Vector¶

class ompy.Vector(values=None, E=None, path=None, std=None, units='keV')[source]¶

Bases: ompy.AbstractArray

Stores 1d array with energy axes (a vector)

Variables

values (np.ndarray) – The values at each bin.
E (np.ndarray) – The energy of each bin. (mid-bin calibration)
path (str or Path) – The path to load a saved vector from
std (np.ndarray) – The standard deviation of the counts
unit (str) – Unit of the energies. Can be “keV” or “MeV”. Defaults to “keV”.

There are several ways to initialize

An initialization with only E, or energy, defaults to zero values.
An initialization using a path loads a vector from said path.

If no std is given, it will default to None

Parameters

values (Optional[Iterable[float]]) – see above
E (Optional[Iterable[float]]) – see above
path (Union[str, Path, None]) – see above
std (Optional[Iterable[float]]) – see above
unit – see above

Raises

ValueError if the given arrays are of differing lenghts. –

Todo

Crean up initialization.

Attributes Summary

shape

rtype: Union[Tuple[int], Tuple[int, int]]

Methods Summary

`calibration`()	Calculate and return the calibration coefficients of the energy axes
`copy`()	Return a deepcopy of the class
`cut`([Emin, Emax, inplace])	Cut the vector at the energy limits
`cut_nan`([inplace])	Cut the vector where elements are np.nan
`error`(other[, std])	Computes the (weighted) χ²
`has_equal_binning`(other, **kwargs)	Check whether other has equal_binning as self within precision.
`index`(E)	Returns the closest index corresponding to the E value
`load`(path[, filetype])	Load to a file of specified format
`plot`([ax, scale, kind])	Plots the vector
`save`(path[, filetype])	Save to a file of specified format
`to_MeV`()	Convert E from keV to MeV if necessary
`to_keV`()	Convert E from MeV to keV if necessary
`transform`([const, alpha, inplace])	Apply a normalization transformation.
`verify_integrity`()	Verify the internal consistency of the vector

Attributes Documentation

shape¶

Return type: Union[Tuple[int], Tuple[int, int]]

Methods Documentation

calibration()[source]¶

Calculate and return the calibration coefficients of the energy axes

Formatted as “a{axis}{power of E}”

Return type: Dict[str, float]

copy()¶

Return a deepcopy of the class

Return type: AbstractArray

cut(Emin=None, Emax=None, inplace=True)[source]¶

Cut the vector at the energy limits

Parameters

Emin (float, optional) – The lower energy limit
Emax (float, optional) – The higher energy limit
inplace (bool, optional) – If True perform the cut on this vector or if False returns a copy. Defaults to True

Return type

Optional[Vector]

Returns

The cut vector if inplace is True.

cut_nan(inplace=True)[source]¶

Cut the vector where elements are np.nan

Parameters: inplace (bool, optional) – If True perform the cut on this vector or if False returns a copy. Defaults to True
Return type: Vector
Returns: The cut vector if inplace is True.

error(other, std=None)[source]¶

Computes the (weighted) χ²

Parameters

other (Vector or ndarray]) – The reference to compare itself to. If an array, assumes it has the same energy binning as itself.
std (Optional[ndarray], optional) – Standard deviations to use as inverse of the weights.

Returns

χ²

Return type

float

has_equal_binning(other, **kwargs)[source]¶

Check whether other has equal_binning as self within precision.

Parameters

other (Vector) – Vector to compare to.
kwargs – Additional kwargs to np.allclose.

Return type

bool

Returns

Returns True if both arrays are equal .

Raises

TypeError – If other is not a Vector.
ValueError – If any of the bins in any of the arrays are not equal.

index(E)[source]¶

Returns the closest index corresponding to the E value

Return type: int

load(path, filetype=None)[source]¶

Load to a file of specified format

Parameters

path (str or Path) – Path to Load
filetype (str, optional) – Filetype. Default uses auto-recognition from suffix.

Raises

ValueError – Filetype is not supported

Return type

None

plot(ax=None, scale='linear', kind='line', **kwargs)[source]¶

Plots the vector

Parameters

ax (matplotlib axis, optional) – The axis to plot onto. If not provided, a new figure is created
scale (str, optional) – The scale to use. Can be linear (default), log, symlog or logit.
kind (str, optional) –
- ‘line’ : line plot (default) evokes ax.plot
- ’plot’ : same as ‘line’
- ’step’ : step plot
- ’bar’ : vertical bar plot
kwargs (optional) – Additional kwargs to plot command.

Return type

Tuple[Any, Any]

Returns

The figure and axis used.

save(path, filetype=None)[source]¶

Save to a file of specified format

Parameters

path (str or Path) – Path to save
filetype (str, optional) – Filetype. Default uses auto-recognition from suffix. Options: [“numpy”, “tar”, “mama”]

Raises

ValueError – Filetype is not supported

Return type

None

to_MeV()[source]¶

Convert E from keV to MeV if necessary

Return type: Vector

to_keV()[source]¶

Convert E from MeV to keV if necessary

Return type: Vector

transform(const=1, alpha=0, inplace=True)[source]¶

Apply a normalization transformation:

vector -> const * vector * exp(alpha*energy)

If the vector has std, the std will be transformed as well.

Parameters

const (float, optional) – The constant. Defaults to 1.
alpha (float, optional) – The exponential coefficient. Defaults to 0.
inplace (bool, optional) – Whether to apply the transformation inplace. If False, returns the transformed vector.

Return type

Optional[Vector]

Returns

Optional[Vector]

verify_integrity()[source]¶

Verify the internal consistency of the vector

Raises: AssertionError or ValueError if any test fails –

calibration()[source]

Calculate and return the calibration coefficients of the energy axes

Formatted as “a{axis}{power of E}”

Return type: Dict[str, float]

cut(Emin=None, Emax=None, inplace=True)[source]

Cut the vector at the energy limits

Parameters

Emin (float, optional) – The lower energy limit
Emax (float, optional) – The higher energy limit
inplace (bool, optional) – If True perform the cut on this vector or if False returns a copy. Defaults to True

Return type

Optional[Vector]

Returns

The cut vector if inplace is True.

cut_nan(inplace=True)[source]

Cut the vector where elements are np.nan

Parameters: inplace (bool, optional) – If True perform the cut on this vector or if False returns a copy. Defaults to True
Return type: Vector
Returns: The cut vector if inplace is True.

error(other, std=None)[source]

Computes the (weighted) χ²

Parameters

other (Vector or ndarray]) – The reference to compare itself to. If an array, assumes it has the same energy binning as itself.
std (Optional[ndarray], optional) – Standard deviations to use as inverse of the weights.

Returns

χ²

Return type

float

has_equal_binning(other, **kwargs)[source]

Check whether other has equal_binning as self within precision.

Parameters

other (Vector) – Vector to compare to.
kwargs – Additional kwargs to np.allclose.

Return type

bool

Returns

Returns True if both arrays are equal .

Raises

TypeError – If other is not a Vector.
ValueError – If any of the bins in any of the arrays are not equal.

index(E)[source]

Returns the closest index corresponding to the E value

Return type: int

load(path, filetype=None)[source]

Load to a file of specified format

Parameters

path (str or Path) – Path to Load
filetype (str, optional) – Filetype. Default uses auto-recognition from suffix.

Raises

ValueError – Filetype is not supported

Return type

None

plot(ax=None, scale='linear', kind='line', **kwargs)[source]

Plots the vector

Parameters

ax (matplotlib axis, optional) – The axis to plot onto. If not provided, a new figure is created
scale (str, optional) – The scale to use. Can be linear (default), log, symlog or logit.
kind (str, optional) –
- ‘line’ : line plot (default) evokes ax.plot
- ’plot’ : same as ‘line’
- ’step’ : step plot
- ’bar’ : vertical bar plot
kwargs (optional) – Additional kwargs to plot command.

Return type

Tuple[Any, Any]

Returns

The figure and axis used.

save(path, filetype=None)[source]

Save to a file of specified format

Parameters

path (str or Path) – Path to save
filetype (str, optional) – Filetype. Default uses auto-recognition from suffix. Options: [“numpy”, “tar”, “mama”]

Raises

ValueError – Filetype is not supported

Return type

None

to_MeV()[source]

Convert E from keV to MeV if necessary

Return type: Vector

to_keV()[source]

Convert E from MeV to keV if necessary

Return type: Vector

transform(const=1, alpha=0, inplace=True)[source]

Apply a normalization transformation:

vector -> const * vector * exp(alpha*energy)

If the vector has std, the std will be transformed as well.

Parameters

const (float, optional) – The constant. Defaults to 1.
alpha (float, optional) – The exponential coefficient. Defaults to 0.
inplace (bool, optional) – Whether to apply the transformation inplace. If False, returns the transformed vector.

Return type

Optional[Vector]

Returns

Optional[Vector]

verify_integrity()[source]

Verify the internal consistency of the vector

Raises: AssertionError or ValueError if any test fails –