Switch over to using cmlibs.maths 0.6.0 for math functions.

setup.py

@@ -25,7 +25,7 @@ def readfile(filename, split=False):
 # into the 'requirements.txt' file.
 requires = [
     # minimal requirements listing
-    "cmlibs.maths >= 0.3",
+    "cmlibs.maths >= 0.6",
     "cmlibs.utils >= 0.6",
     "cmlibs.zinc >= 4.1",
     "scipy",

src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py

@@ -5,6 +5,7 @@
 import copy
 import math
 
+from cmlibs.maths.vectorops import angle
 from cmlibs.zinc.element import Element
 from cmlibs.zinc.field import Field
 from cmlibs.zinc.node import Node
@@ -17,7 +18,6 @@
 from scaffoldmaker.utils import interpolation as interp
 from scaffoldmaker.utils import matrix
 from scaffoldmaker.utils import tubemesh
-from scaffoldmaker.utils import vector
 from scaffoldmaker.utils.geometry import createEllipsePoints
 from scaffoldmaker.utils.tracksurface import TrackSurface
 from scaffoldmaker.utils.zinc_utils import exnode_string_from_nodeset_field_parameters
@@ -528,7 +528,7 @@ def generateBaseMesh(cls, region, options):
         #     v1 = xEllipsoid[n]
         #     v2 = xEllipsoid[n + elementsCountAround // 2]
         #     v1v2 = [v2[c] - v1[c] for c in range(3)]
-        #     mag = vector.magnitude(v1v2)
+        #     mag = magnitude(v1v2)
         #     halfMag = mag / 2
         #     d2path.append([0.0, -halfMag, 0.0])
         #     d3path.append([0.0, 0.0, halfMag])
@@ -567,7 +567,7 @@ def generateBaseMesh(cls, region, options):
 
         # Flat coordinates
         xFlat = d1Flat = d2Flat = []
-        # urethraOpeningRadius = vector.magnitude(sx_neck_group[2][-1])
+        # urethraOpeningRadius = magnitude(sx_neck_group[2][-1])
         # xFlat, d1Flat, d2Flat = obtainBladderFlatNodes(elementsCountAlongBladder, elementsCountAround,
         #                                                elementsCountThroughWall, xFinal, d1Final, d2Final,
         #                                                bladderCentralPathLength, urethraOpeningRadius, wallThickness)
@@ -798,7 +798,7 @@ def findDerivativeBetweenPoints(v1, v2):
     """
     d = [v2[c] - v1[c] for c in range(3)]
     arcLengthAround = interp.computeCubicHermiteArcLength(v1, d, v2, d, True)
-    d = [c * arcLengthAround for c in vector.normalise(d)]
+    d = [c * arcLengthAround for c in normalize(d)]
 
     return d
 
@@ -810,8 +810,8 @@ def findNodesAlongBladderDome(sx_dome_group, elementsCountAround, elementsCountA
     d2 = sx_dome_group[2][0]
     for n1 in range(elementsCountAround):
         rotAngle = n1 * 2.0 * math.pi / elementsCountAround
-        rotAxis = vector.normalise(vector.crossproduct3(vector.normalise(sx_dome_group[2][0]),
-                                                        vector.normalise(sx_dome_group[4][0])))
+        rotAxis = normalize(cross(normalize(sx_dome_group[2][0]),
+                                                        normalize(sx_dome_group[4][0])))
         rotFrame = matrix.getRotationMatrixFromAxisAngle(rotAxis, rotAngle)
         d2Rot = [rotFrame[j][0] * d2[0] + rotFrame[j][1] * d2[1] + rotFrame[j][2] * d2[2] for j in range(3)]
         d2Apex.append(d2Rot)
@@ -946,9 +946,9 @@ def findNodesAlongBladderNeck(sx_dome_group, sx_neck_group, d2SampledDome, domeS
                 v1 = xEllipses_neck[n2 - 1][n1]
                 v2 = xEllipses_neck[n2][n1]
                 d2vec = findDerivativeBetweenPoints(v1, v2)
-                d2mag = vector.magnitude(d2vec)
-                d2dir = vector.normalise(sx_neck_group[1][-1])
-                d2 = vector.setMagnitude(d2dir, d2mag)
+                d2mag = magnitude(d2vec)
+                d2dir = normalize(sx_neck_group[1][-1])
+                d2 = set_magnitude(d2dir, d2mag)
             else:
                 v1 = xEllipses_neck[n2 - 1][n1]
                 v2 = xEllipses_neck[n2][n1]
@@ -1050,7 +1050,7 @@ def obtainBladderFlatNodes(elementsCountAlongBladder, elementsCountAround, eleme
     # Find the angle at the bottom of the bladder neck
     v1 = [0.0, 0.0, bladderLength]
     v2 = [urethraOpeningRadius, 0.0, bladderLength]
-    alpha = vector.angleBetweenVectors(v1, v2)
+    alpha = angle(v1, v2)
 
     # Find apex to urethra arcLength in minor radius
     xApexInner = xFinal[0]
@@ -1167,8 +1167,8 @@ def obtainBladderFlatNodes(elementsCountAlongBladder, elementsCountAround, eleme
     v3 = xfnListRearranged[elementsCountAround // 2]
     v21 = [v2[c] - v1[c] for c in range(3)]
     v31 = [v3[c] - v1[c] for c in range(3)]
-    d1Mag = vector.magnitude(v21)
-    d2Mag = vector.magnitude(v31)
+    d1Mag = magnitude(v21)
+    d2Mag = magnitude(v31)
 
     # Add apex nodes to the list
     xFlat = []
@@ -1314,8 +1314,8 @@ def getBladderCoordinates(elementsCountAlongDome, elementsCountAlongNeck, elemen
     for n2 in range(1, elementsCountAlongBladder + 1):
         d3Around = []
         for n1 in range(elementsCountAround):
-            d3Around.append(vector.normalise(
-                vector.crossproduct3(vector.normalise(d1SampledAll[n2][n1]), vector.normalise(d2SampledAll[n2][n1]))))
+            d3Around.append(normalize(
+                cross(normalize(d1SampledAll[n2][n1]), normalize(d2SampledAll[n2][n1]))))
         d3UnitOuter.append(d3Around)
 
     # Inner nodes
@@ -1349,12 +1349,12 @@ def getBladderCoordinates(elementsCountAlongDome, elementsCountAlongNeck, elemen
     # Arclength between apex point and corresponding point on next face
     mag = interp.getCubicHermiteArcLength(xList[n - 1], d2List[n - 1], xList[2 * n - 1],
                                           d2List[2 * n - 1])
-    d2ApexOuter = vector.setMagnitude(sx_dome_group[2][0], mag)
+    d2ApexOuter = set_magnitude(sx_dome_group[2][0], mag)
 
-    d1ApexOuter = vector.crossproduct3(sx_dome_group[1][0], d2ApexOuter)
-    d1ApexOuter = vector.setMagnitude(d1ApexOuter, mag)
-    d3ApexUnit = vector.normalise(
-        vector.crossproduct3(vector.normalise(d1ApexOuter), vector.normalise(d2ApexOuter)))
+    d1ApexOuter = cross(sx_dome_group[1][0], d2ApexOuter)
+    d1ApexOuter = set_magnitude(d1ApexOuter, mag)
+    d3ApexUnit = normalize(
+        cross(normalize(d1ApexOuter), normalize(d2ApexOuter)))
     d3ApexOuter = [d3ApexUnit[c] * wallThickness / elementsCountThroughWall for c in range(3)]
 
     # Final nodes on the bladder

src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py

@@ -22,7 +22,6 @@
 from scaffoldmaker.utils import interpolation as interp
 from scaffoldmaker.utils import matrix
 from scaffoldmaker.utils import tubemesh
-from scaffoldmaker.utils import vector
 from scaffoldmaker.utils.annulusmesh import createAnnulusMesh3d
 from scaffoldmaker.utils.geometry import createEllipsePoints
 from scaffoldmaker.utils.interpolation import smoothCubicHermiteDerivativesLine
@@ -871,7 +870,7 @@ def generateBaseMesh(cls, region, options):
         innerRadiusAlong = []
         for n2 in range(elementsCountAlong + 1):
             firstNodeAlong = innerNodes_x[n2 * elementsCountAround]
-            radius = vector.magnitude(firstNodeAlong[c] - [0.0, 0.0, firstNodeAlong[2]][c] for c in range(3))
+            radius = magnitude(firstNodeAlong[c] - [0.0, 0.0, firstNodeAlong[2]][c] for c in range(3))
             innerRadiusAlong.append(radius)
 
         # Warp points
@@ -907,11 +906,11 @@ def generateBaseMesh(cls, region, options):
         # Arclength between apex point and corresponding point on next face
         mag = interp.getCubicHermiteArcLength(xList[0], d2List[0], xList[2 * elementsCountAround],
                                               d2List[2 * elementsCountAround])
-        d2ApexInner = vector.setMagnitude(sd2[0], mag)
-        d1ApexInner = vector.crossproduct3(sd1[0], d2ApexInner)
-        d1ApexInner = vector.setMagnitude(d1ApexInner, mag)
-        d3ApexUnit = vector.normalise(
-            vector.crossproduct3(vector.normalise(d1ApexInner), vector.normalise(d2ApexInner)))
+        d2ApexInner = set_magnitude(sd2[0], mag)
+        d1ApexInner = cross(sd1[0], d2ApexInner)
+        d1ApexInner = set_magnitude(d1ApexInner, mag)
+        d3ApexUnit = normalize(
+            cross(normalize(d1ApexInner), normalize(d2ApexInner)))
         d3ApexInner = [d3ApexUnit[c] * bladderWallThickness / elementsCountThroughWall for c in range(3)]
 
         xFinal = []
@@ -1390,7 +1389,7 @@ def generateUreterInlets(region, nodes, mesh, ureterDefaultOptions, elementsCoun
         ureterElementPositionAround + (1 if ureter1Position.xi1 > 0.5 else 0)
     ureter1StartCornerx = xBladder[endPointStartId1 - 1]
     v1 = [(ureter1StartCornerx[c] - centerUreter1_x[c]) for c in range(3)]
-    ureter1Direction = vector.crossproduct3(td3, v1)
+    ureter1Direction = cross(td3, v1)
     nodeIdentifier, elementIdentifier, (o1_x, o1_d1, o1_d2, _, o1_NodeId, o1_Positions) = \
         generateOstiumMesh(region, ureterDefaultOptions, trackSurfaceUreter1, ureter1Position, ureter1Direction,
                            startNodeIdentifier=nextNodeIdentifier, startElementIdentifier=nextElementIdentifier,
@@ -1406,7 +1405,7 @@ def generateUreterInlets(region, nodes, mesh, ureterDefaultOptions, elementsCoun
                        elementsCountAround - ureterElementPositionAround + (-1 if ureter1Position.xi1 > 0.5 else 0)
     ureter2StartCornerx = xBladder[endPointStartId2 - 1]
     v2 = [(ureter2StartCornerx[c] - centerUreter2_x[c]) for c in range(3)]
-    ureter2Direction = vector.crossproduct3(ad3, v2)
+    ureter2Direction = cross(ad3, v2)
     nodeIdentifier, elementIdentifier, (o2_x, o2_d1, o2_d2, _, o2_NodeId, o2_Positions) = \
         generateOstiumMesh(region, ureterDefaultOptions, trackSurfaceUreter2, ureter2Position, ureter2Direction,
                            startNodeIdentifier=nodeIdentifier, startElementIdentifier=elementIdentifier,
@@ -1594,7 +1593,7 @@ def obtainBladderFlatNodes(elementsCountAlongBladder, elementsCountAround, eleme
     # Find the angle at the bottom of the bladder neck
     v1 = [0.0, 0.0, bladderLength]
     v2 = [0.5 * neckDiameter1, 0.0, bladderLength]
-    alpha = vector.angleBetweenVectors(v1, v2)
+    alpha = angle(v1, v2)
 
     # Find apex to urethra arcLength in minor radius
     minorNodeAlong_x.insert(0, xApexInner)
@@ -1708,8 +1707,8 @@ def obtainBladderFlatNodes(elementsCountAlongBladder, elementsCountAround, eleme
     v3 = xfnListRearranged[elementsCountAround // 2]
     v21 = [v2[c] - v1[c] for c in range(3)]
     v31 = [v3[c] - v1[c] for c in range(3)]
-    d1Mag = vector.magnitude(v21)
-    d2Mag = vector.magnitude(v31)
+    d1Mag = magnitude(v21)
+    d2Mag = magnitude(v31)
 
     # Add apex nodes to the list
     xFlat = []

src/scaffoldmaker/meshtypes/meshtype_3d_bone1.py

@@ -7,21 +7,19 @@
 
 import copy
 
+from cmlibs.maths.vectorops import add_vectors
 from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
 from cmlibs.utils.zinc.finiteelement import getMaximumNodeIdentifier, getMaximumElementIdentifier
 from cmlibs.zinc.field import Field
 from cmlibs.zinc.node import Node
 from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1
 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base
 from scaffoldmaker.scaffoldpackage import ScaffoldPackage
-from scaffoldmaker.utils import vector
 from scaffoldmaker.utils.cylindermesh import CylinderMesh, CylinderShape, CylinderEnds, CylinderCentralPath
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
 from scaffoldmaker.utils.shieldmesh import ShieldMesh3D
 from scaffoldmaker.utils.spheremesh import SphereMesh, SphereShape
 from scaffoldmaker.utils.zinc_utils import exnode_string_from_nodeset_field_parameters
-from scaffoldmaker.utils.derivativemoothing import DerivativeSmoothing
-from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm
 
 
 class MeshType_3d_bone1 (Scaffold_base):
@@ -202,7 +200,7 @@ def generateBaseMesh(region, options):
         sphere_centre = sphere_base.centre
         sphere_radius_3 = options['Lower scale_Z']
         axes = [sphere_base.majorAxis, sphere_base.minorAxis,
-                vector.setMagnitude(vector.crossproduct3(sphere_base.majorAxis, sphere_base.minorAxis),
+                set_magnitude(cross(sphere_base.majorAxis, sphere_base.minorAxis),
                                     sphere_radius_3)]
         elementsCountAcross = [cylinder1._elementsCountAcrossMajor, cylinder1._elementsCountAcrossMinor,
                                cylinder1._elementsCountAcrossMajor]
@@ -235,8 +233,7 @@ def generateBaseMesh(region, options):
                 for n1 in range(elementsCountAcross[1] + 1):
                     if n3 < elementsCountAcross[2] // 2:
                         if sphere1._shield3D.px[n3][n2][n1]:
-                            hemisphere.px[n3][n2][n1] = vector.addVectors([sphere1._shield3D.px[n3][n2][n1],
-                                                                            sphere_centre], [1, 1])
+                            hemisphere.px[n3][n2][n1] = add_vectors([sphere1._shield3D.px[n3][n2][n1], sphere_centre], [1, 1])
                     #cylinder end
                     elif n3 == elementsCountAcross[2] // 2:
                         # find nodes on the triple line. Note that cylinder and sphere have a little bit different
@@ -292,7 +289,7 @@ def generateBaseMesh(region, options):
         sphere_centre = sphere_base.centre
         sphere_radius_3 = options['Upper scale_Z']
         axes = [sphere_base.majorAxis, sphere_base.minorAxis,
-                vector.setMagnitude(vector.crossproduct3(sphere_base.majorAxis, sphere_base.minorAxis),
+                set_magnitude(cross(sphere_base.majorAxis, sphere_base.minorAxis),
                                     sphere_radius_3)]
         elementsCountAcross = [cylinder1._elementsCountAcrossMajor, cylinder1._elementsCountAcrossMinor,
                                cylinder1._elementsCountAcrossMajor]
@@ -326,8 +323,7 @@ def generateBaseMesh(region, options):
                 for n1 in range(elementsCountAcross[1] + 1):
                     if n3 > elementsCountAcross[2] // 2:
                         if sphere2._shield3D.px[n3][n2][n1]:
-                            hemisphere2.px[n3][n2][n1] = vector.addVectors([sphere2._shield3D.px[n3][n2][n1],
-                                                                            sphere_centre], [1, 1])
+                            hemisphere2.px[n3][n2][n1] = add_vectors([sphere2._shield3D.px[n3][n2][n1], sphere_centre], [1, 1])
                     #cylinder end
                     elif n3 == elementsCountAcross[2] // 2:
                         # find nodes on the triple line. Note that cylinder and sphere have a little bit different