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Updating branch with main #146

Merged
merged 306 commits into from
Sep 3, 2024
Merged

Updating branch with main #146

merged 306 commits into from
Sep 3, 2024
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Commits on Apr 11, 2023

  1. Merge pull request #82 from usnistgov/summarize-run-performance 

    SST1RSoXSDB: Dramatically improve the performance of `summarize_run`
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Commits on Apr 17, 2023

  1. Updated radius to fix sqrt(2) offset

    @phonghnguyen
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Commits on Apr 18, 2023

  1. Merge pull request #85 from phonghnguyen/fix_radius_WP

    @pbeaucage
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Commits on Apr 24, 2023

  1. Add logo to readme

    @pbeaucage
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Commits on Jul 5, 2023

  1. create initial CMS files

    @andrewjlevin
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  2. add CMSGIWAXSLoader to loader.py

    @andrewjlevin
    andrewjlevin committed Jul 5, 2023
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  3. first attempt at loadSingleImage

    @andrewjlevin
    andrewjlevin committed Jul 5, 2023
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Commits on Jul 6, 2023

  1. add loadMd method

    @andrewjlevin
    andrewjlevin committed Jul 6, 2023
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  2. parameter fix

    @andrewjlevin
    andrewjlevin committed Jul 6, 2023
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  3. wrote loadSeries method

    @andrewjlevin
    andrewjlevin committed Jul 6, 2023
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  4. syntax fix

    @andrewjlevin
    andrewjlevin committed Jul 6, 2023
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  5. add coordinates & minor tweaks

    @andrewjlevin
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  6. syntax

    @andrewjlevin
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  7. syntax

    @andrewjlevin
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  8. round exposure time to 1 decimal

    @andrewjlevin
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Commits on Jul 7, 2023

  1. change default naming scheme from None to []

    @andrewjlevin
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  2. silence draw.load print statements

    @andrewjlevin
    andrewjlevin committed Jul 7, 2023
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Commits on Jul 8, 2023

  1. remove np.flipud and create pg_convert function in GIWAXS.py

    @andrewjlevin
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  2. add GIWAXS.py to util.py

    @andrewjlevin
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  3. time coordinate shows ending time, included in pg_convert output

    @andrewjlevin
    andrewjlevin committed Jul 8, 2023
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  4. syntax fix

    @andrewjlevin
    andrewjlevin committed Jul 8, 2023
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  5. array shaping fix

    @andrewjlevin
    andrewjlevin committed Jul 8, 2023
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  6. array shaping fix

    @andrewjlevin
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  7. added pg_convert_series fxn

    @andrewjlevin
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  8. changed how time dim is handled & added coordinate units

    @andrewjlevin
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  9. fix typo & sortby time

    @andrewjlevin
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  10. sortby series number too

    @andrewjlevin
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  11. syntax

    @andrewjlevin
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  12. series loader fix

    @andrewjlevin
    andrewjlevin committed Jul 8, 2023
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  13. add time units

    @andrewjlevin
    andrewjlevin committed Jul 8, 2023
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  14. undo time unit

    @andrewjlevin
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Commits on Jul 13, 2023

  1. updated util GIWAXS import sytnax

    @andrewjlevin
    andrewjlevin committed Jul 13, 2023
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  2. undoing previous commit

    @andrewjlevin
    andrewjlevin committed Jul 13, 2023
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  3. minor QoL drawmask tweaks

    @andrewjlevin
    andrewjlevin committed Jul 13, 2023
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  4. fixes on previous commit

    @andrewjlevin
    andrewjlevin committed Jul 13, 2023
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  5. more adjustments to drawmask

    @andrewjlevin
    andrewjlevin committed Jul 13, 2023
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  6. more drawmask

    @andrewjlevin
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  7. fix ui to not swap axes, messes up mask arr

    @andrewjlevin
    andrewjlevin committed Jul 13, 2023
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Commits on Jul 14, 2023

  1. added option to load iterables into loadSeries

    @andrewjlevin
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  2. syntax fix

    @andrewjlevin
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  3. another fix, make for iterables

    @andrewjlevin
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  4. added tqdm progress bar

    @andrewjlevin
    andrewjlevin committed Jul 14, 2023
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  5. do not flip masks in pg_convert

    @andrewjlevin
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Commits on Jul 15, 2023

  1. make Transform class for pg functions

    @andrewjlevin
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  2. add Transform to util

    @andrewjlevin
    andrewjlevin committed Jul 15, 2023
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Commits on Jul 17, 2023

  1. updated the Transform class method to accept both .edf and .json files

    Keith White committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. cms-giwaxs-in_situ_processing notebooks

    Andrew Levin committed Jul 18, 2023
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  2. cms-giwaxs-in_situ_processing notebooks take2

    Andrew Levin committed Jul 18, 2023
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  3. adding comments, error handling and delim method variable to loadMd()

    @kewh5868
    kewh5868 committed Jul 18, 2023
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  4. refactored GIWAXS.py Transform class to include generalized load_mask… 

    …() and add_time_coord() methods. previous instance is saved as comments below. Updated CMSGIWAXSLoader() to include a createSampleDictionary() method to construct a sample dictionary from a root_folder, to be able to directly call samples from the stored sample_dict class attribute of the instantiation
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  5. added createSampleDictionary() and selectSampleandSeries() methods to… 

    … the CMSGIWAXSLoader() class to allow the user to autogenerate a sampledictionary and interactively select their sample form metadata information.
    @kewh5868
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  6. updating module imports in cmsgiwaxsloader() class to include correct… 

    …ions
    @kewh5868
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  7. adding save_as_zarr method to the Transform() object, and adding a Pr… 

    …ocess(Transform) subclass to perform 1D azimuthal and boxcut integrations using xarray slice methods (this still needs to be implemented, but placeholder framework is there).
    @kewh5868
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  8. update the Process() class to ProcessData(), and removing inheritance… 

    … from the Transform class. The ProcessData() class constructor should now load a raw_zarr_file_path and pg_transformer object to generate recip_data and caked_data from raw_data if needed. need to add class methods for explicity loading .zarr filesets consisting of exisitng raw, recip and caked .zarr files in complement to one another.
    @kewh5868
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  9. remove corrections module usage

    @kewh5868
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  10. adding error handling for selectsampleandseries and createSampleDicti… 

    …onary() methods
    @kewh5868
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  11. moving return statement

    @kewh5868
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  12. updating selectSampleAndSeries(self) to include quit sequence. updati… 

    …ng CMSGIWAXSLoader() class attribute to include selected sample series list in the initialization
    @kewh5868
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  13. removed "add_time_coord" method as it was broken. only the raw DA con… 

    …tains time and so the the added method is imo not worth the saved coupled of lines
    @andrewjlevin
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  14. Merge branch 'cms-giwaxs-support' of https://github.com/ToneyGroupCU/… 

    …PyHyperScattering into cms-giwaxs-support

add_time_coord fix
    @andrewjlevin
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  15. adding cell on multiple data set loading to the cms-giwaxs_process.ip… 

    …ynb notebook
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  16. added tqdm descriptions for loadSeries & pg_convert_series methods

    @andrewjlevin
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Commits on Jul 20, 2023

  1. Add fix for empty monitors

    @pbeaucage
    pbeaucage committed Jul 20, 2023
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  2. Merge pull request #92 from usnistgov/91_sst1_data_without_monitors 

    Add fix for empty monitors
    @pbeaucage
    pbeaucage authored Jul 20, 2023
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  3. Add flexible logic for finding energy in multiindexes

    @pbeaucage
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  4. added custom energy parameter to Transform

    @andrewjlevin
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Commits on Jul 21, 2023

  1. Add more robustness to energy finding algrithm so it passes tests

    @pbeaucage
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Commits on Jul 22, 2023

  1. Merge pull request #93 from usnistgov/89_integrator_energy_wrong

    @pbeaucage
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  2. remove FileLoader inheritance of CMSGIWAXSLoader

    @andrewjlevin
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Commits on Jul 25, 2023

  1. Merge branch 'usnistgov:main' into cms-giwaxs-support

    @andrewjlevin
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Commits on Jul 26, 2023

  1. added new function "single_images_to_dataset" inside GIWAXS.py, added… 

    … more comments & docstrings
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  2. Merge branches 'cms-giwaxs-support' and 'cms-giwaxs-support' of https… 

    …://github.com/ToneyGroupCU/PyHyperScattering into cms-giwaxs-support
    @andrewjlevin
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  3. add interpolation correction to aforementioned function

    @andrewjlevin
    andrewjlevin committed Jul 26, 2023
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  4. fix save_zarrs option in aforementioned function

    @andrewjlevin
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  5. minor tweak to single_images_to_dataset function zarr saving lines

    @andrewjlevin
    andrewjlevin committed Jul 26, 2023
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  6. typo fixes

    @andrewjlevin
    andrewjlevin committed Jul 26, 2023
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  7. refined example notebooks & added brief readme.txt to CMS tutorial fo… 

    …lder
    Andrew Levin committed Jul 26, 2023
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Commits on Aug 2, 2023

  1. Whack-a-mole changes to fix auto dim hint #94

    @pbeaucage
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  2. Tweaks to multi-polarization AR loading

    @pbeaucage
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  3. Merge branch 'main' into 70-build-tests-for-sst1rsoxsdb-loader

    @pbeaucage
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  4. Merge branch 'main' into 71-sst1rsoxsdb-use_chunked_loading-and-catal… 

    …og_kwargs-incompatible-with-externally-supplied-catalog
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  5. Merge branch 'main' into 56-integratesingleimage-indexing-error

    @pbeaucage
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  6. Merge branch 'main' into 27-datetimes-not-supported-in-loaders-as-ind… 

    …ices
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Commits on Aug 3, 2023

  1. Merge pull request #81 from usnistgov/70-build-tests-for-sst1rsoxsdb-… 

    …loader

add CI tests for sst1rsoxsdb loader
    @BijalBPatel
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  2. Merge pull request #79 from usnistgov/27-datetimes-not-supported-in-l… 

    …oaders-as-indices

Fixes #27 by creating non-varying params in a more reasonable way
    @BijalBPatel
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  3. Merge pull request #80 from usnistgov/71-sst1rsoxsdb-use_chunked_load… 

    …ing-and-catalog_kwargs-incompatible-with-externally-supplied-catalog

SST1RSoXS: error if conflicting constructor arguments are provided
    @BijalBPatel
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  4. Merge pull request #95 from usnistgov/94-bug-sst1rsoxsdb-stapling-too… 

    …-many-indexes-into-multiindex

Fix for #94
    @BijalBPatel
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  5. Delete residual else block from earlier scan logic

    @pbeaucage
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  6. Merge branch 'main' into 56-integratesingleimage-indexing-error

    @pbeaucage
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  7. Update src/PyHyperScattering/PFEnergySeriesIntegrator.py

    @pbeaucage
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Commits on Aug 9, 2023

  1. slight typo fix

    @andrewjlevin
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  2. Merge branch 'usnistgov:main' into cms-giwaxs-support

    @andrewjlevin
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Commits on Aug 11, 2023

  1. Create doc publish workflow

    @pbeaucage
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Commits on Aug 15, 2023

  1. allow maskPath to be a literal numpy ndarray

    @andrewjlevin
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  2. transformer init fix

    @andrewjlevin
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Commits on Sep 4, 2023

  1. Update SST1RSoXSLoader.py 

    Change equality check to assignment
    @J-avery32
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Commits on Sep 6, 2023

  1. Add pip requirements file link to NISTthedocs script

    @pbeaucage
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Commits on Sep 7, 2023

  1. syntax fix pip requirements

    @pbeaucage
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  2. Use newer version of NTD2D

    @pbeaucage
    pbeaucage authored Sep 7, 2023
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  3. Add sphinx rtd theme to dependencies

    @pbeaucage
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  4. Try to fix RTD theme by commenting static dir

    @pbeaucage
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  5. try explicitly including rtd theme

    @pbeaucage
    pbeaucage authored Sep 7, 2023
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  6. Update conf.py

    @pbeaucage
    pbeaucage authored Sep 7, 2023
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  7. Update conf.py

    @pbeaucage
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  8. Update requirements.txt

    @pbeaucage
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Commits on Sep 8, 2023

  1. switch to alabaster

    @pbeaucage
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  2. in progress

    Andrew Levin committed Sep 8, 2023
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Commits on Sep 10, 2023

  1. updated to loader to work for data pre and post cycle 2 2023

    Andrew Levin committed Sep 10, 2023
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  2. update comments

    @andrewjlevin
    andrewjlevin committed Sep 10, 2023
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Commits on Sep 11, 2023

  1. Merge pull request #101 from ToneyGroupCU/main 

    fix for SST1 cycle 2 2023 rsoxs data loading
    @pbeaucage
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  2. Merge branch 'main' into patch-1

    @pbeaucage
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  3. Merge pull request #102 from J-avery32/patch-1 

    Fixed problem where instead of assigning, it checks for equality.
    @pbeaucage
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  4. Merge branch 'main' into update-readme

    @pbeaucage
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  5. Add new docs link to readme and remove readthedocs.

    @pbeaucage
    pbeaucage authored Sep 11, 2023
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  6. remove old theme from requirements

    @pbeaucage
    pbeaucage authored Sep 11, 2023
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  7. Merge pull request #87 from usnistgov/update-readme 

    Switch from ReadTheDocs to NIST Pages docs, and update readme.
    @BijalBPatel
    BijalBPatel authored Sep 11, 2023
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  8. Attempt pydata theme

    Patel authored and Patel committed Sep 11, 2023
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  9. Attempt pydata theme add to requirements

    Patel authored and Patel committed Sep 11, 2023
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  10. Logo on landing page

    Patel authored and Patel committed Sep 11, 2023
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  11. BaselineReorg

    Patel authored and Patel committed Sep 11, 2023
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  12. reorg skeleton

    Patel authored and Patel committed Sep 11, 2023
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  13. Fin skeleton

    Patel authored and Patel committed Sep 11, 2023
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  14. Contributing Above Skeleton

    Patel authored and Patel committed Sep 11, 2023
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  15. fix markdown errors 1

    Patel authored and Patel committed Sep 11, 2023
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  16. fix sphinx errors 2

    Patel authored and Patel committed Sep 11, 2023
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  17. Test without autodoc

    Patel authored and Patel committed Sep 11, 2023
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  18. restore autodoc

    Patel authored and Patel committed Sep 11, 2023
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  19. Attempt SVG Workaround for pdf

    Patel authored and Patel committed Sep 11, 2023
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Commits on Sep 12, 2023

  1. Give up and use png

    Patel authored and Patel committed Sep 12, 2023
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  2. No image

    Patel authored and Patel committed Sep 12, 2023
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  3. added Binder link back

    Patel authored and Patel committed Sep 12, 2023
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  4. SVG only for html

    Patel authored and Patel committed Sep 12, 2023
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  5. Added conf comment

    Patel authored and Patel committed Sep 12, 2023
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  6. Renamed Func, add deprecated stub

    Patel authored and Patel committed Sep 12, 2023
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  7. Troubleshoot summarize_run 1

    Patel authored and Patel committed Sep 12, 2023
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  8. Pin numexpr for CI test

    Patel authored and Patel committed Sep 12, 2023
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  9. add note to numexpr pin

    @pbeaucage
    pbeaucage authored Sep 12, 2023
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  10. Merge pull request #106 from usnistgov/103-rename-summarize_run-to-ma… 

    …tch-tiledbluesky-nomenclature

103 rename summarize run to match tiledbluesky nomenclature
    @pbeaucage
    pbeaucage authored Sep 12, 2023
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  11. Merge branch 'main' into 104-restructure-docs-along-diataxis-framework

    @BijalBPatel
    BijalBPatel authored Sep 12, 2023
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  12. Merge pull request #105 from usnistgov/104-restructure-docs-along-dia… 

    …taxis-framework

Initial NIST Pages Documentation Refresh
    @BijalBPatel
    BijalBPatel authored Sep 12, 2023
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  13. Re-add Peter suggestions I forgot to accept

    Patel authored and Patel committed Sep 12, 2023
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  14. Merge branch '104-restructure-docs-along-diataxis-framework' of https… 

    …://github.com/usnistgov/PyHyperScattering into 104-restructure-docs-along-diataxis-framework
    Patel authored and Patel committed Sep 12, 2023
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Commits on Sep 14, 2023

  1. Fixed Error Handling for integrateImage energy 

    When attempting to integrate data from cycle 2022-2, was getting an
IndexError when integrateImageStack called integrateSingleImage.  The
indexes for finding the energy were switched from what they needed to
be. Perhaps this block of code isn't running for other cycles, or the
index structure is different.

Changes are at lines 62 and 63.
    Camille Bishop committed Sep 14, 2023
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Commits on Oct 2, 2023

  1. Merge pull request #109 from usnistgov/integrateImageStack_energy 

    Fixed Error Handling for integrateImage energy
    @pbeaucage
    pbeaucage authored Oct 2, 2023
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  2. Merge pull request #107 from usnistgov/104-restructure-docs-along-dia… 

    …taxis-framework

104 restructure docs along diataxis frameworkv2
    @pbeaucage
    pbeaucage authored Oct 2, 2023
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Commits on Dec 5, 2023

  1. Rename doc-building action 

    OISM has no sense of humor
    @guyer
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  2. Merge pull request #111 from usnistgov/guyer-patch-1

    @pbeaucage
    pbeaucage authored Dec 5, 2023
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Commits on Mar 6, 2024

  1. Implemented dask backing under use_chunked_loading flag

    @phonghnguyen
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  2. Minor changes to img dimensions from dask_imread

    @phonghnguyen
    phonghnguyen committed Mar 6, 2024
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Commits on Mar 7, 2024

  1. Trying alternative method to convert image to dask array because dask… 

    ….imread.imread does not behave well with subsequent processing
    @phonghnguyen
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Commits on Mar 8, 2024

  1. Finalizing changes to chunk loading for SST1RSoXSLoader after testing

    @phonghnguyen
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Commits on Mar 17, 2024

  1. Apply suggestions from code review

    @pbeaucage
    pbeaucage authored Mar 17, 2024
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  2. Fix numpy/pillow size/shape convention

    @pbeaucage
    pbeaucage authored Mar 17, 2024
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  3. Flip qx/qy which are inverted in pillow/numpy transition

    @pbeaucage
    pbeaucage authored Mar 17, 2024
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  4. Merge pull request #113 from phonghnguyen/SST1RSoXSLoader_chunk_loading 

    Implementing chunk loading for SST1RSoXSLoader
    @pbeaucage
    pbeaucage authored Mar 17, 2024
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Commits on Mar 19, 2024

  1. Update requirements-bluesky.txt

    @pbeaucage
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  2. Merge branch 'main' into 56-integratesingleimage-indexing-error

    @pbeaucage
    pbeaucage authored Mar 19, 2024
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Commits on Mar 20, 2024

  1. Merge pull request #115 from usnistgov/pbeaucage-patch-1

    @pbeaucage
    pbeaucage authored Mar 20, 2024
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Commits on Mar 27, 2024

  1. Add automatic connection to BNL tiled and add Tiled testing using the… 

    … public server.
    @pbeaucage
    pbeaucage authored Mar 27, 2024
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  2. Roll Python versions forward by 1 minor

    @pbeaucage
    pbeaucage authored Mar 27, 2024
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  3. Add tiled install for testing.

    @pbeaucage
    pbeaucage authored Mar 27, 2024
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  4. fix import of module to be tested...

    @pbeaucage
    pbeaucage authored Mar 27, 2024
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  5. exclude tutorial, docs, and all ipynb files from linguist

    @pbeaucage
    pbeaucage authored Mar 27, 2024
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Commits on Mar 29, 2024

  1. Fix typo, was accessing wrong catalog

    @pbeaucage
    pbeaucage committed Mar 29, 2024
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  2. Update dataframe indexing syntax to avoid deprecated usage.

    @pbeaucage
    pbeaucage committed Mar 29, 2024
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  3. Temporarily disable SST1RSoXSDB tests while waiting for public data u… 

    …pload
    @pbeaucage
    pbeaucage authored Mar 29, 2024
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Commits on Apr 2, 2024

  1. Fix bug in #121

    @pbeaucage
    pbeaucage committed Apr 2, 2024
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  2. Add explicit line to avoid new xarray warning

    @pbeaucage
    pbeaucage committed Apr 2, 2024
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  3. Merge pull request #118 from usnistgov/116-feat-natively-support-remo… 

    …te-tiled-connections-to-bnl

`SST1RSoXSDB`: add direct-from-user connections to BNL tiled.
    @pdudenas
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  4. Merge pull request #119 from usnistgov/117-chore-stop-testing-against… 

    …-py37-start-testing-against-py311

Roll Python versions forward by 1 minor
    @pdudenas
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  5. Merge branch 'main' into 121-bug-sst1rsoxsdb-scan-hinting-breaks-if-a… 

    …-scanned-axis-has-negative-value
    @pbeaucage
    pbeaucage authored Apr 2, 2024
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  6. Merge branch 'main' into 120-chore-modify-gitattributes-to-exclude-do… 

    …cs-in-language-stats
    @pbeaucage
    pbeaucage authored Apr 2, 2024
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Commits on Apr 3, 2024

  1. Fix #125

    @pbeaucage
    pbeaucage committed Apr 3, 2024
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  2. Few style and warning fixes

    @pbeaucage
    pbeaucage committed Apr 3, 2024
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  3. Fix import so CI tests work?

    @pbeaucage
    pbeaucage authored Apr 3, 2024
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Commits on Apr 4, 2024

  1. Try to fix import again

    @pbeaucage
    pbeaucage authored Apr 4, 2024
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  2. More robust, duck-friendly type check

    @pbeaucage
    pbeaucage authored Apr 4, 2024
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  3. Merge branch 'main' into 56-integratesingleimage-indexing-error

    @pbeaucage
    pbeaucage authored Apr 4, 2024
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  4. More robust check

    @pbeaucage
    pbeaucage authored Apr 4, 2024
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  5. Merge pull request #123 from usnistgov/120-chore-modify-gitattributes… 

    …-to-exclude-docs-in-language-stats

chore: exclude tutorial, docs, and all ipynb files from linguist
    @BijalBPatel
    BijalBPatel authored Apr 4, 2024
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  6. Merge pull request #126 from usnistgov/125-bug-pfgeneralintegrator-do… 

    …es-not-load-energy-from-a-template-xarray

`PFEnergySeriesIntegrator` bug: fix #125
    @BijalBPatel
    BijalBPatel authored Apr 4, 2024
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  7. Merge branch 'main' into 56-integratesingleimage-indexing-error

    @pbeaucage
    pbeaucage authored Apr 4, 2024
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  8. Merge branch 'main' into 121-bug-sst1rsoxsdb-scan-hinting-breaks-if-a… 

    …-scanned-axis-has-negative-value
    @pbeaucage
    pbeaucage authored Apr 4, 2024
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  9. autoformatter

    @BijalBPatel
    BijalBPatel committed Apr 4, 2024
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  10. Fix to pass in maskpath

    @BijalBPatel
    BijalBPatel committed Apr 4, 2024
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  11. Merge pull request #127 from usnistgov/110-bug-in-loading-image-masks2 

    110 bug in loading image masks2
    @BijalBPatel
    BijalBPatel authored Apr 4, 2024
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  12. Merge branch 'main' into 56-integratesingleimage-indexing-error

    @pdudenas
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  13. Merge branch 'main' into 121-bug-sst1rsoxsdb-scan-hinting-breaks-if-a… 

    …-scanned-axis-has-negative-value
    @pdudenas
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  14. Merge pull request #78 from usnistgov/56-integratesingleimage-indexin… 

    …g-error

Add support for single images in PyFAI integrators
    @pdudenas
    pdudenas authored Apr 4, 2024
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  15. Merge branch 'main' into 121-bug-sst1rsoxsdb-scan-hinting-breaks-if-a… 

    …-scanned-axis-has-negative-value
    @pdudenas
    pdudenas authored Apr 4, 2024
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  16. Merge pull request #122 from usnistgov/121-bug-sst1rsoxsdb-scan-hinti… 

    …ng-breaks-if-a-scanned-axis-has-negative-value

`SST1RSoXSDB`: fix bug described in  #121
    @pdudenas
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Commits on Apr 15, 2024

  1. Tidy up code in PFGeneralIntegrator

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  2. Add zarr saving to fileio

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  3. Change sigma output to unified code that copies dims/coords

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  4. Add ponifile loading to PFGE

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  5. Add edf mask loading to PFGE

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  6. Add missed import

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  7. Rewrite Transform to use PFGeneralIntegrator machinery

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  8. Rename GIWAXS to PGGeneralIntegrator

    @pbeaucage
    pbeaucage committed Apr 15, 2024
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  9. loader: raise error if 'files' is not pathlib.Path or iterable 

    Co-authored-by: Peter Beaucage <github@peterbeaucage.com>
    @andrewjlevin @pbeaucage
    andrewjlevin and pbeaucage authored Apr 15, 2024
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  10. loader: commit 9 suggestions from code review 

    Co-authored-by: Peter Beaucage <github@peterbeaucage.com>
    @andrewjlevin @pbeaucage
    andrewjlevin and pbeaucage authored Apr 15, 2024
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  11. Merge pull request #2 from pbeaucage/pr/100 

    Modify GIWAXS to PGGeneralIntegrator and restructure to use integrator machinery
    @andrewjlevin
    andrewjlevin authored Apr 15, 2024
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Commits on Apr 18, 2024

  1. pin holoviews version

    @pdudenas
    pdudenas committed Apr 18, 2024
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  2. Update env.yml

    @pdudenas
    pdudenas authored Apr 18, 2024
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  3. Merge pull request #136 from usnistgov/135-pin-holoviews-version-to-1… 

    …162-in-requirements-uitxt

135 pin holoviews version to 1162 in requirements uitxt
    @pbeaucage
    pbeaucage authored Apr 18, 2024
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Commits on Apr 23, 2024

  1. fix indentation error

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  2. remove Union syntax in saveZarr function (avoid NameError)

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  3. remove legacy giwaxs import in util.py

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  4. small naming/syntax fixes caught in linting/github test runs

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  5. add PGGeneralIntegrator to integrate.py

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  6. fix naming error for loading pyhyper mask

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  7. remove maskpath argument, so that it only exists in kwargs

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  8. pyfai needs ponifile path input to be a string

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  9. update if statement in ponifile loader

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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  10. add template_xr to ponifile loader for empty masks

    @andrewjlevin
    andrewjlevin committed Apr 23, 2024
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Commits on Apr 24, 2024

  1. add filename as attribute if no md scheme is provided. add unused arg… 

    …uments to loadSingleImage for loadFileSeries compatibility
    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  2. change value comparison to check if img is None in loadFileSeries

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  3. add pygix to requirements

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  4. add file_filter pathlib glob filtering

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  5. file needs to be a string?

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  6. updating, file should be a str of just the filename

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  7. update to how the existing stacking dimension is preserved in integra… 

    …teSingleImage
    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  8. more syntax rearranging to preserve stacking dimension

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  9. consistenty fix, should let loadFileSeries work without needing a fil… 

    …e_filter
    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  10. update single_images_to_dataset function

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  11. update single_image_to_ds function to update incident angle for each … 

    …sample loaded (require incident_angle attribute)
    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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  12. Merge remote-tracking branch 'nist/main' into cms-giwaxs-support

    @andrewjlevin
    andrewjlevin committed Apr 24, 2024
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Commits on Apr 25, 2024

  1. updated time series processing notebook for new branch update

    Andrew Levin committed Apr 25, 2024
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  2. Update main.yml 

    add check-latest: true; attempts at debugging builds not running
    @andrewjlevin
    andrewjlevin authored Apr 25, 2024
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  3. Update main.yml 

    remove python versions 3.8 and 3.9 tests
    @andrewjlevin
    andrewjlevin authored Apr 25, 2024
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  4. remove filetoload argument from a couple mask loaders, already using … 

    …kwargs['maskpath']
    @andrewjlevin
    andrewjlevin committed Apr 25, 2024
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  5. Update requirements.txt; specify version of silx for pygix to work

    @andrewjlevin
    andrewjlevin authored Apr 25, 2024
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  6. update nika mask test

    @andrewjlevin
    andrewjlevin committed Apr 25, 2024
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  7. Merge branch 'cms-giwaxs-support' of https://github.com/ToneyGroupCU/… 

    …PyHyperScattering into cms-giwaxs-support
    @andrewjlevin
    andrewjlevin committed Apr 25, 2024
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  8. logic fix; add single_imgs_to_ds function to a new CMSGIWAXS class in… 

    … IntegrationUtils
    @andrewjlevin
    andrewjlevin committed Apr 25, 2024
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  9. fix missing tqdm import

    @andrewjlevin
    andrewjlevin committed Apr 25, 2024
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Commits on Apr 26, 2024

  1. rearrange order of functions / methods. add more documentation across… 

    … codebase. update tutorial usage readme.txt
    @andrewjlevin
    andrewjlevin committed Apr 26, 2024
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  2. updated cms giwaxs tutorials to reflected updated cms-giwaxs-support

    Andrew Levin committed Apr 26, 2024
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  3. Update requirements.txt: add comment for silx specification

    @andrewjlevin
    andrewjlevin authored Apr 26, 2024
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Commits on Apr 28, 2024

  1. add main.yml wgets & test_CMSLoader.py; also CMS Loader init docstrin… 

    …g update
    @andrewjlevin
    andrewjlevin committed Apr 28, 2024
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Commits on Apr 30, 2024

  1. cmsgiwaxsloader: tidy imports & switch from PIL to fabio for image lo… 

    …ading
    @andrewjlevin
    andrewjlevin committed Apr 30, 2024
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Commits on May 1, 2024

  1. uncomment cmsloader test lines

    @andrewjlevin
    andrewjlevin committed May 1, 2024
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  2. fix: add naming scheme to test loader and correct attribute dim from … 

    …filenames
    @andrewjlevin
    andrewjlevin committed May 1, 2024
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  3. cmsloader: use PIL for tiffs (avoid fabio warning), fabio for anythin… 

    …g else
    @andrewjlevin
    andrewjlevin committed May 1, 2024
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  4. add optional filename md scheme check before making cmsgiwaxsloaders

    Andrew Levin committed May 1, 2024
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Commits on May 2, 2024

  1. move empty template_xr mask creation to __init__, minor dosctring cha… 

    …nges
    @andrewjlevin
    andrewjlevin committed May 2, 2024
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  2. remote init empty mask creation, it's already in pygix integrateSingl… 

    …eImage
    @andrewjlevin
    andrewjlevin committed May 2, 2024
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  3. fix: add empty mask back to calibrationFromTemplateXRParams

    @andrewjlevin
    andrewjlevin committed May 2, 2024
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  4. update tutorial processing notebooks to not used template_xr for inte… 

    …grators
    Andrew Levin committed May 2, 2024
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Commits on May 6, 2024

  1. Merge pull request #100 from ToneyGroupCU/cms-giwaxs-support 

    Cms giwaxs support version 1
    @pbeaucage
    pbeaucage authored May 6, 2024
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