[DOC] Adds Iñigo's blogposts of Weeks 1 and 2 #39

itellaetxe · 2024-06-07T09:54:00Z

Adds @itellaetxe blogposts for Weeks 1 and .

github-actions · 2024-06-07T09:55:04Z

🪓 PR closed, deleted preview at https://github.com/dipy/preview-html/tree/main/dipy.org/pull/39/

itellaetxe · 2024-06-07T09:57:25Z

@skoudoro I cannot request review from other participants, am I overlooking something or is there anything wrong with my permissions?

skoudoro · 2024-06-07T10:21:12Z

@skoudoro I cannot request review from other participants, am I overlooking something or is there anything wrong with my permissions?

done, not sure why you can not, I might look at it this weekend

skoudoro · 2024-06-07T10:23:09Z

Why I see kaustav blog posts? can you rebase or merge master to see only your changes. Thank you

skoudoro · 2024-06-07T10:29:45Z

You blog post failed to compile. see here: https://github.com/dipy/dipy.org/actions/runs/9415155137/job/25935562148?pr=39#step:7:216

Warning, treated as error:
/home/runner/work/dipy.org/dipy.org/posts/2024/2024_06_07_Inigo_week_1.rst:17:Unexpected indentation.

Please, can you update? That's why we have no preview

ps: we also need to update the CI. it should come back as an error

itellaetxe · 2024-06-07T11:44:09Z

Why I see kaustav blog posts? can you rebase or merge master to see only your changes. Thank you

Done, I dropped his commits and squashed mines. Thanks

itellaetxe · 2024-06-07T11:46:41Z

You blog post failed to compile. see here: https://github.com/dipy/dipy.org/actions/runs/9415155137/job/25935562148?pr=39#step:7:216
Warning, treated as error:
/home/runner/work/dipy.org/dipy.org/posts/2024/2024_06_07_Inigo_week_1.rst:17:Unexpected indentation.
Please, can you update? That's why we have no preview

Updated. Should be fine now. I do not get the CI notifications, IDK why.

ps: we also need to update the CI. it should come back as an error

Perhaps I will look into this next week. I opened an issue #40

jhlegarreta

Not sure if this is the latest commit preview:
https://dipy.github.io/preview-html/dipy.org/pull/39/posts/2024/2024_06_07_Inigo_week_1.html

But two of the links are not rendered correctly.

Even for the first one, if I'm not wrong, a single underscore is usually enough.

jhlegarreta · 2024-06-07T13:36:53Z

Also, this blog post is mixing work done during week 1 and week 2, so please split those.

robinroy03

Hi, nice work you've done :)

I found some small RST syntax issues but that's all. Approving ✅

robinroy03 · 2024-06-07T18:27:35Z

posts/2024/2024_06_07_Inigo_week_1.rst

+
+What I did this week
+~~~~~~~~~~~~~~~~~~~~
+On my last post, I wrote about translating the AutoEncoder architecture from PyTorch to TensorFlow. I have successfully done so, and I have attempted to overfit the model with data from the `FiberCup dataset <https://tractometer.org/fibercup/home/>`__ to check whether the architecture is working as intended, and that the training objective is correctly defined (i.e. the loss function is correctly implemented).


The rst URL syntax got an issue.
Fix:

`separate repo <https://github.com/itellaetxe/tractoencoder_gsoc>`_

Fixed, thanks

robinroy03 · 2024-06-07T18:33:35Z

posts/2024/2024_06_07_Inigo_week_1.rst

+
+What is coming up next week
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+With the help of my mentors, we identified possible improvements to the AutoEncoder training process. Yesterday I investigated how PyTorch weights are initialized in convolutional kernels and in Keras Dense layers using the `He Initialization <https://paperswithcode.com/paper/delving-deep-into-rectifiers-surpassing-human>__`. Using custom initializers, one can mimic the same behavior in TensorFlow, which I started to implement also yesterday.


RST url linking

Fixed, thanks

jhlegarreta

Dates and contents still mix week 1 and week 2. Can this be addressed, please?

jhlegarreta · 2024-06-09T14:33:50Z

posts/2024/2024_06_07_Inigo_week_1.rst

+First Week into GSoC 2024: Building the AutoEncoder, preliminary results
+========================================================================
+
+.. post:: June 7 2024


There is still confusion in dates and weeks. If I'm not mistaken there was a blog post (the first one) that corresponded to the community bonding period (week prior to May 27), and since then there have been two weeks: week 1 (ended Fri May 31), and week 2 (ended Fri Jun 7). So I find that this blog post still confuses dates and contents. Can this please be addressed? 2 blog posts are requested. To avoid this in the future, best is to allocate 30-45 minutes every Friday to write about the work that week. I know it is the most scientifically interesting part for the contributor, but it is important for the mentors, to keep track of the project, and the program.

You are right, I messed up the dates. I will split the info into two blogs. Sorry for the confusion.

WassCodeur · 2024-06-09T15:08:16Z

posts/2024/2024_06_07_Inigo_week_1.rst

+    :category: gsoc
+
+
+What I did this week


Hi @itellaetxe!

Nice blog, clear and concise, Great job.

Thanks Wachiou!

jhlegarreta

A minor comment inline.

jhlegarreta · 2024-06-09T15:50:29Z

posts/2024/2024_05_31_Inigo_week_1.rst

+What I did this week
+~~~~~~~~~~~~~~~~~~~~
+I finished becoming familiar with the TensorFlow + Keras basics and I wrote the training loop and a couple of scripts for instantiating and training the AutoEncoder.
+Data loading was also addressed and I am able to load the data from the FiberCup dataset in .trk format using `NiBabel <https://nipy.org/nibabel/>`__, transform it into NumPy arrays, and feed it into the network.


Again, a single underscore is enough in links: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#hyperlinks

fixed, thanks :)

skoudoro · 2024-06-10T07:42:15Z

pinging @deka27

deka27 · 2024-06-10T08:51:15Z

Two weeks progress. Looks fine to me. sorry for the delayed check. If squashing isn't required, GTG.

* [DOC] Adds blogpost Iñigo's blogpost of Week 1 * FIX: RCorrects bad RST URL syntax & deletes mentions to week 0 work * DOC: Adds Iñigo's week 1 and 2 blogposts * FIX: Single underscore instead of two for RST URLs 6219f3c

itellaetxe marked this pull request as draft June 7, 2024 09:57

itellaetxe marked this pull request as ready for review June 7, 2024 09:58

skoudoro requested review from WassCodeur, robinroy03, deka27, jhlegarreta and pjsjongsung June 7, 2024 10:20

itellaetxe force-pushed the gsoc2024_inigo branch from 6755aed to b2d1301 Compare June 7, 2024 11:43

itellaetxe mentioned this pull request Jun 7, 2024

[MAINT] Website fails to compile but action run does not fail #40

Closed

[DOC] Adds blogpost Iñigo's blogpost of Week 1

81d7cee

itellaetxe force-pushed the gsoc2024_inigo branch from b2d1301 to 81d7cee Compare June 7, 2024 12:05

jhlegarreta suggested changes Jun 7, 2024

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robinroy03 approved these changes Jun 7, 2024

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FIX: RCorrects bad RST URL syntax & deletes mentions to week 0 work

7483a03

jhlegarreta suggested changes Jun 9, 2024

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WassCodeur approved these changes Jun 9, 2024

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DOC: Adds Iñigo's week 1 and 2 blogposts

c6bfe87

jhlegarreta reviewed Jun 9, 2024

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FIX: Single underscore instead of two for RST URLs

9ead66d

jhlegarreta approved these changes Jun 9, 2024

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deka27 approved these changes Jun 10, 2024

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skoudoro merged commit 6219f3c into dipy:master Jun 10, 2024
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itellaetxe changed the title ~~[DOC] Adds Iñigo's blogpost of Week 1~~ [DOC] Adds Iñigo's blogposts of Weeks 1 and 2 Jun 14, 2024

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[DOC] Adds Iñigo's blogposts of Weeks 1 and 2 #39

[DOC] Adds Iñigo's blogposts of Weeks 1 and 2 #39

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[DOC] Adds Iñigo's blogposts of Weeks 1 and 2 #39

[DOC] Adds Iñigo's blogposts of Weeks 1 and 2 #39

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