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Adding support for .jpk-qi-data and .bin files#190

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ahobbs7 wants to merge 42 commits intomainfrom
ahobbs7/jpk-qi-data
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Adding support for .jpk-qi-data and .bin files#190
ahobbs7 wants to merge 42 commits intomainfrom
ahobbs7/jpk-qi-data

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@ahobbs7 ahobbs7 commented May 3, 2026

Adds support for .jpk-qi-data files, allowing the loading of the image for the selected channel. It also allows for the raw force-distance curve data as well as metadata for each curve to be loaded efficiently, using a lazy data structure approach that loads each section of the dataset into memory only when it is required.
The updates also allow for the conversion of .jpk-qi-data files into a HDF5 file format (.h5-jpk) for much faster mass analysis. Hence, the h5-jpk loading code has also been updated to support the loading of these converted files.

The update also allows .bin with different binary formats to be loaded.

closes #174 closes #173

…files and removing the ability to run curve analysis directly in the reader
…g to memory then saving in one go when duplicating data to h5
…sampled curves then are streamed directly into h5
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codecov-commenter commented May 4, 2026

Codecov Report

❌ Patch coverage is 14.41441% with 760 lines in your changes missing coverage. Please review.
✅ Project coverage is 47.45%. Comparing base (d65d297) to head (a1764fe).
⚠️ Report is 11 commits behind head on main.

Files with missing lines Patch % Lines
AFMReader/jpk_qi.py 10.07% 491 Missing ⚠️
AFMReader/h5_jpk.py 21.09% 101 Missing ⚠️
AFMReader/general_loader.py 22.95% 47 Missing ⚠️
AFMReader/lazy_data_classes.py 20.40% 39 Missing ⚠️
AFMReader/raw_bin.py 21.21% 26 Missing ⚠️
AFMReader/jpk.py 39.28% 17 Missing ⚠️
AFMReader/spm.py 7.69% 12 Missing ⚠️
AFMReader/asd.py 9.09% 10 Missing ⚠️
AFMReader/ibw.py 9.09% 10 Missing ⚠️
AFMReader/gwy.py 12.50% 7 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #190       +/-   ##
===========================================
- Coverage   79.84%   47.45%   -32.40%     
===========================================
  Files          12       15        +3     
  Lines         928     1806      +878     
===========================================
+ Hits          741      857      +116     
- Misses        187      949      +762     

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@ahobbs7 ahobbs7 marked this pull request as ready for review May 5, 2026 07:54
@ahobbs7 ahobbs7 requested a review from SylviaWhittle May 5, 2026 07:54
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[feature] : Read .jpk-qi-data files [Bug]: .jpk-qi-data files not loading

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