Preserve visualization output

cli/view_command.py

@@ -12,27 +12,30 @@
 #
 # -----------------------------------------------------------------------------
 
-import os, sys, shutil
+import os
 import subprocess as sp
+import sys
+
 from print_command import Print
-from build_command import BuildCommand
 
 
 ## The BioDynaMo CLI command to execute the unit-tests created by default with
 ## the simulation template. Note that we ignore the configuration in bdm.json.
 def ViewCommand(file_id=None):
     Print.success("<bdm view> Opening previous simulation results ...")
-    # 1. Check if paraview is installed and if not, return
-    bdmsys = os.environ.get("BDMSYS")
-    if bdmsys is None:
-        Print.error("<bdm view> BDMSYS is not set.")
+    # 1. Check if ParaView is available on PATH.
+    try:
+        pv_found = sp.run(
+            ["paraview", "--version"],
+            stdout=sp.DEVNULL,
+            stderr=sp.DEVNULL,
+            check=False,
+        )
+    except FileNotFoundError:
+        Print.error("<bdm view> ParaView not found.")
         sys.exit(1)
-    paraview_executable = os.path.join(
-        bdmsys, "third_party/paraview/bin/paraview"
-    )
-    pv_found = sp.run("{} --version".format(paraview_executable), shell=True)
     if pv_found.returncode != 0:
-        Print.error("<bdm view> ParaView not found.")
+        Print.error("<bdm view> ParaView could not be started.")
         sys.exit(1)
 
     # 2. attempt to change into project director if we are in build
@@ -83,9 +86,7 @@ def ViewCommand(file_id=None):
         os.chdir("build")
 
     # 9. Open the latest pvsm file
-    visualize = sp.run(
-        "{} --state={}".format(paraview_executable, pvsm_file), shell=True
-    )
+    visualize = sp.run(["paraview", "--state={}".format(pvsm_file)])
     if visualize.returncode != 0:
         Print.warning(
             "<bdm view> Visualization terminated with return code {}.".format(

paraview_plugin/CMakeLists.txt

@@ -9,7 +9,9 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 
 find_package(MPI REQUIRED)
-find_package(ParaView REQUIRED)
+find_package(ParaView REQUIRED COMPONENTS
+             RemotingServerManager
+             VTKExtensionsFiltersGeneral)
 
 set("_paraview_plugin_default_${CMAKE_PROJECT_NAME}" ON)
 paraview_plugin_scan(

paraview_plugin/Plugin/CMakeLists.txt

@@ -1,5 +1,6 @@
 paraview_add_plugin(BDMGlyphFilter
   VERSION "1.0"
+  XML_DOCUMENTATION OFF
   REQUIRED_ON_SERVER
   REQUIRED_ON_CLIENT
   MODULES BDM

src/core/visualization/paraview/adaptor.cc

@@ -22,8 +22,6 @@
 #include "core/visualization/paraview/vtk_agents.h"
 #include "core/visualization/paraview/vtk_diffusion_grid.h"
 
-#ifndef __ROOTCLING__
-
 #include <vtkCPDataDescription.h>
 #include <vtkCPInputDataDescription.h>
 #include <vtkCPProcessor.h>
@@ -214,7 +212,8 @@ void ParaviewAdaptor::CreateVtkObjects() {
 void ParaviewAdaptor::BuildAgentsVTKStructures() {
   auto* rm = Simulation::GetActive()->GetResourceManager();
   for (auto& pair : impl_->vtk_agents_) {
-    const auto& agents = rm->GetTypeIndex()->GetType(pair.second->GetTClass());
+    const auto& agents =
+        rm->GetTypeIndex()->GetType(pair.second->GetTypeName());
     pair.second->Update(&agents);
   }
 }
@@ -251,10 +250,9 @@ void ParaviewAdaptor::WriteSimulationInfoJsonFile() {
 void ParaviewAdaptor::GenerateParaviewState() {
   auto* sim = Simulation::GetActive();
   std::stringstream python_cmd;
-  std::string pv_dir = std::getenv("ParaView_DIR");
   std::string bdmsys = std::getenv("BDMSYS");
 
-  python_cmd << pv_dir << "/bin/pvbatch " << bdmsys
+  python_cmd << "pvbatch " << bdmsys
              << "/include/core/visualization/paraview/generate_pv_state.py "
              << sim->GetOutputDir() << "/" << kSimulationInfoJson;
   int ret_code = system(python_cmd.str().c_str());
@@ -298,25 +296,3 @@ std::string ParaviewAdaptor::BuildPythonScriptString(
 }
 
 }  // namespace bdm
-
-#else
-
-namespace bdm {
-
-ParaviewAdaptor::ParaviewAdaptor() {}
-
-void ParaviewAdaptor::Visualize() {}
-
-void ParaviewAdaptor::InsituVisualization() {}
-
-void ParaviewAdaptor::ExportVisualization() {}
-
-void ParaviewAdaptor::WriteToFile() {}
-
-void ParaviewAdaptor::GenerateParaviewState() {}
-
-std::string ParaviewAdaptor::BuildPythonScriptString(
-    const std::string& python_script) {}
-}  // namespace bdm
-
-#endif

src/core/visualization/paraview/adaptor.h

@@ -36,7 +36,7 @@
 namespace bdm {
 
 /// The class that bridges the simulation code with ParaView.
-class ParaviewAdaptor : private VisualizationAdaptor {
+class ParaviewAdaptor : public VisualizationAdaptor {
  public:
   /// Initializes Catalyst with the predefined pipeline and allocates memory
   /// for the VTK grid structures
@@ -50,11 +50,11 @@ class ParaviewAdaptor : private VisualizationAdaptor {
   struct ParaviewImpl;
 
  private:
-  std::unique_ptr<ParaviewImpl> impl_;    //!
-  static std::atomic<uint64_t> counter_;  //!
+  std::unique_ptr<ParaviewImpl> impl_;
+  static std::atomic<uint64_t> counter_;
 
   /// only needed for insitu visualization
-  bool initialized_ = false;  //!
+  bool initialized_ = false;
   bool simulation_info_json_generated_ = false;
 
   friend class ParaviewAdaptorTest_GenerateSimulationInfoJson_Test;
@@ -96,8 +96,6 @@ class ParaviewAdaptor : private VisualizationAdaptor {
   /// Combine user-defined python script with biodynamo default python
   /// insitu pipeline.
   static std::string BuildPythonScriptString(const std::string& python_script);
-
-  ClassDefNV(ParaviewAdaptor, 1);
 };
 
 }  // namespace bdm

src/core/visualization/paraview/helper.h

@@ -23,8 +23,6 @@
 #include "core/visualization/paraview/vtk_agents.h"
 #include "core/visualization/paraview/vtk_diffusion_grid.h"
 
-class TClass;
-
 namespace bdm {
 
 static constexpr char const* kSimulationInfoJson = "simulation_info.json";