Python Module Index

a | b | c | d | e | f | g | h | i | l | m | n | o | p | q | r | s | t | u | v | w | x | y
 
a
all_cpus_plugin (Unix) Base class for all plugins which want to use all CPU's on the target machine
arithmetic_operations (Unix) Perform elementary arithmetic operations on data: addition, subtraction, multiplication and division
astra_recon_cpu (Unix) Wrapper around the Astra toolbox for cpu reconstruction
astra_recon_gpu (Unix) Wrapper around the Astra toolbox for gpu reconstruction using vector geometry
 
b
band_pass (Unix) A plugin to low pass each frame with a gaussian
base_absorption_correction (Unix) A set of plugins to correct for absorption effects in xrd and xrf ct.
base_astra_recon (Unix) A base for all Astra toolbox reconstruction algorithms
base_astra_vector_recon (Unix) A base for Astra toolbox reconstruction algorithms using vector geometry
base_azimuthal_integrator (Unix) A plugin to integrate azimuthally "symmetric" signals i.e. SAXS, WAXS or XRD.Requires a calibration file
base_component_analysis (Unix) A base class for all component analysis methods
base_correction (Unix) A base class for dark and flat field corrections
base_dezinger_sinogram (Unix) A base class for CPU/GPU sinogram dezinger
base_driver (Unix) Base class or all driver plugins
base_filter (Unix) A base class for all standard filters
base_fitter (Unix) a base class for all fitting methods
base_image_saver (Unix) Handles common functionality for savers that save separate image files.
base_loader (Unix) A base class for loader plugins
base_median_filter (Unix) A base class for CPU/GPU median filter
base_multi_modal_loader (Unix) Contains a base class from which all multi-modal loaders are derived.
base_recon (Unix) A base class for all reconstruction methods
base_saver (Unix) A base class for all saver plugins
base_tomophantom_loader (Unix) A loader that generates synthetic 3D projection full-field tomo data as hdf5 dataset of any size.
base_transport (Unix) A BaseTransport class which implements functions that control the interaction between the data and plugin layers.
base_transport_data (Unix) Base class for transport mechanism data functions.
base_type (Unix) A base module for different data types.
basic_driver (Unix) Base class or all driver plugins
basic_operations (Unix) Plugin to perform basic mathematical operations on datasets.
basic_plugin_runner (Unix) Plugin list runner, which passes control to the transport layer.
basic_transport (Unix) Transports data to and from file at the beginning and end of the process list respectively.
basic_transport_data (Unix) A data transport class that is inherited by Data class at runtime. It organises the slice list and moves the data.
 
c
camera_rot_correction (Unix) A plugin to apply a rotation to projection images
ccpi_cgls_recon (Unix) Wrapper around the CCPi cgls reconstruction algorithm.
ccpi_denoising_cpu (Unix) "CCPi-Regularisation/denoising Toolkit delivers a variety of variational 2D/3D denoising methods."
ccpi_denoising_cpu_3D (Unix) GPU modules of CCPi-Regularisation Toolkit (CcpiRegulToolkitCpu)
ccpi_denoising_gpu (Unix) GPU modules of CCPi-Regularisation Toolkit (CcpiRegulToolkitGpu)
ccpi_denoising_gpu_3D (Unix) GPU modules of CCPi-Regularisation Toolkit (CcpiRegulToolkitGpu)
ccpi_ring_artefact_filter (Unix) Regularization-based method for removing ring artifacts.
centering360 (Unix) A plugin to find the center of rotation per frame
checkpointing (Unix) A class to organise Savu checkpointing.
chunking (Unix) A class to optimise hdf5 chunking
comparison (Unix) A plugin to compare two datasets, given as input datasets, and print the RMSD between the two. The data is unchanged.
convert_360_180_sinogram (Unix) A plugin working in sinogram space to convert a 360-degree sinogram to a 180-degree sinogram in a half-acquisition scan.
core_utils (Unix) Simple core utility methods.
cpu_iterative_plugin (Unix) Base class for all plugins which use a CPU on the target machine and have the ability to be iterative
cpu_plugin (Unix) Base class for all plugins which use a CPU on the target machine
 
d
dark_flat_field_correction (Unix) A Plugin to apply a simple dark and flatfield correction to raw timeseries data
data (Unix) The Data class dynamically inherits from transport specific data class and holds the data array, along with associated information.
data_additions (Unix) A module containing add_on classes, which have instances encapsulated within the Data class.
data_create (Unix) A class inherited by Data class that deals with data object creation.
data_notes (Unix) A module containing extended doc strings for the data module.
data_removal (Unix) Plugin to remove unwanted data.
data_threshold (Unix) module to threshold the data (less, lessequal, equal, greater, greaterequal) than the given value
data_utils (Unix) Simple data utility methods
data_with_darks_and_flats (Unix) A class for loading data that has associated dark and flat fields.
denoise_bregman_filter (Unix) A plugin to denoise 2D slices of data by using the Split Bregman to solve the Total Variation ROF model
dezinger (Unix) A 3D median-based dezinger plugin to apply to raw projection data
dezinger_gpu A 3D median-based GPU dezinger plugin to apply to raw projection data
dezinger_sinogram (Unix) A 2D/3D median-based dezinger plugin to apply to sinogram data
dezinger_sinogram_gpu (Unix) A 2D/3D GPU median-based dezinger plugin to apply to sinogram data
distortion_correction (Unix) A plugin to apply a distortion correction
docstring_parser (Unix) Parser for the docstring to interpret parameters and plugin info.
dosna_transport (Unix) Transports data using DosNa(which provides several storing backends) at the beginning and end of the process list respectively.
dosna_transport_data (Unix) A data transport class that is inherited by Data class at runtime. It organises the slice list and moves the data.
downsample_filter (Unix) A plugin to downsample and rescale data volume.
dxchange_loader (Unix) Load tomography data in dxchange format.
 
e
elementwise_arrays_arithmetics (Unix) perform elementwise arithmetic operations on two input datasets: addition, subtraction, multiplication and division
experiment (Unix) Contains information specific to the entire experiment.
 
f
find_peaks (Unix) A plugin to find the peaks
forward_projector_gpu (Unix) A forward data projector using ToMoBAR software
framework_citations (Unix) Contains all framework citations.
fresnel_filter (Unix) A plugin for denoising or improving the contrast of reconstruction images.
 
g
geo_distance (Unix) Calculate geodesic distance transforms. Wraps the code for calculating geodesic distance transforms, can be a usefull tool for data segmentation with a proper seed initialisation
geo_distance_3D (Unix) Calculate geodesic distance transforms in 3D. Wraps the code for calculating geodesic distance transforms, can be a usefull tool for data segmentation with a proper seed initialisation.
get_data_statistics (Unix) A plugin to calculate global statistics (max, min, sum, mean) of the input data
gmm_segment3d (Unix) Gaussian mixture models for classification-segmentation routine. Wrapper around scikit GMM function
gpu_plugin (Unix) The driver for GPU plugins.
 
h
hdf5_saver (Unix) A class to save data to a hdf5 output file.
hdf5_template_loader (Unix) A class to load data from a non-standard nexus/hdf5 file using descriptions loaded from a yaml file.
hdf5_transport (Unix) Transport specific plugin list runner, passes the data to and from the plugin.
hdf5_transport_data (Unix) A data transport class that is inherited by Data class at runtime. It organises the slice list and moves the data.
hilbert_filter (Unix) A plugin to apply Hilbert filter horizontally for tomographic reconstruction of phase gradient images.
 
i
ica (Unix) A plugin to fit peaks
image_data (Unix) A module for loading any of the FabIO python module supported image formats (e.g. tiffs)
image_interpolation (Unix) A plugin to interpolate each frame
image_loader (Unix) A plugin for loading standard tomography data in image formats (e.g. tiff).
image_saver (Unix) A class to save output as images
image_stitching (Unix) A plugin for stitching two tomo-datasets.
image_template_loader (Unix) 'A class to load data from a folder of Fabio compatible images using data descriptions loaded from a yaml file.'
inpainting (Unix) A plugin to inpaint missing data. Data inpainting method from Larix software
iterative_ccpi_denoising (Unix) iterative ccpi denoising with changing patterns between Savu (outer) iterations
iterative_plugin (Unix) Driver for iterative plugins
 
l
lfov_loader (Unix) Large field-of-view loader. A class for loading 2 standard tomography scans.
list_to_projections (Unix) A plugin to convert a list (1D array) to image (2D array)
 
m
map_3dto4d_h5 (Unix) A module for loading a 3D hdf5 dataset that contains a set of 4D scans.
mask_initialise (Unix) A plugin to initialise a binary mask for level sets and distance transform segmentations
mc_near_absorption_correction (Unix) A plugin apply hogans xrf absorption correction using stxm data
median_filter (Unix) A plugin to apply 2D/3D median filter (CPU)
median_filter_gpu (Unix) A plugin to apply 2D/3D median filter (GPU)
meta_data (Unix) Contains the MetaData class which holds all information required by the pipeline throughout processing. An instance of MetaData is held by the Experiment class.
min_and_max (Unix) A plugin to calculate the min and max of each frame
mipmap (Unix) 'Mipmapping plugin (a pyramid-like data downampling). A plugin to downsample multidimensional data
mm_loader (Unix) A class for loading multi-modal data
monitor_correction (Unix) A plugin to apply a monitor correction.
morph_proc (Unix) Wrapper around skimage morphology routines for 2D morphological processing of binary datasets
morph_proc_line (Unix) a Larix module to remove inconsistent gaps in the resulted binary mask by merging the boundaries
morph_proc_line3D (Unix) a Larix module to remove inconsistent gaps in the resulted 3D binary mask by merging the boundaries
morph_remove_objects (Unix) Wrapper around skimage morphology to remove objects smaller than the specified size.
morph_snakes (Unix) 2D segmentation using Morphological Level Sets or active countours.
morph_snakes3D (Unix) 3D segmentation using Morphological Level Sets or active countours.
mrc (Unix) A module to load MRC image data.
mrc_loader (Unix) A class for MRC data.
mrc_saver (Unix) Saves data as .mrc file
mtf_deconvolution (Unix) A plugin for MTF (modulation transfer function) deconvolution or PSF (point spread function) correction in the Fourier domain.
multi_nxtomo_loader (Unix) A class for loading multiple standard tomography scans.
multi_savu_loader (Unix) A class for loading multiple savu output nexus files.
multi_threaded_plugin (Unix) Driver to run one instance of a plugin on EACH node.
 
n
no_process_plugin (Unix) Plugin to test loading and saving without processing
nxfluo_loader (Unix) A class for loading nxfluo data
nxmonitor_loader (Unix) A class for loading nxmonitor data
nxstxm_loader (Unix) A class for loading nxstxm data
nxtomo_loader (Unix) A class for loading standard tomography data in Nexus format.
nxxrd_loader (Unix) A class for loading nxxrd data
 
o
ortho_slice (Unix) A plugin render some slices from a volume and save them as images.
 
p
paganin_filter (Unix) A plugin to apply the Paganin filter.
pca (Unix) A plugin to fit peaks
phase_unwrapping (Unix) A plugin for unwrapping phase-retrieved images.
plugin (Unix) Base class for all plugins used by Savu
plugin_data (Unix) Contains the PluginData class. Each Data set used in a plugin has a PluginData object encapsulated within it, for the duration of a plugin run.
plugin_datasets (Unix) Base class of plugin containing all dataset related functions
plugin_datasets_notes (Unix) A module containing extended doc strings for the data module.
plugin_driver (Unix) Base class or all driver plugins
plugin_list (Unix) Contains the PluginList class, which deals with loading and saving the plugin list, and the CitationInformation class. An instance is held by the MetaData class.
plugin_runner (Unix) Plugin list runner, which passes control to the transport layer.
poly_background_estimator (Unix) A plugin to find peaks in spectra
preview (Unix) This class deals with previewing (reduction) of the data and is encapsulated in the Data class.
projection_shift (Unix) Calculate horizontal and vertical shifts in the projection images over time, using template matching.
projection_vertical_alignment (Unix) Align each projection vertically with shift values calculated using the ProjectionShift plugin
pyfai_azimuthal_integrator (Unix) A plugin to integrate azimuthally "symmetric" signals i.e. SAXS, WAXS or XRD.Requires a calibration file
pyfai_azimuthal_integrator_separate (Unix) A plugin to integrate azimuthally "symmetric" signals i.e. SAXS, WAXS or XRD.Requires a calibration file
pyfai_azimuthal_integrator_with_bragg_filter (Unix) A plugin to integrate azimuthally "symmetric" signals i.e. SAXS, WAXS or XRD.Requires a calibration file.
pymca (Unix) A plugin to fit spectral data
 
q
quantisation_filter (Unix) A plugin to to quantise an image into a number of discrete levels
 
r
random_3d_tomo_loader (Unix) A full-field tomography loader that creates a NeXus file in NXtomo format and contains a random number generated hdf5 dataset of a specified size.
random_hdf5_loader (Unix) A loader that creates a random number generated hdf5 dataset of any size.
raven_filter (Unix) FFT-based method for removing ring artifacts.
region_grow (Unix) Fast region-grow type segmentation (2D) from Larix toolbox to evolve a given mask
region_grow3D (Unix) Fast region-grow type segmentation in 3D from Larix toolbox to evolve a given mask
remove_all_rings (Unix) Combination of methods working in the sinogram space to remove most types of ring artefacts.
remove_large_rings (Unix) Method working in the sinogram space to remove large ring artifacts.
remove_unresponsive_and_fluctuating_rings (Unix) Method working in the sinogram space to remove ring artifacts caused by dead pixels.
replicate (Unix) A class to replicate the slice list of a dataset (not the data itself!)
rescale_intensity (Unix) performs stretching or shrinking the data intensity levels based on skimage rescale_intensity module
ring_removal_filtering (Unix) Method working in the sinogram space to remove ring artifacts.
ring_removal_fitting (Unix) Method working in the sinogram space to remove ring artifacts.
ring_removal_interpolation (Unix) Method working in the sinogram space to remove ring artifacts.
ring_removal_normalization (Unix) Method working in the sinogram space to remove ring artifacts.
ring_removal_regularization (Unix) Method working in the sinogram space to remove ring artifacts.
ring_removal_sorting (Unix) Method working in the sinogram space to remove ring artifacts.
ring_removal_wavelengtfft (Unix) Method working in the sinogram space to remove ring artifacts.
 
s
savu_nexus_loader (Unix) A class for loading savu output data.
scikitimage_filter_back_projection (Unix) Wrapper for scikitimage FBP function
scikitimage_sart (Unix) Wrapper for scikitimage SART function
setup
simple_fit (Unix) A plugin to fit peaks
simple_recon (Unix) A simple implementation of a reconstruction routine for testing purposes
sinogram_alignment (Unix) A plugin to determine the centre of rotation of a sinogram and to align the rows of a sinogram e.g. in the case of motor backlash.
sinogram_clean (Unix) A plugin to clean the sinogram.
slice_lists (Unix) Contains classes for creating global and local slice lists
spectrum_crop (Unix) A plugin to crop a spectra
stage_motion (Unix) Calculate stage motion from motor positions.
statistics (Unix) Contains and processes statistics information for each plugin.
stitch_data (Unix) A module for stitching together multiple datasets.
strip_background (Unix) A plugin to automatically strip peaks and subtract background
subpixel_shift (Unix) A plugin to apply a subpixel x-shift to images
sum_dimension (Unix) Sum a chosen dimension of the data.
 
t
thresh_segm (Unix) Segmentation by threhsolding based on lower and upper intensities
threshold_filter (Unix) A plugin to to quantise an image into a number of discrete levels
tiff_saver (Unix) A class to save output in tiff format
time_based_correction (Unix) A time-based dark and flat field correction using linear interpolation
time_based_plus_drift_correction (Unix) A time-based dark and flat field correction that accounts for image drift (Note: A work in progress but please try).
tomo_phantom_artifacts (Unix) Adding artifacts to real or generated synthetic projection data using TomoPhantom
tomo_phantom_quantification (Unix) A Tomophantom plugin to calculate quantitative values e.g. MSE, RMSE, SSIM
tomo_recon (Unix) Runner for the Savu framework
tomobar_recon (Unix) 'A wrapper around TOmographic MOdel-BAsed Reconstruction (ToMoBAR) software for advanced iterative image reconstruction (2D case) using GPU'
tomobar_recon_3D (Unix) A wrapper around TOmographic MOdel-BAsed Reconstruction (ToMoBAR) software for direct and advanced iterative image reconstruction using _3D_ capabilities of regularisation. This plugin will divide 3D projection data into overlapping subsets using padding.
tomobar_recon_cpu (Unix) A wrapper around TOmographic MOdel-BAsed Reconstruction (ToMoBAR) software for advanced iterative image reconstruction using CPU (2D case)
tomophantom_loader (Unix) A full-field tomography loader that creates a NeXus file in NXtomo format and contains tomographic synthetic data generated hdf5 dataset of a specified size.
tomopy_recon (Unix) Wrapper around the tomopy reconstruction algorithms. See 'http://tomopy.readthedocs.io/en/latest/api/tomopy.recon.algorithm.html'
transport_setup (Unix) Module containing classes required for transport setup, e.g MPI.
 
u
utils (Unix) Utilities for plugin management
 
v
value_substitution (Unix) looks for a specific value in the provided second dataset (e.g. a mask image) and substitutes it with a given value
visual_hulls_recon (Unix) simple visual hulls reconstruction
vo_centering (Unix) A plugin to find the center of rotation per frame
 
w
wavelet_denoising_gpu (Unix) GPU Wavelet 2D denoising from pypwt package (Pierre Paleo)
 
x
xrf_saver (Unix) A class to save output in tiff format
 
y
yaml_converter (Unix) 'A class to load data from a non-standard nexus/hdf5 file using descriptions loaded from a yaml file.'