Difference between revisions of "User talk:Tamekue"

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=== Diploma Thesis - Tasks ===
 
=== Diploma Thesis - Tasks ===
  
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1. Task
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== Time line table==
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* Find out how to use .UI files in Python (Slicer4). <font color=green>DONE</font>
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{| border="1" cellpadding="5"
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* Result: Shown at http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers:Projects:QtSlicer/Tutorials/PythonAndUIFile
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|- style="background:#eeeeee; color:black" align="center"
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2. Task (until 03/04/11)
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| style="width:1%" | '''Task number'''
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* Write expose for diploma thesis, find enough references. Write it first in Microsoft Word, later we have to write the text in LaTeX. <font color=red>OPEN</font>
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| style="width:20%" | '''Tasks'''
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* Result: ?
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| style="width:5%" | '''Deadlines'''
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3. Task (until 02/24/11)
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| style="width:4%" | '''Status'''
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* 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 later help to detect stenosis.
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| style="width:20%" | '''Comments'''
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* Result: Loop through array realized. Stenosis are now found when radius is below a hard-coded threshold. <font color=green>DONE</font>
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|-
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4. Task (until 02/21/11)
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| style="background:#CEE3F6; color:black"| '''<font color=black>1</font>'''
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* 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>
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| style="background:#CEE3F6; color:black"; align="left"| Design a prototyp of a wizard based graphical user interface.
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* 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.
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| style="background:#ffffff; color:#522200"| '''<font color=black>12/01/10</font>'''
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5. Task (until 03/04/11)
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| style="background:#dbf3ff; color:#522200"| '''<font color=green>DONE</font>'''
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* Modify VMTKCenterlines in Slicer3 to include a button to perform the code of Task 3 on a vtkPolyData object. The centerlines are polyData. Add your new method to the logic class of VMTKCenterlines. This will later be the algorithm to detect stenosis. <font color=red>OPEN</font>
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| style="background:#dbf3ff; color:#522200"|
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* The following code snippet should help:
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|-
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<pre>for i in range(polyData.GetNumberOfPoints()):
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| style="background:#CEE3F6; color:black"| '''<font color=black>2</font>'''
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| 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.  
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point = polyData.GetPoint(polyData.GetNumberOfPoints() - i - 1)
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| style="background:#ffffff; color:black"| '''<font color=black>12/22/10</font>'''
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| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
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# aktueller punkt ist x: point[0] y: point[1] z: point[2]
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| style="background:#dbf3ff; color:black"|
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|-
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array = polyData.GetPointData().GetArray("MaximumInscribedSphereRadius")
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| style="background:#CEE3F6; color:black"| '''<font color=black>3</font>'''
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| 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.  
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        # hier der radius
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| style="background:#ffffff; color:black"| '''<font color=black>02/08/11</font>'''
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diameter = array[0]
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| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
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| style="background:#dbf3ff; color:black"|
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        #benutze self._parentClass.GetHelper().debug("x") zur ausgabe
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|-
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</pre>
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| style="background:#CEE3F6; color:black"| '''<font color=black>4</font>'''
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6. Task (until 03/04/11)
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| 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>
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* 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>
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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.
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* Result: ?
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| style="background:#ffffff; color:black"|  '''<font color=black>02/20/11</font>'''
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7.Task (until 05/01/11)
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| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
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* 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>
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| style="background:#dbf3ff; color:black"|
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* Result: ?
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|-
 +
| style="background:#CEE3F6; color:black"| '''<font color=black>5</font>'''
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| style="background:#CEE3F6; color:black"; align="left"|Write expose for diploma thesis, find enough references.
 +
| style="background:#ffffff; color:black"| '''<font color=black>03/13/11</font>'''
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| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
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| style="background:#dbf3ff; color:black"|
 +
|-
 +
| style="background:#CEE3F6; color:black"| '''<font color=black>6</font>'''
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| 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.
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| style="background:#ffffff; color:black"| '''<font color=black>03/31/11</font>'''
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| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
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| style="background:#dbf3ff; color:black"|
 +
|-
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| style="background:#CEE3F6; color:black"| '''<font color=black>7</font>'''
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| 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:#ffffff; color:black"| '''<font color=black>05/15/11</font>'''
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| style="background:#dbf3ff; color:black"| '''<font color=green>DONE</font>'''
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| style="background:#dbf3ff; color:black"|
 +
|-"
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| style="background:#CEE3F6; color:black"| '''<font color=black>8</font>'''
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| 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.
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| style="background:#ffffff; color:black"| '''<font color=black>06/20/11</font>'''
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| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
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| style="background:#dbf3ff; color:black"|
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|-
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| style="background:#CEE3F6; color:black"| '''<font color=black>9</font>'''
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| style="background:#CEE3F6; color:black"; align="left"|Evalutation of the tool on testing datasets
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| style="background:#ffffff; color:black"| '''<font color=black>10/20/11</font>'''
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| style="background:#dbf3ff; color:black"|'''<font color=green>DONE</font>'''
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| style="background:#dbf3ff; color:black"|'''Almost..'''
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|-
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| style="background:#CEE3F6; color:black"| '''<font color=black>10</font>'''
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| style="background:#CEE3F6; color:black"; align="left"|Write and complete the thesis  
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| style="background:#ffffff; color:black"| '''<font color=black>10/15/11</font>'''
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| style="background:#dbf3ff; color:black"|'''<font color=green>OPEN</font>'''
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| style="background:#dbf3ff; color:black"|'''Almost..'''
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|}

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..
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