evedata.measurement.entities.measurement module

Entities representing a measurement, typically read from an eveH5 file.

Contents

A measurement generally reflects all the data obtained during a measurement. However, to plot data or to perform some analysis, usually we need data together with an axis (or multiple axes for nD data), where data (“intensity values”) and axis values come from different HDF5 datasets. Furthermore, there may generally be the need/interest to plot arbitrary data against each other, i.e. channel data vs. channel data and axis data vs. axis data, not only channel data vs. axis data. This is the decisive difference between the Measurement entity and the Measurement facade, with the latter having the additional attributes for storing the data to work on.

Overview

A first overview of the classes implemented in this module and their hierarchy is given in the UML diagram below. Key is the Measurement entity. Data and Axis seem not to be used here, but become essential in the corresponding Measurement facade. See Fig. 18 and the measurement.boundaries.measurement module for details.

Fig. 42 Class hierarchy of the measurement.entities.measurement module. Currently, this diagram just reflects first ideas for a more abstract representation of a measurement as compared to the data model of the evefile subpackage. Devices in the scan_modules are all the detector(channel)s and motor(axe)s used in a scan. Distinguishing between detector(channel)s/motor(axe)s, beamline, and machine can (at least partially) happen based on the data type: detector(channel)s are ChannelData, motor(axe)s are AxisData. Machine and beamline parameters are more tricky, as they can be DeviceData (from the “monitor” section) as well as ChannelData (and AxisData for shutters and alike?) from the original “main” and “snapshot” sections. Scan and Setup inherit directly from their counterparts in the evefile.entities.file module. Data and Axis seem not to be used here, but become essential in the corresponding Measurement facade. See Fig. 18 for details.

Key aspects

• The Measurement class, although quite similar on first sight to the EveFile class, does not inherit from there nor from File. Nevertheless, the contents of the attributes are in many cases the same objects as those of these other two classes.

Module documentation

class evedata.measurement.entities.measurement.Measurement

Bases: object

Representation of all information available for a given measurement.

Individual measurements are saved in HDF5 files using a particular schema (eveH5). Besides file-level metadata, there are log messages, a scan description (originally an XML/SCML file), and the actual data.

The data are organised in three functionally different sections: scan_modules, machine, and beamline.

scan_modules

Modules the scan consists of.

Each item is an instance of evedata.evefile.entities.file.ScanModule and contains the data recorded within the given scan module.

In case of no scan description present, a “dummy” scan module will be created containing all data.

Type:

dict

machine

Data recorded from the machine involved in a measurement.

Each item is an instance of evedata.evefile.entities.data.Data.

Type:

dict

beamline

Data recorded from the beamline involved in a measurement.

Each item is an instance of evedata.evefile.entities.data.Data.

Type:

dict

device_snapshots

Snapshot data recorded from the devices involved in a scan.

Each item is an instance of evedata.evefile.entities.data.MeasureData.

Snapshots reflect, as their name says, the state of the devices at a given point in time. Snapshots of devices involved in a scan are used in data joining to get additional reference points.

Type:

dict

metadata

Measurement metadata

Type:

evedata.measurement.entities.metadata.Metadata

log_messages

Log messages from an individual measurement

Each item in the list is an instance of evedata.evefile.entities.file.LogMessage.

Type:

list

scan

Description of the actual scan.

Type:

evedata.scan.boundaries.scan.Scan

station

Description of the actual setup.

Type:

Station

Raises:

exception – Short description when and why raised

class evedata.measurement.entities.measurement.Data(data=array([], dtype=float64), axes=None)

Bases: object

Unit containing both, numeric data and corresponding axes.

The data class ensures consistency in terms of dimensions between numerical data and axes.

Parameters:

• data (numpy.ndarray) – Numerical data

• axes (list) –

  List of objects of type aspecd.dataset.Axis

  The number of axes needs to be consistent with the dimensions of data.

  Axes will be set automatically when setting data. Hence, the easiest is to first set data and only afterwards set axis values.

Raises:

• IndexError – Raised if number of axes is inconsistent with data dimensions

• IndexError – Raised if axes values are inconsistent with data

property data

Get or set (numeric) data.

Note

If you set data that have different dimensions to the data previously stored in the dataset, the axes values will be set to an array with indices corresponding to the size of the respective data dimension. You will most probably assign proper axis values afterwards. On the other hand, all other information stored in the axis object will be retained, namely quantity, unit, and label.

property axes

Get or set axes.

If you set axes, they will be checked for consistency with the data. Therefore, first set the data and only afterwards the axes, with values corresponding to the dimensions of the data.

Raises:

• IndexError – Raised if number of axes is inconsistent with data dimensions

• IndexError – Raised if axes values are inconsistent with data dimensions

class evedata.measurement.entities.measurement.Axis

Bases: object

Axis for data.

An axis contains always both, numerical values as well as the metadata necessary to create axis labels and to make sense of the numerical information.

quantity

quantity of the numerical data, usually used as first part of an automatically generated axis label

Type:

str

unit

unit of the numerical data, usually used as second part of an automatically generated axis label

Type:

str

symbol

symbol for the quantity of the numerical data, usually used as first part of an automatically generated axis label

Type:

str

label

manual label for the axis, particularly useful in cases where no quantity and unit are provided or should be overwritten.

Type:

str

Note

There are three alternative ways of writing axis labels, one with using the quantity name and the unit, one with using the quantity symbol and the unit, and one using both, quantity name and symbol, usually separated by comma. Quantity and unit shall always be separated by a slash. Which way you prefer is a matter of personal taste and given context.

Raises:

• ValueError – Raised when trying to set axis values to another type than numpy array

• IndexError – Raised when trying to set axis values to an array with more than one dimension. Raised if index does not have the same length as values.

property values

Get or set the numerical axis values.

Values require to be a one-dimensional numpy array. Trying to set values to either a different type that cannot be converted to a numpy array or a numpy array with more than one dimension will raise a corresponding error.

Raises:

• ValueError – Raised if axis values are of wrong type

• IndexError – Raised if axis values are of wrong dimension, i.e. not a vector

property equidistant

Return whether the axes values are equidistant.

True if the axis values are equidistant, False otherwise. None in case of no axis values.

The property is set automatically if axis values are set and therefore read-only.

While simple plotting of data values against non-uniform axes with non-equidistant values is usually straightforward, many processing steps rely on equidistant axis values in their simplest possible implementation.