pyuff_ustb.objects.Phantom

class pyuff_ustb.objects.Phantom(_reader: Reader | str | None = None, **kwargs)

Bases: Uff

Uff class for a phantom definition.

Original authors:

Alfonso Rodriguez-Molares <alfonso.r.molares@ntnu.no>

__init__(_reader: Reader | str | None = None, **kwargs)

Methods

__init__([_reader])
copy()	Return a (deep) copy of the Uff object.
read(name)	Read an Uff object from the file.
write(filepath, location[, overwrite, ...])	Write the Uff to a file.

Attributes

Gamma	Reflection coefficient [unitless]
N_points	Number of points
alpha	Medium attenuation [dB/cm/MHz]
author	Contact of the authors
density	Medium density [kg/m3]
info	Other information
name	Name of the dataset
phi	Angle in the elevation direction respect to origin [rad]
points	Matrix of point scaterers [x y z Gamma] - [m m m unitless]
r	Distance from the points to the origin [m]
reference	Reference to the publication where it was used/acquired
sound_speed	Medium sound speed [m/s]
theta	Angle in the azimuth direction respect to origin [rad]
time	Time [s]
version	Version of the dataset
x	Points position in the x axis [m]
y	Points position in the y axis [m]
z	Points position in the z axis [m]

property points: ndarray

Matrix of point scaterers [x y z Gamma] - [m m m unitless]

property time: float

Time [s]

property sound_speed: float

Medium sound speed [m/s]

property density: float

Medium density [kg/m3]

property alpha: float

Medium attenuation [dB/cm/MHz]

property N_points: int

Number of points

property x: ndarray

Points position in the x axis [m]

property y: ndarray

Points position in the y axis [m]

property z: ndarray

Points position in the z axis [m]

property Gamma: ndarray

Reflection coefficient [unitless]

property r: ndarray

Distance from the points to the origin [m]

property author: str | None

Contact of the authors

copy() → Uff

Return a (deep) copy of the Uff object.

In addition to the _reader, all compulsory and optional fields are copied (deeply) iff they are loaded/cached. This means that if a field has not been read from the file, it will not be copied. This is to avoid unintended eager loading of data.

See Uff.__deepcopy__() for implementation details.

Returns:

A deep copy of this object.

Return type:

Uff

property info: str | None

Other information

property name: str | None

Name of the dataset

read(name: str) → Uff

Read an Uff object from the file. A Reader must be provided in order to read.

>> uff = Uff(“/path/to/some/file.uff”) >> scan = uff.read(“scan”)

property reference: str | None

Reference to the publication where it was used/acquired

property theta: ndarray

Angle in the azimuth direction respect to origin [rad]

property version: str | None

Version of the dataset

write(filepath: str, location: str | Tuple[str, ...] | List[str], overwrite: bool = False, ignore_missing_compulsory_fields: bool = False)

Write the Uff to a file.

Parameters:

• filepath (Union[str, h5py.File]) – The filepath (or h5py.File) to write to.

• location (Union[str, Tuple[str, ...], List[str]]) – The location in the h5 file to write to. Can be a tuple/list of strings representing a path into the h5 file, or a string with the path separated by slashes.

• overwrite (bool) – Whether to overwrite the location if it already exists. If the location already exists and overwrite=False, a ValueError is raised. overwrite=False by default.

• ignore_missing_compulsory_fields (bool) – Whether to ignore missing compulsory fields. If a compulsory field is not set then usually a ValueError is raised. Setting ignore_missing_compulsory_fields=True will ignore this error and write the object anyway. ignore_missing_compulsory_fields=False by default.

Examples

We can write an object to a file like this:

>>> import pyuff_ustb as pyuff
>>> point = pyuff.Point(distance=0.0, azimuth=0.0, elevation=0.0)
>>> point.write("my_point.uff", "point")

If we try to write an object to the same location, we get an error:

>>> point.write("my_point.uff", "point")
Traceback (most recent call last):
    ...
ValueError: Location 'point' already exists in the file 'my_point.uff'. Use overwrite=True to overwrite it.

We can choose to overwrite the location by passing overwrite=True:

>>> point.write("my_point.uff", "point", overwrite=True)

We can also write the object to another arbitrary location if we want:

>>> point.write("my_point.uff", "sub_directory/point")

Compulsory fields may not be None when writing an object to an UFF file (unless ignore_missing_compulsory_fields=True).

>>> point.distance = None
>>> point.write("my_point.uff", "point2")
Traceback (most recent call last):
    ...
ValueError: The compulsory field 'distance' is set to None. Compulsory fields
may not be None when writing an object to an UFF file. To ignore this error and write
the object anyway, set ignore_missing_compulsory_fields=True.

Note that even though the previous step failed, the file was still partially written to (we don’t rollback changes when writing fails), so we will have to pass overwrite=True to write the object again.

>>> point.write(
...     "my_point.uff",
...     "point2",
...     overwrite=True,
...     ignore_missing_compulsory_fields=True,
... )

After running these steps, the file will contain the following fields:

>>> uff = pyuff.Uff("my_point.uff")
>>> uff
Uff(point=Point(<...>), point2=Point(<...>), sub_directory=<...>)

property phi: ndarray

Angle in the elevation direction respect to origin [rad]