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Readers

The mimic3benchmark/readers.py contains class Reader and five other task-specific classes derived from it:

  • InHospitalMortalityReader
  • DecompensationReader
  • LengthOfStayReader
  • PhenotypingReader
  • MultitaskReader

All of them have the same structure as the Reader class:

class Reader(object):
    def __init__(self, dataset_dir, listfile=None):
        ...
  
    def get_number_of_examples(self):
        ...
  
    def random_shuffle(self, seed=None):
        ...
  
    def read_example(self, index):
        ...
  
    def read_next(self):
        ...

The initializer requires two paths: dataset_dir and listfile. The former specifies a directory with ICU stays and the latter specifies a listfile that describes the samples. If listfile is not given, the code will try to use listfile.csv file of the dataset_dir.

Two functions are there for reading a sample: read_example and read_next. The read_example function reads the sample with the given index, while read_next reads the next sample by using a cyclic counter inside. Both of them return a dictionary. The details about returned dictionary are written in the documentation of read_example functions. For example, here is the description of the return dictionary of InHospitalMortalityReader.

Example of usage:

from mimic3benchmark.readers import DecompensationReader

reader = DecompensationReader(dataset_dir='data/decompensation/train',
                              listfile='data/decompensation/train/listfile.csv')

print(reader.read_example(10))

The output will be:

{
  'X': array([['0.0455555555556', '', '69.0', ..., '38.111110263400604', '', ''],
         ['0.378888888889', '', '92.0', ..., '', '', ''],
         ['1.04555555556', '', '90.0', ..., '', '', ''],
         ...,
         ['78.0455555556', '', '60.0', ..., '', '', ''],
         ['78.6288888889', '', '', ..., '', '', ''],
         ['79.0455555556', '', '63.0', ..., '', '', '']], dtype='|S18'),
  'y': 0,
  't': 80.0,
  'name': '17378_episode1_timeseries.csv',
  'header': [
    'Hours',
    'Capillary refill rate',
    'Diastolic blood pressure',
    'Fraction inspired oxygen',
    'Glascow coma scale eye opening',
    'Glascow coma scale motor response',
    'Glascow coma scale total',
    'Glascow coma scale verbal response',
    'Glucose',
    'Heart Rate',
    'Height',
    'Mean blood pressure',
    'Oxygen saturation',
    'Respiratory rate',
    'Systolic blood pressure',
    'Temperature',
    'Weight',
    'pH'
  ]
}