Merge pull request #2181 from SCIInstitute/deepssm_phase2

Studio DeepSSM Phase 2/3

Author: akenmorris

Applications/shapeworks/Commands.cpp

@@ -41,31 +41,7 @@ bool Example::execute(const optparse::Values &options, SharedCommandData &shared
 }
 #endif
 
-static void setup_callbacks(bool show_progress, bool xml_status) {
-  if (show_progress) {
-    auto progress_callback = [](double progress, std::string message) {
-      // show status message and percentage complete
-      std::cout << fmt::format("{} ({:.1f}%)        \r", message, progress);
-      std::cout.flush();
-    };
-    Logging::Instance().set_progress_callback(progress_callback);
-  }
 
-  if (xml_status) {
-    auto progress_callback = [](double progress, std::string message) {
-      // print status message and percentage complete
-      std::cout << fmt::format("<xml><status>{}</status><progress>{:.1f}</progress></xml>\n", message, progress);
-      std::cout.flush();
-    };
-    Logging::Instance().set_progress_callback(progress_callback);
-
-    auto error_callback = [](std::string message) {
-      std::cout << fmt::format("<xml><error>{}</error></xml>\n", message);
-      std::cout.flush();
-    };
-    Logging::Instance().set_error_callback(error_callback);
-  }
-}
 
 ///////////////////////////////////////////////////////////////////////////////
 // Seed
@@ -87,7 +63,7 @@ void Seed::buildParser() {
 bool Seed::execute(const optparse::Values& options, SharedCommandData& sharedData) {
   int value = static_cast<int>(options.get("value"));
 
-  ShapeworksUtils::setRngSeed(value);
+  ShapeWorksUtils::set_rng_seed(value);
 
   return true;
 }
@@ -123,7 +99,7 @@ bool OptimizeCommand::execute(const optparse::Values& options, SharedCommandData
   bool isProject = StringUtils::hasSuffix(projectFile, "xlsx") || StringUtils::hasSuffix(projectFile, "swproj");
 
   Optimize app;
-  setup_callbacks(show_progress, xml_status);
+  ShapeWorksUtils::setup_console_logging(show_progress, xml_status);
 
   if (isProject) {
     try {
@@ -161,7 +137,7 @@ bool OptimizeCommand::execute(const optparse::Values& options, SharedCommandData
 
       return success;
     } catch (std::exception& e) {
-      SW_ERROR(e.what());
+      SW_ERROR("{}", e.what());
       return false;
     }
   } else {
@@ -199,7 +175,7 @@ bool GroomCommand::execute(const optparse::Values& options, SharedCommandData& s
     return false;
   }
 
-  setup_callbacks(show_progress, xml_status);
+  ShapeWorksUtils::setup_console_logging(show_progress, xml_status);
 
   try {
     ProjectHandle project = std::make_shared<Project>();
@@ -226,7 +202,7 @@ bool GroomCommand::execute(const optparse::Values& options, SharedCommandData& s
 
     return success;
   } catch (std::exception& e) {
-    SW_ERROR(e.what());
+    SW_ERROR("{}", e.what());
     return false;
   }
 }

Applications/shapeworks/MeshCommands.cpp

@@ -1469,6 +1469,7 @@ bool WarpMesh::execute(const optparse::Values &options, SharedCommandData &share
       movingPoints.resize(3, numParticles);
       movingPoints.transposeInPlace();
       Mesh output = warper.build_mesh(movingPoints);
+      SW_DEBUG("Writing mesh {} with {} points", filenm, output.numPoints());
       output.write(filenm);
       if (warp_along_with_landmarks) {
         std::string warped_landmarks_filename = targetPointsFilenames[i];

Examples/Python/RunUseCase.py

@@ -18,11 +18,11 @@
 import sys
 import shutil
 
-#check if current directory is writable
+# check if current directory is writable
 current_dir = os.getcwd()
-if not os.access(current_dir,os.W_OK):
-    raise OSError("You don't have write permission in the current directory. Please copy the Examples folder to a different location to run the use cases")
-
+if not os.access(current_dir, os.W_OK):
+    raise OSError(
+        "You don't have write permission in the current directory. Please copy the Examples folder to a different location to run the use cases")
 
 if __name__ == '__main__':
 
@@ -31,6 +31,7 @@
         import termcolor
         import DatasetUtils
         import shapeworks as sw
+
         print(f"Using shapeworks module from {sw.__file__}")
 
         # make sure the shapeworks executables can be found
@@ -41,29 +42,35 @@
 
     except ImportError as error:
         print("\nError: Unable to import ShapeWorks executables, Python module, or dependencies\n")
-        print("Users: Please make sure you have run \"source install_shapeworks.sh\" (once) and \"conda activate shapeworks\" (each time)")
+        print(
+            "Users: Please make sure you have run \"source install_shapeworks.sh\" (once) and \"conda activate shapeworks\" (each time)")
         print("\tSee http://sciinstitute.github.io/ShapeWorks/users/install.html for more information")
         print("\nDevelopers: Please make sure you have run \"source ./devenv.sh <SOURCE_DIR> <BUILD_DIR>\"")
-        sys.exit(1)
 
+        print(f"\nError message: {error}")
+        sys.exit(1)
 
     # parse arguments
     parser = argparse.ArgumentParser(description='Example ShapeWorks Pipeline')
     parser.add_argument("use_case", help="Must specify which of these use cases to run.",
-                        choices=["ellipsoid", "ellipsoid_evaluate", "ellipsoid_mesh", "ellipsoid_fd", "ellipsoid_cut", "ellipsoid_pca", \
-                                 "ellipsoid_multiple_domain","ellipsoid_multiple_domain_mesh", "lumps", "left_atrium", \
-                                 "femur_cut","femur_pvalues","deep_ssm", "supershapes_1mode_contour", "thin_cavity_bean",
-                                 "peanut_shared_boundary", "incremental_supershapes","hip_multiple_domain"])
+                        choices=["ellipsoid", "ellipsoid_evaluate", "ellipsoid_mesh", "ellipsoid_fd", "ellipsoid_cut",
+                                 "ellipsoid_pca", \
+                                 "ellipsoid_multiple_domain", "ellipsoid_multiple_domain_mesh", "lumps", "left_atrium", \
+                                 "femur_cut", "femur_pvalues", "deep_ssm", "supershapes_1mode_contour",
+                                 "thin_cavity_bean",
+                                 "peanut_shared_boundary", "incremental_supershapes", "hip_multiple_domain"])
     parser.add_argument("--use_subsample", help="Run the pipeline for a subset of data", action="store_true")
     parser.add_argument("--num_subsample", help="Size of subset to run on (default: %(default)s)", type=int, default=3)
     parser.add_argument("--interactive", help="Run in interactive mode", action="store_true")
-    parser.add_argument("--use_single_scale", help="Use single scale optimization (default: multi scale)", action="store_true")
-    parser.add_argument("--mesh_mode", help="Run optimization on meshes rather than distance transforms.",action="store_true")
+    parser.add_argument("--use_single_scale", help="Use single scale optimization (default: multi scale)",
+                        action="store_true")
+    parser.add_argument("--mesh_mode", help="Run optimization on meshes rather than distance transforms.",
+                        action="store_true")
     parser.add_argument("--tiny_test", help="Run as a short test", action="store_true")
     parser.add_argument("--verify", help="Run as a full test", action="store_true")
+    parser.add_argument("--clean", help="Run from scratch, ignoring intermediate stages", action="store_true")
     args = parser.parse_args()
 
-
     type = ""
     if args.tiny_test:
         type = "tiny_test_"
@@ -78,8 +85,9 @@
     if args.use_subsample:
         dataExists = sw.data.dataset_exists_check(args.use_case)
         args.use_subsample = args.num_subsample
-        if(dataExists==False):
-            print("Please note: For --use_subsample argument the entire dataset will be downloaded. For a quick test use the --tiny_test argument")
+        if (dataExists == False):
+            print(
+                "Please note: For --use_subsample argument the entire dataset will be downloaded. For a quick test use the --tiny_test argument")
             input("Press any key to continue")
 
     # import use case and run