Update neo structure #1026

JuliaSprenger · 2021-09-03T13:42:31Z

This PR is a suggestion on how to update the neo object linking to include RegionsOfInterest and ChannelView in a consistent manner.
Currently, Groups accept also Segments as child objects, which I think is confounding the neo structure. Also RegionOfInterest was not considered as part of a neo structure yet. Since these are supposed to basically fulfill a masking functionality for ImageSequence their functionality is very similar to the one of ChannelViews for Signals. So my suggestion is to have Group and Segment at the same level and RegionOfInterest as well as ChannelView as optional level before linking to data object. This results in the following neo dependencies:

This PR also updates the corresponding neo structure diagram (as well as generation script).

@samuelgarcia @apdavison What do you think of this?

Fixes #1024

pep8speaks · 2021-09-03T13:42:35Z

Hello @JuliaSprenger! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2022-05-13 11:18:49 UTC

JuliaSprenger · 2021-09-06T09:18:08Z

The failing test is already fixed in #1025

samuelgarcia · 2021-10-28T10:58:28Z

Hi Julia.

Thank you for updating the new diagram.

About the hierachy place for RegionOfInterest I don't known what to say.
I don't have in mind totally the goal for this.
Today in calcium Imaging a ROIs can be

"some zone I want to anaylse" in that case the hierachy is OK for me.
"some neuron that have been detected by an algo" : in that case the number of neuron can be enormous
and dealing then as a list of element is a bad choice from the begining. (like we did from spiketrain instead of
spiketrainlist). In that case we should a RegionOfInterestList I think.

I let @apdavison check this new RegionOfInterest place in the tree.

JuliaSprenger · 2022-01-24T14:50:52Z

I think it would be good to discuss the missing links and pieces in the Neo structure rather sooner than later. @apdavison What is your opinion on the suggestions here? Do you have an alternative organization in mind?

JuliaSprenger · 2022-03-31T12:03:39Z

Here's a summary of the last discussion with @samuelgarcia @apdavison and @mdenker on this topic

there is no consensus on whether Groups should permit Segments as child objects. The strongest argument so far is to keep the object structure as little convoluted as possible for discovery/export/import purposes. Therefore I suggest keeping the current version in which Groups only can contain other Groups, DataObjects or masks of data objects (RegionOfInterest, ChannelView).
Another important point to be added (in another PR) would be the (optional) automatic linking of Spiketrains and Analogsignal traces upon loading. This link will not be explicitly saved when the block exported, but is on request generated when a block is loaded. We still need to decide on what criteria need to be fulfilled for a link to be generated. Is an identical channel_index annotation sufficient?
Extension: Channel_index should be a 2-dim sparse matrix linking a SpikeTrainList with traces of an Analogsignal

- do not accept segments as child objects, but accept regionsofinterest - expand base class RegionOfInterest

- add ImageSequence and RegionOfInterest - remove outdated fake_neo reference - take into account if necessary attributes contain references to neo objects - shorted lines if too long for text box

JuliaSprenger · 2023-04-03T12:32:45Z

neo/core/regionofinterest.py



-class RegionOfInterest:
+class RegionOfInterest(Container):


This should be BaseNeo

JuliaSprenger · 2023-04-03T12:34:31Z

neo/core/view.py

 from .basesignal import BaseSignal
 from .dataobject import ArrayDict


-class ChannelView(BaseNeo):


to be reverted or inherit from a BaseView class

apdavison · 2023-07-27T16:15:00Z

This PR is doing a lot of things. I think we should break it up into several PRs, then we can discuss each of them separately.

I'll follow up with PRs to:

fix the figure generation script
remove old documentation

…e#1026

alejoe91 · 2024-01-24T12:54:00Z

@apdavison can we clos this in favor of #1313 and #1314 ?

apdavison · 2024-01-24T12:59:32Z

@alejoe91 we're still missing a PR to fix the figure generation script (the one which shows the Neo object relationship diagram). (That would need #1313 to be merged first.) I'd prefer to keep this PR open until we have either a PR or an issue for the figure generation, in case it gets forgotten.

…ger in NeuralEnsemble#1026

apdavison · 2024-01-29T11:08:44Z

#1384 fixes the figure generation script, and is the final PR needed to replace this one.

JuliaSprenger modified the milestones: 0.10.0, 0.11.0 Sep 6, 2021

JuliaSprenger mentioned this pull request Sep 10, 2021

update documentation images and remove old material #1027

Merged

JuliaSprenger added Core Documentation labels Sep 13, 2021

JuliaSprenger force-pushed the fix/1024 branch from 9fb891d to ca3f4f3 Compare September 29, 2021 11:45

JuliaSprenger requested review from apdavison and samuelgarcia March 3, 2022 14:16

JuliaSprenger added 9 commits May 13, 2022 13:18

[structure] Reorganize groups in neo structure

c19204b

- do not accept segments as child objects, but accept regionsofinterest - expand base class RegionOfInterest

[structure] Adjust tests to group reorganization

9c28595

[structure] Remove unused _child_properties attribute

19214c3

[structure] Make ChannelView a container object

8beba03

[doc] Update class diagram

6949976

- add ImageSequence and RegionOfInterest - remove outdated fake_neo reference - take into account if necessary attributes contain references to neo objects - shorted lines if too long for text box

[doc] update generated plots

549ad2c

[doc] reformatting

0686d00

[pep8]

434ac76

remove outdated doc files

75152db

JuliaSprenger force-pushed the fix/1024 branch from ca3f4f3 to 75152db Compare May 13, 2022 11:18

apdavison modified the milestones: 0.10.3, 0.11.0 Aug 30, 2022

apdavison modified the milestones: 0.11.0, 0.12.0 Sep 29, 2022

JuliaSprenger modified the milestones: 0.12.0, 0.12.1 Apr 2, 2023

JuliaSprenger modified the milestones: 0.12.1, 0.13.0 Apr 2, 2023

JuliaSprenger commented Apr 3, 2023

View reviewed changes

neo/core/regionofinterest.py

class RegionOfInterest:

class RegionOfInterest(Container):

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This should be BaseNeo

JuliaSprenger commented Apr 3, 2023

View reviewed changes

JuliaSprenger assigned apdavison Apr 3, 2023

JuliaSprenger mentioned this pull request May 17, 2023

Automatic handling of relationships between objects #1266

Merged

apdavison mentioned this pull request Jul 27, 2023

make the handling of RegionOfInterest subclasses consistent with ChannelView #1313

Merged

apdavison added a commit to apdavison/python-neo that referenced this pull request Jul 27, 2023

do not allow Groups to contain Segments, as proposed in NeuralEnsembl…

6524d19

…e#1026

apdavison mentioned this pull request Jul 27, 2023

do not allow Groups to contain Segments #1314

Merged

apdavison added a commit to apdavison/python-neo that referenced this pull request Jan 29, 2024

Updated "generate_diagram.py" script, based on changes by Julia Spren…

5fa8bc3

…ger in NeuralEnsemble#1026

apdavison mentioned this pull request Jan 29, 2024

Updated "generate_diagram.py" script #1384

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apdavison closed this Jan 29, 2024

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Update neo structure #1026

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Update neo structure #1026

Update neo structure #1026

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