# Using Segment Editor effects programmatically

**URL:** <https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561>\
**Category:** Development\
**Tags:** segmentation, python\
**Created:** [May 15, 2020, 5:02pm UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561 "2020-05-15T17:02:41Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![mangotee](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Post date:** [May 15, 2020, 5:02pm UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561/1 "2020-05-15T17:02:41Z")

</div>

Hi all,  
I’m wondering how to script some simple steps from the Segment Editor. I know that there are a few recipes from Andras and others in this forum, which are great, thanks for the continuous support.  
In one of the recipes, there is a good example for thresholding:

```auto
#Thresholding
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold","35")
effect.setParameter("MaximumThreshold","695")
effect.self().onApply()

```

Now, the effect I wanna use programmatically is “Logical operators”, specifically I wanna create a hull, i.e. one segment that sums up all the other segments (in other words, a logical\_or of all segments contained in the segmentation node), which is easy to automate. The steps I need to do are:

1. Create a new segment (via node\_seg.GetSegmentation().AddSegment(‘hull’))
2. Copy the first segment into ‘hull’
3. Add all other segments into ‘hull’.

For this, and other simple steps… Is there a documentation on all the parameters of all effects.  
I was trying something like:

```auto
segmentEditorWidget.setActiveEffectByName("Logical operators")
effect = segmentEditorWidget.activeEffect()
effect.setParameter('Operation','Copy')

```

But I have no idea whether these parameters are correct (and there are no error messages, even if I enter random strings).

Thanks in advance!

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<div class="post-metadata">

**Author:** ![mangotee](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Post date:** [May 15, 2020, 6:35pm UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561/2 "2020-05-15T18:35:09Z")

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I found some more information [in this thread](https://discourse.slicer.org/t/scissors-segment-editor-effects-from-a-script/8348/2), and after activating the the “Logical operators” operations one-by-one, I got this list of parameters:

```auto
  Logical operators.BypassMasking:1
  Logical operators.ModifierSegmentID:Segment_11
  Logical operators.Operation:COPY
  Logical operators.Operation:UNION
  Logical operators.Operation:SUBTRACT
  Logical operators.Operation:INTERSECT
  Logical operators.Operation:INVERT
  Logical operators.Operation:CLEAR
  Logical operators.Operation:FILL

```

I will try a bit more, but for future reference, is there a documentation page with the full list of these parameters?

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [May 16, 2020, 4:46am UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561/3 "2020-05-16T04:46:55Z")

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It would be nice to create separate documentation for these - contributions are welcome!

@jcfr, do you have any suggestions for documenting segment editor effect parameters? It would be nice if documentation would be available at the same place for C++ and Python effects. I could create a new markdown file in developer\_guide and describe parameters of the effects there, but it would be a bit nicer if the description could be in each effect’s .py or .h file. Could ReadTheDocs fetch documentation from segment editor effect source files (currently [Developer guide](https://slicer.readthedocs.io/en/latest/developer_guide/api.html) does not seem to be able to get anything from there).

Until separate documentation is written, then open source code is _the_ documentation. You can find the relevant file by Google search. For example first hit when searching for `github slicer Logical operators` takes you to [SegmentEditorLogicalEffect.py](https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorLogicalEffect.py). For all Segment Editor effects, `setMRMLDefaults` method contains the list of parameters that the effect uses. If there are constants then they are typically defined at the bottom of the file.

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<div class="post-metadata">

**Author:** ![Fangwen\_Zhai](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fangwen_zhai/32/6001_2.png) [@Fangwen\_Zhai](https://discourse.slicer.org/u/Fangwen_Zhai)\
**Post date:** [August 3, 2020, 6:00pm UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561/4 "2020-08-03T18:00:21Z")

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Could you please elaborate a bit more on calling python effects from C++, for example, what is the C++ equivalence of `effect.self.OnApply()`?

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 3, 2020, 7:25pm UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561/5 "2020-08-03T19:25:25Z")

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See this topic for details about how to run Python code from C++:

> [@Calling Python from C++](https://discourse.slicer.org/t/calling-python-from-c/7841/10):
>
> There are several options for calling Python from C++ (one of them is shown in my comment above, using evalScript) and it is done at many places in Slicer. However, C++ modules provide low-level infrastructure, so it would not make sense for a C++ module to depend on Python. If you want to implement some performance-critical processing in C++ but other features are in Python then I would recommend to: create a hidden C++ loadable module that just implements performance-critical processing in …

For more complex Python calls, search for “pythonmanager” in Slicer source code.

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<div class="post-metadata">

**Author:** ![mangotee](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Post date:** [August 31, 2020, 10:33am UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561/6 "2020-08-31T10:33:03Z")

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Hi Andras,  
few weeks ago, I found an alternative way to solve my problem, but now I had to come back to using segment editor effects, in more detail. This time I managed to solve a few problems, one of them was how to use the “logical operators” effect programmatically. You already provide a lot of examples for scripted effects [here](https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#How_to_run_segment_editor_effects_from_a_script), but there is no example for the logical effects. Actually it’s simple, but I needed to sift through the source code a bit. Maybe this example will help others to save some time.

```
# Run segment editor effects from script

# Prerequisites 1/2: 
# Create segment editor widget and node to get scripted access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)

# Prerequisites 2/2:
# nvol ... the reference volume node for the segmentation
# nseg ... the segmentation node
# 'tgtseg' is the name of the target segment, i.e. the region that is being edited
# 'srcseg' is the name of the source segment, i.e. the region from which information is being "transferred" by the logical operator
# Setting up the nodes to be edited
segmentEditorWidget.setSegmentationNode(nseg)
segmentEditorWidget.setMasterVolumeNode(nvol)
# Set overwrite mode: 0/1/2 -> overwrite all/visible/none
segmentEditorNode.SetOverwriteMode(2) # i.e. "allow overlap" in UI
# Get the segment IDs
segid_tgt = nseg.GetSegmentation().GetSegmentIdBySegmentName('tgtseg')
segid_src = nseg.GetSegmentation().GetSegmentIdBySegmentName('srcseg')

# Running the effect:
# The logical operation is set via strings
# 'COPY', 'UNION', 'INTERSECT', 'SUBTRACT', 'INVERT', 'CLEAR', 'FILL'
# (see: https://apidocs.slicer.org/master/SegmentEditorLogicalEffect_8py_source.html)    
segmentEditorNode.SetSelectedSegmentID(segid_tgt)
segmentEditorWidget.setActiveEffectByName("Logical operators")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation","COPY") # change the operation here
effect.setParameter("ModifierSegmentID",segid_src)
effect.self().onApply()
```

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 31, 2020, 7:56pm UTC](https://discourse.slicer.org/t/using-segment-editor-effects-programmatically/11561/7 "2020-08-31T19:56:44Z")

</div>

Thanks a lot for sharing.