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Thrombus Training Dec. 2013
 

Thrombus Training Dec. 2013

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A little presentation of control versioning systems, file storage possibilities in the lab., ParaView advanced tools, and others.

A little presentation of control versioning systems, file storage possibilities in the lab., ParaView advanced tools, and others.

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    Thrombus Training Dec. 2013 Thrombus Training Dec. 2013 Presentation Transcript

    • Thrombus Training Ricardo A Corredor J 19/12/2013
    • Content • Storage – Code (CVS -> SVN -> Git / Mercurial) – Data (TUX-FTP / iRods) • Applications – Data Viz (ParaView) – Mesh Tools (MeshLab, FreeCAD, Blender) – Image Tools (MeVisLab, itkSNAP, GDCM, MITK) 2
    • Content • Storage – Code (CVS -> SVN -> Git / Mercurial) – Data (TUX-FTP / iRods) • Applications – Data Viz (ParaView) – Mesh Tools (MeshLab, FreeCAD, Blender) – Image Tools (MeVisLab, itkSNAP, GDCM, MITK) 3
    • Storage PhD Comics 28/05/2010 http://www.phdcomics.com/comics/archive.php?comicid=1323 4
    • Storage • Code – Centralize code in one server (online!) – Keep all the modifications/additions (code/text history) – Create new branches to test or to release a new version – Collaborate (many people in the same code) Cloud CVS 5
    • Version control system A.txt v0.1 6
    • Version control system Commit A.txt A.txt v0.1 v0.2 7
    • Version control system Commit A.txt A.txt v0.1 v0.2 ID: 0002 Message: Adds a new method to multiply two integers. 8
    • Version control system A.txt A.txt A.txt A.txt v0.1 v0.2 v0.3 v0.4 ID: 0002 Message: Adds a new method to multiply two integers. 9
    • Version control system A.txt Branch v0.3.1 A.txt A.txt A.txt A.txt v0.1 v0.2 v0.3 v0.4 ID: 0002 Message: Adds a new method to multiply two integers. 10
    • Version control system A.txt Merge v0.3.1 A.txt A.txt A.txt A.txt A.txt v0.1 v0.2 v0.3 v0.4 v0.5 ID: 0002 Message: Adds a new method to sum two numbers 11
    • Version control system Push 12
    • Version control system Pull 13
    • Git • Install Git (already installed on Linux). • For CREATIS, create a SSH key and send the public key to Fabrice. • For today, GitHub (free Git server and highly used for open-source projects) – User: thrombus – Pass: xxxxxx • It’s easier by command’s console… 14
    • Demo - Git 0- Local configuration (if first time using Git in the PC) git config –-global user.name “Your Name” git config –-global user.email “Your@Ema.il” 1- Download a project from server: git clone https://github.com/rcorredorj/ThrombusTraining.git 2- Add all the modifications to the local Git server: git add . 3- Commit modifications in the local server: git commit -m “I did a modification” 4- Push changes to the server: git push 5- Pull changes from the server: git pull Others: git status, git log, git branch,… 15
    • Git - CREATIS • Public and private projects, e.g.: – Public: clitk (D. Sarrut team) git://git.creatis.insa-lyon.fr/clitk – Private: BioThrombus (R. Corredor) ssh://gitolite@git.creatis.insalyon.fr/BioThrombus • • • • • To create a new project, send a email to Fabrice Simple Web Interface: https://git.creatis.insa-lyon.fr/git/ You can subscribe to changes in Git repository (email) A quick guide in https://www.creatis.insa-lyon.fr/mywiki/Git#Git_at_CREATIS Support: Claire Mouton (info-dev), Fabrice Bellet 16
    • Content • Storage – Code (CVS -> SVN -> Git / Mercurial) – Data (TUX-FTP / iRods) • Applications – Data Viz (ParaView) – Mesh Tools (MeshLab, FreeCAD, Blender) – Image Tools (MeVisLab, itkSNAP, GDCM, MITK) 17
    • TUX-FTP • All persons with a CREATIS account have a storage space in TUX server. Accesed via FTPs (Suggested application: Filezilla) – 600 GiB! • Your public SSH key should be uploaded in the server (Fabrice) • Advantages: – – – – Fast in local network Share files with external people Create a personal or a project website Backup and assign UNIX permissions to files/folders 18
    • iRods • iRODS™ (Integrated Rule-Oriented Data System) https://www.irods.org/ • A Data grid system. One or more interconnected resources (each machine running an iRODS server instance) • A Middleware that constructs a virtual file system to access multiple storage resources • A Data + Metadata manager. More semantic info into the files, all stored in a catalog known as an iCAT • A Rule engine (automatic actions and workflows on the data, apply policies and conditions) • An open-source project 19
    • iRods • Stable server managed by IN2P3 – (Zone Rhone-Alpes) • Access via several clients: iRODS Explorer • • Windows only Can add metadata IN2P3 client: JuX • • Java app Data viewer / download Web client • • Web Data viewer 20
    • iRods icommands • • Windows / Linux / Mac Most stable to transfer data • For Thrombus: – – – – Medical Images (Anonymized!) Big back-ups Simulation results Patient’s tracking for the different studies – No personal data! * Web client: http://escience8.inf.ed.ac.uk/irods * Tutorials: - http://eirods.org/dev/wpcontent/uploads/2012/08/irods-getting-started.pdf - http://research.nesc.ac.uk/files/irodsTutorial1.pdf 21
    • Content • Storage – Code (CVS -> SVN -> Git / Mercurial) – Data (TUX-FTP / iRods) • Applications – Data Viz (ParaView) – Mesh Tools (MeshLab, FreeCAD, Blender) – Image Tools (MeVisLab, itkSNAP, GDCM, MITK) 22
    • ParaView • One of the Kitware open-source projects • Data analysis and visualization tool (3D, 2D, Volumes, Images, Animations, Graphics, Tables, … ) • Quick access to VTK capabilities • Multiple visualization and interaction techniques • Can be used in distributed/parallel environments Python / Macros ParaView VTK OpenGL MPI 23
    • ParaView DataObject • Image data, Rectilinear Grid, Structured Grid, Unstructured Grid, Polygonal Data • Geometry data(point coordinates), topology (points or cells), and/or data attributes (Scalars, Vectors, Normals, Texture Coordinates, Tensors, …) ProcessObject • Filters applied on data objects 24
    • ParaView - Open multiple files Display options Volume Rendering Slicing and Clipping Iso-contours / Iso-surfaces Data Analysis Streamlines Animations 25
    • Content • Storage – Code (CVS -> SVN -> Git / Mercurial) – Data (TUX-FTP / iRods) • Applications – Data Viz (ParaView) – Mesh Tools (MeshLab, FreeCAD, Blender) – Image Tools (MeVisLab, itkSNAP, GDCM, MITK) 26
    • Mesh Tools MeshLab (http://meshlab.sourceforge.net/) - Analyze mesh properties - Many filters for mesh processing: Smooth, Decimate, Fill Holes, Subdivide,… - Opens and exports STL, PLY FreeCAD (http://www.freecadweb.org/) - Analyze mesh properties - Free CAD Tool - Can export IGES solids 27
    • Mesh Tools Blender (http://www.blender.org/) - Advanced tool for mesh edition/creation (flat stents, cut vessel segments, smooth vessel wall, …) - Many filters for mesh processing: Smooth, Decimate, Fill Holes, Subdivide, Boolean operations, … - Opens and exports STL, PLY - Create animations 28
    • Image Tools MeVisLab (http://www.mevislab.de/) - Prototype image processing algorithms - Includes ITK and VTK filters - Changes in parameters affects automatically the views - Opens DICOM, practical to convert DICOM to MHD itkSNAP (http://www.itksnap.org) - Simple tool to make manual segmentations - Open multiple formats of medical image files - Some segmentation algorithms to test GDCM 2 (http://gdcm.sourceforge.net/wiki/index.php/GDCM_Release_2.0) - A C++ Library to read DICOM files. - Practical to read DICOM headers, convert images to other formats, ANONYMIZE, … - Normally, GDCM is also included in ITK MITK (http://www.mitk.org/) - Other tool for medical image viz. - Semi-automatic segmentation methods, manual segmentation tools, 2D/3D Viewers, … 29
    • Others http://software.incf.org/software/sumatra 30