pyselfi.utils module

Generic infrastructure routines.

pyselfi.utils.ExecuteBashCommand(commandString)

Prints and executes a bash command.

Parameters

commandString (str) – command line

pyselfi.utils.ExecuteBashCommandMute(commandString)

Executes a bash command without printing it.

Parameters

commandString (str) – command line

pyselfi.utils.ExecuteBashCommandOutput(commandString)

Prints and executes a bash command, returns the output.

Parameters

commandString (str) – command line

Returns

output – the result of subprocess.check_output

Return type

str

pyselfi.utils.FatalError(message)

Prints an error to screen and ends the script.

Parameters

message (str) – message

pyselfi.utils.INDENT()

Indents the current level of outputs.

pyselfi.utils.PrintCommandLine(message)

Prints a bash command line to screen.

Parameters

message (str) – message

pyselfi.utils.PrintDiagnostic(verbosity, message)

Prints a diagnostic to screen.

Parameters

• verbosity (int) – verbosity of the message

• message (str) – message

pyselfi.utils.PrintError(message)

Prints an error to screen.

Parameters

message (str) – message

pyselfi.utils.PrintInfo(message)

Prints an information to screen.

Parameters

message (str) – message

pyselfi.utils.PrintLeftType(message_type, FONT_COLOR)

Prints the type of output to screen.

Parameters

• message_type (str) – type of message

• FONT_COLOR (str) – font color for this type of message

pyselfi.utils.PrintMessage(verbosity, message)

Prints a message to screen.

Parameters

• verbosity (int) – verbosity of the message

• message (str) – message

pyselfi.utils.PrintPythonCommand()

Prints a python command to screen.

Parameters

message (str) – message

pyselfi.utils.PrintValue(name, value)

Prints the value of a variable to screen.

Parameters

• name (str) – name of variable to be printed

• value (str) – value of variable to be printed

pyselfi.utils.PrintWarning(message)

Prints a warning to screen.

Parameters

message (str) – message

pyselfi.utils.UNINDENT()

Unindents the current level of outputs.

pyselfi.utils.get_index(i, j, k, N1, N2=None, N0=None)

Gets 1D index from 3D indices. Assumes row-major ordering. WARNING: N0 is passed last when all of N0,N1,N2 are specified!

Parameters

• i (int) – 3D index x

• j (int) – 3D index y

• k (int) – 3D index z

• N1 (int) – size of the array y

• N2 (int, optional, default=N1) – size of the array z

• N0 (int, optional, default=N1) – size of the array x

Returns

Id – corresponding 1D index

Return type

int

pyselfi.utils.get_indices(Id, N0, N1=None, N2=None)

Gets 3D indices from 1D index. Assumes row-major ordering.

Parameters

• Id (int) – 1D index

• N0 (int) – size of the array x

• N1 (int, optional, default=N0) – size of the array y

• N2 (int, optional, default=N0) – size of the array z

• Returns

• (i,j,k) (array, int, dimension=3) – corresponding 3D indices

pyselfi.utils.p_load(file, mmap_mode=None, allow_pickle=True, fix_imports=True, encoding='ASCII')

Loads arrays or pickled objects from .npy, .npz or pickled files. (Replacement of numpy.load, see its documentation).

pyselfi.utils.p_loadtxt(file, dtype=None, comments='#', delimiter=None, converters=None, skiprows=0, usecols=None, unpack=True, ndmin=0, encoding='bytes')

Loads data from a text file. Each row in the text file must have the same number of values. (Replacement of numpy.loadtxt, see its documentation). WARNING: contrary to numpy.loadtxt, unpack is set to True by default.

pyselfi.utils.p_save(file, arr, allow_pickle=True, fix_imports=True)

Saves an array to a binary file in NumPy .npy format. (Replacement of numpy.save, see its documentation).

pyselfi.utils.p_savetxt(file, X, fmt='%.18e', delimiter=' ', newline='\n', header='', footer='', comments='# ', encoding=None)

Saves an array to a text file. (Replacement of numpy.savetxt, see its documentation).

pyselfi.utils.p_savez(file, *args, **kwds)

Saves several arrays into a single file in uncompressed .npz format. (Replacement of numpy.savez, see its documentation).

pyselfi.utils.regular_inv(A, EPS_A=1e-07, EPS_residual=0.001)

Computes the inverse of a matrix. Attempts a regularization by adding an epsilon to the diagonal, if the matrix is ill-conditioned.

Parameters

• A (array-like, square) – input matrix

• EPS_A (double, optional, default=1e-7) – epsilon to be added to the diagonal of A, if necessary

• EPS_residual (double, optional, default=1e-3) – maximum residual in A*A^{-1} before attempting regularization

Returns

A^{-1} – numerical inverse of A

Return type

array-like, square

pyselfi.utils.save_replace_attr(hf, address, attr, dtype)

Saves or replaces an attribute in a hdf5 file.

Parameters

• hf (h5py.File) – hdf5 file (already opened with writing permission)

• address (str) – address of the attribute to be written/replaced

• attr (array) – attribute to be saved

• dtype (array) – data type

pyselfi.utils.save_replace_dataset(hf, address, data, maxshape, dtype)

Saves or replaces a dataset in a hdf5 file. The dataset must be resizable (see the HDF5 manual).

Parameters

• hf (h5py.File) – hdf5 file (already opened with writing permission)

• address (str) – address of the dataset to be written/replaced

• data (array) – data to be saved

• maxshape (array or None) – maximum size of the array

• dtype (array) – data type