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Merge branch 'verify-focus' into 'v3'

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Improvements to autofocus and stitching in `smart_scan`.

See merge request openflexure/openflexure-microscope-server!175
This commit is contained in:
Richard Bowman 2024-02-21 20:51:09 +00:00
commit 612b88d58c
4 changed files with 134 additions and 41 deletions
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25
src/openflexure_microscope_server/things/autofocus.py
View file

@ -26,6 +26,7 @@ from pydantic import BaseModel
Stage = direct_thing_client_dependency(SangaboardThing, "/stage/")
Camera = raw_thing_dependency(StreamingPiCamera2)
WrappedCamera = direct_thing_client_dependency(StreamingPiCamera2, "/camera/")
### Autofocus utilities
@ -206,12 +207,14 @@ class AutofocusThing(Thing):
"""
repeat = True
attempts = 0
backlash = 200
with m.run():
while repeat and attempts < 10:
if start == 'centre':
stage.move_relative(x = 0, y = 0, z = -dz / 2)
stage.move_relative(x = 0, y = 0, z = -(backlash + dz / 2))
stage.move_relative(x = 0, y = 0, z = backlash)
i, z = m.focus_rel(dz, block_cancellation=True)
_, heights, sizes = m.move_data(i)
@ -226,8 +229,24 @@ class AutofocusThing(Thing):
):
attempts += 1
start = 'centre'
stage.move_absolute(z = peak_height-backlash)
stage.move_absolute(z = peak_height)
else:
repeat = False
stage.move_relative(x = 0, y = 0, z = -dz)
stage.move_absolute(z = peak_height)
stage.move_relative(x = 0, y = 0, z = -(dz+backlash))
stage.move_absolute(z = peak_height)
return heights.tolist(), sizes.tolist()
@thing_action
def verify_focus_sharpness(self, sweep_sizes: list, camera: WrappedCamera, threshold: float = 0.95):
'''Take the sharpness curve of the autofocus, and the size of the current frame
to see if the autofocus completed successfully. Returns True if current sharpness
is within "leniency" number of frames from the peak of the autofocus'''
current_sharpness = camera.grab_jpeg_size(stream_name='lores')
peak = np.max(sweep_sizes)
base = np.min(sweep_sizes)
cutoff = threshold * (peak - base)
return current_sharpness >= base + cutoff

104
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -15,7 +15,7 @@ from scipy.ndimage import zoom
from scipy.interpolate import interp1d
from copy import deepcopy
from datetime import datetime
from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, run
from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, run, STDOUT
from threading import Event, Thread
import glob
import zipfile
@ -584,6 +584,7 @@ class SmartScanThing(Thing):
"""
try:
capture_start = time.time()
metadata = metadata_getter()
raw_image = cam.capture_array(stream_name="raw")
acquired.set()
acquisition_time = time.time()
@ -601,7 +602,7 @@ class SmartScanThing(Thing):
)
exif_dict = piexif.load(os.path.join(images_folder, name))
exif_dict["Exif"][piexif.ExifIFD.UserComment] = json.dumps(
metadata_getter()
metadata
).encode("utf-8")
piexif.insert(piexif.dump(exif_dict), os.path.join(images_folder, name))
save_time = time.time()
@ -651,24 +652,30 @@ class SmartScanThing(Thing):
attempts = 0
if self.autofocus_dz > 200:
while True:
autofocus.looping_autofocus(dz=self.autofocus_dz, start = 'base')
jpeg_zs, jpeg_sizes = autofocus.looping_autofocus(dz=self.autofocus_dz, start = 'base')
current_height = stage.position["z"]
time.sleep(0.2)
autofocus_success = autofocus.verify_focus_sharpness(sweep_sizes = jpeg_sizes, camera = CamDep, threshold = 0.92)
logger.info(f"We just tested the focus! Result was {autofocus_success}")
# if there have been successful autofocuses in this scan, find the closest one in x-y
# test if the change in z between them exceeds a ratio (indicating a failed autofocus)
if len(focused_path) > 0:
nearest_focused_site = focused_path[closest(loc, focused_path)]
result = limit_focus_change(
nearest_focused_site[0:2],
nearest_focused_site[-1],
loc[0:2],
current_height,
0.3,
)
if autofocus_success:
# if there have been successful autofocuses in this scan, find the closest one in x-y
# test if the change in z between them exceeds a ratio (indicating a failed autofocus)
if len(focused_path) > 0:
nearest_focused_site = focused_path[closest(loc, focused_path)]
result = limit_focus_change(
nearest_focused_site[0:2],
nearest_focused_site[-1],
loc[0:2],
current_height,
0.5,
)
# if there haven't been any previous autofocuses, we have to assume this one worked
# if there haven't been any previous autofocuses, we have to assume this one worked
else:
result = "accept"
else:
result = "accept"
result = "reject"
# if the autofocus worked, add the current position to the list of successful locations
if result == "accept":
@ -727,6 +734,7 @@ class SmartScanThing(Thing):
logger.info(f'Rejected moving to {i} as it is out of range')
path = temp_path.copy()
path = sorted(path, key=lambda x: (steps_from_centre(x, true_path[0][:2], dx, dy), distance_to_site(loc[:2], x)))
self.create_zip_of_scan(logger = logger, scan_name = scan_folder.split('scans/')[1], download_zip = False)
except InvocationCancelledError:
logger.error("Stopping scan because it was cancelled.")
@ -767,12 +775,21 @@ class SmartScanThing(Thing):
@thing_property
def max_range(self) -> int:
"""The maximum distance from the centre of the scan before we break"""
return self.thing_settings.get("max_range", 70000)
return self.thing_settings.get("max_range", 45000)
@max_range.setter
def max_range(self, value: int) -> None:
self.thing_settings["max_range"] = value
@thing_property
def stitch_tiff(self) -> bool:
"""Whether or not to also produce a pyramidal tiff"""
return self.thing_settings.get("stitch_tiff", False)
@stitch_tiff.setter
def stitch_tiff(self, value: bool) -> None:
self.thing_settings["stitch_tiff"] = value
@thing_property
def skip_background(self) -> bool:
"""Whether to detect and skip empty fields of view
@ -999,18 +1016,40 @@ class SmartScanThing(Thing):
) -> 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
p = Popen(cmd, stdout=PIPE, stderr = STDOUT, bufsize=1, universal_newlines=True)
os.set_blocking(p.stdout.fileno(), False)
logger.info(time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(time.time())))
while p.poll() == None:
try:
output = p.stdout.readline()
if output != "" and output != None:
logger.info(output)
except:
pass
for line in p.stdout:
try:
output = p.stdout.readline()
if output != "" and output != None:
logger.info(output)
except:
pass
logger.info('Stitching complete')
return p
@thing_action
def stitch_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None, overlap: float = 0.0) -> None:
"""Generate a stitched image based on stage position metadata"""
images_folder = self.images_folder(scan_name=scan_name)
if self.stitch_tiff:
tiff_arg = '--stitch_tiff'
else:
tiff_arg = '--no-stitch_tiff'
if overlap == 0.0:
try:
with open(os.path.join(images_folder, 'scan_inputs.json')) as data_file:
@ -1019,7 +1058,7 @@ class SmartScanThing(Thing):
overlap = data_loaded['overlap']
except:
overlap = 0.1
self.run_subprocess(logger, [self._script, "--stitching_mode", "all", "--minimum_overlap", f"{round(overlap*0.9,2)}", images_folder])
self.run_subprocess(logger, [self._script, "--stitching_mode", "all", f"{tiff_arg}", "--minimum_overlap", f"{round(overlap*0.9,2)}", images_folder])
@thing_action
def create_zip_of_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None, download_zip = True) -> ZipBlob:
@ -1033,7 +1072,7 @@ class SmartScanThing(Thing):
)
if not os.path.isdir(images_folder):
raise FileNotFoundError(f"Tried to make a zip archive of {images_folder} but it does not exist.")
logger.info("Creating zip archive of images (may take some time)...")
# logger.info("Creating zip archive of images (may take some time)...")
zip_fname = f'{os.path.join(scan_folder, "images")}.zip'
@ -1047,8 +1086,6 @@ class SmartScanThing(Thing):
# get a list of files in the existing zip
current_zip = self.get_files_in_zip(zip_fname)
logger.info(current_zip)
# get a list of files in the folder we're zipping
folder_path = self.scan_folder_path(scan_name)
files = glob.glob(folder_path + '/**/*', recursive=True)
@ -1062,11 +1099,14 @@ class SmartScanThing(Thing):
with zipfile.ZipFile(zip_fname, mode="a") as zip:
for file in files:
if any(banned_name in file for banned_name in files_to_delay):
logger.info(f'we only add {file} into zip at the end of the scan')
# logger.info(f'we only add {file} into zip at the end of the scan')
pass
elif file in current_zip:
logger.info(f'{file} is already in zip')
elif ".zip" in file:
logger.info('Not adding the .zip to itself')
# logger.info(f'{file} is already in zip')
pass
elif ".zip" in file or 'raw' in file:
# logger.info('Not adding the .zip to itself')
pass
else:
logger.info(f'appending {file} to zip')
zip.write(os.path.join(folder_path, file), arcname=file)
@ -1087,7 +1127,7 @@ class SmartScanThing(Thing):
if any(banned_name in file for banned_name in files_to_delay):
logger.info(f'we are finally adding {file} into zip')
zip.write(os.path.join(folder_path, file), arcname=file)
logger.info('about to download zip')
return ZipBlob.from_file(zip_fname)
@thing_action

12
webapp/src/components/tabContentComponents/scanListContent.vue
View file

@ -1,5 +1,8 @@
<template>
<div class="galleryDisplay uk-padding uk-padding-remove-top">
<div
v-observe-visibility="visibilityChanged"
class="galleryDisplay uk-padding uk-padding-remove-top"
>
<!-- Gallery nav bar -->
<nav
class="gallery-navbar uk-navbar-container uk-navbar-transparent"
@ -152,10 +155,15 @@ export default {
},
methods: {
visibilityChanged(isVisible) {
if (isVisible) {
this.updateScans();
}
},
async updateScans() {
let scans = await this.readThingProperty("smart_scan", "scans");
if (!scans | scans.length == 0) {
return;
this.scans = scans;
}
scans.forEach(scan => {
scan.modified = Date.parse(scan.modified);

34
webapp/src/components/tabContentComponents/slideScanContent.vue
View file

@ -97,22 +97,33 @@
<button
v-if="cancellable"
type="button"
class="uk-button uk-button-danger uk-margin-remove uk-float-right uk-width-1-1"
class="uk-button uk-button-danger uk-width-1-1"
@click="$refs.smartScanTaskSubmitter.terminateTask()"
>
Cancel
</button>
<div class="uk-margin uk-grid-small uk-child-width-expand" v-if="!cancellable" uk-grid>
<button
v-if="!cancellable"
type="button"
class="uk-button uk-button-danger uk-margin-remove uk-float-right uk-width-1-1"
class="uk-button"
@click="scanning = false; lastStitchedImage=null;"
>
Close
</button>
<task-submitter
class="uk-button"
submit-label="Download ZIP"
:can-terminate="false"
:submit-data="{'scan_name': lastScanName}"
:button-primary="true"
:submit-url="createZipOfScanUri"
@response="downloadZipFile"
@error="modalError"
/>
</div>
</div>
<h3 v-if="scanning">
Scan ID: {{ scan_name }}
Scan ID: {{ lastScanName }}
</h3>
</div>
<div class="view-image uk-width-expand uk-height-1-1">
@ -157,6 +168,9 @@ export default {
},
computed: {
createZipOfScanUri() {
return this.thingActionUrl("smart_scan", "create_zip_of_scan");
},
backendOK() {
return this.thingAvailable("smart_scan");
},
@ -190,8 +204,20 @@ export default {
if (mtime !== null) {
this.lastStitchedImage = `${this.$store.getters.baseUri}/smart_scan/latest_preview_stitch.jpg?t=${mtime}`;
}
this.lastScanName = await this.readThingProperty("smart_scan", "latest_scan_name");
setTimeout(this.pollScan, 1000); // keep rescheduling until it's stopped
}
},
async downloadZipFile(response) {
const scan_name = response.input.scan_name;
const filename = `${scan_name}_images.zip`
const url = response.output.href;
const link = document.createElement("a");
link.href = url;
link.setAttribute("download", filename);
console.log(link);
document.body.appendChild(link);
link.click();
}
}
};