writing vtk files in case of backward registration

compute_strains.py

@@ -31,8 +31,9 @@ def compute_strains(
     if (ref_folder is not None) and (ref_basename is not None):
         ref_mesh = myVTK.readUGrid(
             filename=ref_folder+"/"+ref_basename+"-WithLocalBasis.vtk",
-            verbose=0)
+            verbose=verbose)
         ref_n_cells = ref_mesh.GetNumberOfCells()
+        if (verbose): print "ref_n_cells = " + str(ref_n_cells)
 
         if (ref_mesh.GetCellData().HasArray("sector_id")):
             iarray_sector_id = ref_mesh.GetCellData().GetArray("sector_id")
@@ -66,7 +67,7 @@ def compute_strains(
     for k_frame in xrange(n_frames):
         mesh = myVTK.readUGrid(
             filename=sol_folder+"/"+sol_basename+"_"+str(k_frame).zfill(n_zfill)+"."+sol_ext,
-            verbose=0)
+            verbose=verbose)
         n_cells = mesh.GetNumberOfCells()
         if (ref_mesh is not None):
             assert (n_cells == ref_n_cells)
@@ -76,11 +77,11 @@ def compute_strains(
             mesh=mesh,
             disp_array_name=disp_array_name,
             ref_mesh=ref_mesh,
-            verbose=0)
+            verbose=verbose)
         myVTK.writeUGrid(
             ugrid=mesh,
             filename=sol_folder+"/"+sol_basename+"_"+str(k_frame).zfill(n_zfill)+"."+sol_ext,
-            verbose=0)
+            verbose=verbose)
 
         if (write_strains) or (write_strain_vs_radius):
             if (ref_mesh is not None):

fedic.py

@@ -13,6 +13,7 @@ import glob
 import math
 import numpy
 import os
+import shutil
 import time
 
 import myVTKPythonLibrary as myVTK
@@ -178,10 +179,12 @@ def fedic(
     if not os.path.exists(working_folder):
         os.mkdir(working_folder)
     pvd_basename = working_folder+"/"+working_basename+"_"
-    file_pvd = dolfin.File(pvd_basename+".pvd")
     for vtu_filename in glob.glob(pvd_basename+"*.vtu"):
         os.remove(vtu_filename)
+    file_pvd = dolfin.File(pvd_basename+".pvd")
     file_pvd << (U, float(images_ref_frame))
+    os.remove(pvd_basename+".pvd")
+    shutil.move(pvd_basename+"".zfill(6)+".vtu", pvd_basename+str(images_ref_frame).zfill(6)+".vtu")
 
     if (print_iterations):
         for filename in glob.glob(working_folder+"/"+working_basename+"-frame=*.*"):
@@ -638,7 +641,10 @@ def fedic(
             file_volume.write(" ".join([str(val) for val in [k_frame, mesh_V]])+"\n")
 
             print_str(tab,"Printing solution…")
+            file_pvd = dolfin.File(pvd_basename+".pvd")
             file_pvd << (U, float(k_frame))
+            os.remove(pvd_basename+".pvd")
+            shutil.move(pvd_basename+"".zfill(6)+".vtu", pvd_basename+str(k_frame).zfill(6)+".vtu")
 
             if (images_dynamic_scaling):
                 p = numpy.empty((2,2))

image_expressions_py.py

@@ -53,7 +53,7 @@ class ExprIm2(dolfin.Expression):
         #print "    Expr = " + str(Expr)
 
 class ExprIm3(dolfin.Expression):
-    def __init__(self, filename, **kwargs):
+    def __init__(self, filename=None, **kwargs):
         if filename is not None:
             self.init_image(filename=filename)
 

plot_strains.py

@@ -8,10 +8,7 @@
 ###                                                                  ###
 ########################################################################
 
-import math
-import numpy
 import os
-import sys
 
 ########################################################################
 

print_tools.py

@@ -8,8 +8,6 @@
 ###                                                                  ###
 ########################################################################
 
-import myVTKPythonLibrary as myVTK
-
 ########################################################################
 
 #class Printer: