Skip to content

rbr

RBR Ltd.

https://rbr-global.com/

rtext(file_path, encoding='UTF-8', output=None)

Read RBR R-Text format. :param errors: default ignore :param encoding: default UTF-8 :param file_path: path to file to read :return: metadata dictionary dataframe

Source code in ocean_data_parser/parsers/rbr.py 
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
def rtext(file_path, encoding="UTF-8", output=None):
    """
    Read RBR R-Text format.
    :param errors: default ignore
    :param encoding: default UTF-8
    :param file_path: path to file to read
    :return: metadata dictionary dataframe
    """
    # MON File Header end
    header_end = "NumberOfSamples"

    with open(file_path, encoding=encoding) as fid:
        line = ""
        section = "header_info"
        metadata = {section: {}}

        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"]:
            raise RuntimeError("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