Processing Perspective - List of Processes
- Jacob Filik
Python Script - Image to Image [Scripting]
Image : Image
Process data using a python script that takes an image and returns an image
Options
File : Enter the path to the script
Python Script - Image to XY [Scripting]
Image : XY
Process data using a python script that takes an image and returns XY data
Options
File : Enter the path to the script
Python Script - XY to XY [Scripting]
XY : XY
Process data using a python script that takes XY data and returns XY data
Options
File : Enter the path to the script
Threshold Mask [Masking]
Image : Image
Create a mask with intensity values below a lower bound and above an upper bound masked.
Options
Lower Value : The lower intensity, below which the mask will mask out the value. If you delete the value no lower intensity will be used for the mask.
Upper Value : The upper intensity, above which the mask will mask out the value. If you delete the value no upper intensity will be used for the mask.
Import Mask From File [Masking]
Image : Image
Import a Mask from .nxs or fit2d mask file. A mask file can be created using the masking tool.
Options
Mask File : Path to the mask file
Dilate Mask [Masking]
Image : Image
Increase the size of masked regions by dilating the mask by a set number of pixels
Options
Dilation Size : Increase size of masked areas by a set number of pixels
Box Integration
Image : XY
Using a box region, select a portion of the data to integrate in X or Y.
Options
Direction of Profile : Either X or Y
Region of Interest : Define the region of interest
Cut Rotated Cartesian Box
Image : Image
Use a rectangular region to crop and rotate a selected data region
Options
Region of Interest : Define a region of interest.
Import Detector Calibration [XRD2 Image Processing]
Image : Image
Import the experimental detector geometry and x-ray energy (can be determined in powder calibration perspective). Required for operations which transform data to 2 theta/q/d-space.
Options
Calibration File: : Path to the calibration NeXus file
Azimuthal Integration [XRD2 Integration]
Image : XY
Azimuthal integration of a 2D powder diffraction/SAXS image to a 1D pattern (Intensity vs q, 2 theta, d or pixel). Requires Detector Calibration information to be in the pipeline (use Import Detector Calibration).
Options
Azimuthal range : Two values, start and end, separated by a comma i.e. -90,90, maximum range is 360
Log Radial Axis : Integrates onto a log axis, has no effect on radial integration
Number of bins : Number of bins for integration axis, leave blank for maximum pixel distance on detector
Pixel splitting :
Radial range : Two values, start and end, separated by a comma i.e. 2,4.The values should match the axis selected (i.e. q, 2 theta, pixel).If you delete the text, the range is cleared and the whole image used.
X axis : Type for radial range
Radial Integration [XRD2 Integration]
Image : XY
Radial integration of a 2D powder diffraction/SAXS image to intenisty vs azimuthal angle. Requires Detector Calibration information to be in the pipeline (use Import Detector Calibration).
Options
Azimuthal range : Two values, start and end, separated by a comma i.e. -90,90, maximum range is 360
Log Radial Axis : Integrates onto a log axis, has no effect on radial integration
Number of bins : Number of bins for integration axis, leave blank for maximum pixel distance on detector
Pixel splitting :
Radial range : Two values, start and end, separated by a comma i.e. 2,4.The values should match the axis selected (i.e. q, 2 theta, pixel).If you delete the text, the range is cleared and the whole image used.
X axis : Type for radial range
Powder Diffraction Intensity Corrections [XRD2 Image Processing]
Image : Image
Solid angle, polarisation and detector transmission corrections. Requires Detector Calibration information to be in the pipeline (use Import Detector Calibration).
Options
Detector transmission : Apply the detector transmission correction to the data
Detector transmitted fraction : Fraction of radiation transmitted for the detector transmission correction
Polarisation : Apply the polarisation correction to the data
Polarisation angular offset : Offset of the polarisation relative to the detector
Polarisation factor : Value used in the polarisation correction
Solid angle : Apply solid angle correction to the data
Cake Remapping [XRD2 Integration]
Image : Image
Remap a powder diffraction/SAXS image to q/2theta vs azimuthal angle. Requires Detector Calibration information to be in the pipeline (use Import Detector Calibration).
Options
Azimuthal range : Two values, start and end, separated by a comma i.e. -90,90, maximum range is 360
Log Radial Axis : Integrates onto a log axis, has no effect on radial integration
Number of azimuthal bins : Number of bins for azimuthal axis
Number of bins : Number of bins for integration axis, leave blank for maximum pixel distance on detector
Pixel splitting :
Radial range : Two values, start and end, separated by a comma i.e. 2,4.The values should match the axis selected (i.e. q, 2 theta, pixel).If you delete the text, the range is cleared and the whole image used.
X axis : Set value for X axis after integration
Rolling Ball Baseline Correction [Background Subtraction]
XY : XY
Rolling ball baseline correction with fixed radius
Options
Set ball radius in pixels : Radius should be smaller than size of features
Gaussian Filter [Image Filter]
Image : Image
Gaussian filter an image using kernal of specified width
Options
Kernel Width : Width of filter kernel in pixels
Median Filter [Image Filter]
Image : Image
Median filter an image with a kernel of a specified width
Options
Kernel Width : Width of filter kernel in pixels
Mean Filter [Image Filter]
Image : Image
Mean filter an image with a kernel of a specified width
Options
Kernel Width : Width of filter kernel in pixels
Export to Text File
XY : XY
Save XY data as text
Options
File Extension : Extension that should be used for the output file
Include explicit location : Include the explicit (slice) location of the data in the full dataset as part of the filename
Output Directory : Path to output directory
Pad with zeros : Leave blank for no padding
Suffix : Custom suffix to be appended to the file name, leave blank for no suffix
Downsample Image [Image Filter]
Image : Image
Downsample an image using the corner, mean, min, or max value. The type the output data should take (int, float etc) can also be specified
Options
Downsample mode : The mode, choose from a list of alternative modes.
Downsample Output datatype : Datatype of the downsample output.
Downsample size X : The width of the downsample box in pixels.
Downsample size Y : The height of the downsample box in pixels.
Integrate Range
XY : XY
Trapezoidal integration of the data between the specified range, with the option to subtract a local linear baseline.
Options
Set integration range : Two values, start and end, separated by a comma, for example 2,4. The values should match the axis . If you delete the text, the range is cleared and the whole range used.
Subtract linear baseline : Subtract a linear base line from the integrated area
Mathematical Expression [1D] [Expressions]
XY : XY
Custom mathematical operation, use "data" for the data variable and "xaxis" for the axis, use the dnp: and dat: namespaces to access different mathematical functions
Options
Data Function : Function to apply to the data e.g. dnp:power(data,2)
X Axis Function : Function to apply to the x-axis e.g. xaxis - dat:min(xaxis,0)
Mathematical Expression [2D] [Expressions]
Image : Image
Custom mathematical operation on an image, use "data" for the data variable and "xaxis" and "yaxis" for the axes, use the dnp: and dat: namespaces to access different mathematical functions
Options
Data Function : Function to apply to the data e.g. dnp:power(data,2)
X Axis Function : Function to apply to the x-axis e.g. xaxis - dat:min(xaxis,0)
Y Axis Function : Function to apply to the y-axis e.g. yaxis - dat:min(yaxis,0)
Mathematical Expression [2D Diffraction] [XRD2 Image Processing]
Image : Image
Custom mathematical operation including q, tth, azimuth and energy, use the dnp: and dat: namespaces to access different mathematical functions
Options
Data Function : Function to apply to the data e.g. dnp:power(data,2)
X Axis Function : Function to apply to the x-axis e.g. xaxis - dat:min(xaxis,0)
Y Axis Function : Function to apply to the y-axis e.g. yaxis - dat:min(yaxis,0)
X Region Profile Normalize
Image : Image
A filter which normalises the data frame by the profile of the selected region of the X axis.
Options
Smoothing Width : Smoothing amount of the integrated line
X Range : Range in X direction (i.e. 10,20)
Standard Normal Variate
XY : XY
Subtract mean and divide by standard deviation to bring all XY data onto the same scale
Options
Set Poisson Error [Error]
Image : Image
Sets the current value of the data as the variance on the dataset
Options
ARPES Gold Calibration Correction [ARPES Analysis]
Image : Image
ARPES Gold Calibration Correction
Options
Calibration File : Path to the calibration NeXus file
energyOffset :
ARPES Axis Conversion [ARPES Analysis]
Image : Image
ARPES Axis Conversion
Options
kxOffset :
kyOffset :
workFunction :
Crop Data [1D]
XY : XY
Crop XY data to a specified range
Options
Start : Set beginning of range to crop data to
Stop : Set end of range to crop data to
Average All Data
Any : Same
Average all the data into a single dataset
Options
Crop Data [2D]
Image : Image
Crop an image to a specified size
Options
X Start : Lower bound of crop in X-direction
X Stop : Upper bound of crop in X-direction
Y Start : Lower bound of crop in Y-direction
Y Stop : Upper bound of crop in Y-direction
Mask Outside Region [Masking]
Image : Image
Mask pixels outside the specified region
Options
Region of Interest : Define the region of interest
Normalisation [External Data]
Any : Same
Normalise data against the value from a corresponding value in an external dataset (if path is empty, dataset from processed file is used)
Options
File : Enter the path to the data file, leave blank to use the file being processed
Dataset : Enter the name of the dataset to be used
Subtract Data [External Data]
Any : Same
Subtract a dataset (or average if stack) in the specified file
Options
File : Enter the path to the data file
Dataset :
First: : Position of first (or only) dataset, leave blank to average all data
Last: : Position of end dataset, leave empty to use a single dataset
Scaling : Scaling of the multiplying data
Diffraction Ellipse Fit [XRD2 Image Processing]
Image : Image
Fit an ellipse to the ring at the specified q value - parameters returned as auxiliary data
Options
Ellipse q : Value of q the ellipse corresponds to
q delta : The range of q to search for the ellipse in
Image Rotation
Image : Image
Rotates an image by a certain angle around the image centre
Options
Angle : The image will be rotated by the angle provided around the centre of the dataset (x=xMax/2, y=yMax/2)
Resize : Resize resulting bounding box
Unit : Angle unit
Affine Transformation
Image : Image
Performs an affine transformation on the image
Options
a11 :
a12 :
a21 :
a22 :
dx :
dy :
Resize : Resize resulting bounding box
Convert Diffraction Axis Type [1D]
XY : XY
Convert XY diffraction data axes between q, 2 theta and d-space
Options
Use Calibrated Wavelength : Use wavelength from detector calibration.
Wavelength : Specify a wavelength to use.
X Axis : Set value for X axis after integration
Rebin XY Data
XY : XY
Rebin data onto new axis with specified start, stop and number of points (defaults to min, max and number of points in first axis
Options
Max : Maximum value to use in rebinning, leave blank to use the max from the first dataset
Min : Minimum value to use in rebinning, leave blank to use the min from the first dataset
Number of bins : Number of bins to rebin the data into, leave blank to use the number of bins from the first dataset
Iterative Polynomial Baseline Subtraction [Background Subtraction]
XY : XY
Subtract a polynomial baseline using an iterative fitting routine. On each iteration any data above the fit is set to the fit value.
Options
Number of Iterations : Number of iterations to use in fitting process
Polynomial Order : Polynomial orde to use for baseline
Subtract Input Data
Any : Same
Subtract a selected dataset of the input data (or average) from all datasets
Options
First: : Position of first (or only) dataset, leave blank to average all data
Last: : Position of end dataset, leave empty to use a single dataset
Scaling : Scaling of the multiplying data
Average Fastest Dimension Only
Any : Same
Averages the data along the fastest non-data dimension of the array. For example, if the data set shape is [a,b,c,X,Y] where X and Y are the data dimensions, c is the fastest axis (row-major order)
Options
Image Threshold [Image Filter]
Image : Image
Applies a threshold across the whole image
Options
Down : If 'down' is true, then pixels with values <= to 'threshold' are set to 1 and the others set to 0. If 'down' is false, then pixels with values >= to 'threshold' are set to 1 and the others set to 0.
Radius : Used for adaptive thresholding algorithms that are computed using a local square region centered on each pixel.
Threshold : Value used for GLOBAL_CUSTOM thresholding
Type : Type of thresholding algorithm
Blob Extraction [Binary Image]
Image : Image
Extracts blobs on binary image
Options
Connect Rule : Connectivity rule: blobs can be defined using a 4 or 8 connect rule
Image Stitching [External Data]
Image : Image
Stitches two images together given X and Y translations
Options
File : Enter the path to the data file, leave blank to use the file being processed
Dataset Name : The name of the dataset or the node path of the data if a .NXS file
X Translation : X translation between two images in pixels
Y Translation : Y translation between two images in pixels
Dataset Concatenation [External Data]
Image : Image
Concatenate two datasets together, taking into account axes scaling
Options
File : Enter the path to the data file, leave blank to use the file being processed
Dataset name : Dataset name (leave empty to use input dataset name
Concatenation axis : The axis along which the concatenation will occur
Derivative
XY : XY
uk.ac.diamond.scisoft.analysis.processing.operations.oned.DerivativeOperation
Options
Derivative Order : Enter the derivative order, between 1 and 5
Smoothing : Enter the smoothing size
Polynomial Smoothing Filter
XY : XY
uk.ac.diamond.scisoft.analysis.processing.operations.oned.PolynomialSmoothingOperation
Options
Polynomial Order : Enter the smoothing polynomial order
Window Size : Enter window size (should be even)
General Detector Error [Error]
Image : Image
Add errors to data
Options
electronicNoise :
gain :
gainFluctuation :
quantumEfficiency :
No Data [Utilities]
Any : Same
Stops data being sent down the pipeline, used to not duplicate your data if you only need the auxiliary output
Options
No Change [Utilities]
Any : Same
Propagates the input data without modifying it, used to convert other data formats to nexus
Options
Export to Text File [Image]
Image : Image
Save image as text with x axis as first column, use with caution, files can get very large
Options
File Extension : Extension that should be used for the output file
Include explicit location : Include the explicit (slice) location of the data in the full dataset as part of the filename
Output Directory : Path to output directory
Pad with zeros : Leave blank for no padding
Suffix : Custom suffix to be appended to the file name, leave blank for no suffix
Average Sections of Fastest Dimension
Any : Same
Averages sections of the data along the fastest non-data dimension of the array. For example, if the data set shape is [a,b,c,X,Y] where X and Y are the data dimensions, c is the fastest axis (row-major order)
Options
number :
start :
stop :
Centroid
Image : Image
Determine the X and Y centroid values (saved to file)
Options
Minimum Maximum Normalization
XY : XY
Normalize the minimum to zero and the maximum to one
Options
Pseudo-Flat Field Filter [Image Filter]
Image : Image
Creates a Gaussian-blurred image using the given kernel and then subtract the blurred image/pseudo flat field from the original image
Options
Kernel Width : Width of filter kernel in pixels
Spline Baseline Subtraction [Background Subtraction]
XY : XY
Subtract a spline from the data
Options
Control point x-values : Enter a list of comma-separated x values for the spline control points.
Image Integration
Image : XY
Integrate an image along a selected axis
Options
Direction of Profile : The direction to see the profile in.
Do average? : Average the data along the chosen axis, rather than sum.
Normalisation [metadata]
Any : Same
Divide data by a value taken from the file metadata
Options
metadataName :
Multiply [External Data]
Any : Same
Multiply dataset by external value
Options
File : Enter the path to the data file, leave blank to use the file being processed
Dataset : Enter the name of the dataset to be used
Subtract [External Data]
Any : Same
Subtract external data from a dataset
Options
File : Enter the path to the data file, leave blank to use the file being processed
Dataset : Enter the name of the dataset to be used
Divide [External Data]
Any : Same
Divide dataset by external value
Options
File : Enter the path to the data file, leave blank to use the file being processed
Dataset : Enter the name of the dataset to be used
Add [External Data]
Any : Same
Add external data to a Dataset
Options
File : Enter the path to the data file, leave blank to use the file being processed
Dataset : Enter the name of the dataset to be used
Two Box Mean Difference
Image : Image
Difference between the mean of two boxes
Options
Box 1 : Define the first region of interest
Box 2 : Define the second region of interest.
Two Box Mean Ratio
Image : Image
Ratio of the mean of two boxes
Options
Box 1 : Define the first region of interest
Box 2 : Define the second region of interest.
Mask by coordinate [Masking]
Image : Image
Mask values inside, or outside a set co-ordinate range
Options
Coordinate : Set coordinate for to mask over
Mask range? : Mask over the range when checked, outside the range otherwise
Range : Please set two values, start and end, separated by a comma i.e. 2,4. The values should match the coordinate selected (i.e. q, 2 theta, pixel).If you delete the text, the range is cleared and the whole image used.
Read Nexus Detector Information
Image : Image
Read calibration and mask from the NeXus file being processed
Options
readGeometry :
readMask :
Fit Imported Function
XY : XY
Fit a function to the data, using a function generated in the function fitting tool and exported as a NeXus file
Options
Function File : Enter the path to the function file
optimiser :
Multiply by Scalar
Any : Same
Multipy by a scalar
Options
value :
Subtract Scalar
Any : Same
Subtract a scalar
Options
value :
Divide by Scalar
Any : Same
Divide by a scalar
Options
value :
Add Scalar
Any : Same
Add a scalar
Options
value :
Box Mean
Image : Image
Returns mean values within a Box
Options
Box : Define the region of interest.
Subtract Average X Regions Integration
Image : XY
Subtract the average of two regions in X from the signal region
Options
Set background 1 range : Please set two values, start and end, separated by a comma, for example 2,4. The values should match the axis . If you delete the text, the range is cleared and the whole range used.
Set background 2 range : Please set two values, start and end, separated by a comma, for example 2,4. The values should match the axis . If you delete the text, the range is cleared and the whole range used.
Set signal range : Please set two values, start and end, separated by a comma, for example 2,4. The values should match the axis . If you delete the text, the range is cleared and the whole range used.
Multiply [Internal Data]
Any : Same
Multiply dataset by internal value
Options
Dataset : Enter the name of the dataset to be used
Subtract [Internal Data]
Any : Same
Subtract internal data from a dataset
Options
Dataset : Enter the name of the dataset to be used
Divide [Internal Data]
Any : Same
Divide dataset by internal value
Options
Dataset : Enter the name of the dataset to be used
Add [Internal Data]
Any : Same
Add internal data to a Dataset
Options
Dataset : Enter the name of the dataset to be used
Multiply Frame [External Data]
Any : Same
Multiply dataset by frame (or average of stack) from external file
Options
File : Enter the path to the data file
Dataset :
First: : Position of first (or only) dataset, leave blank to average all data
Last: : Position of end dataset, leave empty to use a single dataset
Scaling : Scaling of the multiplying data
Subtract Frame [External Data]
Any : Same
Subtract frame (or average of stack) from external file
Options
File : Enter the path to the data file
Dataset :
First: : Position of first (or only) dataset, leave blank to average all data
Last: : Position of end dataset, leave empty to use a single dataset
Scaling : Scaling of the multiplying data
Divide Frame [External Data]
Any : Same
Multiply dataset by frame (or average of stack) from external file
Options
File : Enter the path to the data file
Dataset :
First: : Position of first (or only) dataset, leave blank to average all data
Last: : Position of end dataset, leave empty to use a single dataset
Scaling : Scaling of the multiplying data
Add Frame
Any : Same
Add frame (or average of stack) from external file
Options
File : Enter the path to the data file
Dataset :
First: : Position of first (or only) dataset, leave blank to average all data
Last: : Position of end dataset, leave empty to use a single dataset
Scaling : Scaling of the multiplying data
Polynomial1DReflectivityOperation
Image : Image
uk.ac.diamond.scisoft.analysis.processing.surfacescattering.Polynomial1DReflectivityOperation
Options
angular fudge factor : angular fudge factor
beam height : beam height
Boundary Box Direction : X or Y direction?
Boundary Box size (pixels) : Size of the boundary box used for background calculation
box :
Fit power : Fit power
footprint : footprint of smaple in mm
Path to normalisation file : Path to normalisation file
RodScanPolynomial1DOperation
Image : Image
uk.ac.diamond.scisoft.analysis.processing.sxrdrods.RodScanPolynomial1DOperation
Options
Beam Correction : Beam Correction True/False
Beam In Plane : Beam In Plane
Beam Out Plane : Beam Out Plane
Boundary Box Direction : X or Y direction?
Boundary Box size (pixels) : Size of the boundary box used for background calculation
box :
covar : covar
Detector Slits : Detector Slits
Fit power : Fit power
In Plane Slits : In Plane Slits
Inplane Polarisation : Inplane Polarisation
Out Plane Slits : Out Plane Slits
Outplane Polarisation : Outplane Polarisation
Reflectivity a : Reflectivity a
Sample Size in mm : Sample Size
Scaling/Normalisation Factor : Scaling/Normalisation Factor, if in reflectivity mode, note that this will be the division factor, in CRT mode, the multiplying factor (don't blame me).
Specular : Specular True/False
Normalisation for NCD [NCD]
Any : Same
Normalisation of datasets with errors
Options
Absolute scale value : Absolute scaling value
Absolute scaling value from Nexus file by default : Use absolute scaling value /entry1/detector/scaling_factor from original Nexus file. If false, use scaling value defined here
Calibration channel number : Calibration channel location in scan data
Calibration data location : Location of calibration data in Nexus file
Calibration data path is default path (It) : If true, calibration data will be extracted from the default location, /entry1/It/data. If false, data will be from the calibration data location defined here
Calibration file : File containing calibration data
Calibration file is current data file : If true, calibration data will be extracted from the current data file. If false, data will be from the calibration file defined here
Thickness in file is default : The thickness value in the file at /entry1/sample/thickness is default. If false, use the thickness value in defined here
Thickness of sample : Thickness (mm)
NCD Detector Response [NCD]
Any : Same
Flat field detector response operation
Options
Response file : File containing detector response
NCD Sector Integration [NCD]
Image : XY
uk.ac.diamond.scisoft.analysis.processing.NcdSectorIntegration
Options
Calibration XML File : The path to XML file containing the calibration data.
Integration Type : Azimuthal integration results in radial profile Radial integration results in azimuthal profile
Region of Interest : Define the region of interest
Region of Interest File : The path to the a NeXus file containing a ROI. You can click and drag a file into this field.
Import NCD Mask from File [NCD]
Image : Image
uk.ac.diamond.scisoft.analysis.processing.ImportNcdMask
Options
Mask File : Path to the mask file
NCD Background Subtraction [NCD]
Any : Same
uk.ac.diamond.scisoft.analysis.processing.NcdBackgroundSubtraction
Options
Background file : File containing background data
Background Scale : Value to scale the background data
NCD Background Subtraction From Current Data [NCD]
Any : Same
uk.ac.diamond.scisoft.analysis.processing.NcdBackgroundSubtractionFromData
Options
Selection of Images for Background : Selection of image numbers to use in background subtraction. Use slicing syntax separated by commas
Guinier calculation [NCD]
XY : XY
Calculate Guinier plot and derived Rg and range, I0
Options
NCD Averaging [NCD]
XY : XY
Rg calculation, filtering, then averaging
Options
Use Rg filtering : Use Rg-based filtering to remove bad frames before averaging
NCD Invariant [NCD]
XY : XY
Invariant Calculation
Options
Degree of Orientation [NCD]
XY : XY
Degree of Orientation
Options
Export NCD 1-D Data [NCD]
XY : XY
Allow users to export the results to several different formats
Options
Export Format : Select the export type
Select Output Directory: : Enter the path to output directory
SAXS Tools [NCD]
XY : XY
uk.ac.diamond.scisoft.analysis.processing.operations.ncd.SaxsPlotOperation
Options
SAXS Tool : Select the SAXS tool to use
T parameter calculation [NCD]
XY : XY
uk.ac.diamond.scisoft.analysis.processing.operations.ncd.TParameterOperation
Options
Porod Operation (Interactive) [NCD]
XY : XY
uk.ac.diamond.scisoft.ncd.processing.PorodInteractiveOperation
Options
Get auto-fit limits? : Select this to fit the limits of the straight line fit automatically
Set high-qâ?´ fit region : Two values, start and end, separated by a comma, for example 2,4. The values should match the axis. If you delete the text the range is estimated automatically.
Subtract background? : Subtract the background B parameter from the output data
Kratky From Porod Background [NCD]
XY : XY
uk.ac.diamond.scisoft.ncd.processing.KratkyFromPorodBackgroundOperation
Options
Kratky Fitting (Interactive) [NCD]
XY : XY
uk.ac.diamond.scisoft.ncd.processing.KratkyInteractiveOperation
Options
Get auto-fit limits? : Select this to fit the limits of the straight line fit automatically
Numerical integration region : Two values, start and end, separated by a comma, for example 2,4. The values should match the axis. If you delete the text the range is estimated automatically.
XAFS Normalisation [XAFS Analysis]
XY : XY
uk.ac.diamond.scisoft.spectroscopy.operations.XAFSNormalisationOperation
Options
Pre-edge energy : Define the pre-edge energy.
Post-edge energy : Define the post-edge energy.
Pre-edge polynomial order : Set order of pre-edge polynomial.
Post-edge polynomial order : Set order of post-edge polynomial.
Flatten : Subtract post edge polynomial from edge to flatten data
XAFS EDE background subtraction [XAFS Analysis]
XY : XY
uk.ac.diamond.scisoft.spectroscopy.operations.XAFSEDEPostEdgeBackgroundOperation
Options
K-weight :
offset :
Post-edge polynomial order : Define the polynomial order.
step :
XAFS FFT [XAFS Analysis]
XY : XY
uk.ac.diamond.scisoft.spectroscopy.operations.XAFSFFTOperation
Options
filter :
oversample :
XAFS Normalisation Relative [XAFS Analysis]
XY : XY
uk.ac.diamond.scisoft.spectroscopy.operations.XAFSRelativeNormalisationOperation
Options
Pre-edge energy offset : Define the position pre-edge relative to the edge.
Post-edge energy offset : Define the position post-edge relative to the edge.
Pre-edge polynomial order : Set order of pre-edge polynomial.
Post-edge polynomial order : Set order of post-edge polynomial.
Flatten : Subtract post edge polynomial from edge to flatten data
Attenuation correction [XAFS Analysis]
XY : XY
Correct dataset for attenuation
Options
Attenuation distance : Enter the attenuation distance, expressed in cm
Compound : Enter the compound causing the attenuation
Density : Enter the material density, expressed in g/cm3
XAFS Rebin [XAFS Analysis]
XY : XY
Rebin XAFS dataset onto new energygrid
Options
Guess edge energy : Estimate the edge energy
Edge energy : Edge energy
Edge region start : Edge region start
Edge region end : Edge region end
Pre-edge grid : Grid width before the edge region
XANES grid : Grid width within the XANES region
EXAFS grid : Grid width within the EXAFS region
XAFS Shift Energy Axis [XAFS Analysis]
XY : XY
Shift the energy axis
Options
Energy Axis Shift : The value that will be used to shift the energy axis
Insert XPDF Beam Metadata [XPDF beta]
Any : Same
Insert the XPDF metadata into the main Dataset
Options
Beam Energy (keV) : Enter the beam energy
Beam Height (mm) : Enter the beam height
Beam Width (mm) : Enter the beam width
Counting Time (s) : Enter the experiment counting time
Data File : Enter the path to the file
Dataset : Name of the dataset
Errors Dataset : Name of the dataset containing the errors
Errors File : Enter the path to the file containing the error values
Monitor Relative Flux : Enter the relative flux
Insert XPDF Sample Metadata [XPDF beta]
Any : Same
Insert the sample metadata into the processing pipeline
Options
Counting Time : Enter a counting time for the experiment
Errors Dataset : Name of the dataset containing the errors
Errors File : Enter the path to the file containing the error values
Is x-axis 2θ? : Enter whether the x-axis is angle or momentum transfer
Monitor Relative Flux : Enter the flux relative to the monitor
Physical Params From Input : Read sample parameters from the input NeXus file
Sample Density : Enter the sample material density
Sample Identifier : Enter an identifying name for the sample
Sample Inner Distance : Enter an inner distance for the sample shape
Sample Material : Enter the IUPAC formula for the sample material
Sample NeXus file : NeXus file containing the sample parameters
Sample Outer Distance : Enter an outer distance for the sample shape
Sample Packing Fraction : Enter the sample packing fraction
Sample Shape : Enter the shape of the sample
Insert XPDF Container Metadata [XPDF beta]
Any : Same
Insert a container metadata instance into the processing pipeline
Options
Container Density (g/cm^3) : Enter the container material density
Container Identifier : Enter an identifying name for the container
Container Inner Distance (mm) : Enter an inner distance for the container shape
Container is Downstream? : Enter whether the container exists downstream of the container
Container is Upstream? : Enter whether the container exists upstream of the container
Container Material : Enter the IUPAC formula for the container material
Container Outer Distance (mm) : Enter an outer distance for the container shape
Container Packing Fraction : Enter the container packing fraction
Container Shape : Enter the shape of the container
Counting Time (s) : Enter a counting time for the experiment
Data File : Enter the path to the file
Dataset : Name of the dataset
Errors Dataset : Name of the dataset containing the errors
Errors File : Enter the path to the file containing the error values
Monitor Relative Flux : Enter the flux relative to the monitor
XPDF Lorch Fourier Transform (th_soq to dofr) [XPDF beta]
XY : XY
Apply the Lorch Fourier Transform to enter r-space.
Options
Lorch width : Enter the width of the Lorch Fourier filter
Maximum Q : Enter the maximum Q up to which to take the transform.
Rmax (Angstroms) : Enter the maximum radius to consider
Rstep (Angstroms) : Enter the radius increment
Seek next minimum? : Seek the next extremum after Qmax?
Seek next zero? : Seek the next zero after Qmax?
XPDF D(r) to G(r) [XPDF beta]
XY : XY
Convert from the D(r) PDF to G(r)
Options
XPDF Tophat background subtraction (soq to th_soq) [XPDF beta]
XY : XY
Remove background using a tophat filter
Options
Rmax (Angstroms) : Enter the maximum radius to consider
Rmin (Angstroms) : Enter the minimum radius to consider
Rstep (Angstroms) : Enter the radius increment
Tophat width (Angstroms) : Enter the width of the Tophat filter
XPDF Self-scattering and Normalisation (ABSCOR to soq) [XPDF beta]
Any : Same
Calculate the theoretical self-scattring, and use it to normalise the data
Options
XPDF Normalise Data (count to Normon) [XPDF beta]
Any : Same
Normalise all datasets according to their count time and relative flux
Options
Normalise all container traces? : Normalize all the container data, if unnormalized
Normalise empty beam trace? : Normalize the beam data, if unnormalized
Normalise sample trace? : Normalize the sample data, if unnormalized
XPDF Subtract Background (Normon to SUBBAK) [XPDF beta]
Any : Same
Subtract the empty beam data from the sample and empty container data
Options
Subtract all container backgrounds? : Subtract the background from the container data
Subtract sample background? : Subtract the background from the sample data
XPDF Iterate Calibration Constant (SUBBAK to ABSCOR) [XPDF beta]
Any : Same
Calibrate the data to best match the theoretical scattering, and subtract the sample fluorescence
Options
Calculate fluorescence? : Perform a real fluorescence calculation
Correct fluorescence? : Do the fluorescence calculations as part of the calibration
Fluorescence scale : Fixed user fluorescence scale
Number of iterations : Enter the number of iterations to perform
Parallel threads : Number of parallel threads to use for the fluorescence calibration
Regenerate absorption maps : Regenegerate the absorption maps
Sort containers? : Enter whether to sort the previously inserted containers
XPDF Define Detector [XPDF beta]
Any : Any
Define the detector parameters used to take the data
Options
Detector Density (g/cm^3) : Enter the detector material density
Detector Material : Enter the IUPAC formula detector material
Detector Name : Enter a name for the detector
Detector Thickness (mm) : Enter the detector thickness
Solid Angle (sr) : Enter the solid angle subtended by the detector
XPDF Azimuthal Integration [XPDF beta]
Image : XY
An XPDF-specific version of the azimuthal integration Operation.
Options
Azimuthal range : Please set two values, start and end, separated by a comma i.e. -90,90, maximum range is 360
Number of bins : Set number of bins for integration axis, leave blank for maximum pixel distance on detector
Pixel splitting :
Radial range : Please set two values, start and end, separated by a comma i.e. 2,4.The values should match the axis selected (i.e. q, 2 theta, pixel).If you delete the text, the range is cleared and the whole image used.
XPDF Read Metadata [XPDF beta]
Image : Image
Read the XPDF metadata from a NeXus file
Options
Read beam data :
Read beam information :
Read container data :
Read container information :
Read detector calibration :
Read detector information :
Read mask :
Read sample information :