from lxml import etree as et import sys import numpy as np def remove_boundaries(Boundary_section, parts_to_keep, new_mat_ids): """remove any boundaries that are not between two parts we are keeping""" for boundary in Boundary_section: try: boundary_name = boundary.attrib["name"] parts = boundary_name.split('_') parts.remove('With') if not set(parts).issubset(parts_to_keep): # if all the parts are not in the parts_to_keep list Boundary_section.remove(boundary) else: old_mat_id = boundary.attrib['rb'] new_mat_id = new_mat_ids[old_mat_id] boundary.attrib['rb'] = new_mat_id except KeyError: # in case its a comment pass def remove_contacts(Contact_section, parts_to_keep): """remove any contacts that are not between two parts we are keeping""" for contact in Contact_section: try: contact_name = contact.attrib["surface_pair"] parts = contact_name.split('_') parts.remove('To') if not set(parts).issubset(parts_to_keep): # if all the parts are not in the parts_to_keep list Contact_section.remove(contact) except KeyError: pass def remove_materials(Material_section, parts_to_keep): """ any material that is not one we are keeping will be changed to a rigid body""" new_mat_ids = {} count= 0 for material in Material_section: material_name = material.attrib['name'] material_id = material.attrib['id'] if material_name not in parts_to_keep: Material_section.remove(material) else: # if it is one of the materials we are keeping, change the material number count += 1 new_mat_ids[material_id]= str(count) material.attrib['id'] = str(count) return new_mat_ids def remove_geometries(Geometry_section, parts_to_keep, new_mat_ids): """store all the info from the parts we want to keep, and then write a new geometry section""" Nodes_sections = get_section('Nodes', Geometry_section) Elements_sections = get_section('Elements', Geometry_section) NodeSet_sections = get_section('NodeSet', Geometry_section) Surface_sections = get_section('Surface', Geometry_section) SurfacePair_sections = get_section('SurfacePair', Geometry_section) DiscreteSet_sections = get_section('DiscreteSet', Geometry_section) # remove irrelevant nodes for nodes in Nodes_sections: if nodes.attrib['name'] not in parts_to_keep: Geometry_section.remove(nodes) # remove irrelevant Elements for elements in Elements_sections: if elements.attrib['name'] not in parts_to_keep: Geometry_section.remove(elements) else: old_mat_id = elements.attrib['mat'] new_mat_id = new_mat_ids[old_mat_id] elements.attrib['mat'] = new_mat_id # remove irrelevant NodeSets for nodeset in NodeSet_sections: nodeset_name = nodeset.attrib['name'] parts = nodeset_name.split('_') parts.remove('@') try: parts.remove('TiesNodes') except: parts.remove('ContactNodes') if not set(parts).issubset(parts_to_keep): Geometry_section.remove(nodeset) # remove irrelevant Surfaces for surface in Surface_sections: surface_name = surface.attrib['name'] parts = surface_name.split('_') try: parts.remove('@') except: parts.remove('All') try: parts.remove('ContactFaces') except: try: parts.remove('TiesFaces') except: parts.remove('Faces') if not set(parts).issubset(parts_to_keep): Geometry_section.remove(surface) # remove irrelevant surface pairs for surface_pair in SurfacePair_sections: surface_pair_name = surface_pair.attrib['name'] parts = surface_pair_name.split('_') parts.remove('To') if not set(parts).issubset(parts_to_keep): Geometry_section.remove(surface_pair) # remove DiscreteSets for discrete in DiscreteSet_sections: Geometry_section.remove(discrete) def remove_mesh_data(MeshData_section, parts_to_keep): for ElementData in MeshData_section: elem_set_name = ElementData.attrib['elem_set'] if elem_set_name not in parts_to_keep: MeshData_section.remove(ElementData) def edit_step_boundary(Step_sections, new_mat_ids): for Step in Step_sections: boundary_section = get_section('Boundary', Step) for boundary in boundary_section: old_mat_id = boundary.attrib['mat'] if old_mat_id in new_mat_ids.keys(): new_mat_id = new_mat_ids[old_mat_id] boundary.attrib['mat'] = new_mat_id else: boundary_section.remove(boundary) def ReduceModel(febfile, parts_to_keep): """ Remove anything in the febio file that does not pertain to these parts, and make changes as necessary""" # try first leaving in all the geometry, just removing all ties/contacts with anything not in the list # turn parts to keep into a list again, sys.argv turns it into a string parts_to_keep = parts_to_keep[1:-1] # remove the brackets from the string parts_to_keep = parts_to_keep.split(',') # create a list split by the commas feb_tree = et.parse(febfile) febio_spec_root = feb_tree.getroot() # get the geometry file from the febio file geosection = get_section('Geometry', febio_spec_root) geofile = geosection.attrib['from'] geofile_as_list = febfile.split('/')[:-1] + [geofile] geo_tree = et.parse(('/').join(geofile_as_list)) geo_spec_root = geo_tree.getroot() Material = get_section('Material', febio_spec_root) new_mat_ids = remove_materials(Material, parts_to_keep) # as each section is updated, change the material ids where necessary Geometry = get_section('Geometry', geo_spec_root) remove_geometries(Geometry, parts_to_keep, new_mat_ids) # replace the geometry section in the febio xml with the reduced one section_tags = [c.tag for c in febio_spec_root] febio_spec_root[section_tags.index('Geometry')] = Geometry MeshData = get_section('MeshData', febio_spec_root) remove_mesh_data(MeshData, parts_to_keep) Boundary = get_section('Boundary',febio_spec_root) remove_boundaries(Boundary, parts_to_keep, new_mat_ids) Contact = get_section('Contact', febio_spec_root) remove_contacts(Contact, parts_to_keep) Discrete = get_section('Discrete', febio_spec_root) febio_spec_root.remove(Discrete) Steps = get_section('Step', febio_spec_root) edit_step_boundary(Steps, new_mat_ids) directory = '/'.join(febfile.split('/')[:-1]) + '/' new_filename = directory + '_'.join(parts_to_keep) + '.feb' # Write the New File feb_tree.write(new_filename, xml_declaration=True, pretty_print=True) # make sure that it's pretty printing properly, by parsing and re-writing parser = et.XMLParser(remove_blank_text=True) new_feb_tree = et.parse(new_filename, parser) new_feb_tree.write(new_filename, xml_declaration=True, pretty_print=True) def myElement(tag, parent=None, text=None, attrib={}, **extra): """Shortcut to create an xml element (root or child), add text and other attributes""" e = et.Element(tag, attrib, **extra) if text: e.text = text if parent is not None: parent.append(e) return e def get_section(section_tag, parent, use_other_attribute = None, attribute_value = None): """Get the section from the parent. defualt is to search for the xml tag that matches with section_name. If use_other_attribute is specified, will search based on an xml attribute instead of the tag. if the section doesn't exist, create it. If more than one section exists in the parent with that name, return them as a list""" # if searching by a section tag if use_other_attribute is None: section_tags = [c.tag for c in parent] if section_tags.count(section_tag) == 1: section = parent[section_tags.index(section_tag)] elif section_tags.count(section_tag) > 1: section_indices = [i for i, x in enumerate(section_tags) if x == section_tag] section = [] for i in section_indices: section.append(parent[i]) else: # create it if it doesnt exist section = myElement(section_tag, parent) # if searching by an attribute else: # get all the sections with the tag. = my_sections section_tags = [c.tag for c in parent] section_indices = [i for i, x in enumerate(section_tags) if x == section_tag] my_sections = [] for i in section_indices: my_sections.append(parent[i]) # search those sections for the requested attribute section_attribute = [] for c in my_sections: try: att = c.attrib[use_other_attribute] section_attribute.append(att) except KeyError: section_attribute.append(None) # placeholder if they dont have the attribute # return the section/sections from my_section that have the requested attribute if section_attribute.count(attribute_value) == 0: # create it if it doesnt exist section = myElement(section_tag, parent, **{use_other_attribute:attribute_value}) elif section_attribute.count(attribute_value) == 1: # if only 1 return that one section = my_sections[section_attribute.index(attribute_value)] else: # if multiple return as list section_indices = [i for i, x in enumerate(section_attribute) if x == attribute_value] section = [] for i in section_indices: section.append(my_sections[i]) return section if __name__ == '__main__': ReduceModel(*sys.argv[1:]) # feb_filename = '/home/schwara2/Documents/Open_Knees/knee_hub/oks003/2nd_order/Febio/FeBio_custom.feb' # parts_to_keep = ['FMB','ACL','TBB'] # ReduceModel(feb_filename, parts_to_keep)