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Pr test #1

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b88aa75
Quantal lips simulation changes
connormayer Jun 1, 2020
e548bb9
Removed temp files
connormayer Jun 1, 2020
37bf7fa
Changes for perturbation simulations
connormayer Jun 4, 2020
df201cb
Merge remote-tracking branch 'upstream/master' into quantal_lips
connormayer Jun 10, 2020
df447ff
Merge remote-tracking branch 'origin/master' into quantal_lips
connormayer Jul 29, 2021
6251df6
Merge branch 'master' of https://github.com/artisynth/artisynth_model…
connormayer Nov 3, 2022
5e17e13
Quantal lips stuff
connormayer Nov 15, 2022
f61052e
Got BatchSim working
connormayer Nov 17, 2022
bf6eb07
Added contact points
connormayer Nov 17, 2022
8616e80
Commit
connormayer Dec 7, 2022
564a2f6
Blah
connormayer May 13, 2025
4e406c6
Blah
connormayer May 13, 2025
dec580c
Turned down print rate
connormayer May 13, 2025
51bc0b8
My great commit
connormayer Jun 23, 2025
e32e244
Merge branch 'tentacles' of github.com:connormayer/artisynth_models i…
connormayer Jun 23, 2025
3f991ec
Added new file
connormayer Jun 24, 2025
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6 changes: 6 additions & 0 deletions .project
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Expand Up @@ -5,6 +5,11 @@
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.python.pydev.PyDevBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
Expand All @@ -13,5 +18,6 @@
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.python.pydev.pythonNature</nature>
</natures>
</projectDescription>
1 change: 0 additions & 1 deletion classes/DONT_DELETE
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213 changes: 213 additions & 0 deletions src/_sources_.txt
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@@ -0,0 +1,213 @@
./artisynth/models/dynjaw/DeformedJawDemoX.java
./artisynth/models/dynjaw/DigastricMuscle.java
./artisynth/models/dynjaw/FoodBolus.java
./artisynth/models/dynjaw/JawDemo.java
./artisynth/models/dynjaw/JawGraft.java
./artisynth/models/dynjaw/JawHemi.java
./artisynth/models/dynjaw/JawLarynxDemo.java
./artisynth/models/dynjaw/JawLongPharyngealDemo.java
./artisynth/models/dynjaw/JawMarxGraft.java
./artisynth/models/dynjaw/JawModel.java
./artisynth/models/dynjaw/JawPanel.java
./artisynth/models/dynjaw/OrthoSpring.java
./artisynth/models/dynjaw/PharynxDemo.java
./artisynth/models/dynjaw/PlanarSpring.java
./artisynth/models/dynjaw/RajJawLarynxDemo.java
./artisynth/models/dynjaw/ScarSpring.java
./artisynth/models/face/AnsysFaceMuscleFiberReader.java
./artisynth/models/face/BadinFaceDemo.java
./artisynth/models/face/BadinFaceDemoLipOpening.java
./artisynth/models/face/BadinFemMuscleFaceDemo.java
./artisynth/models/face/BadinJawFaceDemo.java
./artisynth/models/face/BadinJawTongueFaceDemo.java
./artisynth/models/face/BadinJawTongueFaceTension.java
./artisynth/models/face/BadinWithProbe2.java
./artisynth/models/face/JawFaceLarynxDemo.java
./artisynth/models/face/MeshEdit.java
./artisynth/models/face/OpeningTest.java
./artisynth/models/face/RefFaceDemo.java
./artisynth/models/face/RefFaceWithProbe.java
./artisynth/models/face/RefFemMuscleFaceDemo.java
./artisynth/models/jawTongue/AirwaySkin.java
./artisynth/models/jawTongue/AirwaySkinDemo.java
./artisynth/models/jawTongue/AirwayXsectionDemo.java
./artisynth/models/jawTongue/BadinDataDemo.java
./artisynth/models/jawTongue/BadinJawHyoid.java
./artisynth/models/jawTongue/BadinJawHyoidTongue.java
./artisynth/models/jawTongue/BadinJawHyoidTongueContact.java
./artisynth/models/jawTongue/BadinJawHyoidTongueContactBatchWorker.java
./artisynth/models/jawTongue/ContactMeasurer.java
./artisynth/models/jawTongue/DistanceMonitor.java
./artisynth/models/jawTongue/FemBlendController.java
./artisynth/models/jawTongue/IsBatchable.java
./artisynth/models/jawTongue/JawHyoidFemMuscleTongue.java
./artisynth/models/jawTongue/KinematicSoftPalateDemo.java
./artisynth/models/jawTongue/MeshBlendController.java
./artisynth/models/jawTongue/SoftPalateBracingDemo.java
./artisynth/models/jawTongue/StaticJawHyoidTongue.java
./artisynth/models/jawTongue/TongueBracingDemo.java
./artisynth/models/larynx/VHLarynxDemo.java
./artisynth/models/larynx/VHLarynxDemo_intrinsic.java
./artisynth/models/larynx/VHLarynxInvDemo.java
./artisynth/models/larynx_QL2/AbstractSimulation.java
./artisynth/models/larynx_QL2/components/AbstractBody.java
./artisynth/models/larynx_QL2/components/Contractile.java
./artisynth/models/larynx_QL2/components/Diarthrotic.java
./artisynth/models/larynx_QL2/components/HardBody.java
./artisynth/models/larynx_QL2/components/LegacyReaders.java
./artisynth/models/larynx_QL2/components/Ligamentous.java
./artisynth/models/larynx_QL2/components/Names.java
./artisynth/models/larynx_QL2/components/PointBody.java
./artisynth/models/larynx_QL2/components/SoftBody.java
./artisynth/models/larynx_QL2/components/StructureBase.java
./artisynth/models/larynx_QL2/components/Structures.java
./artisynth/models/larynx_QL2/components/Tissue.java
./artisynth/models/larynx_QL2/DriverListener.java
./artisynth/models/larynx_QL2/LarynxQL2.java
./artisynth/models/larynx_QL2/tools/AuxTools.java
./artisynth/models/larynx_QL2/tools/ColorTools.java
./artisynth/models/larynx_QL2/tools/ControlTools.java
./artisynth/models/larynx_QL2/tools/FemTools.java
./artisynth/models/larynx_QL2/tools/GeometryTools.java
./artisynth/models/larynx_QL2/tools/Neighbour.java
./artisynth/models/larynx_QL2/tools/RenderTools.java
./artisynth/models/larynx_QL2/VocalTractBase.java
./artisynth/models/mandibleOpening/mandibleOpening_1_2016_11_26.java
./artisynth/models/palate/JawTongueSoftPalate.java
./artisynth/models/palate/RegisteredSoftPalate.java
./artisynth/models/palate/SoftPalateDemo.java
./artisynth/models/palate/SoftPalateModel.java
./artisynth/models/palate/SoftPalate_spring.java
./artisynth/models/palate/SoftPalate_springPeter.java
./artisynth/models/palateV2/SoftPalateModel.java
./artisynth/models/palateV2/SoftPalateMuscles.java
./artisynth/models/palateV2/SoftPalateProbes.java
./artisynth/models/quantalLips/QuantalLipsBatchWorker.java
./artisynth/models/registration/AttachmentForceUtilities.java
./artisynth/models/registration/correspondences/DirectMeshCorrespondence.java
./artisynth/models/registration/correspondences/GMMMeshCorrespondence.java
./artisynth/models/registration/correspondences/ICPMeshCorrespondence.java
./artisynth/models/registration/correspondences/MeshCorrespondenceComputer.java
./artisynth/models/registration/correspondences/TargetGMMMeshCorrespondence.java
./artisynth/models/registration/demos/ArticulatedRegistrationDemo.java
./artisynth/models/registration/demos/EmbeddedRegistrationDemo.java
./artisynth/models/registration/demos/FemRegistrationDemo.java
./artisynth/models/registration/demos/RigidRegistrationDemo.java
./artisynth/models/registration/demos/SpineRegistrationDemo.java
./artisynth/models/registration/DynamicRegistrationController.java
./artisynth/models/registration/MeshCorrespondenceController.java
./artisynth/models/registration/old/MeshRegistrationController.java
./artisynth/models/registration/old/MeshRegistrationForce.java
./artisynth/models/registration/old/PressureMeshRegistrationForce.java
./artisynth/models/registration/old/pressures/GaussianPressureFunction.java
./artisynth/models/registration/old/pressures/GravityPressureFunction.java
./artisynth/models/registration/old/pressures/LogNormalPressureFunction.java
./artisynth/models/registration/old/pressures/RegistrationPressureFunction.java
./artisynth/models/registration/old/pressures/SpringPressureFunction.java
./artisynth/models/registration/TargetMesh.java
./artisynth/models/registration/test/FrameFrameForceTest.java
./artisynth/models/registration/test/FrameRegistrationTest.java
./artisynth/models/registration/weights/ConstantWeightFunction.java
./artisynth/models/registration/weights/GaussianWeightFunction.java
./artisynth/models/registration/weights/RegistrationWeightFunction.java
./artisynth/models/template/FemMuscleBlock.java
./artisynth/models/template/HybridFemFactoryDemo.java
./artisynth/models/template/ModelTemplate.java
./artisynth/models/template/testFemMuscle.java
./artisynth/models/template/testInverseX.java
./artisynth/models/tongue3d/AnsysMuscleElemReader.java
./artisynth/models/tongue3d/AnsysMuscleFiberReader.java
./artisynth/models/tongue3d/FemMuscleTongueDemo.java
./artisynth/models/tongue3d/HexTongueDemo.java
./artisynth/models/tongue3d/QuadhexTongueDemo.java
./artisynth/models/tongue3d/StableFemMuscleTongueDemo.java
./artisynth/models/tongue3d/TetTongueDemo.java
./artisynth/models/tongue3d/TongueInvDemo.java
./artisynth/models/tongue3d/TongueLollipop.java
./artisynth/models/tubesounds/Airway.java
./artisynth/models/tubesounds/AirwayMesh.java
./artisynth/models/tubesounds/AreaFunctionPlotter.java
./artisynth/models/tubesounds/PolygonalSection.java
./artisynth/models/tubesounds/SectionedMesh.java
./artisynth/models/tubesounds/SectionedMeshNormalizer.java
./artisynth/models/tubesounds/TextSpeechDlg.java
./artisynth/models/tubesounds/TubeData.java
./artisynth/models/tubesounds/VoiceProbeMaker.java
./artisynth/models/tubesounds/VTNTDemo.java
./artisynth/models/vkhUpperAirway/SkinMeshMulti.java
./artisynth/models/vkhUpperAirway/SkinMeshRBF.java
./artisynth/models/vkhUpperAirway/VKHUpperAirwayDemo.java
./artisynth/models/vkhUpperAirway/VKHUpperAirwaySwallowingDemo.java
./artisynth/models/vkhUpperAirway/VKHUpperAirwaySwallowingWA.java
./artisynth/models/vkhUpperAirway/VKHUpperAirwayWA.java
./artisynth/tools/batchsim/BatchWorkerBase.java
./artisynth/tools/batchsim/conditions/Condition.java
./artisynth/tools/batchsim/conditions/ConditionChecker.java
./artisynth/tools/batchsim/conditions/ConditionCheckerBase.java
./artisynth/tools/batchsim/conditions/ConditionMonitor.java
./artisynth/tools/batchsim/conditions/ConvergenceCheckerList.java
./artisynth/tools/batchsim/conditions/EmptyCondition.java
./artisynth/tools/batchsim/conditions/EquilibriumChecker.java
./artisynth/tools/batchsim/conditions/NotChecker.java
./artisynth/tools/batchsim/conditions/package-info.java
./artisynth/tools/batchsim/conditions/StopConditionMonitor.java
./artisynth/tools/batchsim/conditions/TimeChecker.java
./artisynth/tools/batchsim/example/SpringMeshDemoBatchWorker.java
./artisynth/tools/batchsim/manager/BatchManager.java
./artisynth/tools/batchsim/manager/CombinationChecker.java
./artisynth/tools/batchsim/manager/DistributionSampler.java
./artisynth/tools/batchsim/manager/FileParser.java
./artisynth/tools/batchsim/manager/JythonCodeBlock.java
./artisynth/tools/batchsim/manager/Printable.java
./artisynth/tools/batchsim/manager/PropertySpecification.java
./artisynth/tools/batchsim/manager/Utils.java
./artisynth/tools/batchsim/package-info.java
./artisynth/tools/batchsim/SimpleTimedBatchWorker.java
./artisynth/tools/batchsim/test/SimTaskRequester.java
./artisynth/tools/exReader/CmissFileManager.java
./artisynth/tools/exReader/ExElement.java
./artisynth/tools/exReader/ExElementComparator.java
./artisynth/tools/exReader/ExFace.java
./artisynth/tools/exReader/ExLine.java
./artisynth/tools/exReader/ExMeshGenerator.java
./artisynth/tools/exReader/ExNode.java
./artisynth/tools/exReader/ExNodeComparator.java
./artisynth/tools/exReader/ExNodeComponent.java
./artisynth/tools/exReader/ExNodeField.java
./artisynth/tools/exReader/ExParser.java
./artisynth/tools/exReader/ExRegion.java
./artisynth/tools/exReader/ExWriter.java
./artisynth/tools/exReader/NodeInterpolator.java
./artisynth/tools/exReader/NodeOrderingException.java
./artisynth/tools/exReader/TangentFlipper.java
./artisynth/tools/exReader/tests/FemArmTest.java
./artisynth/tools/exReader/tests/FemLegTest.java
./artisynth/tools/exReader/tests/SurfaceMeshes.java
./artisynth/tools/femtool/DynamicFemFixer.java
./artisynth/tools/femtool/DynamicFemFixerController.java
./artisynth/tools/femtool/DynamicFemFixerMultiController.java
./artisynth/tools/femtool/FemFixHexTest.java
./artisynth/tools/femtool/FemFixTest.java
./artisynth/tools/femtool/FemFixTestToy.java
./artisynth/tools/femtool/FemTools.java
./artisynth/tools/femtool/HybridFemFactory.java
./artisynth/tools/femtool/HybridFemGenerator.java
./artisynth/tools/femtool/InteractiveFemCreator.java
./artisynth/tools/femtool/QHullSurfaceForceController.java
./artisynth/tools/femtool/SimpleVolumeGenerator.java
./artisynth/tools/femtool/SurfaceForceController.java
./artisynth/tools/femtool/SymmetricSurfaceForceController.java
./artisynth/tools/femtool/VolumeScalingController.java
./artisynth/tools/femtool/VolumetricMeshGenerator.java
./artisynth/tools/rotation/demos/AxisArmDemo.java
./artisynth/tools/rotation/demos/AxisDemo.java
./artisynth/tools/rotation/IHAComputer.java
./artisynth/tools/rotation/InstantaneousHelicalAxis.java
./artisynth/tools/rotation/PlaneIntersectionRotationAxis.java
./artisynth/tools/rotation/PlaneProjectionRotationAxis.java
./artisynth/tools/rotation/PlaneProjectionRotationComputer.java
./artisynth/tools/rotation/Rotation2DComputer.java
./artisynth/tools/rotation/RotationAxis.java
./artisynth/tools/rotation/RotationAxis2D.java
./artisynth/tools/rotation/RotationAxisComputer.java
./artisynth/tools/rotation/RotationController.java
17 changes: 8 additions & 9 deletions src/artisynth/models/face/BadinFaceDemoLipOpening.java
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Expand Up @@ -281,7 +281,7 @@ public void attach(DriverInterface driver) {
}

getMainViewer().setOrthographicView(true);
getMainFrame ().setSize (1053, 1113); // 1000 x 1000 viewer
getMainFrame ().setSize (1000, 1000); // 1000 x 1000 viewer
getMainViewer().setAxialView (AxisAlignedRotation.NY_Z);

// Chenhao view
Expand All @@ -292,8 +292,8 @@ public void attach(DriverInterface driver) {
setViewerEye (new Point3d(-0.521787, 0.0009809, -0.126136));
setViewerCenter (new Point3d(0.134664, 0.0009809, 0.117214));
//connor view
// setViewerEye (new Point3d(-0.56632, 0.000422501, 0.107807));
// setViewerCenter (new Point3d(0.134409, 0.000422502, 0.107807));
// setViewerEye (new Point3d(-0.56632, 0.000422501, 0.107807));
// setViewerCenter (new Point3d(0.134409, 0.000422502, 0.107807));
getMainViewer().zoom(0.5);
}

Expand All @@ -305,7 +305,6 @@ private static Rectangle getViewerBounds(GLViewer viewer) {
area.y = viewer.getScreenY();
return area;
}


/**
* Method to get the distance between this pixel's color and the passed color
Expand Down Expand Up @@ -363,11 +362,11 @@ public double getLipOpeningArea() {
}
}
}
System.out.println("opening pixels = "+cnt);
for (int i = 0; i < pixelColors.size (); i++) {
System.out.println("pixel color = "+pixelColors.get (i)+" "+pixelCnts.get (i));
}
System.out.println("opening color = "+openingColor+" matching colors = "+cnt);
// System.out.println("opening pixels = "+cnt);
// for (int i = 0; i < pixelColors.size (); i++) {
// System.out.println("pixel color = "+pixelColors.get (i)+" "+pixelCnts.get (i));
// }
// System.out.println("opening color = "+openingColor+" matching colors = "+cnt);
double distPerPixel = getMainViewer().distancePerPixel (Vector3d.ZERO);
openingArea = distPerPixel*distPerPixel*cnt*1000000; // meter to mm conversion
System.out.println("dist-per-pixel = "+distPerPixel+"; opening area = "+openingArea);
Expand Down
2 changes: 1 addition & 1 deletion src/artisynth/models/jawTongue/BadinJawHyoidTongue.java
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Expand Up @@ -63,7 +63,7 @@ public String getAbout() {
boolean useIcpMuscleDefs = true;
boolean useIncompressibleConstraint = true;
boolean doActivationStiffening = true;

// Here's a comment
public static final TongueType DEFAULT_TONGUE_TYPE = TongueType.HexLineMuscles;

public enum TongueType {
Expand Down
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