rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Merge branch 'verify-focus' of https://gitlab.com/openflexure/openflexure-microscope-server into verify-focus

Browse source
This commit is contained in:
Joe Knapper 2024-02-21 15:48:04 +00:00
commit 07b1d3bb7c
1 changed files with 9 additions and 3 deletions
Download patch file Download diff file Expand all files Collapse all files

12
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -654,6 +654,7 @@ class SmartScanThing(Thing):
while True: while True:
jpeg_zs, jpeg_sizes = 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"] current_height = stage.position["z"]
time.sleep(0.2)
autofocus_success = autofocus.verify_focus_sharpness(sweep_sizes = jpeg_sizes, camera = CamDep, threshold = 0.92) 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}") logger.info(f"We just tested the focus! Result was {autofocus_success}")
@ -774,7 +775,7 @@ class SmartScanThing(Thing):
@thing_property @thing_property
def max_range(self) -> int: def max_range(self) -> int:
"""The maximum distance from the centre of the scan before we break""" """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 @max_range.setter
def max_range(self, value: int) -> None: def max_range(self, value: int) -> None:
@ -782,7 +783,7 @@ class SmartScanThing(Thing):
@thing_property @thing_property
def stitch_tiff(self) -> bool: def stitch_tiff(self) -> bool:
"""The maximum distance from the centre of the scan before we break""" """Whether or not to also produce a pyramidal tiff"""
return self.thing_settings.get("stitch_tiff", False) return self.thing_settings.get("stitch_tiff", False)
@stitch_tiff.setter @stitch_tiff.setter
@ -1044,6 +1045,11 @@ class SmartScanThing(Thing):
"""Generate a stitched image based on stage position metadata""" """Generate a stitched image based on stage position metadata"""
images_folder = self.images_folder(scan_name=scan_name) 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: if overlap == 0.0:
try: try:
with open(os.path.join(images_folder, 'scan_inputs.json')) as data_file: with open(os.path.join(images_folder, 'scan_inputs.json')) as data_file:
@ -1052,7 +1058,7 @@ class SmartScanThing(Thing):
overlap = data_loaded['overlap'] overlap = data_loaded['overlap']
except: except:
overlap = 0.1 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 @thing_action
def create_zip_of_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None, download_zip = True) -> ZipBlob: def create_zip_of_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None, download_zip = True) -> ZipBlob: