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Cms giwaxs support version 1 #100

Merged
merged 127 commits into from
May 6, 2024
Merged

Cms giwaxs support version 1 #100

merged 127 commits into from
May 6, 2024

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andrewjlevin
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Addresses issue #77, adding support for loading and transforming CMS GIWAXS data. Adds 2 new scripts with corresponding classes / methods for loading and transforming single images and series. Also adds template & example notebooks in tutorials/instrument-specific/CMS.

andrewjlevin added 30 commits July 5, 2023 12:14
@andrewjlevin
create initial CMS files
e50136b
@andrewjlevin
add CMSGIWAXSLoader to loader.py
ab094c2
@andrewjlevin
first attempt at loadSingleImage
2260022
@andrewjlevin
add loadMd method
8d7847e
@andrewjlevin
parameter fix
c3b78db
@andrewjlevin
wrote loadSeries method
d31f1af
@andrewjlevin
syntax fix
02cca42
@andrewjlevin
add coordinates & minor tweaks
bb2c510
@andrewjlevin
syntax
60874b9
@andrewjlevin
syntax
a4071cc
@andrewjlevin
round exposure time to 1 decimal
9af942e
@andrewjlevin
change default naming scheme from None to []
a2ca96d
@andrewjlevin
silence draw.load print statements
cf6c619
@andrewjlevin
remove np.flipud and create pg_convert function in GIWAXS.py
7bbba85
@andrewjlevin
add GIWAXS.py to util.py
c60d4d1
@andrewjlevin
time coordinate shows ending time, included in pg_convert output
6d944ef
@andrewjlevin
syntax fix
c968f11
@andrewjlevin
array shaping fix
d1de032
@andrewjlevin
array shaping fix
db57990
@andrewjlevin
added pg_convert_series fxn
84d19b8
@andrewjlevin
changed how time dim is handled & added coordinate units
fd83f08
@andrewjlevin
fix typo & sortby time
4dbd307
@andrewjlevin
sortby series number too
2a74072
@andrewjlevin
syntax
2e2c81b
@andrewjlevin
series loader fix
2059af8
@andrewjlevin
add time units
5ce76ed
@andrewjlevin
undo time unit
05951d0
@andrewjlevin
updated util GIWAXS import sytnax
a38231e
@andrewjlevin
undoing previous commit
54c4324
@andrewjlevin
minor QoL drawmask tweaks
1babde7
andrewjlevin and others added 24 commits April 24, 2024 14:45
@andrewjlevin
update to how the existing stacking dimension is preserved in integra…
d8257a0 
…teSingleImage
@andrewjlevin
more syntax rearranging to preserve stacking dimension
7c5f1c0
@andrewjlevin
consistenty fix, should let loadFileSeries work without needing a fil…
f07661a 
…e_filter
@andrewjlevin
update single_images_to_dataset function
e13219b
@andrewjlevin
update single_image_to_ds function to update incident angle for each …
379ce48 
…sample loaded (require incident_angle attribute)
@andrewjlevin
Merge remote-tracking branch 'nist/main' into cms-giwaxs-support
eb93a0b
updated time series processing notebook for new branch update
8f9356a
@andrewjlevin
Update main.yml
05ef956 
add check-latest: true; attempts at debugging builds not running
@andrewjlevin
Update main.yml
0384c34 
remove python versions 3.8 and 3.9 tests
@andrewjlevin
remove filetoload argument from a couple mask loaders, already using …
e87aea4 
…kwargs['maskpath']
@andrewjlevin
Update requirements.txt; specify version of silx for pygix to work
958fe5a
@andrewjlevin
update nika mask test
00731f5
@andrewjlevin
Merge branch 'cms-giwaxs-support' of https://github.com/ToneyGroupCU/…
b67461a 
…PyHyperScattering into cms-giwaxs-support
@andrewjlevin
logic fix; add single_imgs_to_ds function to a new CMSGIWAXS class in…
f714632 
… IntegrationUtils
@andrewjlevin
fix missing tqdm import
fc299f3
@andrewjlevin
rearrange order of functions / methods. add more documentation across…
5bc3e52 
… codebase. update tutorial usage readme.txt
updated cms giwaxs tutorials to reflected updated cms-giwaxs-support
fe57679
@andrewjlevin
Update requirements.txt: add comment for silx specification
ae3f057
@andrewjlevin
add main.yml wgets & test_CMSLoader.py; also CMS Loader init docstrin…
66a17d5 
…g update
@andrewjlevin
cmsgiwaxsloader: tidy imports & switch from PIL to fabio for image lo…
d6d80ec 
…ading
@andrewjlevin
uncomment cmsloader test lines
05c9650
@andrewjlevin
fix: add naming scheme to test loader and correct attribute dim from …
c34babc 
…filenames
@andrewjlevin
cmsloader: use PIL for tiffs (avoid fabio warning), fabio for anythin…
8b7e6eb 
…g else
add optional filename md scheme check before making cmsgiwaxsloaders
7907e5f
pbeaucage
pbeaucage approved these changes May 2, 2024
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This is all great. After one question about mask generation inside loadponifile, this is ready to merge. Thanks SO MUCH for all your effort getting this together and in and your remarkable patience.

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@pbeaucage pbeaucage merged commit 08c3943 into usnistgov:main May 6, 2024
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@pbeaucage pbeaucage pbeaucage approved these changes

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@andrewjlevin @pbeaucage @kewh5868