Library Reference - Functions¶

Auto Centre¶

Centres the input NumPy array by placing the voxel with the largest amplitude at the centre of the array. The output NumPy array will necessarily increase in dimensions when compared to the input if centring is required.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.

Bin¶

Creates an array in which each voxel results from the grouping and addition of neighbouring voxels of the input file. The dimensions used (in each {x,y,z} direction) for each voxel group is dictated by the Bin dimensions parameter.

Parameters:

Input file: User provided path string to the input NumPy file from which bin groups are defined.
Output File: User provided path string for the output bin NumPy file.
Bin dimensions {x,y,z}: Dimensions used for grouping voxels.

Blank Line Fill Array¶

Applies an average filter to the amplitude of non-zero voxels of the input array within the specified region.

Parameters:

Input file: User provided path string to the input NumPy file.
ROI path: Region of interest within the input HDF file.
Output File: User provided path string for the output NumPy file.
Filter kernel dimensions: Dimensions of the averging kernel.

Centred Resize¶

Centres the input NumPy array by placing the voxel with the largest amplitude at the centre of the array and then resizes the cetered array to the specified dimensions.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Dimensions {x,y,z}: Dimensions of the output array.

Conjugate Reflect¶

Takes the complex conjugate and reflects the coordinates of the input NumPy file.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.

Convolve¶

Performs a discrete convolution of the two input NumPy files.

Parameters:

First Input file: User provided path string to the first input NumPy file.
Second Input file: User provided path string to the second input NumPy file.
Output File: User provided path string for the output NumPy file.

Crop Pad¶

Provides a means to crop and zero pad a NumPy array. The input array is first cropped and subsequently zero padded according to the specified parameters.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Crop dimensions: Start: {i,j,k}: Number of indices by which to crop the array along each {i,j,k} direction. Cropping direction begins from the start of the array (and counts forward) for each {i,j,k} direction.
Crop dimensions: End: {i,j,k}: Number of indices by which to crop the array along each {i,j,k} direction. Cropping direction begins from the end of the array (and counts backward) for each {i,j,k} direction.
Pad dimensions: Start: {i,j,k}: Number of indices by which to pad the array along each {i,j,k} direction. Padding direction begins from the start of the array for each {i,j,k} direction.
Pad dimensions: End: {i,j,k}: Number of indices by which to pad the array along each {i,j,k} direction. Padding direction begins from the end of the array for each {i,j,k} direction.

Cuboid Support¶

Creates a support array for use in phase retrieval. Voxels in this array take a value of $1 + 0j$ inside the support and zero everywhere else. The support is automatically centred within the array.

If any array is supplied in the (xyz) from array field, the dimensions of this array will be used for the support array. Otherwise, the specified dimensions will be used.

Parameters:

Support file: User provided path string for the output support NumPy file.
(xyz) from array: Optional user provided path string for NumPy file used to provide the support array dimensions.
(xyz) from dimensions {x,y,z}: Dimensions of the support array. This is overridden if the (xyz) from array field is used.
Support size {x,y,z}: Dimensions of the support. This must be smaller than the size of the array.

Polyhedron Support¶

Creates a support array for use in phase retrieval using the specified planes to form the surface. The vector formed by each terminal and initial point coordinate pair is the normal vector to a surface that encloses the support. Voxels in this array take a value of $1 + 0j$ inside the support and zero everywhere else.

If any array is supplied in the (xyz) from array field, the dimensions of this array will be used for the support array. Otherwise, the specified dimensions will be used.

Parameters:

Support file: User provided path string for the output support NumPy file.
(xyz) from array: Optional user provided path string for NumPy file used to provide the support array dimensions.
(xyz) from dimensions {x,y,z}: Dimensions of the support array. This is overridden if the (xyz) from array field is used.
Initial Point Coordinates: List of initial point coordinates of vector normals to each surface. One per line with comma separated ordinates. Parentheses are ignored.
Terminal Point Coordinates: List of terminal point coordinates of vector normals to each surface. One per line with comma separated ordinates. Parentheses are ignored.

Fourier Transform¶

Performs a Fast Fourier transform (FFT) on the input NumPy file in the specified direction.

Parameters:

Input file

User provided path string to the input NumPy file.

Output File

User provided path string for the output NumPy file.

To

Fourier Space - Transform to Fourier space.
Real Space - Transform to Real space.

Gaussian Fill¶

Fill the input NumPy file with a Gaussian function.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Sigma: Standard Deviation of the Gaussian function.

Interpolate Object¶

Interpolates an input NumPy array and it’s corresponding co-ordinates onto regular grid NumPy array with dimensions dictated by Array grid size. Shepards famous algorithm is used for the interpolation.

Parameters:

Input file: User provided path string to the input NumPy file.
Co-ord’s File: User provided path string to the corresponding co-ordinates NumPy file. Generating coordinates files is achieved using the Coordinate transformation operation.
Output File: User provided path string for the output NumPy file.
Array grid size: Dimensions of the output NumPy array.
Array Bounds: Start: {x,y,z}: Start bounding coordinates. Each value must be smaller than the End bounding coordinates. If all values are zero, they are ignored and the digault bounds are used instead.
Array Bounds: End: {x,y,z}: End bounding coordinates. Each value must be larger than the Start bounding coordinates. If all values are zero, they are ignored and the digault bounds are used instead.
Interpolation range: Fraction of the input array used for interpolating each point. Larger values approaching unity will significantly slow down the interpolation process.

Affine Transform¶

Performs an affine (linear) transformation on the input coordinates file.

Parameters:

Input co-ord’s file: User provided path string to the corresponding co-ordinates NumPy file. Generating coordinates files is achieved using the Coordinate transformation operation.
Output co-ord’s file: User provided path string for the output co-ordinates NumPy file.
Translate: {x,y,z}: Translation of coordinates in each orthogonal direction. Units are equal to those of the original coordinates.
Scale: {x,y,z}: Scaling of each orthogonal axis.
Rotate: {x,y,z}: Rotation about each orthogonal axis. Units are in degrees.

Mask¶

Creates a mask array for use in phase retrieval. Voxels in this array take a value of $1 + 0j$ if the corresponding voxel of the input file is inside the range of Minimum Value to Maximum Value. Voxels outside the same range are set to zero.

Parameters:

Input file: User provided path string to the input NumPy file from which Minimum Value and Maximum Value are obtained.
Output File: User provided path string for the output mask NumPy file.
Maximum Value: Values above (equal or below) Maximum Value in the input file will result in a corresponding voxel value of zero ( $1 + 0j$ ) in the mask.
Minimum Value: Values below (equal or above) Minimum Value in the input file will result in a corresponding voxel value of zero ( $1 + 0j$ ) in the mask.

Median Filter¶

Applies a median filter to the amplitude of the input array. Voxels are only replaced in the array if they deviate from the median filtered equivalent by an amount greater than the Normal deviation.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Filter kernel dimensions: Dimensions of the median filtering kernel.
Normal deviation: Median filter voxel replace cut-off value. This value is compared element-wise to the normalised difference in amplitude of voxels from the input array and from the median filtered equivalent, i.e. the magnitude of (median filtered array - array)/ array. Voxels that exceeed this cut-off are replaced with their median-filtered equivalent.

Python Script¶

Execute python script. Memory arrays are exposed to this function.

Rotate Support¶

Rotates a binary array (such as a support array) by the specified angle in degrees normal to the specified axis. This operation is only intended for binary arrays.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Axis: Axis normal to the rotation. 1,2 and 3 correspond to axis x,y and z.
Angle: Angle of rotation in degrees.

Scale Array¶

Scales the input array by a given amount. Scaling is performed element-wise.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Scale factor: Factor by which each voxel of the array is scaled.

Sum or Subtract Array¶

Takes the sum or difference of two input arrays and places the result in the output array.

Parameters:

Input file 1: User provided path string to the input NumPy file.
Input file 2: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Add or Subtract: Choose whether to add or subtract array 2 from array 1.

Threshold Data¶

Creates an array using data from the input file for which voxels outside the range of Minimum Value to Maximum Value are set to zero.

Parameters:

Input file: User provided path string to the input NumPy file from which Minimum Value and Maximum Value are obtained.
Output File: User provided path string for the output mask NumPy file.
Maximum Value: Values above Maximum Value in the input file will result in a corresponding voxel value of zero in the output file.
Minimum Value: Values below Minimum Value in the input file will result in a corresponding voxel value of zero in the output file.

Transpose Array¶

Transposes an array from dimensions {x,y,z} to dimensions {z,y,x}.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided choice of memory keyword.

Voxel Replace¶

Replaces all voxels with indices in the range of Start dimensions and End dimensions with the specified complex value.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Start dimensions: {i,j,k}: Starting indices from which the replacement will begin.
End dimensions: {i,j,k}: Final indices for which the replacement will end.
Complex Value: Real and imaginary parts of a complex number used repeatedly to replace voxel data in the input file.

Wrap Data¶

Reorders the data of the input NumPy file into wrap-around order.

Parameters:

Input file: User provided path string to the input NumPy file.
Output File: User provided path string for the output NumPy file.
Wrap Direction: If an array dimension has an odd number of elements, a Forward followed by a Reverse wrap is required to obtain the original array.

Library Reference - Functions¶

Auto Centre¶

Bin¶

Blank Line Fill Array¶

Centred Resize¶

Conjugate Reflect¶

Convolve¶

Crop Pad¶

Cuboid Support¶

Polyhedron Support¶

Fourier Transform¶

Gaussian Fill¶

Interpolate Object¶

Affine Transform¶

Mask¶

Median Filter¶

Python Script¶

Rotate Support¶

Scale Array¶

Sum or Subtract Array¶

Threshold Data¶

Transpose Array¶

Voxel Replace¶

Wrap Data¶

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