sas.sascalc.calculator package

Submodules

sas.sascalc.calculator.BaseComponent module

Provide base functionality for all model components

class sas.sascalc.calculator.BaseComponent.BaseComponent

Bases: object

Basic model component

Since version 0.5.0, basic operations are no longer supported.

calculate_ER()

Calculate effective radius

calculate_VR()

Calculate volume fraction ratio

clone()

Returns a new object identical to the current object

evalDistribution(qdist)

Evaluate a distribution of q-values.

• For 1D, a numpy array is expected as input:

  evalDistribution(q)
  

  where q is a numpy array.

• For 2D, a list of numpy arrays are expected: [qx_prime,qy_prime], where 1D arrays,

  qx_prime = [ qx[0], qx[1], qx[2], ....]
  

  and

  qy_prime = [ qy[0], qy[1], qy[2], ....]
  

Then get

q = np.sqrt(qx_prime^2+qy_prime^2)

that is a qr in 1D array;

q = [q[0], q[1], q[2], ....]

Note

Due to 2D speed issue, no anisotropic scattering is supported for python models, thus C-models should have their own evalDistribution methods.

The method is then called the following way:

evalDistribution(q)

where q is a numpy array.

Parameters:qdist – ndarray of scalar q-values or list [qx,qy] where qx,qy are 1D ndarrays

getDispParamList()

Return a list of all available parameters for the model

getParam(name)

Set the value of a model parameter :param name: name of the parameter

getParamList()

Return a list of all available parameters for the model

getParamListWithToken(token, member)

get Param List With Token

getParamWithToken(name, token, member)

get Param With Token

getProfile()

Get SLD profile

: return: (z, beta) where z is a list of depth of the transition points

beta is a list of the corresponding SLD values

is_fittable(par_name)

Check if a given parameter is fittable or not

Parameters:par_name – the parameter name to check

run(x)

run 1d

runXY(x)

run 2d

setParam(name, value)

Set the value of a model parameter

Parameters:

• name – name of the parameter
• value – value of the parameter

setParamWithToken(name, value, token, member)

set Param With Token

set_dispersion(parameter, dispersion)

model dispersions

sas.sascalc.calculator.instrument module

This module is a small tool to allow user to control instrumental parameters

class sas.sascalc.calculator.instrument.Aperture

Bases: object

An object class that defines the aperture variables

set_sample_distance(distance=[])

Set the sample aperture distance

set_sample_size(size=[])

Set the sample aperture size

set_source_size(size=[])

Set the source aperture size

class sas.sascalc.calculator.instrument.Detector

Bases: object

An object class that defines the detector variables

set_distance(distance=[])

Set the detector distance

set_pix_size(size=[])

Set the detector pix_size

set_size(size=[])

Set the detector size

class sas.sascalc.calculator.instrument.Neutron

Bases: object

An object that defines the wavelength variables

get_band()

To get the wavelength band

get_default_spectrum()

get default spectrum

get_intensity()

To get the value of intensity

get_mass()

To get the neutron mass

get_ramdom_value()

To get the value of wave length

get_spectrum()

To get the wavelength spectrum

get_wavelength()

To get the value of wavelength

get_wavelength_spread()

To get the value of wavelength spread

plot_spectrum()

To plot the wavelength spactrum : requirement: matplotlib.pyplot

set_band(band=[])

To set the wavelength band

Parameters:band – array of [min, max]

set_full_band()

set band to default value

set_intensity(intensity=368428)

Sets the intensity in counts/sec

set_mass(mass=1.67492729e-24)

Sets the wavelength

set_spectrum(spectrum)

Set spectrum

Parameters:spectrum – numpy array

set_wavelength(wavelength=6.0)

Sets the wavelength

set_wavelength_spread(spread=0.125)

Sets the wavelength spread

setup_spectrum()

To set the wavelength spectrum, and intensity, assumes wavelength is already within the spectrum

class sas.sascalc.calculator.instrument.Sample

Bases: object

An object class that defines the sample variables

set_distance(distance=[])

Set the sample distance

set_size(size=[])

Set the sample size

set_thickness(thickness=0.0)

Set the sample thickness

class sas.sascalc.calculator.instrument.TOF

Bases: sas.sascalc.calculator.instrument.Neutron

TOF: make list of wavelength and wave length spreads

get_intensity_list()

get list of the intensity wrt wavelength_list

get_wave_list()

Get wavelength and wavelength_spread list

set_wave_list(wavelength=[])

Set wavelength list

Parameters:wavelength – list of wavelengths

set_wave_spread_list(wavelength_spread=[])

Set wavelength_spread list

Parameters:wavelength_spread – list of wavelength spreads

sas.sascalc.calculator.instrument.validate(value=None)

Check if the value is folat > 0.0

Return value:True / False

sas.sascalc.calculator.kiessig_calculator module

This module is a small tool to allow user to quickly determine the size value in real space from the fringe width in q space.

class sas.sascalc.calculator.kiessig_calculator.KiessigThicknessCalculator

Bases: object

compute thickness from the fringe width of data

compute_thickness()

Calculate thickness.

Returns:the thickness.

get_deltaq()

return deltaQ value in 1/A unit

get_thickness_unit()

Returns:the thickness unit.

set_deltaq(dq=None)

Receive deltaQ value

Parameters:dq – q fringe width in 1/A unit

sas.sascalc.calculator.resolution_calculator module

This object is a small tool to allow user to quickly determine the variance in q from the instrumental parameters.

class sas.sascalc.calculator.resolution_calculator.ResolutionCalculator

Bases: object

compute resolution in 2D

compute(wavelength, wavelength_spread, qx_value, qy_value, coord='cartesian', tof=False)

Compute the Q resoltuion in || and + direction of 2D : qx_value: x component of q : qy_value: y component of q

compute_and_plot(qx_value, qy_value, qx_min, qx_max, qy_min, qy_max, coord='cartesian')

Compute the resolution : qx_value: x component of q : qy_value: y component of q

get_all_instrument_params()

Get all instrumental parameters

get_default_spectrum()

Get default_spectrum

get_detector_pix_size()

Get detector pixel size

get_detector_qrange()

get max detector q ranges

: return: qx_min, qx_max, qy_min, qy_max tuple

get_detector_size()

Get detector size

get_image(qx_value, qy_value, sigma_1, sigma_2, sigma_r, qx_min, qx_max, qy_min, qy_max, coord='cartesian', full_cal=True)

Get the resolution in polar coordinate ready to plot : qx_value: qx_value value : qy_value: qy_value value : sigma_1: variance in r direction : sigma_2: variance in phi direction : coord: coordinate system of image, ‘polar’ or ‘cartesian’

get_intensity()

Get intensity

get_intensity_list()

Set wavelength spread

get_neutron_mass()

Get Neutron mass

get_sample2detector_distance()

Get detector sample2detector_distance

get_sample2sample_distance()

Get detector sampleslitsample_distance

get_sample_aperture_size()

Get sample aperture size

get_source2sample_distance()

Get detector source2sample_distance

get_source_aperture_size()

Get source aperture size

get_spectrum()

Get _spectrum

get_variance(size=[], distance=0, phi=0, comp='radial')

Get the variance when the slit/pinhole size is given : size: list that can be one(diameter for circular) or two components(lengths for rectangular) : distance: [z, x] where z along the incident beam, x // qx_value : comp: direction of the sigma; can be ‘phi’, ‘y’, ‘x’, and ‘radial’

: return variance: sigma^2

get_variance_gravity(s_distance, d_distance, wavelength, spread, phi, comp='radial', switch='on')

Get the variance from gravity when the wavelength spread is given

: s_distance: source to sample distance : d_distance: sample to detector distance : wavelength: wavelength : spread: wavelength spread (ratio) : comp: direction of the sigma; can be ‘phi’, ‘y’, ‘x’, and ‘radial’

: return variance: sigma^2

get_variance_wave(A_value, radius, distance, spread, phi, comp='radial', switch='on')

Get the variance when the wavelength spread is given

: radius: the radial distance from the beam center to the pix of q : distance: sample to detector distance : spread: wavelength spread (ratio) : comp: direction of the sigma; can be ‘phi’, ‘y’, ‘x’, and ‘radial’

: return variance: sigma^2 for 2d, sigma^2 for 1d [tuple]

get_wave_list()

Set wavelength spread

get_wavelength()

Get wavelength

get_wavelength_spread()

Get wavelength spread

plot_image(image)

Plot image using pyplot : image: 2d resolution image

: return plt: pylab object

reset_image()

Reset image to default (=[])

set_detector_pix_size(size)

Set detector pixel size

set_detector_size(size)

Set detector size in number of pixels : param size: [pixel_nums] or [x_pix_num, yx_pix_num]

set_intensity(intensity)

Set intensity

set_neutron_mass(mass)

Set Neutron mass

set_sample2detector_distance(distance)

Set detector sample2detector_distance

: param distance: [distance, x_offset]

set_sample2sample_distance(distance)

Set detector sample_slit2sample_distance

: param distance: [distance, x_offset]

set_sample_aperture_size(size)

Set sample aperture size

: param size: [dia_value] or [xheight_value, yheight_value]

set_source2sample_distance(distance)

Set detector source2sample_distance

: param distance: [distance, x_offset]

set_source_aperture_size(size)

Set source aperture size

: param size: [dia_value] or [x_value, y_value]

set_spectrum(spectrum)

Set spectrum

set_wave(wavelength)

Set wavelength list or wavelength

set_wave_list(wavelength_list, wavelengthspread_list)

Set wavelength and its spread list

set_wave_spread(wavelength_spread)

Set wavelength spread or wavelength spread

set_wavelength(wavelength)

Set wavelength

set_wavelength_spread(wavelength_spread)

Set wavelength spread

setup_tof(wavelength, wavelength_spread)

Setup all parameters in instrument

: param ind: index of lambda, etc

sas.sascalc.calculator.sas_gen module

SAS generic computation and sld file readers

class sas.sascalc.calculator.sas_gen.GenSAS

Bases: sas.sascalc.calculator.BaseComponent.BaseComponent

Generic SAS computation Model based on sld (n & m) arrays

evalDistribution(qdist)

Evaluate a distribution of q-values.

Parameters:qdist – ndarray of scalar q-values (for 1D) or list [qx,qy] where qx,qy are 1D ndarrays (for 2D).

getProfile()

Get SLD profile : return: sld_data

run(x=0.0)

Evaluate the model :param x: simple value :return: (I value)

runXY(x=0.0)

Evaluate the model :param x: simple value :return: I value :Use this runXY() for the computation

set_is_avg(is_avg=False)

Sets is_avg: [bool]

set_pixel_volumes(volume)

Set the volume of a pixel in (A^3) unit :Param volume: pixel volume [float]

set_sld_data(sld_data=None)

Sets sld_data

class sas.sascalc.calculator.sas_gen.MagSLD(pos_x, pos_y, pos_z, sld_n=None, sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None)

Bases: object

Magnetic SLD.

get_sldn()

Returns nuclear sld

pos_x = None

pos_y = None

pos_z = None

set_conect_lines(line_x, line_y, line_z)

Set bonding line data if taken from pdb

set_nodes()

Set xnodes, ynodes, and znodes

set_pix_type(pix_type)

Set pixel type :Param pix_type: string, ‘pixel’ or ‘atom’

set_pixel_symbols(symbol='pixel')

Set pixel :Params pixel: str; pixel or atomic symbol, or array of strings

set_pixel_volumes(vol)

Set pixel volumes :Params pixel: str; pixel or atomic symbol, or array of strings

set_sldms(sld_mx, sld_my, sld_mz)

Sets mx, my, mz and abs(m).

set_sldn(sld_n)

Sets neutron SLD

set_stepsize()

Set xtepsize, ystepsize, and zstepsize

sld_mx = None

sld_my = None

sld_mz = None

sld_n = None

class sas.sascalc.calculator.sas_gen.OMF2SLD

Bases: object

Convert OMFData to MAgData

get_magsld()

return MagSLD

get_omfdata()

Return all data

get_output()

Return output

remove_null_points(remove=False, recenter=False)

Removes any mx, my, and mz = 0 points

set_data(omfdata, shape='rectangular')

Set all data

class sas.sascalc.calculator.sas_gen.OMFData

Bases: object

OMF Data.

set_m(mx, my, mz)

Set the Mx, My, Mz values

class sas.sascalc.calculator.sas_gen.OMFReader

Bases: object

Class to load omf/ascii files (3 columns w/header).

ext = ['.omf', '.OMF']

read(path)

Load data file :param path: file path :return: x, y, z, sld_n, sld_mx, sld_my, sld_mz

type = ['OMF files (*.OMF, *.omf)|*.omf']

type_name = 'OMF ASCII'

class sas.sascalc.calculator.sas_gen.PDBReader

Bases: object

PDB reader class: limited for reading the lines starting with ‘ATOM’

ext = ['.pdb', '.PDB']

read(path)

Load data file

Parameters:path – file path Returns:MagSLD Raises:RuntimeError – when the file can’t be opened

type = ['pdb files (*.PDB, *.pdb)|*.pdb']

type_name = 'PDB'

write(path, data)

Write

class sas.sascalc.calculator.sas_gen.SLDReader

Bases: object

Class to load ascii files (7 columns).

ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']

read(path)

Load data file :param path: file path :return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz :raise RuntimeError: when the file can’t be opened :raise ValueError: when the length of the data vectors are inconsistent

type = ['sld files (*.SLD, *.sld)|*.sld', 'txt files (*.TXT, *.txt)|*.txt', 'all files (*.*)|*.*']

type_name = 'SLD ASCII'

write(path, data)

Write sld file :Param path: file path :Param data: MagSLD data object

sas.sascalc.calculator.sas_gen.decode(s)

sas.sascalc.calculator.sas_gen.mag2sld(mag, v_unit=None)

Convert magnetization to magnatic SLD sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton) Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn’t be 2.90636E-12 [A^(-2)]???

sas.sascalc.calculator.sas_gen.test()

Test code

sas.sascalc.calculator.sas_gen.test_load()

Test code

sas.sascalc.calculator.sas_gen.test_save()

sas.sascalc.calculator.sas_gen.transform_center(pos_x, pos_y, pos_z)

re-center :return: posx, posy, posz [arrays]

sas.sascalc.calculator.slit_length_calculator module

This module is a small tool to allow user to quickly determine the slit length value of data.

class sas.sascalc.calculator.slit_length_calculator.SlitlengthCalculator

Bases: object

compute slit length from SAXSess beam profile (1st col. Q , 2nd col. I , and 3rd col. dI.: don’t need the 3rd)

calculate_slit_length()

Calculate slit length.

Returns:the slit length calculated value.

get_slit_length_unit()

Returns:the slit length unit.

set_data(x=None, y=None)

Receive two vector x, y and prepare the slit calculator for computation.

Parameters:

• x – array
• y – array

Module contents