reflectometry

Package reflectometry

DANSE/Reflectometry reduction and analysis libraries.

reduction - load raw data and remove instrumental effects.
model1d - load reflectivity data and model it with 1-D density profiles
model3d - load 2-D/3-D reflectivity data and model with structures in the plane

The 1-D and 3-D modelling libraries can be used alone in simulation studies or used as part of the PARK fitting services to provide simultaneous refinement of a models to multiple datasets using global optimization techniques.

Further details available at:

http://www.reflectometry.org/danse

Version: 1.0.0

Submodules

reflectometry.model1d
- reflectometry.model1d.adaptor: The initialization for package parkAui.builder.refl.
  - reflectometry.model1d.adaptor.calcMagReflTheory
  - reflectometry.model1d.adaptor.calcReflTheory
  - reflectometry.model1d.adaptor.calcReflectivity
  - reflectometry.model1d.adaptor.matDatasetDataPanel
  - reflectometry.model1d.adaptor.matDatasetEditor
  - reflectometry.model1d.adaptor.matDatasetPanel
  - reflectometry.model1d.adaptor.matDatasetViewerPanel
  - reflectometry.model1d.adaptor.matFittingResidual
  - reflectometry.model1d.adaptor.reflData
  - reflectometry.model1d.adaptor.reflDataset
  - reflectometry.model1d.adaptor.reflDatasetDataPanel
  - reflectometry.model1d.adaptor.reflDatasetEditor
  - reflectometry.model1d.adaptor.reflDatasetMeta
  - reflectometry.model1d.adaptor.reflDatasetPanel
  - reflectometry.model1d.adaptor.reflDatasetViewerPanel
  - reflectometry.model1d.adaptor.reflFittingResidual
  - reflectometry.model1d.adaptor.reflModel
  - reflectometry.model1d.adaptor.reflModelBuilder
  - reflectometry.model1d.adaptor.reflModelPage
  - reflectometry.model1d.adaptor.reflParameter: A model implementing the Refl.
  - reflectometry.model1d.adaptor.reflParameterSet
  - reflectometry.model1d.adaptor.reflTheory
  - reflectometry.model1d.adaptor.reflUtil: Set the environments for park.builder.refl.
  - reflectometry.model1d.adaptor.setup
  - reflectometry.model1d.adaptor.thReflUtil: Set the environments
  - reflectometry.model1d.adaptor.xmlProfile: The generic interface for the profile
- reflectometry.model1d.examples
  - reflectometry.model1d.examples.Fittest
  - reflectometry.model1d.examples.demo_chisq_surfaces: Pure numeric python implementation of Parratt's recursion for computing reflectivity as a function of Q and lambda.
  - reflectometry.model1d.examples.reflClient
- reflectometry.model1d.model: 1-D modeling of scattering length density for reflectometry
  - reflectometry.model1d.model.auxs: Supplementary or auxiliary Functions
  - reflectometry.model1d.model.bspline: BSpline functions.
  - reflectometry.model1d.model.calcProfile: Functions for constructing a profile.
  - reflectometry.model1d.model.calcRefl: Basic reflectometry calculations.
  - reflectometry.model1d.model.dataLoader
  - reflectometry.model1d.model.layer: Reflectometry layer times.
  - reflectometry.model1d.model.model
  - reflectometry.model1d.model.profile: Reflectometry profile Class.
  - reflectometry.model1d.model.setup
  - reflectometry.model1d.model.staj
  - reflectometry.model1d.model.staj2model
  - reflectometry.model1d.model.tetheredPolymer
- reflectometry.model1d.profileview: The initialization for package services
  - reflectometry.model1d.profileview.addData2XML
  - reflectometry.model1d.profileview.addLayerDialog
  - reflectometry.model1d.profileview.auiPanel
  - reflectometry.model1d.profileview.baseInteractor: Basic interactor for Reflectometry profile.
  - reflectometry.model1d.profileview.binder: Extension to MPL to support the binding of artists to key/mouse events.
  - reflectometry.model1d.profileview.changeFigureTitle
  - reflectometry.model1d.profileview.changeLayernameDialog
  - reflectometry.model1d.profileview.changeMetaDataDialog
  - reflectometry.model1d.profileview.changeProfileDialog
  - reflectometry.model1d.profileview.fit
  - reflectometry.model1d.profileview.getData2XML
  - reflectometry.model1d.profileview.initModelDialog
  - reflectometry.model1d.profileview.interfaceInteractor: Reflectometry interface interactor.
  - reflectometry.model1d.profileview.layerInteractor: Layer interactor.
  - reflectometry.model1d.profileview.listener
  - reflectometry.model1d.profileview.miscInfo: Some Auxiliary functions for plotInfoPanel
  - reflectometry.model1d.profileview.miscRefl: Some Auxiliary functions for plotReflPanel
  - reflectometry.model1d.profileview.model2MStaj: Save the model to a staj file: Magnetic case
  - reflectometry.model1d.profileview.model2Staj: Save the model to a staj file: Nonmagnetic case
  - reflectometry.model1d.profileview.parseReflModel
  - reflectometry.model1d.profileview.plotInfoPanel
  - reflectometry.model1d.profileview.plotReflBase: A base panel to draw the profile
  - reflectometry.model1d.profileview.plotReflPanel: A panel to draw the profile
  - reflectometry.model1d.profileview.reflInteractor: Reflectometry profile interactor.
  - reflectometry.model1d.profileview.reflutils: Supplementary or auxiliary Functions
  - reflectometry.model1d.profileview.removeLayerDialog
  - reflectometry.model1d.profileview.roughnessInteractor: roughness interactor.
  - reflectometry.model1d.profileview.saveFigureDialog
  - reflectometry.model1d.profileview.saveModelDialog
  - reflectometry.model1d.profileview.saveStajDialog
  - reflectometry.model1d.profileview.setup
  - reflectometry.model1d.profileview.str2Data
  - reflectometry.model1d.profileview.xmlescape: History:
- reflectometry.model1d.setup
- reflectometry.model1d.tableview
- reflectometry.model1d.tests
  - reflectometry.model1d.tests.abeles: Optical matrix form of the reflectivity calculation.
  - reflectometry.model1d.tests.abelescheck
  - reflectometry.model1d.tests.check
  - reflectometry.model1d.tests.check2
  - reflectometry.model1d.tests.compare
  - reflectometry.model1d.tests.factors
  - reflectometry.model1d.tests.fakeCG1
  - reflectometry.model1d.tests.fresnel
  - reflectometry.model1d.tests.mplot3d
  - reflectometry.model1d.tests.opticalmatrix: Pure numeric python implementation of the optical matrix formalism for computing reflectivity as a function of Q and lambda.
  - reflectometry.model1d.tests.parratt: Pure numeric python implementation of Parratt's recursion for computing reflectivity as a function of Q and lambda.
  - reflectometry.model1d.tests.polarizedmatrix: Pure numeric python implementation of the polarized optical matrix formalism.
  - reflectometry.model1d.tests.proj3d
  - reflectometry.model1d.tests.reflTest: Extension to unittest framework with better support for vectors and arrays.
  - reflectometry.model1d.tests.stajutil
  - reflectometry.model1d.tests.test_ReverseLayers: Check Qz=0 works, and Qz<0 = Qz>0 with reversed layers.
  - reflectometry.model1d.tests.test_ThickLayerAppSub: Check that thick layers approximate substrate R(Q) = R'(Q) when P' = P(1:n) and d(n)>>0, mu(n)>0
  - reflectometry.model1d.tests.test_absReflAmp: Check that reflectivity is abs(amplitude**2)
  - reflectometry.model1d.tests.test_approxRough: Cross check approximate rough calculattion.
  - reflectometry.model1d.tests.test_bspline: Unit tests for bspline module
  - reflectometry.model1d.tests.test_reflAtExtreme: Cross check the extreme cases: 1) sigma=0 matches sigma=1e-10 2) reflectivity at Q==0 is 1 3) d=0 is ok, and about equal t0 d=1.0e-10 4) no layers works (only incident and substrate) 5) polarized calculations match non-polarized when rho_m is 0.
  - reflectometry.model1d.tests.test_reflLessOne: Check that reflectivity <= 1 for all Q.
  - reflectometry.model1d.tests.test_reflTest
  - reflectometry.model1d.tests.test_reflcalc
  - reflectometry.model1d.tests.test_reflectivityCalc: Unit cross check model1d reflectivity calc against opticalmatrix, paratt, and polarizedmatrix.
  - reflectometry.model1d.tests.test_splitLayer: Check that a layer can be split so d1+d2=d and produce the same result.
- reflectometry.model1d.theoryview
  - reflectometry.model1d.theoryview.auiBase
  - reflectometry.model1d.theoryview.lineSelector
  - reflectometry.model1d.theoryview.markerDialog
  - reflectometry.model1d.theoryview.markerSelector
  - reflectometry.model1d.theoryview.matBase
  - reflectometry.model1d.theoryview.matChisqPanel: A panel to plot [x1, y1; x2, y2, ...] style data.
  - reflectometry.model1d.theoryview.matLineSelector
  - reflectometry.model1d.theoryview.matMarkerDialog
  - reflectometry.model1d.theoryview.matMarkerSelector
  - reflectometry.model1d.theoryview.matPanelNCNR: Plot X-Y using matplotlib engineer for NCNR data It is fast, and with fancy features.
  - reflectometry.model1d.theoryview.matPenDialog
  - reflectometry.model1d.theoryview.matPlotBase
  - reflectometry.model1d.theoryview.matPlotPanel: Plot X-Y using matplot engineer.
  - reflectometry.model1d.theoryview.matResidualPanel: A panel to plot residual of [x1, y1, dy1, y1'; x2, y2, dy2, y2'; ...] style data:
  - reflectometry.model1d.theoryview.matSelector
  - reflectometry.model1d.theoryview.matUtil: Some useful functions utilities or CONSTANTS
  - reflectometry.model1d.theoryview.penDialog
  - reflectometry.model1d.theoryview.plotChisqPanel: A panel to plot [x1, y1; x2, y2, ...] style data.
  - reflectometry.model1d.theoryview.plotErrorPanel: Plot X-Y using wx.plot.lib engineer for NCNR data It is fast, but without fancy features.
  - reflectometry.model1d.theoryview.plotPanelNCNR: Plot X-Y using wx.plot.lib engineer for NCNR data It is fast, but without fancy features.
  - reflectometry.model1d.theoryview.plotPanelSNS: Plot X-Y using wx.plot.lib engineer for SNS data It is fast, but without fancy features.
  - reflectometry.model1d.theoryview.plotResidualPanel: A panel to plot residual of [x1, y1, dy1, y1'; x2, y2, dy2, y2'; ...] style data:
  - reflectometry.model1d.theoryview.plotSelector
  - reflectometry.model1d.theoryview.plotTheoryErrorPanel: Plot X-Y using wx.plot.lib engineer for NCNR data It is fast, but without fancy features.
  - reflectometry.model1d.theoryview.polyError: Use to draw errorbar, etc in wx.lib.plot
  - reflectometry.model1d.theoryview.polyText: Use to draw chisq, etc in wx.lib.plot
  - reflectometry.model1d.theoryview.reflPlotPanel: Plot X-Y using wx.plot.lib engineer.
  - reflectometry.model1d.theoryview.reflplotCanvas: #---------------------------------------------------------------------- Name: reflplotCanvas.py
  - reflectometry.model1d.theoryview.setup
reflectometry.model3d
- reflectometry.model3d.BornModel
- reflectometry.model3d.GSAXS_orthaganal
- reflectometry.model3d.Modeling_Chuck_Born
- reflectometry.model3d.Modeling_IsGSAXS_Born
- reflectometry.model3d.isigsax_chuck_comparison
- reflectometry.model3d.par_form: Form class for a substrate and a feature and functions for operating on it
- reflectometry.model3d.par_structure: Structure class and function for operating on it
- reflectometry.model3d.plotting: Qz versus Qx and Intensity versus Qz Plots
- reflectometry.model3d.setup
- reflectometry.model3d.test
reflectometry.reduction: The DANSE Reflectometry data reduction library will use a data flow architecture consisting of file readers, various corrections, plotters and file writers.
- reflectometry.reduction.anglecor: Alignment correction.
- reflectometry.reduction.areacor: Correct from counts per pixel to counts per unit area on the detector.
- reflectometry.reduction.binder: Extension to MPL to support the binding of artists to key/mouse events.
- reflectometry.reduction.canvas: DANSE canvas for WxAgg.
- reflectometry.reduction.cmapmenu: Defines CMapMenu, a wx submenu containing colormaps.
- reflectometry.reduction.correction: Correction is an abstract interface for data corrections.
- reflectometry.reduction.corrections: Data corrections for reflectometry.
- reflectometry.reduction.data: Data was the initial foray into a data representation for reflectometry, and in particular for polarization correction, which was the first task.
- reflectometry.reduction.err1d: Error propogation algorithms for simple arithmetic
- reflectometry.reduction.examples
  - reflectometry.reduction.examples.cg1area: Sample data from NCNR-AND/R.
  - reflectometry.reduction.examples.e3a12: Sample data from NG-1:
  - reflectometry.reduction.examples.ng1: Sample data from NCNR-NG1.
  - reflectometry.reduction.examples.ng7: Sample data from NCNR-NG7.
  - reflectometry.reduction.examples.polcorerr: Program to show the monte carlo error estimate of the polarization correction operation, assuming a value and uncertainty for polarizer and flipper efficiencies.
- reflectometry.reduction.formatnum: Format numbers nicely for printing.
- reflectometry.reduction.formats: Reflectometry reduction file formats.
- reflectometry.reduction.fresnel: Pure python Fresnel reflectivity calculator.
- reflectometry.reduction.icpformat: ICP data reader.
- reflectometry.reduction.limits: Data limits for high dynamic range data.
- reflectometry.reduction.ncnr_ng1: Data file reader for NCNR NG-1 data.
- reflectometry.reduction.ncnr_ng7: Data file reader for NCNR NG-7 data.
- reflectometry.reduction.nexus: High level interface to NeXus files.
- reflectometry.reduction.nexusref: Load a NeXus file into a reflectometry data structure.
- reflectometry.reduction.normcor: Monitor normalization correction.
- reflectometry.reduction.nxs: Wrapper for the NeXus shared library.
- reflectometry.reduction.nxstest: NeXus tests converted to python.
- reflectometry.reduction.nxsunit: Define unit conversion support for NeXus style units.
- reflectometry.reduction.polcor: Polarized data corrections
- reflectometry.reduction.polcorgui: GUI driver for the polarization correction code polcor.
- reflectometry.reduction.polcorplot: Plot the data associated with the polarization efficiency correction.
- reflectometry.reduction.polplot: PolPlot2D is a panel for 4 cross-section 2D polarized reflectometry data.
- reflectometry.reduction.properties: Support for rarely varying instrument configuration parameters.
- reflectometry.reduction.qxqz: Translate coordinates between real and reciprical space.
- reflectometry.reduction.ratiocor: RatioIntensity estimates an intensity scan based on the measured intensity from a known scatterer.
- reflectometry.reduction.rebin: 1-D and 2-D rebinning code.
- reflectometry.reduction.rebincor
- reflectometry.reduction.refldata: Reflectometry data representation.
- reflectometry.reduction.registry: File extension registry.
- reflectometry.reduction.reverse: Some machines allow the sample to be rotated by 180 degrees, reversing the usual sense of the angles.
- reflectometry.reduction.selection
- reflectometry.reduction.setup
- reflectometry.reduction.smooth: Data smoothing
- reflectometry.reduction.smoothcor: Data smoothing
- reflectometry.reduction.ticker: Experimental replacements for log formatting and tick marks.
- reflectometry.reduction.uncertainty: Uncertainty propagation class, and log() and exp() functions.
- reflectometry.reduction.wsolve: Solve a potentially over-determined system with uncertainty in the values.
reflectometry.setup
reflectometry.version

Functions

source code