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various improvements july26 - #59

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dp/various_xas_improvements_july26
Open

various improvements july26#59
DanPorter wants to merge 12 commits into
mainfrom
dp/various_xas_improvements_july26

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@DanPorter

@DanPorter DanPorter commented Jul 31, 2026 •
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Various improvements and fixes, plus additions to the documentation and examples.

Alignment for XAS Spectra

ROI definition improvements

  • add_roi added to Experiment
  • Locally defined rois are now propagated properly
  • additional documentation and examples added (Fix for document ROI functionality #51 )

2D mesh grids

NexusScan Time functions

  • add NexusScan.start_end_duration()
  • add default to NexusScan.times()
  • add NexusScan.get_scan_time()
  • add get_file_time() to file_functions.py
  • add use_time option to ExperimentPlotManager.metadata

NexusScan improvements

  • NexusScan.scans() can now accept NexusScan as input, preserving the local_data and namespace
  • add NexusScan.get_max_index()

DanPorter added 12 commits July 28, 2026 11:22
@DanPorter
add i16 xsp3 examples
1a850ed
@DanPorter
add alignment to xas spectra
e07f28e 
## spectra_analysis.py
 - add find_shift

## spectra.py
 - add shift()

## spectra_container.py
 - add align_spectra to average and subtraction
 - add plot()

## tests
 - add tests
@DanPorter
add ROI to i16 vortex spectra
89963ca 
## hdfmap_generic.py
 - add ROI_SUFFIXES

## nexus_scan.py
 - add rois()

## nxxas_loader.py
 - add custom ROI on i16 vortext load.
@DanPorter
Experiment updates
86e6449 
## experiment.py
 - replaced _scan_numbers with all_scan_numbers
 - allow scans to be loaded from NexusScan objects
 - add get_scan_number()
 - add get_nearby_scan_numbers()
 - improved find_scans
 - add get_value_changes()

Add examples and tests.

All tests pass.

## xas/container_functions.py
 - add find_similar_measurements
@DanPorter
fix tests
fdad899
@DanPorter
add docs for ROIs
56b1507 
Fix for #51
@DanPorter
add get_max_index to NexusScan
8ee3996 
Also add tests for NexusScan and improve doc strings
@DanPorter
improve NexusScan time functions
3b5908a 
## nexus_scan.py
 - add NexusScan.start_end_duration()
 - add default to NexusScan.times()
 - add NexusScan.get_scan_time()

## file_functions.py
 - add get_file_time()

## exp_plot_manager.py
 - add use_time option to ExperimentPlotManager.metadata
@DanPorter
add 2D grid mesh and example
fb760e8 
## surface_grid.py
 - add algorithms for creating 2D mesh from coordinates
 - Fix for issue #49
 - add test to test_utils.py

## experiment.py
 - add option to Experiment.generate_mesh

## example_2d_surface_scans.py
 - add example
 - fix for #50

All tests pass.
@DanPorter
Improve examples
b95048f 
## nexus_scan.py
 - add NexusScan.replace_default_names()

## misc_functions.py
 - add multi_replace()

## fit_functions.py
 - add guess for model_fit()

## fitting/results.py
 - add yinit parameter

## Examples
 - improve example_peak_fits.py
 - improve peak_fitting.md
 - add example_peak_fits2.py as old version
@DanPorter
Improve examples
0ca898b 
## nexus_scan.py
 - add NexusScan.replace_default_names()
 - change to NexusScan.get_plot_axis() to include expressions.

## misc_functions.py
 - add multi_replace()

## fit_functions.py
 - add guess for model_fit()

## fitting/results.py
 - add yinit parameter

## Examples
 - improve example_peak_fits.py
 - improve peak_fitting.md
 - add example_peak_fits2.py as old version
@DanPorter
Merge remote-tracking branch 'origin/dp/various_xas_improvements_july…
c0d3efb 
…26' into dp/various_xas_improvements_july26

# Conflicts:
#	mmg_toolbox/nexus/nexus_scan.py
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@DanPorter