Fix missing imports from maths.vectorops.

src/scaffoldmaker/meshtypes/meshtype_3d_lung2.py

@@ -4,7 +4,7 @@
 
 import copy
 import math
-from cmlibs.maths.vectorops import cross, dot, mult, normalize, sub
+from cmlibs.maths.vectorops import cross, dot, mult, normalize, sub, magnitude
 from cmlibs.utils.zinc.field import Field, findOrCreateFieldCoordinates
 from cmlibs.zinc.element import Element
 from cmlibs.zinc.node import Node
@@ -20,7 +20,6 @@
 from scaffoldmaker.utils.interpolation import computeCubicHermiteDerivativeScaling, interpolateCubicHermite, \
     interpolateCubicHermiteDerivative
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
-from scaffoldmaker.utils.vector import magnitude
 from scaffoldmaker.utils.zinc_utils import disconnectFieldMeshGroupBoundaryNodes
 
 

src/scaffoldmaker/meshtypes/meshtype_3d_stellate1.py

@@ -6,6 +6,7 @@
 
 import math
 
+from cmlibs.maths.vectorops import set_magnitude
 from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \
     findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString
 from cmlibs.zinc.element import Element
@@ -19,7 +20,6 @@
 from scaffoldmaker.utils.interpolation import smoothCubicHermiteDerivativesLine
 from scaffoldmaker.utils.matrix import rotateAboutZAxis
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
-from scaffoldmaker.utils.vector import setMagnitude
 
 
 class MeshType_3d_stellate1(Scaffold_base):
@@ -682,7 +682,7 @@ def createArm(halfArmArcAngleRadians, elementLengths, elementLengthCentral, elem
                         ds1 = [dcent[0], -dcent[1], dcent[2]]
                     elif (e1 == 0) and ((e2 == 0) or (e2 == elementsCount2)):
                         ds2 = [dcent[0], -dcent[1], dcent[2]] if (e2 == 0) else dcent
-                        ds2 = setMagnitude(ds2, dipMag)
+                        ds2 = set_magnitude(ds2, dipMag)
                         ds1 = rotateAboutZAxis(ds2, -math.pi / 2)
                     elif e1 == elementsCount1 and e2 == elementsCount2-1: # armEnd
                         ds1 = [elementWidth,0,0]

src/scaffoldmaker/meshtypes/meshtype_3d_wholebody1.py

@@ -7,6 +7,7 @@
 
 import copy
 
+from cmlibs.maths.vectorops import set_magnitude
 from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates
 from cmlibs.utils.zinc.finiteelement import get_element_node_identifiers
 from cmlibs.utils.zinc.general import ChangeManager
@@ -23,7 +24,6 @@
 from scaffoldmaker.utils.cylindermesh import CylinderMesh, CylinderShape, CylinderEnds, CylinderCentralPath
 from scaffoldmaker.utils.eft_utils import remapEftNodeValueLabelsVersion
 from scaffoldmaker.utils.meshrefinement import MeshRefinement
-from scaffoldmaker.utils.vector import setMagnitude
 from scaffoldmaker.utils.zinc_utils import exnode_string_from_nodeset_field_parameters
 
 
@@ -51,11 +51,11 @@ class MeshType_3d_wholebody1(Scaffold_base):
                 [Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
                  Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3],
                 [[
-                    (1, [[0.0, 0.0, 0.0], setMagnitude(axis1, cylinder1Settings['Length']), setMagnitude(axis2, 0.5),
-                         [0.0, 0.0, 0.0], setMagnitude(axis3, 0.5), [0.0, 0.0, 0.0]]),
-                    (2, [setMagnitude(axis1, cylinder1Settings['Length']),
-                         setMagnitude(axis1, cylinder1Settings['Length']),
-                         setMagnitude(axis2, 0.5), [0.0, 0.0, 0.0], setMagnitude(axis3, 0.5), [0.0, 0.0, 0.0]])
+                    (1, [[0.0, 0.0, 0.0], set_magnitude(axis1, cylinder1Settings['Length']), set_magnitude(axis2, 0.5),
+                         [0.0, 0.0, 0.0], set_magnitude(axis3, 0.5), [0.0, 0.0, 0.0]]),
+                    (2, [set_magnitude(axis1, cylinder1Settings['Length']),
+                         set_magnitude(axis1, cylinder1Settings['Length']),
+                         set_magnitude(axis2, 0.5), [0.0, 0.0, 0.0], set_magnitude(axis3, 0.5), [0.0, 0.0, 0.0]])
                 ]])
         })
     }

src/scaffoldmaker/utils/derivativemoothing.py

@@ -5,14 +5,13 @@
 
 import math
 
-from cmlibs.maths.vectorops import magnitude
+from cmlibs.maths.vectorops import magnitude, set_magnitude
 from cmlibs.utils.zinc.field import findOrCreateFieldGroup
 from cmlibs.utils.zinc.general import ChangeManager
 from cmlibs.zinc.element import Element, Elementbasis
 from cmlibs.zinc.field import Field
 from scaffoldmaker.utils.interpolation import DerivativeScalingMode, getCubicHermiteArcLength, \
     interpolateHermiteLagrangeDerivative, interpolateLagrangeHermiteDerivative
-from scaffoldmaker.utils.vector import setMagnitude
 
 
 class EdgeCurve:
@@ -355,7 +354,7 @@ def smooth(self, updateDirections=False, maxIterations=10, arcLengthTolerance=1.
                         if mag <= 0.0:
                             print('Node', nodeIdentifier, 'value', nodeValueLabel, 'version', nodeVersion,
                                   'has negative mag', mag)
-                        x = setMagnitude(x, mag)
+                        x = set_magnitude(x, mag)
                         self._field.setNodeParameters(fieldcache, -1, nodeValueLabel, nodeVersion, x)
                 for derivativeKey, derivativeEdges in self._derivativeMap.items():
                     edgeCount = len(derivativeEdges)
@@ -403,7 +402,7 @@ def smooth(self, updateDirections=False, maxIterations=10, arcLengthTolerance=1.
                             if mag <= 0.0:
                                 print('Derivative smoothing: Node', nodeIdentifier, 'label', nodeValueLabel,
                                       'version', nodeVersion, 'has negative magnitude', mag)
-                        x = setMagnitude(x, mag)
+                        x = set_magnitude(x, mag)
                         self._field.setNodeParameters(fieldcache, -1, nodeValueLabel, nodeVersion, x)
             # record modified nodes while ChangeManager is in effect
             if self._editNodesetGroup:

src/scaffoldmaker/utils/tubenetworkmesh.py

@@ -1,7 +1,7 @@
 """
 Specialisation of Network Mesh for building 2-D and 3-D tube mesh networks.
 """
-from cmlibs.maths.vectorops import add, cross, dot, magnitude, mult, normalize, sub
+from cmlibs.maths.vectorops import add, cross, dot, magnitude, mult, normalize, sub, rejection
 from cmlibs.zinc.element import Element, Elementbasis
 from cmlibs.zinc.node import Node
 from scaffoldmaker.utils.eft_utils import determineCubicHermiteSerendipityEft, HermiteNodeLayoutManager
@@ -13,7 +13,6 @@
 from scaffoldmaker.utils.networkmesh import NetworkMesh, NetworkMeshBuilder, NetworkMeshGenerateData, \
     NetworkMeshJunction, NetworkMeshSegment, pathValueLabels
 from scaffoldmaker.utils.tracksurface import TrackSurface
-from scaffoldmaker.utils.vector import vectorRejection
 from scaffoldmaker.utils.zinc_utils import get_nodeset_path_ordered_field_parameters
 import copy
 import math
@@ -1375,7 +1374,7 @@ def resampleTubeCoordinates(rawTubeCoordinates, fixedElementsCountAlong=None,
         # first smooth to get d1 with new directions not tangential to surface
         td1 = smoothCubicHermiteDerivativesLoop(sx[p], sd1[p])
         # constraint to be tangential to surface
-        td1 = [vectorRejection(td1[q], normalize(cross(sd1[p][q], sd2[p][q]))) for q in range(elementsCountAround)]
+        td1 = [rejection(td1[q], normalize(cross(sd1[p][q], sd2[p][q]))) for q in range(elementsCountAround)]
         # smooth magnitudes only
         sd1[p] = smoothCubicHermiteDerivativesLoop(sx[p], td1, fixAllDirections=True)