PAN Blend tomography packages

CTSim provides an interactive computed tomography simulator. Computed tomography is the technique of estimating the interior of an object by measuring x-ray absorption through that object.

CTSim has both command-line tools and a graphical user interface. CTSim has very educational trace modes for viewing the data collection simulation as well as the reconstruction.

This package provides HTML and PDF documentation files for the ctsim package. CTSim is a graphical computed tomography simulator. This documentation file is included in a separate package so it will not have to be include in the binary ctsim package for every architecture.

This package provides the online help file for the ctsim package. CTSim is a graphical computed tomography simulator. This help file is included in a separate package so it will not have to be include in the binary ctsim package for every architecture.

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.

Geomview는 수학 연구와 교육에 특히 적합한 쌍방향 기하학 도형 소프트웨어입니 다. 특히, geomview는 유클리드 공간의 물체와 마찬가지로, 쌍곡선 및 구형 공간 내 물체를 표시할 수 있습니다.

Geomview는 대상과 카메라를 각각 독립적으로 제어할 수 있습니다. Geomview는 움직임, (조명, 명암, 그리고 재료를 포함하는)외관, 오브젝트 선택, 구석 또는 정점 레벨, SGI 이미지 파일 또는 Renderman RIB 형식에서 snapshot, 그리고 마 우스의 직접 조작을 통해 제공되는 오브젝트 추가 또는 삭제, 페널 조종, 그리고 키보드 단축키등을 위해 쌍방향 제어를 제공합니다. 외부 프로그램은 뷰어외 모 든것을 쌍방향으로 제어하는 동안, 뷰어의 모양을 원하는데로 만들 수 있습니다 (위치의 변화를 계속적으로 로딩하거나, 특정 오브젝트의 외관를 제어하는 것과 같이).

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 is a cross-platform tool for 2-D and 3-D scientific data visualization. Its features include:

• Visualization of scalar, vector and tensor data in 2 and 3 dimensions
• Easy scriptability using Python
• Easy extendability via custom sources, modules, and data filters
• Reading several file formats: VTK (legacy and XML), PLOT3D, etc.
• Saving of visualizations
• Saving rendered visualization in a variety of image formats.

MayaVi2 has been designed with scriptability and extensibility in mind. While the mayavi2 application is usable by itself, it may be used as an Envisage plugin which allows it to be embedded in user applications natively. Alternatively, it may be used as a visualization engine for any application.

This package also provides TVTK, which wraps VTK objects to provide a convenient, Pythonic API, while supporting Traits attributes and NumPy/SciPy arrays. TVTK is implemented mostly in pure Python, except for a small extension module.

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.

ParaView는 크기가 작은것 부터 매우 큰 것까지 매우 다양한 데이타 세트를 시각 화하도록 설계된 오픈소스, 멀티 플랫폼 어플리케이션입니다. ParaView 프로젝트 의 목적은 다음과 같습니다.

• 오픈소스, 멀티 플랫폼 시각화 어플리케이션 개발.
• 대형 데이타 세트 처리를 위한 분산 계산 모델 지원.
• 개방적이며, 유연하고, 직관적인 사용자 인터페이스 생성
• 오픈 표준을 기반으로 확장가능한 아키텍쳐 개발.

ParaView는 분산 및 공유 메모리의 병렬 및 싱글 프로세스 시스템에서 실행되며, Windows, Mac OS X, Linux 그리고 여러 유닉스 워크스테이션, 클러스터 및 슈퍼 컴퓨터에서 성공적으로 테스트가 완료되었습니다. 내부를 보면, ParaView는 데이 타 프로세싱 및 렌더링 엔진으로 시각화 툴킷을 사용하며, Qt를 사용해서 개발된 사용자 인터페이스를 가지고 있습니다.

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.

Plastimatch는 변형 이미지 등록을 위한 오픈 소스 소프트웨어입니다. 이는 X- ray 단층 촬영 (CT), 자기 공명 영상 (MRI), 양전자 방사 단층 촬영 (PET)과 같 은 의학 영상의 고성능 체적 등록을 위해 설계되었습니다. 이 소프트웨어는 아래 기능들을 포함합니다.

• 이미지 마스킹, 랜드 마크 페널티 및 정규화에 대한 지원을 포함하는, 변형 이미지 등록 (GPU 및 멀티 코어 가속)을 위한 B-spline 방법
• 변형 이미지 등록을 위한 데몬 방법 (GPU 가속)
• 멀티 아틀라스 분할
• 번역, 엄격함, 아핀, 멀티 데몬 방법 및 B-spline 등록을 위한 ITK 기반 알고리즘
• 대부분의 알고리즘 및 변환 유형간의 원활한 전환을 갖는 파이프라인, 다단계 등록 프레임워크
• 글로벌 등록을 위해 thinplate spline을 사용하는 랜드마크 기반 변형 등록
• 로컬 수정을 위해 방사형 기본 함수를 사용하는 랜드마크 기반 변형 등록
• DICOM, Nifti, NRRD, MetaImage, Anlyze를 포함하는 3D 이미지 파일 형식 (ITK 사용)을 위한 폭 넓은 지원

• DICOM, DICOM-RT, DICOM SRO, XiO 파일 형식, 감마 분석, 형상 조작, 형상 중첩 분석, 그리고 벡터 필드 분석을 위한 지원을 포함하는, 방사선 치료 연구를 위한 광범위한 툴체인 Plastimatch는 또한 이미지 등록과는 직접적으로 관련이 없지만 두개의 편리한 유틸리티를 제공합니다:

• FDK 콘 빔 CT 재구성 (GPU 및 멀티코어 가속)

• 디지탈 복원 방사선 (DRR) 발생 (GPU 및 멀티코어 가속)

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.

Rheolef는 유한 요소와 유사한 방법으로 응용 수학에서 계산을 위해 편리한 실험실 역활을 하는 컴퓨터 환경입니다. 일련의 명령과 C++ 알고리즘 그리고 컨테이너를 제공합니다.

 .
기본적으로, 컨테이너는 희소 행렬과 유한 요소 메쉬를 위한 고전적 그래프 데이타 구조를 포함합니다. 더 높은 추상적 수준에서, 컨테이너는 거의 정확한 유한 요소 공간, 개별 필드를 처리할 수 있습니다. 유연하고 강력한 표현식은 쌍일자식을 지정하는데 사용됩니다.
 .
현재 어플리케이션은 다음을 포함합니다:

• MPI 기반에 대규모 분산 메모리 유한 요소 환경;
• 2D 및 3D의 탄력성, Stokes 및 Navier-Stokes 문제;
• 복잡한 유체 응용: 점소성, 점탄성, wall 슬립;
• 고정 소수점, 뉴턴 및 연속 방법의 비선형 문제;
• 고차 다항식, 혼합 요소 및 불연속 Galerkin 방법
• 자동 적응 메쉬 방식;
• 축대칭 문제;
• 다중 지역 및 가변 계수 문제 . 이 패키지는 rheolef 명령을 제공합니다. Paraview, gnuplot 같은 메시 생성기 및 수치 데이타 시각화 시스템을 위한 다양한 파일 형식의 입출력 지원합니다.

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.