68 create a widget for vesicle pool assignments #73
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…tation layer's properties attribute
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The logic for the pool assignments could be simplified a lot:
- First find all the vesicles that are in any pool. From previous queries, if any, and the current query.
- That is easy: get the ids matching the current query (currently
valid_vesicle_ids), and combine it with ids from past queries (if any), which you have access to via the layer properties (if it exists). - If the pool name of the current query is already in the past pool names, then you over-write the ids for that poolname.
- That is easy: get the ids matching the current query (currently
- After this you don't need to introduce any special cases, just filter out the vesicle ids not in any pool, construct the properties and over-write the layer data and properties. (Or add a new layer with the properties if this is the first query)
| props=props, | ||
| ) | ||
| self._add_table(coords, radii, props, name="Vesicles") | ||
| self._add_table(coords, radii, props, name="Vesicles Morphology") |
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The proper spelling is "Vesicle Morphology".
| pool_id = len(np.unique(layer.properties["pool"])) + 1 | ||
| # compute vesicles with new pool_id and properties | ||
| for vesicle_id in valid_vesicle_ids: | ||
| new_layer_data[segmentation == vesicle_id] = pool_id |
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There are a few problems here:
- You set the value in the layer to the
pool_id. Instead we should keep the vesicle ids intact, but just filter out the vesicles that are not part of any pool. - The whole pool assignment and property logic could be simplified a lot, see the general comment for how.
- The way you do this is in general inefficient. Instead of solving this with a loop you can for example do
filtered_vesicle_mask = ~np.isin(segmentation, valid_vesicle_ids)
new_layer_data[filtered_vesicle_mask] = 0
|
I have simplified the implementation of the vesicle pool widget. It does not work 100% yet, but it should be easy to finish now. I will merge it despite the widget not 100% working, as I have fixed many other issues in the plugins and did quite some refactoring. |
constantinpape
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@constantinpape
I detected following issue with the current logic: after querying a vesicle pool and then querying a new vesicle pool, you cannot go back to the first one and edit it, as it will be overridden.