ODF-Fingerprinting #2962

filipp02 · 2023-11-02T23:01:19Z

Dear Authors of DIPY,

I'd like to draw your attention to our implementation of ODF-Fingerprinting. It's a fiber reconstruction technique that identifies fiber directions by comparing the ODFs from the signal with the precomputed ODF-dictionary.
We published a few papers on this method, e.g.,
https://doi.org/10.1016/j.neuroimage.2019.05.024
https://doi.org/10.1002/mrm.29208

Our implementation uses DIPY and hopefully can be integrated with it smoothly. I am aware that one file in our repository (rdsi.py) is a fairly rudimentary translation from MATLAB and it uses a number of modules that could be replaced with others or reimplemented locally, but otherwise I hope the rest of the code would meet your standards.

I'm happy to work with you on improving our code to your satisfaction.

Best,
Patryk

Multiple bug fixes

… mask.

Update README.rst

pep8speaks · 2023-11-02T23:01:27Z

Hello @filipp02, Thank you for updating !

In the file dipy/core/dsi_sphere.py:

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Comment last updated at 2023-12-08 16:41:49 UTC

skoudoro · 2023-11-03T01:17:41Z

Hi @filipp02,

Thank you very much for this work!

It is great that it follows already DIPY design!

I think the first step before any deep review would be to:

fix all the pep8 issues and functions/method docstring
create some unit tests for each functions
create a small tutorial for all the users and for us to try.

Then, we can go deeper and deeper to simplify the code, eliminate duplication, etc.

Looking forward for your first update. Thanks !

skoudoro · 2023-11-03T01:20:36Z

.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,3 @@
+eclipse.preferences.version=1


Can you remove this file? thanks !

skoudoro · 2023-11-03T01:21:01Z

README_odffp.rst

@@ -0,0 +1,120 @@
+Orientation Distribution Function Fingerprinting (ODF-FP)


Can you remove this file ? thanks

Garyfallidis · 2023-11-03T01:23:41Z

Thank you @filipp02. @Atharva-Shah-2298 can you refactor @filipp02's PR?

skoudoro

Below, Some easy additional comments

skoudoro · 2023-11-03T01:25:49Z

dipy/reconst/odffp.py

+MAX_FIT_PENALTY = 0.1
+
+
+def plot_odf(odf, filename='odf.png', tessellation=dsiSphere8Fold()):


The plot function will move to dipy.viz.plotting

skoudoro · 2023-11-03T01:27:09Z

dipy/reconst/odffp.py

+
+
+# Base abstract class
+class DiffusionDataGenerator(object):


All the generator functions/class might move to the simulation module dipy.sims.

filipp02 · 2023-11-04T16:41:44Z

Hi guys, Thank you for such a rapid response and for asking Atharva to refactor the code. I guess I'll focus on preparing the manual then. If there's anything unclear in my code, I'll gladly discuss. Best, Patryk

…

On Thu, Nov 2, 2023 at 9:23 PM Eleftherios Garyfallidis < ***@***.***> wrote: Thank you @filipp02 <https://github.com/filipp02>. @Atharva-Shah-2298 <https://github.com/Atharva-Shah-2298> can you refactor @filipp02 <https://github.com/filipp02>'s PR? — Reply to this email directly, view it on GitHub <#2962 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQVAL2AJER4PSMPR35AO57DYCRBSRAVCNFSM6AAAAAA63T26GWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJRG43TGMRQG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

Atharva-Shah-2298 · 2023-11-04T19:27:53Z

Hi @filipp02 ,

Can we setup a zoom meeting to discuss the core functionality? Then I will help with tests and examples.

filipp02 added 30 commits February 18, 2021 16:39

Initial commit

95de87d

dsi_sphere_8fold added

d424199

ODF calculation

ed591ec

ODF peak finding

416a577

ODF rotation to max

ab04f82

Rotations to main peak

4c78bbd

ODF rotation

99e0be8

ODF rotation and matching

1254e62

Alpha version

90ae1e9

Alpha version

8842bfa

Drop ODF amplitude option added.

d1af737

Class _DsiSphere8Fold is a singleton now.

30a678a

Peak dirs rotation

37458d0

FIB file generator handles peak dirs.

e640af5

Bug fix (division by zero in rotation) and refactoring.

6351b14

Export of QAs and ODFs, although BY-axis is still flipped.

41d4bb1

First step towards runtime optimization.

c704741

Refactoring. Peak dirs seem wrong on HCP data.

cb4a032

Cleaning up

b2adbfa

LPS orientation of DSI Studio is handled, but needs refactoring.

efa9d73

Re-orientation to LPS in saveToFib() + refactoring.

d22896b

Something is still wrong for HCP data.

90fc9ab

Bug fix: NaN-fibers now ignored.

45c0177

Bug fix: Rotation matrix corrected

eb175fa

Saving FIB-files as fib.gz now.

7fc82e2

Export dict_idx & dict_micro.

eb22e65

save_as_fib() refactoring

7f9df05

Diffusivity maps added

660a94a

Index maps implemented.

cd1bce3

Warning messages added.

fc5ec33

filipp02 and others added 10 commits June 22, 2023 16:02

Update odffp.py

f052ea1

Multiple bug fixes

Bug fixes in posterior ODF-FP

8b8bcae

Penalization begins at the 2nd fiber

20176af

Adding VOID element of the ODF-dictionary to represent voxels outside…

7b5e7a4

… mask.

Merge branch 'odffp'

315dc82

Update README.rst

c0b8c7c

Merge pull request #1 from filipp02/master-1

3b27b2c

Update README.rst

Rename README.rst to README_odffp.rst

0118593

Add files via upload

c3868f5

Merge branch 'dipy:master' into master

63b241b

skoudoro reviewed Nov 3, 2023

View reviewed changes

.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,3 @@

eclipse.preferences.version=1

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Can you remove this file? thanks !

skoudoro reviewed Nov 3, 2023

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README_odffp.rst

@@ -0,0 +1,120 @@

Orientation Distribution Function Fingerprinting (ODF-FP)

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Can you remove this file ? thanks

skoudoro reviewed Nov 3, 2023

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skoudoro force-pushed the master branch 4 times, most recently from afae75f to 7e158ff Compare December 8, 2023 09:28

add nightly wheel

dda2ffa

skoudoro force-pushed the master branch from 7e158ff to dda2ffa Compare December 8, 2023 16:00

Merge branch 'dipy:master' into master

a7537fa

skoudoro force-pushed the master branch 2 times, most recently from 1419292 to ca6268a Compare December 8, 2023 22:25

skoudoro force-pushed the master branch 3 times, most recently from 5935e1e to 765963e Compare January 24, 2024 19:24

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ODF-Fingerprinting #2962

ODF-Fingerprinting #2962

filipp02 commented Nov 2, 2023

pep8speaks commented Nov 2, 2023 •

edited

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filipp02 commented Nov 4, 2023 via email

Atharva-Shah-2298 commented Nov 4, 2023 •

edited by Garyfallidis

		@@ -0,0 +1,120 @@
		Orientation Distribution Function Fingerprinting (ODF-FP)

		MAX_FIT_PENALTY = 0.1


		def plot_odf(odf, filename='odf.png', tessellation=dsiSphere8Fold()):

ODF-Fingerprinting #2962

Are you sure you want to change the base?

ODF-Fingerprinting #2962

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filipp02 commented Nov 2, 2023

pep8speaks commented Nov 2, 2023 • edited

Comment last updated at 2023-12-08 16:41:49 UTC

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filipp02 commented Nov 4, 2023 via email

Atharva-Shah-2298 commented Nov 4, 2023 • edited by Garyfallidis

pep8speaks commented Nov 2, 2023 •

edited

Atharva-Shah-2298 commented Nov 4, 2023 •

edited by Garyfallidis