diff --git a/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py b/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py index c252fd8fa748c407919518bcaca6cd444c59593f..0d99fe5f5267d0ff6969235a4f44222ea478b5aa 100644 --- a/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py +++ b/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py @@ -22,15 +22,18 @@ if __name__ == '__main__': # write single-position TIF color stacks where_proc = Path(where_output) / 'proc' - for pos in range(0, cf.shape[cf.axes.index('S')]): - fname = f'{czi_filepath.stem}_p{pos:02d}.tif' - write_accessor_data_to_file( - where_proc / fname, - get_accessor_from_multiposition_czi(cf, pos) - ) - print(f'Wrote file {fname}') + # for pos in range(0, cf.shape[cf.axes.index('S')]): + # for pos in [0, 50, 100, 150, 200]: + # fname = f'{czi_filepath.stem}_p{pos:02d}.tif' + # write_accessor_data_to_file( + # where_proc / fname, + # get_accessor_from_multiposition_czi(cf, pos) + # ) + # print(f'Wrote file {fname}') - px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/pxAF405_dim8bit.ilp').__str__() + px_ilp = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/ilastik/px_4ch_02.ilp').__str__() + + where_proc = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/output/batch-output-20240126-0003/proc') params = { 'pxmap_threshold': 0.25,