opal.datasets package¶

Notebooks¶

StatDataSet_Wrapper

opal.datasets.AmrDataset module¶

class opal.datasets.AmrDataset.AmrDataset(directory)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.AmrPlotter.AmrPlotter

Dataset of AMR output. It uses (https://yt-project.org/) to parse the data. An OPAL-AMR fork is found in https://gitlab.psi.ch/frey_m/yt.

__init__(directory)[source]¶

Parameters: directory (list) – Directory name that contains a Header file and Level_x (x = 0, 1, 2, …) directories.

get_ray_along(axis, field, **kwargs)[source]¶

Parameters

axis (str) – Take a line cut along this axis (‘x’, ‘y’, ‘z’)
field (str) – y-axis parameter
center ((float, float), optional) – Center through which line should go

Returns

array
array
tuple – center

Notes

27. May 2018 http://yt-project.org/doc/visualizing/manual_plotting.html

property real_ds¶

opal.datasets.DatasetBase module¶

class opal.datasets.DatasetBase.DatasetBase(directory, fname)[source]¶

Bases: object

Class with member functions common to all datasets.

_directory¶

Directory of file

Type: str

_fname¶

Name of file

Type: str

_ftype¶

Type of file

Type: FileType

__init__(directory, fname)[source]¶: Constructor.

property ds¶: returns: :rtype: reference to dataset. Used in plotting classes.

property filename¶

property filetype¶

getData(var, **kwargs)[source]¶: To be implemented by derived class.

getLabel(var)[source]¶: To be implemented by derived class.

getLabelWithUnit(var)[source]¶

Returns: plotting label with unit
Return type: str

getUnit(var)[source]¶: To be implemented by derived class.

property size¶: To be implemented by derived class.

opal.datasets.FieldDataset module¶

class opal.datasets.FieldDataset.FieldDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.analysis.FieldAnalysis.FieldAnalysis, opal.visualization.FieldPlotter.FieldPlotter

_basename¶

leading name all files have in common

Type: str

_directory¶

the directory of all files

Type: str

_df¶

the data of a single step (vector and scalar fields)

Type: pandas.core.frame.DataFrame

_dim¶

list of number of grid points per dimension

Type: list

_fields¶

the keys are the different fields and the values denotes ‘scalar’ or ‘field’

Type: dict

_loaded_step¶

the number of the loaded file (if -1, no file is loaded)

Type: int

_label_mapper¶

map variable names to nice plotting labels

Type: dict

_npadding¶

the number of digits in the number (used for zero padding)

Type: int

_parser¶

class to parse field data

Type: FieldParser

_stride¶

list of stride per dimension

Type: list

_units¶

the keys are the variable names and the values their units

Type: dict

__init__(directory, fname)[source]¶: Constructor.

_count_files(directory, fname)[source]¶: Count the number of field files (scalar and vector fields). Store the names and the number of files in the dictionary self._fields.

_find_nearest(array, value, dim)[source]¶

Find nearest value in an array.

Parameters

array (numpy.array) – the array where to find value
value (float) – the value to check
dim (int) – the dimension to check
Reference –
--------- –
https (//stackoverflow.com/questions/2566412/find-nearest-value-in-numpy-array (5. June 2020)) –

Returns

array index

Return type

int

_get_combined_filename(step, field)[source]¶

Parameters

step (int) – the time step
field (str) – the field

Returns

the full file name

Return type

str

_load_step(step)[source]¶: Load all fields of a single step. It merges the dataframes of the individual field files of a step.

_zero_padding(step)[source]¶

Get zero padded number as string in order to load a file.

Parameters: step (int) – the time step
Returns: zero padded number as string
Return type: str

property dataframe¶: returns: all the data :rtype: pandas.core.frame.DataFrame

getData(var, step=0)[source]¶

Get the data of a variable.

Parameters

var (str) – variable name
step (int, optional) – time step

Returns

data of a column

Return type

numpy.ndarray

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – variable name
Returns: Plotting label
Return type: str

getSlice(field, normal, pos=0.0, index=0, step=0)[source]¶

Get a 2d slice through the data.

Parameters

field (str) – name of scalar field or vector field component
normal (str) – normal direction. Either ‘x’, ‘y’, or ‘z’
pos (float, optional) – coordinate position of slice
step (int, optional) – time step
index (int, optional) – optional to ‘pos’. If index > 0, pos is ignored.

Returns

numpy.ndarray – coordinate values in the first direction
numpy.ndarray – coordinate values in the second direction
numpy.ndarray – field values

getUnit(var)[source]¶

Returns: the unit of a variable
Return type: str

get_mesh_spacing(step=0)[source]¶

Get the mesh spacings.

Parameters: step (int, optional) – time step
Returns: the mesh spacing per dimension
Return type: list

property indices¶

Get indices of grid points.

Returns: grid points
Return type: numpy.ndarray

property names¶: returns: the variable names :rtype: list

property positions¶

Get coordinates at the grid points.

Returns: coordinates
Return type: numpy.ndarray

property stride¶: returns: stride per dimension :rtype: list

opal.datasets.GridDataset module¶

class opal.datasets.GridDataset.GridDataset(directory, fname)[source]¶

Bases: opal.datasets.SDDSDatasetBase.SDDSDatasetBase, opal.visualization.GridPlotter.GridPlotter

__init__(directory, fname)[source]¶

getNumCores()[source]¶

Obtain the number of cores.

Returns
Return type: int

getNumLevels()[source]¶

Obtain the number of levels.

Returns
Return type: int

opal.datasets.H5Dataset module¶

class opal.datasets.H5Dataset.H5Dataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.H5Plotter.H5Plotter, opal.analysis.H5Statistics.H5Statistics

__parser¶

Actual data holder

Type: H5Parser

__variable_mapper¶

Map user input variable name to file variable name

Type: dict

__label_mapper¶

Map user input variable

Type: dict

__unit_label_mapper¶

Units of variables to plotting style name to plot label name

Type: list

__direction¶

Used to find out the direction in case of vector type data

Type: dict

__init__(directory, fname)[source]¶: Constructor.

getData(var, **kwargs)[source]¶

Obtain data of a variable

Parameters: var (str) – Variable name
Returns: Data (n, dim)
Return type: array

getH5DataFrame(step=0)[source]¶

Get a dataframe with the following columns:

‘id’ particle id

‘px’ momentum in x

‘py’ momentum in y

‘pz’ momentum in z

‘ptype’ particle type

‘x’ position in x

‘y’ position in x

‘z’ position in x

‘q’ particle charge

Parameters: step (int, optional) – the output step
Returns: a dataframe with the columns [‘id’ ,’px’, ‘py’, ‘pz’, ‘ptype’, ‘x’, ‘y’, ‘z’, ‘q’]
Return type: pandas.core.frame.DataFrame

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate name plotting ready
Return type: str

getMonitorDataFrame()[source]¶

Monitor H5 files only. Get a dataframe with the following columns:

‘id’ particle id

‘px’ momentum in x

‘py’ momentum in y

‘pz’ momentum in z

‘time’ time

‘turn’ turn number

‘x’ position in x

‘y’ position in x

‘z’ position in x

‘q’ particle charge

Returns: a dataframe with the columns [‘id’ ,’px’, ‘py’, ‘pz’, ‘time’, ‘turn’, ‘x’, ‘y’, ‘z’]
Return type: pandas.core.frame.DataFrame

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate unit in math mode for plotting
Return type: str

isStepDataset(var, step=0)[source]¶: Check if a variable is contained as a dataset

property size¶: To be implemented by derived class.

opal.datasets.LBalDataset module¶

class opal.datasets.LBalDataset.LBalDataset(directory, fname)[source]¶

Bases: opal.datasets.SDDSDatasetBase.SDDSDatasetBase, opal.visualization.ProfilingPlotter.ProfilingPlotter

__init__(directory, fname)[source]¶

opal.datasets.LossDataset module¶

class opal.datasets.LossDataset.LossDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase

__parser¶

Actual data holder

Type: LossParser

__unit_label_mapper¶

Units of variables to plotting style

Type: list

__init__(directory, fname)[source]¶: Constructor.

getData(var, **kwargs)[source]¶

Obtain the data of a variable

Parameters: var (str) – Variable name
Returns: an array of the data
Return type: array

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate name plotting ready
Return type: str

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate unit in math mode for plotting
Return type: str

property size¶: To be implemented by derived class.

opal.datasets.MemoryDataset module¶

class opal.datasets.MemoryDataset.MemoryDataset(directory, fname)[source]¶

Bases: opal.datasets.SDDSDatasetBase.SDDSDatasetBase, opal.visualization.MemoryPlotter.MemoryPlotter

__init__(directory, fname)[source]¶

opal.datasets.OptimizerDataset module¶

class opal.datasets.OptimizerDataset.OptimizerDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.OptimizerPlotter.OptimizerPlotter, opal.analysis.OptimizerAnalysis.OptimizerAnalysis

__parser¶

Actual data holder

Type: OptimizerParser

__postfix¶

Substring of generation filenames that is identical to all files

Type: str

_loaded_generation¶

Currently loaded generation

Type: int

_loaded_optimizer¶

Currently loaded optimizer

Type: int

_loadedGeneration¶

Load a generation file

Type: function

__init__(directory, fname)[source]¶

Constructor.

Parameters

directory (str) – Directory name
fname (str) – Generation file name

_loadGeneration(gen, opt=0, pareto=False)[source]¶

Load data of generation into memory.

Parameters

gen (int) – Generation
opt (int, optional) – Optimizer (default: 0)
pareto (bool, optional) – Load pareto file (default: False)

property bounds¶: Obtain design variable upper and lower bounds

property design_variables¶: Obtain design variable names

getData(var, **kwargs)[source]¶

Obtain the data of a variable or all data of an individual.

An individual is returned when setting ‘ind’ > 0. In that case the ‘var’ parameter is not considered.

Parameters

var (str) – A design variable or objective
ind (int, optional) – Individual identity number, default: -1, which means all
gen (int, optional) – Generation, default: 1
opt (int, optional) – Optimizer, default: 0
all (bool, optional) – Get all info of an individual (i.e. objectives, design variables) default : True
pareto (bool, optional) – Load pareto file (default: False)

Returns

Array of the data

Return type

array

getGenerationBasename(gen, opt=0)[source]¶

Obtain the basename of a specific generation.

Parameters

gen (int) – Generation
opt (int, optional) – Optimizer number (default: 0)

Returns

A basename of the selected generation

Return type

str

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate name plotting ready
Return type: str

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name

Notes

The optimizer does not yet write the units of each variable to the files. This function raises an error.

individuals(gen, opt=0, pareto=False)[source]¶

Obtain the ID of every individual of the currently loaded generation file

Parameters

gen (int) – Generation
opt (int, optional) – Optimizer (default: 0)
pareto (bool, optional) – Load pareto file (default: False)

property num_generations¶: Obtain the number of generations

property num_optimizers¶

property objectives¶: Obtain objective names

property size¶: Returns the number of individuals

opal.datasets.PeakDataset module¶

class opal.datasets.PeakDataset.PeakDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.PeakPlotter.PeakPlotter

__parser¶

Actual data holder

Type: PeakParser

__variable_mapper¶

Map user input variable

Type: dict

__init__(directory, fname)[source]¶: Constructor.

getData(var, **kwargs)[source]¶

Obtain the data of a variable

Parameters: var (str) – Variable name
Returns: Array of the data
Return type: array

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Variable name
Returns: appropriate name plotting ready
Return type: str

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate unit in math mode for plotting
Return type: str

property size¶: To be implemented by derived class.

opal.datasets.ProbeHistDataset module¶

class opal.datasets.ProbeHistDataset.ProbeHistDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.ProbePlotter.ProbePlotter

__parser¶

Actual data holder

Type: HistogramParser

__variable_mapper¶

Map user input variable

Type: dict

__label_mapper¶

Map user input variable

Type: dict

__init__(directory, fname)[source]¶: Constructor.

getData(var, **kwargs)[source]¶

Obtain the data of a variable

Parameters: var (str) – Variable name
Returns: Array of the data
Return type: array

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate name plotting ready
Return type: str

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate unit in math mode for plotting
Return type: str

property size¶: To be implemented by derived class.

opal.datasets.SDDSDatasetBase module¶

class opal.datasets.SDDSDatasetBase.SDDSDatasetBase(directory, fname, **kwargs)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase

_parser¶

Actual data holder

Type: SDDSParser

_variable_mapper¶

Map user input variable name to file variable name

Type: dict

_label_mapper¶

Map user input variable name to plot label name

Type: dict

_unit_label_mapper¶

Units of variables to plotting style

Type: list

__init__(directory, fname, **kwargs)[source]¶: Constructor.

property dataframe¶

getData(var, **kwargs)[source]¶

Obtain data of a variable

Parameters: var (str) – Variable name
Returns: List of the data
Return type: list

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate name plotting ready
Return type: str

getRow(var, val)[source]¶

Obtain a row of a dataset

Parameters

var (str) – Variable name
val (float) – Value of given variable

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate unit in math mode for plotting
Return type: str

getVariables()[source]¶

Obtain all variables within file.

Returns: List of strings
Return type: list

property size¶: To be implemented by derived class.

opal.datasets.SamplerDataset module¶

class opal.datasets.SamplerDataset.SamplerDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.SamplerPlotter.SamplerPlotter, opal.analysis.SamplerStatistics.SamplerStatistics

__parser¶

Actual data holder

Type: SamplerParser

__nFiles¶

Number of sampler output files found

Type: int

__actual_file_load(i)¶

__init__(directory, fname)[source]¶

Constructor.

Parameters

directory (str) – Directory name
fname (str) – Generation file name

__load_file(ind)¶

Load file

A sampler output might be split into several files. This function first checks if new data needs to be loaded and then reads the data if necessary.

indint: Individual identity number

property bounds¶: Obtain design variable upper and lower bounds

property design_variables¶: Obtain design variable names

getData(var, **kwargs)[source]¶

Get input data

Obtain the input data of a design variable of an individual. In order to select a specific individual set parameter ‘ind’ >= 0. If ‘ind’ is not given, the function takes the default value 0.

Parameters

var (str) – A design variable or objective if var == '' the full dvar (dvar==True) or objective data is returned
ind (int, optional) – Individual identity number (default: 0)
dvar (bool) – Return DVAR data in case of var==’’ (default: True)

Returns

Design variable simulation input value.

Return type

float

getLabel(var)[source]¶

Obtain label for plotting.

varstr: Variable name

Returns: Appropriate name plotting ready
Return type: str

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name

Notes

The sampler does not yet write the units of each variable to the files. This function raises an error.

property loaded_file¶

property objectives¶: Obtain objectives names

property size¶: Returns the number of individuals

opal.datasets.SolverDataset module¶

class opal.datasets.SolverDataset.SolverDataset(directory, fname)[source]¶

Bases: opal.datasets.SDDSDatasetBase.SDDSDatasetBase, opal.visualization.SolverPlotter.SolverPlotter

__init__(directory, fname)[source]¶

opal.datasets.StatDataset module¶

class opal.datasets.StatDataset.StatDataset(directory, fname)[source]¶

Bases: opal.datasets.SDDSDatasetBase.SDDSDatasetBase, opal.visualization.StatPlotter.StatPlotter

__init__(directory, fname)[source]¶: Constructor.

opal.datasets.StdOpalOutputDataset module¶

class opal.datasets.StdOpalOutputDataset.StdOpalOutputDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.StdOpalOutputPlotter.StdOpalOutputPlotter, opal.analysis.StdOpalOutputAnalysis.StdOpalOutputAnalysis

__init__(directory, fname)[source]¶: Constructor.

getData(var, **kwargs)[source]¶

Obtain filename

Parameters: var (str) – Unused
Returns: Filename
Return type: str

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Unused
Returns: Empty string
Return type: str

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Unused
Returns: Empty string
Return type: str

property size¶: To be implemented by derived class.

opal.datasets.TimeDataset module¶

class opal.datasets.TimeDataset.TimeDataset(directory, fname, ttype='ippl')[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.TimingPlotter.TimingPlotter

__parser¶

Actual data holder

Type: TimingParser

__init__(directory, fname, ttype='ippl')[source]¶

Constructor.

Parameters

directory (str) – Directory of file
fname (str) – Basename
ttype (str) – Time file type (‘ippl’ timing or OPAL ‘output’)

getData(var, **kwargs)[source]¶

Obtain the timing data

Parameters

var (str or int) – Timing name or index of timing
prop (str, optional) – Property, i.e. ‘cpu avg’, ‘cpu max’, ‘cpu min’, ‘wall avg’, ‘wall max’, ‘wall min’ or ‘cpu tot’ and ‘wall tot’ (only for main timing)

Returns

The timing data

Return type

float

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – String that is returned
Returns: var – Input variable var
Return type: str

getLabels()[source]¶

Obtain all timing names

Returns: Strings with names
Return type: list

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Unused
Returns: The string ‘s’ for seconds
Return type: str

property size¶: To be implemented by derived class.

opal.datasets.TrackOrbitDataset module¶

class opal.datasets.TrackOrbitDataset.TrackOrbitDataset(directory, fname)[source]¶

Bases: opal.datasets.DatasetBase.DatasetBase, opal.visualization.TrackOrbitPlotter.TrackOrbitPlotter, opal.analysis.TrackOrbitAnalysis.TrackOrbitAnalysis

__parser¶

Actual data holder

Type: TrackOrbitParser

__unit_label_mapper¶

Units of variables to plotting style

Type: list

__init__(directory, fname)[source]¶: Constructor.

getData(var, **kwargs)[source]¶

Obtain the data of a variable

Parameters: var (str) – Variable name
Returns: Array of the data
Return type: array

getLabel(var)[source]¶

Obtain label for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate name plotting ready
Return type: str

getUnit(var)[source]¶

Obtain unit for plotting.

Parameters: var (str) – Variable name
Returns: Appropriate unit in math mode for plotting
Return type: str

property size¶: To be implemented by derived class.

opal.datasets.filetype module¶

class opal.datasets.filetype.FileType(value)[source]¶

Bases: enum.IntEnum

An enumeration.

AMR = 14¶

FIELD = 16¶

GRID = 6¶

H5 = 0¶

HIST = 10¶

LBAL = 3¶

LOSS = 15¶

MEM = 2¶

NONE = 17¶

OPTIMIZER = 11¶

OUTPUT = 4¶

PEAK = 9¶

SAMPLER = 12¶

SMB = 13¶

SOLVER = 7¶

STAT = 1¶

TIMING = 5¶

TRACK_ORBIT = 8¶

checkFileType(fname)[source]¶

classmethod extensionToFileType(fname)[source]¶

classmethod get_extensions()[source]¶

classmethod get_parsers()[source]¶