orsopy.fileio.base

Implementation of the base classes for the ORSO header.

exception orsopy.fileio.base.ORSOResolveError[source]: Bases: ValueError

exception orsopy.fileio.base.ORSOSchemaWarning[source]: Bases: RuntimeWarning

class orsopy.fileio.base.Header[source]

Bases: object

The super class for all the items in the orso module.

classmethod from_dict(data_dict)[source]

Create class from dictionary as is returned from yaml file reader.

If user-supplied attributes are provided, they are not passed to the constructor but applied after instance generation.

property user_data

classmethod empty()[source]

Create an empty instance of this item containing all non-option attributes as None.

Return type:: Header
Returns:: Empty class.

static asdict(header)[source]

Static method for to_dict().

Parameters:: header (Header) – Object to convert to dictionary.
Return type:: dict
Returns:: Dictionary result.

to_dict()[source]

Produces a clean dictionary of the Header object, removing any optional attributes with the value None.

Return type:: dict
Returns:: Cleaned dictionary.

to_yaml()[source]

Return the yaml string for the Header item

Return type:: str
Returns:: Yaml string

yaml_representer(dumper)[source]

yaml_representer_compact(dumper)[source]

to_nexus(root=None, name=None)[source]

Produces an HDF5 representation of the Header object, removing any optional attributes with the value None.

Returns:: HDF5 object

class orsopy.fileio.base.OrsoDumper(stream, default_style=None, default_flow_style=False, canonical=None, indent=None, width=None, allow_unicode=None, line_break=None, encoding=None, explicit_start=None, explicit_end=None, version=None, tags=None, sort_keys=True)[source]

Bases: SafeDumper

represent_data(data)[source]

class orsopy.fileio.base.ErrorValue(error_value, error_type=None, value_is=None, distribution=None, comment=None)[source]

Bases: Header

Information about errors on a value.

error_value: float

error_type: Optional[Literal['uncertainty', 'resolution']] = None

value_is: Optional[Literal['sigma', 'FWHM']] = None

distribution: Optional[Literal['gaussian', 'triangular', 'uniform', 'lorentzian']] = None

yaml_representer(dumper)

property sigma

Return value converted to standard deviation.

The conversion factors can be found in common statistics and experimental physics text books or derived manually solving the variance definition integral. (e.g. Dekking, Michel (2005). A modern introduction to probability and statistics : understanding why and how. Springer, London, UK:) Values and some references available on Wikipedia, too.

comment: Optional[str] = None

class orsopy.fileio.base.Value(magnitude, unit=None, error=None, offset=None, comment=None)[source]

Bases: Header

A value or list of values with an optional unit.

magnitude: float

unit: Optional[str] = None

error: Optional[ErrorValue] = None

offset: Optional[float] = None

yaml_representer(dumper)

as_unit(output_unit)[source]: Returns the value as converted to the given unit.

comment: Optional[str] = None

class orsopy.fileio.base.ComplexValue(real, imag=None, unit=None, error=None, comment=None)[source]

Bases: Header

A value or list of values with an optional unit.

real: float

imag: Optional[float] = None

unit: Optional[str] = None

error: Optional[ErrorValue] = None

yaml_representer(dumper)

as_unit(output_unit)[source]: Returns the complex value as converted to the given unit.

comment: Optional[str] = None

class orsopy.fileio.base.ValueRange(min, max, unit=None, individual_magnitudes=None, offset=None, comment=None)[source]

Bases: Header

A range or list of ranges with mins, maxs, and an optional unit.

min: float

max: float

unit: Optional[str] = None

individual_magnitudes: Optional[List[float]] = None

offset: Optional[float] = None

yaml_representer(dumper)

as_unit(output_unit)[source]: Returns a (min, max) tuple of values as converted to the given unit.

comment: Optional[str] = None

class orsopy.fileio.base.ValueVector(x, y, z, unit=None, error=None, comment=None)[source]

Bases: Header

A vector or list of vectors with an optional unit. For vectors relating to the sample, such as polarisation, the follow definitions are used.

Parameters:

x (float) – is defined as parallel to the radiation beam, positive going with the beam direction.
y (float) – is defined from the other two based on the right hand rule.
z (float) – is defined as normal to the sample surface, positive direction in scattering direction.
unit (Optional[str]) – SI unit string.

x: float

y: float

z: float

unit: Optional[str] = None

error: Optional[ErrorValue] = None

yaml_representer(dumper)

as_unit(output_unit)[source]: Returns a (x, y, z) tuple of values as converted to the given unit.

comment: Optional[str] = None

class orsopy.fileio.base.AlternatingField(amplitude, frequency, phase=None, comment=None)[source]

Bases: Header

A physical field with regular variations as AC magnetic field.

amplitude: Value

frequency: Value

phase: Optional[Value] = None

comment: Optional[str] = None

class orsopy.fileio.base.Person(name, affiliation, contact=None, comment=None)[source]

Bases: Header

Information about a person, including name, affiliation(s), and contact information.

name: str

affiliation: str

contact: Optional[str] = None

comment: Optional[str] = None

class orsopy.fileio.base.Column(name, unit=None, physical_quantity=None, flag_is=None, comment=None)[source]

Bases: Header

Information about a data column.

name: str

unit: Optional[str] = None

physical_quantity: Optional[str] = None

flag_is: Optional[List[str]] = None

yaml_representer(dumper)

comment: Optional[str] = None

class orsopy.fileio.base.ErrorColumn(error_of, error_type=None, value_is=None, distribution=None, comment=None)[source]

Bases: Header

Information about a data column.

error_of: str

error_type: Optional[Literal['uncertainty', 'resolution']] = None

value_is: Optional[Literal['sigma', 'FWHM']] = None

distribution: Optional[Literal['gaussian', 'triangular', 'uniform', 'lorentzian']] = None

yaml_representer(dumper)

property name: A convenience property to allow programs to get a valid name attribute for any column.

property to_sigma

The multiplicative factor needed to convert a FWHM to sigma.

The conversion factors can be found in common statistics and experimental physics text books or derived manually solving the variance definition integral. (e.g. Dekking, Michel (2005). A modern introduction to probability and statistics : understanding why and how. Springer, London, UK:) Values and some references available on Wikipedia, too.

comment: Optional[str] = None

class orsopy.fileio.base.File(file, timestamp=None, comment=None)[source]

Bases: Header

A file with file path and a last modified timestamp.

file: str

timestamp: Optional[datetime] = None

comment: Optional[str] = None

exception orsopy.fileio.base.NotOrsoCompatibleFileError[source]: Bases: ValueError

orsopy.fileio.base.json_datetime_trap(obj)[source]

orsopy.fileio.base.enum_trap(obj)[source]

orsopy.fileio.base.nexus_value_converter(obj)[source]