[WIP] Enhance distance and gpf metrics by vferat · Pull Request #161 · vferat/pycrostates

vferat · 2024-02-16T15:20:34Z

#160

Change correlation computation to use cosine similarity
Change gfp to either use std or rms

TODO:

make sure to use correlation and gfp whenever its needed

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commit 4962016c029a482ea662726c2fd33ac446d3433c Merge: 8bf3cad e486a2c Author: vferat <victor.ferat@live.fr> Date: Tue Apr 16 19:27:30 2024 +0200 Merge branch 'main' into dev_meeg-16042024

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vferat · 2025-02-21T17:36:35Z

pycrostates/cluster/kmeans.py

@@ -317,7 +332,10 @@ def _compute_maps(
        for _ in range(max_iter):
            # Assign each sample to the best matching microstate
            activation = maps.dot(data)


use distance here ?

Sounds good.

vferat · 2025-02-21T17:40:28Z

pycrostates/utils/utils.py

+    return dist
+
+
+def _gev(data, maps, segmentation):


this is only explained variance

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vferat · 2025-03-03T13:18:54Z

This PR addresses also addresses #197 and #220, and brings a significant refactoring of the code. The main goal is to consolidate the distance metric into a single function, which helps avoid confusion between different distance definitions (e.g., Euclidean, correlation, etc.). This refactor also facilitates the introduction of the ignore_polarity parameter, which is essential for resolving issue #116.

Key improvements:

A single function now handles all distance metric calculations, making the code more maintainable and flexible.
The new structure makes it easier to implement additional distance definitions in the future, should they be needed.
The ignore_polarity parameter has been integrated

In my testing, the results from the tutorial builds remain consistent with the previous behavior when ignore_polarity=True. I will conduct a more comprehensive comparison between the current PR code and the main branch to ensure there are no discrepancies before the PR is reviewed.

vferat and others added 30 commits February 16, 2024 16:22

Add dev notebook to test stuff

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Change distance and gfp metrics

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change correlation and gfp

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fix _correlation

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Use pairwise_distances + cosine

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vferat and others added 10 commits April 16, 2024 01:35

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Squashed commit of the following:

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commit 4962016c029a482ea662726c2fd33ac446d3433c Merge: 8bf3cad e486a2c Author: vferat <victor.ferat@live.fr> Date: Tue Apr 16 19:27:30 2024 +0200 Merge branch 'main' into dev_meeg-16042024

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Fix kmeans

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vferat commented Feb 21, 2025

View reviewed changes

pycrostates/utils/utils.py Outdated

return dist

def _gev(data, maps, segmentation):

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vferat Feb 21, 2025

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this is only explained variance

vferat and others added 17 commits February 24, 2025 15:01

Add no implementation error for segmentation with smoothing and polarity

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Delete previous gfp function

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WIP ignore polarity

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[WIP] Enhance distance and gpf metrics#161

[WIP] Enhance distance and gpf metrics#161
vferat wants to merge 89 commits intomainfrom
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vferat commented Feb 16, 2024 •

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vferat commented Feb 16, 2024 •

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