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AnatomicMaps / flatmap-maker

Make anatomical flatmaps from SVG diagrams, Powerpoint slides, and other sources.
Apache License 2.0
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"Node has multiple terminal features" error in cat and pig flatmaps. #29

Open keeran97 opened 1 year ago

keeran97 commented 1 year ago

In the current version of the cat and pig flatmap (repos linked - files are at the head of the keerans_changes branch), there are errors output from mapmaker that state the below:

2022-11-18 09:22:17,217 WARNING: Node myocardium in heart right ventricle, epicardium, heart has multiple terminal features: {'cardio_29-1', 'cardio_29-4', 'cardio_29-3', 'cardio_29-2'}
2022-11-18 09:22:17,223 WARNING: Node endocardium in heart right ventricle, epicardium, heart has multiple terminal features: {'cardio_28-3', 'cardio_28-1', 'cardio_28-2', 'cardio_28-4'}
2022-11-18 09:22:17,230 WARNING: Node myocardium in heart left ventricle, epicardium, heart has multiple terminal features: {'cardio_29-1', 'cardio_29-4', 'cardio_29-3', 'cardio_29-2'}
2022-11-18 09:22:17,237 WARNING: Node endocardium in heart left ventricle, epicardium, heart has multiple terminal features: {'cardio_28-3', 'cardio_28-1', 'cardio_28-2', 'cardio_28-4'}

Note that the above was extracted from the cat flatmap error log. While the pig flatmap error log only produces the error relating to myocardium of left ventricle. Im not sure if it is an issue. These errors do not appear in mouse or rat flatmaps. The myocardium and other heart wall layers must have these multiple features as that is how things are laid out in SCKAN. And things are set up exactly the same way in the mouse. The annotations and SVG seem to be correct. I am wondering if this is something to do with the SVG/JSON files or mapmaker? Or is this something that can be ignored? Only flagging this as its something that appears only for cat and pig flatmaps.

A confirmation on what this relates to (and if I've missed something) would be appreciated. If this is something that isn't an issue - why does it appear for cat and pig flatmaps and not for mouse or rat?

As mentioned, the files on the head of the keerans_changes branch in both the pig and cat flatmap will reproduce this issue. the line used to generate the map in both cases is:

python runmaker.py --source ../flatmap-sources/new_cat/manifest.json --output ../flatmaps --verbose --background-tiles --authoring --debug --log log-files/LOG_513

dbrnz commented 1 year ago

as that is how things are laid out in SCKAN

SCKAN has no species specific information, so any differences are in the SVG markup and/or the properties file.

I suggest being more systematic when comparing things.

keeran97 commented 1 year ago

SCKAN has no species specific information

I meant in terms of why we need multiple features representing the same thing. e.g. aacar path 11 shows connections to myocardium in the left and right atriums, and the left ventricle. image

I have gone through the related things (i.e. the SVGs and the JSON) and cannot find anything obviously different (especially considering cat and pig are copy-paste of mouse). But if you suggest to continue comparing/investigating then I can. Just wanted to clarify before continuing to spend time on it. Thanks.

dbrnz commented 1 year ago

But the myocardium (and the endocardium) in the left atrium is NOT the same as that in the right atrium, no more than the thumb on your left hand is the same bit of tissue as the thumb on your right hand.

Understand how and why the features and their annotations are on the rat and then do the same for the other non-human species.