimum nuber of pixels for motion to be detected
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this_motion_step = {
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'x':np.zeros(np.shape(displacements)[0]),
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'y':np.zeros(np.shape(displacements)[0]),
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'z':0
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}
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this_motion_step[axis] = displacements * direction * -1
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for loop in range(np.shape(displacements)[0]):
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logger.info(f"Testing with step size {this_motion_step[axis][loop]}")
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image1 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
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stage.move_relative(x = this_motion_step['x'][loop], y = this_motion_step['y'][loop], z = this_motion_step['z'])
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image2 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
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offset = [x * 1 for x in fft_image_tracking.displacement_between_images(
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image_0 = image1, image_1 = image2, sigma=10, fractional_threshold=0.1, pad=True)] # Units is pixels
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delta['x'] = int(offset[1])
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delta['y'] = int(offset[0])
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logger.info(f"Offset measured as {np.abs(delta[axis])}")
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if np.abs(delta[axis]) > motion_minimum:
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logger.info("Motion detected.")
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break
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stage.move_absolute(x = starting_position[0], y = starting_position[1], z = starting_position[2], block_cancellation=True)
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except:
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logger.error("Stopping measurement because it was cancelled by the user")
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stage.move_absolute(x = starting_position[0], y = starting_position[1], z = starting_position[2], block_cancellation=True)
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raise Exception
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return focus_data
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@thing_action
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def rom_main(
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self,
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autofocus: AutofocusDep,
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stage: StageDep,
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cam: CamDep,
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csm: CSMDep,
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cancel: CancelHook,
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logger: InvocationLogger
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):
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"""
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Measures the range of motion of the stage across the x and y axes.
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"""
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logger.info("Using the stage to measure the Range of Motion. Please ensure you are using a big enough sample.")
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x_pos_results = self.rom_axis(
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autofocus,
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stage,
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cam,
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csm,
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cancel,
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logger,
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axis = 'x',
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direction = 1
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)
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return x_pos_results
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