Closed jwindhager closed 2 years ago
I got this error when running the updated chunk in the pre-processing script:
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Input In [8], in <cell line: 3>() 3 for acquisition_dir in acquisitions_dir.glob("*"): 4 if acquisition_dir.is_dir(): 5 # Write full stack 6 imcsegpipe.create_analysis_stacks( 7 acquisition_dir=acquisition_dir, 8 analysis_dir=final_images_dir, ----> 9 analysis_channels=sort_channels_by_mass( 10 panel.loc[panel[panel_keep_col] == 1, panel_channel_col].tolist() 11 ), 12 suffix="_full", 13 hpf=50.0, 14 ) 15 # Write ilastik stack 16 imcsegpipe.create_analysis_stacks( 17 acquisition_dir=acquisition_dir, 18 analysis_dir=ilastik_dir, (...) 23 hpf=50.0, 24 ) File ~/Github/ImcSegmentationPipeline/src/imcsegpipe/utils.py:163, in sort_channels_by_mass(channels) 162 def sort_channels_by_mass(channels: Sequence[str]) -> List[str]: --> 163 return sorted(channels, lambda channel: int(re.sub("[^0-9]", "", channel) or 0)) TypeError: sorted expected 1 argument, got 2
Sorry about that, should be fixed now
I got this error when running the updated chunk in the pre-processing script: