jduffield65 / iss Goto Github PK

Collecting coppafish[optimised,plotting]
  Using cached coppafish-0.1.6-py3-none-any.whl.metadata (2.6 kB)
Collecting numpy (from coppafish[optimised,plotting])
  Using cached numpy-1.24.4-cp38-cp38-macosx_11_0_arm64.whl.metadata (5.6 kB)
Collecting numpy-indexed (from coppafish[optimised,plotting])
  Using cached numpy_indexed-0.3.7-py2.py3-none-any.whl.metadata (4.2 kB)
Collecting tqdm (from coppafish[optimised,plotting])
  Using cached tqdm-4.66.4-py3-none-any.whl.metadata (57 kB)
Collecting scipy (from coppafish[optimised,plotting])
  Using cached scipy-1.10.1-cp38-cp38-macosx_12_0_arm64.whl.metadata (53 kB)
Collecting sklearn (from coppafish[optimised,plotting])
  Using cached sklearn-0.0.post12.tar.gz (2.6 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [15 lines of output]
      The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
      rather than 'sklearn' for pip commands.
      
      Here is how to fix this error in the main use cases:
      - use 'pip install scikit-learn' rather than 'pip install sklearn'
      - replace 'sklearn' by 'scikit-learn' in your pip requirements files
        (requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
      - if the 'sklearn' package is used by one of your dependencies,
        it would be great if you take some time to track which package uses
        'sklearn' instead of 'scikit-learn' and report it to their issue tracker
      - as a last resort, set the environment variable
        SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error
      
      More information is available at
      https://github.com/scikit-learn/sklearn-pypi-package
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Round 4 tile 18 already done.
Round 4 tile 19 already done.
Round 4 tile 20 already done.
Warning: xypos empty - using values from previous round 
> In iss/extract_and_filter (line 79)
  In bridge_process_sample1 (line 67) 
Error using sub2ind (line 73)
Out of range subscript.

Error in iss/fstack_modified>gauss3P (line 145)
Index1 = sub2ind([M,N,P], IM(:), IN(:), Ic-STEP);

Error in iss/fstack_modified (line 79)
[u, s, A, fmax] = gauss3P(opts.focus, fm);

Error in iss/extract_and_filter (line 249)
                I_mod = o.fstack_modified(I);

Error in bridge_process_sample1 (line 67)
o = o.extract_and_filter;

Round 4 tile 18 already done.
Round 4 tile 19 already done.
Round 4 tile 20 already done.
Warning: xypos empty - using values from previous round 
> In iss/extract_and_filter (line 79)
  In bridge_process_sample1 (line 67) 
Error using iss/extract_and_filter (line 229)
Some tiles in imaging rounds already exist, but o.ExtractScale = auto.
This will result in different scalings used for different tiles.
If tiles up to this point were obtained with a manual value of o.ExtractScale,
set o.ExtractScale to this value and rerun.
If tiles up to this point were obtained with auto value, delete tile 8 in round 1 and rerun, tile location:
cache/NLF-133genes/sample1/tiles/r0001_t8.tif.

Error in bridge_process_sample1 (line 67)
o = o.extract_and_filter;