cytominer_database.munge.munge(config_file, source, target=None)[source]

Searches source for directories containing a CSV file corresponding to per-object measurements, then splits the CSV file into one CSV file per compartment.

For instance, the CSV file may comprise of measurements combined across Cells, Cytoplasm, and Nuclei. munge will split this CSV file into 3 CSV files: Cells.csv, Cytoplasm.csv, and Nuclei.csv.

  • config_file – Configuration file.
  • source – Directory containing subdirectories that contain an object CSV file.
  • target – Output directory. If not specified, then it is same as source.

list of subdirectories that have an object CSV file.


import cytominer_database.munge

cytominer_database.munge.munge(source, target, config)