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

Implement a linecut of the modulus in postprocessing #246

Merged
merged 33 commits into from
Apr 8, 2022
Merged

Implement a linecut of the modulus in postprocessing #246

merged 33 commits into from
Apr 8, 2022

Conversation

carnisj
Copy link
Owner

@carnisj carnisj commented Apr 5, 2022

Description

I added one step in post-processing, where line cuts through the reconstructed modulus are generated in Z, Y, X, and the gradient of the line cuts is fitted with a Gaussian line shape to estimate the resolution.

linecut_amp
linecut_amp_fits

Fixes #195

Type of change

  • New feature (non-breaking change which adds functionality)

How has this been tested?

I added unit tests and ran the example dataset.

Checklist:

  • I have made corresponding changes to the documentation
  • I have added corresponding unit tests
  • I have run doit and all tasks have passed

@carnisj carnisj marked this pull request as draft April 5, 2022 20:28
Jerome Carnis added 3 commits April 7, 2022 11:21
@carnisj carnisj marked this pull request as ready for review April 7, 2022 09:28
@clatlan
Copy link
Collaborator

clatlan commented Apr 8, 2022

Nice ! Is this how the pixel size is derived by default ?

@carnisj
Copy link
Owner Author

carnisj commented Apr 8, 2022

Nice ! Is this how the pixel size is derived by default ?

No, this is unrelated. The voxel sizes are chosen by the user beforehand because they are required for the interpolation into an orthonormal grid. The linecut and fits are done on this already interpolated object to get an idea about the resolution of the reconstruction. They take as well the user-defined voxel sizes to convert from a pixel number to a length scale in nm.

@carnisj carnisj merged commit 93a6cf7 into main Apr 8, 2022
@carnisj carnisj deleted the linecut branch April 8, 2022 14:02
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.

[FEAT] Line profile extraction method in post-processing
2 participants