opal.datasets package
Notebooks
opal.datasets.AmrDataset module
- class opal.datasets.AmrDataset.AmrDataset(directory)[source]
Bases:
DatasetBase,AmrPlotterDataset 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:
objectClass with member functions common to all datasets.
- _directory
Directory of file
- Type:
str
- _fname
Name of file
- Type:
str
- property ds
rtype: reference to dataset. Used in plotting classes.
- property filename
- property filetype
- property size
To be implemented by derived class.
opal.datasets.FieldDataset module
- class opal.datasets.FieldDataset.FieldDataset(directory, fname)[source]
Bases:
DatasetBase,FieldAnalysis,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:
- _stride
list of stride per dimension
- Type:
list
- _units
the keys are the variable names and the values their units
- Type:
dict
- _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
- 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:
SDDSDatasetBase,GridPlotter
opal.datasets.H5Dataset module
- class opal.datasets.H5Dataset.H5Dataset(directory, fname)[source]
Bases:
DatasetBase,H5Plotter,H5Statistics- __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
- 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
- property size
To be implemented by derived class.
opal.datasets.LBalDataset module
- class opal.datasets.LBalDataset.LBalDataset(directory, fname)[source]
Bases:
SDDSDatasetBase,ProfilingPlotter
opal.datasets.LossDataset module
- class opal.datasets.LossDataset.LossDataset(directory, fname)[source]
Bases:
DatasetBase- __parser
Actual data holder
- Type:
- __unit_label_mapper
Units of variables to plotting style
- Type:
list
- 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:
SDDSDatasetBase,MemoryPlotter
opal.datasets.OptimizerDataset module
- class opal.datasets.OptimizerDataset.OptimizerDataset(directory, fname)[source]
Bases:
DatasetBase,OptimizerPlotter,OptimizerAnalysis- __parser
Actual data holder
- Type:
- __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:
DatasetBase,PeakPlotter- __parser
Actual data holder
- Type:
- __variable_mapper
Map user input variable
- Type:
dict
- 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:
DatasetBase,ProbePlotter- __parser
Actual data holder
- Type:
- __variable_mapper
Map user input variable
- Type:
dict
- __label_mapper
Map user input variable
- Type:
dict
- 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:
DatasetBase- _parser
Actual data holder
- Type:
- _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
- 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:
DatasetBase,SamplerPlotter,SamplerStatistics- __parser
Actual data holder
- Type:
- __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 returnedind (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:
SDDSDatasetBase,SolverPlotter
opal.datasets.StatDataset module
- class opal.datasets.StatDataset.StatDataset(directory, fname)[source]
Bases:
SDDSDatasetBase,StatPlotter
opal.datasets.StdOpalOutputDataset module
- class opal.datasets.StdOpalOutputDataset.StdOpalOutputDataset(directory, fname)[source]
Bases:
DatasetBase,StdOpalOutputPlotter,StdOpalOutputAnalysis- 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:
DatasetBase,TimingPlotter- __parser
Actual data holder
- Type:
- __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
- 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:
DatasetBase,TrackOrbitPlotter,TrackOrbitAnalysis- __parser
Actual data holder
- Type:
- __unit_label_mapper
Units of variables to plotting style
- Type:
list
- 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.