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Crash in scheme._prepare_data when number of spectral points > time points #597

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jsnel opened this issue Mar 14, 2021 · 0 comments · Fixed by #618
Closed

Crash in scheme._prepare_data when number of spectral points > time points #597

jsnel opened this issue Mar 14, 2021 · 0 comments · Fixed by #618
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@jsnel
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Priority: High Nasty bugs leading to incorrect results or crashes Status: In Progress Issues being worked on Type: Serious Bug Crashes, Broken code, Security Issues

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jsnel commented Mar 14, 2021

  • glotaran version: v0.3.2
  • Python version: all
  • Operating System: all

Description

The code to manipulate SVD related attributes in scheme.py is out of date and can result in a crash when the code path is executed, and happens when the global_dimension > model_dimension. This is more of an issue since merging PR #575.

What I Did

Example traceback of crash

Traceback (most recent call last):
  File "guidance_case_study/ex_two_datasets_guidance_no_area_irf.py", line 91, in <module>
    result = main()
  File "guidance_case_study/ex_two_datasets_guidance_no_area_irf.py", line 44, in main
    scheme = Scheme(
  File "pyglotaran\glotaran\analysis\scheme.py", line 53, in __init__
    self._prepare_data(data)
  File "pyglotaran\glotaran\analysis\scheme.py", line 215, in _prepare_data
    dataset = dataset.rename(right_singular_vectors="right_singular_value_vectorsTMP")
  File "site-packages\xarray\core\dataset.py", line 3005, in rename
    raise ValueError(
ValueError: cannot rename 'right_singular_vectors' because it is not a variable or dimension in this dataset
@jsnel jsnel added Type: Serious Bug Crashes, Broken code, Security Issues Status: In Progress Issues being worked on Priority: High Nasty bugs leading to incorrect results or crashes labels Mar 14, 2021
@jsnel jsnel self-assigned this Mar 14, 2021
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 15, 2021
@jsnel
Force recalculation of SVD attributes in scheme._prepare_data
d49faaf 
Force recalculation of SVD attributes after (possible) transposing of dataset matrix dimension, rather than renaming attributes.
Fixes glotaran#597
@jsnel jsnel mentioned this issue Mar 15, 2021
Merged
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 18, 2021
@jsnel
Force recalculation of SVD attributes in scheme._prepare_data
1a21331 
Force recalculation of SVD attributes after (possible) transposing of dataset matrix dimension, rather than renaming attributes.
Fixes glotaran#597
jsnel added a commit that referenced this issue Mar 18, 2021
@jsnel
Maintenance/patches for v0.3.3 (#599)
67dacce 
* Force recalculation of SVD attributes in scheme._prepare_data Fixes #597
* 🔨 Remove no-op code related to new_dims 
* Remove unneeded check in spectral_penalties._get_area Fixes #598
* Add python 3.9 support (#450)
* Bump numba dependencies as needed for Python 3.9
@jsnel jsnel mentioned this issue Mar 18, 2021
Merged
@jsnel jsnel mentioned this issue Mar 28, 2021
Merged
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 28, 2021
@jsnel
Maintenance/patches for v0.3.3 (glotaran#599) 2/2
6ee801c 
* Force recalculation of SVD attributes in scheme._prepare_data Fixes glotaran#597
* 🔨 Remove no-op code related to new_dims

Changes that were lost because code was moved from scheme.py to problem.py
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 28, 2021
@jsnel
Maintenance/patches for v0.3.3 (glotaran#599) 2/2
4baa65a 
* Force recalculation of SVD attributes in scheme._prepare_data Fixes glotaran#597
* 🔨 Remove no-op code related to new_dims

Changes that were lost because code was moved from scheme.py to problem.py
@jsnel jsnel linked a pull request Mar 28, 2021 that will close this issue
Maintenance/forward port v0.3.3 changes #618
Merged
jsnel added a commit that referenced this issue Mar 28, 2021
@jsnel
Maintenance/forward port v0.3.3 changes (#618)
0d41d63 
* Prepare v0.3.3 release (#603)
Bumped version and added release notes

* Maintenance/patches for v0.3.3 (#599) 1/2
* Remove unneeded check in spectral_penalties._get_area Fixes #598
* Maintenance/patches for v0.3.3 (#599) 2/2
* Force recalculation of SVD attributes in scheme._prepare_data Fixes #597
* 🔨 Remove no-op code related to new_dims
Changes that were lost because code was moved from scheme.py to problem.py

* Add a Zenodo config file
Added config file based on the example generated by zenodo
JSON Export example found at: https://zenodo.org/account/settings/github/repository/glotaran/pyglotaran#
Closes #579

* Update readme
Clarified Python version support
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Priority: High Nasty bugs leading to incorrect results or crashes Status: In Progress Issues being worked on Type: Serious Bug Crashes, Broken code, Security Issues
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Maintenance/forward port v0.3.3 changes jsnel/pyglotaran
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