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Fiddle instrument #1761

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bnmajor
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@bnmajor bnmajor commented Nov 27, 2024 •
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  • New instrument option in LLNL Import: FIDDLE
  • Two modes: With Image PLate and Without Image Plate
  • With no image plate = load image per detector w/ dark subtraction for each image
  • With image plate = images + dark + IP w/ template & masking
  • Try to automatically find remaining images + dark after first image is loaded
  • Support manually loading images + dark if automatic find fails
  • Add hdf5 path as known path so users do not need to select it
  • Need correct default config file (See Fiddle instrument hexrd#736)
  • Need template boundary(ies) file (See Fiddle instrument hexrd#736)
  • Imageseries should say frame or timestep instead of omega
  • Image + dark = 4 frames per image file/dark file
    • Subtract each dark frame from each image frame
    • Create 4 frame imageseries from results
  • All 4 frames are in single hdf5 file. Need to handle multiple hdf5 paths for this new case
  • Need 4th config option: ATLAS coordinates - Saransh will provide script and example data (Will put up in separate PR)
  • Add new intensity correction option: median w/ kernel (default to 7; user can change)
  • On load for FIDDLE instrument pop up dialog w/ option to apply new median filter and set kernel size before Physics Package dialog

@pep8speaks
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pep8speaks commented Nov 27, 2024 •
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Hello @bnmajor! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 554:80: E501 line too long (95 > 79 characters)

Line 81:80: E501 line too long (83 > 79 characters)

Line 101:9: E122 continuation line missing indentation or outdented
Line 235:9: E122 continuation line missing indentation or outdented
Line 258:13: E122 continuation line missing indentation or outdented
Line 265:13: E122 continuation line missing indentation or outdented
Line 273:13: E122 continuation line missing indentation or outdented
Line 305:9: E122 continuation line missing indentation or outdented
Line 494:32: W605 invalid escape sequence '\d'
Line 495:31: W605 invalid escape sequence '\d'
Line 496:31: W605 invalid escape sequence '\d'
Line 532:13: E122 continuation line missing indentation or outdented
Line 588:13: E122 continuation line missing indentation or outdented
Line 665:9: E122 continuation line missing indentation or outdented
Line 736:9: E122 continuation line missing indentation or outdented
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Line 782:9: E122 continuation line missing indentation or outdented
Line 786:9: E122 continuation line missing indentation or outdented
Line 836:9: E122 continuation line missing indentation or outdented
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Comment last updated at 2025-01-03 17:29:26 UTC

@bnmajor bnmajor force-pushed the fiddle-instrument branch 4 times, most recently from 1f3eb43 to dadc297 Compare December 17, 2024 21:55
Brianna Major added 14 commits December 18, 2024 13:43
Add the new FIDDLE instrument
9998652 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Add hdf5 path to known paths list
297bfa2 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Support manually loading images and dark files
6e886a8 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Try to automatically match images and dark files
dc715ae 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Improve naming for clarity
1f36107 
Update variable names to better reflect the two paths: one for image plates
and one for detectors.

Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Make sure that the transform option is enabled on image load
471736e 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Add property to simplify check for template
ea4432b 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Add some inline comments for clarity
1756531 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
PEP8 fixes & use consistent formatting
0e007a3 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Infer which values are detectors and which are image plates
339e3d1 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Add support for median filter intensity correction
53c2281 
It will automatically be applied once the LLNL import concludes. Kernel size
defaults to 7 but users will be prompted to change this value after import if
they'd like to. Median filtering can also be applied/removed from the
"Intensity Corrections" menu, where users will always be allowed to change the
kernel size.

Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Only apply one template to an image at a time
8578522 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Duplicate image plate image if it exists
94b808e 
The UI expects that all imageseries are the same length. To keep this in sync,
for now we simply create for copies of the image plate image and create the
imageseries from those frames.

Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
PEP8 fixes
9ca3ae5 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Brianna Major and others added 2 commits December 22, 2024 12:08
Add default config for FIDDLE instrument
c0f7fe0 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
@psavery
Memoize median filter results for FIDDLE
f7286bf 
This takes up about ~200 MB to contain the results for all 21 FIDDLE
images. We may want to multi-thread across images as well...

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
Brianna Major added 6 commits January 3, 2025 12:28
Refactor median kernel into its own dialog
85a64b1 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Make sure kernel size is always stored as an int
9820ace 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Do not apply the median filter during import
5b5f95b 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Re-organize reset function for readability
ce63da5 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
Automatically flip FIDDLE image plate
9c28ecc
Replace frame spinner with forward/back buttons
ac00f50 
Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>
@bnmajor bnmajor force-pushed the fiddle-instrument branch from 9b17b7b to ac00f50 Compare January 3, 2025 17:29
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3 participants
@bnmajor @pep8speaks @psavery