Fix incomplete_fov_check to not require a channel named Au
#474
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…of if Au was found
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…y imaged, and last test for only one
| channels = io_utils.list_files(os.path.join(extraction_dir, fovs[0]), ".tiff") | ||
| channels_subset = channels[:num_channels] | ||
| if "Au.tiff" not in channels_subset: | ||
| channels_subset = channels_subset[:-1] + ["Au.tiff"] |
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Noah specifically noted here that Au should always be a default channel when checking for incomplete fovs. So if some panels don't have gold, then we need this if statement to change instead of removing it completely.
if "Au.tiff" in channels and not in channels_subset:
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@camisowers in line with adding an explicit argument to set intensity_channels to the callback creation function, what about adding another explicit argument defining a custom name for the gold channel? By default, it will be set to "Au", and even if the user leaves it as None, it'll still assume an "Au.tiff" is found.
In cases where some channels fail to load, instead of erroring out completely, check if the error is specifically caused by a failure to load in gold, and if so, throw a warning that the specific gold channel could not be located and to ask the user to double-check that this is indeed correct.
What is the purpose of this PR?
Closes #473.
How did you implement your changes
Remove the addition of the
"Au"channel inincomplete_fov_check.Add specific lists in the
3aand3bnotebooks to allow the user to change their intensity channels they wish to extract (or leave as blank of none specified).