Documentation/4.3/Modules/SurfaceToolbox - Revision history

Lantiga at 23:41, 7 November 2013

2013-11-07T23:41:55Z

Lantiga at 22:55, 7 November 2013

2013-11-07T22:55:14Z

Lantiga at 22:53, 7 November 2013

2013-11-07T22:53:04Z

Lantiga at 22:35, 7 November 2013

2013-11-07T22:35:06Z

Lantiga at 22:33, 7 November 2013

2013-11-07T22:33:39Z

Lantiga at 22:15, 7 November 2013

2013-11-07T22:15:05Z

Lantiga at 22:14, 7 November 2013

2013-11-07T22:14:40Z

Lantiga at 22:03, 7 November 2013

2013-11-07T22:03:20Z

Lantiga at 22:02, 7 November 2013

2013-11-07T22:02:57Z

Lantiga at 21:55, 7 November 2013

2013-11-07T21:55:58Z

← Older revision		Revision as of 23:41, 7 November 2013
Line 48:		Line 48:

	Connectivity can be employed after the extraction of an isosurface using Grayscale Model Maker, in order to get rid of tiny pieces of surface associated to noise with intensity greater than the isosurface level.		Connectivity can be employed after the extraction of an isosurface using Grayscale Model Maker, in order to get rid of tiny pieces of surface associated to noise with intensity greater than the isosurface level.
		+
		+	{\|
		+	\|[[Image:SurfaceToolbox_Original.png\|thumb\|520px\|Surface obtained using Grayscale Model Maker]]
		+	\|[[Image:SurfaceToolbox_Filtered.png\|thumb\|520px\|Filtered surface]]
		+	\|}

	<!-- ---------------------------- -->		<!-- ---------------------------- -->

← Older revision		Revision as of 22:55, 7 November 2013
Line 107:		Line 107:

	An updateGUI function is defined within the setup method, where controls take values from the state object. At the end of the setup method, self.updateGUI is set to the updateGUI function defined in setup. This allows updateGUI to close over (see [http://en.wikipedia.org/wiki/Closure_(computer_science) closures]), all widget objects instantiated in the setup method. This bypasses the need for making every widget an instance variable and having it connect to an instance method, achieving greater conciseness. An analogous technique is used for the onApply and onToggleModels functions, which are defined in the setup method body and then directly passed to the connect method of the respective widgets.		An updateGUI function is defined within the setup method, where controls take values from the state object. At the end of the setup method, self.updateGUI is set to the updateGUI function defined in setup. This allows updateGUI to close over (see [http://en.wikipedia.org/wiki/Closure_(computer_science) closures]), all widget objects instantiated in the setup method. This bypasses the need for making every widget an instance variable and having it connect to an instance method, achieving greater conciseness. An analogous technique is used for the onApply and onToggleModels functions, which are defined in the setup method body and then directly passed to the connect method of the respective widgets.
		+
		+	The SurfaceToolboxLogic class is in charge of executing the filtering pipeline. It is a stateless class, its applyFilters method takes the state defined in SurfaceToolboxWidget's setup method as an argument and configures the processing pipeline accordingly.

	The module internally uses the following VTK filters:		The module internally uses the following VTK filters:

@@ Line 38: / Line 38: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Use Cases}}
 The module is appropriate when a surface has been extracted (e.g. with the Model Maker module) but its appearance has to be improved.
@@ Line 59: / Line 57: @@
 {|
-|[[Image:SurfaceToolbox.png|thumb|640px|SurfaceToolbox User Interface]]
+|[[Image:SurfaceToolbox.png|thumb|520px|SurfaceToolbox User Interface]]
 |}
@@ Line 103: / Line 101: @@
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
 {{documentation/{{documentation/version}}/module-developerinfo}}
 The module internally uses the following VTK filters:

@@ Line 39: / Line 39: @@
 {{documentation/{{documentation/version}}/module-section|Use Cases}}
@@ Line 60: / Line 57: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Panels}}
 Select the input and output models, and then enable the stages of the pipeline by selecting the buttons. Stages that include parameters will open up when they are enabled. Click apply to activate the pipeline and then click the Toggle button to compare the model before and after the operation.
 ** ''Input Model'': the input model

@@ Line 27: / Line 27: @@
 * Decimation: topology-preserving reduction of surface triangles
-* Smoothing: surface regularization using a Laplacian filter or Taubin's non-shrinking algorithm
+* Smoothing: surface regularization using a Laplacian filter or Taubin's [1] non-shrinking algorithm
 * Normals: generation of surface normals (for geometry algorithms or for improving visualization, since surface shading rendering needs normals to be defined on the surface)
 * Cleaner: merging of coincident points, removal of unused points (i.e. not used by any cell), treatment of degenerate cells
@@ Line 44: / Line 44: @@
-The module is appropriate when a surface has been extracted (e.g. with the Modelmaker module) but its appearance has to be improved.
+The module is appropriate when a surface has been extracted (e.g. with the Model Maker module) but its appearance has to be improved.
 This module supports various cleanup and optimization processes on surface models.  For example, a noisy image data set can lead to models that have bumpy surfaces which do not accurately depict the actual anatomy of interest.  In this case, the model can be smoothed to better approximate the actual surface.
@@ Line 73: / Line 73: @@
 * '''Smoothing:'''
 ** ''Enabled'': enable surface smoothing.
-** ''Smoothing method'': choose between Laplace or Taubin surface smoothing algorithms (while Taubin is a non-shrinking filter, Laplace will tend to shrink the surface under the effect of curvature).
+** ''Smoothing method'': choose between Laplace or Taubin [1] surface smoothing algorithms (while Taubin is a non-shrinking filter, Laplace will tend to shrink the surface under the effect of curvature).
 ** ''Boundary smoothing'': allow smoothing of points located on the boundary of the surface.
 ** ''Laplace number of iterations'': number of iterations set when the Laplace algorithm is selected.
@@ Line 97: / Line 97: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
-N/A
 <!-- ---------------------------- -->

@@ Line 92: / Line 92: @@
 ** ''Clicked'': toggle the visualization of the input or the output model, allowing to compare them and visualize the effect of filtering.
 * '''Apply:'''
-* ''Clicked'': apply the pipeline of all Enabled filters to the input model and produce the output model.
+** ''Clicked'': apply the pipeline of all Enabled filters to the input model and produce the output model.

@@ Line 50: / Line 50: @@
 Another application is to reduce the geometric complexity of surface models using decimation to reduce the file size or rendering time of the models.
-Normals are used to improve the visual appearance of STL surfaces rendered as flat polygons due to a lack in normal information. Activating Splitting, feature edges (i.e. seams in the surface) will be visually enhanced through the creation of a discontinuity in surface normal orientation producing a discontinuity in surface shading.
+Normals are used to improve the visual appearance of STL surfaces rendered as flat polygons due to a lack in normal information. Normals should also be recomputed after smoothing, since smoothing doesn't re-orient normals and shading depends on normal orientation. Activating Splitting, feature edges (i.e. seams in the surface) will be visually enhanced through the creation of a discontinuity in surface normal orientation producing a discontinuity in surface shading.
 Connectivity can be employed after the extraction of an isosurface using Grayscale Model Maker, in order to get rid of tiny pieces of surface associated to noise with intensity greater than the isosurface level.
@@ Line 64: / Line 64: @@
-* '''Surface Decimation:'''
+** ''Input Model'': the input model
 ** ''Enabled'': enable topology-preserving surface decimation.
 ** ''Target reduction'': target percentage reduction in number of triangles (this target reduction may not be achieved depending on the constraints on the topology).
 ** ''Boundary vertex deletion'': allow deletion of points located on the boundary of the surface.
-* '''Surface Smoothing:'''
+* '''Smoothing:'''
 ** ''Enabled'': enable surface smoothing.
 ** ''Smoothing method'': choose between Laplace or Taubin surface smoothing algorithms (while Taubin is a non-shrinking filter, Laplace will tend to shrink the surface under the effect of curvature).
@@ Line 76: / Line 79: @@
 ** ''Taubin number of iterations'': number of iterations set when the Taubin algorithm is selected.
 ** ''Taubin passband'': spatial frequency cutoff for the Taubin algorithm.
-* '''Surface Normals:'''
+* '''Normals:'''
 ** ''Enabled'': enable computation of consistently-oriented surface normals (advised after smoothing - smoothing algorithms only move points and do not update normals accordingly, so the surface might still look non-smooth after smoothing when Gouraud shading is used).
 ** ''Flip normals'': toggle direction of normals - the algorithm will do its best to orient the normals consistently "outwards" a surface, if the surface is orientable. This switch will make normals point "inwards"
 ** ''Splitting'': toggle splitting of surface when angle between the normals of two neighboring triangles is above the Feature angle. This improves the shading appearance of sharp edges but produces topological holes in the surface.
 ** ''Feature angle'': angle (in degrees) between two neighboring triangles beyond which the edge between the triangles is split.
-* '''Surface Cleaner:'''
+* '''Cleaner:'''
 ** ''Enabled'': enable cleaning (merging of coincident points, elimination of unused points, treatment of degenerate cells) of the surface.
-* '''IO:'''
+* '''Connectivity:'''
-** ''Input Surface'': the input surface
+** ''Enabled'': enable extracting the largest connected portion of the surface and getting rid of the rest.
-** ''Output Surface'': the output surface, i.e. the input surface filtered through all the "Enabled" filters.
 <!-- ---------------------------- -->

@@ Line 7: / Line 7: @@
 {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
-* Luca Antiga: Orobix Srl & Mario Negri Institute
+* Luca Antiga: Orobix Srl
 * Daniel Blezek: Mayo Clinic
 * Ron Kikinis, BWH
@@ Line 23: / Line 23: @@
 {{documentation/{{documentation/version}}/module-section|Module Description}}
 {{documentation/{{documentation/version}}/module-description}}
 <!-- ---------------------------- -->