beamtime/nappFileList.m
- Fix h5 LensMode: translate numeric codes to descriptive text (e.g. 1 ->
T_HiPPHAXPES) to match what .ibw files already store, applied across all
three h5read fallback branches, not just the oldest-format one
beamtime/nappGenerateSpectra.m
- Bug fixes
beamtime/nappPlot.m
- Bug fixes
import/importData.m (new)
- Ground script for one beamtime: import (nappFileList,
nappGenerateSpectra), sample/spot and photon-energy assignment per row
range, campaign metadata (CustomProperties) and column
descriptions/units set inline, tidy-up, and export to .csv/.mat/.h5
(via nappExportH5). Leaves FileList in the workspace for PublishReport.m
and callOpenbisSync.m to run against afterward.
import/nappExportH5.m (new)
- Export FileList + campaign metadata + raw source files to a
self-contained HDF5 archive
- Low-level HDF5 API (H5F/H5G/H5D/H5A/H5T/H5S/H5P) to fix
H5FD_truncate/"too many open files" errors from the top-level
h5create/h5write functions each reopening the file internally
- Explicit rowIndex attribute per row group, since HDF5 group listing
order isn't guaranteed to match table row order
openBIS/ (new)
- nappSyncToOpenbis.py, callOpenbisSync.m, testpybis.m, README.md
- openBIS sync pipeline: create-or-update per row matched by $name,
correct lowercase property codes, timestamp formatting, parent linking,
raw file upload, plot/photo/video thumbnail embedding, config/engine
split for maintainability -- see README.md for full details
* Transitioned nappNorm, nappDetermineShift, and nappCopyShift to use modern MATLAB arguments blocks, removing their legacy functionSignatures.json entries.
* Refactored nappNorm to rely on prior peak fitting results (e.g., from nappFitGaussXps) for normalization rather than performing the fitting internally.
* Decoupled energy calibration: nappDetermineShift now solely calculates internal binding energy shifts, and nappCopyShift distributes them using a unified matching engine ('earlier', 'after', 'spectrumNumber').
* Implemented a Universal Logging Block to track data provenance, automatically appending execution timestamps and caller script names to processed rows.
* Updated nappCombineSpectra to output a logDataSource cell array and cleanly name combined spectra.
* Created nappSaveDataTable for automatic, script-named .mat file saving, complete with a Live Editor interceptor.
* Added a publish-mode silencer to nappFitGaussXps to prevent optimizer spam in generated PDFs.
* Updated readme.md to document the new arguments structure, the 3-step calibration workflow, the matching engine, and the new table variables.
Both Scienta (.ibw) and SpecsLab (.xy) raw files capture multidimensional XPS data but use different terminology to structure it. Scienta uses "Region Iterations" and "Sequence Iterations". SpecsLab organizes data by "Groups" or "Regions" (different elemental energy sweeps), "Scans" (time-resolved repetitions), and "Curves". Scienta Region Iterations are automatically averaged to improve the signal-to-noise ratio, while Scienta Sequence Iterations and SpecsLab Scans are preserved to keep the time-resolved data. For SpecsLab files specifically, distinct Regions are split into separate table rows. Ultimately, the preserved time-resolved data is saved in the table's image variable as a 2D matrix ([Energy bins × Sequence iterations/Scans]).
File type handling: Added .xy as a recognized XPS format. Currently, the script differentiates data types strictly by file extension (NEXAFS: .h5, XPS: .ibw and .xy). This extension-based differentiation needs to be improved in future updates.
Metadata parsing: Implemented global header scanning for .xy files to correctly extract instrument parameters (Acquisition Mode, Lens Mode, Slit, Workfunction) located before the first region block.
Timezone alignment: Added timestamp conversion for .xy files from UTC to local time (Europe/Zurich) to ensure synchronization with LabView logs.
Region separation: Modified .xy parsing to append a _RegX suffix to filenames. This correctly splits single .xy files that contain multiple elements or energy sweeps into distinct table rows so they can be processed individually.
Import efficiency: Added an originalFileName variable. The script now cross-references the input DataTable and skips files that have already been imported to reduce execution time on re-runs.
Testing status: Processing of .xy data has currently only been tested and debugged with nappGenerateSpectra and nappPlot. Compatibility with other functions in the suite remains untested.
bartels-rausch
florez_j