Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added praire vole atlas #336

Open
wants to merge 20 commits into
base: main
Choose a base branch
from
Open

Conversation

sacha091
Copy link

@sacha091 sacha091 commented Aug 1, 2024

Before submitting a pull request (PR), please read the contributing guide.

Please fill out as much of this template as you can, but if you have any problems or questions, just leave a comment and we will help out :)

Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

Why is this PR needed?

What does this PR do?

References

Please reference any existing issues/PRs that relate to this PR.

How has this PR been tested?

Please explain how any new code has been tested, and how you have ensured that no existing functionality has changed.

Is this a breaking change?

If this PR breaks any existing functionality, please explain how and why.

Does this PR require an update to the documentation?

If any features have changed, or have been added. Please explain how the documentation has been updated (and link to the associated PR). See here for details.

Checklist:

  • The code has been tested locally
  • Tests have been added to cover all new functionality (unit & integration)
  • The documentation has been updated to reflect any changes
  • The code has been formatted with pre-commit

@adamltyson adamltyson marked this pull request as draft August 1, 2024 10:21
@adamltyson adamltyson self-requested a review August 1, 2024 10:43
ATLAS_BASE_URL = "https://ndownloader.figshare.com/files/"
ORIENTATION = "..."
ROOT_ID = 997
ATLAS_PACKAGER = "..."
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

You can add your name here.



def create_atlas(working_dir):
ATLAS_NAME = "..."
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I've emailed the lab that originally made this atlas to see if they have a preference for the name, but for now it can just be prairie_vole_brain.


def create_atlas(working_dir):
ATLAS_NAME = "..."
SPECIES = "..."
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This can be Microtus ochrogaster

def create_atlas(working_dir):
ATLAS_NAME = "..."
SPECIES = "..."
ATLAS_LINK = "https://elifesciences.org/articles/87029#data"
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This can be Gustison et al. 2024, https://doi.org/10.7554/eLife.87029

ATLAS_LINK = "https://elifesciences.org/articles/87029#data"
CITATION = "..."
ATLAS_BASE_URL = "https://ndownloader.figshare.com/files/"
ORIENTATION = "..."
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is the orientation of the raw data (before packaging), and should be asr. Details here if you're interested.

)

with zipfile.ZipFile(
r"C:\Users\sacha\Downloads\atlas shit\PrV_results_datasets.zip", "r"
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This should be a relative path, defined by Pathlib so it will work on any system, e.g. atlas_path / "PrV_results_datasets.zip"

decimate_fraction = 0.2
smooth = False # smooth meshes after creation
start = time.time()
if PARALLEL:
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Our parallel mesh extraction is broken, so all of this part can be removed, and just keep the stuff after else:.

@adamltyson adamltyson changed the title Added praire vole file Added praire vole atlas Oct 21, 2024
@adamltyson adamltyson marked this pull request as ready for review October 21, 2024 16:23
@adamltyson
Copy link
Member

Thanks @sacha091, this runs well now on my machine. The atlas looks ok, but the main issue is that there seems to be some meshes missing in the packaged atlas. There are 876 structures in structures.csv, but only 258 meshes generated. It may be that the meshes higher up the hierarchy haven't been generated. I think these meshes are also the wrong size, they don't seem to overlap with the images.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants