nabu.resources.utils

source module nabu.resources.utils

Functions

• get_values_from_file — Read a text file and scan the values inside. This function expects one value per line, or values separated with a separator defined with the sep parameter.

• get_memory_per_node — Get the available memory per node in GB.

• get_threads_per_node — Get the available memory per node in GB.

• extract_parameters — Extract the named parameters from a string.

• compact_parameters — Compact the parameters from a dict into a string.

• is_hdf5_extension

• get_quantities_and_units — Return a dictionary with quantities as keys, and values in SI.

source get_values_from_file(fname, n_values=None, shape=None, sep=None, any_size=False)

Read a text file and scan the values inside. This function expects one value per line, or values separated with a separator defined with the sep parameter.

Parameters

• fname : str — Path of the text file

• n_values : int, optional — If set to a value, this function will check that it scans exactly this number of values. Ignored if shape is provided

• shape : tuple, optional — Generalization of n_values for higher dimensions.

• sep : str, optional — Separator between values. Default is white space

• any_size : bool, optional — If set to True, then the parameters 'n_values' and 'shape' are ignored.

Returns

• arr : numpy.ndarray — An array containing the values scanned from the text file

Raises

• ValueError

source get_memory_per_node(max_mem, is_percentage=True)

Get the available memory per node in GB.

Parameters

• max_mem : float — If is_percentage is False, then number is interpreted as an absolute number in GigaBytes. Otherwise, it should be a number between 0 and 100 and is interpreted as a percentage.

• is_percentage : bool — A boolean indicating whether the parameter max_mem is to be interpreted as a percentage of available system memory.

source get_threads_per_node(max_threads, is_percentage=True)

Get the available memory per node in GB.

Parameters

• max_threads : float — If is_percentage is False, then number is interpreted as an absolute number of threads. Otherwise, it should be a number between 0 and 100 and is interpreted as a percentage.

• is_percentage : bool — A boolean indicating whether the parameter max_threads is to be interpreted as a percentage of available system memory.

source extract_parameters(params_str, sep=';')

Extract the named parameters from a string.

Example

The function can be used as follows:

extract_parameters("window_width=None; median_filt_shape=(3,3); padding_mode='wrap'")
{'window_width': None, 'median_filt_shape': (3, 3), 'padding_mode': 'wrap'}

source compact_parameters(params_dict, sep=';')

Compact the parameters from a dict into a string.

This is the inverse of extract_parameters. It can be used for example in tomwer to convert parameters into a string, for example for cor_options, prior to calling a nabu method which is expecting an argument to be in the form of a string containing options.

Example

The function can be used as follows:

compact_parameters( {"side":"near", "near_pos":300 } )
"side=near; nearpos= 300;"

source is_hdf5_extension(ext)

source get_quantities_and_units(string, sep=';')

Return a dictionary with quantities as keys, and values in SI.

Example

get_quantities_and_units("pixel_size = 1.2 um ; distance = 1 m") Will return

Raises

• ValueError