diff --git a/src/libcode/vx_shapedata/mode_conf_info.cc b/src/libcode/vx_shapedata/mode_conf_info.cc
index 03e806c663..e2db27326f 100644
--- a/src/libcode/vx_shapedata/mode_conf_info.cc
+++ b/src/libcode/vx_shapedata/mode_conf_info.cc
@@ -966,13 +966,14 @@ dict = conf.lookup_dictionary(conf_key_obs);
 if ( dict->lookup(conf_key_multivar_logic) )   obs_multivar_logic = dict->lookup_string(conf_key_multivar_logic);
 
 multivar_intensity.clear();
-BoolArray ba = lookup_bool_array("multivar_intensity_flag", dict);
-ba.dump(cout);
-for (int i=0; i<ba.n(); ++i) {
-  multivar_intensity.push_back((ba[i] == 1 ? true:false));
+if ( dict->lookup("multivar_intensity_flag")) {
+  BoolArray ba = lookup_bool_array("multivar_intensity_flag", dict);
+  //ba.dump(cout);
+  for (int i=0; i<ba.n(); ++i) {
+    multivar_intensity.push_back((ba[i] == 1 ? true:false));
+  }
 }
 return;
-
 }
 
 
diff --git a/src/tools/core/mode/mode_exec.cc b/src/tools/core/mode/mode_exec.cc
index d2ceeae5cd..87b984359e 100644
--- a/src/tools/core/mode/mode_exec.cc
+++ b/src/tools/core/mode/mode_exec.cc
@@ -144,7 +144,6 @@ void ModeExecutive::init()
 
 {
 
-GrdFileType ftype, otype;
 Met2dDataFileFactory mtddf_factory;
 
 R_index = T_index = 0;
@@ -208,6 +207,79 @@ return;
 
 }
 
+///////////////////////////////////////////////////////////////////////
+
+
+void ModeExecutive::init_final(const MultiVarData &mvd)
+
+{
+
+GrdFileType ftype, otype;
+//Met2dDataFileFactory mtddf_factory;
+
+R_index = T_index = 0;
+
+   // Create the default config file name
+   default_config_file = replace_path(default_config_filename);
+
+   // If the merge config file was not set, use the match config file
+   if(merge_config_file.length() == 0)
+        merge_config_file = match_config_file;
+
+   // List the config files
+   mlog << Debug(1)
+        << "Default Config File: " << default_config_file << "\n"
+        << "Match Config File: "   << match_config_file   << "\n"
+        << "Merge Config File: "   << merge_config_file   << "\n";
+
+   // Read the config files
+   engine.conf_info.read_config(default_config_file.c_str(), match_config_file.c_str());
+
+   // Get the forecast and observation file types from config, if present
+   ftype = parse_conf_file_type(engine.conf_info.conf.lookup_dictionary(conf_key_fcst));
+   otype = parse_conf_file_type(engine.conf_info.conf.lookup_dictionary(conf_key_obs));
+
+
+   // Read observation file
+   // if(!(obs_mtddf = mtddf_factory.new_met_2d_data_file(obs_file.c_str(), otype))) {
+   //    mlog << Error << "\nTrouble reading observation file \""
+   //         << obs_file << "\"\n\n";
+   //    exit(1);
+   // }
+
+
+   // Read forecast file
+   // if(!(fcst_mtddf = mtddf_factory.new_met_2d_data_file(fcst_file.c_str(), ftype))) {
+   //    mlog << Error << "\nTrouble reading forecast file \""
+   //         << fcst_file << "\"\n\n";
+   //    exit(1);
+   // }
+
+   // Store the input data file types
+   // ftype = fcst_mtddf->file_type();
+   // otype = obs_mtddf->file_type();
+
+   ftype = mvd.ftype;
+   otype = mvd.otype;
+
+   // Process the configuration
+   engine.conf_info.process_config(ftype, otype);
+
+   // const int shift = engine.conf_info.shift_right;
+
+   // fcst_mtddf->set_shift_right(shift);
+   //  obs_mtddf->set_shift_right(shift);
+
+   // List the input files
+   // mlog << Debug(1)
+   //      << "Forecast File: "    << fcst_file << "\n"
+   //      << "Observation File: " << obs_file  << "\n";
+
+   engine.conf_info.nc_info.compress_level = engine.conf_info.get_compression_level();
+
+return;
+
+}
 
 ///////////////////////////////////////////////////////////////////////
 
@@ -1022,6 +1094,8 @@ MultiVarData *ModeExecutive::get_multivar_data()
   mvd->Fcst_sd = new ShapeData(Fcst_sd);
   mvd->Obs_sd = new ShapeData(Obs_sd);
   mvd->grid = new Grid(grid);
+  mvd->ftype = ftype;
+  mvd->otype = otype;
   return mvd;
 }
 
@@ -1271,9 +1345,6 @@ if ( info.all_false() )  return;
 
    }
 
-   vector<int> fcstValues, obsValues;
-   vector<int> fcstCValues, obsCValues;
-
    for(x=0; x<grid.nx(); x++) {
 
       for(y=0; y<grid.ny(); y++) {
@@ -1299,11 +1370,6 @@ if ( info.all_false() )  return;
 	   }
            if ( info.do_object_id && fcst_obj_data != nullptr && engine.fcst_split != nullptr ) {
              fcst_obj_data[n] = nint(engine.fcst_split->data(x, y));
-	     if (find(fcstValues.begin(), fcstValues.end(), fcst_obj_data[n]) == fcstValues.end())
-	       {
-		 printf("FcstValue=%d\n", fcst_obj_data[n]);
-		 fcstValues.push_back(fcst_obj_data[n]);
-	       }
            }
          }
          else {
@@ -1321,11 +1387,6 @@ if ( info.all_false() )  return;
 	   }
 	   if ( info.do_object_id && obs_obj_data != nullptr ) {
 	     obs_obj_data[n] = nint(engine.obs_split->data(x, y));
-	     if (find(obsValues.begin(), obsValues.end(), obs_obj_data[n]) == obsValues.end())
-	       {
-		 printf("ObsValue=%d\n", obs_obj_data[n]);
-		 obsValues.push_back(obs_obj_data[n]);
-	       }
 	   }
          }
          else {
diff --git a/src/tools/core/mode/mode_exec.h b/src/tools/core/mode/mode_exec.h
index 73f889f200..75f574b5cd 100644
--- a/src/tools/core/mode/mode_exec.h
+++ b/src/tools/core/mode/mode_exec.h
@@ -77,6 +77,7 @@ class ModeExecutive {
       void clear();
 
       void init();
+      void init_final(const MultiVarData &mvd);
 
       int n_conv_radii   () const;
       int n_conv_threshs () const;
@@ -113,6 +114,8 @@ class ModeExecutive {
 
       ShapeData Fcst_sd, Obs_sd;
 
+      GrdFileType ftype, otype;
+
       void clear_internal_r_index();
       void setup_fcst_obs_data();
       void setup_fcst_obs_data(const MultiVarData &mvd);
diff --git a/src/tools/core/mode/mode_frontend.cc b/src/tools/core/mode/mode_frontend.cc
index e8697d51c5..7ade93261b 100644
--- a/src/tools/core/mode/mode_frontend.cc
+++ b/src/tools/core/mode/mode_frontend.cc
@@ -64,7 +64,7 @@ if ( mode_exec ) {
 int ModeFrontEnd::run(const StringArray & Argv)
 
 {
-  Argv.dump(cout, 0);
+  // Argv.dump(cout, 0);
 
 
    //
@@ -117,7 +117,7 @@ return (0);
 
 int ModeFrontEnd::run(const StringArray & Argv, const MultiVarData &mvd)
 {
-  Argv.dump(cout, 0);
+//Argv.dump(cout, 0);
 
 
    //
@@ -127,9 +127,9 @@ if ( mode_exec )  { delete mode_exec;  mode_exec = 0; }
 
 mode_exec = new ModeExecutive;
 compress_level = -1;
-field_index = -1;
+//field_index = -1;
 
-process_command_line(Argv);
+process_command_line_final(Argv, mvd);
 
 
    //
@@ -138,7 +138,7 @@ process_command_line(Argv);
 
 ModeConfInfo & conf = mode_exec->engine.conf_info;
 
-if ( field_index >= 0 )  conf.set_field_index(field_index);
+//if ( field_index >= 0 )  conf.set_field_index(field_index);
 
  mode_exec->setup_fcst_obs_data(mvd);
 
@@ -317,6 +317,56 @@ void ModeFrontEnd::process_command_line(const StringArray & argv)
 
 }
 
+void ModeFrontEnd::process_command_line_final(const StringArray & argv,
+					      const MultiVarData &mvd)
+{
+
+   CommandLine cline;
+   ConcatString s;
+   const int argc = argv.n();
+
+
+   // Set the default output directory
+   mode_exec->out_dir = replace_path(default_out_dir);
+
+   // Check for zero arguments
+   if(argc == 1) singlevar_usage();  // wrong, need something else
+
+   // Parse the command line into tokens
+   cline.set(argv);
+
+   // Set the usage function
+   cline.set_usage(singlevar_usage);  // wrong, need something else
+
+   // Add the options function calls
+   cline.add(set_config_merge_file, "-config_merge", 1);
+   cline.add(set_outdir,            "-outdir",       1);
+   cline.add(set_logfile,           "-log",          1);
+   cline.add(set_verbosity,         "-v",            1);
+   cline.add(set_compress,          "-compress",     1);
+
+      //
+      //  add for mode multivar ... undocumented
+      //
+   //cline.add(set_field_index, "-field_index", 1);
+
+   // Parse the command line
+   cline.parse();
+
+   // Check for error. There should be 1 argument left:
+   // config filename
+   if(cline.n() != 1) singlevar_usage();  // wrong need something else
+
+   // Store the input forecast and observation file names, placeholders
+   mode_exec->fcst_file         = "not set";
+   mode_exec->obs_file          = "not set";
+   mode_exec->match_config_file = cline[0];
+   mode_exec->init_final(mvd);
+
+   return;
+
+}
+
 ///////////////////////////////////////////////////////////////////////
 
 void ModeFrontEnd::set_config_merge_file(const StringArray & a)
diff --git a/src/tools/core/mode/mode_frontend.h b/src/tools/core/mode/mode_frontend.h
index cfcff9c983..2440851416 100644
--- a/src/tools/core/mode/mode_frontend.h
+++ b/src/tools/core/mode/mode_frontend.h
@@ -45,6 +45,8 @@ class ModeFrontEnd {
   MultiVarData *get_multivar_data();
 
   void process_command_line(const StringArray &);
+  void process_command_line_final(const StringArray & argv,
+				  const MultiVarData &mvd);
   static void set_config_merge_file (const StringArray &);
   static void set_outdir            (const StringArray &);
   static void set_logfile           (const StringArray &);
diff --git a/src/tools/core/mode/multivar_data.h b/src/tools/core/mode/multivar_data.h
index 7eb0077925..401d97274d 100644
--- a/src/tools/core/mode/multivar_data.h
+++ b/src/tools/core/mode/multivar_data.h
@@ -36,7 +36,9 @@ class MultiVarData {
     obs_raw_data(0),
     nx(0), ny(0),
     Fcst_sd(0), Obs_sd(0),
-    grid(0)
+    grid(0),
+    ftype(FileType_None),
+    otype(FileType_None)
     {}
       
     inline ~MultiVarData() {
@@ -57,6 +59,8 @@ class MultiVarData {
      ShapeData *Fcst_sd;
      ShapeData *Obs_sd;
      Grid *grid;
+     GrdFileType ftype;
+     GrdFileType otype;
      
   /* int get_fcst_obj_nx(); */
   /* int get_fcst_obj_ny(); */
diff --git a/src/tools/core/mode/multivar_frontend.cc b/src/tools/core/mode/multivar_frontend.cc
index 852060e9dd..6f3bfcc773 100644
--- a/src/tools/core/mode/multivar_frontend.cc
+++ b/src/tools/core/mode/multivar_frontend.cc
@@ -96,6 +96,19 @@ static void set_outdir    (const StringArray &);
 static void set_logfile   (const StringArray &);
 static void set_verbosity (const StringArray &);
 
+static void multivar_consistency_checks(StringArray &fcst_filenames, StringArray &obs_filenames,
+					BoolCalc &f_calc, BoolCalc &o_calc, int &n_files);
+
+static ConcatString set_multivar_dir(int j);
+
+static MultiVarData *process_multivar_data(int j, const string &fcst_filename,
+					   const string &obs_filename,
+					   const ConcatString &dir);
+
+static void process_masked_multivar_data(int j, const BoolPlane &f_result, const BoolPlane &o_result,
+					 int nx, int ny, const ConcatString &dir,
+					 MultiVarData &mvd);
+
 static void mask_data(int nx, int ny, const BoolPlane &mask, DataPlane &data);
 
 static void read_config(const string & filename);
@@ -118,238 +131,56 @@ const int Argc = Argv.n();
 
 if ( Argc < 4 )  multivar_usage();
 
-int j;
+int j, n_files;
 StringArray fcst_filenames;
 StringArray  obs_filenames;
-ConcatString dir;
-
+BoolCalc f_calc, o_calc ;
 
 process_command_line(Argv);
 
-
 read_config(config_file);
 
-if ( config.fcst_multivar_logic.empty() )  {
-
-   mlog << Error << "\n" << program_name
-        << ": fcst multivar logic not specified!\n\n";
-
-   exit ( 1 );
-
-}
-
-
-if ( config.obs_multivar_logic.empty() )  {
-
-   mlog << Error << "\n" << program_name
-        << ": obs multivar logic not specified!\n\n";
-
-   exit ( 1 );
-
-}
-
-  //
-  //  make sure the multivar logic programs are in the config file
-  //
-
-fcst_filenames = parse_ascii_file_list(fcst_fof.c_str());
- obs_filenames = parse_ascii_file_list(obs_fof.c_str());
-
-if ( fcst_filenames.n() != obs_filenames.n() )  {
-
-   mlog << Error << "\n" << program_name
-        << ": number of fcst and obs files should be the same!\n\n";
-
-   exit ( 1 );
-
-}
-
-const int n_files = fcst_filenames.n();
-StringArray nc_files;
- 
-//ConcatString mode_args;
+multivar_consistency_checks(fcst_filenames, obs_filenames, f_calc, o_calc, n_files);
 
 mlog << Debug(2) << "\n" << sep << "\n";
 
-   //
-   //  check for no inputs
-   //
-
-if ( n_files == 0 )  {
-
-   mlog << Error << "\n" << program_name
-        << ": no input forecast files to process!\n\n";
-
-   exit ( 1 );
-
-}
-
-   //
-   // create the BoolCalc objects now and check that the logic is in
-   // range and the right length before proceeding
- 
-
-BoolCalc f_calc, o_calc ;
-f_calc.set(config.fcst_multivar_logic.text());
-o_calc.set(config.obs_multivar_logic.text());
-if (!f_calc.check_args(n_files)) {
-  exit ( 1 );
-}
-if (!o_calc.check_args(n_files)) {
-  exit ( 1 );
-}
-
-   //
-   // check that the multivar_intensity vector is the right length
-   //
-if ((int)config.multivar_intensity.size() != n_files) {
-  mlog << Error << "\nmultivar_frontend() -> "
-       << "wrong size multivar_intensity array, wanted "
-       << n_files << " got " << config.multivar_intensity.size() << "\n\n";
-  exit ( 1 );
- }
-
    //
    //  do the individual mode runs
    //
 
- vector<MultiVarData *> mvd;
+vector<MultiVarData *> mvd;
+StringArray nc_files;
 
 for (j=0; j<n_files; ++j)  {
 
-  ConcatString command;
-  StringArray a, mode_argv;
-  int status;
-  char junk [256];
    mlog << Debug(2) 
         << "\n starting mode run " << (j + 1) << " of " << n_files
         << "\n" << sep << "\n";
-
-      //
-      //  test to see of the output directory for this
-      //    mode runs exists, and if not, create it
-      //
-
-   dir.clear();
-
-   if ( outdir.length() > 0 )  dir << outdir << '/';
-
-   snprintf(junk, sizeof(junk), "%02d", j);
-
-   dir << junk;
-
-   if ( ! directory_exists(dir.c_str()) )  {
-
-      mlog << Debug(2)
-           << program_name << ": creating output directory \""
-           << dir << "\"\n\n";
-
-      status = mkdir(dir.c_str(), dir_creation_mode);       
-
-      if ( status < 0 )  {
-
-         mlog << Error << "\n" << program_name
-              << ": unable to create output directory \""
-              << dir << "\"\n\n";
-
-         exit ( 1 );
-
-      }
-
-   }
-
-      //
-      //  build the command for running mode
-      //
-
-   mode_argv.clear();
-
-   mode_argv.add(mode_path);
-   mode_argv.add(fcst_filenames[j]);
-   mode_argv.add(obs_filenames[j]);
-   mode_argv.add(config_file);
-
-   command << cs_erase
-           << mode_path         << ' '
-           << fcst_filenames[j] << ' '
-           <<  obs_filenames[j] << ' '
-           << config_file;
-
-   mode_argv.add("-v");
-   snprintf(junk, sizeof(junk), "%d", mlog.verbosity_level());
-   mode_argv.add(junk);
-
-   mode_argv.add("-outdir");
-   mode_argv.add(dir);
-
-   command << " -v " << mlog.verbosity_level();
-
-   command << " -outdir " << dir;
-
-   mode_argv.add("-field_index");
-   snprintf(junk, sizeof(junk), "%d", j);
-   mode_argv.add(junk);
-
-   command << " -field_index " << j;
-
-      //
-      //  run mode
-      //
-
-   mlog << Debug(1) << "Running mode command: \"" << command << "\"\n\n";
-
-   
-
-   //run_command(command);
-   // [TODO] MET #1238: run MODE in memory instead of via system calls.
-   // (void) mode_frontend(mode_argv);
-
-   ModeFrontEnd *frontend = new ModeFrontEnd;
-   status = frontend->run(mode_argv);
-   MultiVarData *mvdi = frontend->get_multivar_data();
+   ConcatString dir = set_multivar_dir(j);
+   MultiVarData *mvdi = process_multivar_data(j, fcst_filenames[j], obs_filenames[j], dir);
    mvd.push_back(mvdi);
-   
-   // int nx = frontend->get_fcst_obj_nx();
-   // int ny = frontend->get_fcst_obj_ny();
-   // int *fcst_obj_data = frontend->get_fcst_obj_data();
-   // int *obs_obj_data = frontend->get_obs_obj_data();
-   // float *fcst_raw_data = frontend->get_fcst_raw_data();
-   // float *obs_raw_data = frontend->get_obs_raw_data();
-   // mode_fcst_objects.push_back(fcst_obj_data);
-   // mode_fcst_raw_data.push_back(fcst_raw_data);
-   // mode_obs_objects.push_back(obs_obj_data);
-   // mode_obs_raw_data.push_back(obs_raw_data);
-   // mode_nx.push_back(nx);
-   // mode_ny.push_back(ny);
-
-   delete frontend;
    mlog << Debug(2) << "\n finished mode run " << (j + 1) << " of " << n_files
         << "\n" << sep << "\n";
-
-   a = get_filenames_from_dir(dir.text(), "mode_", ".nc");
-
+   StringArray a = get_filenames_from_dir(dir.text(), "mode_", ".nc");
    nc_files.add(a);
 
 }   //  for j
 
-mlog << Debug(2) << "\n finished with individual mode runs "
-     << "\n" << sep << "\n";
+mlog << Debug(2) << "\n finished with individual mode runs " << "\n" << sep << "\n";
+nc_files.dump(cout, 0);
 
 BoolPlane * f_plane = new BoolPlane [n_files];
 BoolPlane * o_plane = new BoolPlane [n_files];
 BoolPlane f_result, o_result;
-Pgm image;
 
    //
-   //  load the objects from the mode output files
+   //  set the BoolPlane objects using the mvd content
    //
-nc_files.dump(cout, 0);
-
 
 for (j=0; j<n_files; ++j)  {
 
   //objects_from_netcdf(nc_files[j].c_str(), do_clusters, f_plane[j], o_plane[j]);  
-  objects_from_arrays(nc_files[j].c_str(), do_clusters, mvd[j]->fcst_obj_data, mvd[j]->obs_obj_data, mvd[j]->nx, mvd[j]->ny, f_plane[j], o_plane[j]);  
+  objects_from_arrays(do_clusters, mvd[j]->fcst_obj_data, mvd[j]->obs_obj_data, mvd[j]->nx, mvd[j]->ny, f_plane[j], o_plane[j]);  
 
 }
 
@@ -367,111 +198,37 @@ o_result.set_size(nx, ny);
 combine_boolplanes(f_plane, n_files, f_calc, f_result);
 combine_boolplanes(o_plane, n_files, o_calc, o_result);
 
-   // Filter the data to within the superobjects only
+   //
+   // Filter the data to within the superobjects only and do statistics by invoking mode algorithm again
+   //
+ 
 for (j=0; j<n_files; ++j) {
-  // see if this one is getting stats or not
+
   if (!config.multivar_intensity[j]) {
-    printf("SKIPPING field for intensities..%d\n", j);
+    mlog << Debug(2) << "\n SKIPPING field " << j << " for masked intensities \n";
     continue;
   }
-  mask_data(nx, ny, f_result, mvd[j]->Fcst_sd->data);
-  mask_data(nx, ny, o_result, mvd[j]->Obs_sd->data);
-  ConcatString command;
-  StringArray a, mode_argv;
-  int status;
-  char junk [256];
+
   mlog << Debug(2) 
        << "\n starting filtered data mode run " << (j + 1) << " of " << n_files
        << "\n" << sep << "\n";
 
-    //
-    //  test to see of the output directory for this
-    //    mode runs exists, and if not, create it
-    //
-
-  dir.clear();
-
-  if ( outdir.length() > 0 )  dir << outdir << '/';
-
-  snprintf(junk, sizeof(junk), "%02d", j);
-
-  dir << junk;
-
-  if ( ! directory_exists(dir.c_str()) )  {
-
-    mlog << Debug(2)
-	 << program_name << ": creating output directory \""
-	 << dir << "\"\n\n";
-
-    status = mkdir(dir.c_str(), dir_creation_mode);       
-
-    if ( status < 0 )  {
-
-      mlog << Error << "\n" << program_name
-	   << ": unable to create output directory \""
-	   << dir << "\"\n\n";
-
-      exit ( 1 );
-
-    }
-  }
-    //
-    //  build the command for running mode again
-    //
-  mode_argv.clear();
-
-  mode_argv.add(mode_path);
-  mode_argv.add(fcst_filenames[j]);
-  mode_argv.add(obs_filenames[j]);
-  mode_argv.add(config_file);
-
-  command << cs_erase
-	  << mode_path         << ' '
-	  << fcst_filenames[j] << ' '
-	  <<  obs_filenames[j] << ' '
-	  << config_file;
-
-  mode_argv.add("-v");
-  snprintf(junk, sizeof(junk), "%d", mlog.verbosity_level());
-  mode_argv.add(junk);
-
-  mode_argv.add("-outdir");
-  mode_argv.add(dir);
-
-  command << " -v " << mlog.verbosity_level();
-
-  command << " -outdir " << dir;
-
-  mode_argv.add("-field_index");
-  snprintf(junk, sizeof(junk), "%d", j);
-  mode_argv.add(junk);
-
-  command << " -field_index " << j;
+  // same here as above, overwriting contents written to previously 
+  ConcatString dir = set_multivar_dir(j);
 
-  //
-  //  run mode
-  //
-
-  mlog << Debug(1) << "Running filtered mode command: \"" << command << "\"\n\n";
-
-   
-
-  //run_command(command);
-  // [TODO] MET #1238: run MODE in memory instead of via system calls.
-  // (void) mode_frontend(mode_argv);
-
-  ModeFrontEnd *frontend = new ModeFrontEnd;
-  status = frontend->run(mode_argv, *mvd[j]);
+  process_masked_multivar_data(j, f_result, o_result, nx, ny, dir, *mvd[j]);
+  delete mvd[j];
+  mvd[j] = 0;
  }
  
+mlog << Debug(2) << "\n finished with individual masked mode runs " << "\n" << sep << "\n";
+
    //
    //  write the superobject output files
    //
 
 MetNcFile met;   //  mostly to get grid
 ConcatString path;
-
-
 path = nc_files[0];
 
 if ( ! met.open(path.text()) )  {
@@ -494,10 +251,6 @@ write_output_nc_file( obs_file.text(), met, o_result);
    //
    //  done
    //
-for (size_t i=0; i<mvd.size(); ++i) {
-  delete mvd[i];
- }
-
 return ( 0 );
 
 }
@@ -633,7 +386,228 @@ return;
 
 }
 
+////////////////////////////////////////////////////////////////////////
+
+void multivar_consistency_checks(StringArray &fcst_filenames, StringArray &obs_filenames,
+				 BoolCalc &f_calc, BoolCalc &o_calc, int &n_files)
+{
+
+  //
+  //  make sure the multivar logic programs are in the config file
+  //
+
+if ( config.fcst_multivar_logic.empty() )  {
+
+   mlog << Error << "\n" << program_name
+        << ": fcst multivar logic not specified!\n\n";
+   exit ( 1 );
+
+}
+
+if ( config.obs_multivar_logic.empty() )  {
+
+   mlog << Error << "\n" << program_name
+        << ": obs multivar logic not specified!\n\n";
+   exit ( 1 );
+
+}
+
+  //
+  // make sure there are the same number of obs and fcst files
+  //
+
+fcst_filenames = parse_ascii_file_list(fcst_fof.c_str());
+obs_filenames = parse_ascii_file_list(obs_fof.c_str());
+
+if ( fcst_filenames.n() != obs_filenames.n() )  {
+
+   mlog << Error << "\n" << program_name
+        << ": number of fcst and obs files should be the same!\n\n";
+   exit ( 1 );
+
+}
+
+   //
+   //  check for multivar being actually multi.
+   //
+
+n_files = fcst_filenames.n();
+if ( n_files < 2 )  {
+
+   mlog << Error << "\n" << program_name
+        << ": want at least 2 input forecast files in multivar mode, got " << n_files << "\n\n";
+   exit ( 1 );
+
+}
+   //
+   // create the BoolCalc objects and check that the logic is in range and the right length
+   //
+
+f_calc.set(config.fcst_multivar_logic.text());
+o_calc.set(config.obs_multivar_logic.text());
+
+if (!f_calc.check_args(n_files)) {
+  exit ( 1 );
+}
+
+if (!o_calc.check_args(n_files)) {
+  exit ( 1 );
+}
+
+   //
+   // check that the multivar_intensity vector is the right length.
+   // If empty set to the default of all FALSE
+   //
+
+int num_multivar = (int)config.multivar_intensity.size();
+if (num_multivar == n_files) {
+  return;
+}
+
+if (num_multivar == 0) {
 
+  mlog << Warning << "\nmultivar_frontend() -> "
+       << "empty multivar intensity array, setting to all FALSE \n\n";
+
+  for (int i=0; i<n_files; ++i) {
+    config.multivar_intensity.push_back(false);
+  }
+
+} else {
+
+  mlog << Error << "\n" << program_name 
+       << ": wrong size multivar_intensity array, wanted "
+       << n_files << " got " << config.multivar_intensity.size() << "\n\n";
+  exit ( 1 );
+}
+}
+
+////////////////////////////////////////////////////////////////////////
+
+ConcatString set_multivar_dir(int j)
+{
+ConcatString dir;
+int status;
+char junk [256];
+
+    //
+    //  test to see of the output directory for this
+    //    mode runs exists, and if not, create it
+    //
+
+dir.clear();
+if ( outdir.length() > 0 )  dir << outdir << '/';
+snprintf(junk, sizeof(junk), "%02d", j);
+dir << junk;
+
+if ( ! directory_exists(dir.c_str()) )  {
+
+   mlog << Debug(2)
+        << program_name << ": creating output directory \""
+        << dir << "\"\n\n";
+
+   status = mkdir(dir.c_str(), dir_creation_mode);       
+
+   if ( status < 0 )  {
+
+      mlog << Error << "\n" << program_name
+           << ": unable to create output directory \""
+           << dir << "\"\n\n";
+
+      exit ( 1 );
+   }
+}
+return dir;
+}
+
+////////////////////////////////////////////////////////////////////////
+
+MultiVarData *process_multivar_data(int j, const string &fcst_filename, const string &obs_filename,
+				    const ConcatString &dir)
+{
+ConcatString command;
+StringArray a, mode_argv;
+
+   //
+   //  build the command for running mode
+   //
+
+mode_argv.clear();
+mode_argv.add(mode_path);
+mode_argv.add(fcst_filename);
+mode_argv.add(obs_filename);
+mode_argv.add(config_file);
+
+command << cs_erase
+        << mode_path         << ' '
+        << fcst_filename << ' '
+        <<  obs_filename << ' '
+        << config_file;
+
+mode_argv.add("-v");
+char junk [256];
+snprintf(junk, sizeof(junk), "%d", mlog.verbosity_level());
+mode_argv.add(junk);
+
+mode_argv.add("-outdir");
+mode_argv.add(dir);
+
+command << " -v " << mlog.verbosity_level();
+
+command << " -outdir " << dir;
+
+mode_argv.add("-field_index");
+snprintf(junk, sizeof(junk), "%d", j);
+mode_argv.add(junk);
+
+command << " -field_index " << j;
+
+   //
+   //  run mode (sort of)
+   //
+
+mlog << Debug(1) << "Running mode command: \"" << command << "\"\n\n";
+ModeFrontEnd *frontend = new ModeFrontEnd;
+// clean up this status thing, not used
+int status = frontend->run(mode_argv);
+MultiVarData *mvdi = frontend->get_multivar_data();
+delete frontend;
+return mvdi;
+}
+
+////////////////////////////////////////////////////////////////////////
+
+void process_masked_multivar_data(int j, const BoolPlane &f_result,
+				  const BoolPlane &o_result, int nx, int ny,
+				  const ConcatString &dir, MultiVarData &mvd)
+{
+  
+  mask_data(nx, ny, f_result, mvd.Fcst_sd->data);
+  mask_data(nx, ny, o_result, mvd.Obs_sd->data);
+
+
+  StringArray mode_argv;
+  char junk [256];
+
+    //
+    //  build the command for running mode again, sort of mode
+    //
+  mode_argv.clear();
+  mode_argv.add(mode_path);
+  mode_argv.add(config_file);
+  mode_argv.add("-v");
+  snprintf(junk, sizeof(junk), "%d", mlog.verbosity_level());
+  mode_argv.add(junk);
+  mode_argv.add("-outdir");
+  mode_argv.add(dir);
+
+  mlog << Debug(1) << "Running filtered mode \n\n";
+
+  ModeFrontEnd *frontend = new ModeFrontEnd;
+  int status = frontend->run(mode_argv, mvd);
+  delete frontend;
+}
+ 
 ////////////////////////////////////////////////////////////////////////
 
 
diff --git a/src/tools/core/mode/objects_from_netcdf.cc b/src/tools/core/mode/objects_from_netcdf.cc
index ffcfa25f25..6b22bb2004 100644
--- a/src/tools/core/mode/objects_from_netcdf.cc
+++ b/src/tools/core/mode/objects_from_netcdf.cc
@@ -50,7 +50,7 @@ static const string  obs_cluster_id_var_name =  "obs_clus_id";
 static void populate_bool_plane(const int * buf, const int nx, const int ny, BoolPlane & bp_out);
 
 
-void  objects_from_arrays(const char *netcf_filename, bool do_clusters,
+void  objects_from_arrays(bool do_clusters,
 			  int *fcst_objects, int *obs_objects, int nx, int ny,
 			  BoolPlane & fcst_out, 
 			  BoolPlane & obs_out)
diff --git a/src/tools/core/mode/objects_from_netcdf.h b/src/tools/core/mode/objects_from_netcdf.h
index 4192e4033a..20f553791c 100644
--- a/src/tools/core/mode/objects_from_netcdf.h
+++ b/src/tools/core/mode/objects_from_netcdf.h
@@ -29,7 +29,7 @@
 
 
 ////////////////////////////////////////////////////////////////////////
-extern void  objects_from_arrays(const char *netcf_filename, bool do_clusters,
+extern void  objects_from_arrays(bool do_clusters,
 				 int *fcst_objects, int *obs_objects, int nx, int ny,
 				 BoolPlane & fcst_out, 
 				 BoolPlane & obs_out);