old_contents: import argparse
  import sys
  import numpy as np
  import skimage.io
  import pandas as pd
  import warnings
  
  def points2label(labels, shape, output_file=None, has_header=False, is_TSV=False):
      labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32)
  
      if is_TSV:
          if has_header:
              df = pd.read_csv(labels, sep='\t', skiprows=1, header=None)
          else:
              df = pd.read_csv(labels, sep='\t', header=None)
      else:
          if has_header:
              df = pd.read_csv(labels, skiprows=1, header=None)
          else:
              df = pd.read_csv(labels, header=None)
  
      for i in range(0, len(df)):
          a_row = df.iloc[i]
          labelimg[a_row[0], a_row[1]] = i+1
  
      if output_file is not None:
          with warnings.catch_warnings():
              warnings.simplefilter("ignore")
              skimage.io.imsave(output_file, labelimg, plugin='tifffile')
      else:
          return labelimg
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser()
      parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file')
      parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file')
      parser.add_argument('org_file', type=argparse.FileType('r'), default=sys.stdin, help='input original file')
      parser.add_argument('--has_header', dest='has_header', type=bool, default=False, help='label file has header')
      parser.add_argument('--is_tsv', dest='is_tsv', type=bool, default=False, help='label file is TSV')
      args = parser.parse_args()
  
      original_shape = skimage.io.imread(args.org_file.name, plugin='tifffile').shape
  
      points2label(args.label_file.name, original_shape, args.out_file.name, args.has_header, args.is_tsv)
  
new_contents: import argparse
  import sys
  import numpy as np
  import skimage.io
  import pandas as pd
  import warnings
  
  def points2label(labels, shape, output_file=None, has_header=False, is_TSV=True):
      labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32)
  
      if is_TSV:
          if has_header:
              df = pd.read_csv(labels, sep='\t', skiprows=1, header=None)
          else:
              df = pd.read_csv(labels, sep='\t', header=None)
      else:
          if has_header:
              df = pd.read_csv(labels, skiprows=1, header=None)
          else:
              df = pd.read_csv(labels, header=None)
  
      for i in range(0, len(df)):
          a_row = df.iloc[i]
          labelimg[a_row[0], a_row[1]] = i+1
  
      if output_file is not None:
          with warnings.catch_warnings():
              warnings.simplefilter("ignore")
              skimage.io.imsave(output_file, labelimg, plugin='tifffile')
      else:
          return labelimg
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser()
      parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file')
      parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file')
      parser.add_argument('org_file', type=argparse.FileType('r'), default=sys.stdin, help='input original file')
      parser.add_argument('--has_header', dest='has_header', type=bool, default=False, help='label file has header')
      parser.add_argument('--is_tsv', dest='is_tsv', type=bool, default=True, help='label file is TSV')
      args = parser.parse_args()
  
      original_shape = skimage.io.imread(args.org_file.name, plugin='tifffile').shape
  
      points2label(args.label_file.name, original_shape, args.out_file.name, args.has_header, args.is_tsv)
  
subject: change default to tsv