Skip to content

hdf5

__all__ module-attribute 

__all__ = [
    "parse_channel_hdf5",
    "parse_chromatogram_hdf5",
    "parse_experiment_hdf5",
]

parse_channel_hdf5 

parse_channel_hdf5(
    path: str | Path,
) -> ChannelChromatograms

Parse a standalone ChromStream channel HDF5 file into a ChannelChromatograms object.

Parameters:

  • path (str | Path) –

    Path to the channel HDF5 file written by ChromStream.

Raises:

Source code in src/chromstream/parsers/hdf5.py 
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
def parse_channel_hdf5(path: str | Path) -> ChannelChromatograms:
    """Parse a standalone ChromStream channel HDF5 file into a ChannelChromatograms object.

    Args:
        path: Path to the channel HDF5 file written by ChromStream.

    Raises:
        FileNotFoundError: If the file does not exist.
        ValueError: If the file schema or layout does not match the expected format.
    """
    input_path = Path(path)
    if not input_path.exists():
        raise FileNotFoundError(f"File not found: {input_path}")

    with h5py.File(input_path, "r") as hdf:
        _require_schema(hdf, SCHEMA_CHANNEL)
        channel = _read_channel_group(hdf, path=input_path)

    return channel

parse_chromatogram_hdf5 

parse_chromatogram_hdf5(path: str | Path) -> Chromatogram

Parse a standalone ChromStream chromatogram HDF5 file into a Chromatogram object.

Parameters:

  • path (str | Path) –

    Path to the chromatogram HDF5 file written by ChromStream.

Raises:

Source code in src/chromstream/parsers/hdf5.py 
156
157
158
159
160
161
162
163
164
165
166
def parse_chromatogram_hdf5(path: str | Path) -> Chromatogram:
    """Parse a standalone ChromStream chromatogram HDF5 file into a Chromatogram object.

    Args:
        path: Path to the chromatogram HDF5 file written by ChromStream.

    Raises:
        FileNotFoundError: If the file does not exist.
        ValueError: If the file schema or layout does not match the expected format.
    """
    return _parse_chromatogram_hdf5_with_index(path)[1]

parse_experiment_hdf5 

parse_experiment_hdf5(path: str | Path) -> Experiment

Parse a ChromStream HDF5 experiment file into an Experiment object.

Parameters:

  • path (str | Path) –

    Path to the HDF5 file written by ChromStream.

Returns:

  • Experiment ( Experiment ) –

    Reconstructed experiment containing persisted channels and chromatograms.

Raises:

  • FileNotFoundError –

    If the file does not exist.

  • ValueError –

    If the file schema or layout does not match the expected format.

  • OSError –

    If the file cannot be opened as HDF5.

Source code in src/chromstream/parsers/hdf5.py 
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
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
def parse_experiment_hdf5(path: str | Path) -> Experiment:
    """Parse a ChromStream HDF5 experiment file into an Experiment object.

    Args:
        path: Path to the HDF5 file written by ChromStream.

    Returns:
        Experiment: Reconstructed experiment containing persisted channels and chromatograms.

    Raises:
        FileNotFoundError: If the file does not exist.
        ValueError: If the file schema or layout does not match the expected format.
        OSError: If the file cannot be opened as HDF5.
    """
    input_path = Path(path)
    if not input_path.exists():
        raise FileNotFoundError(f"File not found: {input_path}")

    with h5py.File(input_path, "r") as hdf:
        schema = _require_schema(hdf, SCHEMA_EXPERIMENT)

        label = _require_attr(hdf.attrs, "label", "file root")
        creation_date = (
            _parse_timestamp(
                hdf.attrs["creation_date"], "file root attribute 'creation_date'"
            )
            if "creation_date" in hdf.attrs
            else None
        )
        author = (
            _from_hdf5_attr(hdf.attrs["author"]) if "author" in hdf.attrs else None
        )
        metadata = {
            key: _from_hdf5_attr(value)
            for key, value in hdf.attrs.items()
            if key not in RESERVED_EXPERIMENT_ATTRS
        }

        if "Channels" not in hdf:
            raise ValueError("Missing required group 'Channels' in file root.")
        channels_group = hdf["Channels"]
        if not isinstance(channels_group, h5py.Group):
            raise ValueError("'Channels' must be an HDF5 group.")

        experiment = Experiment(
            name=str(label),
            schema=str(schema),
            author=str(author) if author is not None else None,
            creation_date=creation_date,
            metadata=metadata,
        )

        for channel_name in channels_group:
            channel_group = channels_group[channel_name]
            if not isinstance(channel_group, h5py.Group):
                raise ValueError(
                    f"Channel entry {channel_name!r} must be an HDF5 group."
                )
            channel = _read_channel_group(
                channel_group, path=input_path, expected_name=channel_name
            )
            experiment.add_channel(channel_name, channel)

    return experiment