Spectrum

The position of spectra is not yet completely set in ixdat.

A spectrum is in essence just a 1-D field where a response variable (e.g. counts, detector current, adsorption) lives on a space defined by a scanning variable (e.g. wavelength, mass-to-charge ratio, two-theta). As such it could be a DataSeries on par with ValueSeries (a 1-D field with a value living in a space defined by a TimeSeries). A Spectrum is however a stand-alone output of an experimental technique. It could also be a type of Measurement.

As it is now, Spectrum is its own base class on par with Measurement, with its own table (i.e. the Spectrum class inherits directly from Saveable). It has properties which give quick access to the scanning variable and response as x and y, respectively. It also has its own plotter and exporter.

Similar questions can be raised about a sequence of spectra - whether it is a Measurement or a 2-D field. As it is now, sequences of spectra are represented by SpectrumSeries, which inherits from Spectrum.

The spectra module

class ixdat.spectra.Spectrum(name, technique='spectrum', metadata=None, sample_name=None, reader=None, tstamp=None, field=None, field_id=None)

The Spectrum class.

A spectrum is a data structure including one-dimensional arrays of x and y variables of equal length. Typically, information about the state of a sample can be obtained from a plot of y (e.g. absorbance OR intensity OR counts) vs x (e.g energy OR wavelength OR angle OR mass-to-charge ratio). Even though in reality it takes time to require a spectrum, a spectrum is considered to represent one instance in time.

In ixdat, the data of a spectrum is organized into a Field, where the y-data is considered to span a space defined by the x-data and the timestamp. If the x-data has shape (N, ), then the y-data has shape (N, 1) to span the x-axis and the single-point t axis.

The Spectrum class makes the data in this field intuitively available. If spec is a spectrum, spec.x and spec.y give access to the x and y data, respectively, while spec.xseries and spec.yseries give the corresponding DataSeries.

data_objects

The data-containing objects that need to be saved when the spectrum is saved.

For a field to be correctly saved and loaded, its axes_series must be saved first. So there are three series in the data_objects to return FIXME: with backend-specifying id’s, field could check for itself whether FIXME: its axes_series are already in the database.

field

Since a spectrum can be loaded lazily, we make sure the field is loaded

field_id

The id of the field

classmethod from_data(x, y, tstamp=None, x_name='x', y_name='y', x_unit_name=None, y_unit_name=None, **kwargs)

Initiate a spectrum from data. Does so via cls.from_series

Parameters:

• x (np array) – x data
• y (np array) – y data
• tstamp (timestamp) – the timestamp of the spectrum. Defaults to None.
• x_name (str) – Name of the x variable. Defaults to ‘x’
• y_name (str) – Name of the y variable. Defaults to ‘y’
• x_unit_name (str) – Name of the x unit. Defaults to None
• y_unit_name (str) – Name of the y unit. Defaults to None
• kwargs – key-word arguments are passed on ultimately to cls.__init__

classmethod from_field(field, **kwargs)

Initiate a spectrum from data. Does so via cls.from_field

Parameters:

• field (Field) – The field containing all the data of the spectrum. field.data is the y-data, which is considered to span x and t. field.axes_series[0] is a DataSeries with the x data. field.axes_series[1] is a TimeSeries with one time point.
• kwargs – key-word arguments are passed on ultimately to cls.__init__

classmethod from_series(xseries, yseries, tstamp, **kwargs)

Initiate a spectrum from data. Does so via cls.from_field

Parameters:

• xseries (DataSeries) – a series with the x data
• yseries (DataSeries) – a series with the y data. The y data should be a vector of the same length as the x data.
• tstamp (timestamp) – the timestamp of the spectrum. Defaults to None.
• kwargs – key-word arguments are passed on ultimately to cls.__init__

plotter

The default plotter for Measurement is ValuePlotter.

classmethod read(path_to_file, reader, **kwargs)

Return a Measurement object from parsing a file with the specified reader

Parameters:

• path_to_file (Path or str) – The path to the file to read
• reader (str or Reader class) – The (name of the) reader to read the file with.
• kwargs – key-word arguments are passed on to the reader’s read() method.

series_list

A Spectrum’s series list includes its field and its axes_series.

tseries

The TimeSeries of a spectrum is a single point [0] and its tstamp

x

The x data is the data attribute of the xseries

x_name

The name of the x variable is the name attribute of the xseries

xseries

The x DataSeries is the first axis of the field

y

The y data is the data attribute of the field

y_name

The name of the y variable is the name attribute of the field

yseries

The yseries is a DataSeries reduction of the field

class ixdat.spectra.SpectrumSeries(*args, **kwargs)

plotter

The default plotter for Measurement is ValuePlotter.

t

The time array of a SectrumSeries is the data of its tseries. Note that it it is not sorted!

t_name

The name of the time variable of the spectrum series

tseries

The TimeSeries of a SectrumSeries is the 0’th axis of its field. Note that its data is not sorted!

x

The x (scanning variable) data

x_name

The name of the scanning variable

xseries

The x-axis DataSeries of a SectrumSeries is the 1’st axis of its field

y_average

The y-data of the average spectrum

yseries

The yseries is a DataSeries reduction of the field