Documentation/4.3/Modules/Annotations - Revision history

Grundlett: Text replacement - "slicerWiki/index.php" to "wiki"

2019-11-21T16:59:52Z

Text replacement - "slicerWiki/index.php" to "wiki"

Nicole: /* Selection and interaction */

2013-09-24T16:11:40Z

Selection and interaction

Nicole at 16:10, 24 September 2013

2013-09-24T16:10:53Z

Nicole at 20:13, 10 September 2013

2013-09-10T20:13:48Z

Nicole at 20:03, 10 September 2013

2013-09-10T20:03:11Z

UpdateBot: Nightly -> 4.3

2013-09-05T03:43:33Z

Nightly -> 4.3

New page

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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:'''Author(s)/Contributor(s):''' Nicole Aucoin (SPL, BWH), Kilian Pohl (UPenn), Daniel Haehn (UPenn), Yong Zhang (BWH), Alex Yarmarkovich (Isomics)
: '''Acknowledgements:''' This work is part of the [http://www.na-mic.org/ National Alliance for Medical Image Computing] (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br>
: '''Contact:''' Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br>
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|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
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{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description}}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1: placing fiducial markers at points of interest on images
* Use Case 2: using fiducials to seed tractography
* Use Case 3: using rulers to measure tumor diameters
* Use Case 4: using ROIs to crop volume rendering


{{documentation/{{documentation/version}}/module-section|Tutorials}}

To delete multiple fiducials from a list press down the Control key and left click to select fiducials in the Annotations GUI, then click on the trash can to delete them.

To move multiple fiducials from one list to another, hold down the Shift key and left click to select a group of fiducials, then while still holding down the shift key, left click on the selection to drag and drop it.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

A list of all the panels in the interface, their features, what they mean, and how to use them.

{|
|[[Image:Slicer4-1-Annotations-GUI.jpeg|thumb|200px|Annotations]]
|[[Image:Slicer4-Annotations-ModifyPropeties.jpeg|thumb|200px|Modify Annotation Properties]]
|[[Image:Slicer4-Annotations-ModifyHierarchy.jpeg|thumb|200px|Modify Hierarchy Properties]]
|[[Image:Slicer4-Annotations-Toolbar.jpeg|thumb|200px|Annotation tool bar]]
|}
{{documentation/{{documentation/version}}/module-parametersdescription}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* The Annotations tool bar at the top of the main Slicer window is used to add new annotations to the scene.


{{documentation/{{documentation/version}}/module-section|References}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}

=== Access to Fiducial Locations from Python ===

Starting from the ID of an Annotation hierarchy node that collects a group of fiducials, you can get a fiducial location using the following python code:
# get the first list of annotations
listNodeID = "vtkMRMLAnnotationHierarchyNode2"
annotationHierarchyNode = slicer.mrmlScene.GetNodeByID(listNodeID)
# get the first in the list
listIndex = 0
annotation = annotationHierarchyNode.GetNthChildNode(listIndex).GetAssociatedNode()
coords = [0,0,0]
annotation.GetFiducialCoordinates(coords)
print coords

If you have the id of the fiducial node, it's more direct:
fidID = "vtkMRMLAnnotationFiducialNode1"
fid = slicer.mrmlScene.GetNodeByID(fidID)
coords = [0,0,0]
fid.GetFiducialCoordinates(coords)
print coords[0], coords[1], coords[2]

You can also look at the sample code in the [https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Scripts/Endoscopy.py#L287 Endoscopy module] to see how python is used to access fiducials.

=== Transforms ===
Individual annotations are transformable (able to be placed under a transform node), but lists are not. In order to apply a transform to a set of annotations, open the python console (View -> Python Interctor) and use the following code. First you'll need to get the transform node MRML id from the Data module (click on Display MRML IDs), and save it to a variable:
transformNodeID = "vtkMRMLLinearTransformNode5"
Then get the id of the annotation hierarchy list node that holds the annotations that you wish to transform:
listNodeID = "vtkMRMLAnnotationHierarchyNode3"
Then use this code snippet to apply the transform to all the annotations under the hierarchy node:
annotationHierarchyNode = slicer.mrmlScene.GetNodeByID(listNodeID)
numNodes = annotationHierarchyNode.GetNumberOfChildrenNodes()
for i in range(numNodes):
annotation = annotationHierarchyNode.GetNthChildNode(i).GetAssociatedNode()
annotation.SetAndObserveTransformNodeID(transformNodeID)
* [[Documentation/{{documentation/version}}/Modules/Transforms#Information_for_Developers|Read more]] about transforming MRML nodes

=== Programmatic Access to Fiducials ===

This section explains how to access fiducial nodes added into the scene by the user.

In your module's Logic class, overwrite SetMRMLSceneInternal to observe the NodeAddedEvent of the scene:
void vtkSlicerMYMODULEModuleLogic::SetMRMLSceneInternal(vtkMRMLScene * newScene)
{
vtkIntArray *events = vtkIntArray::New();
events->InsertNextValue(vtkMRMLScene::NodeAddedEvent);
// Optionally you can add here more events
// you can be interested in such as vtkMRMLScene::NodeRemovedEvent
this->SetAndObserveMRMLSceneEventsInternal(newScene, events);
events->Delete();
}
Via the set and observe mrml scene macro, anytime a node is added into the scene, it will trigger the base Logic class method
[http://slicer.org/doc/html/classvtkMRMLAbstractLogic.html#a51fdf00ecfc18c1a1465d4bccb789ef1 vtkMRMLAbstractLogic::ProcessMRMLNodesEvents] which calls the virtual method <code>vtkMRMLAbstractLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* node)</code> to reimplement in your logic:
void vtkSlicerMYMODULEModuleLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* addedNode)
{
vtkMRMLAnnotationFiducialNode* fidNode =
vtkMRMLAnnotationFiducialNode::SafeDownCast(addedNode);
if (fidNode)
{
// here you write what you need to do when a
// fiducial node is added into the scene
}
}

===Selection and interaction===
This section indicates how to change in the GUI the mouse placing mode to start placing nodes.

For the selection and interaction nodes, make sure that you access the singleton nodes already in the scene (rather than making your own) via (caveat: this call works on displayable managers, you may have to go a different route to get at the application logic):
vtkMRMLApplicationLogic *mrmlAppLogic = this->GetMRMLApplicationLogic();
vtkMRMLInteractionNode *inode = mrmlAppLogic->GetInteractionNode();
vtkMRMLSelectionNode *snode = mrmlAppLogic->GetSelectionNode();
If you can't get at the mrml application logic, you can get the nodes from the scene:
vtkMRMLInteractionNode *interactionNode = vtkMRMLInteractionNode::SafeDownCast(this->GetMRMLScene()->GetNodeByID("vtkMRMLInteractionNodeSingleton"));

You can then call methods on the nodes or add your own event observers as in
vtkSlicerAnnotationModuleLogic::ObserveMRMLScene
You can see vtkSlicerAnnotationModuleLogic::ProcessMRMLNodesEvents to see how to respond to interaction node changes, but I don't think you'll need to do that.

Slicer4/Base/QTGUI/qSlicerMouseModeToolBar.cxx has a lot of the code you'll need as well, with a slightly different way of getting at the mrml app logic to access the nodes.

The calls you need to make to switch into placing fiducials with the mouse are:
selectionNode->SetActiveAnnotationID ("vtkMRMLAnnotationFiducialNode");
interactionNode->SetCurrentInteractionMode(vtkMRMLInteractionNode::Place);
If you don't set PlaceModePersistence on the interaction node, the mouse mode/current interaction mode will automatically go back to view transform after one fiducial has been placed, and you just need to reset the current interaction mode for future placing (the active annotation id is persistent).


{{documentation/{{documentation/version}}/module-footer}}

@@ Line 67: / Line 67: @@
 === Use the Markups module for fiducials ===
-'''Fiducials have been moved to the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Markups  Markups module].'''
+'''Fiducials have been moved to the [http://www.slicer.org/wiki/Documentation/Nightly/Modules/Markups  Markups module].'''
 === Access to Ruler Locations from Python ===

@@ Line 137: / Line 137: @@
 The calls you need to make to switch into placing rulers with the mouse are:
-   selectionNode->SetReferencePlaceNodeClassName("vtkMRMLAnnotationRulerNode");
+   selectionNode->SetReferenceActivePlaceNodeClassName("vtkMRMLAnnotationRulerNode");
    interactionNode->SetCurrentInteractionMode(vtkMRMLInteractionNode::Place);
 If you don't set PlaceModePersistence on the interaction node, the mouse mode/current interaction mode will automatically go back to view transform after one ruler has been placed, and you just need to reset the current interaction mode for future placing (the active place node class name is persistent).

@@ Line 65: / Line 65: @@
 {{documentation/{{documentation/version}}/module-developerinfo}}
-=== Access to Annotation Coordinates from Python ===
+=== Use the Markups module for fiducials ===
-Starting from the ID of an Annotation hierarchy node that collects a group of annotations, you can get ruler end point locations using the following python code:
+'''Fiducials have been moved to the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Markups  Markups module].'''
    # get the first list of annotations
-   listNodeID = "vtkMRMLAnnotationHierarchyNode4"
+   listNodeID = "vtkMRMLAnnotationHierarchyNode2"
    annotationHierarchyNode = slicer.mrmlScene.GetNodeByID(listNodeID)
    # get the first in the list
@@ Line 75: / Line 79: @@
    annotation = annotationHierarchyNode.GetNthChildNode(listIndex).GetAssociatedNode()
    coords1 = [0,0,0]
    annotation.GetPosition1(coords1)
-   print coords1
+  annotation.GetPosition2(coords2)
 If you have the id of the ruler node, it's more direct:
@@ Line 86: / Line 92: @@
    ruler.GetPosition2(coords2)
    print coords1, coords2
 === Transforms ===
@@ Line 99: / Line 119: @@
      annotation.SetAndObserveTransformNodeID(transformNodeID)
 * [[Documentation/{{documentation/version}}/Modules/Transforms#Information_for_Developers|Read more]] about transforming MRML nodes
 ===Selection and interaction===
@@ Line 147: / Line 137: @@
 The calls you need to make to switch into placing rulers with the mouse are:
-   selectionNode->SetActivePlaceNodeID ("vtkMRMLAnnotationRulerNode");
+   selectionNode->SetReferencePlaceNodeClassName("vtkMRMLAnnotationRulerNode");
    interactionNode->SetCurrentInteractionMode(vtkMRMLInteractionNode::Place);
-If you don't set PlaceModePersistence on the interaction node, the mouse mode/current interaction mode will automatically go back to view transform after one ruler has been placed, and you just need to reset the current interaction mode for future placing (the active annotation id is persistent).
+If you don't set PlaceModePersistence on the interaction node, the mouse mode/current interaction mode will automatically go back to view transform after one ruler has been placed, and you just need to reset the current interaction mode for future placing (the active place node class name is persistent).
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-footer}}
 <!-- ---------------------------- -->

@@ Line 44: / Line 44: @@
 {|
-|[[Image:Slicer4-1-Annotations-GUI.jpeg|thumb|200px|Annotations]]
+|[[Image:Slicer4-3-Annotations-GUI.jpeg|thumb|200px|Annotations]]
 |[[Image:Slicer4-Annotations-ModifyPropeties.jpeg|thumb|200px|Modify Annotation Properties]]
 |[[Image:Slicer4-Annotations-ModifyHierarchy.jpeg|thumb|200px|Modify Hierarchy Properties]]
-|[[Image:Slicer4-Annotations-Toolbar.jpeg|thumb|200px|Annotation tool bar]]
+|[[Image:Slicer4-3-Annotations-Toolbar.jpeg|thumb|200px|Annotation tool bar with Markups fiducial at the bottom]]
 |}
 {{documentation/{{documentation/version}}/module-parametersdescription}}

@@ Line 27: / Line 27: @@
 Most frequently used for these scenarios:
-* Use Case 1: placing fiducial markers at points of interest on images
+* Use Case 1: using rulers to measure tumor diameters
-* Use Case 2: using fiducials to seed tractography
+* Use Case 2: using ROIs to crop volume rendering
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-To delete multiple fiducials from a list press down the Control key and left click to select fiducials in the Annotations GUI, then click on the trash can to delete them.
+To delete multiple rulers or ROIs from a list press down the Control key and left click to select annotations in the Annotations GUI, then click on the trash can to delete them.
-To move multiple fiducials from one list to another, hold down the Shift key and left click to select a group of fiducials, then while still holding down the shift key, left click on the selection to drag and drop it.
+To move multiple rulers or ROIs from one list to another, hold down the Shift key and left click to select a group of annotations, then while still holding down the shift key, left click on the selection to drag and drop it.
@@ Line 56: / Line 54: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
 * The Annotations tool bar at the top of the main Slicer window is used to add new annotations to the scene.
@@ Line 66: / Line 65: @@
 {{documentation/{{documentation/version}}/module-developerinfo}}
-=== Access to Fiducial Locations from Python ===
+=== Access to Annotation Coordinates from Python ===
-Starting from the ID of an Annotation hierarchy node that collects a group of fiducials, you can get a fiducial location using the following python code:
+Starting from the ID of an Annotation hierarchy node that collects a group of annotations, you can get ruler end point locations using the following python code:
    # get the first list of annotations
-   listNodeID = "vtkMRMLAnnotationHierarchyNode2"
+   listNodeID = "vtkMRMLAnnotationHierarchyNode4"
    annotationHierarchyNode = slicer.mrmlScene.GetNodeByID(listNodeID)
    # get the first in the list
    listIndex = 0
    annotation = annotationHierarchyNode.GetNthChildNode(listIndex).GetAssociatedNode()
-   coords = [0,0,0]
+   coords1 = [0,0,0]
-   annotation.GetFiducialCoordinates(coords)
+   annotation.GetPosition1(coords1)
-   print coords
+   print coords1
-If you have the id of the fiducial node, it's more direct:
+If you have the id of the ruler node, it's more direct:
-   fidID = "vtkMRMLAnnotationFiducialNode1"
+   rulerID = "vtkMRMLAnnotationRulerNode1"
-   fid = slicer.mrmlScene.GetNodeByID(fidID)
+   ruler = slicer.mrmlScene.GetNodeByID(rulerID)
-   coords = [0,0,0]
+   coords1 = [0,0,0]
-   fid.GetFiducialCoordinates(coords)
+   coords2 = [0,0,0]
-  print coords[0], coords[1], coords[2]
+  ruler.GetPosition1(coords1)
+  ruler.GetPosition2(coords2)
-You can also look at the sample code in the [https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Scripts/Endoscopy.py#L287  Endoscopy module] to see how python is used to access fiducials.
+  print coords1, coords2
 === Transforms ===
@@ Line 100: / Line 99: @@
      annotation.SetAndObserveTransformNodeID(transformNodeID)
 * [[Documentation/{{documentation/version}}/Modules/Transforms#Information_for_Developers|Read more]] about transforming MRML nodes
 === Programmatic Access to Fiducials ===
@@ Line 127: / Line 128: @@
+      }
+    }
 ===Selection and interaction===
@@ Line 144: / Line 146: @@
 Slicer4/Base/QTGUI/qSlicerMouseModeToolBar.cxx has a lot of the code you'll need as well, with a slightly different way of getting at the mrml app logic to access the nodes.
-The calls you need to make to switch into placing fiducials with the mouse are:
+The calls you need to make to switch into placing rulers with the mouse are:
-   selectionNode->SetActiveAnnotationID ("vtkMRMLAnnotationFiducialNode");
+   selectionNode->SetActivePlaceNodeID ("vtkMRMLAnnotationRulerNode");
    interactionNode->SetCurrentInteractionMode(vtkMRMLInteractionNode::Place);
-If you don't set PlaceModePersistence on the interaction node, the mouse mode/current interaction mode will automatically go back to view transform after one fiducial has been placed, and you just need to reset the current interaction mode for future placing (the active annotation id is persistent).
+If you don't set PlaceModePersistence on the interaction node, the mouse mode/current interaction mode will automatically go back to view transform after one ruler has been placed, and you just need to reset the current interaction mode for future placing (the active annotation id is persistent).
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-footer}}
 <!-- ---------------------------- -->