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Millerjv: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Module Name=== Voting Binary Hole Filling {| |Caption 1 |[[Image:…'

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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
Voting Binary Hole Filling

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
Applies a voting operationin order to fill-in cavities.
This can be used for smoothing contours and for filling holes in binary
images.

Similar capabilities are available in the Editor module as the Island Removal tool.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module can be used to fill in small holes in a segmentation, such as segmentations resulting from simple thresholding.
* This technique is used frequently when segmenting complete organs that may have ducts or vasculature that may not have been included in the initial segmentation, e.g. lungs, kidneys, liver.

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Binary Hole Filling Parameters:'''
** '''Maximum radius''' The radius of the hole to be filled
** '''Majority threshold''' The number of pixels over 50% that will decide whether an OFF pixel
will become ON or not. For example, if the neighborhood of a pixel has
124 pixels (excluding itself), the 50% will be 62, and if you set upd
a Majority threshold of 5, that means that the filter will require 67
or more neighbor pixels to be ON in order to switch the current OFF
pixel to ON.
** '''Background''' The value associated with the background (not object)
** '''Foreground''' The value associated with the foreground (object)
* '''IO panel:'''
** '''Input volume''' Volume to be processed
** '''Output volume''' Volume with holes filled by the algorithm

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/VotingBinaryHoleFillingImageFilter.cxx?view=annotate VotingBinaryholeFillingImageFilter.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/VotingBinaryHoleFillingImageFilter.cxx?view=co VotingBinaryholeFillingImageFilter.xml]

Usage:
<pre>
./VotingBinaryHoleFillingImageFilter [--processinformationaddress
<std::string>] [--xml] [--echo]
[--foreground <int>] [--background
<int>] [--majorityThreshold <int>]
[--radius <std::vector<int>>] [--]
[--version] [-h] <std::string>
<std::string>

Where:

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--foreground <int>
The value associated with the foreground (object) (default: 255)

--background <int>
The value associated with the background (not object) (default: 0)

--majorityThreshold <int>
The number of pixels over 50% that will decide whether an OFF pixel
will become ON or not. For example, if the neighborhood of a pixel has
124 pixels (excluding itself), the 50% will be 62, and if you set upd
a Majority threshold of 5, that means that the filter will require 67
or more neighbor pixels to be ON in order to switch the current OFF
pixel to ON. (default: 1)

--radius <std::vector<int>>
The radius of a hole to be filled (default: 1,1,1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Output filtered

Description: Applies a voting operationin order to fill-in cavities.
This can be used for smoothing contours and for filling holes in binary
images.

Author(s): Bill Lorensen

Acknowledgements: This command module was derived from
Insight/Examples/Filtering/MedianImageFilter (copyright) Insight
Software Consortium
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

@@ Line 5: / Line 5: @@
 {|
-|[[Image:VotingBinaryHoleFilling.png |thumb|600px|(Red) Original image. (Yellow) Otsu threshold. (Green) Voting binary hole filling of Otsu threshold.]]
+|[[Image:VotingBinaryHoleFilling.png |thumb|600px|(Red) Original image. (Yellow) Otsu threshold. (Green) Voting binary hole filling with a "Maximum radius" of "15,15,1" on the Otsu thresholded image.]]
 |}

@@ Line 5: / Line 5: @@
 {|
-|[[Image:VotingBinaryHoleFilling.png |thumb|280px|(Red) Original image. (Yellow) Otsu threshold. (Green) Voting binary hole filling of Otsu threshold.]]
+|[[Image:VotingBinaryHoleFilling.png |thumb|600px|(Red) Original image. (Yellow) Otsu threshold. (Green) Voting binary hole filling of Otsu threshold.]]
 |}

@@ Line 5: / Line 5: @@
 {|
-|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
+|[[Image:VotingBinaryHoleFilling.png |thumb|280px|(Red) Original image. (Yellow) Otsu threshold. (Green) Voting binary hole filling of Otsu threshold.]]
 |}

@@ Line 60: / Line 60: @@
 ===Known bugs===
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.
 ===Usability issues===

Modules:VotingBinaryHoleFilling-Documentation-3.6 - Revision history

Millerjv: /* Module Name */

Millerjv: /* Module Name */

Millerjv: /* Module Name */

Millerjv: /* Known bugs */

Millerjv: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Voting Binary Hole Filling {| |Caption 1 |[[Image:…'

Millerjv: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Module Name=== Voting Binary Hole Filling {| |Caption 1 |[[Image:…'