parent/child grouping

[swharden]

It's often convenient to have a simple way to group related ABFs (e.g., all recordings from a single cell) within a folder that contains a long series of consecutively-named ABF files.

I often achieve this by taking a picture of a cell and saving it with the same basename as the first ABF for that cell. This "parent" abf indicates the start of a sequence of related ABF files, and the subsequent ABF files are "children".

This may be useful to consider including in the pyabf tools submodule.

Code

import pathlib


class AbfParents:
    """
    This class helps group ABFs together using filenames.
    If an ABF file is adjacent to a non-ABF file with the same basename,
    it indicates that ABF file is a "parent" and subsequent ABFs are grouped together.
    Typically the non-abf file is a .tif or .jpg photograph of the sample being recorded.
    """

    def __init__(self):
        self.abfs_by_parent = {}

    def add_folder(self, folder: str):
        folder = pathlib.Path(folder)
        abfs = folder.glob("*.abf")
        others = [x.stem for x in folder.glob("*.*") if x.suffix != ".abf"]
        last_parent = None
        for abf in abfs:
            is_parent = abf.stem in others
            if is_parent:
                self.abfs_by_parent[abf] = []
                last_parent = abf
            self.abfs_by_parent[last_parent].append(abf)

    def add_subfolders(self, folder: str):
        folder = pathlib.Path(folder)
        sub_folders = [x for x in folder.glob("*") if x.is_dir()]
        for sub_folder in sub_folders:
            self.add_folder(sub_folder)

    def __str__(self):
        total = sum([len(x) for x in self.abfs_by_parent.values()])
        return f"{total} ABFs ({len(self.abfs_by_parent)} parents)"

Example

if __name__ == "__main__":
    parents = AbfParents()
    parents.add_subfolders("/path/to/data/")

    for parent in parents.abfs_by_parent.keys():
        print("\n" + parent.name)
        for child in parents.abfs_by_parent[parent]:
            print("  " + child.name)

2023_06_26_0000.abf
  2023_06_26_0000.abf
  2023_06_26_0001.abf

2023_06_26_0002.abf
  2023_06_26_0002.abf
  2023_06_26_0003.abf
  2023_06_26_0004.abf
  2023_06_26_0005.abf
  2023_06_26_0006.abf

2023_06_26_0007.abf
  2023_06_26_0007.abf
  2023_06_26_0008.abf
  2023_06_26_0009.abf

2023_06_26_0010.abf
  2023_06_26_0010.abf
  2023_06_26_0011.abf
  2023_06_26_0012.abf
  2023_06_26_0013.abf
  2023_06_26_0014.abf
  2023_06_26_0015.abf
  2023_06_28_0000.abf
  2023_06_28_0001.abf

2023_06_26_0000.abf
  2023_06_26_0000.abf
  2023_06_26_0001.abf
  2023_06_26_0002.abf
  2023_06_26_0003.abf

2023_06_27_0000.abf
  2023_06_27_0000.abf
  2023_06_27_0001.abf
  2023_06_27_0002.abf
  2023_06_27_0003.abf
  2023_06_27_0004.abf
  2023_06_27_0005.abf

2023_06_27_0006.abf
  2023_06_27_0006.abf
  2023_06_27_0007.abf
  2023_06_27_0008.abf
  2023_06_27_0009.abf

2023_06_27_0010.abf
  2023_06_27_0010.abf
  2023_06_27_0011.abf
  2023_06_27_0012.abf
  2023_06_27_0013.abf
  2023_06_27_0014.abf
  2023_06_27_0015.abf

2023_06_27_0016.abf
  2023_06_27_0016.abf
  2023_06_27_0017.abf
  2023_06_27_0018.abf
  2023_06_27_0019.abf
  2023_06_27_0020.abf
  2023_06_27_0021.abf

2023_06_27_0022.abf
  2023_06_27_0022.abf
  2023_06_27_0023.abf
  2023_06_27_0024.abf
  2023_06_27_0025.abf
  2023_06_27_0026.abf
  2023_06_27_0027.abf