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Merge pull request #135 from arti-sukasem/human2DAnnotation
created lung fissure annotation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,180 @@ | ||
| import unittest | ||
| import copy | ||
| 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 scaffoldmaker.annotation.annotationgroup import AnnotationGroup, getAnnotationGroupForTerm | ||
| from scaffoldmaker.annotation.lung_terms import get_lung_term | ||
| from scaffoldmaker.meshtypes.meshtype_3d_lung1 import MeshType_3d_lung1 | ||
| from scaffoldmaker.utils.meshrefinement import MeshRefinement | ||
| from testutils import assertAlmostEqualList | ||
|
|
||
| class LungScaffoldTestCase(unittest.TestCase): | ||
|
|
||
| def test_lung1(self): | ||
| """ | ||
| Test creation of heart scaffold. | ||
| """ | ||
| scaffold = MeshType_3d_lung1 | ||
| parameterSetNames = scaffold.getParameterSetNames() | ||
| self.assertEqual(parameterSetNames, [ "Default", "Human 1", "Mouse 1" ]) | ||
| options = scaffold.getDefaultOptions(["Human"]) | ||
| self.assertEqual(3, len(options)) | ||
| self.assertFalse(scaffold.checkOptions(options)) | ||
|
|
||
| context = Context("Test") | ||
| region = context.getDefaultRegion() | ||
| self.assertTrue(region.isValid()) | ||
| annotationGroups = scaffold.generateMesh(region, options) | ||
| self.assertEqual(11, len(annotationGroups)) | ||
| fieldmodule = region.getFieldmodule() | ||
| mesh3d = fieldmodule.findMeshByDimension(3) | ||
| self.assertEqual(88, mesh3d.getSize()) | ||
| mesh2d = fieldmodule.findMeshByDimension(2) | ||
| self.assertEqual(292, mesh2d.getSize()) | ||
| mesh1d = fieldmodule.findMeshByDimension(1) | ||
| self.assertEqual(334, mesh1d.getSize()) | ||
| nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) | ||
| self.assertEqual(138, nodes.getSize()) | ||
| datapoints = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS) | ||
| self.assertEqual(0, datapoints.getSize()) | ||
|
|
||
| # check coordinates range, outside surface area and volume | ||
| coordinates = fieldmodule.findFieldByName("coordinates").castFiniteElement() | ||
| self.assertTrue(coordinates.isValid()) | ||
| minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes) | ||
| assertAlmostEqualList(self, minimums, [ 14.153, 62.444, -354.889 ], 1.0E-6) | ||
| assertAlmostEqualList(self, maximums, [ 297.502, 234.911, -23.486 ], 1.0E-6) | ||
| with ChangeManager(fieldmodule): | ||
| one = fieldmodule.createFieldConstant(1.0) | ||
| upperRightFissureGroup = fieldmodule.findFieldByName('upper lobe of right lung').castGroup() | ||
| self.assertTrue(upperRightFissureGroup.isValid()) | ||
| upperRightFissureMeshGroup = upperRightFissureGroup.getFieldElementGroup(mesh2d).getMeshGroup() | ||
| self.assertTrue(upperRightFissureMeshGroup.isValid()) | ||
| surfaceAreaField = fieldmodule.createFieldMeshIntegral(one, coordinates, upperRightFissureMeshGroup) | ||
| surfaceAreaField.setNumbersOfPoints(4) | ||
| volumeField = fieldmodule.createFieldMeshIntegral(one, coordinates, mesh3d) | ||
| volumeField.setNumbersOfPoints(3) | ||
| fieldcache = fieldmodule.createFieldcache() | ||
| result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1) | ||
| self.assertEqual(result, RESULT_OK) | ||
| self.assertAlmostEqual(surfaceArea, 139195.03021771502, delta=1.0E-2) | ||
| result, volume = volumeField.evaluateReal(fieldcache, 1) | ||
| self.assertEqual(result, RESULT_OK) | ||
| self.assertAlmostEqual(volume, 7169261.158690422, delta=1.0E-2) | ||
|
|
||
| # check some annotationGroups: | ||
| expectedSizes3d = { | ||
| "lung": 88, | ||
| "left lung": 44, | ||
| "right lung": 44, | ||
| "upper lobe of left lung": 24, | ||
| "lower lobe of left lung": 20, | ||
| "upper lobe of right lung": 16, | ||
| "middle lobe of right lung": 8, | ||
| "lower lobe of right lung": 20, | ||
| # "right lung accessory lobe": 0 | ||
| } | ||
| for name in expectedSizes3d: | ||
| group = getAnnotationGroupForTerm(annotationGroups, get_lung_term(name)) | ||
| size = group.getMeshGroup(mesh3d).getSize() | ||
| self.assertEqual(expectedSizes3d[name], size, name) | ||
| expectedSizes2d = { | ||
| "horizontal fissure of right lung": 4, | ||
| "oblique fissure of left lung": 8, | ||
| "oblique fissure of right lung": 8 | ||
| } | ||
| for name in expectedSizes2d: | ||
| group = getAnnotationGroupForTerm(annotationGroups, get_lung_term(name)) | ||
| size = group.getMeshGroup(mesh2d).getSize() | ||
| self.assertEqual(expectedSizes2d[name], size, name) | ||
|
|
||
| # test finding a marker in scaffold | ||
| markerGroup = fieldmodule.findFieldByName("marker").castGroup() | ||
| markerNodes = markerGroup.getFieldNodeGroup(nodes).getNodesetGroup() | ||
| self.assertEqual(6, markerNodes.getSize()) | ||
| markerName = fieldmodule.findFieldByName("marker_name") | ||
| self.assertTrue(markerName.isValid()) | ||
| markerLocation = fieldmodule.findFieldByName("marker_location") | ||
| self.assertTrue(markerLocation.isValid()) | ||
| # test apex marker point | ||
| cache = fieldmodule.createFieldcache() | ||
| node = findNodeWithName(markerNodes, markerName, "apex of left lung") | ||
| self.assertTrue(node.isValid()) | ||
| cache.setNode(node) | ||
| element, xi = markerLocation.evaluateMeshLocation(cache, 3) | ||
| self.assertEqual(37, element.getIdentifier()) | ||
| assertAlmostEqualList(self, xi, [ 0.0, 0.0, 1.0 ], 1.0E-10) | ||
|
|
||
| # refine 4 and check result | ||
| # first remove any face (but not point) annotation groups as they are re-added by defineFaceAnnotations | ||
| removeAnnotationGroups = [] | ||
| for annotationGroup in annotationGroups: | ||
| if (not annotationGroup.hasMeshGroup(mesh3d)) and (annotationGroup.hasMeshGroup(mesh2d) or annotationGroup.hasMeshGroup(mesh1d)): | ||
| removeAnnotationGroups.append(annotationGroup) | ||
| for annotationGroup in removeAnnotationGroups: | ||
| annotationGroups.remove(annotationGroup) | ||
| self.assertEqual(8, len(annotationGroups)) | ||
|
|
||
| refineRegion = region.createRegion() | ||
| refineFieldmodule = refineRegion.getFieldmodule() | ||
| options['Refine'] = True | ||
| options['Refine number of elements'] = 4 | ||
| refineNumberOfElements = options['Refine number of elements'] | ||
| meshrefinement = MeshRefinement(region, refineRegion, annotationGroups) | ||
| scaffold.refineMesh(meshrefinement, options) | ||
| annotationGroups = meshrefinement.getAnnotationGroups() | ||
|
|
||
| refineFieldmodule.defineAllFaces() | ||
| oldAnnotationGroups = copy.copy(annotationGroups) | ||
| for annotationGroup in annotationGroups: | ||
| annotationGroup.addSubelements() | ||
| scaffold.defineFaceAnnotations(refineRegion, options, annotationGroups) | ||
| for annotation in annotationGroups: | ||
| if annotation not in oldAnnotationGroups: | ||
| annotationGroup.addSubelements() | ||
| self.assertEqual(11, len(annotationGroups)) | ||
|
|
||
| mesh3d = refineFieldmodule.findMeshByDimension(3) | ||
| self.assertEqual(5632, mesh3d.getSize()) | ||
| mesh2d = refineFieldmodule.findMeshByDimension(2) | ||
| self.assertEqual(17344, mesh2d.getSize()) | ||
| mesh1d = refineFieldmodule.findMeshByDimension(1) | ||
| self.assertEqual(17848, mesh1d.getSize()) | ||
| nodes = refineFieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) | ||
| self.assertEqual(6144, nodes.getSize()) | ||
| datapoints = refineFieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS) | ||
| self.assertEqual(0, datapoints.getSize()) | ||
|
|
||
| # check some refined annotationGroups: | ||
| for name in expectedSizes3d: | ||
| group = getAnnotationGroupForTerm(annotationGroups, get_lung_term(name)) | ||
| size = group.getMeshGroup(mesh3d).getSize() | ||
| self.assertEqual(expectedSizes3d[name]*(refineNumberOfElements**3), size, name) | ||
| for name in expectedSizes2d: | ||
| group = getAnnotationGroupForTerm(annotationGroups, get_lung_term(name)) | ||
| size = group.getMeshGroup(mesh2d).getSize() | ||
| self.assertEqual(expectedSizes2d[name]*(refineNumberOfElements**2), size, name) | ||
|
|
||
| # test finding a marker in refined scaffold | ||
| markerGroup = refineFieldmodule.findFieldByName("marker").castGroup() | ||
| refinedNodes = refineFieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES) | ||
| markerNodes = markerGroup.getFieldNodeGroup(refinedNodes).getNodesetGroup() | ||
| self.assertEqual(6, markerNodes.getSize()) | ||
| markerName = refineFieldmodule.findFieldByName("marker_name") | ||
| self.assertTrue(markerName.isValid()) | ||
| markerLocation = refineFieldmodule.findFieldByName("marker_location") | ||
| self.assertTrue(markerLocation.isValid()) | ||
| # test apex marker point | ||
| cache = refineFieldmodule.createFieldcache() | ||
| node = findNodeWithName(markerNodes, markerName, "apex of left lung") | ||
| self.assertTrue(node.isValid()) | ||
| cache.setNode(node) | ||
| element, xi = markerLocation.evaluateMeshLocation(cache, 3) | ||
| self.assertEqual(2353, element.getIdentifier()) | ||
| assertAlmostEqualList(self, xi, [ 0.0, 0.0, 1.0 ], 1.0E-10) | ||
|
|
||
| if __name__ == "__main__": | ||
| unittest.main() |