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rbr

RBR Ltd. is a company that specializes in oceanographic instruments and sensors.

They provide a range of instruments for measuring various parameters in the ocean, including temperature, salinity, pressure, and more.

rtext(file_path, encoding='UTF-8', header_end='NumberOfSamples', errors='raise')

Read RBR legacy R-Text Engineering format.

Parameters:

Name Type Description Default
file_path Path

RBR R-Text file path

 required
encoding str

File encoding. Defaults to "UTF-8".

 'UTF-8'
header_end str

End of the metadata header. Defaults to "NumberOfSamples".

 'NumberOfSamples'
errors str

Error handling. Defaults to "raise".

 'raise'

Raises:

Type Description
RuntimeError

File length do not match expected Number of Samples

Returns:

Name Type Description
Dataset Dataset

Parsed Dataset
Source code in ocean_data_parser/parsers/rbr.py 
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def rtext(
    file_path: str,
    encoding="UTF-8",
    header_end: str = "NumberOfSamples",
    errors: str = "raise",
) -> Dataset:
    """Read RBR legacy R-Text Engineering format.

    Args:
        file_path (Path): RBR R-Text file path
        encoding (str, optional): File encoding. Defaults to "UTF-8".
        header_end (str, optional): End of the metadata header.
            Defaults to "NumberOfSamples".
        errors (str, optional): Error handling. Defaults to "raise".

    Raises:
        RuntimeError: File length do not match expected Number of Samples

    Returns:
        Dataset: Parsed Dataset
    """
    line = ""
    metadata = {}
    with open(file_path, encoding=encoding) as fid:
        while not line.startswith(header_end):
            # Read line by line
            line = fid.readline()

            if re.match(r"\s*.*(=).*", line):
                key, item = re.split(r"\s*[:=]\s*", line, 1)

                # If line has key[index].subkey format
                if re.match(r".*\[\d+\]\..*", key):
                    items = re.search(r"(.*)\[(\d+)\]\.(.*)", key)
                    key = items[1]
                    index = items[2]
                    subkey = items[3].strip()

                    if key not in metadata:
                        metadata[key] = {}
                    if index not in metadata[key]:
                        metadata[key][index] = {}

                    metadata[key][index][subkey] = item.strip()

                else:
                    metadata[key] = item.strip()
            elif re.match(r"^\s+$", line):
                continue
            else:
                print(f"Ignored: {line}")
        # Read NumberOFSamples line
        metadata["number_of_samples"] = int(line.rsplit("=")[1])

        # Read data
        ds = pd.read_csv(fid, sep=r"\s\s+", engine="python").to_xarray()

        # Make sure that line count is good
        if ds.dims["index"] != metadata["number_of_samples"]:
            if errors == "raise":
                raise RuntimeError(
                    "Data length do not match expected Number of Samples"
                )
            else:
                logger.warning("Data length do not match expected Number of Samples")

        # Convert to datset
        ds.attrs = {
            **metadata,
            "instrument_manufacturer": "RBR",
            "instrument_model": metadata["Model"],
            "instrument_sn": metadata["Serial"],
        }

        ds = standardize_dataset(ds)
        return ds