Advanced Masking of Fields

[bryn]

A user recently asked me:

I have a field distribution from an EM solver in the brain. I would like to mask the field in the left amygdala, but I my model does not separate the left/right amygdala. How can this be done?

There are different approaches, but here are some suggestions:

1. Split the amygdala in the model BEFORE running the simulation. You can select the amygdala and use the Mesh Tools -> Separate Meshes. Assign the same material property to both (left/right) solid regions and then AFTER running the simulation mask e.g. just the left amygdala.

2. You already have run the simulation.

   • Mask the field to remove everything outside the amygdala,
   • Create a sphere around the left amygdala (e.g. called "Sphere Amygdala_left"
   • Mask the masked field with only the sphere region (by dragging it onto the masking list). This will remove everything outside the sphere, i.e., the field in the right amygdala.

Here is the second option in code:

simulation_extractor = simulation.Results()

# Add a EmSensorExtractor
em_sensor_extractor = simulation_extractor["Overall Field"]
em_sensor_extractor.FrequencySettings.ExtractedFrequency = u"All"
document.AllAlgorithms.Add(em_sensor_extractor)

# Add a FieldMaskingFilter
inputs = [em_sensor_extractor.Outputs["EM E(x,y,z,f0)"]]
field_masking_filter = analysis.core.FieldMaskingFilter(inputs=inputs)
field_masking_filter.UpdateAttributes()
for id, name in zip(field_masking_filter.MaterialIds(), field_masking_filter.MaterialNames()):
    field_masking_filter.SetMaterial(id, name == "Amygdala")
field_masking_filter.UpdateAttributes()
document.AllAlgorithms.Add(field_masking_filter)

# Add a second FieldMaskingFilter
inputs = [field_masking_filter.Outputs["EM E(x,y,z,f0)"]]
field_masking_filter_2 = analysis.core.FieldMaskingFilter(inputs=inputs)
field_masking_filter_2.UpdateAttributes()
for mat in field_masking_filter_2.MaterialIds():
    field_masking_filter_2.SetMaterial(mat, False)
field_masking_filter_2.SetEntities([model.AllEntities()["Sphere Amygdala_left"]])
field_masking_filter_2.UpdateAttributes()
document.AllAlgorithms.Add(field_masking_filter_2)

# Add a SliceFieldViewer
inputs = [field_masking_filter_2.Outputs["EM E(x,y,z,f0)"]]
slice_field_viewer = analysis.viewers.SliceFieldViewer(inputs=inputs)
slice_field_viewer.Data.Mode = slice_field_viewer.Data.Mode.enum.QuantityComplexModulus
slice_field_viewer.Data.Component = slice_field_viewer.Data.Component.enum.ComponentsAll
slice_field_viewer.Slice.Index = 23
slice_field_viewer.Update()
document.AllAlgorithms.Add(slice_field_viewer)

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