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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 :

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