2025.1.1

• bugfix for generating and running Feff for XAFS calculations -- fixed PRINT flag
• more error checking in find_e0 for coercing to numpy arrays.
• add spline interpolation option for XAFS re-binning
• updated the binary Installers and GetLarch Installation scripts to use the latest conda/mamba packages.
• some doc updates

Full Changelog:

2025.1.0...2025.1.1

2024.12.0

Main changes:

• Saving Athena File from Larch/Larix now gives files that Athena can read
• CIF and XRD and CIF->Feff.inp conversion has been improved and migrated to the separate larixite project.

Bug fixes:

• make sure multi-column imports sets 'mu' array

• multiple improvements to reading data lines, including respecting allow_dates, allowing semicolon- or tab-delimited lines.kk

• avoid system bell on invalid floats for parameter widgets

• add R^2 to fit stats for pre-edge peak fitting

• add spline option for rebinning xafs (now set as default)

• fix bug when saving athena projects that prevented them to be read by athena.

• make athena project writing for consistency with Athena

• reorder pyFAI imports for Windows

• fix pre_edge docstring

• relax requirement for pymatgen for Py3.9

• using utilities from pyshortcuts where possibie

• xrd1d: fix core-dump on exit, add check for currrent CIF before calculating HKLs

• add larixite as dependency, use dbs and code from there

• using larixite as a separate repo for cif2feff and general CIF/XRD data

• use epicsscan to connect to ScanDB

• better retain datatype when reading column frame data

• fixes for Rixs reader

• fix saving feffit result chi in all spaces

• more dependency version updates, drop Python 3.8

• change license to MIT for consistency with other projects, update requirements

• update to BLISS/HDF5 files

• only set shell wx if LarchWxApp is imported, for whatever reaseon

• fix storing of port for larch_server

• Bug fix for using feff6l and feff8l

• update to Struct2xas v2407 (before refactoring)

• better mapping of unique xtal sites to feff input formatting tweaks

• better saving of chi(q) outputs

• feffit_panel: make sure FT params are used on data

• add support for XAFS pre-edge that is a constant value

• remove dups (and nans) when merging groups

• remove duplicate energies when reading athena projects

• some more fixes for CIF processing

• remove pycifrw from dependencies and github workflows

• github actions now use conda, no longer needing mamba

2024.12.0rc1

many bugfixes

0.9.81

version 0.9.81

0.9.80

Several of the changes here represent the start of an effort to make the Larix GUI more configurable, especially for non XAS tasks, allowing for additional optional Analysis Tasks to be added for certain types of data and analyses. This is a work-in-progress.

General bugfixes:

• allow shorter pre-edge range, selecting by number of energy points (#517)
• fix bug reading very short XDI files (#519)
• remove _larch argument from write_ascii() (#521)
• tweak scaling and fitting tolerances used for XRF fitting.
• scale reconstructed tomography data to have the same mean value as the original sinogram.
• fix many Numpy uses that have been deprecated in Numpy2.
• require Numpy<2, at least until other packages (pymatgen, scikit-image) support it.
• drop requirement for peakutils, add function to reproduce peakutils.peak_indices
• improve debugtime utility, use tabulate module for output.
• add support for Python 3.12, and drop testing of Python 3.8.

Larix features and fixes:

• Feffit Panel: fixes for handling cases with no data, to allow EXAFS simulations without data.
• Feffit Panel: fix plotting individual paths (#515).
• PCA Panel: fix plotting of group with model and other plot variations (#520).
• fix getting config when a datagroup might be missing.
• Add splash screen at startup
• Better placement of Plot window at startup.
• support enabling wx inspection.
• better sizing of results pages, and Parameters windows on all platforms
• reorganize menus to have more drop-down menus with fewer, better organized categories.
• Analysis Panels/Tabs can be re-arranged or removed.
• Analysis Panels can be selected or deselected from the Preferences Menu.
• remove "XY data" (was "raw data") from XAS Normalization Panel
• reading general "XY data" (was "raw data") into separate Panel
• "Spin Arrows" to in/decrement numbers are now acceptably sized on Linux/Gtk3.
• Horizontal Lines are shown on macOS.

XRF Fitting interface:

• fix many display issues, especially on Linux.

0.9.79

Several of the changes here represent the start of an effort to make the Larix GUI more configurable, especially for non XAS tasks, allowing for additional optional Analysis Tasks to be added for certain types of data and analyses. This is a work-in-progress.

General bugfixes:

• allow shorter pre-edge range, selecting by number of energy points (#517)
• fix bug reading very short XDI files (#519)
• remove _larch argument from write_ascii() (#521)
• tweak scaling and fitting tolerances used for XRF fitting.
• scale reconstructed tomography data to have the same mean value as the original sinogram.
• fix many Numpy uses that have been deprecated in Numpy2.
• require Numpy<2, at least until other packages (pymatgen, scikit-image) support it.
• drop requirement for peakutils, add function to reproduce peakutils.peak_indices
• improve debugtime utility, use tabulate module for output.
• add support for Python 3.12, and drop testing of Python 3.8.

Larix features and fixes:

• Feffit Panel: fixes for handling cases with no data, to allow EXAFS simulations without data.
• Feffit Panel: fix plotting individual paths (#515).
• PCA Panel: fix plotting of group with model and other plot variations (#520).
• fix getting config when a datagroup might be missing.
• Add splash screen at startup
• Better placement of Plot window at startup.
• support enabling wx inspection.
• reorganize menus to have more drop-down menus with fewer, better organized categories.
• Analysis Panels/Tabs can be re-arranged or removed.
• Analysis Panels can be selected or deselected from the Preferences Menu.
• remove "XY data" (was "raw data") from XAS Normalization Panel
• reading general "XY data" (was "raw data") into separate Panel
• "Spin Arrows" to in/decrement numbers are now acceptably sized on Linux/Gtk3.
• Horizontal Lines are shown on macOS.

XRF Fitting interface:

• fix many display issues, especially on Linux.

0.9.78

Bug fixes only:

• more fixes for reading in Larix Sessions with Feffit, Pre-edge Peak results.
• Larix Feffit: better recall and fill in FT window parameters and displayed windows for results.
• Larix displays more accurate times in the list of auto-saved sessions.
• better handling of NaNs when importing and sorting XAS data.

0.9.76

Bug fixes, mostly for Larix GUI application

Larix Bug fixes:

• fix critical bug in 0.9.75 for saving and loading projects with lmfit Models, such as pre-edge peak fitting.
• several tweaks and fixes for peak-fitting with step functions, reflecting changes in lmfit 1.3.0
• fixes for scaling non-xas data, including using pin icon to pick scale, and fixes for merging non-xas data
• more safety checks on fit for energy alignment
• use dict.get() with default for plot selection to avoid error messages with broken groups
• remove deleted groups from _xasgroups when loading session that had been cleared

Larch code bug fixes:

• fixes for interpolation data with non-stricly-increasing x
• merge_groups: skip interpolation for raw data with non-increasing x
• find_e0: add sanity checks for handling out-of-strict-order mu(E) data

Doc and Maintenance:

• updated doc to more uniformly refer to Larix as "Larix" or "Larix (was XAS Viewer)".

0.9.75

General

• using miniforge3 and mamba as "normal" installer.
• bash installer properly installs "xraylarch[larix]".
• 1D XRD viewer can use, set, unset mask when reading XRD TIFF images.
• cleanup "plugins", "modules", other out-dated code.
• work towards "XasDataSource" to generalize the API for reading XAS data.
• better reading of ESRF Bliss data.

Jupyter Notebook examples:

• better handling of plotting with plotly_xafsplots now having many more working functions
• add example of plotting XAFS data with wxPython/wxmplot/larch plotting calls
• add Feffit example with Jupyter and plotly.
• update repr_html for Larch group to better display in Jupyter.
• update ReadAthena example.
• add example of reading data and writing Athena Projet files.
• add PCA exmple.
• add example to read Larix Session

XAFS processing improvements:

• improve removing of duplicate energies
• more careful setting of smoothing to fine E0.
• E0 and edge are guessed earlier in the "data installation" phase.
• better remember element/edge from configuration.
• use interpolated univariate spline for cubic spline in interp()
• speed up autobk, delay and separate calculation of delta_chi
• feffit will call autobk_delta_chi() if needed when initializing feffit dataset
• add refine_bkg option to feffit_dataset to allow refining background during fit
• update feffit examples
• add feffit_conf_maps() for making confidence/parameter ellipse maps.
• tweaks to feffit report.
• updates for using lmfit's conf_interval2d()
• continued migration from larch ParameterGroup to lmfit Parameters object.
• hash dataset, use in Path parameter names to make finding expressions more robust
• CIF to Feff: allow seeding RNG to make results with partial occupancy reproducible.
• fixes for use of deprecated scikit-learn function arguments.

Larix Bug Fixes:

• improvements in save/restore of Larix sessions.
• better(?) showing of selection on checkbox select of file.
• more consistent button labels
• deglitching dialog fixes, and now show points that will be removed.
• column_file_reader: add plot selected columns to multicolumn selected on columnfile importer
• normalization_panel: correctly force 'norm' for plots.
• normalization_panel: "auto" normalization polynomial now sets and shows its automated choice.
• normalization_panel: improvements to using "last arguments" used to call XAFS functions to set normalization config
• exafs_panel: fix error with "Copy to Selected"
• exafs_panel: fix error with processing all groups on Select All.
• exafs_panel: add "name and save these plotting options"
• exafs_panel: plot bkg(E) can now show location of E_k0.
• feffit_panel: avoid very slow loading.
• feffit_panel: add warning when rmin goes below rbkg
• feffit_panel: allow specifyitng kweight used for plots.
• feffit_panel: add refine background checkbox, allow plotting of bkg-refined data.

0.9.74

minor bug fixes to 0.9.73:

[Bug Fixes, Code improvements]

• fix release version and date
• fix update link formatting