Some problem when running ilastik fix（KeyError: 'Patient1_s0_a1_ac_ilastik_x593_y590_w500_h500'）

[yibulaxin]

Dear Sirs, Thank you for developing steinbock,which is a wonderful package used for IMC image processing. However,when trying to run your sample program: ` steinbock classify ilastik prepare --cropsize 500 --seed 123

rm pixel_classifier.ilp && mv IMCWorkflow.ilp pixel_classifier.ilp

rm -r ilastik_crops && mv analysis/crops ilastik_crops

steinbock classify ilastik fix --no-backup

I met the following problem: Traceback (most recent call last): File "D:\python\IMCprocess\imc_classification_cmd.py", line 45, in ilastik_fix("analysis/official_classification.ilp","analysis/official_cropped","analysis/classification_result") File "D:\python\IMCprocess\imc_classification_cmd.py", line 41, in ilastik_fix ilastik.fix_ilastik_project_file_inplace(project_file,crop_img_dir,output_dir,ilastik_crop_shapes,last_transpose_axes,) File "E:\anconda\envs\medsam_data_processor\lib\site-packages\steinbock\classification\ilastik_ilastik.py", line 385, in fix_ilastik_project_file_inplace _fix_input_data_group_inplace( File "E:\anconda\envs\medsam_data_processor\lib\site-packages\steinbock\classification\ilastik_ilastik.py", line 421, in _fix_input_data_group_inplace shape=ilastik_crop_shapes[ilastik_crop_file.stem], KeyError: 'Patient1_s0_a1_ac_ilastik_x593_y590_w500_h500'`

I've read your source code and found that you implemented the function as follows: ` ilastik_crop_shapes = {}

last_transpose_axes = None

for (

    ilastik_crop_file,

    transpose_axes,

    ilastik_crop,

) in ilastik.try_fix_ilastik_crops_from_disk(

    ilastik_crop_files, orig_axis_order=orig_axis_order

):

    if last_transpose_axes not in (None, transpose_axes):

        raise SteinbockCLIException("Inconsistent axis orders across crops")

    ilastik.write_ilastik_crop(ilastik_crop, ilastik_crop_file)

    ilastik_crop_shapes[ilastik_crop_file.stem] = ilastik_crop.shape

    last_transpose_axes = transpose_axes

    logger.info(ilastik_crop_file)

    del ilastik_crop

ilastik.fix_ilastik_project_file_inplace(

    ilastik_project_file,

    ilastik_crop_dir,

    ilastik_probab_dir,

    ilastik_crop_shapes,

    last_transpose_axes,

)`

However,the ilastik.try_fix_ilastik_crops_from_disk function returns noting (because it always continue in the loop) when "steinbock" is True in the dataset,and the ilastik_crop_shape keeps an empty dict.Therefore,when the program runs into the fix_ilastik_project_file_inplace function ,it might occur an error in the following part because the ilastik_crop_shapes contains nothing: ` _fix_raw_data_group_inplace(

                raw_data_group,

                file_path=str(

                    rel_ilastik_crop_dir

                    / ilastik_crop_file.name

                    / _crop_dataset_path

                ),

                nickname=ilastik_crop_file.stem,

                shape=ilastik_crop_shapes[ilastik_crop_file.stem],

            )`

I wonder whether I use the function wrongly or there might be some problem with the code. Thanks a lot!!!