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Please refer to our FAQ and look at our known issues before opening a bug report.
Describe the bug
There is a logic error in alpineer.load_utils.load_tiled_img_data for the case when the number of FOVs is the same as spots in the grid (i.e. there are no black spaces in the stitched image).
The code runs, but the images are instead stitched in acquisition order and not the intended tiled shape.
Expected behavior
We want the images to stitch in the correct order.
Solution
Remove the following lines of code from the load_tiled_img_data function. in alpineer Even if there are no blank spots in the image, we should just always load in the images one at a time to ensure they are put in the correct location within the array.
# no missing fov images, load data normally and return array
if len(fov_list) == len(expected_fovs):
if single_dir:
img_xr = load_imgs_from_dir(
data_dir,
match_substring=channel,
xr_dim_name="channels",
trim_suffix="_" + channel,
xr_channel_names=[channel],
)
else:
img_xr = load_imgs_from_tree(
data_dir, img_sub_folder, fovs=fov_list, channels=[channel]
)
return img_xr
This is probably happened because the same function is used by both toffy and ark; however, in ark the folders have already been renamed and could be loaded in alphabetical order without issue.
The text was updated successfully, but these errors were encountered:
Please refer to our FAQ and look at our known issues before opening a bug report.
Describe the bug
There is a logic error in
alpineer.load_utils.load_tiled_img_data
for the case when the number of FOVs is the same as spots in the grid (i.e. there are no black spaces in the stitched image).The code runs, but the images are instead stitched in acquisition order and not the intended tiled shape.
Expected behavior
We want the images to stitch in the correct order.
Solution
Remove the following lines of code from the
load_tiled_img_data
function. in alpineer Even if there are no blank spots in the image, we should just always load in the images one at a time to ensure they are put in the correct location within the array.This is probably happened because the same function is used by both toffy and ark; however, in ark the folders have already been renamed and could be loaded in alphabetical order without issue.
The text was updated successfully, but these errors were encountered: