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

If not provided, find resize from image size when stitching

Browse source
This commit is contained in:
jaknapper 2025-06-23 14:58:57 +01:00
parent c659ba8f5e
commit 62a07622fa
1 changed files with 24 additions and 2 deletions
Download patch file Download diff file Expand all files Collapse all files

26
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -1080,7 +1080,7 @@ class SmartScanThing(Thing):
self,
logger: InvocationLogger,
scan_name: str,
stitch_resize: float,
stitch_resize: Optional[float] = None,
overlap: float = 0.0,
) -> None:
"""Generate a stitched image based on stage position metadata
@ -1100,7 +1100,6 @@ class SmartScanThing(Thing):
try:
with open(json_fpath, "r", encoding="utf-8") as data_file:
data_loaded = json.load(data_file)
logger.info(data_loaded)
overlap = data_loaded["overlap"]
except (json.decoder.JSONDecodeError, FileNotFoundError, TypeError):
# As there is no schema or pydantic model this should handle
@ -1117,6 +1116,29 @@ class SmartScanThing(Thing):
"Attempting stitch with overlap value of 0.1"
)
overlap = 0.1
if stitch_resize is None:
try:
with open(json_fpath, "r", encoding="utf-8") as data_file:
data_loaded = json.load(data_file)
capture_resolution = data_loaded["capture resolution"]
stitch_resize = STITCHING_RESOLUTION[0] / capture_resolution[0]
except (json.decoder.JSONDecodeError, FileNotFoundError, TypeError):
# As there is no schema or pydantic model this should handle
# the file not being there, it not being json in the file,
# or the imported data not being indexable
logger.warning(
f"Couldn't read scan data, is {SCAN_DATA_FILENAME} missing or corrupt? "
"Attempting stitch with resize value of 0.5"
)
stitch_resize = 0.5
except KeyError:
logger.warning(
"Value for capture resolution not found in scan data. "
"Attempting stitch with resize value of 0.5"
)
stitch_resize = 0.5
self.run_subprocess(
logger,
[