From aa3120963ac034923ff83d3092ab68f4c62c6ee0 Mon Sep 17 00:00:00 2001 From: Hugh Sorby Date: Fri, 31 Mar 2023 15:00:13 +1300 Subject: [PATCH 1/2] Rename opencmiss to cmlibs. --- README.rst | 6 +++--- docs/index.rst | 6 +++--- setup.py | 8 ++++---- src/scaffoldmaker/annotation/annotationgroup.py | 16 ++++++++-------- .../meshtypes/meshtype_1d_bifurcationtree1.py | 12 ++++++------ src/scaffoldmaker/meshtypes/meshtype_1d_path1.py | 10 +++++----- .../meshtypes/meshtype_2d_plate1.py | 8 ++++---- .../meshtypes/meshtype_2d_platehole1.py | 8 ++++---- .../meshtypes/meshtype_2d_sphere1.py | 8 ++++---- src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py | 8 ++++---- .../meshtypes/meshtype_2d_tubebifurcation1.py | 8 ++++---- .../meshtype_2d_tubebifurcationtree1.py | 6 +++--- .../meshtypes/meshtype_3d_bladder1.py | 8 ++++---- .../meshtypes/meshtype_3d_bladderurethra1.py | 8 ++++---- src/scaffoldmaker/meshtypes/meshtype_3d_box1.py | 8 ++++---- .../meshtypes/meshtype_3d_boxhole1.py | 8 ++++---- .../meshtypes/meshtype_3d_brainstem.py | 12 ++++++------ .../meshtypes/meshtype_3d_cecum1.py | 4 ++-- .../meshtypes/meshtype_3d_colon1.py | 4 ++-- .../meshtypes/meshtype_3d_colonsegment1.py | 8 ++++---- .../meshtypes/meshtype_3d_esophagus1.py | 8 ++++---- .../meshtypes/meshtype_3d_heart1.py | 10 +++++----- .../meshtypes/meshtype_3d_heart2.py | 2 +- .../meshtypes/meshtype_3d_heartarterialroot1.py | 10 +++++----- .../meshtypes/meshtype_3d_heartarterialvalve1.py | 12 ++++++------ .../meshtypes/meshtype_3d_heartatria1.py | 14 +++++++------- .../meshtypes/meshtype_3d_heartatria2.py | 10 +++++----- .../meshtypes/meshtype_3d_heartventricles1.py | 8 ++++---- .../meshtypes/meshtype_3d_heartventricles2.py | 8 ++++---- .../meshtypes/meshtype_3d_heartventricles3.py | 10 +++++----- .../meshtype_3d_heartventriclesbase1.py | 10 +++++----- .../meshtype_3d_heartventriclesbase2.py | 10 +++++----- src/scaffoldmaker/meshtypes/meshtype_3d_lens1.py | 4 ++-- src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py | 8 ++++---- src/scaffoldmaker/meshtypes/meshtype_3d_lung2.py | 12 ++++++------ .../meshtypes/meshtype_3d_musclefusiform1.py | 4 ++-- .../meshtypes/meshtype_3d_ostium1.py | 6 +++--- .../meshtypes/meshtype_3d_smallintestine1.py | 2 +- .../meshtypes/meshtype_3d_solidcylinder1.py | 4 ++-- .../meshtypes/meshtype_3d_solidsphere1.py | 8 ++++---- .../meshtypes/meshtype_3d_solidsphere2.py | 2 +- .../meshtypes/meshtype_3d_sphereshell1.py | 8 ++++---- .../meshtypes/meshtype_3d_sphereshellseptum1.py | 8 ++++---- .../meshtypes/meshtype_3d_stellate1.py | 8 ++++---- .../meshtypes/meshtype_3d_stomach1.py | 12 ++++++------ .../meshtypes/meshtype_3d_stomachhuman1.py | 12 ++++++------ src/scaffoldmaker/meshtypes/meshtype_3d_tube1.py | 8 ++++---- .../meshtypes/meshtype_3d_tubeseptum1.py | 8 ++++---- .../meshtypes/meshtype_3d_wholebody1.py | 12 ++++++------ src/scaffoldmaker/meshtypes/scaffold_base.py | 4 ++-- src/scaffoldmaker/scaffoldpackage.py | 10 +++++----- src/scaffoldmaker/utils/annulusmesh.py | 6 +++--- src/scaffoldmaker/utils/bifurcation.py | 6 +++--- src/scaffoldmaker/utils/cylindermesh.py | 6 +++--- src/scaffoldmaker/utils/derivativemoothing.py | 10 +++++----- src/scaffoldmaker/utils/eft_utils.py | 6 +++--- .../utils/eftfactory_bicubichermitelinear.py | 4 ++-- .../utils/eftfactory_tricubichermite.py | 10 +++++----- src/scaffoldmaker/utils/exportvtk.py | 8 ++++---- src/scaffoldmaker/utils/geometry.py | 2 +- src/scaffoldmaker/utils/meshrefinement.py | 10 +++++----- src/scaffoldmaker/utils/shieldmesh.py | 6 +++--- src/scaffoldmaker/utils/spheremesh.py | 4 ++-- src/scaffoldmaker/utils/tubemesh.py | 8 ++++---- src/scaffoldmaker/utils/zinc_utils.py | 16 ++++++++-------- tests/test_bladder.py | 12 ++++++------ tests/test_cecum.py | 12 ++++++------ tests/test_colon.py | 14 +++++++------- tests/test_colonsegment.py | 12 ++++++------ tests/test_cylinder.py | 10 +++++----- tests/test_esophagus.py | 12 ++++++------ tests/test_general.py | 12 ++++++------ tests/test_heart.py | 10 +++++----- tests/test_lung.py | 10 +++++----- tests/test_smallintestine.py | 14 +++++++------- tests/test_sphere.py | 10 +++++----- tests/test_stomach.py | 12 ++++++------ tests/test_wholebody1.py | 10 +++++----- 78 files changed, 334 insertions(+), 334 deletions(-) diff --git a/README.rst b/README.rst index 8dd94bb5..3523a036 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ Scaffold Maker ============== -Anatomical scaffold generator using OpenCMISS-Zinc. +Anatomical scaffold generator using Zinc. Install with:: pip install scaffoldmaker @@ -14,8 +14,8 @@ For developing scaffolds:: Requires the following Python libraries to be installed. -* opencmiss.zinc -* opencmiss.utils +* cmlibs.zinc +* cmlibs.utils We recommend installing scaffoldmaker into a virtual python environment. See `python virtual environment documentation `__ for information on virtual environments. diff --git a/docs/index.rst b/docs/index.rst index 2040027c..68d61e8f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,7 +1,7 @@ -*scaffoldmaker library* -======================= +scaffoldmaker library +===================== -The *scaffoldmaker library* contains scripts for programmatically generating anatomical scaffolds for a range of organs and other structures, and includes utility code for building common geometric shapes, annotation, and refinement. The scripts generate the scaffold model in the data structures of the underlying *OpenCMISS-Zinc library*, and through the Zinc API clients can interrogate the model or export it for subsequent use. +The *scaffoldmaker library* contains scripts for programmatically generating anatomical scaffolds for a range of organs and other structures, and includes utility code for building common geometric shapes, annotation, and refinement. The scripts generate the scaffold model in the data structures of the underlying *Zinc library*, and through the Zinc API clients can interrogate the model or export it for subsequent use. Most users will make scaffolds using the ABI Mapping Tools' **Scaffold Creator** user interface for this library, and its documentation gives a good introduction to anatomical scaffolds and some common features of them. diff --git a/setup.py b/setup.py index 48e1227e..399bf87b 100644 --- a/setup.py +++ b/setup.py @@ -25,9 +25,9 @@ def readfile(filename, split=False): # into the 'requirements.txt' file. requires = [ # minimal requirements listing - "opencmiss.maths", - "opencmiss.utils >= 0.3", - "opencmiss.zinc >= 3.10.2", + "cmlibs.maths", + "cmlibs.utils >= 0.3", + "cmlibs.zinc >= 3.99", "scipy", "numpy", ] @@ -36,7 +36,7 @@ def readfile(filename, split=False): setup( name="scaffoldmaker", version="0.8.1", - description="Python client for generating anatomical scaffolds using OpenCMISS-Zinc", + description="Python client for generating anatomical scaffolds using Zinc", long_description="\n".join(readme) + source_license, long_description_content_type="text/x-rst", classifiers=[ diff --git a/src/scaffoldmaker/annotation/annotationgroup.py b/src/scaffoldmaker/annotation/annotationgroup.py index 00345a40..e9280f3e 100644 --- a/src/scaffoldmaker/annotation/annotationgroup.py +++ b/src/scaffoldmaker/annotation/annotationgroup.py @@ -3,16 +3,16 @@ """ import sys -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.utils.zinc.field import find_or_create_field_coordinates, find_or_create_field_group, \ +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.utils.zinc.field import find_or_create_field_coordinates, find_or_create_field_group, \ find_or_create_field_stored_mesh_location, find_or_create_field_stored_string -from opencmiss.zinc.element import Element, Mesh -from opencmiss.zinc.field import Field, FieldFiniteElement, FieldGroup, FieldStoredMeshLocation, FieldStoredString, \ +from cmlibs.zinc.element import Element, Mesh +from cmlibs.zinc.field import Field, FieldFiniteElement, FieldGroup, FieldStoredMeshLocation, FieldStoredString, \ FieldFindMeshLocation -from opencmiss.zinc.fieldcache import Fieldcache -from opencmiss.zinc.fieldmodule import Fieldmodule -from opencmiss.zinc.node import Node -from opencmiss.zinc.result import RESULT_OK +from cmlibs.zinc.fieldcache import Fieldcache +from cmlibs.zinc.fieldmodule import Fieldmodule +from cmlibs.zinc.node import Node +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.utils.zinc_utils import get_highest_dimension_mesh, get_next_unused_node_identifier, \ group_get_highest_dimension, identifier_ranges_from_string, identifier_ranges_to_string, \ mesh_group_add_identifier_ranges, mesh_group_to_identifier_ranges, \ diff --git a/src/scaffoldmaker/meshtypes/meshtype_1d_bifurcationtree1.py b/src/scaffoldmaker/meshtypes/meshtype_1d_bifurcationtree1.py index 4fdf6228..0340b772 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_1d_bifurcationtree1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_1d_bifurcationtree1.py @@ -5,12 +5,12 @@ from __future__ import division from math import cos, radians, sin -from opencmiss.maths.vectorops import add, cross, magnitude, mult, normalize, sub -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldFiniteElement -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.maths.vectorops import add, cross, magnitude, mult, normalize, sub +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldFiniteElement +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_1d_path1.py b/src/scaffoldmaker/meshtypes/meshtype_1d_path1.py index 7a8dc880..ca9c1f23 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_1d_path1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_1d_path1.py @@ -4,11 +4,11 @@ from __future__ import division -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils import vector from scaffoldmaker.utils.interpolation import smoothCubicHermiteCrossDerivativesLine diff --git a/src/scaffoldmaker/meshtypes/meshtype_2d_plate1.py b/src/scaffoldmaker/meshtypes/meshtype_2d_plate1.py index 6a80220f..ae7e6aa0 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_2d_plate1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_2d_plate1.py @@ -4,10 +4,10 @@ from __future__ import division -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_2d_platehole1.py b/src/scaffoldmaker/meshtypes/meshtype_2d_platehole1.py index e277f662..77049d9e 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_2d_platehole1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_2d_platehole1.py @@ -9,10 +9,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative diff --git a/src/scaffoldmaker/meshtypes/meshtype_2d_sphere1.py b/src/scaffoldmaker/meshtypes/meshtype_2d_sphere1.py index ce02d97c..e2323f56 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_2d_sphere1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_2d_sphere1.py @@ -6,10 +6,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py b/src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py index b2f56497..c0e834a2 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_2d_tube1.py @@ -6,10 +6,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcation1.py b/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcation1.py index de61dd73..d5dd6294 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcation1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcation1.py @@ -6,10 +6,10 @@ import math -from opencmiss.maths.vectorops import cross, mult, normalize, sub -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.maths.vectorops import cross, mult, normalize, sub +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.bifurcation import get_tube_bifurcation_connection_elements_counts, \ make_tube_bifurcation_points, make_tube_bifurcation_elements_2d diff --git a/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcationtree1.py b/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcationtree1.py index 9bd34097..98327f74 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcationtree1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_2d_tubebifurcationtree1.py @@ -5,9 +5,9 @@ from __future__ import division import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.meshtype_1d_bifurcationtree1 import MeshType_1d_bifurcationtree1 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.scaffoldpackage import ScaffoldPackage diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py index 921dbb46..da16f129 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py @@ -7,10 +7,10 @@ import copy import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm from scaffoldmaker.annotation.bladder_terms import get_bladder_term from scaffoldmaker.meshtypes.meshtype_3d_ostium1 import MeshType_3d_ostium1, generateOstiumMesh diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py index 405add15..0a008b9e 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py @@ -7,11 +7,11 @@ import copy import math -from opencmiss.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \ findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, \ getAnnotationGroupForTerm from scaffoldmaker.annotation.bladder_terms import get_bladder_term diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_box1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_box1.py index 1028cb8e..c7ee73c7 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_box1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_box1.py @@ -4,10 +4,10 @@ from __future__ import division -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite from scaffoldmaker.utils.meshrefinement import MeshRefinement diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py index ce5d2e91..4af71c04 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_boxhole1.py @@ -9,10 +9,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py b/src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py index df05dcc2..0ebf8b57 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py @@ -6,13 +6,13 @@ import copy -from opencmiss.zinc.element import Element -from opencmiss.zinc.node import Node -from opencmiss.zinc.field import FieldFindMeshLocation -from opencmiss.utils.zinc.field import Field, findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, \ +from cmlibs.zinc.element import Element +from cmlibs.zinc.node import Node +from cmlibs.zinc.field import FieldFindMeshLocation +from cmlibs.utils.zinc.field import Field, findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, \ findOrCreateFieldStoredString -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.utils.zinc.finiteelement import getMaximumNodeIdentifier +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.utils.zinc.finiteelement import getMaximumNodeIdentifier from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm from scaffoldmaker.annotation.brainstem_terms import get_brainstem_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_cecum1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_cecum1.py index 6cbb2cc7..05eaf559 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_cecum1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_cecum1.py @@ -7,8 +7,8 @@ import copy import math -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.annotation.colon_terms import get_colon_term from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py index ca4bb936..9675f69d 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py @@ -6,8 +6,8 @@ import copy -from opencmiss.zinc.node import Node -from opencmiss.zinc.element import Element +from cmlibs.zinc.node import Node +from cmlibs.zinc.element import Element from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm from scaffoldmaker.annotation.colon_terms import get_colon_term from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py index 4ae1810c..7c6abef1 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_colonsegment1.py @@ -8,10 +8,10 @@ import copy import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, mergeAnnotationGroups, \ findOrCreateAnnotationGroupForTerm, findAnnotationGroupByName, getAnnotationGroupForTerm from scaffoldmaker.annotation.colon_terms import get_colon_term diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_esophagus1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_esophagus1.py index ea2d3452..308262f4 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_esophagus1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_esophagus1.py @@ -6,11 +6,11 @@ import copy import math -from opencmiss.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldStoredString, \ +from cmlibs.utils.zinc.field import findOrCreateFieldGroup, findOrCreateFieldStoredString, \ findOrCreateFieldStoredMeshLocation, findOrCreateFieldNodeGroup -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationGroupForTerm, \ findOrCreateAnnotationGroupForTerm from scaffoldmaker.annotation.esophagus_terms import get_esophagus_term diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py index f3965b3c..17cf6e5a 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heart1.py @@ -4,12 +4,12 @@ from __future__ import division -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm, mergeAnnotationGroups from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.meshtype_3d_heartatria1 import MeshType_3d_heartatria1 diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heart2.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heart2.py index aa21258d..f3dd6ac8 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heart2.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heart2.py @@ -4,7 +4,7 @@ from __future__ import division -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates from scaffoldmaker.annotation.annotationgroup import mergeAnnotationGroups from scaffoldmaker.meshtypes.meshtype_3d_heartatria2 import MeshType_3d_heartatria2 from scaffoldmaker.meshtypes.meshtype_3d_heartventriclesbase2 import MeshType_3d_heartventriclesbase2 diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialroot1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialroot1.py index 5f7d93f5..f5c2082d 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialroot1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialroot1.py @@ -7,11 +7,11 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialvalve1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialvalve1.py index 7f9da0fb..8403208e 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialvalve1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartarterialvalve1.py @@ -8,12 +8,12 @@ import math -from opencmiss.maths.vectorops import eulerToRotationMatrix3 -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.maths.vectorops import eulerToRotationMatrix3 +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils import vector from scaffoldmaker.utils.eft_utils import setEftScaleFactorIds diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria1.py index a713716c..da9a61f9 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria1.py @@ -8,14 +8,14 @@ import copy import math -from opencmiss.maths.vectorops import add, cross, dot, magnitude, mult, normalize, sub -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.maths.vectorops import add, cross, dot, magnitude, mult, normalize, sub +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field, FieldGroup -from opencmiss.zinc.node import Node -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field, FieldGroup +from cmlibs.zinc.node import Node +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findAnnotationGroupByName, \ findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm from scaffoldmaker.annotation.heart_terms import get_heart_term diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria2.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria2.py index 74deb158..dd04231c 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria2.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartatria2.py @@ -7,11 +7,11 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles1.py index c8cfd494..9edff6f4 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles1.py @@ -7,11 +7,11 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles2.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles2.py index 549cf081..7dfcbd21 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles2.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles2.py @@ -6,10 +6,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles3.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles3.py index 318113ca..2a83a008 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles3.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventricles3.py @@ -7,12 +7,12 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase1.py index 4d5d7928..ed4a1207 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase1.py @@ -9,12 +9,12 @@ import copy import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field, FieldGroup -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field, FieldGroup +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationGroupForTerm from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.meshtype_3d_heartatria1 import MeshType_3d_heartatria1, getAtriumBasePoints diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase2.py b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase2.py index 5d6dc32e..8eb13761 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase2.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_heartventriclesbase2.py @@ -8,11 +8,11 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.finiteelement import getMaximumElementIdentifier, getMaximumNodeIdentifier +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationGroupForTerm from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.meshtype_3d_heartventricles2 import MeshType_3d_heartventricles2 diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_lens1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_lens1.py index e107a294..3a605072 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_lens1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_lens1.py @@ -7,8 +7,8 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.field import Field +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.field import Field from scaffoldmaker.meshtypes.meshtype_3d_solidsphere1 import MeshType_3d_solidsphere1 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.meshrefinement import MeshRefinement diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py index 97a7822a..7b01c9f8 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py @@ -2,11 +2,11 @@ Generates 3D lung surface mesh. ''' -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm from scaffoldmaker.annotation.lung_terms import get_lung_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_lung2.py b/src/scaffoldmaker/meshtypes/meshtype_3d_lung2.py index 596643d4..80c58892 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_lung2.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_lung2.py @@ -12,7 +12,7 @@ from scaffoldmaker.utils.eft_utils import remapEftLocalNodes, remapEftNodeValueLabel, remapEftNodeValueLabelsVersion, setEftScaleFactorIds from scaffoldmaker.utils.cylindermesh import createEllipsePerimeter from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite -from opencmiss.utils.zinc.general import ChangeManager +from cmlibs.utils.zinc.general import ChangeManager from scaffoldmaker.utils.geometry import createEllipsoidPoints, getEllipseRadiansToX, getEllipseArcLength, \ getApproximateEllipsePerimeter, sampleEllipsePoints, updateEllipseAngleByArcLength, getEllipsoidPlaneA, \ getEllipsoidPolarCoordinatesFromPosition, getEllipsoidPolarCoordinatesTangents @@ -20,13 +20,13 @@ interpolateCubicHermiteDerivative from scaffoldmaker.utils.meshrefinement import MeshRefinement from scaffoldmaker.utils.vector import magnitude, setMagnitude, crossproduct3, normalise -from opencmiss.maths.vectorops import add, cross, dot, mult, normalize, sub +from cmlibs.maths.vectorops import add, cross, dot, mult, normalize, sub from scaffoldmaker.utils.zinc_utils import disconnectFieldMeshGroupBoundaryNodes -from opencmiss.utils.zinc.field import Field, findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.utils.zinc.field import Field, findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString, createFieldEulerAnglesRotationMatrix -from opencmiss.utils.zinc.finiteelement import get_element_node_identifiers -from opencmiss.zinc.element import Element -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.finiteelement import get_element_node_identifiers +from cmlibs.zinc.element import Element +from cmlibs.zinc.node import Node class MeshType_3d_lung2(Scaffold_base): ''' diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_musclefusiform1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_musclefusiform1.py index bb341e0a..4e20af65 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_musclefusiform1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_musclefusiform1.py @@ -7,8 +7,8 @@ import copy -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1 from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_ostium1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_ostium1.py index 9d09761d..ee5a20e2 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_ostium1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_ostium1.py @@ -7,9 +7,9 @@ import copy import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils import interpolation as interp from scaffoldmaker.utils import vector diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_smallintestine1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_smallintestine1.py index f8757bb3..a5797cda 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_smallintestine1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_smallintestine1.py @@ -6,7 +6,7 @@ import copy -from opencmiss.zinc.node import Node +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.annotation.smallintestine_terms import get_smallintestine_term from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_solidcylinder1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_solidcylinder1.py index ebf459b9..61cfa5be 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_solidcylinder1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_solidcylinder1.py @@ -7,8 +7,8 @@ import copy -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +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 diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere1.py index 407f2dba..76bb1b33 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere1.py @@ -7,10 +7,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils import interpolation as interp from scaffoldmaker.utils import vector diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere2.py b/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere2.py index 682859c9..89efe9ed 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere2.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_solidsphere2.py @@ -5,7 +5,7 @@ from __future__ import division -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils import vector diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshell1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshell1.py index 96a395f8..e062a0f3 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshell1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshell1.py @@ -7,10 +7,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.eftfactory_bicubichermitelinear import eftfactory_bicubichermitelinear from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshellseptum1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshellseptum1.py index a72e03b8..49ec6e63 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshellseptum1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_sphereshellseptum1.py @@ -11,10 +11,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite from scaffoldmaker.utils.interpolation import interpolateCubicHermite, interpolateCubicHermiteDerivative diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_stellate1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_stellate1.py index aab0b280..a94d75b3 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_stellate1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_stellate1.py @@ -6,11 +6,11 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, findOrCreateFieldStoredMeshLocation, \ findOrCreateFieldStoredString -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm, getAnnotationGroupForTerm from scaffoldmaker.annotation.stellate_terms import get_stellate_term from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_stomach1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_stomach1.py index 7bcdedda..8d17d7b0 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_stomach1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_stomach1.py @@ -9,12 +9,12 @@ import copy import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.utils.zinc.finiteelement import get_element_node_identifiers, getMaximumNodeIdentifier -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.finiteelement import get_element_node_identifiers, getMaximumNodeIdentifier +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, mergeAnnotationGroups, \ getAnnotationGroupForTerm, findOrCreateAnnotationGroupForTerm from scaffoldmaker.annotation.stomach_terms import get_stomach_term diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_stomachhuman1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_stomachhuman1.py index 4d156d17..6df30375 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_stomachhuman1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_stomachhuman1.py @@ -6,11 +6,11 @@ from __future__ import division import numpy as np -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldFibres -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldFibres +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite from scipy.interpolate import splprep, splev @@ -9506,7 +9506,7 @@ def getInitialValues(self,fieldNames,circumferentialElements,axialElements,wallE def generateMesh(self,region,circumferentialElements,axialElements,wallElements,normalizeCircumferentialSegmentLengths,refineAtLength={},refineAtTheta={}): ''' - region - opencmiss zinc region where mesh needs to be created + region - zinc region where mesh needs to be created circumferentialElements - number of elements along the circumference axialElements - number of elements along the axis wallElements - number of elements along the wall diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_tube1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_tube1.py index 94df9d63..e3f39d89 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_tube1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_tube1.py @@ -7,10 +7,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite from scaffoldmaker.utils.meshrefinement import MeshRefinement diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_tubeseptum1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_tubeseptum1.py index 8d372f2f..fb8c5824 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_tubeseptum1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_tubeseptum1.py @@ -10,10 +10,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_wholebody1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_wholebody1.py index 6ca8656b..87b4565b 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_wholebody1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_wholebody1.py @@ -7,13 +7,13 @@ import copy -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, \ findOrCreateFieldStoredString, findOrCreateFieldStoredMeshLocation, findOrCreateFieldNodeGroup -from opencmiss.utils.zinc.finiteelement import getMaximumNodeIdentifier, get_element_node_identifiers -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.finiteelement import getMaximumNodeIdentifier, get_element_node_identifiers +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation import heart_terms, bladder_terms, lung_terms, stomach_terms, brainstem_terms from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findOrCreateAnnotationGroupForTerm from scaffoldmaker.annotation.annotationgroup import getAnnotationGroupForTerm diff --git a/src/scaffoldmaker/meshtypes/scaffold_base.py b/src/scaffoldmaker/meshtypes/scaffold_base.py index 7a196785..4823e548 100644 --- a/src/scaffoldmaker/meshtypes/scaffold_base.py +++ b/src/scaffoldmaker/meshtypes/scaffold_base.py @@ -4,8 +4,8 @@ """ import copy -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.field import Field +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.field import Field from scaffoldmaker.utils.derivativemoothing import DerivativeSmoothing from scaffoldmaker.utils.interpolation import DerivativeScalingMode from scaffoldmaker.utils.meshrefinement import MeshRefinement diff --git a/src/scaffoldmaker/scaffoldpackage.py b/src/scaffoldmaker/scaffoldpackage.py index 650201c5..51a2dc84 100644 --- a/src/scaffoldmaker/scaffoldpackage.py +++ b/src/scaffoldmaker/scaffoldpackage.py @@ -6,11 +6,11 @@ import copy import math -from opencmiss.maths.vectorops import euler_to_rotation_matrix -from opencmiss.utils.zinc.field import createFieldEulerAnglesRotationMatrix -from opencmiss.utils.zinc.finiteelement import get_maximum_node_identifier -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.field import Field, FieldGroup +from cmlibs.maths.vectorops import euler_to_rotation_matrix +from cmlibs.utils.zinc.field import createFieldEulerAnglesRotationMatrix +from cmlibs.utils.zinc.finiteelement import get_maximum_node_identifier +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.field import Field, FieldGroup from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, findAnnotationGroupByName, \ getAnnotationMarkerLocationField # , getAnnotationMarkerNameField from scaffoldmaker.meshtypes.scaffold_base import Scaffold_base diff --git a/src/scaffoldmaker/utils/annulusmesh.py b/src/scaffoldmaker/utils/annulusmesh.py index a4d1f9f9..3c4e5820 100644 --- a/src/scaffoldmaker/utils/annulusmesh.py +++ b/src/scaffoldmaker/utils/annulusmesh.py @@ -6,9 +6,9 @@ import copy from collections.abc import Sequence -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.node import Node from scaffoldmaker.utils import interpolation as interp from scaffoldmaker.utils import vector from scaffoldmaker.utils.eft_utils import remapEftNodeValueLabel, setEftScaleFactorIds diff --git a/src/scaffoldmaker/utils/bifurcation.py b/src/scaffoldmaker/utils/bifurcation.py index 31b90fe0..bf852c50 100644 --- a/src/scaffoldmaker/utils/bifurcation.py +++ b/src/scaffoldmaker/utils/bifurcation.py @@ -4,9 +4,9 @@ from __future__ import division -from opencmiss.maths.vectorops import add, cross, dot, magnitude, mult, normalize, sub -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.node import Node +from cmlibs.maths.vectorops import add, cross, dot, magnitude, mult, normalize, sub +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.node import Node from scaffoldmaker.utils.eft_utils import remapEftNodeValueLabel, scaleEftNodeValueLabels, setEftScaleFactorIds from scaffoldmaker.utils.geometry import createCirclePoints from scaffoldmaker.utils.interpolation import DerivativeScalingMode, interpolateCubicHermite, interpolateCubicHermiteDerivative, \ diff --git a/src/scaffoldmaker/utils/cylindermesh.py b/src/scaffoldmaker/utils/cylindermesh.py index b960b6f0..29af8661 100644 --- a/src/scaffoldmaker/utils/cylindermesh.py +++ b/src/scaffoldmaker/utils/cylindermesh.py @@ -7,9 +7,9 @@ import math from enum import Enum -from opencmiss.utils.zinc.finiteelement import getMaximumNodeIdentifier, getMaximumElementIdentifier -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +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 extractPathParametersFromRegion from scaffoldmaker.utils import vector, geometry from scaffoldmaker.utils.interpolation import sampleCubicHermiteCurves, interpolateSampleCubicHermite, \ diff --git a/src/scaffoldmaker/utils/derivativemoothing.py b/src/scaffoldmaker/utils/derivativemoothing.py index 3f52060f..23d6e532 100644 --- a/src/scaffoldmaker/utils/derivativemoothing.py +++ b/src/scaffoldmaker/utils/derivativemoothing.py @@ -5,11 +5,11 @@ import math -from opencmiss.maths.vectorops import magnitude -from opencmiss.utils.zinc.field import findOrCreateFieldGroup -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field +from cmlibs.maths.vectorops import 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 diff --git a/src/scaffoldmaker/utils/eft_utils.py b/src/scaffoldmaker/utils/eft_utils.py index 4ed72b4d..be47b5ac 100644 --- a/src/scaffoldmaker/utils/eft_utils.py +++ b/src/scaffoldmaker/utils/eft_utils.py @@ -1,9 +1,9 @@ ''' Utility functions for element field templates shared by mesh generators. ''' -from opencmiss.utils.zinc.finiteelement import getElementNodeIdentifiers -from opencmiss.zinc.element import Elementfieldtemplate -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import getElementNodeIdentifiers +from cmlibs.zinc.element import Elementfieldtemplate +from cmlibs.zinc.result import RESULT_OK def getEftTermScaling(eft, functionIndex, termIndex): diff --git a/src/scaffoldmaker/utils/eftfactory_bicubichermitelinear.py b/src/scaffoldmaker/utils/eftfactory_bicubichermitelinear.py index 44abaf92..58c261c6 100644 --- a/src/scaffoldmaker/utils/eftfactory_bicubichermitelinear.py +++ b/src/scaffoldmaker/utils/eftfactory_bicubichermitelinear.py @@ -1,8 +1,8 @@ ''' Definitions of standard element field templates using bicubic Hermite x linear Lagrange basis. ''' -from opencmiss.zinc.element import Elementbasis -from opencmiss.zinc.node import Node +from cmlibs.zinc.element import Elementbasis +from cmlibs.zinc.node import Node from scaffoldmaker.utils.eft_utils import remapEftLocalNodes, remapEftNodeValueLabel, setEftScaleFactorIds diff --git a/src/scaffoldmaker/utils/eftfactory_tricubichermite.py b/src/scaffoldmaker/utils/eftfactory_tricubichermite.py index fc304baa..0adf3ef5 100644 --- a/src/scaffoldmaker/utils/eftfactory_tricubichermite.py +++ b/src/scaffoldmaker/utils/eftfactory_tricubichermite.py @@ -3,11 +3,11 @@ ''' import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.utils.zinc.finiteelement import getElementNodeIdentifiers -from opencmiss.zinc.element import Element, Elementbasis, Elementfieldtemplate -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.finiteelement import getElementNodeIdentifiers +from cmlibs.zinc.element import Element, Elementbasis, Elementfieldtemplate +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.utils import vector from scaffoldmaker.utils.eft_utils import mapEftFunction1Node1Term, remapEftLocalNodes, remapEftNodeValueLabel, scaleEftNodeValueLabels, setEftScaleFactorIds diff --git a/src/scaffoldmaker/utils/exportvtk.py b/src/scaffoldmaker/utils/exportvtk.py index 3ec632d9..7c1bf934 100644 --- a/src/scaffoldmaker/utils/exportvtk.py +++ b/src/scaffoldmaker/utils/exportvtk.py @@ -7,10 +7,10 @@ import sys from sys import version_info -from opencmiss.utils.zinc.finiteelement import getElementNodeIdentifiersBasisOrder -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import getElementNodeIdentifiersBasisOrder +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK class ExportVtk: diff --git a/src/scaffoldmaker/utils/geometry.py b/src/scaffoldmaker/utils/geometry.py index a4771915..5e852580 100644 --- a/src/scaffoldmaker/utils/geometry.py +++ b/src/scaffoldmaker/utils/geometry.py @@ -7,7 +7,7 @@ import copy import math -from opencmiss.maths.vectorops import magnitude, mult +from cmlibs.maths.vectorops import magnitude, mult from scaffoldmaker.utils import vector from scaffoldmaker.utils.tracksurface import calculate_surface_delta_xi diff --git a/src/scaffoldmaker/utils/meshrefinement.py b/src/scaffoldmaker/utils/meshrefinement.py index e79b575d..ff3b04f5 100644 --- a/src/scaffoldmaker/utils/meshrefinement.py +++ b/src/scaffoldmaker/utils/meshrefinement.py @@ -5,12 +5,12 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \ +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldGroup, findOrCreateFieldNodeGroup, \ findOrCreateFieldStoredMeshLocation, findOrCreateFieldStoredString -from opencmiss.zinc.element import Element, Elementbasis -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node -from opencmiss.zinc.result import RESULT_OK as ZINC_OK +from cmlibs.zinc.element import Element, Elementbasis +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node +from cmlibs.zinc.result import RESULT_OK as ZINC_OK from scaffoldmaker.annotation.annotationgroup import AnnotationGroup from scaffoldmaker.utils.octree import Octree diff --git a/src/scaffoldmaker/utils/shieldmesh.py b/src/scaffoldmaker/utils/shieldmesh.py index 415994ce..812e4369 100644 --- a/src/scaffoldmaker/utils/shieldmesh.py +++ b/src/scaffoldmaker/utils/shieldmesh.py @@ -8,9 +8,9 @@ import copy from enum import Enum -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.utils import vector from scaffoldmaker.utils.eft_utils import remapEftNodeValueLabel, setEftScaleFactorIds from scaffoldmaker.utils.eftfactory_tricubichermite import eftfactory_tricubichermite diff --git a/src/scaffoldmaker/utils/spheremesh.py b/src/scaffoldmaker/utils/spheremesh.py index 7bdd7c29..896478a8 100644 --- a/src/scaffoldmaker/utils/spheremesh.py +++ b/src/scaffoldmaker/utils/spheremesh.py @@ -6,8 +6,8 @@ import math -from opencmiss.utils.zinc.finiteelement import getMaximumNodeIdentifier, getMaximumElementIdentifier -from opencmiss.zinc.field import Field +from cmlibs.utils.zinc.finiteelement import getMaximumNodeIdentifier, getMaximumElementIdentifier +from cmlibs.zinc.field import Field from scaffoldmaker.utils import vector from scaffoldmaker.utils.interpolation import sampleCubicHermiteCurves, smoothCubicHermiteDerivativesLine from scaffoldmaker.utils.cylindermesh import Ellipse2D, EllipseShape diff --git a/src/scaffoldmaker/utils/tubemesh.py b/src/scaffoldmaker/utils/tubemesh.py index 34be1555..c40c4466 100644 --- a/src/scaffoldmaker/utils/tubemesh.py +++ b/src/scaffoldmaker/utils/tubemesh.py @@ -6,10 +6,10 @@ import math -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldTextureCoordinates -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates, findOrCreateFieldTextureCoordinates +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node from scaffoldmaker.annotation.annotationgroup import mergeAnnotationGroups from scaffoldmaker.utils import interpolation as interp from scaffoldmaker.utils import matrix diff --git a/src/scaffoldmaker/utils/zinc_utils.py b/src/scaffoldmaker/utils/zinc_utils.py index 72385026..d4494b1a 100644 --- a/src/scaffoldmaker/utils/zinc_utils.py +++ b/src/scaffoldmaker/utils/zinc_utils.py @@ -2,14 +2,14 @@ Utility functions for easing use of Zinc API. ''' -from opencmiss.utils.zinc.field import findOrCreateFieldCoordinates -from opencmiss.utils.zinc.general import ChangeManager, HierarchicalChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Mesh, MeshGroup -from opencmiss.zinc.field import Field, FieldGroup -from opencmiss.zinc.fieldmodule import Fieldmodule -from opencmiss.zinc.node import Node, Nodeset -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.field import findOrCreateFieldCoordinates +from cmlibs.utils.zinc.general import ChangeManager, HierarchicalChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Mesh, MeshGroup +from cmlibs.zinc.field import Field, FieldGroup +from cmlibs.zinc.fieldmodule import Fieldmodule +from cmlibs.zinc.node import Node, Nodeset +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.utils import interpolation as interp from scaffoldmaker.utils import vector diff --git a/tests/test_bladder.py b/tests/test_bladder.py index 84dd0d49..9ee1d75c 100644 --- a/tests/test_bladder.py +++ b/tests/test_bladder.py @@ -1,12 +1,12 @@ import copy import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import getAnnotationGroupForTerm from scaffoldmaker.annotation.bladder_terms import get_bladder_term from scaffoldmaker.meshtypes.meshtype_3d_bladderurethra1 import MeshType_3d_bladderurethra1 diff --git a/tests/test_cecum.py b/tests/test_cecum.py index 715d6a83..0e36dec0 100644 --- a/tests/test_cecum.py +++ b/tests/test_cecum.py @@ -1,11 +1,11 @@ import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.meshtypes.meshtype_3d_cecum1 import MeshType_3d_cecum1 from scaffoldmaker.utils.zinc_utils import createFaceMeshGroupExteriorOnFace diff --git a/tests/test_colon.py b/tests/test_colon.py index 9537c220..73e9f2a9 100644 --- a/tests/test_colon.py +++ b/tests/test_colon.py @@ -1,13 +1,13 @@ import copy import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion from scaffoldmaker.meshtypes.meshtype_3d_colon1 import MeshType_3d_colon1 from scaffoldmaker.meshtypes.meshtype_3d_colonsegment1 import MeshType_3d_colonsegment1 diff --git a/tests/test_colonsegment.py b/tests/test_colonsegment.py index 786181d3..7c469478 100644 --- a/tests/test_colonsegment.py +++ b/tests/test_colonsegment.py @@ -1,11 +1,11 @@ import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.meshtypes.meshtype_3d_colonsegment1 import MeshType_3d_colonsegment1 from scaffoldmaker.utils.zinc_utils import createFaceMeshGroupExteriorOnFace diff --git a/tests/test_cylinder.py b/tests/test_cylinder.py index 01b64fca..3c262217 100644 --- a/tests/test_cylinder.py +++ b/tests/test_cylinder.py @@ -1,10 +1,10 @@ import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.meshtypes.meshtype_3d_solidcylinder1 import MeshType_3d_solidcylinder1 from testutils import assertAlmostEqualList diff --git a/tests/test_esophagus.py b/tests/test_esophagus.py index 139a77c4..a5503f10 100644 --- a/tests/test_esophagus.py +++ b/tests/test_esophagus.py @@ -1,12 +1,12 @@ import copy import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import getAnnotationGroupForTerm from scaffoldmaker.annotation.esophagus_terms import get_esophagus_term from scaffoldmaker.meshtypes.meshtype_3d_esophagus1 import MeshType_3d_esophagus1 diff --git a/tests/test_general.py b/tests/test_general.py index 7deac83e..36d45bc5 100644 --- a/tests/test_general.py +++ b/tests/test_general.py @@ -1,12 +1,12 @@ import math import unittest -from opencmiss.maths.vectorops import dot, magnitude, normalize, sub -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName -from opencmiss.zinc.context import Context -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node -from opencmiss.zinc.result import RESULT_OK +from cmlibs.maths.vectorops import dot, magnitude, normalize, sub +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName +from cmlibs.zinc.context import Context +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationMarkerNameField from scaffoldmaker.meshtypes.meshtype_3d_box1 import MeshType_3d_box1 from scaffoldmaker.meshtypes.meshtype_3d_brainstem import MeshType_3d_brainstem1 diff --git a/tests/test_heart.py b/tests/test_heart.py index 430dff84..93f0b9d7 100644 --- a/tests/test_heart.py +++ b/tests/test_heart.py @@ -1,11 +1,11 @@ import copy import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import getAnnotationGroupForTerm from scaffoldmaker.annotation.heart_terms import get_heart_term from scaffoldmaker.meshtypes.meshtype_3d_heart1 import MeshType_3d_heart1 diff --git a/tests/test_lung.py b/tests/test_lung.py index 7d3b6a75..2e2a3dde 100644 --- a/tests/test_lung.py +++ b/tests/test_lung.py @@ -2,11 +2,11 @@ import math import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import getAnnotationGroupForTerm from scaffoldmaker.annotation.lung_terms import get_lung_term from scaffoldmaker.meshtypes.meshtype_3d_lung1 import MeshType_3d_lung1 diff --git a/tests/test_smallintestine.py b/tests/test_smallintestine.py index 5e5e1025..09d2abd7 100644 --- a/tests/test_smallintestine.py +++ b/tests/test_smallintestine.py @@ -1,13 +1,13 @@ import copy import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.node import Node -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.node import Node +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.meshtypes.meshtype_1d_path1 import MeshType_1d_path1, extractPathParametersFromRegion from scaffoldmaker.meshtypes.meshtype_3d_smallintestine1 import MeshType_3d_smallintestine1 from scaffoldmaker.scaffoldpackage import ScaffoldPackage diff --git a/tests/test_sphere.py b/tests/test_sphere.py index 9881ad63..42e294d1 100644 --- a/tests/test_sphere.py +++ b/tests/test_sphere.py @@ -1,11 +1,11 @@ import unittest from testutils import assertAlmostEqualList -from opencmiss.zinc.context import Context -from opencmiss.zinc.field import Field -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.result import RESULT_OK +from cmlibs.zinc.context import Context +from cmlibs.zinc.field import Field +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationGroupForTerm from scaffoldmaker.meshtypes.meshtype_3d_solidsphere2 import MeshType_3d_solidsphere2 from scaffoldmaker.utils.meshrefinement import MeshRefinement diff --git a/tests/test_stomach.py b/tests/test_stomach.py index dad9be55..d6a59219 100644 --- a/tests/test_stomach.py +++ b/tests/test_stomach.py @@ -1,12 +1,12 @@ import copy import unittest -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.context import Context -from opencmiss.zinc.element import Element -from opencmiss.zinc.field import Field -from opencmiss.zinc.result import RESULT_OK +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange, findNodeWithName +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.context import Context +from cmlibs.zinc.element import Element +from cmlibs.zinc.field import Field +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import getAnnotationGroupForTerm from scaffoldmaker.annotation.stomach_terms import get_stomach_term from scaffoldmaker.meshtypes.meshtype_3d_stomach1 import MeshType_3d_stomach1 diff --git a/tests/test_wholebody1.py b/tests/test_wholebody1.py index d6be7d13..022d23e9 100644 --- a/tests/test_wholebody1.py +++ b/tests/test_wholebody1.py @@ -1,11 +1,11 @@ import unittest from testutils import assertAlmostEqualList -from opencmiss.zinc.context import Context -from opencmiss.zinc.field import Field -from opencmiss.utils.zinc.finiteelement import evaluateFieldNodesetRange -from opencmiss.utils.zinc.general import ChangeManager -from opencmiss.zinc.result import RESULT_OK +from cmlibs.zinc.context import Context +from cmlibs.zinc.field import Field +from cmlibs.utils.zinc.finiteelement import evaluateFieldNodesetRange +from cmlibs.utils.zinc.general import ChangeManager +from cmlibs.zinc.result import RESULT_OK from scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationGroupForTerm from scaffoldmaker.meshtypes.meshtype_3d_wholebody1 import MeshType_3d_wholebody1 from scaffoldmaker.utils.meshrefinement import MeshRefinement From 44db6b9c297954000a7f1e7e6c34658d8786a3c2 Mon Sep 17 00:00:00 2001 From: Hugh Sorby Date: Tue, 4 Apr 2023 13:33:54 +1200 Subject: [PATCH 2/2] Tidy docs/index.rst. --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index 68d61e8f..71aeb6fe 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,4 +1,4 @@ -scaffoldmaker library +ScaffoldMaker library ===================== The *scaffoldmaker library* contains scripts for programmatically generating anatomical scaffolds for a range of organs and other structures, and includes utility code for building common geometric shapes, annotation, and refinement. The scripts generate the scaffold model in the data structures of the underlying *Zinc library*, and through the Zinc API clients can interrogate the model or export it for subsequent use.