Fix Time Axis [i20-1] [XAFS Analysis]
XY : XY
org.dawnsci.ede.processing.EdeAxesFixOperation
Options
Python Script - Image to Image [Scripting]
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Process data using a python script that takes an image and returns an image
Options
File : Enter the path to the script
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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
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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.
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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
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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
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Using a box region, select a portion of the data to integrate in X or Y.
Options
Direction of Profile : Either X or Y
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Use a rectangular region to crop and rotate a selected data region
Options
Region of Interest : Define a region of interest.
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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
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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
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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
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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
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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
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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
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Gaussian filter an image using kernal of specified width
Options
Kernel Width : Width of filter kernel in pixels
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Median filter an image with a kernel of a specified width
Options
Kernel Width : Width of filter kernel in pixels
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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
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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.
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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.
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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)
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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)
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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)
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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]
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Sets the current value of the data as the variance on the dataset
Options
ARPES Gold Calibration Correction [ARPES Analysis]
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ARPES Gold Calibration Correction
Options
Calibration File : Path to the calibration NeXus file
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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
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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
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Mask pixels outside the specified region
Options
Region of Interest : Define the region of interest
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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
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Subtract a dataset (or average if stack) in the specified file
Options
File : Enter the path to the data file
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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
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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)
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Performs an affine transformation on the image
Options
a11 :
a12 :
a21 :
a22 :
dx :
dy :
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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.
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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
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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
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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
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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]
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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.
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Extracts blobs on binary image
Options
Connect Rule : Connectivity rule: blobs can be defined using a 4 or 8 connect rule
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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
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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
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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
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Polynomial Smoothing Filter
XY : XY
uk.ac.diamond.scisoft.analysis.processing.operations.oned.PolynomialSmoothingOperation
Options
Polynomial Order : Enter the smoothing polynomial order
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Image : Image
Add errors to data
Options
electronicNoise :
gain :
gainFluctuation :
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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]
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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
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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
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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]
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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.
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Integrate an image along a selected axis
Options
Direction of Profile : The direction to see the profile in.
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Divide data by a value taken from the file metadata
Options
metadataName :
Multiply [External Data]
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Multiply dataset by external value
Options
File : Enter the path to the data file, leave blank to use the file being processed
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Subtract external data from a dataset
Options
File : Enter the path to the data file, leave blank to use the file being processed
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Divide dataset by external value
Options
File : Enter the path to the data file, leave blank to use the file being processed
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Add external data to a Dataset
Options
File : Enter the path to the data file, leave blank to use the file being processed
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Difference between the mean of two boxes
Options
Box 1 : Define the first region of interest
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Ratio of the mean of two boxes
Options
Box 1 : Define the first region of interest
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Mask values inside, or outside a set co-ordinate range
Options
Coordinate : Set coordinate for to mask over
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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
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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.
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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.
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Multiply dataset by internal value
Options
Dataset : Enter the name of the dataset to be used
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Subtract internal data from a dataset
Options
Dataset : Enter the name of the dataset to be used
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Divide dataset by internal value
Options
Dataset : Enter the name of the dataset to be used
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Add internal data to a Dataset
Options
Dataset : Enter the name of the dataset to be used
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Multiply dataset by frame (or average of stack) from external file
Options
File : Enter the path to the data file
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Subtract frame (or average of stack) from external file
Options
File : Enter the path to the data file
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Multiply dataset by frame (or average of stack) from external file
Options
File : Enter the path to the data file
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Add frame (or average of stack) from external file
Options
File : Enter the path to the data file
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uk.ac.diamond.scisoft.analysis.processing.surfacescattering.Polynomial1DReflectivityOperation
Options
angular fudge factor : angular fudge factor
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uk.ac.diamond.scisoft.analysis.processing.sxrdrods.RodScanPolynomial1DOperation
Options
Beam Correction : Beam Correction True/False
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Specular : Specular True/False
Mask Outliers in Q
Image : Image
uk.ac.diamond.scisoft.analysis.processing.operations.mask.MaskOutliersInQOperation
Options
Mask High : Check to mask high outliers
Mask Low : Check to mask low outliers
Scale Multiplier : Set outlier scale factor
Normalisation for NCD [NCD]
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Normalisation of datasets with errors
Options
Absolute scale value : Absolute scaling value
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Flat field detector response operation
Options
Response file : File containing detector response
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uk.ac.diamond.scisoft.analysis.processing.NcdSectorIntegration
Options
Calibration XML File : The path to XML file containing the calibration data.
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Import NCD Mask from File [NCD]
Image : Image
uk.ac.diamond.scisoft.analysis.processing.ImportNcdMask
Options
Mask File : Path to the mask file
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uk.ac.diamond.scisoft.analysis.processing.NcdBackgroundSubtraction
Options
Background file : File containing background data
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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
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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
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XAFS Normalisation [XAFS Analysis]
XY : XY
uk.ac.diamond.scisoft.spectroscopy.operations.XAFSNormalisationOperation
Options
Pre-edge energy : Define the pre-edge energy.
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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.
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Attenuation correction [XAFS Analysis]
XY : XY
Correct dataset for attenuation
Options
Attenuation distance : Enter the attenuation distance, expressed in cm
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XAFS Rebin [XAFS Analysis]
XY : XY
Rebin XAFS dataset onto new energygrid
Options
Guess edge energy : Estimate the edge energy
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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
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Insert the XPDF metadata into the main Dataset
Options
Beam Energy (keV) : Enter the beam energy
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Insert the sample metadata into the processing pipeline
Options
Counting Time : Enter a counting time for the experiment
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Insert a container metadata instance into the processing pipeline
Options
Container Density (g/cm^3) : Enter the container material density
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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
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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
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Calculate the theoretical self-scattring, and use it to normalise the data
Options
XPDF Normalise Data (count to Normon) [XPDF beta]
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Normalise all datasets according to their count time and relative flux
Options
Normalise all container traces? : Normalize all the container data, if unnormalized
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Subtract the empty beam data from the sample and empty container data
Options
Subtract all container backgrounds? : Subtract the background from the container data
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Calibrate the data to best match the theoretical scattering, and subtract the sample fluorescence
Options
Calculate fluorescence? : Perform a real fluorescence calculation
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Define the detector parameters used to take the data
Options
Detector Density (g/cm^3) : Enter the detector material density
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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
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XPDF Read Metadata [XPDF beta]
Image : Image
Read the XPDF metadata from a NeXus file
Options
Read beam data :
Read beam information :
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