Welcome to bnlcrl

CRL simulator

bnlcrl package

Subpackages

bnlcrl.pkcli package

Submodules

bnlcrl.pkcli.simulate module

Utilities for X-Ray beamlines.

The module to perform the following operations:

• simulate Compound Refractive Lenses (CRL) in the approximation of thick lens;
• get the Index of Refraction (Delta) value;
• calculate ideal focal distance.

bnlcrl.pkcli.simulate.calc_ideal_focus(delta, n, p0, radius)

Calculate ideal focus for the CRL with specified parameters.

Parameters:

• delta (float) – the index of refraction.
• n (int) – number of lenses in the CRL.
• p0 (float) – distance from source to the CRL [m].
• radius (float) – radius on tip of parabola [m].

Returns:

dictionary with the result.

Return type:

dict

bnlcrl.pkcli.simulate.find_delta(energy, calc_delta=False, characteristic='delta', data_file='', e_max=30000.0, e_min=30.0, e_step=10.0, formula='Be', n_points=500, outfile='', plot=False, precise=False, save=False, save_output=False, show_plot=False, thickness=0.1, use_numpy=False, verbose=False)

Determine the Index of Refraction (delta).

The index of refraction can be defined by three different methods/approaches:

1. Get delta for the closest energy from the saved *.dat files (see bnlcrl/package_data/dat/).
2. Get delta from http://henke.lbl.gov/optical_constants/getdb2.html.
3. Calculate delta analytically (requires periodictable package installed).

Parameters:

• calc_delta (bool) – a flag to calculate delta analytically.
• characteristic (str) – characteristic to be extracted (atten - attenuation length, delta - index of refraction, transmission - filter transmission).
• data_file (str) – a *.dat data file in bnlcrl/package_data/dat/ directory with delta values for the material of the CRL (e.g., Be).
• e_max (float) – the highest available energy [eV].
• e_min (float) – the lowest available energy [eV].
• e_step (float) – energy step size used for saving data to a file [eV].
• energy (float) – photon energy [eV].
• formula (str) – material’s formula of the interest.
• n_points (int) – number of points to get from the server.
• outfile (str) – optional output file.
• plot (bool) – a flag to plot the obtained data.
• precise (bool) – a flag to find delta within the energy interval +/- 1 eV from the specified energy.
• save (bool) – a flag to save the obtained data.
• save_output (bool) – a flag to save the output dictionary in JSON format.
• show_plot (bool) – a flag to show the show the plot.
• thickness (float) – thickness of the material.
• use_numpy (bool) – a flag to use NumPy.
• verbose (bool) – a flag to print output to console.

Returns:

dictionary with the result.

Return type:

dict

bnlcrl.pkcli.simulate.simulate_crl(cart_ids, energy, beamline='smi', calc_delta=False, d_ssa_focus=8.1, data_file='Be_delta.dat', dl_cart=0.03, dl_lens=0.002, lens_array=[1, 2, 4, 8, 16], outfile='False', output_format='csv', p0=6.2, r_array=[50, 200, 500], radii_tolerance=1e-08, teta0=6e-05, use_numpy=False, verbose=False)

Runner of the CRL simulator.

Calculate real CRL under-/over-focusing comparing with the ideal lens.

Example:

d = default_command(
    cart_ids=['2', '4', '6', '7', '8'],
    energy=21500,
    p0=6.52,
    verbose=True
)

Output:

"d","d_ideal","f","p0","p1","p1_ideal"
0.00120167289264,-0.0661303590822,1.0480597835,6.52,1.24879832711,1.31613035908

Parameters:

• beamline (str) – beamline name.
• calc_delta (bool) – a flag to calculate delta analytically.
• cart_ids (list) – cartridges ids.
• d_ssa_focus (float) – Distance from SSA [m].
• data_file (str) – data file with delta values for the material of the CRL (e.g., Be).
• dl_cart (float) – distance between centers of two neighbouring cartridges [m].
• dl_lens (float) – distance between two lenses within a cartridge [m].
• energy (float) – photon energy [eV].
• lens_array (list) – possible number of lenses in cartridges.
• outfile (str) – output file.
• output_format (str) – output file format (CSV, JSON, plain text).
• p0 (float) – distance from z=50.9 m to the first lens in the most upstream cartridge at the most upstream position of the transfocator [m].
• r_array (list) – radii of available lenses in different cartridges [um].
• radii_tolerance (float) – tolerance to compare radii [m].
• teta0 (float) – divergence of the beam before CRL [rad].
• use_numpy (bool) – a flag to use NumPy for operations with matrices.
• verbose (bool) – a flag to print output to console.

Returns:

dictionary with the result.

Return type:

dict

Module contents

Submodules

bnlcrl.base_pkconfig module

Default config

bnlcrl.base_pkconfig.alpha()

bnlcrl.base_pkconfig.beta()

bnlcrl.base_pkconfig.dev()

bnlcrl.base_pkconfig.prod()

bnlcrl.bnlcrl_console module

Front-end command line for bnlcrl.

See pykern.pkcli for how this module is used.

copyright:Copyright (c) 2016 mrakitin. All Rights Reserved. license:http://www.apache.org/licenses/LICENSE-2.0.html

bnlcrl.bnlcrl_console.main()

bnlcrl.crl_simulator module

class bnlcrl.crl_simulator.CRLSimulator(**kwargs)

calc_T_total()

calc_delta_focus(p)

static calc_ideal_focus(**kwargs)

calc_ideal_lens()

calc_lens_array(radius, n)

Calculate accumulated T_fs for one cartridge with fixed radius.

Parameters:

• radius – radius.
• n – number of lenses in one cartridge.

Return T_fs_accum:  

accumulated T_fs.

calc_real_lens()

calc_y_teta()

get_inserted_lenses()

print_result(output_format=None)

read_config_file()

bnlcrl.delta_finder module

A library to get index of refraction (delta) or attenuation length.

Author: Maksim Rakitin (BNL) 2016

class bnlcrl.delta_finder.DeltaFinder(**kwargs)

calculate_delta()

print_info()

save_to_file()

bnlcrl.plot_delta module

bnlcrl.utils module

bnlcrl.utils.console(class_name, parameters_file)

bnlcrl.utils.convert_types(input_dict)

Convert types of values from specified JSON file.

bnlcrl.utils.create_cli_function(function_name, parameters, config)

The function creates the content of the CLI functions with the input from JSON config.

Parameters:

• function_name (str) – name of the function.
• parameters (dict) – dictionary with the parameters of the arguments (default value, help info, type).
• config (dict) – dictionary with the parameters (descriptions, used class name, returns, parameters (optional)).

Returns:

resulted function represented as a string.

Return type:

str

bnlcrl.utils.defaults_file(suffix=None, defaults_file_path=None)

bnlcrl.utils.get_cli_functions(config)

Get list of CLI functions’ content with the input from JSON config.

Parameters:config (dict) – dictionary with the configuration in JSON format. Returns:list of functions’ contents. Return type:list

bnlcrl.utils.read_json(file_name)

bnlcrl.visualize module

bnlcrl.visualize.plot_data(df, elements, property, thickness, e_min, e_max, n_points, file_name='data', x_label=None, figsize=(10, 6), show_plot=False)

bnlcrl.visualize.save_to_csv(df, file_name='data', index=False)

bnlcrl.visualize.to_dataframe(d, elements)

Convert a list of strings, each representing the read data, to a Pandas DataFrame object.

Parameters:

• d – a list of strings, each representing the read data.
• elements – Chemical elements of interest.

Returns:

a tuple of DataFrame and the parsed columns.

Module contents

bnlcrl

Indices and tables

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• Module Index
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