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