content: from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json
  from nnunetv2.paths import nnUNet_raw, nnUNet_preprocessed
  import tifffile
  from batchgenerators.utilities.file_and_folder_operations import *
  import shutil
  
  
  if __name__ == '__main__':
      """
      This is going to be my test dataset for working with tif as input and output images
      
      All we do here is copy the files and rename them. Not file conversions take place 
      """
      dataset_name = 'Dataset073_Fluo_C3DH_A549_SIM'
  
      imagestr = join(nnUNet_raw, dataset_name, 'imagesTr')
      imagests = join(nnUNet_raw, dataset_name, 'imagesTs')
      labelstr = join(nnUNet_raw, dataset_name, 'labelsTr')
      maybe_mkdir_p(imagestr)
      maybe_mkdir_p(imagests)
      maybe_mkdir_p(labelstr)
  
      # we extract the downloaded train and test datasets to two separate folders and name them Fluo-C3DH-A549-SIM_train
      # and Fluo-C3DH-A549-SIM_test
      train_source = '/home/fabian/Downloads/Fluo-C3DH-A549-SIM_train'
      test_source = '/home/fabian/Downloads/Fluo-C3DH-A549-SIM_test'
  
      # with the old nnU-Net we had to convert all the files to nifti. This is no longer required. We can just copy the
      # tif files
  
      # tif is broken when it comes to spacing. No standards. Grr. So when we use tif nnU-Net expects a separate file
      # that specifies the spacing. This file needs to exist for EVERY training/test case to allow for different spacings
      # between files. Important! The spacing must align with the axes.
      # Here when we do print(tifffile.imread('IMAGE').shape) we get (29, 300, 350). The low resolution axis is the first.
      # The spacing on the website is griven in the wrong axis order. Great.
      spacing = (1, 0.126, 0.126)
  
      # train set
      for seq in ['01', '02']:
          images_dir = join(train_source, seq)
          seg_dir = join(train_source, seq + '_GT', 'SEG')
          # if we were to be super clean we would go by IDs but here we just trust the files are sorted the correct way.
          # Simpler filenames in the cell tracking challenge would be soooo nice.
          images = subfiles(images_dir, suffix='.tif', sort=True, join=False)
          segs = subfiles(seg_dir, suffix='.tif', sort=True, join=False)
          for i, (im, se) in enumerate(zip(images, segs)):
              target_name = f'{seq}_image_{i:03d}'
              # we still need the '_0000' suffix for images! Otherwise we would not be able to support multiple input
              # channels distributed over separate files
              shutil.copy(join(images_dir, im), join(imagestr, target_name + '_0000.tif'))
              # spacing file!
              save_json({'spacing': spacing}, join(imagestr, target_name + '.json'))
              shutil.copy(join(seg_dir, se), join(labelstr, target_name + '.tif'))
              # spacing file!
              save_json({'spacing': spacing}, join(labelstr, target_name + '.json'))
  
      # test set, same a strain just without the segmentations
      for seq in ['01', '02']:
          images_dir = join(test_source, seq)
          images = subfiles(images_dir, suffix='.tif', sort=True, join=False)
          for i, im in enumerate(images):
              target_name = f'{seq}_image_{i:03d}'
              shutil.copy(join(images_dir, im), join(imagests, target_name + '_0000.tif'))
              # spacing file!
              save_json({'spacing': spacing}, join(imagests, target_name + '.json'))
  
      # now we generate the dataset json
      generate_dataset_json(
          join(nnUNet_raw, dataset_name),
          {0: 'fluorescence_microscopy'},
          {'background': 0, 'cell': 1},
          60,
          '.tif'
      )
  
      # custom split to ensure we are stratifying properly. This dataset only has 2 folds
      caseids = [i[:-4] for i in subfiles(labelstr, suffix='.tif', join=False)]
      splits = []
      splits.append(
          {'train': [i for i in caseids if i.startswith('01_')], 'val': [i for i in caseids if i.startswith('02_')]}
      )
      splits.append(
          {'train': [i for i in caseids if i.startswith('02_')], 'val': [i for i in caseids if i.startswith('01_')]}
      )
      save_json(splits, join(nnUNet_preprocessed, dataset_name, 'splits_final.json'))