SimEx.Analysis package

SimEx.Analysis.AbstractAnalysis module

module AbstractAnalysis

Hosts the abstract base class for all analysis classes.

class SimEx.Analysis.AbstractAnalysis.AbstractAnalysis(input_path=None)

Bases: object

Class AbstractAnalysis

Abstract base class for all data analysis classes.

Parameters

input_path (str) – Path to hdf5 file holding the data to analyze. Single file or directory.

classmethod dumpLoader(fname)

Creates calculator object from a dump file

Parameters

fname – path to the dump file.

Returns

Created calculator object.

Raises

RuntimeError – if cannot create object.

dumpToFile(fname)

dump class instance to file.

Parameters

fname – Path to file to dump.

property input_path

Query for the input file path(s).

classmethod runFromCLI()

Method to start calculator computations from command line.

Returns

exit with status code

SimEx.Analysis.AbstractAnalysis.checkAndSetBaseCalculator(var=None, default=None)

Check if passed object is an AbstractAnalysis instance. If non is given, set to given default.

Parameters

• var – The object to check.

• default – The default to use.

Returns

The checked object.

Raises

RuntimeError – if no valid Analysis object was given.

SimEx.Analysis.DiffractionAnalysis module

module DiffractionAnalysis

Module that hosts the DiffractionAnalysis class.

class SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis(input_path=None, pattern_indices=None, poissonize=True, mask=None)

Bases: SimEx.Analysis.AbstractAnalysis.AbstractAnalysis

Class DiffractionAnalysis

Class that implements common data analysis tasks for diffraction data.

Parameters

• input_path (str) – Name of file or directory that contains data to analyse.

• pattern_indices (int || sequence of int || "all") – Identify which patterns to include in the analysis (default “all”).

• poissonize (bool) – Whether to add Poisson noise to the integer photon numbers (default True).

• mask (numpy.array) – Mask to multiply on each pattern.

Example pattern_indices

pattern_indices=1

pattern_indices=[1,2,3]

pattern_indices=range(1,10)

pattern_indices=”all”

animatePatterns(output_path=None, logscale=False, offset=0.1)

Make an animated gif out of the given patterns.

Parameters

• output_path (str) – Where to save the animated git.

• logscale (bool) – Whether to apply logarithmic scaling to the z axis (color).

• offset (float) – Offset to apply if logarithmic scaling is on.

Raises

IOError – File exists or parent directory not found.

property mask

Query the mask.

property npattern

get the number of the selected patterns in this analysis object

numpyPattern(operation=None)

Return the pattern after opentation over the patterns defined in DiffractionAnalysis class.

Parameters

operation (python function) – Operation to apply to selected patterns (default none).

Note operation

Operation must accept a 3D numpy.array as first input argument and the “axis” keyword-argument. Operation must return a 2D numpy.array. Axis will always be chosen as axis=0.

Example operation

numpy.mean, numpy.std, numpy.sum

property parameters

patternGenerator()

Yield an iterator over a given pattern sequence from a diffraction file.

property pattern_indices

Query pattern indices attribute.

property patterns_iterator

plotPattern(operation=None, logscale=False, offset=0.1, symlog=False, *argv, **kwargs)

Plot a pattern.

Parameters

• operation (python function) – Operation to apply to selected patterns (default numpy.sum).

• logscale (bool) – Whether to plot the intensity on a logarithmic scale (z-axis) (default False).

• offset (float) – Offset to apply if logarithmic scaling is on.

Note operation

Operation must accept a 3D numpy.array as first input argument and the “axis” keyword-argument. Operation must return a 2D numpy.array. Axis will always be chosen as axis=0.

Example operation

numpy.mean, numpy.std, numpy.sum

plotRadialProjection(operation=None, logscale=False, offset=1e-05, unit='q_nm^-1')

Plot the radial projection of a pattern.

Parameters

• operation (python function) – Operation to apply to selected patterns (default numpy.sum).

• logscale (bool) – Whether to plot the intensity on a logarithmic scale (z-axis) (default False).

Note operation

Operation must accept a 3D numpy.array as first input argument and the “axis” keyword-argument. Operation must return a 2D numpy.array. Axis will always be chosen as axis=0.

Example operation

numpy.mean, numpy.std, numpy.sum

:param unit:can be “q_nm^-1”, “q_A^-1”, “2th_deg”, “2th_rad”, “r_mm”. :type unit: str

property poissonize

Query whether to read data with (True) or without (False) Poisson noise.

property qMap

q of each pixel

shannonPixelPhoton(resolution)

Get the average number of photons per shannon pixel

Parameters

resolution (float) – The full periodic resolution (A) for shannon pixels

property solidAngles

Solid angle of each pixel

statistics()

Get statistics of photon numbers per pattern (mean and rms) over selected patterns and plot a historgram.

SimEx.Analysis.DiffractionAnalysis.azimuthalIntegration(pattern, parameters, unit='q_nm^-1')

SimEx.Analysis.DiffractionAnalysis.diffractionParameters(path)

Extract beam parameters and geometry from given file or directory.

Parameters

path (str) – Path to file that holds the parameters to extract.

SimEx.Analysis.DiffractionAnalysis.photonStatistics(stack)

SimEx.Analysis.DiffractionAnalysis.plotImage(pattern, logscale=False, offset=0.1, symlog=False, *argv, **kwargs)

Workhorse function to plot an image

Parameters

• logscale (bool) – Whether to show the data on logarithmic scale (z axis) (default False).

• offset (float) – Offset to apply if logarithmic scaling is on.

• symlog (bool) – If logscale is True, to show the data on symlogarithmic scale (z axis) (default False).

Returns

the handles of figure and axis

Return type

figure,axis

SimEx.Analysis.DiffractionAnalysis.plotRadialProjection(pattern, parameters, logscale=True, offset=1e-05, unit='q_nm^-1')

Perform integration over azimuthal angle and plot as function of radius.

:param unit:can be “q_nm^-1”, “q_A^-1”, “2th_deg”, “2th_rad”, “r_mm”. :type unit: str

SimEx.Analysis.DiffractionAnalysis.plotResolutionRings(parameters, rings=(10, 5.0, 3.5), half=True)

Show resolution rings on current plot.

Parameters

• parameters (dict) – Parameters needed to construct the resolution rings.

• rings (list) – the rings shown on the figure

• half (bool) – show half period resolution (True, default) or full period resolution (False)

SimEx.Analysis.DiffractionAnalysis.totalNPattern(input_path)

get the number of the diffraction patterns in the h5file

SimEx.Analysis.XFELPhotonAnalysis module

module XFELPhotonAnalysis

Module that hosts the XFELPhotonAnalysis class.

class SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis(input_path=None)

Bases: SimEx.Analysis.AbstractAnalysis.AbstractAnalysis

Class XFELPhotonAnalysis

Class that implements common data analysis tasks for wavefront (radiation field) data.

Parameters

input_path (str) – Name of file or directory that contains data to analyse.

animate(qspace=False, logscale=False)

Generate an animated gif from the wavefront data.

property intensity

Query for the intensity.

numpyTotalPower(spectrum=False, all=False)

Method to dump meaningful total power.

Parameters

• spectrum (bool) – Whether to dump the power density in energy domain (True) or time domain (False, default).

• all (bool) – True to extract all the points, False to extract only meaningful points

plotIntensityMap(qspace=False, logscale=False)

Plot the integrated intensity as function of x,y or qx, qy on a colormap.

Parameters

• qspace (bool) – Whether to plot the reciprocal space intensity map (default False).

• logscale (bool) – Whether to plot the intensity on a logarithmic scale (z-axis) (default False).

plotOnAxisPowerDensity(spectrum=False)

Method to plot the on-axis power density.

Parameters

spectrum (bool) – Whether to plot the power density in energy domain (True) or time domain (False, default).

plotTotalPower(spectrum=False)

Method to plot the total power.

Parameters

spectrum (bool) – Whether to plot the power density in energy domain (True) or time domain (False, default).

property wavefront

Query for the wavefront.

SimEx.Analysis.XFELPhotonAnalysis.calculate_fwhm(wfr)

Calculate FWHM of the beam calculating number of point bigger then max/2 throuhgt center of the image

Parameters

wfr – wavefront

Returns

{‘fwhm_x’:fwhm_x, ‘fwhm_y’: fwhm_y} in [m]

SimEx.Analysis.XFELPhotonAnalysis.mask_nans(a, replacement=0.0)

Find nans in an array and replace. :param a: Array to mask. :type a: numpy.array

Parameters

replacement (numeric) – The value to replace nans.

Returns

The array of booleans indicating which values of a are nan, numpy.isnan(a)

Return type

numpy.array(dtype=bool)

SimEx.Analysis.XMDYNPhotonMatterAnalysis module

module XMDYNPhotonMatterAnalysis

Hosting utilities to analyse and visualize photon-matter trajectories generated by XMDYN.

class SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis(input_path=None, snapshot_indices=None, elements=None, sample_path=None)

Bases: SimEx.Analysis.AbstractAnalysis.AbstractAnalysis

Class XMDYNPhotonMatterAnalysis

Class to encapsulate diagnostics of photon matter interaction trajectories.

Parameters

• input_path (str) – Path to the data to analyze.

• snapshot_indices (list) – Snapshot (indices or IDs) to analyze (Default: All).

• elements (list) – Which elements to include in the analysis (Default: All).

animate()

Generate an animation of atom trajectories and their ionization.

property elements

Query the elements to include.

property input_path

Query the input path.

load_snapshot(snapshot_index)

Load snapshot data from hdf5 file into memory.

load_trajectory()

Load the selected snapshots and extract data to analyze.

number_of_snapshots()

Get number of valid snapshots.

plot_charge()

Plot the average number of electrons per atom per atomic species as function of time.

plot_displacement()

Plot the average displacement per atomic species as function of time.

plot_energies()

Plot the evolution of MD energies over the simulation time.

property sample_path

Query the sample path.

property snapshot_indices

Query the snapshot indices.

SimEx.Analysis.XMDYNPhotonMatterAnalysis.calculate_displacement(snapshot, r0, sample)

Calculate the average displacement per atomic species in a snapshot.

Parameters

• snapshot (dict) – The snapshot to analyze

• r0 (numpy.array (shape=(Natoms, 3))) – Unperturbed positions of the sample atoms.

### CHECKME: Can’t we read r0 from the sample dict?

Parameters

sample (dict) – Sample data

SimEx.Analysis.XMDYNPhotonMatterAnalysis.calculate_ion_charge(snapshot, sample)

Calculate the remaining electric charge per atomic species of a given snapshot.

Parameters

• snapshot (dict) – The snapshot to analyze

• sample (dict) – The sample data.

SimEx.Analysis.XMDYNPhotonMatterAnalysis.load_sample(sample_path)

Load a sample file into memory.

SimEx.Analysis.XMDYNPhotonMatterAnalysis.read_h5_dataset(path, dataset)

Read a dataset from hdf5 file.