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improve compute_god_map and moved graph stuff to specific module
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,129 @@ | ||
| from pymicro.crystal.microstructure import Microstructure, Orientation | ||
| import networkx as nx | ||
| import numpy as np | ||
| import vtk | ||
| from vtk.util import numpy_support | ||
| from BasicTools.Bridges import vtkBridge | ||
| try: | ||
| from skimage.future import graph | ||
| except ImportError: | ||
| from skimage import graph | ||
|
|
||
| def create_graph(m: Microstructure) -> graph.RAG: | ||
| """Create the graph of this microstructure. | ||
| This method processes a `Microstructure` instance using a Region Adgency | ||
| Graph built with the crystal misorientation between neighbors as weights. | ||
| The graph has a node per grain and a connection between neighboring | ||
| grains of the same phase. The misorientation angle is attach to each edge. | ||
| :return rag: the region adjency graph of this microstructure. | ||
| """ | ||
|
|
||
| print('build the region agency graph for this microstructure') | ||
| rag = graph.RAG(m.get_grain_map(), connectivity=1) | ||
|
|
||
| # remove node and connections to the background | ||
| if 0 in rag.nodes: | ||
| rag.remove_node(0) | ||
|
|
||
| # get the grain infos | ||
| grain_ids = m.get_grain_ids() | ||
| rodrigues = m.get_grain_rodrigues() | ||
| centers = m.get_grain_centers() | ||
| volumes = m.get_grain_volumes() | ||
| phases = m.grains[:]['phase'] | ||
| for grain_id, d in rag.nodes(data=True): | ||
| d['label'] = [grain_id] | ||
| index = grain_ids.tolist().index(grain_id) | ||
| d['rod'] = rodrigues[index] | ||
| d['center'] = centers[index] | ||
| d['volume'] = volumes[index] | ||
| d['phase'] = phases[index] | ||
|
|
||
| # assign grain misorientation between neighbors to each edge of the graph | ||
| for x, y, d in rag.edges(data=True): | ||
| if rag.nodes[x]['phase'] != rag.nodes[y]['phase']: | ||
| # skip edge between neighboring grains of different phases | ||
| continue | ||
| sym = m.get_phase(phase_id=rag.nodes[x]['phase']).get_symmetry() | ||
| o_x = Orientation.from_rodrigues(rag.nodes[x]['rod']) | ||
| o_y = Orientation.from_rodrigues(rag.nodes[y]['rod']) | ||
| mis = np.degrees(o_x.disorientation(o_y, crystal_structure=sym)[0]) | ||
| d['misorientation'] = mis | ||
|
|
||
| # return our graph | ||
| return rag | ||
|
|
||
| def store_graph(m: Microstructure, rag: graph.RAG): | ||
| """Store the microstructure graph in a form that can be visualized in ParaView.""" | ||
| if rag is None: | ||
| rag = create_graph(m) | ||
| # create points for each node in the graph | ||
| points = vtk.vtkPoints() | ||
| # vtkUnstructuredGrid instance for all the cells | ||
| grid = vtk.vtkUnstructuredGrid() | ||
| grid.SetPoints(points) | ||
| for grain_id, d in rag.nodes(data=True): | ||
| # scale coordinates with the grain size and center on the grain | ||
| points.InsertNextPoint(d['center']) | ||
| # allocate memory for the cells representing the edges | ||
| grid.Allocate(len(rag.edges), 1) | ||
| for e in rag.edges: | ||
| Ids = vtk.vtkIdList() | ||
| Ids.InsertNextId(e[0] - 1) | ||
| Ids.InsertNextId(e[1] - 1) | ||
| grid.InsertNextCell(vtk.VTK_LINE, Ids) | ||
| # add arrays containing useful information to the grid | ||
| grain_ids = m.get_grain_ids() | ||
| grain_sizes = m.compute_grain_equivalent_diameters() | ||
| grain_ids_array = numpy_support.numpy_to_vtk(grain_ids) | ||
| grain_sizes_array = numpy_support.numpy_to_vtk(grain_sizes) | ||
| grain_ids_array.SetName('grain_ids') | ||
| grain_sizes_array.SetName('grain_sizes') | ||
| grid.GetCellData().AddArray(grain_ids_array) | ||
| grid.GetCellData().AddArray(grain_sizes_array) | ||
|
|
||
| # now add the created mesh to the microstructure | ||
| mesh = vtkBridge.VtkToMesh(grid) | ||
| m.add_mesh(mesh_object=mesh, location='/MeshData', meshname='graph', indexname='mesh_graph', replace=True) | ||
|
|
||
| def segment_mtr(m: Microstructure, labels_seg=None, mis_thr=20., min_area=500, store=False): | ||
| """Segment micro-textured regions (MTR). | ||
| This method processes a `Microstructure` instance to segment the MTR | ||
| with the specified parameters. | ||
| :param ndarray labels_seg: a pre-segmentation of the grain map, the full | ||
| grain map will be used if not specified. | ||
| :param float mis_thr: threshold in misorientation used to cut the graph. | ||
| :param int min_area: minimum area used to define a MTR. | ||
| :param bool store: flag to store the segmented array in the microstructure. | ||
| :return mtr_labels: array with the labels of the segmented regions. | ||
| """ | ||
| rag_seg = m.graph() | ||
|
|
||
| # cut our graph with the misorientation threshold | ||
| rag = rag_seg.copy() | ||
| edges_to_remove = [(x, y) for x, y, d in rag.edges(data=True) | ||
| if d['misorientation'] >= mis_thr] | ||
| rag.remove_edges_from(edges_to_remove) | ||
|
|
||
| comps = nx.connected_components(rag) | ||
| map_array = np.arange(labels_seg.max() + 1, dtype=labels_seg.dtype) | ||
| for i, nodes in enumerate(comps): | ||
| # compute area of this component | ||
| area = np.sum(np.isin(labels_seg, list(nodes))) | ||
| if area < min_area: | ||
| # ignore small MTR (simply assign them to label zero) | ||
| i = 0 | ||
| for node in nodes: | ||
| for label in rag.nodes[node]['label']: | ||
| map_array[label] = i | ||
| mtr_labels = map_array[labels_seg] | ||
| print('%d micro-textured regions were segmented' % len(np.unique(mtr_labels))) | ||
| if store: | ||
| m.add_field(gridname='CellData', fieldname='mtr_segmentation', | ||
| array=mtr_labels, replace=True) | ||
| return mtr_labels | ||
|
|
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