filenames

Auxiliary functions related to filenames of Yokogawa-microscope images.

_get_plate_name(plate_prefix)

Two kinds of plate_prefix values are handled in a special way:

1. Filenames from FMI, with successful barcode reading: 210305NAR005AAN_210416_164828 with plate name 210305NAR005AAN;
2. Filenames from FMI, with failed barcode reading: yymmdd_hhmmss_210416_164828 with plate name RS{yymmddhhmmss}.

For all non-matching filenames, plate name is plate_prefix.

PARAMETER	DESCRIPTION
plate_prefix	TBD TYPE: str

Source code in fractal_tasks_core/cellvoyager/filenames.py

def _get_plate_name(plate_prefix: str) -> str:
    """
    Two kinds of plate_prefix values are handled in a special way:

    1. Filenames from FMI, with successful barcode reading:
       `210305NAR005AAN_210416_164828` with plate name `210305NAR005AAN`;
    2. Filenames from FMI, with failed barcode reading:
       `yymmdd_hhmmss_210416_164828` with plate name `RS{yymmddhhmmss}`.

    For all non-matching filenames, plate name is `plate_prefix`.

    Args:
        plate_prefix: TBD
    """

    fields = plate_prefix.split("_")

    # FMI (successful barcode reading)
    if (
        len(fields) == 3
        and len(fields[1]) == 6
        and len(fields[2]) == 6
        and fields[1].isdigit()
        and fields[2].isdigit()
    ):
        barcode, img_date, img_time = fields[:]
        plate = barcode
    # FMI (failed barcode reading)
    elif (
        len(fields) == 4
        and len(fields[0]) == 6
        and len(fields[1]) == 6
        and len(fields[2]) == 6
        and len(fields[3]) == 6
        and fields[0].isdigit()
        and fields[1].isdigit()
        and fields[2].isdigit()
        and fields[3].isdigit()
    ):
        scan_date, scan_time, img_date, img_time = fields[:]
        plate = f"RS{scan_date + scan_time}"
    # All non-matching cases
    else:
        plate = plate_prefix

    return plate

glob_with_multiple_patterns(*, folder, include_patterns=None, exclude_patterns=None)

List all the items (files and folders) in a given folder that simultaneously match a series of glob include_patterns and do not match any of the exclude_patterns.

PARAMETER	DESCRIPTION
folder	Base folder where items will be searched. TYPE: str
include_patterns	If specified, the list of patterns (defined as in https://docs.python.org/3/library/fnmatch.html) that item names will match with. TYPE: Sequence[str] DEFAULT: None

Source code in fractal_tasks_core/cellvoyager/filenames.py

def glob_with_multiple_patterns(
    *,
    folder: str,
    include_patterns: Sequence[str] = None,
    exclude_patterns: Sequence[str] = None,
) -> set[str]:
    """
    List all the items (files and folders) in a given folder that
    simultaneously match a series of glob include_patterns and do not match
    any of the exclude_patterns.

    Args:
        folder: Base folder where items will be searched.
        include_patterns: If specified, the list of patterns (defined as in
            https://docs.python.org/3/library/fnmatch.html) that item
            names will match with.
    """
    # Sanitize base-folder path
    if folder.endswith("/"):
        actual_folder = folder[:-1]
    else:
        actual_folder = folder[:]

    # If not pattern is specified, look for *all* items in the base folder
    if not include_patterns:
        include_patterns = ["*"]
    if not exclude_patterns:
        exclude_patterns = []

    # Combine multiple glob searches (via set intersection)
    logging.info(f"[glob_with_multiple_patterns] {include_patterns=}")
    items = None
    for pattern in include_patterns:
        new_matches = glob(f"{actual_folder}/{pattern}")
        if items is None:
            items = set(new_matches)
        else:
            items = items.intersection(new_matches)
    items = items or set()

    # Combine all exclude patterns
    exclude_items = set()
    for pattern in exclude_patterns:
        new_matches = glob(f"{actual_folder}/{pattern}")
        if len(exclude_items) == 0:
            exclude_items = set(new_matches)
        else:
            exclude_items.update(new_matches)
    exclude_items = exclude_items or set()

    # Remove exclude_items from included list
    consensus_items = items - exclude_items

    logging.info(
        f"[glob_with_multiple_patterns] Found {len(consensus_items)} items"
    )

    return consensus_items

parse_filename(filename)

Parse image metadata from filename.

PARAMETER	DESCRIPTION
filename	Name of the image. TYPE: str

RETURNS	DESCRIPTION
dict[str, str]	Metadata dictionary.

Source code in fractal_tasks_core/cellvoyager/filenames.py

def parse_filename(filename: str) -> dict[str, str]:
    """
    Parse image metadata from filename.

    Args:
        filename: Name of the image.

    Returns:
        Metadata dictionary.
    """

    # Remove extension and folder from filename
    filename = Path(filename).with_suffix("").name

    output = {}

    # Split filename into plate_prefix + well + TFLAZC
    filename_fields = filename.split("_")
    if len(filename_fields) < 3:
        raise ValueError(f"{filename} not valid")
    output["plate_prefix"] = "_".join(filename_fields[:-2])
    output["plate"] = _get_plate_name(output["plate_prefix"])

    # Assign well
    output["well"] = filename_fields[-2]

    # Assign TFLAZC
    TFLAZC = filename_fields[-1]
    metadata = re.split(r"([0-9]+)", TFLAZC)
    if metadata[-1] != "" or len(metadata) != 13:
        raise ValueError(f"Something wrong with {filename=}, {TFLAZC=}")
    # Remove 13-th (and last) element of the metadata list (an empty string)
    metadata = metadata[:-1]
    # Fill output dictionary
    for ind, key in enumerate(metadata[::2]):
        value = metadata[2 * ind + 1]
        if key.isdigit() or not value.isdigit():
            raise ValueError(
                f"Something wrong with {filename=}, for {key=} {value=}"
            )
        output[key] = value
    return output