Merge pull request #51 from rchristie/transfer-data

Add common fit utils for transferring data and matching field names

Author: hsorby

src/cmlibs/utils/zinc/group.py

@@ -4,12 +4,17 @@
 
 from enum import Enum
 
+from cmlibs.utils.zinc.field import get_group_list
 from cmlibs.utils.zinc.finiteelement import evaluate_mesh_centroid, evaluate_nearest_mesh_location, \
     evaluate_field_nodeset_mean
 from cmlibs.utils.zinc.general import ChangeManager, HierarchicalChangeManager
 from cmlibs.zinc.element import Element
 from cmlibs.zinc.field import Field, FieldGroup
 from cmlibs.zinc.result import RESULT_OK
+import logging
+
+
+logger = logging.getLogger(__name__)
 
 
 class GroupOperator(Enum):
@@ -487,3 +492,40 @@ def group_remove_group_local_contents(group, source_group):
                 nodeset_group = group.getNodesetGroup(nodeset)
                 if nodeset_group.isValid() and (nodeset_group.getSize() > 0):
                     nodeset_group.removeNodesConditional(source_group)
+
+
+def match_fitting_group_names(data_fieldmodule, model_fieldmodule, log_diagnostics=False):
+    """
+    Used for fitting problems. Rename any group names in the data fieldmodule that differ only in
+    case and whitespace from any in the model fieldmodule, to the accepted values from the model,
+    which are expected to be lower case without leading or trailing whitespace characters.
+    Note that internal whitespace must be exactly matched.
+    :param data_fieldmodule:  Data Fieldmodule whose group names may be modified.
+    :param model_fieldmodule:  Model Fieldmodule containing preferred group names.
+    :param log_diagnostics:  Set to True to write diagonstic messages about name matches and changes to logging.
+    """
+    # future: match with annotation terms
+    model_names = [group.getName() for group in get_group_list(model_fieldmodule)]
+    for data_group in get_group_list(data_fieldmodule):
+        data_name = data_group.getName()
+        compare_name = data_name.strip().casefold()
+        for model_name in model_names:
+            if model_name == data_name:
+                if log_diagnostics:
+                    logger.info("Data group '" + data_name + "' found in model")
+                break
+            elif model_name.strip().casefold() == compare_name:
+                result = data_group.setName(model_name)
+                if result == RESULT_OK:
+                    if log_diagnostics:
+                        logger.info("Data group '" + data_name + "' found in model as '" +
+                                    model_name + "'. Renaming to match.")
+                else:
+                    logger.error("Error: Data group '" + data_name + "' found in model as '" +
+                          model_name + "'. Renaming to match FAILED.")
+                    if fieldmodule.findFieldByName(model_name).isValid():
+                        logger.error("    Reason: field of that name already exists.")
+                break
+        else:
+            if log_diagnostics:
+                logger.info("Data group '" + data_name + "' not found in model")

src/cmlibs/utils/zinc/mesh.py

@@ -278,3 +278,18 @@ def undefine_field(field):
             mesh = fm.findMeshByDimension(i)
             mesh_group = mesh
             _undefine_field_on_elements(field, mesh_group)
+
+
+def element_or_ancestor_is_in_mesh(element, mesh):
+    """
+    Query whether element is in mesh or is from its tree of faces, lines etc.
+    :param element: Element to query.
+    :param mesh: Equal or higher dimension ancestor mesh or mesh group to check.
+    :return: True if element or any parent/ancestor is in mesh.
+    """
+    if mesh.containsElement(element):
+        return True
+    for p in range(1, element.getNumberOfParents() + 1):
+        if element_or_ancestor_is_in_mesh(element.getParentElement(p), mesh):
+            return True
+    return False

src/cmlibs/utils/zinc/region.py

@@ -1,4 +1,4 @@
-from cmlibs.utils.zinc.finiteelement import get_identifiers, evaluate_field_nodeset_range
+from cmlibs.utils.zinc.finiteelement import evaluate_field_nodeset_range, get_identifiers, get_maximum_node_identifier
 from cmlibs.zinc.field import Field
 from cmlibs.zinc.result import RESULT_OK
 
@@ -10,11 +10,25 @@ def _find_missing(lst):
             for i in range(x + 1, y) if y - x > 1]
 
 
-def convert_nodes_to_datapoints(target_region, source_region):
+def convert_nodes_to_datapoints(target_region, source_region, source_nodeset_type=Field.DOMAIN_TYPE_NODES,
+                                destroy_after_conversion=True):
+    """
+    Converts nodes in the source region to datapoints in the target region, renumbering any existing
+    datapoints in target region to not clash.
+    When the source nodeset type is Field.DOMAIN_TYPE_DATAPOINTS, then datapoints are transferred from the
+    source region to the target region.
+    :param target_region: Zinc Region to read data into. Existing data points are renumbered to avoid nodes.
+    :param source_region: Zinc Region containing nodes to transfer.
+    :param source_nodeset_type:  Set to Field.DOMAIN_TYPE_DATAPOINTS or Field.DOMAIN_TYPE_NODES to transfer datapoints
+    or convert nodes. Datapoint transfer should only be to different regions [default: Field.DOMAIN_TYPE_NODES].
+    :param destroy_after_conversion:  Set to True to destroy nodes that have been successfully converted, or False
+    to leave intact in source region [default: True].
+    """
     source_fieldmodule = source_region.getFieldmodule()
     target_fieldmodule = target_region.getFieldmodule()
     with ChangeManager(source_fieldmodule), ChangeManager(target_fieldmodule):
-        nodes = source_fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
+        # Could be nodes or datapoints.
+        nodes = source_fieldmodule.findNodesetByFieldDomainType(source_nodeset_type)
         if nodes.getSize() > 0:
             datapoints = target_fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
             if datapoints.getSize() > 0:
@@ -44,11 +58,27 @@ def convert_nodes_to_datapoints(target_region, source_region):
                     datapoint.setIdentifier(new_identifier)
 
             # transfer nodes as datapoints to target_region
-            buffer = write_to_buffer(source_region, resource_domain_type=Field.DOMAIN_TYPE_NODES)
-            buffer = buffer.replace(bytes("!#nodeset nodes", "utf-8"), bytes("!#nodeset datapoints", "utf-8"))
+            buffer = write_to_buffer(source_region, resource_domain_type=source_nodeset_type)
+            if source_nodeset_type == Field.DOMAIN_TYPE_NODES:
+                buffer = buffer.replace(bytes("!#nodeset nodes", "utf-8"), bytes("!#nodeset datapoints", "utf-8"))
             result = read_from_buffer(target_region, buffer)
             assert result == RESULT_OK, "Failed to load nodes as datapoints"
-            nodes.destroyAllNodes()
+            if destroy_after_conversion:
+                # note this cannot destroy nodes in use by elements
+                nodes.destroyAllNodes()
+
+
+def copy_fitting_data(target_region, source_region):
+    """
+    Copy nodes and data points from source_region to target_region, converting nodes to data points and
+    offsetting data point identifiers to not clash. All groups and fields in use are transferred.
+    This is used for setting up fitting problems where data needs to be in datapoints only.
+    :param target_region: Zinc Region to read nodes/data into.
+    :param source_region: Zinc Region containing nodes/data to transfer. Unmodified.
+    """
+    for domain_type in [Field.DOMAIN_TYPE_DATAPOINTS, Field.DOMAIN_TYPE_NODES]:
+        convert_nodes_to_datapoints(target_region, source_region, source_nodeset_type=domain_type,
+                                    destroy_after_conversion=False)
 
 
 def copy_nodeset(region, nodeset):

tests/test_zinc.py

@@ -1,12 +1,14 @@
 import unittest
-from cmlibs.utils.zinc.field import createFieldMeshIntegral, findOrCreateFieldCoordinates, \
-    findOrCreateFieldGroup
-from cmlibs.utils.zinc.finiteelement import createCubeElement, createSquareElement, createNodes, \
-    createTriangleElements, evaluateFieldNodesetMean
+from cmlibs.utils.zinc.field import (
+    createFieldMeshIntegral, findOrCreateFieldCoordinates, findOrCreateFieldGroup)
+from cmlibs.utils.zinc.mesh import element_or_ancestor_is_in_mesh
+from cmlibs.utils.zinc.finiteelement import (
+    createCubeElement, createSquareElement, createNodes, createTriangleElements, evaluateFieldNodesetMean)
 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 utilities import assert_almost_equal_list
+from utilities import assert_almost_equal_list, get_test_resource_name
 
 
 class ZincUtilsTestCase(unittest.TestCase):
@@ -105,6 +107,41 @@ def test_create_nodes_and_elements(self):
         self.assertEqual(RESULT_OK, result)
         self.assertAlmostEqual(0.9, volume, delta=1.0E-7)
 
+    def test_element_or_ancestor_is_in_mesh(self):
+        exf_file = get_test_resource_name('two_element_cube.exf')
+
+        context = Context("test")
+        source_region = context.createRegion()
+        result = source_region.readFile(exf_file)
+        self.assertTrue(result == RESULT_OK)
+
+        fm = source_region.getFieldmodule()
+        mesh3d = fm.findMeshByDimension(3)
+        mesh2d = fm.findMeshByDimension(2)
+        mesh1d = fm.findMeshByDimension(1)
+        element2 = mesh3d.findElementByIdentifier(2)
+        self.assertTrue(element2.isValid())
+        self.assertTrue(element_or_ancestor_is_in_mesh(element2, mesh3d))
+        self.assertFalse(element_or_ancestor_is_in_mesh(element2, mesh2d))
+        self.assertFalse(element_or_ancestor_is_in_mesh(element2, mesh1d))
+        face4 = mesh2d.findElementByIdentifier(4)
+        self.assertTrue(face4.isValid())
+        self.assertTrue(element_or_ancestor_is_in_mesh(face4, mesh3d))
+        self.assertTrue(element_or_ancestor_is_in_mesh(face4, mesh2d))
+        self.assertFalse(element_or_ancestor_is_in_mesh(face4, mesh1d))
+        line5 = mesh1d.findElementByIdentifier(5)
+        self.assertTrue(line5.isValid())
+        self.assertTrue(element_or_ancestor_is_in_mesh(line5, mesh3d))
+        self.assertTrue(element_or_ancestor_is_in_mesh(line5, mesh2d))
+        self.assertTrue(element_or_ancestor_is_in_mesh(line5, mesh1d))
+
+        elementtemplate = mesh1d.createElementtemplate()
+        elementtemplate.setElementShapeType(Element.SHAPE_TYPE_LINE)
+        new_line = mesh1d.createElement(-1, elementtemplate)
+        self.assertFalse(element_or_ancestor_is_in_mesh(new_line, mesh3d))
+        self.assertFalse(element_or_ancestor_is_in_mesh(new_line, mesh2d))
+        self.assertTrue(element_or_ancestor_is_in_mesh(new_line, mesh1d))
+
 
 if __name__ == "__main__":
     unittest.main()

tests/test_zinc_group.py

@@ -1,8 +1,9 @@
 import os
 import unittest
+from cmlibs.utils.zinc.field import find_or_create_field_group
 from cmlibs.utils.zinc.group import (
     group_add_group_local_contents, group_evaluate_centroid, group_remove_group_local_contents,
-    group_evaluate_representative_point, groups_have_same_local_contents)
+    group_evaluate_representative_point, groups_have_same_local_contents, match_fitting_group_names)
 from cmlibs.zinc.context import Context
 from cmlibs.zinc.element import Element
 from cmlibs.zinc.field import Field
@@ -134,3 +135,27 @@ def test_group_add_compare_group_local_contents(self):
         self.assertEqual(0, group1.getMeshGroup(mesh2d).getSize())
         self.assertEqual(0, group1.getMeshGroup(mesh1d).getSize())
         self.assertEqual(0, group1.getNodesetGroup(nodes).getSize())
+
+
+    def test_match_fitting_group_names(self):
+        """
+        Test utility functions for adding and comparing group local contents.
+        """
+        context = Context("test")
+        model_region = context.createRegion()
+        model_fieldmodule = model_region.getFieldmodule()
+        find_or_create_field_group(model_fieldmodule, "bob", managed=True)
+        find_or_create_field_group(model_fieldmodule, "fred", managed=True)
+        find_or_create_field_group(model_fieldmodule, "two names", managed=True)
+
+        data_region = context.createRegion()
+        data_fieldmodule = data_region.getFieldmodule()
+        data_group_bob = find_or_create_field_group(data_fieldmodule, " Bob")
+        data_group_fred = find_or_create_field_group(data_fieldmodule, "  fRed\t")
+        data_group_two_names = find_or_create_field_group(data_fieldmodule, "\t two NAMES  ")
+
+        match_fitting_group_names(data_fieldmodule, model_fieldmodule, log_diagnostics=True)
+
+        self.assertEqual(data_group_bob.getName(), "bob")
+        self.assertEqual(data_group_fred.getName(), "fred")
+        self.assertEqual(data_group_two_names.getName(), "two names")