Naming convention

__init__.py

@@ -2,41 +2,41 @@
 
 from .generate_images_Mapping import *
 from .fedic import *
+from .expressions_imaging_models_cpp import *
 from .plot_binned_strains_vs_radius import *
 from .NonlinearSolver import *
 from .MeshSeries import *
-from .generated_image_expressions_cpp import *
 from .plot_strains_vs_radius import *
 from .Energy_GeneratedImage import *
 from .compute_unwarped_images import *
 from .mesh2ugrid import *
 from .Problem_ImageRegistration import *
+from .compute_downsampled_images import *
+from .expressions_images_py import *
 from .compute_quadrature_degree import *
+from .expressions_static_scaling_cpp import *
 from .Energy_Regularization import *
 from .compute_warped_images import *
+from .expressions_generated_grad_cpp import *
 from .plot_strains import *
-from .image_expressions_cpp import *
 from .plot_twist_vs_height import *
+from .compute_projected_image import *
 from .Energy import *
+from .compute_normalized_images import *
 from .compute_warped_mesh import *
 from .Energy_WarpedImage import *
 from .write_VTU_file import *
 from .generate_undersampled_images import *
-from .normalize_images import *
 from .plot_regional_strains import *
-from .image_expressions_py import *
 from .compute_displacements_from_ref import *
 from .ImageIterator import *
-from .static_scaling_cpp import *
 from .fedic2 import *
-from .generated_grad_expressions_cpp import *
 from .plot_displacement_error import *
+from .expressions_generated_images_cpp import *
 from .Problem import *
 from .generate_images import *
 from .ImageSeries import *
 from .compute_displacement_error import *
-from .downsample_images import *
-from .imaging_models_cpp import *
-from .project import *
+from .expressions_images_cpp import *
 from .compute_strains import *
 from .generate_images_Image import *

downsample_images.py → compute_downsampled_images.py

@@ -25,7 +25,7 @@ import dolfin_dic as ddic
 
 ################################################################################
 
-def downsample_images(
+def compute_downsampled_images(
         images_folder,
         images_basename,
         downsampling_factors,
@@ -35,7 +35,7 @@ def downsample_images(
         write_temp_images=0,
         verbose=0):
 
-    mypy.my_print(verbose, "*** downsample_images ***")
+    mypy.my_print(verbose, "*** compute_downsampled_images ***")
 
     images_filenames = glob.glob(images_folder+"/"+images_basename+"_[0-9]*"+"."+images_ext)
     images_nframes = len(images_filenames)

normalize_images.py → compute_normalized_images.py

@@ -25,7 +25,7 @@ import dolfin_dic as ddic
 
 ################################################################################
 
-def normalize_images(
+def compute_normalized_images(
         images_folder,
         images_basename,
         images_datatype,
@@ -33,7 +33,7 @@ def normalize_images(
         overwrite_orig_images=1,
         verbose=0):
 
-    mypy.my_print(verbose, "*** normalize_images ***")
+    mypy.my_print(verbose, "*** compute_normalized_images ***")
 
     images_filenames = glob.glob(images_folder+"/"+images_basename+"_[0-9]*"+"."+images_ext)
     images_nframes = len(images_filenames)

project.py → compute_projected_image.py

@@ -22,7 +22,7 @@ import dolfin_dic as ddic
 
 ################################################################################
 
-def project(
+def compute_projected_image(
         mesh,
         image_filename,
         image_field_name="displacement",

image_expressions_cpp.py → expressions_images_cpp.py

@@ -10,11 +10,29 @@
 
 # from future.utils import native_str
 
+import dolfin
+
 import dolfin_dic as ddic
 
 ################################################################################
 
 def get_ExprIm_cpp(
+        *args,
+        **kwargs):
+
+    if (int(dolfin.dolfin_version().split('.')[0]) >= 2018):
+        return get_ExprIm_cpp_pybind(
+            *args,
+            **kwargs)
+    else:
+        return get_ExprIm_cpp_swig(
+            *args,
+            **kwargs)
+
+
+################################################################################
+
+def get_ExprIm_cpp_swig(
         im_dim, # 2, 3
         im_type="im", # im, grad, grad_no_deriv
         im_is_def=0,

generate_images.py

@@ -184,7 +184,7 @@ def generate_images(
     else:
         downsampling = True
 
-        ddic.downsample_images(
+        ddic.compute_downsampled_images(
             images_folder=images["folder"],
             images_basename=images["basename"],
             downsampling_factors=images["upsampling_factors"],
@@ -207,7 +207,7 @@ def generate_images(
     elif (images["data_type"] in ("unsigned char", "unsigned short", "unsigned int", "unsigned long", "unsigned float", "uint8", "uint16", "uint32", "uint64", "ufloat")):
         normalizing = True
 
-        ddic.normalize_images(
+        ddic.compute_normalized_images(
             images_folder=images["folder"],
             images_basename=images["basename"],
             images_datatype=images["data_type"],