Merge branch 'integrated-stitching' into 'v3'
Run `openflexure-stitch` on the server See merge request openflexure/openflexure-microscope-server!169
This commit is contained in:
Richard Bowman
commit
13f39d5303
9 changed files with 495 additions and 176 deletions
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@ -11,6 +11,7 @@ from .things.system_control import SystemControlThing
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from .things.settings_manager import SettingsManager
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from .things.auto_recentre_stage import RecentringThing
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from .things.smart_scan import SmartScanThing, BackgroundDetectThing
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from .things.stitching import Stitcher
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from .things.test import APITestThing
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from .serve_static_files import add_static_files
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from .logging import configure_logging, retrieve_log
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@ -25,7 +26,7 @@ thing_server.add_thing(AutofocusThing(), "/autofocus/")
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thing_server.add_thing(CameraStageMapper(), "/camera_stage_mapping/")
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thing_server.add_thing(SystemControlThing(), "/system_control/")
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thing_server.add_thing(SettingsManager(), "/settings/")
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thing_server.add_thing(SmartScanThing(), "/smart_scan/")
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thing_server.add_thing(SmartScanThing("application/openflexure-stitching/.venv/bin/openflexure-stitch"), "/smart_scan/")
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thing_server.add_thing(BackgroundDetectThing(), "/background_detect/")
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thing_server.add_thing(APITestThing(), "/api_test/")
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try:
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@ -1,4 +1,5 @@
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import shutil
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import threading
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from typing import Mapping, Optional
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import cv2
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from fastapi import HTTPException
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@ -9,14 +10,15 @@ import time
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from PIL import Image
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from pydantic import BaseModel
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from scipy.stats import norm
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import logging
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from copy import deepcopy
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from datetime import datetime
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from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, run
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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, fastapi_endpoint
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from labthings_fastapi.outputs.blob import BlobOutput
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from labthings_sangaboard import SangaboardThing
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from labthings_picamera2.thing import StreamingPiCamera2
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from openflexure_microscope_server.things.autofocus import AutofocusThing
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@ -279,11 +281,18 @@ class BackgroundDetectThing(Thing):
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BackgroundDep = direct_thing_client_dependency(BackgroundDetectThing, "/background_detect/")
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class NotEnoughFreeSpaceError(IOError):
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pass
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def ensure_free_disk_space(path: str, min_space: int = 500000000) -> None:
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"""Raise an exception if we are running out of disk space"""
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du = shutil.disk_usage(path)
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if du.free < min_space:
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raise IOError(f"There is not enough free disk space to continue {du}")
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raise NotEnoughFreeSpaceError(
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"There is not enough free disk space to continue."
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f"(Required: {min_space}, {du})."
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)
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class ScanInfo(BaseModel):
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@ -298,24 +307,47 @@ DOWNLOADABLE_SCAN_FILES = (
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"images.zip",
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)
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class JPEGBlob(BlobOutput):
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media_type = "image/jpeg"
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class SmartScanThing(Thing):
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def __init__(self, path_to_openflexure_stitch: str):
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self._script = path_to_openflexure_stitch
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self._preview_stitch_popen_lock = threading.Lock()
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self._correlate_popen_lock = threading.Lock()
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self._scan_lock = threading.Lock()
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@property
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def scan_folder_path(self) -> str:
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def scans_folder_path(self) -> str:
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"""This folder will hold all the scans we do."""
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# TODO: This should be determined using sensible configuration.
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# If the working directory is `/var/openflexure` this will result
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# in scans being saved at `/var/openflexure/scans/`
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return "scans"
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_latest_scan_name = None
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@thing_property
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def latest_scan_name(self) -> Optional[str]:
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"""The name of the last scan to be started."""
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return self._latest_scan_name
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def scan_folder_path(self, scan_name: Optional[str]=None):
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"""The path to the scan folder with a given name"""
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if not scan_name:
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if not self.latest_scan_name:
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raise IOError("There is no latest scan to return")
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scan_name = self.latest_scan_name
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return os.path.join(self.scans_folder_path, scan_name)
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def new_scan_folder(self) -> str:
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"""Create a new empty folder, into which we can save scan images"""
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if not os.path.exists(self.scan_folder_path):
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os.makedirs(self.scan_folder_path)
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if not os.path.exists(self.scans_folder_path):
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os.makedirs(self.scans_folder_path)
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for j in range(999999):
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folder_path = os.path.join(self.scan_folder_path, f"scan_{j:06}")
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folder_path = os.path.join(self.scans_folder_path, f"scan_{j:06}")
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if not os.path.exists(folder_path):
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os.makedirs(folder_path)
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self._latest_scan_name = os.path.basename(folder_path)
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return folder_path
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raise FileExistsError("Could not create a new scan folder: all names in use!")
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@ -330,7 +362,6 @@ class SmartScanThing(Thing):
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csm: CSMDep,
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background_detect: BackgroundDep,
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recentre: RecentreStage,
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sample_check
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):
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"""Move the stage to cover an area, taking images that can be tiled together.
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@ -343,82 +374,84 @@ class SmartScanThing(Thing):
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* `overlap` is the fraction by which images should overlap, i.e.
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`0.3` means we will move by 70% of the field of view each time.
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"""
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# Before anything else, check that we've got a background set
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# It's annoying to have to wait to find out!
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max_dist = self.max_range
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if sample_check:
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d = background_detect.background_distributions
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if not d:
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raise RuntimeError("Background is not set: you need to calibrate background detection.")
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else:
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logger.warning(
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"This scan will run in a spiral from the starting point "
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f"until you cancel it, or until it has moved by {max_dist} steps "
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"in every direction. Make sure you watch it run to stop it leaving "
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"the area of interest, or (worse) leading the microscope's range "
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"of motion."
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)
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names = []
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positions = []
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# Record the starting position so we can move back there afterwards
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starting_position = stage.position
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r = cam.grab_jpeg()
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arr = np.array(Image.open(r.open()))
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if list(arr.shape[:2]) != [int(i) for i in csm.image_resolution]:
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logger.error(
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f"Images are, by default, {arr.shape[:2]}, but the CSM was "
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f"calibrated at {csm.image_resolution}."
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)
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# Here, we calculate the x and y step size based on the desired overlap
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# TODO: Consider using CSM calibration size instead
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# TODO: generalise to have 2D displacements for x and y (as the
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# camera and stage may not be aligned).
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CSM = csm.image_to_stage_displacement_matrix
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csm_calibration_width = csm.last_calibration["image_resolution"][1]
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# TODO: this downsampling by two is to deal with a camera issue
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img_width = int(arr.shape[1] / 2)
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overlap = self.overlap
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dx = int(np.abs(np.dot(np.array([0, arr.shape[1] * (1 - overlap)]), CSM)[0]))
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dy = int(np.abs(np.dot(np.array([arr.shape[0] * (1 - overlap), 0]), CSM)[1]))
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logger.info(f"Based on an overlap of {overlap}, we will make steps of {dx}, {dy}")
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# construct a 2D scan path
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path = [[stage.position["x"], stage.position["y"]]]
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focused_path = [] # This holds a list of all points where focus succeeded
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true_path = [] # This holds a list of all points visited
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i = 0
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ids = []
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start_time = time.strftime("%H_%M_%S-%d_%m_%Y")
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scan_path = self.new_scan_folder()
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images_folder = os.path.join(scan_path, "images")
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os.mkdir(images_folder)
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raw_images_folder = os.path.join(scan_path, "raw_images")
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os.mkdir(raw_images_folder)
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logger.info(f"Saving images to {images_folder}")
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self._scan_lock.acquire(timeout=0.1)
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try:
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# Before anything else, check that we've got a background set
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# It's annoying to have to wait to find out!
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max_dist = self.max_range
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if self.skip_background:
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d = background_detect.background_distributions
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if not d:
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raise RuntimeError("Background is not set: you need to calibrate background detection.")
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else:
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logger.warning(
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"This scan will run in a spiral from the starting point "
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f"until you cancel it, or until it has moved by {max_dist} steps "
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"in every direction. Make sure you watch it run to stop it leaving "
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"the area of interest, or (worse) leading the microscope's range "
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"of motion."
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)
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names = []
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positions = []
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# Record the starting position so we can move back there afterwards
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starting_position = stage.position
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r = cam.grab_jpeg()
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arr = np.array(Image.open(r.open()))
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if list(arr.shape[:2]) != [int(i) for i in csm.image_resolution]:
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logger.error(
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f"Images are, by default, {arr.shape[:2]}, but the CSM was "
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f"calibrated at {csm.image_resolution}."
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)
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# Here, we calculate the x and y step size based on the desired overlap
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# TODO: Consider using CSM calibration size instead
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# TODO: generalise to have 2D displacements for x and y (as the
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# camera and stage may not be aligned).
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CSM = csm.image_to_stage_displacement_matrix
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csm_calibration_width = csm.last_calibration["image_resolution"][1]
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# TODO: this downsampling by two is to deal with a camera issue
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img_width = int(arr.shape[1] / 2)
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overlap = self.overlap
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dx = int(np.abs(np.dot(np.array([0, arr.shape[1] * (1 - overlap)]), CSM)[0]))
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dy = int(np.abs(np.dot(np.array([arr.shape[0] * (1 - overlap), 0]), CSM)[1]))
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logger.info(f"Based on an overlap of {overlap}, we will make steps of {dx}, {dy}")
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# construct a 2D scan path
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path = [[stage.position["x"], stage.position["y"]]]
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focused_path = [] # This holds a list of all points where focus succeeded
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true_path = [] # This holds a list of all points visited
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i = 0
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ids = []
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start_time = time.strftime("%H_%M_%S-%d_%m_%Y")
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scan_folder = self.new_scan_folder()
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images_folder = os.path.join(scan_folder, "images")
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os.mkdir(images_folder)
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raw_images_folder = os.path.join(images_folder, "raw")
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os.mkdir(raw_images_folder)
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logger.info(f"Saving images to {images_folder}")
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# TODO: I think this is unnecessary, we do a looping autofocus at the first point in the loop, unless
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# it's flagged as background (which is a wierd case anyway)
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recentre.looping_autofocus()
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# move to each x-y position. in z, move to the height of the closest x-y position that successfully focused
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while len(path) > 0:
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ensure_free_disk_space(scan_folder)
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loc = [path[0][0], path[0][1], stage.position["z"]]
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path.remove(path[0])
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# TODO: combine this with the move below for speed (I think this could just be "else")
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logger.info(f"Moving to {loc}")
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stage.move_absolute(x=int(loc[0]), y=int(loc[1]), z=int(loc[2]))
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if len(focused_path) > 1:
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@ -430,7 +463,7 @@ class SmartScanThing(Thing):
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)
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# Check if the image is background
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if sample_check:
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if self.skip_background:
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image_is_sample = background_detect.image_is_sample()
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else:
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image_is_sample = True
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@ -501,7 +534,7 @@ class SmartScanThing(Thing):
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width, height = img.size
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img = img.resize((int(width*0.5), int(height*0.5)))
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logger.info(f"Saving {name} at {stage.position}")
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logger.info(f"Saving {name}")
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img.save(
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os.path.join(images_folder, name),
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exif=exif,
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@ -511,6 +544,11 @@ class SmartScanThing(Thing):
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positions.append(loc[:2])
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names.append(name)
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if not self.preview_stitch_running():
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self.preview_stitch_start(images_folder)
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if not self.correlate_running():
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self.correlate_start(images_folder)
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# add the current position to the list of all positions visited
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true_path.append(loc)
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@ -533,17 +571,34 @@ class SmartScanThing(Thing):
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break
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except InvocationCancelledError:
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logger.error("Stopping scan because it was cancelled.")
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except IOError as e:
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except NotEnoughFreeSpaceError as e:
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logger.exception(
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f"Stopping scan because of an IOError (most likely a full disk): {e}",
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f"Stopping scan to avoid filling up the disk: {e}",
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)
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raise e
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except Exception as e:
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logger.exception(
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f"The scan stopped because of an error: {e}",
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"We will attempt to stitch and archive the images acquired "
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"so far."
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)
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raise e
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finally:
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logger.info("Waiting for background processes to finish...")
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self.preview_stitch_wait()
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self.correlate_wait()
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logger.info("Stitching final image (may take some time)...")
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try:
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self.stitch_scan(logger, os.path.basename(scan_folder))
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except SubprocessError as e:
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logger.exception(f"Stitching failed: {e}")
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logger.info("Creating zip archive of images (may take some time)...")
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shutil.make_archive(
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os.path.join(scan_path, "images"), "zip", images_folder
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os.path.join(scan_folder, "images"), "zip", images_folder
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)
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logger.info("Returning to starting position.")
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stage.move_absolute(**starting_position, block_cancellation=True)
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self._scan_lock.release()
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@thing_property
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def max_range(self) -> int:
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@ -554,6 +609,18 @@ class SmartScanThing(Thing):
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def max_range(self, value: int) -> None:
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self.thing_settings["max_range"] = value
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@thing_property
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def skip_background(self) -> bool:
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"""Whether to detect and skip empty fields of view
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This uses the settings from the `background_detect` Thing.
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"""
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return self.thing_settings.get("skip_background", True)
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@skip_background.setter
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def skip_background(self, value: bool) -> None:
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self.thing_settings["skip_background"] = value
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@thing_property
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def autofocus_dz(self) -> int:
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"""The z distance to perform an autofocus"""
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@ -583,8 +650,10 @@ class SmartScanThing(Thing):
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in the `images` folder.
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"""
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scans: list[ScanInfo] = []
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for f in os.listdir(self.scan_folder_path):
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path = os.path.join(self.scan_folder_path, f)
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if not os.path.isdir(self.scans_folder_path):
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return scans
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for f in os.listdir(self.scans_folder_path):
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path = os.path.join(self.scans_folder_path, f)
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if os.path.isdir(path):
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images_folder = os.path.join(path, "images")
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if os.path.isdir(images_folder):
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@ -624,7 +693,7 @@ class SmartScanThing(Thing):
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raise HTTPException(
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403, f"You may only download files named {DOWNLOADABLE_SCAN_FILES}"
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)
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path = os.path.join(self.scan_folder_path, scan_name, file)
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path = os.path.join(self.scans_folder_path, scan_name, file)
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if not os.path.isfile(path):
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raise HTTPException(404, "File not found")
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return FileResponse(path)
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@ -642,7 +711,7 @@ class SmartScanThing(Thing):
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This endpoint allows scans to be deleted from disk.
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"""
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path = os.path.join(self.scan_folder_path, scan_name)
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path = os.path.join(self.scans_folder_path, scan_name)
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if not os.path.isdir(path):
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print(f"can't find {path}")
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raise HTTPException(404, "Scan not found")
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@ -660,4 +729,108 @@ class SmartScanThing(Thing):
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Use with extreme caution.
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"""
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for scan in self.scans:
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self.delete_scan(scan.name)
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self.delete_scan(scan.name)
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def images_folder(self, scan_name: Optional[str]=None) -> str:
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scan_folder = self.scan_folder_path(scan_name=scan_name)
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return os.path.join(scan_folder, "images")
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@property
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def latest_preview_stitch_path(self):
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"""The path of the latest preview stitched image"""
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return os.path.join(self.images_folder(), "stitched_from_stage.jpg")
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@thing_property
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def latest_preview_stitch_time(self) -> Optional[datetime]:
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"""The modification time of the latest preview image"""
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fpath = self.latest_preview_stitch_path
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if not os.path.exists(fpath):
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return None
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||||
else:
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return os.path.getmtime(fpath)
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|
||||
@fastapi_endpoint(
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||||
"get",
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||||
"latest_preview_stitch.jpg",
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||||
responses = {
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||||
200: {
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||||
"description": "A preview-quality stitched image",
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||||
"content": {"image/jpeg": {}}
|
||||
},
|
||||
404: {"description": "File not found"}
|
||||
},
|
||||
)
|
||||
def get_latest_preview(self) -> FileResponse:
|
||||
"""Retrieve the latest preview image.
|
||||
"""
|
||||
path = self.latest_preview_stitch_path
|
||||
if not os.path.isfile(path):
|
||||
raise HTTPException(404, "File not found")
|
||||
return FileResponse(path)
|
||||
|
||||
_preview_stitch_popen = None
|
||||
def preview_stitch_start(self, images_folder: str) -> None:
|
||||
"""Start stitching a preview of the scan in a subprocess"""
|
||||
if self.preview_stitch_running():
|
||||
raise RuntimeError("Only one subprocess is allowed at a time")
|
||||
with self._preview_stitch_popen_lock:
|
||||
self._preview_stitch_popen = Popen(
|
||||
[self._script, "--stitching_mode", "only_stage_stitch", images_folder]
|
||||
)
|
||||
|
||||
def preview_stitch_running(self) -> bool:
|
||||
"""Whether there is a preview stitch running in a subprocess"""
|
||||
with self._preview_stitch_popen_lock:
|
||||
if self._preview_stitch_popen is None:
|
||||
return False
|
||||
if self._preview_stitch_popen.poll() is None:
|
||||
return True
|
||||
return False
|
||||
|
||||
def preview_stitch_wait(self):
|
||||
if self.preview_stitch_running():
|
||||
with self._preview_stitch_popen_lock:
|
||||
self._preview_stitch_popen.wait()
|
||||
|
||||
_correlate_popen = None
|
||||
def correlate_start(self, images_folder: str) -> None:
|
||||
"""Start stitching a preview of the scan in a subprocess"""
|
||||
if self.correlate_running():
|
||||
raise RuntimeError("Only one subprocess is allowed at a time")
|
||||
with self._correlate_popen_lock:
|
||||
self._correlate_popen = Popen(
|
||||
[self._script, "--stitching_mode", "only_correlate", images_folder]
|
||||
)
|
||||
|
||||
def correlate_running(self) -> bool:
|
||||
"""Whether there is a preview stitch running in a subprocess"""
|
||||
with self._correlate_popen_lock:
|
||||
if self._correlate_popen is None:
|
||||
return False
|
||||
if self._correlate_popen.poll() is None:
|
||||
return True
|
||||
return False
|
||||
|
||||
def correlate_wait(self):
|
||||
if self.correlate_running():
|
||||
with self._correlate_popen_lock:
|
||||
self._correlate_popen.wait()
|
||||
|
||||
def run_subprocess(
|
||||
self, logger: InvocationLogger, cmd: list[str],
|
||||
) -> CompletedProcess:
|
||||
"""Run a subprocess and log any output"""
|
||||
logger.info(f"Running command in subprocess: `{' '.join(cmd)}")
|
||||
output = run(cmd, stdout=PIPE, stderr=PIPE, universal_newlines=True)
|
||||
for pipe in [output.stdout, output.stderr]:
|
||||
if pipe:
|
||||
logger.info(pipe)
|
||||
output.check_returncode()
|
||||
return output
|
||||
|
||||
@thing_action
|
||||
def stitch_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None, downsample: float=1.0) -> None:
|
||||
"""Generate a stitched image based on stage position metadata"""
|
||||
images_folder = self.images_folder(scan_name=scan_name)
|
||||
self.run_subprocess(logger, [self._script, "--stitching_mode", "all", images_folder])
|
||||
|
||||
|
|
|
|||
85
src/openflexure_microscope_server/things/stitching.py
Normal file
85
src/openflexure_microscope_server/things/stitching.py
Normal file
|
|
@ -0,0 +1,85 @@
|
|||
from typing import Optional
|
||||
import os
|
||||
from subprocess import CompletedProcess, run, PIPE
|
||||
|
||||
from labthings_fastapi.thing import Thing
|
||||
from labthings_fastapi.dependencies.raw_thing import raw_thing_dependency
|
||||
from labthings_fastapi.dependencies.invocation import InvocationLogger
|
||||
from labthings_fastapi.decorators import thing_action
|
||||
from labthings_fastapi.outputs.blob import BlobOutput
|
||||
|
||||
from .smart_scan import SmartScanThing
|
||||
|
||||
SmartScanDep = raw_thing_dependency(SmartScanThing)
|
||||
|
||||
|
||||
class JPEGBlob(BlobOutput):
|
||||
media_type = "image/jpeg"
|
||||
|
||||
|
||||
class Stitcher(Thing):
|
||||
def __init__(self, path_to_openflexure_stitch: str):
|
||||
self._script = path_to_openflexure_stitch
|
||||
|
||||
def run_subprocess(
|
||||
self, logger: InvocationLogger, cmd: list[str],
|
||||
) -> CompletedProcess:
|
||||
"""Run a subprocess and log any output"""
|
||||
logger.info(f"Running command in subprocess: `{' '.join(cmd)}")
|
||||
output = run(cmd, stdout=PIPE, stderr=PIPE, universal_newlines=True)
|
||||
for pipe in [output.stdout, output.stderr]:
|
||||
if pipe:
|
||||
logger.info(pipe)
|
||||
output.check_returncode()
|
||||
return output
|
||||
|
||||
def images_folder(self, smart_scan: SmartScanDep, scan_name: Optional[str]=None) -> str:
|
||||
scan_folder = smart_scan.scan_folder_path(scan_name=scan_name)
|
||||
return os.path.join(scan_folder, "images")
|
||||
|
||||
@staticmethod
|
||||
def output_up_to_date(folder: str, output_filename: str, image_prefix: str="image", image_suffix: str=".jpg") -> bool:
|
||||
"""Check if any of the images in a folder are newer than a file
|
||||
|
||||
If there are no images (files with the prefix and suffix) newer than the
|
||||
`output_filename`, we return `True`, i.e. the output is up to date. If
|
||||
any image in the folder is newer, we return `False`.
|
||||
|
||||
This is not flawless logic - if an update process is slow, images might be
|
||||
saved between starting that process and saving the output. Consequently,
|
||||
a `True` from this function does not guarantee the output is up to date.
|
||||
|
||||
If the output file is missing, we also return `False`.
|
||||
"""
|
||||
output_path = os.path.join(folder, output_filename)
|
||||
if not os.path.exists(output_path):
|
||||
return False
|
||||
mtime = os.path.getmtime(output_path)
|
||||
for fname in os.listdir(folder):
|
||||
if fname.startswith(image_prefix) and fname.endswith(image_suffix):
|
||||
if os.path.getmtime(os.path.join(folder, fname)) > mtime:
|
||||
return False
|
||||
return True
|
||||
|
||||
@thing_action
|
||||
def stitch_scan_from_stage(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None, downsample: float=1.0) -> JPEGBlob:
|
||||
"""Generate a stitched image based on stage position metadata"""
|
||||
output_fname = "stitched_from_stage.jpg"
|
||||
images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
|
||||
if self.output_up_to_date(images_folder, output_fname):
|
||||
logger.info(f"No images are newer than {output_fname}, skipping.")
|
||||
else:
|
||||
self.run_subprocess(logger, [self._script, "--stitching_mode", "only_stage_stitch", images_folder])
|
||||
return JPEGBlob.from_file(os.path.join(images_folder, output_fname))
|
||||
|
||||
@thing_action
|
||||
def update_scan_correlations(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None) -> None:
|
||||
"""Generate a stitched image based on stage position metadata"""
|
||||
images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
|
||||
self.run_subprocess(logger, [self._script, "--stitching_mode", "only_correlate", images_folder])
|
||||
|
||||
@thing_action
|
||||
def stitch_scan(self, logger: InvocationLogger, smart_scan: SmartScanDep, scan_name: Optional[str]=None, downsample: float=1.0) -> None:
|
||||
"""Generate a stitched image based on stage position metadata"""
|
||||
images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
|
||||
self.run_subprocess(logger, [self._script, "--stitching_mode", "all", images_folder])
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
<template>
|
||||
<div ref="logContainer" class="log-container">
|
||||
<div ref="logContainer" class="log-container uk-margin-left uk-margin-right uk-margin">
|
||||
<div v-if="log">
|
||||
<div v-for="(item, index) in log" :key="`log_entry_${index}`">
|
||||
{{ item.message }}
|
||||
|
|
@ -57,5 +57,8 @@ export default {
|
|||
position: relative;
|
||||
overflow-y: auto;
|
||||
overflow-x: auto;
|
||||
background-color: white;
|
||||
padding: 0.5em;
|
||||
border: 1px solid black;
|
||||
}
|
||||
</style>
|
||||
|
|
|
|||
|
|
@ -235,18 +235,18 @@ export default {
|
|||
);
|
||||
if (response.status == "completed") {
|
||||
this.$emit("response", response);
|
||||
this.$emit("completed", response.output);
|
||||
} else if (response.status == "cancelled") {
|
||||
this.$emit("cancelled", response);
|
||||
this.modalNotify(`The action '${this.submitLabel}' was cancelled.`);
|
||||
}
|
||||
this.$emit("finished");
|
||||
} catch (error) {
|
||||
this.$emit("error", error | Error("Unknown error"));
|
||||
this.$emit("finished");
|
||||
} finally {
|
||||
// Reset taskRunning and taskId
|
||||
this.taskRunning = false;
|
||||
this.taskStarted = false;
|
||||
this.$emit("finished");
|
||||
// Update the form data if we're self-updating
|
||||
if (this.selfUpdate) {
|
||||
this.getFormData();
|
||||
|
|
@ -300,19 +300,12 @@ export default {
|
|||
return new Promise(checkCondition);
|
||||
},
|
||||
|
||||
pollProgress: function() {
|
||||
axios.get(this.taskUrl).then(response => {
|
||||
this.progress = response.data.progress;
|
||||
});
|
||||
},
|
||||
|
||||
hideModal() {
|
||||
UIkit.modal(this.$refs.statusModal).hide();
|
||||
},
|
||||
|
||||
terminateTask: function() {
|
||||
console.log(`deleting task at ${this.taskUrl}`);
|
||||
axios.delete(this.taskUrl);
|
||||
axios.delete(this.taskUrl, { baseURL: this.$store.getters.baseUri });
|
||||
}
|
||||
}
|
||||
};
|
||||
|
|
|
|||
|
|
@ -1,57 +1,79 @@
|
|||
<template>
|
||||
<div>
|
||||
<label class="uk-form-label">{{ label }}</label>
|
||||
<div v-if="dataType == 'number'" class="input-and-buttons-container">
|
||||
<input
|
||||
v-model="value"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="number"
|
||||
@focusin="focusIn"
|
||||
@focusout="focusOut"
|
||||
@keydown="keyDown"
|
||||
/>
|
||||
<label v-if="dataType == 'number'" class="uk-form-label">{{ label }}
|
||||
<div class="input-and-buttons-container">
|
||||
<input
|
||||
v-model="value"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="number"
|
||||
@focusin="focusIn"
|
||||
@focusout="focusOut"
|
||||
@keydown="keyDown"
|
||||
/>
|
||||
<a class="button-next-to-input" @click="readProperty">
|
||||
<span class="material-symbols-outlined">refresh</span>
|
||||
</a>
|
||||
</div>
|
||||
</label>
|
||||
<div v-if="dataType == 'boolean'" class="input-and-buttons-container">
|
||||
<label class="uk-form-label numeric-setting-line-input">
|
||||
<input
|
||||
ref="checkbox"
|
||||
v-model="value"
|
||||
class="uk-checkbox"
|
||||
type="checkbox"
|
||||
@change="writeProperty"
|
||||
/>
|
||||
{{ label }}
|
||||
</label>
|
||||
<a class="button-next-to-input" @click="readProperty">
|
||||
<span class="material-symbols-outlined">refresh</span>
|
||||
</a>
|
||||
</div>
|
||||
<div v-if="dataType == 'number_array'" class="input-and-buttons-container">
|
||||
<input
|
||||
v-for="i in valueLength"
|
||||
:key="i"
|
||||
v-model="value[i - 1]"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="number"
|
||||
@focusin="focusIn"
|
||||
@focusout="focusOut"
|
||||
@keydown="keyDown"
|
||||
/>
|
||||
<a class="button-next-to-input" @click="readProperty">
|
||||
<span class="material-symbols-outlined">refresh</span>
|
||||
</a>
|
||||
</div>
|
||||
<div v-if="dataType == 'number_object'" class="input-and-buttons-container">
|
||||
<input
|
||||
v-for="(_v, key) in value"
|
||||
:key="key"
|
||||
v-model="value[key]"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="number"
|
||||
@focusin="focusIn"
|
||||
@focusout="focusOut"
|
||||
@keydown="keyDown"
|
||||
/>
|
||||
<a class="button-next-to-input" @click="readProperty">
|
||||
<span class="material-symbols-outlined">refresh</span>
|
||||
</a>
|
||||
</div>
|
||||
<div v-if="dataType == 'other'" class="input-and-buttons-container">
|
||||
<input
|
||||
:value="value"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="text"
|
||||
disabled="true"
|
||||
/>
|
||||
</div>
|
||||
<label v-if="dataType == 'number_array'" class="uk-form-label">{{ label }}
|
||||
<div class="input-and-buttons-container">
|
||||
<input
|
||||
v-for="i in valueLength"
|
||||
:key="i"
|
||||
v-model="value[i - 1]"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="number"
|
||||
@focusin="focusIn"
|
||||
@focusout="focusOut"
|
||||
@keydown="keyDown"
|
||||
/>
|
||||
<a class="button-next-to-input" @click="readProperty">
|
||||
<span class="material-symbols-outlined">refresh</span>
|
||||
</a>
|
||||
</div>
|
||||
</label>
|
||||
<label v-if="dataType == 'number_object'" class="uk-form-label">{{ label }}
|
||||
<div class="input-and-buttons-container">
|
||||
<input
|
||||
v-for="(_v, key) in value"
|
||||
:key="key"
|
||||
v-model="value[key]"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="number"
|
||||
@focusin="focusIn"
|
||||
@focusout="focusOut"
|
||||
@keydown="keyDown"
|
||||
/>
|
||||
<a class="button-next-to-input" @click="readProperty">
|
||||
<span class="material-symbols-outlined">refresh</span>
|
||||
</a>
|
||||
</div>
|
||||
</label>
|
||||
<label v-if="dataType == 'other'" class="uk-form-label">{{ label }}
|
||||
<div class="input-and-buttons-container">
|
||||
<input
|
||||
:value="value"
|
||||
class="uk-form-small numeric-setting-line-input"
|
||||
type="text"
|
||||
disabled="true"
|
||||
/>
|
||||
</div>
|
||||
</label>
|
||||
</div>
|
||||
</template>
|
||||
|
||||
|
|
@ -129,6 +151,9 @@ export default {
|
|||
}
|
||||
}
|
||||
}
|
||||
if (prop.type == "boolean") {
|
||||
return "boolean";
|
||||
}
|
||||
if (prop.type == "object") {
|
||||
let numeric = true;
|
||||
for (let key in prop.properties) {
|
||||
|
|
@ -173,6 +198,7 @@ export default {
|
|||
writeProperty: async function() {
|
||||
try {
|
||||
let requestedValue = this.value;
|
||||
console.log("writing", requestedValue);
|
||||
await this.writeThingProperty(
|
||||
this.thingName,
|
||||
this.propertyName,
|
||||
|
|
@ -195,6 +221,12 @@ export default {
|
|||
this.modalError(error); // Let mixin handle error
|
||||
}
|
||||
},
|
||||
checkboxUpdated: function() {
|
||||
if (this.value != this.$refs.checkbox.checked) {
|
||||
this.value = this.$refs.checkbox.checked;
|
||||
this.writeProperty();
|
||||
}
|
||||
},
|
||||
focusIn: function(event) {
|
||||
this.valueOnEnter = event.target.value;
|
||||
},
|
||||
|
|
|
|||
|
|
@ -135,6 +135,9 @@ export default {
|
|||
methods: {
|
||||
async updateScans() {
|
||||
let scans = await this.readThingProperty("smart_scan", "scans");
|
||||
if (!scans | scans.length == 0) {
|
||||
return;
|
||||
}
|
||||
scans.forEach(scan => {
|
||||
scan.modified = Date.parse(scan.modified);
|
||||
scan.created = Date.parse(scan.created);
|
||||
|
|
|
|||
|
|
@ -16,20 +16,32 @@
|
|||
property-name="max_range"
|
||||
label="Maximum Distance (steps)"
|
||||
/>
|
||||
<div class="uk-margin">
|
||||
<propertyControl
|
||||
thing-name="smart_scan"
|
||||
property-name="autofocus_dz"
|
||||
label="Autofocus range (steps)"
|
||||
/>
|
||||
</div>
|
||||
<div class="uk-margin">
|
||||
<propertyControl
|
||||
thing-name="smart_scan"
|
||||
property-name="overlap"
|
||||
label="Image overlap (0-1)"
|
||||
/>
|
||||
</div>
|
||||
</div>
|
||||
<div class="uk-margin">
|
||||
<propertyControl
|
||||
thing-name="smart_scan"
|
||||
property-name="autofocus_dz"
|
||||
label="Autofocus range (steps)"
|
||||
/>
|
||||
</div>
|
||||
<div class="uk-margin">
|
||||
<propertyControl
|
||||
thing-name="smart_scan"
|
||||
property-name="overlap"
|
||||
label="Image overlap (0-1)"
|
||||
/>
|
||||
</div>
|
||||
</div>
|
||||
</li>
|
||||
<li class="uk-open">
|
||||
<a class="uk-accordion-title" href="#">Scan Settings</a>
|
||||
<div class="uk-accordion-content">
|
||||
<div class="uk-margin">
|
||||
<propertyControl
|
||||
thing-name="smart_scan"
|
||||
property-name="skip_background"
|
||||
label="Detect and skip empty fields"
|
||||
/>
|
||||
</div>
|
||||
</div>
|
||||
</li>
|
||||
|
|
@ -40,19 +52,7 @@
|
|||
:submit-url="smartScanUri"
|
||||
submit-label="Start smart scan"
|
||||
:can-terminate="true"
|
||||
:submit-data="{ sample_check: true }"
|
||||
@taskStarted="scanning = true"
|
||||
@update:taskStatus="taskStatus = $event"
|
||||
@update:progress="progress = $event"
|
||||
@update:log="log = $event"
|
||||
/>
|
||||
</div>
|
||||
<div class="uk-margin">
|
||||
<taskSubmitter
|
||||
:submit-url="smartScanUri"
|
||||
submit-label="Start manual scan"
|
||||
:can-terminate="true"
|
||||
:submit-data="{ sample_check: false }"
|
||||
@taskStarted="startScanning"
|
||||
@update:taskStatus="taskStatus = $event"
|
||||
@update:progress="progress = $event"
|
||||
@update:log="log = $event"
|
||||
|
|
@ -60,6 +60,7 @@
|
|||
</div>
|
||||
</div>
|
||||
<div v-show="scanning">
|
||||
<mini-stream-display v-if="displayImageOnRight" />
|
||||
<action-log-display
|
||||
id="log-display"
|
||||
:log="log"
|
||||
|
|
@ -78,14 +79,15 @@
|
|||
v-if="!cancellable"
|
||||
type="button"
|
||||
class="uk-button uk-button-danger uk-margin-remove uk-float-right uk-width-1-1"
|
||||
@click="scanning = false"
|
||||
@click="scanning = false; lastStitchedImage=null;"
|
||||
>
|
||||
Close
|
||||
</button>
|
||||
</div>
|
||||
</div>
|
||||
<div class="view-component uk-width-expand">
|
||||
<streamDisplay />
|
||||
<img v-if="displayImageOnRight" :src="lastStitchedImage" id="last-stitched-image"/>
|
||||
<streamDisplay v-else />
|
||||
</div>
|
||||
</div>
|
||||
</template>
|
||||
|
|
@ -96,6 +98,7 @@ import taskSubmitter from "../genericComponents/taskSubmitter";
|
|||
import propertyControl from "../labThingsComponents/propertyControl.vue";
|
||||
import actionLogDisplay from "../genericComponents/actionLogDisplay.vue";
|
||||
import actionProgressBar from "../genericComponents/actionProgressBar.vue";
|
||||
import MiniStreamDisplay from '../genericComponents/miniStreamDisplay.vue';
|
||||
|
||||
export default {
|
||||
name: "SlideScanContent",
|
||||
|
|
@ -105,7 +108,8 @@ export default {
|
|||
taskSubmitter,
|
||||
propertyControl,
|
||||
actionLogDisplay,
|
||||
actionProgressBar
|
||||
actionProgressBar,
|
||||
MiniStreamDisplay
|
||||
},
|
||||
|
||||
data() {
|
||||
|
|
@ -113,8 +117,11 @@ export default {
|
|||
lastScanName: null,
|
||||
scanning: false,
|
||||
taskStatus: "pending",
|
||||
correlateStatus: "",
|
||||
stitchFromStageStatus: "",
|
||||
progress: null,
|
||||
log: []
|
||||
log: [],
|
||||
lastStitchedImage: null,
|
||||
};
|
||||
},
|
||||
|
||||
|
|
@ -127,6 +134,9 @@ export default {
|
|||
},
|
||||
cancellable() {
|
||||
return (this.taskStatus == "running") | (this.taskStatus == "pending");
|
||||
},
|
||||
displayImageOnRight() {
|
||||
return this.scanning & this.lastStitchedImage !== null;
|
||||
}
|
||||
},
|
||||
|
||||
|
|
@ -134,6 +144,23 @@ export default {
|
|||
onScanError: function(error) {
|
||||
this.scanRunning = false;
|
||||
this.modalError(error);
|
||||
},
|
||||
correlateCurrentScan() {
|
||||
|
||||
},
|
||||
startScanning() {
|
||||
this.lastStitchedImage = null;
|
||||
this.scanning = true;
|
||||
setTimeout(this.pollScan, 1000);
|
||||
},
|
||||
async pollScan() {
|
||||
if (this.cancellable) { // while the scan is running
|
||||
let mtime = await this.readThingProperty("smart_scan", "latest_preview_stitch_time");
|
||||
if (mtime !== null) {
|
||||
this.lastStitchedImage = `${this.$store.getters.baseUri}/smart_scan/latest_preview_stitch.jpg?t=${mtime}`;
|
||||
}
|
||||
setTimeout(this.pollScan, 1000); // keep rescheduling until it's stopped
|
||||
}
|
||||
}
|
||||
}
|
||||
};
|
||||
|
|
|
|||
|
|
@ -63,11 +63,13 @@ Vue.mixin({
|
|||
"writeproperty",
|
||||
false
|
||||
);
|
||||
try {
|
||||
await axios.put(url, value);
|
||||
} catch (error) {
|
||||
this.modalError(error);
|
||||
// `false` fails because axios somehow eats it!
|
||||
// Other values should not be stringified or pydantic
|
||||
// can't parse them.
|
||||
if (value===false | value===true) {
|
||||
value=JSON.stringify(value);
|
||||
}
|
||||
await axios.put(url, value);
|
||||
},
|
||||
thingActionUrl(thing, action) {
|
||||
let url = this.$store.getters["wot/thingActionUrl"](
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue