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Code Issues 14 Pull requests 2 Packages Activity Actions

[MARKER]: (f)ALFF #35

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fraimondo merged 10 commits from enh/falff into main 2022-12-19 21:17:40 +00:00
Conversation 7 Commits 10 Files changed 13 +1367 -4
fraimondo commented 2022-11-24 15:47:56 +00:00 (Migrated from github.com)
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Which marker do you want to include?

ALFF and fALFF

They can be calculated simultaneously as fALFF is just a scaling of ALFF in the full frequency range.

Inputs:
List of 3D MNI coordinates OR a mask file

Output:
Two arrays with one value per voxel, one for ALFF and one for fALFF

Is there any publication or available code?

https://pubmed.ncbi.nlm.nih.gov/18501969/

Do you have a sample code that implements this outside of junifer?

No response

Anything else to say?

Equations here can be used:
https://web.conn-toolbox.org/fmri-methods/connectivity-measures/other#h.p_uBWGEgvizNhI

### Which marker do you want to include? ALFF and fALFF They can be calculated simultaneously as fALFF is just a scaling of ALFF in the full frequency range. Inputs: List of 3D MNI coordinates OR a mask file Output: Two arrays with one value per voxel, one for ALFF and one for fALFF ### Is there any publication or available code? https://pubmed.ncbi.nlm.nih.gov/18501969/ ### Do you have a sample code that implements this outside of junifer? _No response_ ### Anything else to say? Equations here can be used: https://web.conn-toolbox.org/fmri-methods/connectivity-measures/other#h.p_uBWGEgvizNhI
github-actions[bot] commented 2022-11-24 15:52:39 +00:00 (Migrated from github.com)
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PR Preview Action v1.2.0
Preview removed because the pull request was closed.
2022-12-19 21:22 UTC
[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.2.0 :---: Preview removed because the pull request was closed. 2022-12-19 21:22 UTC <!-- Sticky Pull Request Commentpr-preview -->
codecov[bot] commented 2022-11-24 15:59:02 +00:00 (Migrated from github.com)
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Codecov Report

Merging #35 (ade3974) into main (ade3974) will not change coverage.
The diff coverage is n/a.

❗ Current head ade3974 differs from pull request most recent head 08154f9. Consider uploading reports for the commit 08154f9 to get more accurate results

Impacted file tree graph

@@           Coverage Diff           @@
##             main      #35   +/-   ##
=======================================
  Coverage   93.53%   93.53%           
=======================================
  Files          66       66           
  Lines        2616     2616           
  Branches      483      483           
=======================================
  Hits         2447     2447           
  Misses        116      116           
  Partials       53       53
Flag Coverage Δ
docs 100.00% <0.00%> (ø)
junifer 93.52% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

# [Codecov](https://codecov.io/gh/juaml/junifer/pull/35?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report > Merging [#35](https://codecov.io/gh/juaml/junifer/pull/35?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (ade3974) into [main](https://codecov.io/gh/juaml/junifer/commit/ade3974b677d2617bd8109db2fae08f37210e2bd?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (ade3974) will **not change** coverage. > The diff coverage is `n/a`. > :exclamation: Current head ade3974 differs from pull request most recent head 08154f9. Consider uploading reports for the commit 08154f9 to get more accurate results [![Impacted file tree graph](https://codecov.io/gh/juaml/junifer/pull/35/graphs/tree.svg?width=650&height=150&src=pr&token=5H21JuZXMw&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)](https://codecov.io/gh/juaml/junifer/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #35 +/- ## ======================================= Coverage 93.53% 93.53% ======================================= Files 66 66 Lines 2616 2616 Branches 483 483 ======================================= Hits 2447 2447 Misses 116 116 Partials 53 53 ``` | Flag | Coverage Δ | | |---|---|---| | docs | `100.00% <0.00%> (ø)` | | | junifer | `93.52% <0.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#carryforward-flags-in-the-pull-request-comment) to find out more.
synchon (Migrated from github.com) requested changes 2022-12-19 10:49:57 +00:00
junifer/markers/falff/falff_base.py
@ -0,0 +1,180 @@
"""Provide abstract class for computing fALFF."""
synchon (Migrated from github.com) commented 2022-12-19 10:18:25 +00:00
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Please add a newline after this for consistency.

Please add a newline after this for consistency.
synchon (Migrated from github.com) commented 2022-12-19 10:19:42 +00:00
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highpass : positive float?

`highpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:19:57 +00:00
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lowpass : positive float?

`lowpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:20:44 +00:00
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tr : positive float, optional?

`tr : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:29:50 +00:00
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Maybe return the list directly?

Maybe return the list directly?
synchon (Migrated from github.com) commented 2022-12-19 10:31:37 +00:00
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I don't think the class is abstract.

I don't think the class is abstract.
synchon (Migrated from github.com) commented 2022-12-19 10:35:05 +00:00
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Use raise_error?

Use `raise_error`?
junifer/markers/falff/falff_base.py
@ -0,0 +33,4 @@
if available (default None).
name : str, optional
The name of the marker. If None, it will use the class name
(default None).
synchon (Migrated from github.com) commented 2022-12-19 10:21:20 +00:00
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Please add a newline after this.

Please add a newline after this.
junifer/markers/falff/falff_estimator.py
@ -0,0 +1,338 @@
"""Provide estimator class for (f)ALFF."""
synchon (Migrated from github.com) commented 2022-12-19 10:35:29 +00:00
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The docstring needs to be updated.

The docstring needs to be updated.
synchon (Migrated from github.com) commented 2022-12-19 10:37:32 +00:00
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highpass : positive float?

`highpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:37:45 +00:00
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lowpass : positive float?

`lowpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:39:06 +00:00
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highpass : positive float?

`highpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:39:19 +00:00
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lowpass : positive float?

`lowpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:39:38 +00:00
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tr : positive float, optional

`tr : positive float, optional`
synchon (Migrated from github.com) commented 2022-12-19 10:39:52 +00:00
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tr : positive float, optional?

`tr : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:40:44 +00:00
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highpass : positive float?

`highpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:40:55 +00:00
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lowpass : positive float?

`lowpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:41:09 +00:00
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tr : positive float, optional?

`tr : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:41:29 +00:00
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highpass : positive float?

`highpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:41:39 +00:00
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lowpass : positive float?

`lowpass : positive float`?
synchon (Migrated from github.com) commented 2022-12-19 10:42:04 +00:00
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tr : positive float, optional?

`tr : positive float, optional`?
junifer/markers/falff/falff_parcels.py
@ -0,0 +1,126 @@
"""Provide class for computing fALFF on parcels."""
synchon (Migrated from github.com) commented 2022-12-19 10:42:43 +00:00
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highpass : positive float, optional?

`highpass : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:42:59 +00:00
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lowpass : positive float, optional?

`lowpass : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:43:22 +00:00
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tr : positive float, optional?

`tr : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:44:07 +00:00
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``tr``
``` ``tr`` ```
synchon (Migrated from github.com) commented 2022-12-19 10:44:43 +00:00
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Extra newline here, can be removed.

Extra newline here, can be removed.
junifer/markers/falff/falff_spheres.py
@ -0,0 +1,134 @@
"""Provide class for computing fALFF on spheres."""
synchon (Migrated from github.com) commented 2022-12-19 10:45:27 +00:00
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highpass : positive float, optional?

`highpass : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:45:43 +00:00
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lowpass : positive float, optional?

`lowpass : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:45:56 +00:00
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tr : positive float, optional?

`tr : positive float, optional`?
synchon (Migrated from github.com) commented 2022-12-19 10:46:16 +00:00
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Extra newline here, can be removed.

Extra newline here, can be removed.
junifer/markers/falff/falff_spheres.py
@ -0,0 +116,4 @@
keys:
* ``data`` : the actual computed values as a numpy.ndarray
* ``columns`` : the column labels for the computed values as a list
synchon (Migrated from github.com) commented 2022-12-19 10:46:47 +00:00
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Needs a newline after the listing.

Needs a newline after the listing.
junifer/markers/falff/tests/test_falff_estimator.py
@ -0,0 +206,4 @@
_check_afni() is False, reason="requires afni to be in PATH"
)
def test_AmplitudeLowFrequencyFluctuationEstimator_afni_vs_python() -> None:
"""Test that the cache works properly when using afni."""
synchon (Migrated from github.com) commented 2022-12-19 10:47:30 +00:00
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Docstring needs to be updated.

Docstring needs to be updated.
junifer/markers/falff/tests/test_falff_parcels.py
@ -0,0 +17,4 @@
from junifer.storage import SQLiteFeatureStorage
from junifer.utils import logger
synchon (Migrated from github.com) commented 2022-12-19 10:48:39 +00:00
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As the parcellations used are same, maybe create a module-level variable and reuse it.

As the parcellations used are same, maybe create a module-level variable and reuse it.
junifer/markers/falff/tests/test_falff_spheres.py
@ -0,0 +1,165 @@
"""Provide test for sphere-aggregated (f)ALFF."""
synchon (Migrated from github.com) commented 2022-12-19 10:49:03 +00:00
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Docstring needs to be updated.

Docstring needs to be updated.
junifer/markers/falff/tests/test_falff_spheres.py
@ -0,0 +18,4 @@
from junifer.storage import SQLiteFeatureStorage
from junifer.utils import logger
synchon (Migrated from github.com) commented 2022-12-19 10:49:32 +00:00
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As the coordinates used are same, maybe create a module-level variable and reuse it.

As the coordinates used are same, maybe create a module-level variable and reuse it.
fraimondo (Migrated from github.com) reviewed 2022-12-19 12:24:52 +00:00
junifer/markers/falff/falff_base.py
@ -0,0 +33,4 @@
if available (default None).
name : str, optional
The name of the marker. If None, it will use the class name
(default None).
fraimondo (Migrated from github.com) commented 2022-12-19 12:24:51 +00:00
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done

done
synchon (Migrated from github.com) reviewed 2022-12-19 12:41:35 +00:00
synchon (Migrated from github.com) reviewed 2022-12-19 20:46:02 +00:00
synchon (Migrated from github.com) approved these changes 2022-12-19 21:16:53 +00:00
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