AHM 2007:Slicer3 Developer Feedback - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:30Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Melonakos at 18:38, 6 November 2008

2008-11-06T18:38:29Z

Lauren: /* Module Architecture */

2007-01-10T18:24:22Z

Module Architecture

Lauren: /* Feedback on Slicer3 */

2007-01-10T18:23:40Z

Feedback on Slicer3

Lauren: /* Module Architecture */

2007-01-10T18:22:57Z

Module Architecture

Lauren: /* Module Architecture */

2007-01-10T18:21:50Z

Module Architecture

Lauren: /* What I would like in Slicer3 base... */

2007-01-10T18:20:27Z

What I would like in Slicer3 base...

Davisb: /* Feedback */

2007-01-10T18:17:01Z

Feedback

Lauren: /* What I would like in Slicer3 base... */

2007-01-10T18:15:41Z

What I would like in Slicer3 base...

Lauren: /* What I would like in Slicer3 base... */

2007-01-10T18:15:12Z

What I would like in Slicer3 base...

@@ Line 68: / Line 68: @@
 ===Module Description===
-The following description is from the [http://www.slicer.org/slicerWiki/index.php/Slicer3:EM#Old_.282007.29_Tutorial project wiki page]:
+The following description is from the [https://www.slicer.org/wiki/Slicer3:EM#Old_.282007.29_Tutorial project wiki page]:
 The goal of this project is the creation of a module in Slicer 3 integrating the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data set. However, the configuration of the algorithm is greatly simplified in Slicer 3 as the user is guided by a work flow. The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist.
@@ Line 106: / Line 106: @@
 The EM GUI includes eight steps implemented with KWWidgets and vtkKWWizardWorkflow framework. Each step is written as a single class, derived from a super class vtkEMSegmentStep. All steps are initialized with parameters from the vtkKWEMSegmentLogic class, and once a user interacts with the UI, the new parameters (if there are) will be passed to the logic class immediately.
-There is also a brief description of these steps in the [http://www.slicer.org/slicerWiki/index.php/Slicer3:EM#Old_.282007.29_Tutorial project wiki page]:
+There is also a brief description of these steps in the [https://www.slicer.org/wiki/Slicer3:EM#Old_.282007.29_Tutorial project wiki page]:
 *1/8 vtkEMSegmentParametersSetStep: Select parameter set or create new parameters

@@ Line 68: / Line 68: @@
 ===Module Description===
-The following description is from the [[Slicer3:EM |project wiki page]]:
+The following description is from the [http://www.slicer.org/slicerWiki/index.php/Slicer3:EM#Old_.282007.29_Tutorial project wiki page]:
 The goal of this project is the creation of a module in Slicer 3 integrating the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data set. However, the configuration of the algorithm is greatly simplified in Slicer 3 as the user is guided by a work flow. The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist.
@@ Line 106: / Line 106: @@
 The EM GUI includes eight steps implemented with KWWidgets and vtkKWWizardWorkflow framework. Each step is written as a single class, derived from a super class vtkEMSegmentStep. All steps are initialized with parameters from the vtkKWEMSegmentLogic class, and once a user interacts with the UI, the new parameters (if there are) will be passed to the logic class immediately.
-There is also a brief description of these steps in the [[Slicer3:EM |project wiki page]]:
+There is also a brief description of these steps in the [http://www.slicer.org/slicerWiki/index.php/Slicer3:EM#Old_.282007.29_Tutorial project wiki page]:
 *1/8 vtkEMSegmentParametersSetStep: Select parameter set or create new parameters

@@ Line 40: / Line 40: @@
 * MRML details
 ** Tractography is represented as a vtkMRMLFiberBundleNode.  Display parameters are stored in a vtkMRMLFiberBundleDisplayNode, and storage (load/save) handled by vtkMRMLFiberBundleStorageNode.  Basic operations of adding new fiber bundles, etc. are in vtkMRMLFiberBundleLogic.
-** vtkMRMLFiberBundleDisplayLogic is needed to create "hidden" slicer models that will be rendered in the MRML scene. Otherwise base classes would have to be heavily edited to handle tractography display using the display node.
+** NEW: vtkMRMLFiberBundleDisplayLogic is needed to create "hidden" slicer models that will be rendered in the MRML scene. Otherwise base classes would have to be heavily edited to handle tractography display using the display node.
 * Base edited to add this new type (list under construction)
 ** Slicer3.cxx

@@ Line 47: / Line 47: @@
 ===Feedback on Slicer3 ===
 * Most of my feedback is that there is a bit of a learning curve and I spent a few weeks reading over code before doing anything in my module. However Steve and Alex have been very helpful. Specific things that were/are difficult include:
-* When adding a new module and a new datatype, it is difficult to find the places in Base code that must be edited.
+** When adding a new module and a new datatype, it is difficult to find the places in Base code that must be edited.
-* It is also difficult to understand how the MRML callback happens, and how to set a new one up.  It would be great to have a simple overview on the observers somewhere.
+** It is also difficult to understand how the MRML callback happens, and how to set a new one up.  It would be great to have a simple overview on the observers somewhere.
-* If a vtkMRMLNode inherits from another one used in slicer (for example mine inherits from the modelNode currently) then the subclass will show up on all of the superclass menus. This is because the vtk "IsA" function is used rather than a direct match.  I believe this is feature that is not desired.
+** I also have trouble understanding how the MRML file is read in, and how my module can do the "special" things it needs to do (set up logic for display of nodes read in).
-* I also have trouble understanding how the MRML file is read in, and how my module can do the "special" things it needs to do (set up logic for display of nodes read in).
+** Finally, I would love a tutorial or documentation on the existing interactor functionality in 2D/3D (how do I get mouse clicks in RAS coordinates?, what's the best way to add a picker to the scene?)
 * Finally, I would love a tutorial or documentation on the existing interactor functionality in 2D/3D (how do I get mouse clicks in RAS coordinates?, what's the best way to add a picker to the scene?)
 ===What I would like in Slicer3 base...===

@@ Line 41: / Line 41: @@
 ** Tractography is represented as a vtkMRMLFiberBundleNode.  Display parameters are stored in a vtkMRMLFiberBundleDisplayNode, and storage (load/save) handled by vtkMRMLFiberBundleStorageNode.  Basic operations of adding new fiber bundles, etc. are in vtkMRMLFiberBundleLogic.
 ** vtkMRMLFiberBundleDisplayLogic is needed to create "hidden" slicer models that will be rendered in the MRML scene. Otherwise base classes would have to be heavily edited to handle tractography display using the display node.
-* Base edited (list under construction)
+* Base edited to add this new type (list under construction)
 ** Slicer3.cxx
 ** vtkMRMLScene.cxx

@@ Line 54: / Line 54: @@
 * For CLP tractography in whole brain: ability to seed in RAS, return tracts as models with an attribute (?) saying they're tracts for subsequent conversion to fiberBundleNodes (Should this be CLP or interactive where user can see fibers as seeded?)
 * Efficient bundle display...
 =EM=

@@ Line 135: / Line 135: @@
 *seperating logic from GUI was a key aspect of developing this module, as it allowed Brad David to focus on the logic, while Yumin and myself (Sebastien) would write the GUI. We started by defining a clean API for the logic and a Powerpoint mockup for the GUI. Brad wrote the corresponding API header and an empty implementation, while we would code the GUI elements and connect them to the logic through the API. Soon after, we added methods to stress-test the API and populate Slicer3 nodes with fake-data so as to test the functionalities of both th elogic and the GUI. Once the piece of the puzzles were in and the most critical bugs were found, we included a real-life dataset for testing.
-[[Media:EMFeedback2.ppt | Feedback slides]]
+[[Media:EMFeedback3.ppt | Feedback slides]]
 =IGT =

@@ Line 53: / Line 53: @@
 * More documentation, comments, etc.
 * For CLP tractography in whole brain: ability to seed in RAS, return tracts as models with an attribute (?) saying they're tracts for subsequent conversion to fiberBundleNodes
 =EM=