Library Reference - Functions¶
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.
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.
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.
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.
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.
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.
HDF5 to Numpy¶
Provides a means to browse and import data within a Hierarchical Data Format (HDF) file. HDF5 is supported via the python H5Py package.
Parameters:
- Input HDF file
- User provided path string to the input HDF file.
- HDF key path
- Comma separated list of HDF keys found within the
input HDF file
. - Output File
- User provided path string for the output NumPy file.
SPE to Numpy¶
Provides a means to import data from SPE format into NumPy format. During conversion, additional information is provided and appears in the Log.
Parameters:
- Input SPE file
- User provided path string to the input SPE file.
- Output File
- User provided path string for the output NumPy file.
Image to Numpy¶
Provides a means to import image data into NumPy format. Accepted formats include Portable Network Graphics (PNG), JPEG, Portable PixMap (PPM) and Tagged Image File (TIF) format. Output Numpy arrays are three dimensional with unit length in the third dimension.
Parameters:
- Input Image file
- User provided path string to the input image file.
- Output File
- User provided path string for the output NumPy file.
Array to Memory¶
Provides a means to load a NumPy array from disk directly into a memory by using either of the 10 keywords memory0
, memory1
, … , memory9
as a string in place of a NumPy file path. See Array Creation and Storage for furthr details.
Parameters:
- Input file
- User provided path string to the input NumPy file.
- Output File
- User provided choice of memory keyword.
Memory to Array¶
Provides a means to save to disk a NumPy array stored in memory. See Array to Memory for furthr details.
Parameters:
- Input file
- User provided path string to the input NumPy file.
- Output File
- User provided choice of memory keyword.
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 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.
Mask¶
Creates a mask
array for use in phase retrieval. Voxels in this array take a value of 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
andMaximum 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 theinput file
will result in a corresponding voxel value of zero () in the
mask
. - Minimum Value
- Values below (equal or above)
Minimum Value
in theinput file
will result in a corresponding voxel value of zero () in the
mask
.
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.
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.
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.
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.
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.
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.
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.
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.
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
andMaximum Value
are obtained. - Output File
- User provided path string for the output
mask
NumPy file. - Maximum Value
- Values above
Maximum Value
in theinput file
will result in a corresponding voxel value of zero in theoutput file
. - Minimum Value
- Values below
Minimum Value
in theinput file
will result in a corresponding voxel value of zero in theoutput file
.
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
.
Load Co-ordinates¶
Initialises or replaces the internally stored Co-ordinates data
with the supplied array.
Parameters:
- Input file
- User provided path string to the input NumPy file.
Median Filter¶
Applies a median filter to the amplitude of the input NumPy file. Voxels are only replaced if they deviate in amplitude by an amount greater than the Normal deviation
between the input NumPy array and the median filtered NumPy array.
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: {x,y,z}
- Size of the kernel in pixels.
- Normal deviaton
- Element-wise normalised deviation of the intensity between the input NumPy array and the median filtered NumPy array. Voxels with amplitude above this value are replaced with the median filtered alternative. All other voxels remain unfiltered.
Array to VTK¶
Convert an input NumPy array into VTK file format. Uses either the amplitude or phase of the array.
Parameters:
- Input file
- User provided path string to the input NumPy file.
- Output File
- User provided path string for the output VTK file.
- Type
- Use either the amplitude or the phase of the complex
input file
in order to construct a VTK array.
Object to VTK¶
Convert an input NumPy array and it’s corresponding co-ordinates array into VTK file format. Uses either the amplitude or phase of the array.
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 VTK file.
- Type
- Use either the amplitude or the phase of the complex
input file
in order to construct a VTK array.
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.
- Interpolation range
- fraction of the input array used for interpolating each point. Larger values approaching unity will significantly slow down the interpolation process.
View Array¶
Render an image of the two or three-dimensional input Numpy array to the Visualisation tab.
Parameters:
- Input file
- User provided path string to the input NumPy file.
- Type
- Amplitude - An iso-surface of the array amplitude.
- Phase - An interactive scalar cut plane of the array phase.
- Amplitude and Phase - An iso-surface of the array amplitude and an interactive scalar cut plane of the array phase.
- Amplitude with Phase - An iso-surface of the array amplitude with the array phase mapped onto the iso-surface.
- Amplitude (cut plane) - An interactive scalar cut plane of the array amplitude.
- Amplitude
- Iso-surface - Scalar value for the rendered iso-surface.
- Opacity - Opacity of the isosurface when viewing
Amplitude and Phase
. - Feature angle - Minimum angle between two surface normals of the rendered object.
- Phase
- Max - Maximum phase.
- Min - Minimum phase.
- Origin
- Origin point of the interactive scalar cut plane.
- Normal
- Normal vector to the interactive scalar cut plane.
- Spacing
- Spacing of the input array indices.
- View Axes
- Optionally view the axes of the array.
View Object¶
Render an object of the three-dimensional input Numpy array with it’s corresponding co-ordinates array to the Visualisation tab.
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 array file. Alternatively, the memory array keyword
memorycoords
provides access to the internally stored coordinate array. Generating a coordinate array is achieved using the Coordinate transformation operation. - Type
- Amplitude - An iso-surface of the object amplitude.
- Phase - An interactive scalar cut plane of the object phase.
- Amplitude and Phase - An iso-surface of the object amplitude and an interactive scalar cut plane of the object phase.
- Amplitude with Phase - An iso-surface of the object amplitude with the object phase mapped onto the iso-surface.
- Amplitude (cut plane) - An interactive scalar cut plane of the object amplitude.
- Amplitude
- Iso-surface - Scalar value for the rendered iso-surface.
- Opacity - Opacity of the isosurface when viewing
Amplitude and Phase
. - Feature angle - Minimum angle between two surface normals of the rendered object.
- Phase
- Max - Maximum phase.
- Min - Minimum phase.
- Origin
- Origin point of the interactive scalar cut plane.
- Normal
- Normal vector to the interactive scalar cut plane.
- View Axes
- Optionally view the axes of the object.
View VTK Array¶
Render an input VTK array to the Visualisation tab.
Parameters:
- Input file
- User provided path string to the input NumPy file.
- Type
- Amplitude - An iso-surface of the array amplitude.
- Phase - An interactive scalar cut plane of the array phase.
- Amplitude (cut plane) - An interactive scalar cut plane of the array amplitude.
- Amplitude
- Iso-surface - Scalar value for the rendered iso-surface.
- Feature angle - Minimum angle between two surface normals of the rendered object.
- Phase
- Max - Maximum phase.
- Min - Minimum phase.
- Origin
- Origin point of the interactive scalar cut plane.
- Normal
- Normal vector to the interactive scalar cut plane.
- View Axes
- Optionally view the axes of the array.
View Support¶
Render an image of a three-dimensional input Numpy data array and its Support array to the Visualisation tab.
Parameters:
- Support file
- User provided path string to the NumPy array file.
- Data array file
- User provided path string to the NumPy array file.
- Isosurface options
- Support iso-surface - Scalar value for the rendered iso-surface on the interval [0,1].
- Opacity - Opacity of the support isosurface.
- Data file iso-surface - Scalar value for the rendered iso-surface.
- Feature angle - Minimum angle between two surface normals of the rendered object.
- View Axes
- Optionally view the axes of the array.
Comments¶
Input comments into the pipeline.
Python Script¶
Execute python script. Memory arrays are exposed to this function.