amep.trajectory.FieldTrajectory#

class amep.trajectory.FieldTrajectory(reader)#

Bases: BaseTrajectory

Field trajectory object.Time-series of per spatial point field values.

__init__(reader)#

Creates a trajectory object containing data frames for multiple time steps.

Can be viewed as a Sequence of BaseField.

Parameters:: reader (BaseReader) – Reader of the data.
Return type:: None.

Methods

`__init__`(reader)	Creates a trajectory object containing data frames for multiple time steps.
`add_author_info`(author, key, value)	Adds author information for the given author to the trajectory.
`add_field_info`(ftype, key, value)	Adds information for the given field to the fields group of the trajectory file.
`add_param`(param, value)	Adds a parameter to the trajectory.
`add_script`(path)	Adds a script in text format to the hdf5 file.
`add_software_info`(key, value)	Add software information to the hdf5 trajectory file.
`animate`(filename, **kwargs)	Wrapper to amep.plot.animate_trajectory.
`delete_author_info`(author[, key])	Deletes all information (key=None) or specific information given by the key keyword of the given author.
`delete_field_info`(ftype[, key])	Deletes specific field information.
`delete_param`(param)	Deletes the given parameter.
`delete_script`(filename)	Deletes the script of the given filename.
`delete_software_info`([key])	Deletes all software information (key=None) or specific information given by the key keyword.
`get_author_info`(author)	Returns all information for the given author.
`get_field_info`([ftype])	Returns all parameters of the given field as a dictionary.
`get_script`(filename[, store, directory])	Returns a stored script as a list of lines and stores it as a file in the given directory if store is True.

Attributes

`authors`	Returns a list of all author names.
`dim`	Spatial dimension of the simnulation.
`dt`	Size of the time step used for the simulation.
`info`	Returns all stored metadata information as a dictionary.
`nframes`	Total number of loaded frames.
`nth`	Every which dump file was loaded.
`params`	Returns all parameters stored within the trajectory as a dictionary.
`reader`
`savedir`	Trajectory file directory.
`scripts`	Returns a list of all scripts (filenames) that are stored in the trajectory object.
`software`	Returns all software information.
`start`	Start fraction.
`steps`	Array of the number of time steps for each frame.
`stop`	Stop fraction.
`times`	Physical times.
`type`	Returns the data type ('particles' or 'field').
`version`	AMEP version with which the trajectory file has been created.

Get an individual frame or field of a simulation.

Supports slicing as well as iterables of valid integer indices. The return type depends on the type of the trajectory. Also it depends if only one frame or a collection of frames is requested. If a collection of frames is requested a list of frames is returned.

Parameters:: item (int | slice | Iterable[int]) –
Return type:: BaseFrame | BaseField | list[BaseField | BaseFrame]

add_author_info(author: str, key: str, value: int | float | str) → None#

Adds author information for the given author to the trajectory.

Parameters:

author (str) – Author name.
key (str) – Name or category of the information to be added.
value (int or float or str) – Information to be added.

Return type:

None.

add_field_info(ftype: str, key: str, value: int | float | str) → None#

Adds information for the given field to the fields group of the trajectory file.

Parameters:

ftype (str) – Field.
key (str) – Name of the parameter.
value (int/float/str) – Value of the parameter.

Return type:

None.

Examples

>>> import amep
>>> traj = amep.load.traj("../examples/data/continuum.h5amep")
>>> traj.add_field_info('p', 'name', 'particle density')
>>> traj.add_field_info('c', 'name', 'chemical concentration')
>>> print(traj.get_field_info())
{'c': {'name': 'chemical concentration'}, 'p': {'name': 'particle density'}}
>>> traj.delete_field_info(None)
>>>

add_param(param: str, value: int | float | str) → None#

Adds a parameter to the trajectory.

Parameters:

param (str) – Parameter.
value (str or float or int) – Value of the parameter.

Raises:

ValueError – Raises an error if param is not of type str.

Return type:

None.

add_script(path: Path | str) → None#

Adds a script in text format to the hdf5 file.

Parameters:: path (str or Path) – Path of the script to add.
Return type:: None.

add_software_info(key: str, value: str | int | float) → None#

Add software information to the hdf5 trajectory file.

Parameters:

key (str) – Name of the parameter.
value (str or int or float) – Value of the parameter.

Return type:

None.

animate(filename: str, **kwargs) → None#

Wrapper to amep.plot.animate_trajectory.

Parameters:

filename (str) – File in which the video should be saved.
**kwargs – All keyword arguments are forwarded to amep.plot.animate_trajectory.

Return type:

None

property authors: list[str]#

Returns a list of all author names.

Returns:: keys – List of author names.
Return type:: list

delete_author_info(author: str, key: str | None = None) → None#

Deletes all information (key=None) or specific information given by the key keyword of the given author.

Parameters:

author (str) – Author name.
key (str or None, optional) – Info that should be deleted. If None, all info is deleted. The default is None.

Return type:

None.

delete_field_info(ftype: str | None, key: str | None = None) → None#

Deletes specific field information.

Parameters:

ftype (str or None) – Field. If None, the information of all fields is deleted.
key (str, optional) – Parameter to delete. If None, all parameters of the given field are deleted. The default is None.

Return type:

None.

Examples

>>> import amep
>>> traj = amep.load.traj("../examples/data/continuum.h5amep")
>>> traj.add_field_info('p', 'name', 'particle density')
>>> traj.add_field_info('c', 'name', 'chemical concentration')
>>> print(traj.get_field_info())
{'c': {'name': 'chemical concentration'}, 'p': {'name': 'particle density'}}
>>> traj.delete_field_info(None)
>>> print(traj.get_field_info())
{}
>>>

delete_param(param: str) → None#

Deletes the given parameter.

Parameters:: param (str) – Parameter.
Raises:: ValueError – Raises an error if param is not of type str.
Return type:: None.

delete_script(filename: str) → None#

Deletes the script of the given filename.

Parameters:: filename (str) – Filename.
Return type:: None.

delete_software_info(key: str | None = None) → None#

Deletes all software information (key=None) or specific information given by the key keyword.

Parameters:: key (str or None, optional) – Information that should be deleted. If None, all information is deleted. The default is None.
Return type:: None.

property dim: int#

Spatial dimension of the simnulation.

Returns:: x – Spatial dimension.
Return type:: int

property dt#: Size of the time step used for the simulation.

get_author_info(author: str) → dict#

Returns all information for the given author.

Parameters:: author (str) – Author name.
Returns:: p – Author information.
Return type:: dict

get_field_info(ftype: str | None = None) → dict#

Returns all parameters of the given field as a dictionary.

Parameters:: ftype (str or None, optional) – Field. If None, the information of all fields is returned. The default is None.
Returns:: p – Parameters.
Return type:: dict

Examples

>>> import amep
>>> traj = amep.load.traj("../examples/data/continuum.h5amep")
>>> traj.add_field_info('p', 'name', 'particle density')
>>> traj.add_field_info('c', 'name', 'chemical concentration')
>>> print(traj.get_field_info())
{'c': {'name': 'chemical concentration'}, 'p': {'name': 'particle density'}}
>>> traj.delete_field_info(None)
>>>

get_script(filename: str, store: bool = False, directory: str = '.') → list#

Returns a stored script as a list of lines and stores it as a file in the given directory if store is True.

Parameters:

filename (str) – File name.
store (bool, optional) – If True, the script is stored in a file. The default is False.
directory (str, optional) – Directory in which the file is stored if store is True. The default is ‘.’.

Returns:

decoded – List of lines.

Return type:

list

property info: dict#

Returns all stored metadata information as a dictionary.

Returns:: Metadata.
Return type:: dict

property nframes#: Total number of loaded frames.

property nth#: Every which dump file was loaded.

property params: dict#

Returns all parameters stored within the trajectory as a dictionary.

Returns:: p – Parameter dictionary.
Return type:: dict

property savedir#: Trajectory file directory.

property scripts: list#

Returns a list of all scripts (filenames) that are stored in the trajectory object.

Returns:: keys – List of filenames.
Return type:: list

property software: dict#

Returns all software information.

Returns:: keys – Software information.
Return type:: dict

property start#: Start fraction.

property steps#: Array of the number of time steps for each frame.

property stop#: Stop fraction.

property times#: Physical times.

property type: str#

Returns the data type (‘particles’ or ‘field’).

Returns:: Data type.
Return type:: str

property version#

AMEP version with which the trajectory file has been created.

Returns:: ver – Version.
Return type:: str