Extend MRC to Nexus converter to work with TVIPS #300
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Extend ED_mrc_to_nexus command to work with TVIPS cameras (besides eBIC Ceta-D detector). The command now has an option --detector that could be set either to cetad or tvips.
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
noemifrisina
reviewed
Feb 3, 2025
Collaborator
noemifrisina
left a comment
noemifrisina
left a comment
There was a problem hiding this comment.
Lgtm, thanks. Definitely much tidier with one command line tool.
I added a couple of comments but nothing big.
Please rebase on top of main before merging - although there shouldn't be any conflicts.
Also, a lot of bits in the code look to be unformatted, could you please run pre-commits on them?
| parser.add_argument( | ||
| "--detector", | ||
| type=str, | ||
| default="cetad", |
Collaborator
There was a problem hiding this comment.
You can add a choices=["cetad", "tvips"] option to the argument so that it will accept only those values and show them as part of the help.
src/nexgen/tools/mrc_tools.py
Outdated
| return n, out_file, np.array(angles) | ||
| else: | ||
| msg = "The converter expects either a list of MRC images\n" | ||
| msg = "or a single MRC file with a stack of images." |
Collaborator
There was a problem hiding this comment.
I think this is complaining because the next msg is missing a '+'
src/nexgen/tools/mrc_tools.py
Outdated
| import numpy as np | ||
|
|
||
|
|
||
| def cal_wavelength(V0): |
Collaborator
There was a problem hiding this comment.
Could: add some typing to these functions?
Also it would be good to have a couple of tests...
Bumps [h5py](https://github.com/h5py/h5py) from 3.11.0 to 3.13.0. - [Release notes](https://github.com/h5py/h5py/releases) - [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst) - [Commits](h5py/h5py@3.11.0...3.13.0) --- updated-dependencies: - dependency-name: h5py dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Noemi Frisina <54588199+noemifrisina@users.noreply.github.com>
Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.10.3 to 2.11.4. - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@v2.10.3...v2.11.4) --- updated-dependencies: - dependency-name: pydantic dependency-version: 2.11.4 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [numpy](https://github.com/numpy/numpy) from 2.2.2 to 2.2.6. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v2.2.2...v2.2.6) --- updated-dependencies: - dependency-name: numpy dependency-version: 2.2.6 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update pydantic things * A start and some notes * Replace old namedtuples * Start rethinking parameter model * Add utility function to be used by nexgen server for serial * Update changelog * Fix test * Add a couple of dumb tests * Tidy up where possible * For now comment out before refactoring * Pass timestamps as datetime * Replace deprecated function * Fix iso timestamp bug and add test * Improve validation * Small test detail * Small improvements on general writer * Tidy ups * Update changelog * Start adding to CLI to make it nicer * Update command line for i19 * Update changelog * Add docstring * Fix typo
noemifrisina
approved these changes
May 20, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Extend ED_mrc_to_nexus command to work with TVIPS cameras (besides eBIC Ceta-D detector). The command now has an option --detector that could be set either to cetad or tvips.