move models to own files/simplify view #123
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in view of moving to a separate version managing widget
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #123 +/- ##
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+ Coverage 97.44% 97.72% +0.28%
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Files 8 9 +1
Lines 391 396 +5
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+ Hits 381 387 +6
+ Misses 10 9 -1 ☔ View full report in Codecov by Sentry. |
| def refresh_data(self) -> None: | ||
| """Refresh model data by calling atlas API""" | ||
| all_atlases = get_all_atlases_lastversions() | ||
| data = [] | ||
| for name, latest_version in all_atlases.items(): | ||
| if name in get_atlases_lastversions().keys(): | ||
| data.append( | ||
| [ | ||
| name, | ||
| self._format_name(name), | ||
| get_local_atlas_version(name), | ||
| latest_version, | ||
| ] | ||
| ) | ||
| else: | ||
| data.append( | ||
| [name, self._format_name(name), "n/a", latest_version] | ||
| ) | ||
|
|
||
| self._data = data | ||
|
|
||
| def _format_name(self, name: str) -> str: | ||
| formatted_name = name.split("_") | ||
| formatted_name[0] = formatted_name[0].capitalize() | ||
| formatted_name[-1] = f"({formatted_name[-1].split('um')[0]} \u03BCm)" | ||
| return " ".join([formatted for formatted in formatted_name]) |
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These are the new functions added to the atlas table model.
| for hidden_column in [0, 2, 3]: | ||
| # hide raw name(0), local and latest versions(2,3) in this view | ||
| self.hideColumn(hidden_column) |
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Is there any way to avoid hard coding the hidden columns? I can foresee a situation where the column order is changed, or new columns are added throwing this off.
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Good point - I can implement this with a simple refactor of our custom model.
| for name, latest_version in all_atlases.items(): | ||
| if name in get_atlases_lastversions().keys(): | ||
| data.append( | ||
| [ | ||
| name, | ||
| self._format_name(name), | ||
| get_local_atlas_version(name), | ||
| latest_version, | ||
| ] | ||
| ) | ||
| else: | ||
| data.append( | ||
| [name, self._format_name(name), "n/a", latest_version] | ||
| ) |
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What does 'get_local_atlas_version' return if the atlas isn't downloaded? If it's something sensible can that be used instead of querying 'get_atlases_lastversions()'?
| for name, latest_version in all_atlases.items(): | |
| if name in get_atlases_lastversions().keys(): | |
| data.append( | |
| [ | |
| name, | |
| self._format_name(name), | |
| get_local_atlas_version(name), | |
| latest_version, | |
| ] | |
| ) | |
| else: | |
| data.append( | |
| [name, self._format_name(name), "n/a", latest_version] | |
| ) | |
| for name, latest_version in all_atlases.items(): | |
| local_version = get_local_atlas_version(name) if get_local_atlas_version else "n/a" | |
| data.append( | |
| [ | |
| name, | |
| self._format_name(name), | |
| local_version, | |
| latest_version, | |
| ] | |
| ) |
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Don't think it currently returns something sensible unfortunately - I've tested locally and it gives a list index out of range error. I've opened brainglobe/brainglobe-atlasapi#187 as a possibility for the future.
Co-authored-by: Igor Tatarnikov <[email protected]>
Description
What is this PR
Why is this PR needed?
It is a step on the way towards being able to download new atlases, and update local atlases to newer versions, through a napari GUI.
What does this PR do?
This PR does two things (I should have split this into two PRs - sorry!) in preparation for moving atlas download functionality to a different widget/adding atlas update functionality in the GUI.
Make the model/views more flexible to allow several (kinds of) views on the same model
AtlasTableViewtoAtlasViewerView, which is the view that allows users to "view" atlases innapari. This paves the way to have other atlas views, e.g. anAtlasUpdaterViewor so, which is a view that allows updating the atlas version, using the same data model.BrainrenderWidget, as this will be for visualisation purposes only.Minor refactor of the atlas table model
This PR does a minor refactor of
AtlasTableModel(see below for details).I've sign-posted these new functions with a comment.
The data model code has not changed otherwise (beyond moving files).
References
Will facilitate #21 by separating concerns further.
How has this PR been tested?
Existing tests refactored in line with changes detailed above, pass locally and on CI.
Is this a breaking change?
Yes, in the sense that downloading atlases will now not be possible via the viewer widget.
Does this PR require an update to the documentation?
Once #21 is addressed, yes, we'll need to update https://brainglobe.info/tutorials/visualise-atlas-napari.html
Checklist: