Source code for extractor

#!/usr/bin/env python
"""
Extract information from a SfePy multi-time-step results file (HDF5
format) and/or linearize results with stored higher order DOFs.

For the linearization, the original input (problem description) file must
be specified as the first argument. Use the option --linearization below
to override linearization parameters defined in the input file. The
linearization forces --dump option, i.e., output to VTK files.

Examples
--------

$ ./extractor.py -e "p e 0 1999" bone.h5
$ ./extractor.py -e "p e 0 1999" bone.h5 -a
$ ./extractor.py -e "p e 0 1999" bone.h5 -o extracted.h5
$ ./extractor.py -e "p e 0 1999" bone.h5 -o extracted.h5 -a
"""
from __future__ import print_function
from __future__ import absolute_import
import os
from argparse import ArgumentParser, RawDescriptionHelpFormatter

import sfepy
from sfepy.base.base import nm, dict_to_struct, get_default, Struct
from sfepy.base.ioutils import get_trunk
import sfepy.postprocess.time_history as th

[docs]def create_problem(filename): from sfepy.discrete import Problem problem = Problem.from_conf_file(filename, init_equations=False, init_solvers=False) return problem
[docs]def parse_linearization(linearization): out = {} for item in linearization.split(','): key, val = item.split(':') if key == 'eps': val = float(val) elif key in ('min_level', 'max_level'): val = int(val) elif key == 'kind': pass else: raise ValueError('wrong linearization option key! (%s)' % key) out[key] = val return dict_to_struct(out)
helps = { 'debug': 'automatically start debugger when an exception is raised', 'filename' : 'basename of output file(s) [default: <basename of input file>]', 'dump' : 'dump to sequence of VTK files', 'same_dir' : 'store the dumped VTK files in the directory of filename_in', 'linearization' : 'linearization options. Default values apply if neither command' ' line nor input file options are set.' " [default: 'kind:adaptive,min_level:0,max_level:2,eps:1e-2']", 'times' : 'extract and print times of individual time steps', 'from' : 'start dumping from time step ii [default: %(default)s]', 'to' : 'stop dumping at time step ii [default: <last step>]', 'step' : 'use every ii-th step for dumping [default: %(default)s]', 'extract' : 'extract variables according to extraction list.' " Example: 'u n 10 15, p e 0' means variable 'u' in nodes 10, 15" " and variable 'p' in element 0", 'average' : 'average vertex variable into cells ("e" extraction mode)' }
[docs]def main(): parser = ArgumentParser(description=__doc__, formatter_class=RawDescriptionHelpFormatter) parser.add_argument('--version', action='version', version='%(prog)s ' + sfepy.__version__) parser.add_argument('--debug', action='store_true', dest='debug', default=False, help=helps['debug']) parser.add_argument('-o', metavar='filename', action='store', dest='output_filename_trunk', default=None, help=helps['filename']) parser.add_argument('-d', '--dump', action='store_true', dest='dump', default=False, help=helps['dump']) parser.add_argument('--same-dir', action='store_true', dest='same_dir', default=False, help=helps['same_dir']) parser.add_argument('-l', '--linearization', metavar='options', action='store', dest='linearization', default=None, help=helps['linearization']) parser.add_argument('--times', action='store_true', dest='times', default=False, help=helps['times']) parser.add_argument('-f', '--from', type=int, metavar='ii', action='store', dest='step_from', default=0, help=helps['from']) parser.add_argument('-t', '--to', type=int, metavar='ii', action='store', dest='step_to', default=None, help=helps['to']) parser.add_argument('-s', '--step', type=int, metavar='ii', action='store', dest='step_by', default=1, help=helps['step']) parser.add_argument('-e', '--extract', metavar='list', action='store', dest='extract', default=None, help=helps['extract']) parser.add_argument('-a', '--average', action='store_true', dest='average', default=False, help=helps['average']) parser.add_argument('input_file', nargs='?', default=None) parser.add_argument('results_file') options = parser.parse_args() if options.debug: from sfepy.base.base import debug_on_error; debug_on_error() filename_in = options.input_file filename_results = options.results_file if filename_in is None: linearize = False else: linearize = True options.dump = True if options.times: steps, times, nts, dts = th.extract_times(filename_results) for ii, time in enumerate(times): step = steps[ii] print('%d %e %e %e' % (step, time, nts[ii], dts[ii])) if options.dump: trunk = get_default(options.output_filename_trunk, get_trunk(filename_results)) if options.same_dir: trunk = os.path.join(os.path.dirname(filename_results), os.path.basename(trunk)) args = {} if linearize: problem = create_problem(filename_in) linearization = Struct(kind='adaptive', min_level=0, max_level=2, eps=1e-2) aux = problem.conf.options.get('linearization', None) linearization.update(aux) if options.linearization is not None: aux = parse_linearization(options.linearization) linearization.update(aux) args.update({'fields' : problem.fields, 'linearization' : linearization}) if options.step_to is None: args.update({'step0' : options.step_from}) else: args.update({'steps' : nm.arange(options.step_from, options.step_to + 1, options.step_by, dtype=nm.int)}) th.dump_to_vtk(filename_results, output_filename_trunk=trunk, **args) if options.extract: ths, ts = th.extract_time_history(filename_results, options.extract) if options.average: ths = th.average_vertex_var_in_cells(ths) if options.output_filename_trunk: th.save_time_history(ths, ts, options.output_filename_trunk + '.h5') else: print(dict_to_struct(ths, flag=(1, 1, 1)).str_all())
if __name__ == '__main__': main()