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Cms giwaxs support version 1#100

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pbeaucage merged 127 commits intousnistgov:mainusnistgov/PyHyperScattering:mainfrom ToneyGroupCU:cms-giwaxs-supportToneyGroupCU/PyHyperScattering:cms-giwaxs-supportCopy head branch name to clipboardMay 6, 2024

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Commits

Commits on Jul 5, 2023

• create initial CMS files

  andrewjlevin

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• add CMSGIWAXSLoader to loader.py

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• first attempt at loadSingleImage

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Commits on Jul 6, 2023

• add loadMd method

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• parameter fix

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• wrote loadSeries method

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• syntax fix

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• add coordinates & minor tweaks

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• syntax

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• syntax

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• round exposure time to 1 decimal

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Commits on Jul 7, 2023

• change default naming scheme from None to []

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• silence draw.load print statements

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Commits on Jul 8, 2023

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

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• add GIWAXS.py to util.py

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• time coordinate shows ending time, included in pg_convert output

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• syntax fix

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• array shaping fix

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• array shaping fix

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• added pg_convert_series fxn

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• changed how time dim is handled & added coordinate units

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• fix typo & sortby time

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• sortby series number too

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• syntax

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• series loader fix

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• add time units

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• undo time unit

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Commits on Jul 13, 2023

• updated util GIWAXS import sytnax

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• undoing previous commit

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• minor QoL drawmask tweaks

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• fixes on previous commit

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• more adjustments to drawmask

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• more drawmask

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• fix ui to not swap axes, messes up mask arr

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Commits on Jul 14, 2023

• added option to load iterables into loadSeries

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• syntax fix

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• another fix, make for iterables

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• added tqdm progress bar

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• do not flip masks in pg_convert

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Commits on Jul 15, 2023

• make Transform class for pg functions

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• add Transform to util

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Commits on Jul 17, 2023

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

  

  Keith White

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Commits on Jul 18, 2023

• cms-giwaxs-in_situ_processing notebooks

  

  Andrew Levin

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• cms-giwaxs-in_situ_processing notebooks take2

  

  Andrew Levin

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• adding comments, error handling and delim method variable to loadMd()

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• 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 createSamp…

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• added createSampleDictionary() and selectSampleandSeries() methods to the CMSGIWAXSLoader() class to allow the user to autogenerate a sampledictionary and interactively select their sample form met…

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• updating module imports in cmsgiwaxsloader() class to include corrections

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• adding save_as_zarr method to the Transform() object, and adding a Process(Transform) subclass to perform 1D azimuthal and boxcut integrations using xarray slice methods (this still needs to be imp…

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• 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…

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• remove corrections module usage

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• adding error handling for selectsampleandseries and createSampleDictionary() methods

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• moving return statement

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• updating selectSampleAndSeries(self) to include quit sequence. updating CMSGIWAXSLoader() class attribute to include selected sample series list in the initialization

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• removed "add_time_coord" method as it was broken. only the raw DA contains time and so the the added method is imo not worth the saved coupled of lines

  andrewjlevin

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• Merge branch 'cms-giwaxs-support' of https://github.com/ToneyGroupCU/PyHyperScattering into cms-giwaxs-support

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• adding cell on multiple data set loading to the cms-giwaxs_process.ipynb notebook

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• added tqdm descriptions for loadSeries & pg_convert_series methods

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Commits on Jul 20, 2023

• added custom energy parameter to Transform

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Commits on Jul 22, 2023

• remove FileLoader inheritance of CMSGIWAXSLoader

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Commits on Jul 25, 2023

• Merge branch 'usnistgov:main' into cms-giwaxs-support

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Commits on Jul 26, 2023

• added new function "single_images_to_dataset" inside GIWAXS.py, added more comments & docstrings

  andrewjlevin

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• Merge branches 'cms-giwaxs-support' and 'cms-giwaxs-support' of https://github.com/ToneyGroupCU/PyHyperScattering into cms-giwaxs-support

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• add interpolation correction to aforementioned function

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• fix save_zarrs option in aforementioned function

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• minor tweak to single_images_to_dataset function zarr saving lines

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• typo fixes

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• refined example notebooks & added brief readme.txt to CMS tutorial folder

  

  Andrew Levin

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Commits on Aug 9, 2023

• slight typo fix

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• Merge branch 'usnistgov:main' into cms-giwaxs-support

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Commits on Aug 15, 2023

• allow maskPath to be a literal numpy ndarray

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• transformer init fix

  andrewjlevin

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Commits on Apr 15, 2024

• Tidy up code in PFGeneralIntegrator

  pbeaucage

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• Add zarr saving to fileio

  pbeaucage

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• Change sigma output to unified code that copies dims/coords

  pbeaucage

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• Add ponifile loading to PFGE

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• Add edf mask loading to PFGE

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• Add missed import

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• Rewrite Transform to use PFGeneralIntegrator machinery

  pbeaucage

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• Rename GIWAXS to PGGeneralIntegrator

  pbeaucage

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• loader: raise error if 'files' is not pathlib.Path or iterable

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  pbeaucage

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• loader: commit 9 suggestions from code review

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• Merge pull request #2 from pbeaucage/pr/100

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Commits on Apr 23, 2024

• fix indentation error

  andrewjlevin

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• remove Union syntax in saveZarr function (avoid NameError)

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• remove legacy giwaxs import in util.py

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• small naming/syntax fixes caught in linting/github test runs

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• add PGGeneralIntegrator to integrate.py

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• fix naming error for loading pyhyper mask

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• remove maskpath argument, so that it only exists in kwargs

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• pyfai needs ponifile path input to be a string

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• update if statement in ponifile loader

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• add template_xr to ponifile loader for empty masks

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Commits on Apr 24, 2024

• add filename as attribute if no md scheme is provided. add unused arguments to loadSingleImage for loadFileSeries compatibility

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• change value comparison to check if img is None in loadFileSeries

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• add pygix to requirements

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• add file_filter pathlib glob filtering

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• file needs to be a string?

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• updating, file should be a str of just the filename

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• update to how the existing stacking dimension is preserved in integrateSingleImage

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• more syntax rearranging to preserve stacking dimension

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• consistenty fix, should let loadFileSeries work without needing a file_filter

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• update single_images_to_dataset function

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• update single_image_to_ds function to update incident angle for each sample loaded (require incident_angle attribute)

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• Merge remote-tracking branch 'nist/main' into cms-giwaxs-support

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Commits on Apr 25, 2024

• updated time series processing notebook for new branch update

  

  Andrew Levin

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• Update main.yml

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• Update main.yml

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• remove filetoload argument from a couple mask loaders, already using kwargs['maskpath']

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• Update requirements.txt; specify version of silx for pygix to work

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• update nika mask test

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• Merge branch 'cms-giwaxs-support' of https://github.com/ToneyGroupCU/PyHyperScattering into cms-giwaxs-support

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• logic fix; add single_imgs_to_ds function to a new CMSGIWAXS class in IntegrationUtils

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• fix missing tqdm import

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Commits on Apr 26, 2024

• rearrange order of functions / methods. add more documentation across codebase. update tutorial usage readme.txt

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• updated cms giwaxs tutorials to reflected updated cms-giwaxs-support

  

  Andrew Levin

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• Update requirements.txt: add comment for silx specification

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Commits on Apr 28, 2024

• add main.yml wgets & test_CMSLoader.py; also CMS Loader init docstring update

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Commits on Apr 30, 2024

• cmsgiwaxsloader: tidy imports & switch from PIL to fabio for image loading

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Commits on May 1, 2024

• uncomment cmsloader test lines

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• fix: add naming scheme to test loader and correct attribute dim from filenames

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• cmsloader: use PIL for tiffs (avoid fabio warning), fabio for anything else

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• add optional filename md scheme check before making cmsgiwaxsloaders

  

  Andrew Levin

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Commits on May 2, 2024

• move empty template_xr mask creation to __init__, minor dosctring changes

  andrewjlevin

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• remote init empty mask creation, it's already in pygix integrateSingleImage

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• fix: add empty mask back to calibrationFromTemplateXRParams

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• update tutorial processing notebooks to not used template_xr for integrators

  

  Andrew Levin

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