adding kalman

kalman/run.py

@@ -0,0 +1,75 @@
+from roukf.core import ROUKF
+import argparse
+import importlib
+from dolfin import *
+import dolfin
+import logging
+
+logging.getLogger().setLevel(logging.INFO)
+
+parameters['form_compiler']['optimize'] = True
+parameters['form_compiler']['cpp_optimize'] = True
+parameters['form_compiler']['cpp_optimize_flags'] = ('-O3 -ffast-math '
+                                                     '-march=native')
+
+
+def print_timing():
+    if dolfin.__version__ >= '2018':
+        list_timings(TimingClear.clear, [TimingType.wall])
+    else:
+        list_timings(TimingClear_clear, [TimingType_wall])
+
+
+def main(fwd_solver_module, inputfile):
+    ''' Run ROUKF parameter estimation.
+
+    Imports the given forward solver module and initializes the forward solver
+    with the specified input file.
+    Creates a ROUKF solver from the same input file and the instantiated
+    forward solver object and solves the optimization problem specified in the
+    input file.
+
+    Args:
+        fwd_solver_module (str): forward solver module to be imported and
+            passed to the ROUKF solver
+        inputfile (str): YAML input file with configuration of both
+            forward and ROUKF solver
+    '''
+
+    fwd_solver = importlib.import_module(fwd_solver_module)
+    fwd_solver = fwd_solver.init(inputfile)
+    fwd_solver.logger.setLevel(logging.WARNING)
+
+    kf = ROUKF(inputfile, fwd_solver)
+    kf.logger.setLevel(logging.INFO)
+    kf.solve()
+
+    print_timing()
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description='''\
+Run ROUKF parameter estimation.
+
+1. Imports the given forward solver module and initializes the forward solver
+   with the specified input file. The solver module is required to have a
+   method `init()` which handles the complete setup and returns self.
+2. Creates a ROUKF solver from the same input file and the instantiated
+   forward solver object and solves the optimization problem specified in the
+   input file.''',
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument('fwd_solver', type=str,
+                        help='Name of the forward solver module (see full'
+                        ' documentation), such that it can be imported.\n'
+                        'For example:\n navierstokes.solver or '
+                        'hyperelasticity.solver')
+    parser.add_argument('inputfile', type=str, help='path to YAML input file')
+    return parser
+
+
+if __name__ == '__main__':
+
+    args = get_parser().parse_args()
+
+    main(args.fwd_solver, args.inputfile)