Difference between revisions of "User talk:Tamekue"

From NAMIC Wiki
Jump to: navigation, search
 
(28 intermediate revisions by the same user not shown)
Line 3: Line 3:
 
== Time line table==  
 
== Time line table==  
 
{| border="1" cellpadding="5"
 
{| border="1" cellpadding="5"
−
|- style="background:#eeeeee; color:black" align="left"  
+
|- style="background:#eeeeee; color:black" align="center"  
−
| style="width:4%" | '''Time'''
+
| style="width:1%" | '''Task number'''
−
| style="width:12%" | '''Monday, January 10'''  
+
| style="width:20%" | '''Tasks'''
−
| style="width:12%" | '''Tuesday, January 11'''
+
| style="width:5%" | '''Deadlines'''  
−
| style="width:12%" | '''Wednesday, January 12'''  
+
| style="width:4%" | '''Status'''
−
| style="width:32%" | '''Thursday, January 13 '''
+
| style="width:20%" | '''Comments'''
−
| style="width:12%" | '''Friday, January 14'''  
+
|-
 +
| style="background:#CEE3F6; color:black"| '''<font color=black>1</font>'''
 +
| style="background:#CEE3F6; color:black"; align="left"| Design a prototyp of a wizard based graphical user interface.
 +
| style="background:#ffffff; color:#522200"| '''<font color=black>12/01/10</font>'''
 +
| style="background:#dbf3ff; color:#522200"| '''<font color=green>DONE</font>'''
 +
| style="background:#dbf3ff; color:#522200"|
 +
|-
 +
| style="background:#CEE3F6; color:black"| '''<font color=black>2</font>'''
 +
| style="background:#CEE3F6; color:black"; align="left"|Implement the designed graphical user interface so that we can run it and navigate through the different wizard steps.
 +
| style="background:#ffffff; color:black"| '''<font color=black>12/22/10</font>'''
 +
| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
 +
| style="background:#dbf3ff; color:black"|
 
|-
 
|-
−
| style="background:#eeeeee; color:black"|
+
| style="background:#CEE3F6; color:black"| '''<font color=black>3</font>'''
−
| style="background:#ffffff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
+
| style="background:#CEE3F6; color:black"; align="left"|Implement a separate algorithm in python, which parse an array containing array elements representing centerline points with associated diameter. <br> Define a threshold value for diameters. The algorithm should detect all line segments, where associated diameters are less than the defined threshold value and save them in a container.  
−
| style="background:#dbf3ff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
+
| style="background:#ffffff; color:black"| '''<font color=black>02/08/11</font>'''
−
| style="background:#dbf3ff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
+
| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
−
| style="background:#F2E5D3; color:#522200"| '''AHM, EAB''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons, Arches, Deer Valley)]
+
| style="background:#dbf3ff; color:black"|
−
| style="background:#dbf3ff; color:#522200"|'''[[2011_Winter_Project_Week|Project Activities]] ''' <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
 
 
|-
 
|-
−
| style="background:#eeeeee; color:black"|'''7:30-8:00'''  
+
| style="background:#CEE3F6; color:black"| '''<font color=black>4</font>'''
−
| style="background:#ffffff; color:black"|
+
| style="background:#CEE3F6; color:black"; align="left"|Use the VMTK modules avaible in Slicer 3 to extract and generate a sample of lumen line from a chosen dataset containing stenosis. <br>
−
| style="background:#dbf3ff; color:black"| Breakfast
+
Create a temporary stenosis detector molude in Slicer 3.  <br>Import and customize the algorithm implemented at task 3, so that stenosis may be marked and visualized in 3D view. Run and test the created module.
−
| style="background:#dbf3ff; color:black"| Breakfast
+
| style="background:#ffffff; color:black"| '''<font color=black>02/20/11</font>'''
−
| style="background:#F2E5D3; color:black"| Breakfast
+
| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
−
| style="background:#dbf3ff; color:black"| Breakfast
+
| style="background:#dbf3ff; color:black"|  
 
|-
 
|-
−
| style="background:#eeeeee; color:black"|'''8:00-10:00'''  
+
| style="background:#CEE3F6; color:black"| '''<font color=black>5</font>'''
−
| style="background:#ffffff; color:black"|
+
| style="background:#CEE3F6; color:black"; align="left"|Write expose for diploma thesis, find enough references.
−
| style="background:#dbf3ff; color:black"|8:00-9:00 [[AHM_2011:DBP-Briefing|DBP Briefing]] (Ron Kikinis) <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br>9:30-10:00 [[AHM_2011:2011TrainingCoreVision|Training Core Strategy Session]] <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br>*<br> Project Work <br>
+
| style="background:#ffffff; color:black"| '''<font color=black>03/13/11</font>'''
−
| style="background:#dbf3ff; color:black"|Project Work <br> 8-9:30am: [[2011 Winter Project Week:Breakout Multi-Image Engineering|Breakout: Engineering of Multi-Volume Data in Slicer]] <br>  [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)]<br>
+
| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
−
| style="background:#F2E5D3; color:black"|'''8:00''' Introduction, [http://www.spl.harvard.edu/~kikinis Ron Kikinis] <br>
+
| style="background:#dbf3ff; color:black"|
−
'''8:05-10:00 Roadmap Projects'''<br>
 
−
: 8:05-8:25 Atrial Fibrillation, Rob MacLeod ([[Media:DBP-Afib-1up.pdf|slides (1up)‎]] and [[Media:DBP-Afib-2up.pdf|slides (2up)‎]]) <br>
 
−
: 8:25-8:45 Huntington's Diseases, Hans Johnson ([[Media:20110113_DTI_Intro.pdf|slides]]) <br>
 
−
: 8:45-9:05 Head and Neck Cancer, Greg Sharp  ([[Media:AHM2011-DBP3-HN-Cancer.pdf|slides]])<br>
 
−
: 9:05-9:25 Traumatic Brain Injury, Jack Van Horn ([[Media:NAMIC-DBP-AHM-2011_pptold.ppt|slides]])<br>
 
−
: 9:25-9:45 Image Guided Therapy, Nobuhiko Hata ([[Media:AHM2011-IGT-Hata-talk.pptx|slides]]) <br>
 
−
| style="background:#dbf3ff; color:black"|Project Review <br>
 
 
|-
 
|-
−
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
+
| style="background:#CEE3F6; color:black"| '''<font color=black>6</font>'''
−
| style="background:#ffffff; color:black"|
+
| style="background:#CEE3F6; color:black"; align="left"|Transcribe the implemented graphical user interface with all wizard steps using python and import it into the module created above.
−
| style="background:#dbf3ff; color:black"| Coffee
+
| style="background:#ffffff; color:black"| '''<font color=black>03/31/11</font>'''
−
| style="background:#dbf3ff; color:black"| Coffee
+
| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
−
| style="background:#F2E5D3; color:black"| Coffee
+
| style="background:#dbf3ff; color:black"|
−
| style="background:#dbf3ff; color:black"| Coffee
 
 
|-
 
|-
−
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
+
| style="background:#CEE3F6; color:black"| '''<font color=black>7</font>'''
−
| style="background:#ffffff; color:black"| '''Vision10'''
+
| style="background:#CEE3F6; color:black"; align="left"|Extend the implementation of the module adding and customizing all different image processing steps (vessel enhancement, level-set segmentation, network extraction, centerline extraction and stenosis detection). <br> We will hereby be dealing with the automation of our tool, which improves the user-friendliness by reducing the number of parameters usually required through the graphical user interface and with interactions between the different wizard steps.
−
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout Slicer|Breakout: Slicer 4 - Looking Forward]] (Steve Pieper, Julien Finet, Jean-Christophe Fillion-Robin)<br>[http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)]<br>*<br> Project Work
+
| style="background:#ffffff; color:black"| '''<font color=black>05/15/11</font>'''
−
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout DTI|Breakout: DTI - Next Generation]] (Hans Johnson, C-F Westin) <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br>*<br>  Project Work
+
| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
−
 
+
| style="background:#dbf3ff; color:black"|
−
| style="background:#F2E5D3; color:black"|
+
|-"
−
'''10:30-12:00: Algorithms''' <br>
+
| style="background:#CEE3F6; color:black"| '''<font color=black>8</font>'''
−
:10:30-10:45 Overview, Ross Whitaker  ([[media:NAMIC_AHM_C1_intro_Jan11.ppt‎|slides]]) <br>
+
| style="background:#CEE3F6; color:black"; align="left"|Design and implement and test a diagramm, which gives an estimation of the stenosis detection results with different stenosis stages.  <br>This will be include into evaluation step (last wizard step) of our module.
−
:10:45-11:00 Statistical models of anatomy and pathology, Polina Golland ([[media:NAMIC-AHM-2011-StatisticalModels.ppt‎|slides]]) <br>
+
| style="background:#ffffff; color:black"| '''<font color=black>06/20/11</font>'''
−
:11:00-11:15 Geometric correspondence,  Guido Gerig ([[media:NAMIC-AHM-Geom-Registration.pdf‎|pdf slides]]) ([[media:NAMIC-AHM-Geom-Registration.ppt‎|ppt slides w movies]]) <br>
+
| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
−
:11:15-11:30 User interactive tools for segmentation, Allen Tannenbaum  ([[media:Interactive.segmentation.january.2011.pdf‎|pdf slides]]) ([[media:Interactive.segmentation.january.2011.pdf‎‎|pdf slides]])  <br>
+
| style="background:#dbf3ff; color:black"|
−
:11:30-11:45 Longitudinal and time-series analysis,  Martin Styner ([[media:2011_01_NAMIC_LongTimeSeries.pptx‎|slides]])<br>
 
−
| style="background:#dbf3ff; color:black"|Project Review
 
−
|-
 
−
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
 
−
| style="background:#dbf3ff; color:black"| Lunch
 
−
| style="background:#dbf3ff; color:black"| Lunch <br>  
 
−
| style="background:#dbf3ff; color:black"| Lunch<br>  
 
−
| style="background:#F2E5D3; color:black"| Lunch
 
−
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn
 
 
|-
 
|-
−
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
+
| style="background:#CEE3F6; color:black"| '''<font color=black>9</font>'''
−
| style="background:#dbf3ff; color:black"|1:00 '''Welcome''' <br> Ron Kikinis <br> [[2011_Winter_Project_Week:Segment-a-spine|Segment a spine challenge]] <br><br>1:10pm '''Project Introductions''' <br> All Project Leads <br>
+
| style="background:#CEE3F6; color:black"; align="left"|Evalutation of the tool on testing datasets
−
| style="background:#dbf3ff; color:black"|1-2pm: [[2011 Winter Project Week:Breakout Pathology and Longitudinal Followup|Breakout: Pathology and Longitudinal Followup]] <br> (Guido Gerig) <br> [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)]<br>
+
| style="background:#ffffff; color:black"| '''<font color=black>10/20/11</font>'''
−
2-3pm: [[2011 Winter Project Week:Breakout ShapeWorks|Breakout: Particle Shape Correspondence]] <br> (Martin Styner, Tom Fletcher, Ross Whitaker) <br> (Arches)<br>
+
| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
−
| style="background:#dbf3ff; color:black"|Project Work 
+
| style="background:#dbf3ff; color:black"|'''Almost..'''
−
| style="background:#F2E5D3; color:black"|
 
−
 
 
−
'''1:00-2:30 Engineering'''<br>
 
−
:1:00-1:15 2010 Highlights, Aims, Architecture, Will Schroeder ([[Media:AHM2011-Core1b-Engineering-Architecture.ppt|slides]])<br>
 
−
:1:15-1:30 End User Platform Slicer 4, Steve Pieper ([[Media:AHM2011-Core1b-Engineering-EndUserPlatform.ppt|slides]])<br>
 
−
:1:30-1:45 Computational Platform, CLI, Jim Miller ([[Media:AHM2011-Core1b-Engineering-ComputationalPlatform.ppt|slides]])<br>
 
−
:1:45-2:00 Data Management Platform, Stephen Aylward ([[Media:AHM2011-Core1b-Engineering-DataManagement.ppt|slides]])<br>
 
−
:2:00-2:15 Software Process, Stephen Aylward ([[Media:AHM2011-Core1b-Engineering-SoftwareProcess.ppt|slides]])<br>
 
−
'''2:30-3:00 Outreach and Training''' (Sonia Pujol) ([[Media:NA-MIC_TrainingOutreach_AHM2011_SoniaPujol.ppt‎|slides]])
 
−
| style="background:#ffffff; color:black"|
 
 
|-
 
|-
−
| style="background:#eeeeee; color:black"|'''05:00-07:00'''  
+
| style="background:#CEE3F6; color:black"| '''<font color=black>10</font>'''
−
| style="background:#dbf3ff; color:black"|
+
| style="background:#CEE3F6; color:black"; align="left"|Write and complete the thesis
−
| style="background:#dbf3ff; color:black"|4:30-6:30<br>[[2011_Winter_Project_Week:Breakout_Slicer#Afternoon_Qt_Loadable_Module_Tutorial|How to write a loadable module]](J2, JC)
+
| style="background:#ffffff; color:black"| '''<font color=black>10/15/11</font>'''
−
| style="background:#dbf3ff; color:black"|
+
| style="background:#dbf3ff; color:black"|'''<font color=green>OPEN</font>'''
−
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
+
| style="background:#dbf3ff; color:black"|'''Almost..'''
−
| style="background:#ffffff; color:black"|
 
 
|}
 
|}
−
 
−
 
−
 
−
 
−
1. Task
 
−
* Find out how to use .UI files in Python (Slicer4). <font color=green>DONE</font>
 
−
* Result: Shown at http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers:Projects:QtSlicer/Tutorials/PythonAndUIFile
 
−
2. Task (until 03/11/11)
 
−
* Write expose for diploma thesis, find enough references. <font color=red>OPEN</font>
 
−
* Result:
 
−
3. Task (until 02/24/11)
 
−
* Implement a simple program in Python to run through an array (x,y,z,radius), find the points where the radius is < THRESHOLD and save the detected segments in an array. Select a reasonable threshold. This will help to detect stenosis.
 
−
* Result: Loop through array realized. Stenosis are now found when radius is below a hard-coded threshold and put into a container <font color=green>DONE</font>
 
−
4. Task
 
−
* Look at Slicer4/QTScriptedModules/Scripts/Editor.py and Slicer4/QTScriptedModules/EditorLib to figure out how to split Python module to different files in Slicer4. <font color=green>DONE</font>
 
−
* Result: The module itself is a .py file in QTScriptedModules/Scripts. It is possible to include a directory with other Python Scripts in QTScriptedModules/XXX where XXX is a custom name. Then, in the .py File in Scripts, an import XXX has to be placed. This will call the XXX/__init__.py file and can include other files.
 
−
5. Task
 
−
* Modify VMTKCenterlines in Slicer3 to include a button to perform the code of Task 3 on a vtkPolyData object. The centerlines are polyData. Add the new method to the logic class of VMTKCenterlines. This will be the algorithm to detect stenosis. <font color=green>DONE</font>
 
−
6. Task (until 03/16/11)
 
−
* A pixel in 2D has always 8 neighbors. Write code in Python to do the following: Create a 2D array (maybe a 16x16 matrix?). Take a random element in the middle of the array and loop in the directions of all 8 neighbors (top, bottom, left, right, diagonal left to top, diagonal left to bottom, diagonal right to top, diagonal right to bottom) until you reach the end of the matrix. If this is finished we can modify it to detect the maximal diameter of a vessel through one click. We will extend it then to 3D. If you want, skip 2D and start directly with 3D (16x16x16 matrix). <font color=red>OPEN</font>
 
−
* Result:
 
−
7.Task (until 04/01/11)
 
−
* We use the gradient (deltaX) to compute the difference between radii of two points to distinguish if a stenosis is present or not in a relative fashion. Prepare the derivation for the formulas used and proof them for the thesis! <font color='red'>OPEN</font>
 
−
* Result:
 
−
8. Task (until 03/18/11)
 
−
* Write a container class in Python to save two coordinates (x,y,z) and a radius. <font color='red'>OPEN</font>
 
−
9. Task (until 03/23/11)
 
−
* Write code in Python to do the following: Use the container from Task 8 to save the results from Task 6. So, these two tasks have to be completed before starting this one. Then, extend Task 6 to store the user click and the touch of the diameter in the container. Finally, use the values of the container to probe an intensity value exactly at the following location: the point on the line between the two coordinates in the container and the distance 2*radius from the first coordinate. <font color='red'>OPEN</font>
 
−
10. Task (until 03/25/11)
 
−
* Use the intensity values from the user clicked point of Task 6 and the probed position of Task 9 to calculate a contrast measure between these two points. The measure should be low (less than 50) if the intensity values are similar and high (around 100-200) if the contrast is high. <font color='red'>OPEN</font>
 
−
11. Task (until 04/15/11)
 
−
* Use the output of task 10 as parameter gamma for Frangi's VesselEnhancement. Use also proper values as discussed for alpha and beta. Also, Integrate the click-to-diameter functionality. Then, you should have a parameter free vesselness module where the user only clicks once to configure the filter. <font color='red'>OPEN</font>
 

Latest revision as of 12:19, 18 October 2011

Home < User talk:Tamekue

Diploma Thesis - Tasks

Time line table

Task number Tasks Deadlines Status Comments
1 Design a prototyp of a wizard based graphical user interface. 12/01/10 DONE
2 Implement the designed graphical user interface so that we can run it and navigate through the different wizard steps. 12/22/10 DONE
3 Implement a separate algorithm in python, which parse an array containing array elements representing centerline points with associated diameter.
Define a threshold value for diameters. The algorithm should detect all line segments, where associated diameters are less than the defined threshold value and save them in a container. 		02/08/11 DONE
4 Use the VMTK modules avaible in Slicer 3 to extract and generate a sample of lumen line from a chosen dataset containing stenosis.

Create a temporary stenosis detector molude in Slicer 3.
Import and customize the algorithm implemented at task 3, so that stenosis may be marked and visualized in 3D view. Run and test the created module.

02/20/11 DONE
5 Write expose for diploma thesis, find enough references. 03/13/11 DONE
6 Transcribe the implemented graphical user interface with all wizard steps using python and import it into the module created above. 03/31/11 DONE
7 Extend the implementation of the module adding and customizing all different image processing steps (vessel enhancement, level-set segmentation, network extraction, centerline extraction and stenosis detection).
We will hereby be dealing with the automation of our tool, which improves the user-friendliness by reducing the number of parameters usually required through the graphical user interface and with interactions between the different wizard steps. 		05/15/11 DONE
8 Design and implement and test a diagramm, which gives an estimation of the stenosis detection results with different stenosis stages.
This will be include into evaluation step (last wizard step) of our module. 		06/20/11 DONE
9 Evalutation of the tool on testing datasets 10/20/11 DONE Almost..
10 Write and complete the thesis 10/15/11 OPEN Almost..
Retrieved from "https://www.na-mic.org/w/index.php?title=User_talk:Tamekue&oldid=71450"