diff --git a/_index.db b/_index.db index d8b6cebde..ad2557ae7 100644 Binary files a/_index.db and b/_index.db differ diff --git a/data/en.wikipedia.org/wiki/3D_Slicer-0.md b/data/en.wikipedia.org/wiki/3D_Slicer-0.md new file mode 100644 index 000000000..e11dd9eb8 --- /dev/null +++ b/data/en.wikipedia.org/wiki/3D_Slicer-0.md @@ -0,0 +1,85 @@ +--- +title: "3D Slicer" +chunk: 1/1 +source: "https://en.wikipedia.org/wiki/3D_Slicer" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T10:10:20.011628+00:00" +instance: "kb-cron" +--- + +3D Slicer (Slicer) is a free and open source software package for image analysis and scientific visualization. Slicer is used in a variety of medical applications, including autism, multiple sclerosis, systemic lupus erythematosus, prostate cancer, lung cancer, breast cancer, schizophrenia, orthopedic biomechanics, COPD, cardiovascular disease and neurosurgery. + + +== About == +3D Slicer is a free open source software (BSD-style license) that is a flexible, modular platform for image analysis and visualization. 3D Slicer is extended to enable development of both interactive and batch processing tools for a variety of applications. +3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the addition of new functionality and provides a number of generic features. +The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and hardware accelerated volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized color maps). +Slicer's capabilities include: + +Handling DICOM images and reading/writing a variety of other formats +Interactive visualization of volumetric Voxel images, polygonal meshes, and volume renderings +Manual editing +Fusion and co-registering of data using rigid and non-rigid algorithms +Automatic image segmentation +Analysis and visualization of diffusion tensor imaging data +Tracking of devices for image-guided procedures. +Slicer is compiled for use on multiple computing platforms, including Windows, Linux, and macOS. +Slicer is distributed under a BSD style, free, open source license. The license has no restrictions on use of the software in academic or commercial projects. However, no claims are made on the software being useful for any particular task. It is entirely the responsibility of the user to ensure compliance with local rules and regulations. The slicer has not been formally approved for clinical use by the FDA in the US or by any other regulatory body elsewhere. + + +== Image gallery == + + +== History == +Slicer started as a master's thesis project between the Surgical Planning Laboratory at the Brigham and Women's Hospital and the MIT Artificial Intelligence Laboratory in 1998. 3D Slicer version 2 has been downloaded several thousand times. In 2007 a completely revamped version 3 of Slicer was released. The next major refactoring of Slicer was initiated in 2009, which transitioned the GUI of Slicer from using KWWidgets to Qt. Qt-enabled Slicer version 4 was released in 2011. As of 2022, Slicer 4 had been downloaded over one million times by users around the world. +Slicer software has enabled a variety of research publications, all aimed at improving image analysis. + +This significant software project has been enabled by the participation of several large-scale NIH funded efforts, including the NA-MIC, NAC, BIRN, CIMIT, Harvard Catalyst and NCIGT communities. The funding support comes from several federal funding sources, including NCRR, NIBIB, NIH Roadmap, NCI, NSF and the DOD. + + +== Users == +Slicer's platform provides functionalities for segmentation, registration and three-dimensional visualization of multimodal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided radiation therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software. +Slicer has been used in a variety of clinical research. In image-guided therapy research, Slicer is frequently used to construct and visualize collections of MRI data that are available pre- and intra-operatively to allow for the acquiring of spatial coordinates for instrument tracking. In fact, Slicer has already played such a pivotal role in image-guided therapy, it can be considered as growing up alongside that field, with over 200 publications referencing Slicer since 1998. +In addition to producing 3D models from conventional MRI images, Slicer has also been used to present information derived from fMRI (using MRI to assess blood flow in the brain related to neural or spinal cord activity), DTI (using MRI to measure the restricted diffusion of water in imaged tissue), and electrocardiography. For example, Slicer's DTI package allows the conversion and analysis of DTI images. The results of such analysis can be integrated with the results from analysis of morphologic MRI, MR angiograms and fMRI. Other uses of Slicer include paleontology and neurosurgery planning. +There is an active community at Slicer's Discourse server. + + +== Developers == +The Slicer Developer Orientation offers resources for developers new to the platform. Slicer development is coordinated on the Slicer Discourse forum, and a summary of development statistics is available on Ohloh. +3D Slicer is built on VTK, a pipeline-based graphical library that is widely used in scientific visualization and ITK, a framework widely used for the development of image segmentation and image registration. In version 4, the core application is implemented in C++, and the API is available through a Python wrapper to facilitate rapid, iterative development and visualization in the included Python console. The user interface is implemented in Qt, and may be extended using either C++ or Python. +Slicer supports several types of modular development. Fully interactive, custom interfaces may be written in C++ or Python. Command-line programs in any language may be wrapped using a light-weight XML specification, from which a graphical interface is automatically generated. +For modules that are not distributed in the Slicer core application, a system is available to automatically build and distribute for selective download from within Slicer. This mechanism facilitates the incorporation of code with different license requirements from the permissive BSD-style license used for the Slicer core. +The Slicer build process utilizes CMake to automatically build prerequisite and optional libraries (excluding Qt). The core development cycle incorporates automatic testing, as well as incremental and nightly builds on all platforms, monitored using an online dashboard. +Slicer's development is managed primarily through its GitHub repository. + + +== External dependencies == +VTK +ITK +CMake +CPack +Python +Nrrd +MRML +IGSTK +Qt + + +== See also == +Analyze +GIMIAS +List of free and open-source software packages +Mimics + + +== Notes == +1.^For a list of publications citing Slicer usage since 1998, visit: slicer.org Archived 2016-03-29 at the Wayback Machine + + +== References == + + +== External links == + +Slicer \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/ANUGA_Hydro-0.md b/data/en.wikipedia.org/wiki/ANUGA_Hydro-0.md new file mode 100644 index 000000000..54d731f5a --- /dev/null +++ b/data/en.wikipedia.org/wiki/ANUGA_Hydro-0.md @@ -0,0 +1,32 @@ +--- +title: "ANUGA Hydro" +chunk: 1/3 +source: "https://en.wikipedia.org/wiki/ANUGA_Hydro" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T10:10:23.608024+00:00" +instance: "kb-cron" +--- + +ANUGA Hydro is a free and open source software tool for hydrodynamic modelling, suitable for predicting the consequences of hydrological disasters such as riverine flooding, storm surges and tsunamis. For example, ANUGA can be used to create predicted inundation maps based on hypothetical tsunami or flood scenarios. The ANUGA name without qualification is used informally to mean the ANUGA Hydro tool. + +== ANUGA == + +=== Background === +Modelling the effects on the built environment of natural hazards such as riverine flooding, storm surges and tsunami is critical for understanding their economic and social impact on our urban communities. +ANUGA has its genesis as a MatLab program developed for ACTEW (an Australian Capital Territory owned utility providing electricity, water and wastewater treatment to the residents of the Australian Capital Territory). Its development was instigated by Dr Christopher Zoppou, a senior engineer in the Hydrographics Section of ACTEW in 1998 and a former student of Professor Stephen Roberts from the Australian National University (ANU). Stephen Roberts and Christopher Zoppou embarked on the development of a two-dimensional hydrodynamic shallow water wave equation solver. Written by Stephen Roberts, the MatLab code was used by Christopher Zoppou to simulate the impact of the catastrophic collapse of water supply reservoirs maintained by ACTEW. The code's ownership is shared between ANU and ACTEW. +In 2002 Christopher Zoppou left ACTEW to lead the Risk Modelling Section at Geoscience Australia (an Australian Government agency responsible for providing geo-scientific advice and information). The Risk Modelling Section was formed because Geoscience Australia was diversifying its interest from the impact of earthquakes on the built environment to the impact of other natural hazards. These included cyclones, storm surges and landslides. Christopher Zoppou initiated the development of a generic open source storm surge model within the Risk Modelling Section, that was based on the MatLab model developed for ACTEW. A small group was formed in 2002, consisting of Dr Ole Nielsen, who joined Geoscience Australia from the ANU and Mr Duncan Gray, a software developer to produce a comprehensive storm surge model in the Risk Modelling Section. Stephen Roberts was involved in the development of the hydrodynamic solver, Ole Nielsen led the modelling framework using Python, Duncan Gray participated in the coding and Christopher Zoppou provided hydraulic engineering advice on the model development. The open source model is jointly owned by ANU and Geoscience Australia and is called ANUGA. +In the wake of the 2004 Indian Ocean earthquake and tsunami. the emphasis of ANUGA shifted from a storm surge model due to cyclones to inundation modelling caused by tsunamis resulting from earthquakes. This was not a quantum leap as the shallow water wave equations are applicable to tsunami, storm surge, flash and riverine flooding. +The first public open source release of ANUGA took place in December 2006. In 2007 after approaches from Local Government Engineers, a rainfall routine was added. This allows rainfall to be placed directly over the topography described in the computational domain. A time series can be applied to a polygon, or a series of polygons. Alternatively a rainfall grid can be applied. This is particularly useful for applying RADAR rainfall. ANUGA can model culverts and bridges with code from the open source Watershed Bounded Network Model (WBNM){Boyd, Rigby, VanDrie}, having a pipe, box and trapezoid routine. Development continues to create an arbitrary shape culvert solver that links to a 1D piped network model such as SWMM. ANUGA is stable even in extreme flow with high Froude numbers. An example of this is the 1928 St Francis Dam Break in California that resulted in extreme flow velocities and complex waves in a tortuous valley. ANUGA ran this model with full volumetric mass balance preserved at all times and no instabilities anywhere in the model. +In the ensuing years ANUGA has involved contributions form a number of individuals and organisations. These include: a sediment transport module etc. + +=== Simulation engine === +The fluid dynamics in ANUGA are based on a Finite volume method for solving the Shallow Water Wave Equation. The study area is represented by a mesh of triangular cells that can vary in size in order to capture detail where it is required. By solving the governing equation within each cell, water surface, bed elevation (hence depth) and horizontal (X-y) momentum are tracked over time. +A major capability of ANUGA is that it can model the process of wetting and drying as water enters and leaves an area. This means that it is suitable for simulating water flow onto a beach or dry land and around structures such as buildings. ANUGA is also capable of modelling hydraulic jumps due to the ability of the finite-volume method to accommodate discontinuities in the solution. While ANUGA works with discontinuities in the conserved momentum quantities, only the discontinuous elevation solvers allow discontinuities in the bed elevation. The latter were added to the code in 2013 and include the default algorithm as of ANUGA 2.0. + +=== User Interface === +Most ANUGA components are written in the object-oriented programming language Python. Software written in Python can be produced quickly and can be readily adapted to changing requirements throughout its lifetime. Computationally intensive components are written for efficiency in C routines working directly with Python numpy structures. +To set up a model of a scenario the user specifies the geometry (bathymetry and topography), the initial water level, boundary conditions such as tide, and any forcing terms that may drive the system such as rainfall, water abstraction, wind stress or atmospheric pressure gradients. Gravity and Frictional resistance from the different terrains in the model are represented by predefined forcing terms. + +=== ANUGA viewer === +The ANUGA Viewer is a graphical 3D rendering program suitable for animating the output files from ANUGA. \ No newline at end of file diff --git a/data/en.wikipedia.org/wiki/ANUGA_Hydro-1.md b/data/en.wikipedia.org/wiki/ANUGA_Hydro-1.md new file mode 100644 index 000000000..5e0bec02e --- /dev/null +++ b/data/en.wikipedia.org/wiki/ANUGA_Hydro-1.md @@ -0,0 +1,71 @@ +--- +title: "ANUGA Hydro" +chunk: 2/3 +source: "https://en.wikipedia.org/wiki/ANUGA_Hydro" +category: "reference" +tags: "science, encyclopedia" +date_saved: "2026-05-05T10:10:23.608024+00:00" +instance: "kb-cron" +--- + +Additional viewing capability is available via several other options: +– Using Commercial Software such as WaterRide (Ref to WebSite) +– Using Free tools Such as Mirone (Grid viewing software) which has a specific tool called Aquamoto +– Using SWW2DEM in combination with any GIS platform +– Using Crayfish viewer as plugin in QGIS +– Possibly using tools such as VisIt (Ref to Web Site) + +=== Validation studies === +ANUGA has been extensively validated against wave tank experiments and field studies where available, and ships with a validation test suite with about 30 analytical solutions, wave tank and field tests. Examples include validation against the wave tank experiment for the Okushiri 1995 tsunami, wave tank runup experiments at University of Queensland, the 2004 Indian Ocean tsunami impact at Patong Beach, comparison to other models, ANUGA was a late entry in the UK 2D model Benchmarking project in 2010 using version 1.1beta_7501. As a result, not all tests were completed. However of the basic tests ANUGA was well within the comparable range of results of other models. Since late 2013 the standard test suite for the model also includes a full catchment model (Towradgi Creek Catchment) which has been validated against the 17 August 1998 storm event. + +=== ANUGA software development methodology === +ANUGA was developed as an AGILE project so with strong adherence to Test Driven Development and Continuous Integration. ANUGA has more than 1200 individual tests that can be run by users or developers to verify that a given installation works as expected. ANUGA is fully versioned using the source code control system git, which allows a user to replicate a model run from a previous version at any time. It also of course thereby allows comparison with the current version. + +=== ANUGA development timeline summary === +Noting that ANUGA runs both in serial (1 core) and parallel (many cores) tested on 1000s. +Here is a rough time line of major developments: +Date : Version : Comment +1999 : ------- : Zoppou Roberts Paper +2004 : ------- : Storm Surge Open Source project started at Geoscience Australia in collaboration with the ANU. In: AusGEO news, No. 75, September 2004; pages: 8-9. Availability: +2006/08/16: 3500 : Moved code to SVN +2006/09/07: 3548 : Offline viewer with Animation capability +2006/09/20: : Published work on Tsunami Modelling answers tsunami questions. In: AusGEO news, No. 83, September 2006; Availability: