Save and show neurostim points

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In GitLab by @RolandGuichard on Jul 18, 2019, 11:51

From the transform an actual point coordinates (?) save the location into a timestamped file and show the point under another sphere model (?) in the 3D viewer.

This is a sub-issue of #66

[tdowrick]

In GitLab by @RolandGuichard on Jul 18, 2019, 11:51

changed the description

[tdowrick]

In GitLab by @RolandGuichard on Jul 18, 2019, 12:04

changed the description

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In GitLab by @AnastasisGeorgoulas on Jul 18, 2019, 12:25

There are (at least) two options for showing the points. The first is to create a spherical model:

• Create a model

radius = 5  # for example
sphere = slicer.modules.createmodels.logic().CreateSphere(radius)
slicer.mrmlScene.AddNode(sphere)  # maybe not needed

• Set its display options

sphere.GetDisplayNode().SetColor(255, 0, 0)  # for red (RGB triplet)
# To show sphere outline in slice viewers:
sphere.GetDisplayNode().SetSliceIntersectionVisibility(True)

• Set its location, based on a transform neurostim_location_tf:

functions.set_parent_of_transform_hierarchy_node(sphere, neurostim_location_tf)

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In GitLab by @AnastasisGeorgoulas on Jul 18, 2019, 15:53

The second way is using the Markups module to add fiducials. In this case, we need the coordinates of the point rather than a transform:

• Create a fiducial:

slicer.modules.markups.logic().AddFiducial(coord_x, coord_y, coord_z)

• Change the colour of all points:

# Assuming there is only fiducial node
fidNode = slicer.util.getNode("vtkMRMLMarkupsFiducialNode1")
fidNode.GetDisplayNode().SetSelectedColor(255, 0, 0)

To show points in different colours (for example, depending on whether there was a response), we can use multiple fiducial lists. Can also check the Fiducial Registration module, which uses a transform instead of coordinates.

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In GitLab by @DavidPerez-Suarez on Aug 20, 2019, 17:13

I believe !20 implements this.

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In GitLab by @AnastasisGeorgoulas on Aug 21, 2019, 07:20

@DavidPerez-Suarez There is actually more work on that in the ageorgou/form-to-get-neurostim-point branch. That contains the code for showing the points and saving the voltage, among other things.