Permalink
Comparing changes
Choose two branches to see what’s changed or to start a new pull request.
If you need to, you can also or
learn more about diff comparisons.
Open a pull request
Create a new pull request by comparing changes across two branches. If you need to, you can also .
Learn more about diff comparisons here.
...
- 14 commits
- 62 files changed
- 10 contributors
Commits on May 9, 2023
-
DEBUG: Deleting intermeadiate generated file. (#109)
Co-authored-by: RubelMozumder <rubelmozumder@outlook.com>
Commits on May 19, 2023
-
Transmission reader: Fixes reading of detector ranges (#112)
* Fixes reading of detector ranges * Make linting happy
Commits on May 23, 2023
-
Full visit and support for attribute inheritances (#113)
* replace the use of built-in recursive visititems by a full_visit which visits the objects again if connected to different concept * linting * fix test reference for MPES * Support for annotating an hdf_node when referenced not only in its default path. Hence, hdf_node can be annotated based on a new parameter hdf_path added alongside in a dict hdf_info. note that hdf_root can also be added in future when data is linked from multiple files * changing input parametes for get_inherited_nodes to enable hash based caching * reflect changes in definitions to test reference file * 0.000 for the newly appearing analyser/data * linting * elist (inheritance chain) support for attributes, too * better printing of attribute inheritance and support for attributes using the option --concept * fixing the merge
Commits on May 25, 2023
-
Ellips reader attribute issues (#115)
* Update writer.py trying to fix issues with writing attributes * testing writing attributes to plot(NXdata) * fix for adding units to existing elements * Updated reader to be consisent with NXellipsometry * fixing pycodestyle errors in reader * fixing pycodestyle errors in reader * fixing pycodestyle errors in reader * fixing pylint errors * removed redundant backslash --------- Co-authored-by: Sandor Brockhauser <sandor.brockhauser@xfel.eu>
Commits on May 26, 2023
Commits on May 30, 2023
-
Fixes interface for failing nomad tests (#119)
* Fixes interface for failing nomad tests * Fixes linting * Allow input file name to be a list or a str
Commits on May 31, 2023
Commits on Jun 1, 2023
-
Reader for native SPECS SLE format (#110)
* Add reader for .sle XPS files (SPECS Prodigy) Initial commit for XPS reader for SLE files (native format of SPECS Prodigy) - Add sle_parsers which read the schedule (as xml) as well as the data from the SLE datafiles (which are SQLlite databases) - Implement interface in dataconverter/xps/reader_utils for SLE readers for different versions of .sle files Currently missing: - mapping from output format of parse_file method of the different SleParsers to get_dict method of parse_xml of XML reader -> SleParser output cannot be mapped to Nxmpes at the moment * Pylinting, minor naming updates * Map from SleParser to common format The output of the SleParsers is a flattened list of dictionaries, which each dict containing the data and metadata of one spectrum (including the individual channel scans). This list is mapped to a dictionary that has a similar structure as the output of the XmlSpecs parser, which can then be used to write the nxmpes structure using config files. * Small updates to SleParsers - Individual channel scans are stored in the data field of the spectrum dictionaries - Fix some data type errors during reading - Read out transmission data. Note: Channel readout and calibration is currently not working ( see method _get_calibrated_data). Therefore, the "calibrated" data is currently just the scan of the first channel. * Small changes to reader.py, multiple config files - Restructure CONVERT_DICT - Add "NXmpes_xps" to supported NXDLs - Config files: either the config files in the xps folder are used (based on the file extension of the input) or a config file can be explicitly passed during the reading * Fix error in transmission data parsing - Read both TF data and the file it was stored in. * Allow kwargs passing to the SleParsers * Small update to config file parsing * Pycodestyle linting * Temporarily remove NXmpes_xps from supported_nxdls Since there is no NXDL for the NXmpes_xps application definition, the pytests are failing. Temporarily remove it until NXDL is available. * Implement abstractmethod for flattening XML Different SLE parsers have different xml schedules. Implement abstractmethod for abstract SleParser base class. * pylinting * Linting * some more linting * Mypy changes
-
* 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>
-
Ellips reader and eln_data (#120)
* Reader for NXellipsometry(NXopt) * mock function for NXellipsometry(NXopt) * eln_data.yaml for NXellipsometry(NXopt) * New reader for NXellipsometry(NXopt) * Update mock.py * indentation * indentation * Update mock.py * Update mock.py * Updated metadata file to be consistent with new NXellipsometry * corrected some pycodestyle errors in the reader * corrected some pycodestyle errors * indentation * shortened lines * Added argument to FlattenSettings used in ellips reader * correcting some pylint errors * pycodestyle problems * Update reader.py * Update reader.py * Update reader.py * label function * removing err_labels * fixing header_labels args * Update reader.py * derived prms * data array functions * Update reader.py * removing unused argument header * Update reader.py * Update reader.py * removed blocks from config keys * update eln_data file * changing ang. spread unit * Corrections in the reader * Renamed black_list to ignore_keys * moved import math * Updating reader to be consistent with new eln * new eln file * Updated writer to handle attributs in ellips reader * updating definitions * Update pynxtools/dataconverter/readers/ellips/reader.py Co-authored-by: Florian Dobener <florian.dobener@physik.hu-berlin.de> * Updates eln_data to nomad generated one * Fixes key mapping --------- Co-authored-by: Florian Dobener <florian.dobener@physik.hu-berlin.de>
Loading
This comparison is taking too long to generate.
Unfortunately it looks like we can’t render this comparison for you right now. It might be too big, or there might be something weird with your repository.
You can try running this command locally to see the comparison on your machine:
git diff v0.0.2...v0.0.3