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| """ | ||
| Extractors for data files generated by various proprietary Agilent software. | ||
| """ |
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| @@ -1,7 +1,173 @@ | ||
| from yadg.parsers.chromtrace.agilentch import process as extract | ||
| """ | ||
| **agilent.ch** | ||
| -------------- | ||
| supports = { | ||
| "agilent.ch", | ||
| Extractor of Agilent OpenLab binary signal trace files (``.ch`` and ``.it``). | ||
| Currently supports version "179" of the files. Version information is defined in | ||
| the ``magic_values`` (parameters & metadata) and `data_dtypes` (data) dictionaries. | ||
| Adapted from `ImportAgilent.m <https://bit.ly/3HSelIR>`_ and | ||
| `aston <https://github.com/bovee/Aston>`_. | ||
| Usage | ||
| ````` | ||
| Available since ``yadg-4.0``. | ||
| .. autopydantic_model:: dgbowl_schemas.yadg.dataschema_5_1.filetype.Agilent_ch | ||
| Schema | ||
| `````` | ||
| .. code-block:: yaml | ||
| datatree.DataTree: | ||
| {{ detector_name }}: | ||
| coords: | ||
| uts: !!float # Unix timestamp | ||
| elution_time: !!float # Elution time | ||
| data_vars: | ||
| signal: (uts, elution_time) # Signal data | ||
| Metadata | ||
| ```````` | ||
| The following metadata is extracted: | ||
| - ``sampleid``: Sample name. | ||
| - ``username``: User name used to generate the file. | ||
| - ``method``: Name of the chromatographic method. | ||
| - ``version``: Version of the CH file (only "179" is currently supported.) | ||
| Notes on file structure | ||
| ``````````````````````` | ||
| The following magic values are used: | ||
| .. code :: | ||
| 0x0000 "version magic" | ||
| 0x0108 "data offset" | ||
| 0x011a "x-axis minimum (ms)" | ||
| 0x011e "x-axis maximum (ms)" | ||
| 0x035a "sample ID" | ||
| 0x0559 "description" | ||
| 0x0758 "username" | ||
| 0x0957 "timestamp" | ||
| 0x09e5 "instrument name" | ||
| 0x09bc "inlet" | ||
| 0x0a0e "method" | ||
| 0x104c "y-axis unit" | ||
| 0x1075 "detector name" | ||
| 0x1274 "y-axis intercept" | ||
| 0x127c "y-axis slope" | ||
| Data is stored in a consecutive set of ``<f8``, starting at the offset (calculated | ||
| as ``offset = ("data offset" - 1) * 512``) until the end of the file. | ||
| .. codeauthor:: | ||
| Peter Kraus | ||
| """ | ||
|
|
||
| import numpy as np | ||
| from yadg import dgutils | ||
| from yadg.dgutils.dateutils import str_to_uts | ||
| import xarray as xr | ||
| from datatree import DataTree | ||
|
|
||
| magic_values = {} | ||
| magic_values["179"] = { | ||
| 0x035A: ("sampleid", "utf-16"), | ||
| 0x0559: ("description", "utf-16"), | ||
| 0x0A0E: ("method", "utf-16"), | ||
| 0x0758: ("username", "utf-16"), | ||
| 0x0957: ("timestamp", "utf-16"), | ||
| 0x09E5: ("instrument", "utf-16"), | ||
| 0x09BC: ("inlet", "utf-16"), | ||
| 0x104C: ("yunit", "utf-16"), | ||
| 0x1075: ("tracetitle", "utf-16"), | ||
| 0x0108: ("offset", ">i4"), # (x-1) * 512 | ||
| 0x011A: ("xmin", ">f4"), # / 60000 | ||
| 0x011E: ("xmax", ">f4"), # / 60000 | ||
| 0x1274: ("intercept", ">f8"), | ||
| 0x127C: ("slope", ">f8"), | ||
| } | ||
|
|
||
| __all__ = ["supports", "extract"] | ||
| data_dtypes = {} | ||
| data_dtypes["179"] = (8, "<f8") | ||
|
|
||
|
|
||
| def extract( | ||
| *, | ||
| fn: str, | ||
| timezone: str, | ||
| **kwargs: dict, | ||
| ) -> DataTree: | ||
| with open(fn, "rb") as inf: | ||
| ch = inf.read() | ||
|
|
||
| magic = dgutils.read_value(ch, 0, "utf-8") | ||
| pars = {} | ||
| if magic in magic_values.keys(): | ||
| for offset, (tag, dtype) in magic_values[magic].items(): | ||
| v = dgutils.read_value(ch, offset, dtype) | ||
| pars[tag] = v | ||
| pars["end"] = len(ch) | ||
| dsize, ddtype = data_dtypes[magic] | ||
| pars["start"] = (pars["offset"] - 1) * 512 | ||
| nbytes = pars["end"] - pars["start"] | ||
| assert nbytes % dsize == 0 | ||
| npoints = nbytes // dsize | ||
|
|
||
| metadata = dict() | ||
| for k in ["sampleid", "username", "method"]: | ||
| metadata[k] = pars[k] | ||
| metadata["version"] = str(magic) | ||
|
|
||
| xsn = np.linspace(pars["xmin"] / 1000, pars["xmax"] / 1000, num=npoints) | ||
| xss = np.ones(npoints) * xsn[0] | ||
| ysn = ( | ||
| np.frombuffer( | ||
| ch, | ||
| offset=pars["start"], | ||
| dtype=ddtype, | ||
| count=npoints, | ||
| ) | ||
| * pars["slope"] | ||
| ) | ||
| yss = np.ones(npoints) * pars["slope"] | ||
|
|
||
| detector, title = pars["tracetitle"].split(",") | ||
|
|
||
| uts = str_to_uts( | ||
| timestamp=pars["timestamp"], format="%d-%b-%y, %H:%M:%S", timezone=timezone | ||
| ) | ||
|
|
||
| ds = xr.Dataset( | ||
| data_vars={ | ||
| "signal": ( | ||
| ["uts", "elution_time"], | ||
| [ysn], | ||
| {"units": pars["yunit"], "ancillary_variables": "signal_std_err"}, | ||
| ), | ||
| "signal_std_err": ( | ||
| ["uts", "elution_time"], | ||
| [yss], | ||
| {"units": pars["yunit"], "standard_name": "signal standard_error"}, | ||
| ), | ||
| "elution_time_std_err": ( | ||
| ["elution_time"], | ||
| xss, | ||
| {"units": "s", "standard_name": "elution_time standard_error"}, | ||
| ), | ||
| }, | ||
| coords={ | ||
| "elution_time": ( | ||
| ["elution_time"], | ||
| xsn, | ||
| {"units": "s", "ancillary_variables": "elution_time_std_err"}, | ||
| ), | ||
| "uts": (["uts"], [uts]), | ||
| }, | ||
| attrs={"title": title}, | ||
| ) | ||
| dt = DataTree.from_dict({detector: ds}) | ||
| dt.attrs = metadata | ||
| return dt |
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