rahix/openflexure-microscope-server
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Produce tiff as property

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jaknapper 2024-02-21 14:42:52 +00:00
parent 169df15fd1
commit 43cf7e837a
1 changed files with 7 additions and 2 deletions
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9
src/openflexure_microscope_server/things/smart_scan.py
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@ -783,7 +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
@ -1045,6 +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:
@ -1053,7 +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: