NRSS.morphology#

class NRSS.morphology.Material(materialID=1, Vfrac=None, S=None, theta=None, psi=None, NumZYX=None, energies=None, opt_constants=None, name=None)#

Bases: OpticalConstants

Object to hold the voxel-level data for a CyRSoXS morphology. Inherits from the OpticalConstants class.

materialID#

Integer value denoting the material number. Used in CyRSoXS

Type:

int

Vfrac#

Volume fractions for a Material

Type:

ndarray

theta#

The second Euler angle (ZYZ convention)

Type:

ndarray

psi#

The third Euler angle (ZYZ convention)

Type:

ndarray

NumZYX#

Dimensions of the Material arrays (NumZ, NumY, NumX)

Type:

tuple or list

name#

Name of the Material (e.g. ‘Polystyrene’)

Type:

str

copy()#
class NRSS.morphology.Morphology(numMaterial, materials=None, PhysSize=None, config={'CaseType': 0, 'EAngleRotation': [0.0, 1.0, 0.0], 'Energies': [270.0], 'MorphologyType': 0}, create_cy_object=True)#

Bases: object

Object used to hold all the components necessary for a complete CyRSoXS morphology

input_mapping#

A dictionary to handle specific configuration input types

Type:

dict

numMaterial#

Number of materials present in the morphology

Type:

int

materials#

A dictionary of Material objects

Type:

dict

PhysSize#

The physical size of each cubic voxel’s three dimensions

Type:

float

NumZYX#

Number of voxels in the Z, Y, and X directions (NumZ, NumY, NumX)

Type:

tuple or list

config#

A dictionary of configuration parameters for CyRSoXS

Type:

dict

create_cy_object#

Boolean value that decides if the CyRSoXS objects are created upon instantiation

Type:

bool

simulated#

Boolean value that tracks whether or not the simulation has been run

Type:

bool

load_morph_hdf5(hdf5_file, create_cy_object=True)#

Class method that creates a Morphology object from a morphology HDF5 file

create_inputData()#

Creates a CyRSoXS InputData object and populates it with parameters from self.config

create_optical_constants()#

Creates a CyRSoXS RefractiveIndex object and populates it with optical constants from the materials dict

create_voxel_data()#

Creates a CyRSoXS VoxelData object and populates it with the voxel information from the materials dict

run(stdout=True, stderr=True, return_xarray=True, print_vec_info=False)#

Creates a CyRSoXS ScatteringPattern object if not already created, and submits all CyRSoXS objects to run the simulation

scattering_to_xarray(return_xarray=True, print_vec_info=False)#

Copies the CyRSoXS ScatteringPattern arrays to an xarray in the format used by PyHyperScattering for further analysis

property AlgorithmType#
property CaseType#
property EAngleRotation#
property Energies#
property EwaldsInterpolation#
property MorphologyType#
property PhysSize#
property ReferenceFrame#
property RotMask#
property WindowingType#
check_materials(quiet=True)#
property config#
config_default = {'AlgorithmType': 0, 'CaseType': 0, 'EAngleRotation': [0.0, 1.0, 0.0], 'Energies': [270.0], 'EwaldsInterpolation': 1, 'MorphologyType': 0, 'ReferenceFrame': 1, 'RotMask': 0, 'WindowingType': 0}#
config_to_inputData()#
create_inputData()#
create_optical_constants()#
create_update_cy()#
create_voxel_data()#
input_mapping = {'AlgorithmType': ['setAlgorithm', [0, 1]], 'CaseType': ['setCaseType', [<CaseType.Default: 0>, <CaseType.BeamDivergence: 1>, <CaseType.GrazingIncidence: 2>]], 'EwaldsInterpolation': ['interpolationType', [<InterpolationType.NearestNeighour: 0>, <InterpolationType.Linear: 1>]], 'MorphologyType': ['setMorphologyType', [<MorphologyType.EulerAngles: 0>, <MorphologyType.VectorMorphology: 1>]], 'ReferenceFrame': ['referenceFrame', [0, 1]], 'RotMask': ['rotMask', [False, True]], 'WindowingType': ['windowingType', [<FFTWindowing.NoPadding: 0>, <FFTWindowing.Hanning: 1>]]}#
load_config(config_file)#
load_matfile(matfile)#
classmethod load_morph_hdf5(hdf5_file, create_cy_object=False)#
property numMaterial#
run(stdout=True, stderr=True, return_xarray=True, print_vec_info=False, validate=False)#
scattering_to_xarray(return_xarray=True, print_vec_info=False)#
property simulated#
update_optical_constants()#
update_voxel_data()#
validate_all(quiet=True)#
visualize_materials(*args, **kwargs)#

Reads in morphology HDF5 file and checks that the format is consistent for CyRSoXS. Optionally plots and returns select quantities.

Parameters:

  • z_slice (int) – Which z-slice of the array to plot.

  • subsample (int) – Number of voxels to display in X and Y

  • translate_x (int) – Number of voxels to translate image in x; meant for use with subsample

  • translate_y (int) – Number of voxels to translate image in y; meant for use with subsample

  • screen_euler (bool) – Suppress visualization of euler angles where vfrac < 0.05 or S < 0.05; intended to hilight edges

  • add_quiver (bool) – Adds lines to every voxel on the psi plot that indicate in-plane direction. Not recommended for resolutions larger than 128x128, best for resolutions 64x64 or lower.

  • quiver_bw (bool) – Intended to be used when add_quiver == True, when quiver_bw is True, the quiver arrows will be black and white instead of colored.

  • outputmat (list of ints) – Number of which materials to return

  • outputplot (list of strings) – Number of which plots to return, can include ‘vfrac’, ‘S’, ‘theta’, ‘psi’

  • outputaxes (bool) – If a plot is returned, include its axes

  • vfrac_range (list of tuples as [float, float]) – A custom range for vfrac colorbar

  • S_range (list of tuples as [float, float]) – A custom range for S colorbar

  • vfrac_cmap (str) – A custom substitution for vfrac colormap

  • S_cmap (str) – A custom substitution for vfrac colormap

  • runquiet (bool) – Boolean flag for running without plotting or outputting to console

  • batchMode (bool) – if true, prints console output and generates plots but doesnt show (provide exportDir for export)

  • plotstyle (str) – Use a light or dark background for plots. ‘dark’ - dark, ‘light’ - light

  • dpi (int) – The dpi at which the plot is generated. Per-material plot dimensions are 8.5” x 12.75”

  • exportDir (str, optional) – if provided, export directory to save any generated figures into, by default, will respect dpi and save as png, use exportParams to override

  • exportParams (dict, optional) – additional params to unpack into matplotlib.pyplot.savefig. Overrides existing params. ex: exportParams = {‘dpi’:600, format=’svg’}

Return type:

If outputmat and outputplot are correctly entered, will return an index list of images of the selected material and plot. Each list element will be a numpy array in RGB format that be displayed with imshow

write_config()#
write_constants(path=None)#
write_to_file(fname, author='NIST')#
class NRSS.morphology.OpticalConstants(energies, opt_constants=None, name='unknown')#

Bases: object

Object to hold dielectric optical constants in a format compatible with CyRSoXS

energies#

List of energies

Type:

list or array

opt_constants#

Dictionary of optical constants, where each energy is a key in the dict

Type:

dict

name#

String identifying the element or material for these optical constants

Type:

str

calc_constants(energies, reference_data, name='unkown')#

Interpolates optical constant data to the list of energies provided

load_matfile(matfile, name='unknown')#

Creates an OpticalConstants object from a previously written MaterialX.txt file

create_vacuum(energies)#

Convenience function to populate zeros for all optical constants

classmethod calc_constants(energies, reference_data, name='unknown')#
create_vacuum(energies)#
classmethod load_matfile(matfile, name='unknown')#
NRSS.morphology.check_NumMat(f, morphology_type)#

Checks and validates the number of materials in the HDF5 file

Parameters:

  • f (file object) –

  • morphology_type (int) – 0 - Euler, 1 - Vector

Returns:

num_mat – Number of materials in file

Return type:

int

NRSS.morphology.morphology_visualizer(morphology, z_slice: int = 0, subsample: int = None, translate_x: int = None, translate_y: int = None, screen_euler: bool = True, add_quiver: bool = False, quiver_bw: bool = True, outputmat: list = None, outputplot: list = None, outputaxes: bool = True, vfrac_range: list = None, S_range: list = None, vfrac_cmap: str = None, S_cmap: str = None, runquiet: bool = False, batchMode: bool = False, plotstyle: str = 'light', dpi: int = 300, exportDir: str = None, exportParams: dict = None)#

Reads in morphology HDF5 file and checks that the format is consistent for CyRSoXS. Optionally plots and returns select quantities.

Parameters:

  • z_slice (int) – Which z-slice of the array to plot.

  • subsample (int) – Number of voxels to display in X and Y

  • translate_x (int) – Number of voxels to translate image in x; meant for use with subsample

  • translate_y (int) – Number of voxels to translate image in y; meant for use with subsample

  • screen_euler (bool) – Suppress visualization of euler angles where vfrac < 0.05 or S < 0.05; intended to hilight edges

  • add_quiver (bool) – Adds lines to every voxel on the psi plot that indicate in-plane direction. Not recommended for resolutions larger than 128x128, best for resolutions 64x64 or lower.

  • quiver_bw (bool) – Intended to be used when add_quiver == True, when quiver_bw is True, the quiver arrows will be black and white instead of colored.

  • outputmat (list of ints) – Number of which materials to return

  • outputplot (list of strings) – Number of which plots to return, can include ‘vfrac’, ‘S’, ‘theta’, ‘psi’

  • outputaxes (bool) – If a plot is returned, include its axes

  • vfrac_range (list of tuples as [float, float]) – A custom range for vfrac colorbar

  • S_range (list of tuples as [float, float]) – A custom range for S colorbar

  • vfrac_cmap (str) – A custom substitution for vfrac colormap

  • S_cmap (str) – A custom substitution for vfrac colormap

  • runquiet (bool) – Boolean flag for running without plotting or outputting to console

  • batchMode (bool) – if true, prints console output and generates plots but doesnt show (provide exportDir for export)

  • plotstyle (str) – Use a light or dark background for plots. ‘dark’ - dark, ‘light’ - light

  • dpi (int) – The dpi at which the plot is generated. Per-material plot dimensions are 8.5” x 12.75”

  • exportDir (str, optional) – if provided, export directory to save any generated figures into, by default, will respect dpi and save as png, use exportParams to override

  • exportParams (dict, optional) – additional params to unpack into matplotlib.pyplot.savefig. Overrides existing params. ex: exportParams = {‘dpi’:600, format=’svg’}

Return type:

If outputmat and outputplot are correctly entered, will return an index list of images of the selected material and plot. Each list element will be a numpy array in RGB format that be displayed with imshow

NRSS.morphology.read_config(config_file)#
NRSS.morphology.read_material(filename)#
NRSS.morphology.write_hdf5(material_list, PhysSize, fname, MorphologyType=0, ordering='ZYX', author='NIST')#

Writes Euler or Vector Morphology format into CyRSoXS-compatible HDF5 file and returns the hdf5 filename

Parameters:

  • material_list (lists) – List of material lists. Euler Ex. [[Mat_1_Vfrac, Mat_1_S, Mat_1_Theta, Mat_1_Psi],[Mat_2_Vfrac, Mat_2_S, Mat_2_Theta, Mat_2_Psi]] Vector Ex. [[Mat_1_alignment, Mat_1_unaligned],[Mat_2_alignment, Mat_2_unaligned]]

  • PhysSize (float) – Voxel size

  • fname (str or path) – name of hdf5 file to write

  • MorphologyType (int) – 0 - Euler 1 - Vector

  • ordering (str) – String denoting the axes ordering. ‘ZYX’ or ‘XYZ’

  • author (str) – Name of author writing the morphology

Returns:

Name of hdf5 file written

Return type:

fname

NRSS.morphology.write_opts(optical_constants, material_num, path)#