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Add delmic load function #139

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@noemiebonnet noemiebonnet commented Jun 13, 2023

Description of the change

  • Addition of a delmic reader

Progress of the PR

  • basic parsing of the file
  • basic testing
  • add metadata handling
  • ... (additional functionalities)
  • add tests,
  • update docstring (if appropriate),
  • add an changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
  • Check formatting changelog entry in the readthedocs doc build of this PR (link in github checks)
  • ready for review.

@jlaehne
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jlaehne commented Jun 13, 2023

Tests are failing, because docstrings has been made private _docstrings in #132. Could you rename that in line 4 of your _api.py

@noemiebonnet
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noemiebonnet commented Jun 13, 2023 via email

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codecov bot commented Jun 15, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 87.70%. Comparing base (e499110) to head (b7bf8f7).
Report is 2 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #139      +/-   ##
==========================================
+ Coverage   87.67%   87.70%   +0.02%     
==========================================
  Files          83       85       +2     
  Lines       11149    11173      +24     
  Branches     2414     2414              
==========================================
+ Hits         9775     9799      +24     
  Misses        860      860              
  Partials      514      514              

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@jlaehne
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jlaehne commented Jun 15, 2023

Thanks for putting this forward @noemiebonnet

As far as I understand, it only reads spectral images and not other types of Delmic-HDF5 files (e.g. single spectra, intensity maps, angle-resolved data) so far?

Note that we changed the placement and handling of the test data files in #123

Concerning the metadata, it would be great if the full metadata tree from the hdf5 file could be placed under original_metadata.

For the fields mentioned in https://docs.lumispy.org/en/latest/user_guide/metadata_structure.html it would be great if they can be mapped to the metadata tree at some point.

@@ -0,0 +1,8 @@
name: delmic
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Suggested change
name: delmic
name: Delmic

},
]

metadata = {"signal": {"signal_type": "", "quantity": "Intensity (counts)"}}
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If LumiSpy is installed, signal_type should be set to CL to provide the CL specific functions.


metadata = {"signal": {"signal_type": "", "quantity": "Intensity (counts)"}}

original_metadata = dict(DimensionScaleX="182", DimensionScaleY="132")
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I guess these fixed values are just from testing so far?

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jlaehne commented Jun 15, 2023

I added a progress tracker to the initial comment. It helps show others how far this PR is, feel free to amend the list by editing the comment.

@ericpre ericpre added this to the v0.2 milestone Jul 8, 2023
@ericpre ericpre modified the milestones: v0.2, v0.3 Nov 8, 2023
@ericpre ericpre removed this from the v0.3 milestone Dec 13, 2023
@noemiebonnet noemiebonnet force-pushed the add-delmic-load-function branch 4 times, most recently from ceea371 to 3f5c79d Compare August 14, 2024 14:36
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jlaehne commented Aug 21, 2024

pre-commit.ci autofix

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3 participants