Modules:GrayscaleModelMaker-Documentation-3.6 - Revision history

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2019-11-27T13:16:25Z

Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

Lorensen: Updated links

2013-07-23T03:43:58Z

Updated links

Kikinis: /* Module Name */

2011-10-20T02:10:43Z

Module Name

Kikinis: /* Module Name */

2011-10-20T02:09:28Z

Module Name

Pieper: /* References */

2011-10-17T11:41:52Z

References

Nicole: /* Use Cases, Examples */

2010-06-10T20:22:41Z

Use Cases, Examples

Nicole at 20:22, 10 June 2010

2010-06-10T20:22:13Z

Lorensen at 11:39, 29 April 2010

2010-04-29T11:39:50Z

Lorensen: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Module Name=== Grayscale Model Maker {| |Input Image |[[Image:Sample2.pn…'

2010-04-29T11:26:24Z

Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Grayscale Model Maker {| |thumb|280px|Input Image |[[Image:Sample2.pn…'

New page

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Grayscale Model Maker

{|
|[[Image:Sample1.png|thumb|280px|Input Image]]
|[[Image:Sample2.png|thumb|280px|Median Filtered Image]]
|}

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

Type: CLI

Category: Surface Models

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

===Module Description===
Create 3D surface models from grayscale data. This module
uses Marching Cubes to create an isosurface at a given threshold. The
resulting surface consists of triangles that separate a volume into
regions below and above the threshold. The resulting surface can be
smoothed and decimated. This model works on continuous data while the
module Model Maker works on labeled (or discrete) data.

== Usage ==
<pre>
GrayscaleModelMaker
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--pointnormals] [--splitnormals]
[--decimate <float>] [--smooth
<int>] [-n <std::string>] [-t
<float>] [--] [--version] [-h]
<std::string> <std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--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)

--pointnormals
Calculate the point normals? Calculated point normals make the surface
appear smooth. Without point normals, the surface will appear faceted.
(default: 0)

--splitnormals
Splitting normals is useful for visualizing sharp features. However it
creates holes in surfaces which affect measurements (default: 0)

--decimate <float>
Target reduction during decimation, as a decimal percentage reduction
in the number of polygons. If 0, no decimation will be done. (default:
0.25)

--smooth <int>
Number of smoothing iterations. If 0, no smoothing will be done.
(default: 15)

-n <std::string>, --name <std::string>
Name to use for this model. (default: Model)

-t <float>, --threshold <float>
Grayscale threshold of isosurface. The resulting surface of triangles
separates the volume into voxels that lie above (inside) and below
(outside) the threshold. (default: 100)

--, --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) Volume containing the input grayscale data.

<std::string>
(required) Output that contains geometry model.
</pre>

== Development ==

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

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

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/GrayscaleModelMakerTest.cxx?rev=11537&view=log GrayscaleModelMakerTest.cxx]

== 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 36: / Line 36: @@
 |-
-|Program documentation-url || http://www.slicer.org/slicerWiki/index.php/Modules:GrayscaleModelMaker-Documentation-3.6
+|Program documentation-url || https://www.slicer.org/wiki/Modules:GrayscaleModelMaker-Documentation-3.6 |-
 |}

@@ Line 6: / Line 6: @@
 {|
-|[[Image:GMMSkin.png|thumb|280px|CT Study, Skin. Threshold=-300 Hounsfield]]
+|[[Image:GMMSkin.png|thumb|280px|CT Study, Skin. Threshold=-300 [http://en.wikipedia.org/wiki/Hounsfield_scale Hounsfield Units]]]
-|[[Image:GMMBone.png|thumb|280px|CT Study, Bone. Threshold=200 Hounsfield]]
+|[[Image:GMMBone.png|thumb|280px|CT Study, Bone. Threshold=200 [http://en.wikipedia.org/wiki/Hounsfield_scale Hounsfield Units]]]
 |}

@@ Line 6: / Line 6: @@
 {|
-|[[Image:GMMSkin.png|thumb|280px|CT Study, Skin. Threshold=-300 hounsfeld]]
+|[[Image:GMMSkin.png|thumb|280px|CT Study, Skin. Threshold=-300 Hounsfield]]
-|[[Image:GMMBone.png|thumb|280px|CT Study, Bone. Threshold=200 hounsfeld]]
+|[[Image:GMMBone.png|thumb|280px|CT Study, Bone. Threshold=200 Hounsfield]]
 |}

← Older revision		Revision as of 11:41, 17 October 2011
Line 102:		Line 102:

	===References===		===References===
		+	Model smoothing is done using the windowed sinc algorithm:
		+	http://www.vtk.org/doc/nightly/html/classvtkWindowedSincPolyDataFilter.html#details

@@ Line 51: / Line 51: @@
 Examples of the module in use:
-* Example 1: to
+* Example 1: to create a model of the skin or bone from a volume
 * Example 2

@@ Line 86: / Line 86: @@
 ===Source code & documentation===
-Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GrayscaleModelMaker.cxx?view=annotate GrayscaleModelMaker.cxx]
+Source Code: [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.cxx?view=co GrayscaleModelMaker.cxx]
-XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/GrayscaleModelMaker.xml?view=co  GrayscaleModelMaker.xml]
+XML Description: [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.xml?view=co  GrayscaleModelMaker.xml]
 == More Information ==

@@ Line 22: / Line 22: @@
 ===Module Description===
 Create 3D surface models from grayscale data. This module
-uses Marching Cubes to create an isosurface at a given threshold. The
+{| style="color:green" border="1"
 resulting surface consists of triangles that separate a volume into
-regions below and above the threshold. The resulting surface can be
+|Program title || Grayscale Model Maker
-smoothed and decimated. This model works on continuous data while the
-module Model Maker works on labeled (or discrete) data.
+|-
 == Usage ==
-   --returnparameterfile <std::string>
+===Use Cases, Examples===
-   --processinformationaddress <std::string>
+This module is especially appropriate for these use cases:
-   --xml
+* Use Case 1: when have a continuous data set as input (ie grey scale volume)
-   --echo
+Examples of the module in use:
-   --pointnormals
+* Example 1: to
-     Calculate the point normals? Calculated point normals make the surface
+* Example 2
-   --splitnormals
+===Tutorials===
-   --decimate <float>
+* Tutorial 1
-     Target reduction during decimation, as a decimal percentage reduction
+** Data Set 1
-   --smooth <int>
+===Quick Tour of Features and Use===
-   -n <std::string>,  --name <std::string>
+A list panels in the interface, their features, what they mean, and how to use them.
-   -t <float>,  --threshold <float>
+{|
-     Grayscale threshold of isosurface. The resulting surface of triangles
-     separates the volume into voxels that lie above (inside) and below
+* <span style="color:blue">'''''IO''''' </span>
-     (outside) the threshold. (default: 100)
+** <span style="color:green">'''Input Volume'''</span>  : Volume containing the input grayscale data.
-   --version
+* <span style="color:blue">'''''Grayscale Model Maker Parameters''''' </span>
-     Displays version information and exits.
+** <span style="color:green">'''Threshold'''</span> [<span style="color:orange">----threshold</span>] [<span style="color:pink">--t</span>]: Grayscale threshold of isosurface. The resulting surface of triangles separates the volume into voxels that lie above (inside) and below (outside) the threshold. ''Default value: 100.0''
-   <std::string>
+|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
-     (required)  Volume containing the input grayscale data.
+|}
 == Development ==

Modules:GrayscaleModelMaker-Documentation-3.6 - Revision history

Grundlett: Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

Lorensen: Updated links

Kikinis: /* Module Name */

Kikinis: /* Module Name */

Pieper: /* References */

Nicole: /* Use Cases, Examples */

Nicole at 20:22, 10 June 2010

Lorensen at 11:39, 29 April 2010

Lorensen: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Grayscale Model Maker {| |Input Image |[[Image:Sample2.pn…'

Lorensen: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Module Name=== Grayscale Model Maker {| |Input Image |[[Image:Sample2.pn…'