Thrombus
Training
Ricardo A Corredor J
19/12/2013
Content
• Storage
– Code (CVS -> SVN -> Git / Mercurial)
– Data (TUX-FTP / iRods)

• Applications
– Data Viz (ParaView)
– ...
Content
• Storage
– Code (CVS -> SVN -> Git / Mercurial)
– Data (TUX-FTP / iRods)

• Applications
– Data Viz (ParaView)
– ...
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)
– Crea...
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 multipl...
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...
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
Mes...
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 ...
Demo - Git
0- Local configuration (if first time using Git in the PC)
git config –-global user.name “Your Name”
git config...
Git - CREATIS
• Public and private projects, e.g.:
– Public: clitk (D. Sarrut team) git://git.creatis.insa-lyon.fr/clitk
–...
Content
• Storage
– Code (CVS -> SVN -> Git / Mercurial)
– Data (TUX-FTP / iRods)

• Applications
– Data Viz (ParaView)
– ...
TUX-FTP
• All persons with a CREATIS account have a storage space in
TUX server. Accesed via FTPs (Suggested application: ...
iRods
• iRODS™ (Integrated Rule-Oriented Data System)
https://www.irods.org/

• A Data grid system. One or more interconne...
iRods
• Stable server managed by IN2P3 – (Zone Rhone-Alpes)
• Access via several clients:
iRODS Explorer

•
•

Windows onl...
iRods
icommands
•
•

Windows / Linux / Mac
Most stable to transfer data

• For Thrombus:
–
–
–
–

Medical Images (Anonymiz...
Content
• Storage
– Code (CVS -> SVN -> Git / Mercurial)
– Data (TUX-FTP / iRods)

• Applications
– Data Viz (ParaView)
– ...
ParaView
• One of the Kitware open-source projects
• Data analysis and visualization tool (3D, 2D, Volumes, Images,
Animat...
ParaView
DataObject
• Image data, Rectilinear Grid, Structured Grid, Unstructured
Grid, Polygonal Data
• Geometry data(poi...
ParaView
-

Open multiple files
Display options
Volume Rendering
Slicing and Clipping
Iso-contours / Iso-surfaces
Data Ana...
Content
• Storage
– Code (CVS -> SVN -> Git / Mercurial)
– Data (TUX-FTP / iRods)

• Applications
– Data Viz (ParaView)
– ...
Mesh Tools
MeshLab (http://meshlab.sourceforge.net/)
- Analyze mesh properties
- Many filters for mesh processing:
Smooth,...
Mesh Tools
Blender (http://www.blender.org/)
- Advanced tool for mesh edition/creation (flat stents, cut vessel
segments, ...
Image Tools
MeVisLab (http://www.mevislab.de/)
- Prototype image processing algorithms
- Includes ITK and VTK filters
- Ch...
Others
http://software.incf.org/software/sumatra

30
Upcoming SlideShare
Loading in...5
×

Thrombus Training Dec. 2013

279

Published on

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

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
279
On Slideshare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
1
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Thrombus Training Dec. 2013

  1. 1. Thrombus Training Ricardo A Corredor J 19/12/2013
  2. 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) 2
  3. 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) 3
  4. 4. Storage PhD Comics 28/05/2010 http://www.phdcomics.com/comics/archive.php?comicid=1323 4
  5. 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 5
  6. 6. Version control system A.txt v0.1 6
  7. 7. Version control system Commit A.txt A.txt v0.1 v0.2 7
  8. 8. Version control system Commit A.txt A.txt v0.1 v0.2 ID: 0002 Message: Adds a new method to multiply two integers. 8
  9. 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. 9
  10. 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. 10
  11. 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 11
  12. 12. Version control system Push 12
  13. 13. Version control system Pull 13
  14. 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… 14
  15. 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,… 15
  16. 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 16
  17. 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) 17
  18. 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 18
  19. 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 19
  20. 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 20
  21. 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 21
  22. 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) 22
  23. 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 23
  24. 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 24
  25. 25. ParaView - Open multiple files Display options Volume Rendering Slicing and Clipping Iso-contours / Iso-surfaces Data Analysis Streamlines Animations 25
  26. 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) 26
  27. 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 27
  28. 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 28
  29. 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, … 29
  30. 30. Others http://software.incf.org/software/sumatra 30
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×