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nexus_scan

NeXus Scan Classes

NexusScan - NeXus Scan class, lazy loader of scan files NexusDataHolder - Loads scan data and meta data into attributes

NexusDataHolder

Bases: DataHolder, NexusScan

Nexus data holder class - Automatically reads scannable and metadata from file - acts like the old .dat DataHolder class - has additional functions to read data from NeXus file

Example: scan = NexusDataHolder('12345.nxs') scan.eta -> returns array scan.metadata.metadata -> returns value scan('signal') -> evaluate expression

Parameters:

Name Type Description Default
filename str | None

path to Nexus file

 required
hdf_map NexusMap | None

NexusMap object or None to generate

 None
flatten_scannables bool

if True, flattens all scannable arrays to 1D

 True
Source code in mmg_toolbox/nexus/nexus_scan.py 
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class NexusDataHolder(DataHolder, NexusScan):
    """
    Nexus data holder class
     - Automatically reads scannable and metadata from file
     - acts like the old .dat DataHolder class
     - has additional functions to read data from NeXus file

    Example:
        scan = NexusDataHolder('12345.nxs')
        scan.eta -> returns array
        scan.metadata.metadata -> returns value
        scan('signal') -> evaluate expression

    :param filename: path to Nexus file
    :param hdf_map: NexusMap object or None to generate
    :param flatten_scannables: if True, flattens all scannable arrays to 1D
    """
    filename: str
    map: NexusMap
    metadata: DataHolder

    def __init__(self, filename: str | None, hdf_map: NexusMap | None = None, flatten_scannables: bool = True):
        NexusScan.__init__(self, filename, hdf_map)

        with load_hdf(filename) as hdf:
            metadata = self.map.get_metadata(hdf)
            scannables = self.map.get_scannables(hdf, flatten=flatten_scannables)
        DataHolder.__init__(self, **scannables)
        self.metadata = DataHolder(**metadata)

    def __repr__(self):
        return f"NexusDataHolder('{self.filename}')"

NexusScan

Bases: NexusLoader

Light-weight NeXus file reader

Example: scan = NexusScan('scan.nxs') scan('scan_command') -> returns value

Parameters:

Name Type Description Default
nxs_filename str

path to nexus file

 required
hdf_map NexusMap | None

NexusMap object or None

 None
Source code in mmg_toolbox/nexus/nexus_scan.py 
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class NexusScan(NexusLoader):
    """
    Light-weight NeXus file reader

    Example:
        scan = NexusScan('scan.nxs')
        scan('scan_command') -> returns value

    :param nxs_filename: path to nexus file
    :param hdf_map: NexusMap object or None
    """
    MAX_STR_LEN: int = 100

    def __init__(self, nxs_filename: str, hdf_map: NexusMap | None = None):
        super().__init__(nxs_filename, hdf_map)

        from mmg_toolbox.utils.fitting import ScanFitManager, poisson_errors
        self.fit = ScanFitManager(self)
        self._error_function = poisson_errors
        from mmg_toolbox.plotting.scan_plot_manager import ScanPlotManager
        self.plot = ScanPlotManager(self)

    def __repr__(self):
        return f"NexusScan('{self.filename}')"

    def scan_number(self) -> int:
        return get_scan_number(self.filename)

    def title(self) -> str:
        return f"#{self.scan_number()}"

    def label(self) -> str:
        return f"#{self.scan_number()}"

    def load_hdf(self) -> h5py.File:
        """Load the Hdf file"""
        return load_hdf(self.filename)

    def datasets(self, *args) -> list[h5py.Dataset]:
        """Return HDF5 datasets from NeXus file (leaves file in open state)"""
        with self.load_hdf() as hdf:
            return [hdf[self.map.combined[name]] for name in args]

    def arrays(self, *args, units: str = '', default: np.ndarray = np.array([np.nan])) -> list[np.ndarray]:
        """Return Numpy arrays"""
        with self.load_hdf() as hdf:
            return [
                get_dataset_value(self.map.combined[name], hdf, units=units, default=default)
                for name in args
            ]

    def values(self, *args, value_func=np.mean,
               units: str = '', default: np.ndarray = np.array(np.nan)) -> list[np.floating]:
        """Return float values"""
        with self.load_hdf() as hdf:
            return [
                value_func(get_dataset_value(self.map.combined[name], hdf, units=units, default=default))
                for name in args
            ]

    def times(self, *args) -> list[datetime.datetime]:
        """Return datetime object"""
        with self.load_hdf() as hdf:
            return [dataset2data(hdf[self.map.combined[name]]) for name in args]

    def strings(self, *args, units=False) -> list[str]:
        """Return string value"""
        with self.load_hdf() as hdf:
            return [dataset2str(hdf[self.map.combined[name]], units=units) for name in args]

    def image(self, index: int | tuple | slice | None = None) -> np.ndarray:
        """Return image or selection from default detector"""
        with self.load_hdf() as hdf:
            return self.map.get_image(hdf, index)

    def table(self, delimiter=', ', string_spec='', format_spec='f', default_decimals=8) -> str:
        """Return data table"""
        with self.load_hdf() as hdf:
            return self.map.create_scannables_table(hdf, delimiter, string_spec, format_spec, default_decimals)

    #TODO: Remove this?
    def get_plot_data(self, x_axis: str = 'axes0', y_axis: str = 'signal0') -> dict:
        with self.load_hdf() as hdf:
            cmd = self.map.eval(hdf, Md.cmd)
            if len(cmd) > self.MAX_STR_LEN:
                cmd = shorten_string(cmd)
            xdata = self.map.eval(hdf, x_axis)
            ydata = self.map.eval(hdf, y_axis)
            yerror = self._error_function(ydata)
            x_lab, y_lab = self.map.generate_ids(x_axis, y_axis, modify_missing=False)
            return {
                'x': xdata,
                'y': ydata,
                'yerror': yerror,
                'xlabel': x_lab,
                'ylabel': y_lab,
                'title': f"#{self.scan_number()}\n{cmd}"
            }

    def xas_scan(self) -> SpectraContainer:
        """Load XAS Spectra"""
        return load_xas_scans(self.filename)[0]

    def instrument_model(self) -> NXInstrumentModel:
        """return instrument model"""
        with self.load_hdf() as hdf:
            return NXInstrumentModel(hdf)

arrays(*args, units='', default=np.array([np.nan]))

Return Numpy arrays

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def arrays(self, *args, units: str = '', default: np.ndarray = np.array([np.nan])) -> list[np.ndarray]:
    """Return Numpy arrays"""
    with self.load_hdf() as hdf:
        return [
            get_dataset_value(self.map.combined[name], hdf, units=units, default=default)
            for name in args
        ]

datasets(*args)

Return HDF5 datasets from NeXus file (leaves file in open state)

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def datasets(self, *args) -> list[h5py.Dataset]:
    """Return HDF5 datasets from NeXus file (leaves file in open state)"""
    with self.load_hdf() as hdf:
        return [hdf[self.map.combined[name]] for name in args]

image(index=None)

Return image or selection from default detector

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def image(self, index: int | tuple | slice | None = None) -> np.ndarray:
    """Return image or selection from default detector"""
    with self.load_hdf() as hdf:
        return self.map.get_image(hdf, index)

instrument_model()

return instrument model

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def instrument_model(self) -> NXInstrumentModel:
    """return instrument model"""
    with self.load_hdf() as hdf:
        return NXInstrumentModel(hdf)

load_hdf()

Load the Hdf file

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def load_hdf(self) -> h5py.File:
    """Load the Hdf file"""
    return load_hdf(self.filename)

strings(*args, units=False)

Return string value

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def strings(self, *args, units=False) -> list[str]:
    """Return string value"""
    with self.load_hdf() as hdf:
        return [dataset2str(hdf[self.map.combined[name]], units=units) for name in args]

table(delimiter=', ', string_spec='', format_spec='f', default_decimals=8)

Return data table

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def table(self, delimiter=', ', string_spec='', format_spec='f', default_decimals=8) -> str:
    """Return data table"""
    with self.load_hdf() as hdf:
        return self.map.create_scannables_table(hdf, delimiter, string_spec, format_spec, default_decimals)

times(*args)

Return datetime object

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def times(self, *args) -> list[datetime.datetime]:
    """Return datetime object"""
    with self.load_hdf() as hdf:
        return [dataset2data(hdf[self.map.combined[name]]) for name in args]

values(*args, value_func=np.mean, units='', default=np.array(np.nan))

Return float values

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def values(self, *args, value_func=np.mean,
           units: str = '', default: np.ndarray = np.array(np.nan)) -> list[np.floating]:
    """Return float values"""
    with self.load_hdf() as hdf:
        return [
            value_func(get_dataset_value(self.map.combined[name], hdf, units=units, default=default))
            for name in args
        ]

xas_scan()

Load XAS Spectra

Source code in mmg_toolbox/nexus/nexus_scan.py 
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def xas_scan(self) -> SpectraContainer:
    """Load XAS Spectra"""
    return load_xas_scans(self.filename)[0]