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don't attempt ROI stats on big images #223

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don't attempt ROI stats on big images #223

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efdee36
don't attempt ROI stats on big images
will-moore Sep 13, 2024
d33f646
Call is_big_image() once per image
will-moore Sep 13, 2024
d8b2bbd
Flake8 fix
will-moore Sep 13, 2024
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9 changes: 8 additions & 1 deletion omero/export_scripts/Batch_ROI_Export.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,12 @@ def log(data):
print(data)


def is_big_image(image):
"""Return True if image is tiled."""
max_size = image._conn.getMaxPlaneSize()
return (image.getSizeX() * image.getSizeY()) > (max_size[0] * max_size[1])


def get_export_data(conn, script_params, image, units=None):
"""Get pixel data for shapes on image and returns list of dicts."""
log("Image ID %s..." % image.id)
Expand All @@ -58,6 +64,7 @@ def get_export_data(conn, script_params, image, units=None):
all_planes = script_params["Export_All_Planes"]
include_points = script_params.get("Include_Points_Coords", False)
size_c = image.getSizeC()
big_image = is_big_image(image)
# Channels index
channels = script_params.get("Channels", [1])
ch_indexes = []
Expand Down Expand Up @@ -110,7 +117,7 @@ def get_export_data(conn, script_params, image, units=None):
# get pixel intensities
for z in z_indexes:
for t in t_indexes:
if z is None or t is None:
if z is None or t is None or big_image:
stats = None
else:
stats = roi_service.getShapeStatsRestricted(
Expand Down