Documentation/Nightly/Developers/Tutorials/MigrationGuide/Slicer - Revision history

JChris.FillionR: /* Slicer 5.3: Organization name and domain changed from NA-MIC to Slicer */

2023-08-22T14:55:07Z

Slicer 5.3: Organization name and domain changed from NA-MIC to Slicer

Jamesobutler: /* Slicer backward incompatible changes */

2023-03-04T19:46:57Z

Slicer backward incompatible changes

JChris.FillionR at 02:18, 28 February 2023

2023-02-28T02:18:57Z

Lasso: /* Slicer 5.3: Removed Annotation module */

2022-09-14T16:43:06Z

Slicer 5.3: Removed Annotation module

Lasso: /* Slicer 5.0: Fiducial List was renamed to Point List */

2022-09-14T16:42:19Z

Slicer 5.0: Fiducial List was renamed to Point List

Lasso: /* Volume rendering */

2022-08-27T22:51:21Z

Volume rendering

JChris.FillionR: /* Slicer 5.0: Removed Charts and DoubleArrays module */

2022-03-21T22:48:03Z

Slicer 5.0: Removed Charts and DoubleArrays module

Lasso: /* Slicer 5.0: Fiducial List was renamed to Point List */

2022-02-03T20:33:30Z

Slicer 5.0: Fiducial List was renamed to Point List

Lasso: /* Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead */

2021-11-09T15:31:35Z

Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead

Lasso: /* Removed classes */

2021-11-06T02:31:23Z

Removed classes

@@ Line 2: / Line 2: @@
 ==Slicer backward incompatible changes==
-===Slicer 5.3: Organization name and domain changed from NA-MIC to Slicer===
+===Slicer 5.3: Organization name and domain changed from NA-MIC to slicer.org===
-To address the [https://discourse.slicer.org/t/inconsistency-between-organization-name-used-for-settings-files-and-for-macos-bundle-identifier/26547 inconsistency between organization name used for settings files and for macOS bundle identifier], the 3D Slicer application has updated the <code>Slicer_ORGANIZATION_NAME</code> from "NA-MIC" to "Slicer" and <code>Slicer_ORGANIZATION_DOMAIN</code> from <code>www.na-mic.org</code> to <code>www.slicer.org</code>. At the time of this change, 3D Slicer is developed primarily by the Slicer community rather than the NA-MIC community. Distribution of 3D Slicer is hosted at [https://www.slicer.org www.slicer.org] rather than at [https://www.na-mic.org www.na-mic.org].
+To address the [https://discourse.slicer.org/t/inconsistency-between-organization-name-used-for-settings-files-and-for-macos-bundle-identifier/26547 inconsistency between organization name used for settings files and for macOS bundle identifier], the 3D Slicer application has updated the <code>Slicer_ORGANIZATION_NAME</code> from "NA-MIC" to "slicer.org" and <code>Slicer_ORGANIZATION_DOMAIN</code> from <code>www.na-mic.org</code> to <code>slicer.org</code>. At the time of this change, 3D Slicer is developed primarily by the Slicer community rather than the NA-MIC community. Distribution of 3D Slicer is hosted at [https://slicer.org slicer.org] rather than at [https://www.na-mic.org www.na-mic.org].
 Slicer settings will now be under a Slicer directory location rather than NA-MIC. Please review the [https://slicer.readthedocs.io/en/latest/user_guide/settings.html#settings-file-location Settings File Location documentation] for details about the settings location on various platforms.

@@ Line 1: / Line 1: @@
 <noinclude>__TOC__</noinclude>
 ==Slicer backward incompatible changes==
 ===Slicer 5.3: Removed Annotation module===

@@ Line 1: / Line 1: @@
 <noinclude>__TOC__</noinclude>
 ==Slicer backward incompatible changes==
 ===Slicer 5.0: API changes since 4.10===
@@ Line 204: / Line 224: @@
 * qMRMLChartViewControllerWidget is replaced by qMRMLPlotViewControllerWidget
 * qMRMLChartWidget is replaced by qMRMLPlotWidget
 ===Slicer 5.0: Fiducial List was renamed to Point List===

@@ Line 215: / Line 215: @@
 Tips for updating a module to use markups:
-- In node selectors, wherever `vtkMRMLAnnotationROINode` is accepted, add `vtkMRMLMarkupsLineNode` _before_ it (so they are both accepted, but markups are preferred)
+* In node selectors, wherever `vtkMRMLAnnotationROINode` is accepted, add `vtkMRMLMarkupsLineNode` _before_ it (so they are both accepted, but markups are preferred)
-- In node selectors, wherever `vtkMRMLAnnotationRuler` is accepted, add `vtkMRMLMarkupsLine` _before_ it (so they are both accepted, but markups are preferred)
+* In node selectors, wherever `vtkMRMLAnnotationRuler` is accepted, add `vtkMRMLMarkupsLine` _before_ it (so they are both accepted, but markups are preferred)
-- For ROIs:
+* For ROIs:
-  - When only non-rotated ROIs are used: you can still use `GetXYZ()` and `GetRadiusXYZ()` methods work the same way for markups ROI
+** When only non-rotated ROIs are used: you can still use `GetXYZ()` and `GetRadiusXYZ()` methods work the same way for markups ROI
-  - When ROIs are rotated, markups ROIs support built-in rotation and scaling, therefore it is recommended to use the `exportRoi.GetObjectToWorldMatrix()` method to get all the transforms (including the transform inside the markup node and any transforms applied using transform nodes) that are applied to the bounding box object (that has its center in the origin and its diameter returned by `GetSize()`).
+** When ROIs are rotated, markups ROIs support built-in rotation and scaling, therefore it is recommended to use the `exportRoi.GetObjectToWorldMatrix()` method to get all the transforms (including the transform inside the markup node and any transforms applied using transform nodes) that are applied to the bounding box object (that has its center in the origin and its diameter returned by `GetSize()`).
-- For rulers:
+* For rulers:
-  - Use `GetNthControlPointPosition(0)` and `GetNthControlPointPosition(1)` methods to get the endpoints of the line.
+** Use `GetNthControlPointPosition(0)` and `GetNthControlPointPosition(1)` methods to get the endpoints of the line.
-  - Use `GetNumberOfDefinedControlPoints()` method to check if both endpoints of the line are defined.
+** Use `GetNumberOfDefinedControlPoints()` method to check if both endpoints of the line are defined.
-  - Use `GetMeasurement('length').GetValue()` to get the line length (or for the displayed string, with units: `getNode('L').GetMeasurement('length').GetValueWithUnitsAsPrintableString()`)
+** Use `GetMeasurement('length').GetValue()` to get the line length (or for the displayed string, with units: `getNode('L').GetMeasurement('length').GetValueWithUnitsAsPrintableString()`)
 ===Slicer 5.0: Fiducial List was renamed to Point List===

@@ Line 204: / Line 204: @@
 * qMRMLChartViewControllerWidget is replaced by qMRMLPlotViewControllerWidget
 * qMRMLChartWidget is replaced by qMRMLPlotWidget
 ===Slicer 5.0: Fiducial List was renamed to Point List===

← Older revision		Revision as of 22:51, 27 August 2022
Line 157:		Line 157:

	vtkMRMLVolumeRenderingDisplayNode::SetAndObserveVolumeNodeID method was removed, as display node base class already maintains a pointer to the displayed (volume) node. To associate a volume display node with a volume node, call <pre>volumeNode->AddAndObserveDisplayNodeID(volumeRenderingDisplayNode->GetID());</pre> after both nodes are added to the scene.		vtkMRMLVolumeRenderingDisplayNode::SetAndObserveVolumeNodeID method was removed, as display node base class already maintains a pointer to the displayed (volume) node. To associate a volume display node with a volume node, call <pre>volumeNode->AddAndObserveDisplayNodeID(volumeRenderingDisplayNode->GetID());</pre> after both nodes are added to the scene.
		+
		+	''vtkSlicerVolumeRenderingLogic::CreateDefaultVolumeRenderingNodes'' method unnecessarily polluted the scene with ROI node even though the user did not need cropping. In Slicer-5.x we fixed the issue by not creating the ROI nodes automatically. To create a ROI node, you can call ''vtkSlicerVolumeRenderingLogic::CreateROINode'' method.

	====Extract skeleton====		====Extract skeleton====

← Older revision		Revision as of 22:48, 21 March 2022
Line 291:		Line 291:

	Charts and DoubleArrays module have been deprecated since about 2018 and got removed in November 2021. They are replaced by Plots and Tables modules.		Charts and DoubleArrays module have been deprecated since about 2018 and got removed in November 2021. They are replaced by Plots and Tables modules.
		+
		+	'''Example of commits'''
		+	* [https://github.com/SlicerRt/SlicerRT/commit/8f9155f94399be71e747d3d45b1f6c4152caa139 SlicerRT@8f9155f94] ENH: Update DVH module to use plots infrastructure instead of charts

	===Slicer 5.0 : Avoid typedef of anonymous structure===		===Slicer 5.0 : Avoid typedef of anonymous structure===

← Older revision		Revision as of 20:33, 3 February 2022
Line 209:		Line 209:

	See discussion of the topic [https://discourse.slicer.org/t/delete-control-point-delete-fiducial-pop-up-confirm-box/20430/18 here].		See discussion of the topic [https://discourse.slicer.org/t/delete-control-point-delete-fiducial-pop-up-confirm-box/20430/18 here].
		+
		+	===Slicer 5.0: SliceIntersectionVisibility was moved from vtkMRMLSliceCompositeNode to vtkMRMLSliceDisplayNode===
		+
		+	SliceIntersectionVisibility property (that controls if intersections of other slices should be displayed in the slice view) was stored in vtkMRMLSliceCompositeNode. This was not a good choice because the composite node stores what image layers should be displayed in the slice view and how (what opacity, what blending method, etc.). The property was kept in that class for a long time to preserve backward compatibility, but when interactive slice intersection feature was added and additional properties had to be added that control appearance and behavior of slice intersections, this property was moved into the new vtkMRMLSliceDisplayNode node type and renamed to IntersectingSlicesVisibility.
		+
		+	Scripts that previously used SliceIntersectionVisibility property will now fail with this error:
		+
		+	AttributeError: 'MRMLCore.vtkMRMLSliceCompositeNode' object has no attribute 'SetSliceIntersectionVisibility'
		+
		+	Those failing scripts can be updated with this example in the script repository: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#turn-on-slice-intersections

	===Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead===		===Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead===

@@ Line 190: / Line 190: @@
 * vtkImageErode was removed, vtkImageDilateErode3D (in VTK) can be used instead
 * vtkImageLabelChange was removed, vtkImageThreshold (in VTK) can be used instead
-* vtkImageSlicePaint was removed, ***
+* vtkImageSlicePaint was replaced by logic built into qSlicerSegmentEditorPaintEffect
 * vtkImageStash is replaced by vtkSegmentationHistory
 * vtkPichonFastMarching moved to SegmentEditorExtraEffects extension (https://github.com/lassoan/SlicerSegmentEditorExtraEffects)