IndexError: list index out of range

[josenimo]

Dear @VictorDidier,

Thank you for developing this nice package. I am currently testing the docker container implementation and I am running into an isssue. I am using a small sample data set, which has 000 -> 003 cycles. Thank you for your help and let me know what other information I can provide.

Output before crashing (for every exposure level):

(base) mambauser@b2a9af1b8e0f:/stack_macsima$ python macsima2mc.py -i /data -o /data/output -c 1 3
extracting antigen cycle: 1
extracting bleaching cycle: 0
extracting bleaching cycle: 0
extracting bleaching cycle: 0
extracting antigen cycle: 2
extracting bleaching cycle: 1
extracting bleaching cycle: 1
extracting bleaching cycle: 1
extracting antigen cycle: 3
Traceback (most recent call last):
  File "/stack_macsima/macsima2mc.py", line 611, in <module>
    main()
  File "/stack_macsima/macsima2mc.py", line 568, in main
    antigen_stack_info=create_stack(antigen_info,antigen_cycle_no=i,exp_level=e)
  File "/stack_macsima/macsima2mc.py", line 473, in create_stack
    exp=groupB.loc[(groupB['marker']==s) & (groupB['fov']==1) & (groupB['exposure_level']==exp_level),'exposure'].tolist()[0]
IndexError: list index out of range

Link to sample dataset:
https://filetransfer.mdc-berlin.de/?u=dTzagkaQ&p=C6fa7U32

Best,
Jose

[migueLib]

@josenimo We recently created a pip version to install macsima2mc could you perhaps try it (if you have time) and let us know if this fixed the issue?

[josenimo]

installation worked, will get my hands on some macsima data and let you know

[josenimo]

nvm, failed with jax

❯ macsima2mc
Traceback (most recent call last):
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/bin/macsima2mc", line 5, in <module>
    from macsima2mc.macsima2mc import main
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/macsima2mc/__init__.py", line 3, in <module>
    from macsima2mc import illumination_corr
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/macsima2mc/illumination_corr.py", line 1, in <module>
    from basicpy import BaSiC
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/basicpy/__init__.py", line 7, in <module>
    from basicpy.basicpy import BaSiC
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/basicpy/basicpy.py", line 27, in <module>
    from basicpy._jax_routines import ApproximateFit, LadmapFit
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/basicpy/_jax_routines.py", line 10, in <module>
    from basicpy.tools.dct_tools import JaxDCT
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/basicpy/tools/__init__.py", line 3, in <module>
    from basicpy.tools import dct_tools
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/basicpy/tools/dct_tools.py", line 13, in <module>
    import basicpy.tools._jax_idct
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/basicpy/tools/_jax_idct.py", line 6, in <module>
    from jax._src.numpy.util import _wraps
ImportError: cannot import name '_wraps' from 'jax._src.numpy.util' (/opt/homebrew/Caskroom/mambaforge/base/envs/test_macsima2mcmicro/lib/python3.13/site-packages/jax/_src/numpy/util.py)