Skip to content

don't attempt ROI stats on big images #223

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
sbesson merged 3 commits into from
Nov 26, 2025
Merged

don't attempt ROI stats on big images #223

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 8 additions & 1 deletion omero/export_scripts/Batch_ROI_Export.py
View file
Open in desktop
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