Thrombus Training Dec. 2013
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Transcript of Thrombus Training Dec. 2013
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)
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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)
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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
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Version control system
A.txt
v0.1
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Version control system
A.txt A.txt
v0.1 v0.2
Commit
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Version control system
A.txt A.txt
v0.1 v0.2
ID: 0002 Message: Adds a new method to multiply two integers.
Commit
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Version control system
A.txt A.txt
v0.1 v0.2
A.txt
v0.3
ID: 0002 Message: Adds a new method to multiply two integers.
A.txt
v0.4
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Version control system
A.txt A.txt
v0.1 v0.2
A.txt
v0.3
ID: 0002 Message: Adds a new method to multiply two integers.
A.txt
v0.3.1
A.txt
v0.4
Branch
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Version control system
A.txt A.txt
v0.1 v0.2
A.txt
v0.3
ID: 0002 Message: Adds a new method to sum two numbers
A.txt
v0.3.1
A.txt
v0.4
A.txt
v0.5
Merge
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Version control system
Push
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Version control system
Pull
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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…
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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 “[email protected]”
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,…
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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://[email protected]/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
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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)
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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
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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
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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
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iRods
• For Thrombus: – Medical Images (Anonymized!)
– Big back-ups
– Simulation results
– Patient’s tracking for the different studies
– No personal data!
icommands
• Windows / Linux / Mac
• Most stable to transfer data
* Web client: http://escience8.inf.ed.ac.uk/irods * Tutorials: - http://eirods.org/dev/wp-content/uploads/2012/08/irods-getting-started.pdf
- http://research.nesc.ac.uk/files/irodsTutorial1.pdf
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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)
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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
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ParaView
- Open multiple files
- Display options
- Volume Rendering
- Slicing and Clipping
- Iso-contours / Iso-surfaces
- Data Analysis
- Streamlines
- Animations
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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)
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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
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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
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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, …
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