Merge pull request #134 from KVSlab/update-probe-import

Update probe import

src/vampy/automatedPostprocessing/compute_velocity_and_pressure.py

@@ -10,14 +10,15 @@
     pass
 
 
-def compute_velocity_and_pressure(folder, dt, velocity_degree, pressure_degree, step):
+def compute_velocity_and_pressure(folder, dt, save_frequency, velocity_degree, pressure_degree, step):
     """
     Loads velocity and pressure from compressed .h5 CFD solution and
     converts and saves to .xdmf format for visualization (in e.g. ParaView).
 
     Args:
         folder (str): Path to results from simulation
         dt (float): Time step of simulation
+        save_frequency (int): Frequency that velocity and pressure has been stored
         velocity_degree (int): Finite element degree of velocity
         pressure_degree (int): Finite element degree of pressure
         step (int): Step size determining number of times data is sampled
@@ -74,8 +75,10 @@ def compute_velocity_and_pressure(folder, dt, velocity_degree, pressure_degree,
     if MPI.rank(MPI.comm_world) == 0:
         print("=" * 10, "Start post processing", "=" * 10)
 
-    file_counter = 1
+    counter = 1
     for i in range(len(dataset_u)):
+        # Set physical time (in [ms])
+        t = dt * counter * save_frequency
 
         file_u.read(u, dataset_u[i])
         file_p.read(p, dataset_p[i])
@@ -86,31 +89,31 @@ def compute_velocity_and_pressure(folder, dt, velocity_degree, pressure_degree,
 
         # Store velocity
         u.rename("velocity", "velocity")
-        u_writer.write(u, dt * file_counter)
+        u_writer.write(u, t)
 
         # Store pressure
         p.rename("pressure", "pressure")
-        p_writer.write(p, dt * file_counter)
+        p_writer.write(p, t)
 
         # Store deformation
         # NB: Storing together with velocity.
         if file_d is not None:
             file_d.read(d, dataset_d[i])
             d.rename("deformation", "deformation")
-            u_writer.write(d, dt * file_counter)
+            u_writer.write(d, t)
 
         # Update file_counter
-        file_counter += step
+        counter += step
 
     print("========== Post processing finished ==========")
     print("Results saved to: {}".format(folder))
 
 
 def main_convert():
-    folder, _, _, dt, velocity_degree, pressure_degree, _, _, _, _, _, step, _ = read_command_line()
-    compute_velocity_and_pressure(folder, dt, velocity_degree, pressure_degree, step)
+    folder, _, _, dt, velocity_degree, pressure_degree, _, _, save_frequency, _, _, step, _ = read_command_line()
+    compute_velocity_and_pressure(folder, dt, save_frequency, velocity_degree, pressure_degree, step)
 
 
 if __name__ == '__main__':
-    folder, _, _, dt, velocity_degree, pressure_degree, _, _, _, _, _, step, _ = read_command_line()
-    compute_velocity_and_pressure(folder, dt, velocity_degree, pressure_degree, step)
+    folder, _, _, dt, velocity_degree, pressure_degree, _, _, save_frequency, _, _, step, _ = read_command_line()
+    compute_velocity_and_pressure(folder, dt, save_frequency, velocity_degree, pressure_degree, step)

src/vampy/automatedPostprocessing/postprocessing_common.py

@@ -211,7 +211,7 @@ def norm_l2(self, u):
         return pow(inner(u, u), 0.5)
 
 
-def get_dataset_names(data_file, num_files=100000, step=1, start=1, print_info=True,
+def get_dataset_names(data_file, num_files=100000, step=1, start=0, print_info=True,
                       vector_filename="/velocity/vector_%d"):
     """
     Read velocity fields datasets and extract names of files

src/vampy/simulation/MovingAtrium.py

@@ -1,7 +1,6 @@
 import json
 import pickle
 from os import makedirs
-from pprint import pprint
 from dolfin import set_log_level, UserExpression
 
 from oasismove.problems.NSfracStep import *
@@ -96,11 +95,6 @@ def problem_parameters(commandline_kwargs, scalar_components, NS_parameters, **N
             print("-- Computing blood residence time --")
         scalar_components += ["blood"]
 
-    if MPI.rank(MPI.comm_world) == 0:
-        print("=== Starting simulation for MovingAtrium.py ===")
-        print("Running with the following parameters:")
-        pprint(NS_parameters)
-
 
 def scalar_source(scalar_components, **NS_namespace):
     """Return a dictionary of scalar sources."""

src/vampy/simulation/Probe.py

@@ -15,8 +15,9 @@
 ProbeObject = object
 
 try:
-    probe11 = cppimport.imp('probe.probe11')
+    probe11 = cppimport.imp('vampy.simulation.probe.probe11')
     ProbeObject = probe11.Probes
+    print("Successfully imported probe.probe11")
 except ImportError:
     print("Failed to import probe.probe11")
 

tests/test_compute_velocity_and_pressure.py

@@ -7,12 +7,13 @@ def test_compute_velocity_and_pressure():
     # Path to test results and params
     results_path = "tests/test_data/results/Solutions"
     dt = 0.951
+    save_frequency = 5
     velocity_degree = 1
     pressure_degree = 1
     step = 1
 
     # Run post-processing
-    compute_velocity_and_pressure(results_path, dt, velocity_degree, pressure_degree, step)
+    compute_velocity_and_pressure(results_path, dt, save_frequency, velocity_degree, pressure_degree, step)
 
     # Check that output files exist
     metric_names = ["velocity", "pressure"]