PAN Blend tomography packages

CTSim enthält einen interaktiven Simulator für berechnete Tomografien. Berechnete Tomografie ist die Technik, das Innere eines Objektes, durch Messung der Absorption der Röntgenstrahlung durch das Objekt, zu schätzen.

Es enthält sowohl Befehlszeilenprogramme als auch eine grafische Benutzeroberfläche. CTSim besitzt sehr lehrreiche Modi zum Betrachten der Datensammelsimulation als auch für die Rekonstruktion.

Dieses Paket enthält HTML- und PDF-Dokumentationsdateien für das Paket ctsim. CTSim ist ein grafischer Simulator für berechnete Computer-Tomografie (computed tomography). Diese Dokumentationsdatei ist in einem separaten Paket enthalten, damit es nicht in dem Binärpaket ctsim für jede Architektur enthalten sein muss.

Dieses Paket enthält die Online-Hilfedatei für CTSim. CTSim ist ein grafischer Simulator für berechnete Computer-Tomografie (computed tomography). Diese Hilfedatei ist in einem separaten Paket enthalten, so dass sie nicht im Binärpaket ctsim für jede Architektur mitgeliefert werden muss.

The presented ParaView plugin allows easy access to the algorithm described in Ref 1. It enables analysis of faceted objects that exhibit distortions in their digital representation, e.g. due to tomographic reconstruction artifacts. The contributed functionality can also be used outside ParaView in e.g. command-line programs. The code, data, a test and an example program are included.

Ref 1: Roman Grothausmann, Sebastian Fiechter, Richard Beare, Gaëtan Lehmann, Holger Kropf, Goarke Sanjeeviah Vinod Kumar, Ingo Manke, and John Banhart. Automated quantitative 3D analysis of faceting of particles in tomographic datasets. Ultramicroscopy, 122(0):65 – 75, 2012. ISSN 0304- 3991. doi: 10.1016/j.ultramic.2012.07.024.

Geomview ist ein interaktiver Geometriebetrachter, der besonders für mathematische Forschung und Ausbildung geeignet ist. Insbesondere kann geomview Dinge in hyperbolischen, sphärischen und Euklidischen Räumen darstellen.

Geomviev erlaubt mehrere, unabhängig kontrollierbare Objekte und Kameras. Es bietet eine interaktive Kontrolle für Bewegung, Erscheinung (einschließlich Beleuchtung, Schatten und Beschaffenheit der Materialien), Aufnehmen eines Objektes, Kanten oder Eckpunkte, Schnappschüsse im SGI-Bild-Format oder Renderman-RIB-Format. Das Hinzufügen und Löschen von Objekten wird über direkte Bearbeitung mit der Maus, Kontrollleisten und Tastenkürzel bereitgestellt. Externe Programme können gewünschte Aspekte des Betrachters (wie kontinuierliches Laden wechselnder Geometrie oder Kontrolle der Bewegungen bestimmter Objekte) steuern, während die interaktive Kontrolle des Restes weiter möglich ist.

The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. It is extensively used at the Karlsruhe Institute of Technology for Ultra-fast X-ray Imaging (radiography, tomography and laminography).

A gobject-instrospection binding is also provided to write scripts or user interfaces.

This package can be used by other packages using the GIRepository format to generate dynamic bindings.

MayaVi2 ist ein plattformübergreifendes Werkzeug zur 2D- und 3D-Visualisierung wissenschaftlicher Daten. Die Merkmale:

• Visualisierung von skalaren, vektoriellen und Tensor-Daten in 2 und 3 Dimensionen
• Einfache Skriptmöglichkeit mittels Python
• Einfache Erweiterung mittels externer Quellen, Module und Datenfilter
• Liest einige Datenformate: VTK (alt und XML), PLOT3D, usw.
• Speichert Visualisierungen
• Speichert berechnete Bilder in mehreren Bildformaten.

MayaVi2 wurde hinsichtlich Skriptschnittstelle und Erweiterbarkeit konzipiert. Während die Anwendung MayaVi2 an sich schon einsetzbar ist, kann sie auch als ein Envisage-Plugin verwendet werden, was die direkte Integration in Benutzerprogramme ermöglicht. Alternativ kann sie auch als Visualisierungs-Engine für beliebige Anwendungen verwendet werden.

Dieses Paket stellt auch eine Hülle für VTK-Objekte bereit (TVTK), um eine komfortable Python-API zu liefern, wobei Traits-Attribute und NumPy/SciPy-Arrays unterstützt werden. TVTK ist - bis auf ein kleines Erweiterungsmodul - in reinem Python implementiert.

Meshio can read from and write to various data formats representing unstructured meshes, such as DOLFIN, Gmsh, H5M or VTK.

This package provides the command-line tools, and a plugin for paraview.

This package also provides Flavien Loiseau's msh2xdmf tool to convert from MSH to XDMF mesh formats.

This is an open source, portable, and extendible system for the processing and editing of unstructured 3D triangular meshes. The system is aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning, providing a set of tools for editing, cleaning, healing, inspecting, rendering and converting this kind of meshes.

Meshlab can read files in these formats: PLY, STL, OFF, OBJ, 3DS, COLLADA and PTX. It can write PLY, STL, OFF, OBJ, 3DS, COLLADA, VRML, and DXF.

ParaView ist eine quelloffene, Multi-Plattform-Anwendung, konzipiert um Datensätze unterschiedlichster Größe zu visualisieren. Die Ziele des ParaView-Projekts:

* Entwickle eine quelloffene, Multi-Plattform-Visualisierungsanwendung.
* Unterstütze verteilt berechnete Modelle, um große Datensätze zu
  verarbeiten.
* Erstelle eine offene, flexible und intuitive Benutzerschnittstelle.
* Entwickele eine erweiterbare Architektur, basierend auf offenen
  Standards.

ParaView läuft auf verteiltem (distributed) und geteiltem (shared) Speicher parallel ebenso wie auf Einzelprozessorsystemen und wurde erfolgreich unter Windows, MacOS X, Linux und verschiedenen Unix-Arbeitsstationen, Rechner-Clustern und Supercomputern getestet. Unter der Haube gesehen verwendet ParaView das Visualization Toolkit als Datenverarbeitungs- und Render-Maschine, und hat eine in Qt programmierte Benutzerschnittstelle.

ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large. The goals of the ParaView project include the following:

* Develop an open-source, multi-platform visualization application.
* Support distributed computation models to process large data sets.
* Create an open, flexible, and intuitive user interface.
* Develop an extensible architecture based on open standards.

ParaView runs on distributed and shared memory parallel as well as single processor systems and has been successfully tested on Windows, Mac OS X, Linux and various Unix workstations, clusters and supercomputers. Under the hood, ParaView uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using Qt. Development header files

ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large. The goals of the ParaView project include the following:

* Develop an open-source, multi-platform visualization application.
* Support distributed computation models to process large data sets.
* Create an open, flexible, and intuitive user interface.
* Develop an extensible architecture based on open standards.

ParaView runs on distributed and shared memory parallel as well as single processor systems and has been successfully tested on Windows, Mac OS X, Linux and various Unix workstations, clusters and supercomputers. Under the hood, ParaView uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using Qt. Comprehensive documentation.

Plastimatch is an open source software for deformable image registration. It is designed for high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography(PET). Software features include:

• B-spline method for deformable image registration (GPU and multicore accelerated), including support for image masking, landmark penalties, and regularization
• Demons method for deformable image registration (GPU accelerated)
• Multi-atlas segmentation
• ITK-based algorithms for translation, rigid, affine, multiple demons methods, and B-spline registration
• Pipelined, multi-stage registration framework with seamless conversion between most algorithms and transform types
• Landmark-based deformable registration using thinplate splines for global registration
• Landmark-based deformable registration using radial basis functions for local corrections
• Broad support for 3D image file formats (using ITK), including DICOM, Nifti, NRRD, MetaImage, and Analyze

• Extensive toolchain for radiotherapy research, including support for DICOM, DICOM-RT, DICOM SRO, XiO file format, gamma analysis, contour manipulation, contour overlap analysis, and vector field analysis Plastimatch also features two handy utilities which are not directly related to image registration:

• FDK cone-beam CT reconstruction (GPU and multicore accelerated)

• Digitally reconstructed radiograph (DRR) generation (GPU and multicore accelerated)

Freeart is a tomographic image reconstruction library using Algebraic Reconstruction Technique (ART). It is able to deal with absorption and emission sinograms. Freeart core is written in C++ using template classes to have simple or double precision. A python interface is provided to access the core functionalities. A set of utils such as configuration files, interpreter to run reconstruction from configuration files are provided in python.

Nabu can be used in several ways:

• As a Python library, by features like Backprojector, FlatField, etc
• As a standalone application with the command line interface
• From Tomwer (https://gitlab.esrf.fr/tomotools/tomwer/)

ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large. The goals of the ParaView project include the following:

* Develop an open-source, multi-platform visualization application.
* Support distributed computation models to process large data sets.
* Create an open, flexible, and intuitive user interface.
* Develop an extensible architecture based on open standards.

ParaView runs on distributed and shared memory parallel as well as single processor systems and has been successfully tested on Windows, Mac OS X, Linux and various Unix workstations, clusters and supercomputers. Under the hood, ParaView uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using Qt. Enables python support.

scikit-image is a collection of image processing algorithms for Python. It performs tasks such as image loading, filtering, morphology, segmentation, color conversions, and transformations.

This package provides the Python 3 module.

Tomogui offers a Graphical User Interface to run tomographic reconstruction based on freeart and silx algorithms

Tomogui contains two main applications:

• tomogui project : to create a new project from scratch
• tomogui recons : to run reconstruction from a configuration file created by 'tomogui project'

This library is offering an abstraction to access tomography data from various file formats.

It can read:

• acquisitions from spec (.edf) and bliss (.hdf5)
• volumes:
• single frame file: EDF, JP2K, tiff
• multi frame: HDF5, multitiff

This repository contains Python data processing scripts to be used with the UFO framework. At the moment they are targeted at high-performance reconstruction of tomographic data sets.

Vispy is a high-performance interactive 2D/3D data visualization library.

Vispy leverages the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets.

This package provides VisPy for the Python 3 interpreter.

Rheolef is a computer environment that serves as a convenient laboratory for computations in applied mathematics involving finite element-like methods. It provides a set of commands and C++ algorithms and containers.

Most basically, containers cover the classic graph data structure for sparse matrix formats and finite element meshes. At a higher level of abstraction, they can handle approximate finite element spaces, discrete fields. Flexible and powerful expressions are used to specify bilinear forms.

Current applications include:

• massively distributed memory finite element environment, based on MPI;
• elasticity, Stokes and Navier-Stokes problems in 2D and 3D;
• complex fluids applications: viscoplasticity, viscoelasticity, wall slip;
• nonlinear problems with fixed-point, Newton and continuation methods;
• high order polynomials, mixed elements and discontinuous Galerkin methods;
• auto-adaptive mesh approaches;
• axisymmetric problems;
• multi-regions and variable coefficient problems.

This package provides the rheolef commands. These support input and output in various file formats for mesh-generators and numerical data visualization systems such as paraview, and gnuplot.

The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. It is extensively used at the Karlsruhe Institute of Technology for Ultra-fast X-ray Imaging (radiography, tomography and laminography).

A gobject-instrospection binding is also provided to write scripts or user interfaces.

This package provides the documentation for libufo.

The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. It is extensively used at the Karlsruhe Institute of Technology for Ultra-fast X-ray Imaging (radiography, tomography and laminography).

This package contains average',backproject', bin',blur', buffer',calculate', camera',clip', contrast',crop', denoise',duplicate', fftmult',fft', filter',flatten', flip',forwardproject', gemm',ifft', interpolate',loop', measure',merge', metaballs',monitor', null',opencl', ordfilt',pad', read',reduce', refeed',replicate', rescale',ringwriter', sleep',slice', stack',stdin', stdout',subtract', transpose',write' and `zeropad' plugins

The UFO data processing framework is a C library suited to build general purpose streams data processing on heterogeneous architectures such as CPUs, GPUs or clusters. It is extensively used at the Karlsruhe Institute of Technology for Ultra-fast X-ray Imaging (radiography, tomography and laminography).

This package provides the documentation for the plugins

It supports 2D parallel and fan beam geometries, and 3D parallel and cone beam. All of them have highly flexible source/detector positioning.

A large number of 2D and 3D algorithms are available, including FBP, SIRT, SART, CGLS.

The basic forward and backward projection operations are GPU-accelerated, and directly callable from Octave and Python to enable building new algorithms.

This is the Octave library.

It supports 2D parallel and fan beam geometries, and 3D parallel and cone beam. All of them have highly flexible source/detector positioning.

A large number of 2D and 3D algorithms are available, including FBP, SIRT, SART, CGLS.

The basic forward and backward projection operations are GPU-accelerated, and directly callable from Octave and Python to enable building new algorithms.

This is the Python3 library.

PyHST is a Python program for Tomographic data reconstruction based on direct filtered back-projection algorithm

This is the CUDA version

Features:

• Image reconstruction algorithms for tomography.
• Various filters, ring removal algorithms, phase retrieval algorithms.
• Forward projection operator for absorption and wave propagation.

RabbitCT provides an open platform for worldwide performance-comparison of backprojection implementations on different architectures using one specific, clinical, high resolution C-arm CT dataset of a rabbit. This includes a sophisticated benchmark interface, a prototype implementation in C++, and image quality measures.

provided prior to the tomography experiment.