Irena manual

Manual 1.5.3 for Irena version 2.71 for Igor 8.0 and higher (will NOT work on Igor 7)

• Introduction
• Important Information
  • Loading the macros
  • Unload the macros
  • Data naming conventions
  • Data naming conventions - QRS
  • Data naming conventions - QIS
  • Data naming conventions - USAXS
  • Slit smeared (USAXS) data
  • Per point smeared data by Q resolution
  • Kill all Irena panels and graphs
  • Irena manual
  • Irena youtube channel
  • Open Form factor description
  • Check for updates
  • Location of items in SAS menu
  • GUI controls and common controls
  • Data selection
  • MultiData selection
  • Using Irena on small displays
  • Using Irena on high resolution displays
  • Use of XOP
  • Genetic optimization
• Import data
  • Description
  • Importing ASCII SAS data
  • Importing ASCII WAXS data
  • Importing Nexus canSAS data
  • Importing XML data
  • Walk through Importing test file
• Export data
  • Export all data as NXcanSAS
  • Export data GUI
• Plotting tools
  • List of Tools
  • Plotting tool I
    • How to use
    • Scripting
    • Contour plot
    • Waterfall 3D graph
    • Gizmo 3D graph
    • Fitting
    • Remove a data set
    • Creating user style
    • Import & Export of styles
    • Modifying the data
    • Storing graphs for future use, exporting Figures
    • Movie making
  • Plotting tool II
  • Multi-Sample Plotting tool
• Data manipulation tools
  • List of Tools
  • Data manipulation I
  • Data manipulation II
  • Data merging
  • Data manipulation III
• Metadata Browser
• Modeling
  • Theory behind this tool
  • SINGLE input data set - size distribution
  • “Unified level”, “Surface Fractal”, “Mass Fractal”, and “Diffraction peak”
  • Fitting data with one input data set
  • Uncertainty evaluation
  • Fitting data with multiple input data set
• Model description
  • Size distribution
  • Unified Fit
  • Diffraction Peaks
  • Surface and Mass Fractal
• Simple fits tool
  • Models supported:
• Unified Fit
  • Constructing Unified fit
  • Uncertainty evaluation
  • Analyze results
• Size Distribution
  • Basic description of methods
    • Maximum entropy method
    • Regularization method
    • Total non-negative least square method
  • Use of Size Distribution
  • Uncertainty analysis of Size distribution
  • Graph information and controls
• System specific models
  • Tool overview and use
  • Controls
  • Models details
  • Debye-Bueche model for gels
  • Treubner-Strey for small-angle diffraction
  • Ciccariello–Benedetti model for coated smooth surfaces
  • Hermans model for lamellar systems
  • Modified Hermans model for lamellar systems
  • Unified Born Green model for lamellar systems
• Small-angle diffraction tool
• Bio SAXS support
  • List of Tools
  • Import bioSAXS ASCII Data
  • Importing ASCII SAS data
  • BioSAXS Data manipulation - Average, Subtract, Scale
  • Naming of files
  • Average
  • Subtract
  • Scale
  • Concentration series extrapolation
  • bioSAXS PDDF and Molecular weight
• Powder diffraction (WAXS) fitting
• Guinier-Porod
• Fractal model
• Pair distance distribution function
• Reflectivity
• Mass Fractal Aggregate model
  • Mass Fractal model parameters
  • The parameters user uses to control growth are:
  • Grow the particles:
  • Find Best Match Aggregate
• Two Phase Solid model
  • Input model values :
    • Fitting procedure
    • Advanced Parameters
    • 3D data generation
    • Results display
    • Model resolution
• Display 3D data
• Import POV or PDB files
• Anisotropy Analysis - HOP
  • Main GUI
• Scattering contrast calculator
  • Basic calculator
  • Anomalous calculator
• Data mining tool
• Evaluate size distributions
• Slit smearing in Irena
• Desmearing
• Form Factors & Structure factors
  • Form factors & their parameters
  • Structure factors & their parameters
  • Form Factor description
    • Spheroid
    • Integrated_Spheroid
    • Cylinder, Disk, and CylinderAR
    • CoreShell
    • CoreShellPrecipitate
    • CoreShell Cylinder
    • Fractal Aggregate
    • CoreShellShell
      • NOTE – GUI panel input parameters – NOTE
    • SphereWHSLocMonoSq
    • Janus CoreShell Micelle
    • RectParallelepiped
  • User Form Factor
    • Example of these functions for sphere:
  • Testing and using Form factors in users own code
    • Structure factors description
    • Interferences
    • HardSpheres
    • StickyHardSpheres
    • SquareWell
    • HayerPenfoldMSA
    • InterPrecipitate
    • DisorderedCrystal
    • Calling the library and use
  • Following Form factors have been removed from Irena in version 2.67
    • Unified_Sphere - removed in version 2.67
    • Unified_Rod - removed in version 2.67
    • Unified_RodAR - removed in version 2.67
    • Unified_Disk - removed in version 2.67
• Other Tools
  • QRS data folder creation tool
  • Results Notebook
  • Logging feature
• Final Comments
• Analyze results
• Scripting tool
• Analytical models - obsolete
  • Debye-Bueche model for gels
  • Treubner-Strey for small-angle diffraction
  • Ciccariello–Benedetti model for coated smooth surfaces
• Frequently asked questions Irena
  • List of Subjects
• FAQs:
  • Citation to use in publications
  • Do modeling populations have required order?
  • What do I do if I need different Form Factor?
  • Why does Modeling warn against use of multiple Unified levels?
  • What is RgCo in Unified fit and why do I need to understand it?
  • How do Irena tools get absolute volume fractions, specific sufc areas etc?

Indices and tables

• Index

• Search Page