I changed the names of two of my segmentation annotations and when I ran PFE, there were no metadata generated for those two annotations.
I changed the names back to what Multi Compartment Segmentation outputs, and it worked, suggesting the changed name was the issue and PFE is hardcoded to run on the named outputs of MCS (I can't find the repo to check the code.)
If that is the case, this should be changed because it is easy for users to change annotation names (I did this to differentiate and compare between raw annotations and QC'd annotations), or there should be some message about using caution when changing names etc. so it isn't a mystery why PFE doesn't generate output for those annotations (if the above is correct, that is.)
I changed the names of two of my segmentation annotations and when I ran PFE, there were no metadata generated for those two annotations.
I changed the names back to what Multi Compartment Segmentation outputs, and it worked, suggesting the changed name was the issue and PFE is hardcoded to run on the named outputs of MCS (I can't find the repo to check the code.)
If that is the case, this should be changed because it is easy for users to change annotation names (I did this to differentiate and compare between raw annotations and QC'd annotations), or there should be some message about using caution when changing names etc. so it isn't a mystery why PFE doesn't generate output for those annotations (if the above is correct, that is.)