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Reformatting generation scripts #15

Merged
merged 8 commits into from
May 28, 2020
Merged

Reformatting generation scripts #15

merged 8 commits into from
May 28, 2020

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vigji
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@vigji vigji commented May 28, 2020

Here's my take at writing some utility functions to keep atlases consistent.

I have updated only the test_atlas.py script, so have a look at that for the current state of atlas generation! I hope that the flow is fully descripted there.

Random notes:

  • The generation of the readable files we were discussing is still not addressed, I am happy if you want to take care of that!
  • I thought that it might also be good to enforce consistency on the reference and annotations stacks. What do you think?
  • Some controls might be a bit tight and could be tested/handled better. But deciding those things require some crash tests so let me know what you think trying them out
  • I cleaned out the allenSDK dependency, @FedeClaudi feel free to improve structure classes for your taste :)
  • tests are still not updated;
  • I did some try at automatic docs conversion using pyment and I was positively impressed. Moving the doc style of entire packages should require only some fixing here and there, so I would definitively keep numpydoc style for the project

@FedeClaudi
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Looks good, it will have to be integrated with
#14 (comment)

and

https:/brainglobe/atlas-scripts/pull/1#issue-424342060

but it should be fairly easy

@adamltyson
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To be clear, are we scrapping atlas-scripts, and keeping everything together in this repo? In which case, can we have tools like allensdk as optional dependencies (we could just stick them into the [dev] group.

I removed the allensdk dependency in #14, so I propose that:

@adamltyson
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Dammit Fede beat me to it

@adamltyson
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Once these are merged (and if you guys ever stop working), I'll start to work on:

@vigji
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vigji commented May 28, 2020

To be clear, are we scrapping atlas-scripts, and keeping everything together in this repo? In which case, can we have tools like allensdk as optional dependencies (we could just stick them into the [dev] group.

Yep, makes perfect sense!

Well, sorry for the overlaps, I hope that as things grow the niches get more separated :D

@FedeClaudi
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Automatic generation of this other mouse atlas

Yes please!

Well, sorry for the overlaps, I hope that as things grow the niches get more separated :D

No worries, it's bound to happen as we are all working on this at the same time.

@FedeClaudi
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Let's archive https:/brainglobe/atlas-scripts once we have finished merging everything?

@adamltyson
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Let's archive https:/brainglobe/atlas-scripts once we have finished merging everything?

agree

@vigji vigji merged commit 41d803d into master May 28, 2020
@vigji
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vigji commented May 28, 2020 •
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Let's archive https:/brainglobe/atlas-scripts once we have finished merging everything?

agree!

@FedeClaudi
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are the latest changes to atlas-scripts integrted here or do you need me to move stuff over?

@vigji
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vigji commented May 28, 2020

No, I think you would need to move stuff over, there's only the allen and the zebrafish scripts right now

@vigji
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vigji commented May 28, 2020

On a different note, I added the config file for configuring the pre-commits hooks according to these instructions.
To install them it should be enough to do pre-commit install in the project dir. There's black formatting and flake8, with a previsionary but expandable list of exceptions.

@adamltyson
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On a different note, I added the config file for configuring the pre-commits hooks according to these instructions.

This looks to work well. We should add flake8 tests to the test script too.

@adamltyson adamltyson mentioned this pull request May 28, 2020
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@vigji vigji deleted the reformatting_generation_scripts branch August 21, 2020 10:58
willGraham01 pushed a commit that referenced this pull request Feb 14, 2024
@FedeClaudi @vigji
Mesh cleaning improvements (#15)
4384efb 
* gitignore: added vscode

* gitignore: added vscode

* added rich fancy traceback for easier debugging

* replaced mesh cleaning with decimation

* pre-commit cleanup

* added TEST mode to atlas creation

* added smoothing options to all atlas gen scripts

* removed ratlas.py since outdated and theres a better atlas

* atlas gen update

* added smoothing and decimation to adult zebrafish atlas

Co-authored-by: Luigi Petrucco <[email protected]>
willGraham01 added a commit that referenced this pull request Feb 23, 2024
@willGraham01 @vigji
@adamltyson @MathieuBo @bkntr @kailynkfields @FedeClaudi @Gubra-ApS @JohannaPerens @yoda-vid @samclothier @JoeZiminski @novafae @dstansby @pre-commit-ci @alessandrofelder @viktorpm
Merge with atlasgen (#199)
e34a84a 
* Initial commit

* Update README.md

* First commit

* gitignore

* Almost at complete atlas autogeneration

* Finalized script for automatic atlas generation

* Added template script for atlas generation

* Template description

* First working version of script for auto deployment

* Fixed metadata link

* Trying to fix windows permission error when deleting folders

* add 50um to allen mouse

* v1.2 for allen mouse

* blacked

* Update requirements

* vtkplotter -> vedo

* Format with black

* Update kim mouse atlas generation

* Improve downsampling

* revert roations

* add kim to main script

* rotate annotation volume for meshes

* add osten mouse atlas

* Added function for creating intermediate hierarchy structures masks

* Fix extract_largest_region and compare_mesh_volume

* reformat with black

* save additional metadata

* consistent syntax for empty dict

* Update docstring

* Add atlas packager metadata

* python 3.8 compatibility

* Add mouse spinal cord atlas

* add WHS SD Rat atlas

* add xmltodict to requirements.txt

* remove structures that are missing from annotation volume

* remove structures that are missing from annotation volume

* Fixed vedo Slicer import issue

* Update mesh_utils.py

* Create azba_zfish.py

* Standardise temporary output directory

* add [allenmouse] extra dependency (#17)

* Allow multiple downloads at once, updated citation

* Mesh cleaning improvements (#15)

* gitignore: added vscode

* gitignore: added vscode

* added rich fancy traceback for easier debugging

* replaced mesh cleaning with decimation

* pre-commit cleanup

* added TEST mode to atlas creation

* added smoothing options to all atlas gen scripts

* removed ratlas.py since outdated and theres a better atlas

* atlas gen update

* added smoothing and decimation to adult zebrafish atlas

Co-authored-by: Luigi Petrucco <[email protected]>

* Update azba_zfish.py

Changing the reference file to be af and the additional references to be topro

* some fixes for mpin atlas

* Fix tiny typo (#22)

* Update README.md

* Add lsfm atlas script (#18)

* Update lsfm mouse atlas script

* 2nd update LSFM mouse atlas script

Co-authored-by: Johanna <[email protected]>
Co-authored-by: Johanna Perens <[email protected]>

* Update requirements.txt

* Add ADMBA 3D developing mouse atlases (#25)

* Add ADMBA 3D developing mouse atlases

Extend the `mouse_e15_5` script by @pr4deepr to build all the atlases in the 3D reconstructed version of the Allen Developing Mouse Brain Atlas series. This build script is essentially the same except for the addition of a data class to configure the atlas parameters, which is implemented for each atlas.

* Fix atlas orientation to LSA

Change the input orientation to LSA to fit the NumPy convention used in BrainGlobe. Add docstrings describing the orientation and resolution assumptions in the configuration data class.

* Update package authors

* Add script for the Princeton mouse brain atlas. (#27)

* Added atlas generation script for the Princeton mouse brain atlas. Modified mesh_utils.py for fix.

* Modified atlas minor version, changed atlas orientation, and removed unnecessary html fetch of region hierarchy.

* Finalised atlas minor version.

Co-authored-by: Sam <[email protected]>

* KimLabDevCCFv001 (neuroinformatics team form) (#31)

* Create KimLabDevCCFv001.py

* Update KimLabDevCCFv001.py

* Update and rename KimLabDevCCFv001.py to KimLabDevCCF.py

* Update KimLabDevCCF.py

* first commit

* updated up to mesh creation, working through VTK type error

* kimlabdevccf working version 1 reference only

* rename atlasgen file

* start adding additional references

* add filenames for additional references

* fix unfinished handling of multi-templates

* update pre-commit black version to fix error with _unicode fun import from click

* tidy and install pre-commit

* fix change of plotter I erronoeusly made when using older python version

* testing kim atlsa with additional references

* Update requirements.txt

* add loguru requirement (at least windows 10)

* fix VTK type error

* remove path

* remove test code

* update to new download dir

* used to run atlas

* update atlas code for general use

* remove standard tempalte from additional references

* further clean up

* edit to run in single script

* fix False flag used to not run meshes

* get working on UNIX

* use PARALLEL and update atlas name

* update template key STP to stp

Co-authored-by: NovaFae <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>

* Add testing config (#35)

* Add testing config

* Specify branchs for workflow trigger

* Bump pre-commit versions

* Fix cov flag

* Run black on code base

* Clean up requirements

* Move requirements to setup.py

* Fix setup.py black

* Replace brainglobe with NI actions (#37)

* Use pyproject.toml

* Update supported Python metadata

* Clean manifest check

* Remove cibuildwheel config

* Catch warnings during tests (#39)

* Add standard pre-commit config (#40)

* Add standard pre-commit config

* Add automated pre-commit fixes

* Ignore line too long

* Fix branches that CI is run on (#42)

* Update link (#48)

* [pre-commit.ci] pre-commit autoupdate (#49)

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* Update to newer vedo API (#58)

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* scale mesh points before mapping to new anatomical space (#62)

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* [pre-commit.ci] pre-commit autoupdate (#95)

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* draft validation functions (#90)

* draft validation functions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* run on all atlases, don't crash on assertion error

* fixing atlas path

* Clearer output printing

* tidy up validation script, remove weird test_git

* add dev install, make test structure, initial tests

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* restructuring validate_mesh_matches_image_extents function, adding comments

* testing expected files and  meshes directory separately

* looping through validation functions and parameters to catch individual errors

* removing hard coded path, generalising to all atlases

* adding successful_validations list

* tidying up duplications

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* addressing Niko's final comments, cleaning code

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* Structure validation (#110)

* draft validation functions

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* fixing atlas path

* Clearer output printing

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* checkout finished validate_atlases.py from validation branch

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* adding assertion to validate_mesh_structure_pairs function

* checking IDs via bg_atlasapi, checking if IDs have mesh files and accesible through the atlas

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* simplify validation function (#113)

* simplify validation function

- all validation functions just take an atlas object
- means we don't need a parameters list
- also simplify output list to be dicts of lists mapping the atlas name to values

- another advantage of this is that it simplifies mocking of atlas functions in the tests

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* bg-atlasapi -> brainglobe-atlasapi

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* Revert "Prepare for merge and rename (#198)"

This reverts commit 9d5317d.

* Update pyproject.toml

Co-authored-by: Alessandro Felder <[email protected]>

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Co-authored-by: Luigi Petrucco <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Mathieu <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Ben Kantor <[email protected]>
Co-authored-by: Kailyn Fields <[email protected]>
Co-authored-by: Federico Claudi <[email protected]>
Co-authored-by: Gubra-ApS <[email protected]>
Co-authored-by: Johanna <[email protected]>
Co-authored-by: Johanna Perens <[email protected]>
Co-authored-by: David Young <[email protected]>
Co-authored-by: Sam Clothier <[email protected]>
Co-authored-by: Sam <[email protected]>
Co-authored-by: Joe Ziminski <[email protected]>
Co-authored-by: NovaFae <[email protected]>
Co-authored-by: David Stansby <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>
Co-authored-by: viktorpm <[email protected]>
Co-authored-by: alessandrofelder <[email protected]>
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@vigji @FedeClaudi @adamltyson