This document provides an overview of various tools for code storage, data storage, data visualization, mesh editing, and medical image analysis available on the CREATIS computing cluster. It describes version control systems like Git and SVN for code storage, data storage options like TUX-FTP and iRODS, the ParaView application for scientific visualization, mesh editing tools like MeshLab, FreeCAD and Blender, and medical image analysis tools including MeVisLab, itkSNAP, GDCM and MITK. Tutorials and support contacts are provided for many of the applications.

1. Thrombus
Training
Ricardo A Corredor J
19/12/2013

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)
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3. 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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4. Storage
PhD Comics 28/05/2010
http://www.phdcomics.com/comics/archive.php?comicid=1323
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5. 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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6. Version control system
A.txt
v0.1
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7. Version control system
Commit
A.txt
A.txt
v0.1
v0.2
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8. Version control system
Commit
A.txt
A.txt
v0.1
v0.2
ID: 0002
Message: Adds a new
method to multiply two
integers.
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9. 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.
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10. 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.
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11. 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
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12. Version control system
Push
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13. Version control system
Pull
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14. 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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15. 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,…
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16. 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
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17. 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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18. 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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19. 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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20. 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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21. 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
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22. 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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23. 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
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24. 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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25. ParaView
-
Open multiple files
Display options
Volume Rendering
Slicing and Clipping
Iso-contours / Iso-surfaces
Data Analysis
Streamlines
Animations
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26. 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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27. 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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28. 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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29. 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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30. Others
http://software.incf.org/software/sumatra
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