added codes

python_code/unwrap_simple.py

@@ -0,0 +1,64 @@
+################################################################
+#
+# Workspace
+#
+################################################################
+
+# Import modules here
+from __future__ import print_function
+import numpy as np
+import sys
+from fenics import *
+import glob
+from unwrapper import Unwrapper
+
+def read_parameters(infile):
+    ''' Read in parameters yaml file.
+
+    Args:
+        infile      path to yaml file
+
+    Return:
+        prms        parameters dictionary
+    '''
+    import ruamel.yaml as yaml
+    with open(infile, 'r+') as f:
+        prms = yaml.load(f, Loader=yaml.Loader)
+    return prms
+
+def getfiles(path):
+    #get the velocities from the input files
+    files = glob.glob(path + '/**/[0-9]*/u.h5', recursive=True)
+    if files == []:
+        files = glob.glob(path + 'u[0-9]*.h5', recursive=True)
+    files.sort(key=lambda f: int(''.join(filter(str.isdigit, f))))
+    return files
+
+def ROUTINES(options):
+    ''' 
+
+    All the process activated in the input file should be coded here
+    
+    '''
+    #unwrap from filenames for h5 files:
+    velocity_files = getfiles(options['io']['in_file'])
+    unwrapper = Unwrapper(options)
+    unwrapper.unwrap(velocity_files)
+
+    #unwrap from numpy file:
+    #unwrapper.set_method('Laplacian')
+    #unwrapper.unwrap(options['io']['in_file'] + 'u.npy')
+     
+
+if __name__ == '__main__':
+
+    # This lines are necessary in order to read the input file as well of the 'read_parameters' function.
+
+    inputfile = sys.argv[1]
+    print('Found input file ' + inputfile)
+
+    # this part will be executed first and will call all the other process. 
+    options =	read_parameters(inputfile)
+    ROUTINES(options)
+
+