Documentation/Nightly/Modules/PlusRemote - Revision history

Grundlett: Text replacement - "\[https:\/\/www\.slicer\.org\/slicerWiki\/index.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:42:47Z

Text replacement - "\[https:\/\/www\.slicer\.org\/slicerWiki\/index.php\/([^ ]+) ([^]]+)]" to "$2"

Sunderlandkyl: Update link to PLUS user documentation

2019-11-14T20:06:01Z

Update link to PLUS user documentation

Rankin: Updating link to plus server commands

2016-01-05T18:26:03Z

Updating link to plus server commands

Lasso at 19:06, 12 June 2015

2015-06-12T19:06:33Z

Ameliemeyer at 14:05, 26 August 2014

2014-08-26T14:05:55Z

Ameliemeyer at 20:40, 25 August 2014

2014-08-25T20:40:40Z

Ameliemeyer at 20:17, 25 August 2014

2014-08-25T20:17:53Z

Ameliemeyer at 20:10, 25 August 2014

2014-08-25T20:10:33Z

Ameliemeyer at 19:49, 25 August 2014

2014-08-25T19:49:23Z

Ameliemeyer at 19:31, 25 August 2014

2014-08-25T19:31:53Z

← Older revision		Revision as of 02:42, 27 November 2019
Line 66:		Line 66:
	**Volume Reconstructor ID		**Volume Reconstructor ID

−	These parameters are essential. Therefore all commands are disabled when these parameters are not set. List of available OpenIGTLinkConnector is available once you created connections in [~~https://www.slicer.org/slicerWiki/index.php/~~Documentation/Nightly/Modules/OpenIGTLinkIF OpenIGTLinkIF] module. When a connector is selected, capture device ID and volume reconstruction ID lists are automatically filled.	+	These parameters are essential. Therefore all commands are disabled when these parameters are not set. List of available OpenIGTLinkConnector is available once you created connections in [[Documentation/Nightly/Modules/OpenIGTLinkIF\|OpenIGTLinkIF]] module. When a connector is selected, capture device ID and volume reconstruction ID lists are automatically filled.

@@ Line 1: / Line 1: @@
-<noinclude>{{documentation/versioncheck}}</noinclude>
+<noinclude>{{documentation/versioncheck}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-header}}
@@ Line 20: / Line 21: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-Convenience module for sending commands through OpenIGTLink Remote to PLUS. Requires OpenIGTLink Remote module available in the SlicerIGT extension. See PLUS [https://www.assembla.com/spaces/plus/wiki/Users_guide user guide] and [http://perk-software.cs.queensu.ca/plus/doc/nightly/user/PlusServerCommands.html manual] for more information about PLUS server commands.
+Convenience module for sending commands through OpenIGTLink Remote to PLUS. Requires OpenIGTLink Remote module available in the SlicerIGT extension. See PLUS [https://plustoolkit.github.io/usersguide user guide] and [http://perk-software.cs.queensu.ca/plus/doc/nightly/user/PlusServerCommands.html manual] for more information about PLUS server commands.
 '''Demo video:''' https://youtu.be/lfZeXabDjMg
 The module provides the following features:
 * Recording of 2D tracked ultrasound frames
-* Volume reconstruction of recorded frames
+*Recording of 2D tracked ultrasound frames
-* Live ultrasound volume reconstruction using scout scanning
+*Volume reconstruction of recorded frames
-* Sending Transform Update command to PLUS server
+*Live ultrasound volume reconstruction using scout scanning
 <!-- ---------------------------- -->
@@ Line 52: / Line 54: @@
 *'''Parameters sets:''' saving of all parameters
-** Create a new parameter set to save your parameters
+**Create a new parameter set to save your parameters
-** Select previously saved ones
+**Select previously saved ones
-** Default parameter set is selected when entering the module
+**Default parameter set is selected when entering the module
 This is useful when user knows optimal parameters for a specific procedure. The parameters set is saved when saving the scene and is reloaded when opening a saved scene.
 *'''Parameters:''' parameters for communication with PLUS server, recording and reconstruction
-** OpenIGTLinkConnector
+**OpenIGTLinkConnector
-** Capture Device ID
+**Capture Device ID
-** Volume Reconstructor ID
+**Volume Reconstructor ID
 These parameters are essential. Therefore all commands are disabled when these parameters are not set. List of available OpenIGTLinkConnector is available once you created connections in [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/OpenIGTLinkIF OpenIGTLinkIF] module. When a connector is selected, capture device ID and volume reconstruction ID lists are automatically filled.
 *'''Recording:'''
-** Start and stop recording
+**Start and stop recording
-** Advanced parameters:
+**Advanced parameters:
-*** Modify default output filename "Recording.mha"
+***Modify default output filename "Recording.mha"
-*** Add timestamp (YYYYMMDD_HHMMSS) to filename
+***Add timestamp (YYYYMMDD_HHMMSS) to filename
 *'''Offline reconstruction of recorded volume:'''
-** Offline reconstruction
+**Offline reconstruction
-** Advanced parameters:
+**Advanced parameters:
-*** Spacing (default value is 3mm)
+***Spacing (default value is 3mm)
-*** Output volume device name
+***Output volume device name
-*** Volume to reconstruct filename (automatically filled when user record a file, but user can also edit this line and reconstruct previously saved files)
+***Volume to reconstruct filename (automatically filled when user record a file, but user can also edit this line and reconstruct previously saved files)
-*** Show results on completion (display reconstructed volume in the green, yellow and 3D views)
+***Show results on completion (display reconstructed volume in the green, yellow and 3D views)
 *'''Scout scan and live reconstruction:'''
-** Start and stop scout scan
+**Start and stop scout scan
-** Advanced parameters:
+**Advanced parameters:
-*** Spacing (default value is 3mm as we expect a low resolution scout scan)
+***Spacing (default value is 3mm as we expect a low resolution scout scan)
-*** Modify default output filename "ScoutScanRecording.mha"
+***Modify default output filename "ScoutScanRecording.mha"
-*** Add timestamp (YYYYMMDD_HHMMSS) to filename
+***Add timestamp (YYYYMMDD_HHMMSS) to filename
-*** Show results on completion (display reconstructed volume in the green, yellow and 3D views)
+***Show results on completion (display reconstructed volume in the green, yellow and 3D views)
 Scout scan button record a file and automatically performs the volume reconstruction once the recording is over. The result of scout scan volume reconstruction is saved in "scoutFile.mha"
 ** Start and stop live volume reconstruction:
-** Display and modify ROI using eye icon (initialized to fit scout scan volume)
+**Start and stop live volume reconstruction:
-** Spacing (default value is 1mm for high resolution reconstruction)
+**Display and modify ROI using eye icon (initialized to fit scout scan volume)
-** Advanced parameters:
+**Spacing (default value is 1mm for high resolution reconstruction)
-*** Output volume device name (read only)
+**Advanced parameters:
-*** Modify default output filename "LiveReconstructedVolume.mha"
+***Output volume device name (read only)
-*** Add timestamp (YYYYMMDD_HHMMSS) to filename
+***Modify default output filename "LiveReconstructedVolume.mha"
-*** Display volume extent values (updated when clicking on scout scan or live reconstruction command buttons)
+***Add timestamp (YYYYMMDD_HHMMSS) to filename
-*** Display snapshots during live volume reconstruction (if 0, no snapshots)
+***Display volume extent values (updated when clicking on scout scan or live reconstruction command buttons)
-*** Show results on completion (display reconstructed volume in the green, yellow and 3D views)
+***Display snapshots during live volume reconstruction (if 0, no snapshots)
@@ Line 110: / Line 116: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
 * [http://perk-software.cs.queensu.ca/plus/doc/nightly/user/PlusServerCommands.html PlusServer commands]
 <!-- ---------------------------- -->

@@ Line 110: / Line 110: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
-* [https://www.assembla.com/spaces/plus/wiki/PlusServer_commands PlusServer commands]
+* [http://perk-software.cs.queensu.ca/plus/doc/nightly/user/PlusServerCommands.html PlusServer commands]
 <!-- ---------------------------- -->

@@ Line 21: / Line 21: @@
 {{documentation/{{documentation/version}}/module-section|Module Description}}
 Convenience module for sending commands through OpenIGTLink Remote to PLUS. Requires OpenIGTLink Remote module available in the SlicerIGT extension. See PLUS [https://www.assembla.com/spaces/plus/wiki/Users_guide user guide] and [http://perk-software.cs.queensu.ca/plus/doc/nightly/user/PlusServerCommands.html manual] for more information about PLUS server commands.
 The module provides the following features:
@@ Line 112: / Line 114: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}

@@ Line 140: / Line 140: @@
 *'''Saving parameters:'''
 <pre>
 self.parameterValueList = {'parameterName': GUIObject, 'ScoutScanSpacing': self.outputVolumeSpacingBox,...}
@@ Line 150: / Line 163: @@
 </pre>
-For the ROI node it has to be done using reference:
+For the ROI node:
 <pre>
 self.roiNode = self.parameterNode.GetNthNodeReference('ROI', 0)
 </pre>

@@ Line 126: / Line 126: @@
 * [http://slicer.org/doc/html/classvtkMRMLAnnotationROINode.html vtkMRMLAnnotationROINode] controls the ROI widget
 * [http://slicer.org/doc/html/classvtkMRMLAnnotationTextNode.html vtkMRMLAnnotationTextNode] represents the command reply text
 ===Parameters set===

@@ Line 182: / Line 182: @@
    roiCenterInit[i] = (bounds[i+1] + bounds[i])/2
    roiRadiusInit[i] = (bounds[i+1] - bounds[i])/2
-  if self.roiNode:
+...
-    self.roiNode.SetXYZ(roiCenterInit[0], roiCenterInit[2], roiCenterInit[4])
+   self.roiNode = slicer.vtkMRMLAnnotationROINode()
-    self.roiNode.SetRadiusXYZ(roiRadiusInit[0], roiRadiusInit[2], roiRadiusInit[4])
+  self.roiNode.SetXYZ(roiCenterInit[0], roiCenterInit[2], roiCenterInit[4])
-   else:
+  self.roiNode.SetRadiusXYZ(roiRadiusInit[0], roiRadiusInit[2], roiRadiusInit[4])
-    self.roiNode = slicer.vtkMRMLAnnotationROINode()
+  self.roiNode.Initialize(slicer.mrmlScene)
 </pre>

@@ Line 127: / Line 127: @@
 * [http://slicer.org/doc/html/classvtkMRMLAnnotationTextNode.html vtkMRMLAnnotationTextNode] represents the command reply text
-===How Tos===
+===Parameters set===
-* '''Parameters set:'''
+* '''Parameters set observer:'''
 Need to add an observer to save the new parameter value when user changes it, or to update the GUI when user select another parameter set.
@@ Line 162: / Line 162: @@
 roiNodeID = self.roiNode.GetID()
 self.parameterNode.SetNthNodeReferenceID('ROI', 0, roiNodeID)
 </pre>

← Older revision		Revision as of 19:49, 25 August 2014
Line 128:		Line 128:

	===How Tos===		===How Tos===
−	*~~How~~ to programmatically ~~volume render your volume~~ node?	+	* '''Parameters set:'''
		+	Need to add an observer to save the new parameter value when user changes it, or to update the GUI when user select another parameter set.
		+
		+	<pre>
		+	self.parameterNodeObserver = self.parameterNode.AddObserver('currentNodeChanged(vtkMRMLNode*)', functionToCall)
		+	</pre>
		+
		+	*'''Saving parameters:'''
		+	<pre>
		+	self.parameterValueList = {'parameterName': GUIObject, 'ScoutScanSpacing': self.outputVolumeSpacingBox,...}
		+	for parameter in self.parameterValueList:
		+	if self.parameterNode.GetParameter(parameter):
		+	#Block Signal to avoid call of updateParameterNodeFromGui when parameter is set programmatically - we only want to catch when user change values
		+	self.parameterValueList[parameter].blockSignals(True)
		+	self.parameterValueList[parameter].setValue(float(self.parameterNode.GetParameter(parameter)))
		+	self.parameterValueList[parameter].blockSignals(False)
		+	</pre>
		+
		+	For the ROI node it has to be done using reference:
		+	<pre>
		+	self.roiNode = self.parameterNode.GetNthNodeReference('ROI', 0)
		+	</pre>
		+
		+	*'''Getting a saved parameter and updating the GUI when selecting a parameter set:'''
		+	<pre>
		+	self.parametersList = {'parameterNode': GUIObject.currentObject, 'ScoutScanSpacing': self.outputVolumeSpacingBox.value,...}
		+	for parameter in self.parametersList:
		+	self.parameterNode.SetParameter(parameter, str(self.parametersList[parameter]))
		+	</pre>
		+
		+	For ROI node:
		+	<pre>
		+	roiNodeID = self.roiNode.GetID()
		+	self.parameterNode.SetNthNodeReferenceID('ROI', 0, roiNodeID)
		+	</pre>

@@ Line 115: / Line 115: @@
 ===Limitations===
-*To date,
+* Extent values are updated only when clicking on scout scan or live reconstruction command buttons, not in "real-time" when user modifies the ROI
 ===Key [[Documentation/{{documentation/version}}/Developers/MRML|nodes]] and classes===