Updated docstrings and fixed ruff errors
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Chish36
Julian Stirling
parent
1c7527c2ef
commit
d494761cbb
1 changed files with 30 additions and 46 deletions
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@ -1,15 +1,24 @@
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"""File contains all the functions used to measure the range of motion of the OpenFlexure Microscope translation stage.
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The range of motion is measured by first taking 5 'medium' sized steps which gives enough positions to predict future z positions. Next, one 'big' step is taken followed by 3
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'small' steps to test that the stage is still moving as expected and has not reached the edge. Once the edge has been found and too account for the possibility that a 'big'
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step was take just before the edge was reached, the stage is moved in a sequence of increasing pixel sizes in the opposite direction until motion is detected. This is
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position is taken as the true final position.
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Throughout the test, parasitic motion(motion in the axis not being measured) is tracked and an error is raised if it exceeds a reasonable amount.
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"""
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import numpy as np
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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 Dict, Optional
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from scipy.optimize import curve_fit
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from camera_stage_mapping import fft_image_tracking
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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
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from labthings_fastapi.decorators import thing_action, thing_property
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from labthings_fastapi.decorators import thing_action
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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 DenumpifyingDict
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@ -21,17 +30,6 @@ 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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'''
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This file contains all the functions used to measure the range of motion of the OpenFlexure Microscope translation stage.
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The range of motion is measured by first taking 5 'medium' sized steps which gives enough positions to predict future z positions. Next, one 'big' step is taken followed by 3
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'small' steps to test that the stage is still moving as expected and has not reached the edge. Once the edge has been found and too account for the possibility that a 'big'
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step was take just before the edge was reached, the stage is moved in a sequence of increasing pixel sizes in the opposite direction until motion is detected. This is
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position is taken as the true final position.
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Throughout the test, parasitic motion(motion in the axis not being measured) is tracked and an error is raised if it exceeds a reasonable amount.
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'''
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def quadratic(x, a, b, c):
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"""Quadratic function. Used for predicting z.
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@ -43,8 +41,8 @@ def quadratic(x, a, b, c):
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"""
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return a * x**2 + b * x + c
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def dict_generate(fov_perc: int, stream_resolution: list[int], direction: int, factor: float = 1) -> dict[str, float]:
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"""Creates a single dictionary of x and y moves for moving in image coordinates.
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def generate_move_dicts(fov_perc: int, stream_resolution: list[int], direction: int, factor: float = 1) -> dict[str, float]:
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"""Create a single dictionary of x and y moves for moving in image coordinates.
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:param fov_perc: The percentage of field of view the stage should move by.
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:param stream_resolution: The resolution of the stream from the camera.
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@ -52,15 +50,14 @@ def dict_generate(fov_perc: int, stream_resolution: list[int], direction: int, f
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:param factor: Multiplicative factor which changes the final result.
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:return: A dictionary with keys 'x' and 'y' with a pixel distance move the stage can make.
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"""
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xy_dict = {
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return {
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"x": (fov_perc / 100) * stream_resolution[0] * factor * direction,
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"y": (fov_perc / 100) * stream_resolution[1] * factor * direction,
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}
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return xy_dict
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def predict_z(positions: list, axis: str, relative_move: float, stage: StageDep, csm: CSMDep) -> float:
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"""Predicts the next z position for a 'big' move using an array of previous positions. This avoids long autofocuses and reduces the possibility of colliding with
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the sample.
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"""Predict the next z position for a move using previous positions.
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:params positions: The list of positions used for predicting z. This will usually be a list of all previuos positions.
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:params axis: The axis in which the stage is moving. This must be 'x' or 'y'.
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@ -76,9 +73,8 @@ def predict_z(positions: list, axis: str, relative_move: float, stage: StageDep,
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z_positions = [i['z'] for i in positions]
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parameters, _ = curve_fit(quadratic, lateral_positions, z_positions)
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z_dest = quadratic(stage.position[axis] + (relative_move/pixel_step[axis]), *parameters)
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z_diff = z_dest - stage.position['z']
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return z_diff
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return z_dest - stage.position["z"]
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def move_and_measure(
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step_size: dict[str, float],
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@ -88,7 +84,7 @@ def move_and_measure(
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csm: CSMDep,
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autofocus: AutofocusDep,
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cam:CamDep) -> tuple:
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"""Moves the stage and measures the offset between the two positions.
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"""Move the stage and measure the offset between the two positions.
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:params step_size: A dictionary with keys 'x' and 'y' with pixel distances.
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:params axis: The axis in which the stage is moving. This must be 'x' or 'y'.
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@ -127,7 +123,7 @@ def medium_moves(
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autofocus: AutofocusDep,
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logger: InvocationLogger
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) -> tuple:
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"""Carries out the medium sized steps section of the range of motion test to get 5 points to make z position predictions with
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"""Carries out the medium sized steps section of the range of motion test to get 5 points to make z position predictions with.
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:params stream_resolution: The resolution of the stream from the camera.
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:param direction: The direction the stage moves.
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@ -138,9 +134,8 @@ def medium_moves(
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:params cor_lat_steps: A list of all correlation values.
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:return: Stage_coords and cor_lat_steps are lists of data tracked throughout the test. Delta is updated and tracked after each move.
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"""
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medium_step = 50
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wrong_axis_max_medium = dict_generate(
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wrong_axis_max_medium = generate_move_dicts(
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medium_step, stream_resolution, direction, factor=0.1
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)
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for loop in range(5):
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@ -148,7 +143,7 @@ def medium_moves(
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np.array(Image.open(cam.grab_jpeg().open())), dsize=(0, 0), fx=1, fy=1
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)
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delta, offset, focus_data, wrong_axis = move_and_measure(
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step_size=dict_generate(medium_step, stream_resolution, direction),
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step_size=generate_move_dicts(medium_step, stream_resolution, direction),
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axis=axis,
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delta=delta,
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image1=image1,
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@ -181,7 +176,7 @@ def small_moves(
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autofocus: AutofocusDep,
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logger: InvocationLogger,
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) -> tuple:
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"""Carries out the medium sized steps section of the range of motion test to get 5 points to make z position predictions with
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"""Carries out 3 small moves in a given direction and axis.
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:params small_step: The integer value used to generate the small step sizes.
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:params stream_resolution: The resolution of the stream from the camera.
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@ -195,14 +190,14 @@ def small_moves(
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:return: Stage_coords and cor_lat_steps are lists of data tracked throughout the test. Delta is updated and tracked after each move.
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"""
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failure_count = 0
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wrong_axis_max_small = dict_generate(small_step, stream_resolution, direction, factor=0.1)
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wrong_axis_max_small = generate_move_dicts(small_step, stream_resolution, direction, factor=0.1)
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for loop in range(3):
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image1 = cv2.resize(
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np.array(Image.open(cam.grab_jpeg().open())), dsize=(0, 0), fx=1, fy=1
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)
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delta, offset, focus_data, wrong_axis = move_and_measure(
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step_size=dict_generate(small_step, stream_resolution, direction),
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step_size=generate_move_dicts(small_step, stream_resolution, direction),
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axis=axis,
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delta=delta,
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image1=image1,
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@ -253,8 +248,7 @@ def small_moves(
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return stage_coords, cor_lat_steps, delta
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def motion_detection(axis: str, direction: int, csm: CSMDep, stage: StageDep, cam: CamDep, logger: InvocationLogger) -> dict:
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"""Moves the stage until motion is detected. This happens at the end of each axis and direction and where the stage is moved in the opposite direction until
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motion is detected.
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"""Move the stage until motion is detected along a specified axis and direction.
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:params axis: The axis in which the stage is moving. This must be 'x' or 'y'.
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:params direction: The direction in which the stage was moving previous to motion detection being used.
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@ -288,18 +282,17 @@ def motion_detection(axis: str, direction: int, csm: CSMDep, stage: StageDep, ca
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logger.info("Motion detected.")
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break
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true_final = stage.position
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return true_final
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return stage.position
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class RangeofMotionThing(Thing):
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"""A class used to measure the range of motion of the stage in X and Y."""
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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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@ -310,7 +303,6 @@ class RangeofMotionThing(Thing):
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:params direction: The direction which is being measured. This must be 1 or -1.
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:return: Results dictionary containing stage positions, correlations and the final position.
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"""
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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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@ -332,7 +324,7 @@ class RangeofMotionThing(Thing):
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big_step = 200
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small_step = 20
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step_sizes_big = dict_generate(big_step, stream_resolution, direction)
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step_sizes_big = generate_move_dicts(big_step, stream_resolution, direction)
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delta = {
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'x':0,
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@ -360,7 +352,7 @@ class RangeofMotionThing(Thing):
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# 1 big step followed by 3 small steps
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minimum_offset_small = dict_generate(
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minimum_offset_small = generate_move_dicts(
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small_step, stream_resolution, direction, factor=0.65
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)
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@ -470,11 +462,3 @@ class RangeofMotionThing(Thing):
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return rom_results
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@thing_property
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def rom_data(self) -> Optional[Dict]:
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"""The results of the last range of motion calibration that was run."""
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filename = '/var/openflexure/settings/range_of_motion/settings.json'
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with open(filename) as f:
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rom_object = json.load(f)
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return rom_object
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