[algorithm] Clean up of the InsertionAlgorithm class (#45)

* [src] Added the .clang-format file from main SOFA repository

* [algorithm] Removed commented outputDist variable

* [algorithm] Added transparency to RGBAColor for the coupling points drawn

* [algorithm] Bring back the mstate that was deleted

* [algorithm] Set default boolean values for drawing to false

* [algorithm] Change name of sphereRadius to drawPointsScale

[scene] Adjust scene files

* [algorithm] Simplified syntax using typedefs for code brevity

* [algorithm] Removed unnecessary sofa:: namespace qualifier

* [algorithm] Re-organized variables' definition

* [algorithm] Renamed detection output variables to distinguish their use for either puncture or insertion

* [algorithm] Renamed link variables to BaseGeometry components

[scene] Changed scenes accordingly

    * Signify that the link is directed at a Geometry object
    * For the needle, the name signifies whether the Geometry refers to the tip or the shaft
    * For the punctured volume, the name signifies whether the Geometry will be used for:
        1. the puncture and, thus, only the surface is of interest or
        2. the insertion and, thus, the volume is now of interest
    * The user should not care whether puncture/insertion happens "from" the
      needle to the "destination" surface/volume. The user should be concerned
      with appropriately defining the tip and shaft geometry as well as the
      geometries of the punctured volumes and surfaces.

* [algorithm] Renamed Geometry iterators, Operations specializations and returned proximities

* [algorithm] Renamed threshold variables and re-wrote descriptions

[scene] Adjusted scenes accordingly

* [algorithm] Simplified link check in doDetection

* [algorithm] Simplified pointer checks against nullptr

* [algorithm] Format code using .clang-format shipped with main SOFA distro

* [algorithm] Replaced auto with ElementIterator::SPtr for clarity for iterators

* [algorithm] Replaced auto with BaseProximity::SPtr when returned from Operations functions

* [algorithm] Re-use tipProx pointer instead of re-creating one when projective is set to true

* [src] Delete .clang-format

Not really needed

Author: th-skam

scenes/InsertionGeomagic.py

@@ -180,18 +180,18 @@ def createScene(root):
 
 
     root.addObject("InsertionAlgorithm", name="InsertionAlgo", 
-        fromGeom="@Needle/tipCollision/geom_tip", 
-        destGeom="@Volume/collision/geom_tri", 
-        fromVol="@Needle/bodyCollision/geom_body", 
-        destVol="@Volume/geom_tetra", 
-        punctureThreshold=2., 
-        slideDistance=0.003,
+        tipGeom="@Needle/tipCollision/geom_tip", 
+        surfGeom="@Volume/collision/geom_tri", 
+        shaftGeom="@Needle/bodyCollision/geom_body", 
+        volGeom="@Volume/geom_tetra", 
+        punctureForceThreshold=2., 
+        tipDistThreshold=0.003,
         drawcollision=True,
-        sphereRadius=0.0001
+        drawPointsScale=0.0001
     )
     root.addObject("DistanceFilter",algo="@InsertionAlgo",distance=0.01)
     root.addObject("SecondDirection",name="punctureDirection",handler="@Volume/collision/SurfaceTriangles")
-    root.addObject("ConstraintUnilateral",input="@InsertionAlgo.output",directions="@punctureDirection",draw_scale=0.001, mu=0.001)
+    root.addObject("ConstraintUnilateral",input="@InsertionAlgo.collisionOutput",directions="@punctureDirection",draw_scale=0.001, mu=0.001)
 
     root.addObject("FirstDirection",name="bindDirection", handler="@Needle/bodyCollision/NeedleBeams")
-    root.addObject("ConstraintInsertion",input="@InsertionAlgo.outputList", directions="@bindDirection",draw_scale="0.01", frictionCoeff=0.000)
+    root.addObject("ConstraintInsertion",input="@InsertionAlgo.insertionOutput", directions="@bindDirection",draw_scale="0.01", frictionCoeff=0.000)

scenes/NeedleInsertion.py

@@ -179,18 +179,18 @@ def createScene(root):
 
 
     root.addObject("InsertionAlgorithm", name="InsertionAlgo", 
-        fromGeom="@Needle/tipCollision/geom_tip", 
-        destGeom="@Volume/collision/geom_tri", 
-        fromVol="@Needle/bodyCollision/geom_body", 
-        destVol="@Volume/geom_tetra", 
-        punctureThreshold=2., 
-        slideDistance=0.003,
+        tipGeom="@Needle/tipCollision/geom_tip", 
+        surfGeom="@Volume/collision/geom_tri", 
+        shaftGeom="@Needle/bodyCollision/geom_body", 
+        volGeom="@Volume/geom_tetra", 
+        punctureForceThreshold=2., 
+        tipDistThreshold=0.003,
         drawcollision=True,
-        sphereRadius=0.0001
+        drawPointsScale=0.0001
     )
     root.addObject("DistanceFilter",algo="@InsertionAlgo",distance=0.01)
     root.addObject("SecondDirection",name="punctureDirection",handler="@Volume/collision/SurfaceTriangles")
-    root.addObject("ConstraintUnilateral",input="@InsertionAlgo.output",directions="@punctureDirection",draw_scale=0.001)
+    root.addObject("ConstraintUnilateral",input="@InsertionAlgo.collisionOutput",directions="@punctureDirection",draw_scale=0.001)
 
     root.addObject("FirstDirection",name="bindDirection", handler="@Needle/bodyCollision/NeedleBeams")
-    root.addObject("ConstraintInsertion",input="@InsertionAlgo.outputList", directions="@bindDirection",draw_scale=0.002, frictionCoeff=0.05)
+    root.addObject("ConstraintInsertion",input="@InsertionAlgo.insertionOutput", directions="@bindDirection",draw_scale=0.002, frictionCoeff=0.05)

scenes/NeedleInsertionCycles.py

@@ -195,18 +195,18 @@ def createScene(root):
 
 
     root.addObject("InsertionAlgorithm", name="InsertionAlgo", 
-        fromGeom="@Needle/tipCollision/geom_tip", 
-        destGeom="@Volume/collision/geom_tri", 
-        fromVol="@Needle/bodyCollision/geom_body", 
-        destVol="@Volume/geom_tetra", 
-        punctureThreshold=2., 
-        slideDistance=0.003,
+        tipGeom="@Needle/tipCollision/geom_tip", 
+        surfGeom="@Volume/collision/geom_tri", 
+        shaftGeom="@Needle/bodyCollision/geom_body", 
+        volGeom="@Volume/geom_tetra", 
+        punctureForceThreshold=2., 
+        tipDistThreshold=0.003,
         drawcollision=True,
-        sphereRadius=0.0001
+        drawPointsScale=0.0001
     )
     root.addObject("DistanceFilter",algo="@InsertionAlgo",distance=0.01)
     root.addObject("SecondDirection",name="punctureDirection",handler="@Volume/collision/SurfaceTriangles")
-    root.addObject("ConstraintUnilateral",input="@InsertionAlgo.output",directions="@punctureDirection",draw_scale=0.001, mu=0.001)
+    root.addObject("ConstraintUnilateral",input="@InsertionAlgo.collisionOutput",directions="@punctureDirection",draw_scale=0.001, mu=0.001)
 
     root.addObject("FirstDirection",name="bindDirection", handler="@Needle/bodyCollision/NeedleBeams")
-    root.addObject("ConstraintInsertion",input="@InsertionAlgo.outputList", directions="@bindDirection",draw_scale=0.002, frictionCoeff=0.0023)
+    root.addObject("ConstraintInsertion",input="@InsertionAlgo.insertionOutput", directions="@bindDirection",draw_scale=0.002, frictionCoeff=0.0023)