Documentation/Nightly/Modules/Volumes - Revision history

Lasso: Replaced content with "{{documentation/versioncheck}} {{documentation/banner | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/volumes.html This page..."

2020-08-21T16:42:03Z

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Hillarylia at 19:26, 5 July 2016

2016-07-05T19:26:34Z

Hillarylia at 15:05, 29 June 2016

2016-06-29T15:05:48Z

Hillarylia: Updated tutorial link

2016-05-12T15:50:05Z

Updated tutorial link

Lasso: /* How to create a volume node from scratch? */

2016-01-27T19:26:28Z

How to create a volume node from scratch?

Pinter: Convert scalar volume to labelmap how-to

2015-11-18T20:46:22Z

Convert scalar volume to labelmap how-to

Lasso: /* How to create a volume node from scratch? */

2015-11-10T21:22:10Z

How to create a volume node from scratch?

Lasso: /* How to create a volume node from scratch? */

2015-11-10T21:15:33Z

How to create a volume node from scratch?

Lasso at 21:12, 10 November 2015

2015-11-10T21:12:52Z

Nicole at 20:06, 5 May 2015

2015-05-05T20:06:52Z

@@ Line 25: / Line 25: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Use Cases}}
-*Use the SampleData module to load the MR Head volume.  You can control the scalar display options using this module.
+*Lookup tables/Colour palettes
-*Use the SampleData module to download the DTI Head volume.  A tensor-specific display interface will allow you to display a variety of scalar modes and display glyphs.
+**Information about the color nodes associated to volumes
 <!-- ---------------------------- -->

@@ Line 25: / Line 25: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Use Cases}}
-# Examples:
+*Use the SampleData module to load the MR Head volume.  You can control the scalar display options using this module.
-## Use the SampleData module to load the MR Head volume.  You can control the scalar display options using this module.
+*Use the SampleData module to download the DTI Head volume.  A tensor-specific display interface will allow you to display a variety of scalar modes and display glyphs.
-## Use the SampleData module to download the DTI Head volume.  A tensor-specific display interface will allow you to display a variety of scalar modes and display glyphs.
-# FAQ:
+<!-- ---------------------------- -->
-## [[Documentation/{{documentation/version}}/FAQ#How_to_overlay_2_volumes.3F|How to overlay 2 volumes?]]
+{{documentation/{{documentation/version}}/module-section|How to Use}}
-## [[Documentation/{{documentation/version}}/FAQ#How_to_load_data_from_a_sequence_of_jpg_files.3F|How to load data from a sequence of JPG files?]]
+*[[Documentation/{{documentation/version}}/FAQ#How_to_overlay_2_volumes.3F|How to overlay two volumes]]
-# When loading a 2D image(jpg, png, tiff ...), the window level(colors) might be skewed. To see the original colors switch the ''Window Level'' combobox to '''Manual Min/Max''', then set ''Min'' to '''0''' and ''Max'' to '''255'''.
+*[[Documentation/{{documentation/version}}/FAQ#How_to_load_data_from_a_sequence_of_jpg_files.3F|How to load data from a sequence of JPG files]]
-## Also use the Spacing field to enter the volumetric pixel sizes of the image data.
+*When loading a 2D image(jpg, png, tiff ...), the window level(colors) might be skewed. To see the original colors switch the ''Window Level'' combobox to '''Manual Min/Max''', then set ''Min'' to '''0''' and ''Max'' to '''255'''.
-## While you can display color volumes as slices, most slicer modules do not work natively with RGB or RGBA data, the new [http://slicer.org/doc/html/VectorToScalarVolume_8py_source.html VectorToScalarVolume] converter can be used to create a volume for use, for example, with the Editor. (added post-4.1).
+**Also use the Spacing field to enter the volumetric pixel sizes of the image data.
 <!-- ---------------------------- -->

@@ Line 38: / Line 38: @@
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-* Tutorial about [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training loading and viewing data].
+* Tutorial about [https://www.slicer.org/slicerWiki/images/5/51/3DDataLoadingandVisualization_Slicer4.5_SoniaPujol.pdf loading and viewing data].
 <!-- ---------------------------- -->

@@ Line 84: / Line 84: @@
 <pre>
 vtkNew<vtkImageData> imageData;
-imageData->SetDimensions(10,10,10);
+imageData->SetDimensions(10,10,10); // image size
-imageData->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+imageData->AllocateScalars(VTK_UNSIGNED_CHAR, 1); // image type and number of components
-// initialize the pixels here.
+// initialize the pixels here
 vtkNew<vtkMRMLScalarVolumeNode> volumeNode;
@@ Line 94: / Line 94: @@
 mrmlScene->AddNode( volumeNode.GetPointer() );
-vtkNew<vtkMRMLScalarVolumeDisplayNode> displayNode;
+volumeNode->CreateDefaultDisplayNodes()
 </pre>
@@ Line 102: / Line 100: @@
 <pre>
 imageData = vtk.vtkImageData()
-imageData.SetDimensions(10,10,10)
+imageData.SetDimensions(10,10,10) # image size
-imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
+imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1) # image type and number of components
 volumeNode = slicer.vtkMRMLScalarVolumeNode()
 volumeNode.SetAndObserveImageData(imageData)
-displayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
+volumeNode = slicer.mrmlScene.AddNode(volumeNode)
-slicer.mrmlScene.AddNode(volumeNode)
+volumeNode.CreateDefaultDisplayNodes()
 </pre>

@@ Line 54: / Line 54: @@
 |[[Image:VolumesModuleWindowLevelSliderPopup.gif|frame|On mouse over, a second popup appears under the window level double slider. Large dynamic range can be controlled using the slider. Moving the handles of the popup double slider changes the whole range of the window level double slider.]]
 |}
 <!-- ---------------------------- -->

@@ Line 73: / Line 73: @@
 ===How to create a volume node from scratch? ===
 You need to create a vtkImageData, a vtkMRMLScalarVolumeNode and a vtkMRMLScalarVolumeDisplayNode.
 <pre>
 vtkNew<vtkImageData> imageData;
@@ Line 88: / Line 90: @@
 mrmlScene->AddNode( displayNode.GetPointer() );
 volumeNode->SetAndObserveDisplayNodeID(displayNode->GetID());
 </pre>
 Note that the origin and spacing must be set on the volume node instead of the image data.
 The [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]] extension module creates a volume from scratch.

@@ Line 80: / Line 80: @@
 vtkNew<vtkMRMLScalarVolumeNode> volumeNode;
-volumeNode->SetAndObserveImageData(volume);
+volumeNode->SetAndObserveImageData(imageData);
 volumeNode->SetOrigin( -10., -10., -10.);
 volumeNode->SetSpacing( 2., 2., 2. );

@@ Line 44: / Line 44: @@
 {|
-| {{documentation/{{documentation/version}}/module-parametersdescription}}
+| rowspan=2 | {{documentation/{{documentation/version}}/module-parametersdescription}}
-| [[Image:VolumesModule-2011-11-25.png|400px]]
+| [[Image:VolumesModule-2011-11-25.png|400px]]  Greyscale volume
 |}
 {|
 |[[Image:VolumesModuleWindowLevelSliderPopup.gif|frame|On mouse over, a second popup appears under the window level double slider. Large dynamic range can be controlled using the slider. Moving the handles of the popup double slider changes the whole range of the window level double slider.]]