Source code for gemseo.utils.ggobi_export

# Copyright 2021 IRT Saint Exupéry,
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License version 3 as published by the Free Software Foundation.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
# Contributors:
#    INITIAL AUTHORS - API and implementation and/or documentation
#       :author : Francois Gallard
GGOBI : interactive data visualization software

Export data to the XML file format needed by GGOBI
from __future__ import annotations

import os
from pathlib import Path
from typing import Sequence
from xml.dom import minidom
from xml.etree import ElementTree
from xml.etree.ElementTree import Comment
from xml.etree.ElementTree import Element
from xml.etree.ElementTree import SubElement

from numpy import ndarray

[docs]def prettify(elem): """Return a pretty-printed XML string for the Element. Args: elem: The xml element. """ rough_string = ElementTree.tostring(elem, "utf-8") reparsed = minidom.parseString(rough_string) return reparsed.toprettyxml(indent="\t")
[docs]def save_data_arrays_to_xml( variables_names: Sequence[str], values_array: ndarray, file_path: str | Path = "opt_hist.xml", ) -> None: """Save an optimization history in NumPy format to an xml file to be read by ggobi. Args: variables_names: The names of the variables. values_array: The history of the variables, of the form *(number of variables, number of iterations)*. file_path: The file path of the generated xml file. """ if os.path.exists(file_path): os.remove(file_path) nb_records = values_array.shape[0] nb_variables = len(variables_names) root = Element("ggobidata") comment = Comment('DOCTYPE ggobidata SYSTEM "ggobi.dtd"') root.append(comment) ggobidata = SubElement(root, "ggobidata") SubElement(ggobidata, "brush", attrib={"colo": "6", "glyph": "fc 3"}) data = SubElement(ggobidata, "data", attrib={"name": "opt_history"}) SubElement(data, "description", attrib={"source": "Optimization history"}) variables = SubElement(data, "variables", attrib={"count": str(nb_variables)}) for var in variables_names: variables_attr = {"name": str(var)} SubElement(variables, "realvariable", attrib=variables_attr) records = SubElement( data, "records", attrib={"color": str(2), "count": str(nb_records), "missingValue": "NA"}, ) for i_rec in range(nb_records): rec = SubElement( records, "record", attrib={"color": str(1), "label": "Iter_" + str(i_rec)} ) rec.text = str(values_array[i_rec, :]).replace("[", "").replace("]", "") with open(file_path, "w") as xml_file: xml_file.write(prettify(root))