rahix/openflexure-microscope-server
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Make overlap value consistent

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jaknapper 2024-02-01 15:31:14 +00:00
parent e6e809cea4
commit db51cd8067
1 changed files with 3 additions and 5 deletions
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8
src/openflexure_microscope_server/things/smart_scan.py
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@ -597,8 +597,6 @@ class SmartScanThing(Thing):
if not self.correlate_running(): if not self.correlate_running():
self.correlate_start(images_folder, overlap=overlap) self.correlate_start(images_folder, overlap=overlap)
self.create_zip_of_scan(logger = logger, scan_name = scan_folder.split('scans/')[1], download_zip = False)
# add the current position to the list of all positions visited # add the current position to the list of all positions visited
true_path.append(loc) true_path.append(loc)
@ -640,6 +638,7 @@ class SmartScanThing(Thing):
stage.move_absolute(**starting_position, block_cancellation=True) stage.move_absolute(**starting_position, block_cancellation=True)
finally: finally:
self._scan_lock.release() self._scan_lock.release()
self.create_zip_of_scan(logger = logger, scan_name = scan_folder.split('scans/')[1], download_zip = False)
logger.info("Waiting for background processes to finish...") logger.info("Waiting for background processes to finish...")
self.preview_stitch_wait() self.preview_stitch_wait()
self.correlate_wait() self.correlate_wait()
@ -905,8 +904,7 @@ class SmartScanThing(Thing):
overlap = data_loaded['overlap'] overlap = data_loaded['overlap']
except: except:
overlap = 0.1 overlap = 0.1
logger.info(overlap) 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", "--minimum_overlap", f"{round(overlap*0.9,3)}", 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:
@ -944,7 +942,7 @@ class SmartScanThing(Thing):
# This is a list of file names that are updated as the scan goes, # This is a list of file names that are updated as the scan goes,
# and should only be zipped at the end of the scan - otherwise they'll # and should only be zipped at the end of the scan - otherwise they'll
# be appended on every loop as we can't overwrite files in the zip # be appended on every loop as we can't overwrite files in the zip
files_to_delay = ['TileConfiguration', 'tiling_cache', 'stitched.jp'] files_to_delay = ['TileConfiguration', 'tiling_cache', 'stitched.jp', 'stitched_from']
with zipfile.ZipFile(zip_fname, mode="a") as zip: with zipfile.ZipFile(zip_fname, mode="a") as zip:
for file in files: for file in files: