Apm em sprint14 p2 #117
Merged
Apm em sprint14 p2 #117
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
added 15 commits
May 22, 2023 17:21
…, inspect get_display_items_from_nszip.ipynb in em_nion/development for the next steps
…types of display_items from swift and added code for classifying cases on unique NeXus concepts and recovery of dimension scale axes, next steps: i) create mapping table, ii) modify nx classes
…xImageRealSpace, next step i) complete this, ii) carry the code over to reader.py
…ce mapping table and code for interpreting modifiers working, next step, carry over to reader code to get a first nxs example with instances of NxImageRealSpace as event_data_em
…i.e. reads zip file in place and reads from these the individual ndata and hdf5 files in place, next step implement assigning into the template
…a.yaml to pass verification, ii) add default plots, iii) check if nd array correctly arranged
…ot explicit constraining this enough but using the default tzlocal today (5.0) in combination with py3.10 yields problems as tzlocal>4.3 and backport.zoneinfo is not supported any longer, seems that swift developers should use newer zoneinfo syntax
… issue that backports.zoneinfo does not compile with 3.10
…ng, added paths to default, successful linting and mypy, next step add and test the standalone ipynb for running the em_nion reader and ask Benedikt for permission to upload the multimodal imaging dataset so that we can make a complete nomad example
…opment ipynbs for em_nion
… upload example from Benedikt and i) upload zenodo reference, ii) test with nomad
|
From my side I am waiting now for Benedikt to grant permission for uploading the example file, in the meantime I continue testing this with nomad, please observe that the definitions have been updated also to point now to the latest (permission was happily granted by Benedikt and data were uploaded on Zenodo https://doi.org/10.5281/zenodo.7979668 |
|
Timeout from coveralls :( |
|
Please check if the updated dependencies still work with the dependencies in nomad before merging this. Doing this currently based on the nomad-FAIR update-north branch, current situation is that this works I push relevant changes from this testing to the following branch update-north-markus |
sanbrock
requested changes
May 26, 2023
...s/data/dataconverter/readers/apm/nomad_oasis_eln_schema_for_nx_apm/nxapm.schema.archive.yaml
Show resolved
Hide resolved
Just checked this in the nomad/update-north-markus branch and the requirements are successfully generated 👍️
|
domna
reviewed
May 30, 2023
|
This line will probably fail in nomad: pynxtools/pynxtools/nexus/nexus.py Line 1225 in 9143bc0 Should be: This is fixed in master already. So after merging this it should be fine (but the respective MR in nomad with this branch will fail). |
added 3 commits
May 30, 2023 18:53
…branch of nomad integrated, also missing link to Benedikts dataset for the new em_nion reader added in the standalone example ipynb
sanbrock
approved these changes
May 30, 2023
RubelMozumder
pushed a commit
that referenced
this pull request
Jun 28, 2023
* Initial commit new em_nion swift project reader * Added code for parsing nsproj, ndata, and h5 file metadata from nszip, inspect get_display_items_from_nszip.ipynb in em_nion/development for the next steps * Added remaining examples from Benedikts Nion session and image concept dict * Added code for analyzing which metadata come with specific different types of display_items from swift and added code for classifying cases on unique NeXus concepts and recovery of dimension scale axes, next steps: i) create mapping table, ii) modify nx classes * Added close to jsonmap_reader mapping table exemplarily for concept NxImageRealSpace, next step i) complete this, ii) carry the code over to reader.py * Time zone converting from swift local time to utc and NxImageReaslSpace mapping table and code for interpreting modifiers working, next step, carry over to reader code to get a first nxs example with instances of NxImageRealSpace as event_data_em * Parser skeleton carried over from ipynb to reader.py tested working, i.e. reads zip file in place and reads from these the individual ndata and hdf5 files in place, next step implement assigning into the template * Support for NxImageRealSpace implemented, next steps i) parse eln_data.yaml to pass verification, ii) add default plots, iii) check if nd array correctly arranged * Mapping table for concept eels * Added generic ELN loading * CI fixes, intentional downgrading of tzlocal to 4.3 as nionswift is not explicit constraining this enough but using the default tzlocal today (5.0) in combination with py3.10 yields problems as tzlocal>4.3 and backport.zoneinfo is not supported any longer, seems that swift developers should use newer zoneinfo syntax * Generated dev-requirements within py310 to check if one can avoid the issue that backports.zoneinfo does not compile with 3.10 * Fixed buges with 3d axes, fixed default plotting, and instance indexing, added paths to default, successful linting and mypy, next step add and test the standalone ipynb for running the em_nion reader and ask Benedikt for permission to upload the multimodal imaging dataset so that we can make a complete nomad example * integrated changes from testing with local NOMAD OASIS, removed development ipynbs for em_nion * added standalone ipynb, updated all other standalone ipynb, next step upload example from Benedikt and i) upload zenodo reference, ii) test with nomad * Feature-development closed and feedback from tests with update-north branch of nomad integrated, also missing link to Benedikts dataset for the new em_nion reader added in the standalone example ipynb * Removed nionswift_tool as it seems that this is not called * Removed deprecated distutils for setuputils * More robust locating of NXtest example appdef * fixing linting error toomanylocals * Resolve merge conflict * Fix merge conflict --------- Co-authored-by: markus.kuehbach <markus.kuehbach@hu-berlin.de>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
No description provided.