Move PythonWorker, implement deepssm CLI command

Author: akenmorris

Applications/shapeworks/Commands.cpp

@@ -2,6 +2,7 @@
 
 #include <Analyze/Analyze.h>
 #include <Application/DeepSSM/DeepSSMJob.h>
+#include <Application/Job/PythonWorker.h>
 #include <Groom/Groom.h>
 #include <Logging.h>
 #include <Optimize/Optimize.h>
@@ -11,6 +12,7 @@
 #include <ShapeworksUtils.h>
 #include <Utils/StringUtils.h>
 
+#include <QApplication>
 #include <boost/filesystem.hpp>
 
 namespace shapeworks {
@@ -350,7 +352,7 @@ void DeepSSMCommand::buildParser() {
       .action("store")
       .type("choice")
       .choices(prep_choices.begin(), prep_choices.end())
-      .set_default("all")
+      //.set_default("all")
       .help("Preparation step to run");
 
   // Boolean flag options
@@ -366,6 +368,11 @@ void DeepSSMCommand::buildParser() {
 }
 
 bool DeepSSMCommand::execute(const optparse::Values& options, SharedCommandData& sharedData) {
+  // Create a non-gui QApplication instance
+  int argc = 0;
+  char** argv = nullptr;
+  QApplication app(argc, argv);
+
   // Handle project file: either from --name or first positional argument
   std::string project_file;
   if (options.is_set_by_user("name")) {
@@ -379,13 +386,26 @@ bool DeepSSMCommand::execute(const optparse::Values& options, SharedCommandData&
     parser.error("Project file must be provided either as --name or as a positional argument");
   }
 
+  // Handle prep option with manual default
+  std::string prep_step;
+  if (options.is_set_by_user("prep")) {
+    prep_step = options["prep"];
+  } else {
+    prep_step = "all";  // Manual default
+  }
+
   std::cout << "DeepSSM: Using project file: " << project_file << std::endl;
 
   bool do_prep = options.is_set("prep") || options.is_set("all");
-  std::string prep_step = options["prep"];
   bool do_augment = options.is_set("augment") || options.is_set("all");
   bool do_train = options.is_set("train") || options.is_set("all");
   bool do_test = options.is_set("test") || options.is_set("all");
+
+  std::cout << "Prep step:    " << (do_prep ? "on" : "off") << "\n";
+  std::cout << "Augment step: " << (do_augment ? "on" : "off") << "\n";
+  std::cout << "Train step:   " << (do_train ? "on" : "off") << "\n";
+  std::cout << "Test step:    " << (do_test ? "on" : "off") << "\n";
+
   if (!do_prep && !do_augment && !do_train && !do_test) {
     do_prep = true;
     do_augment = true;
@@ -396,42 +416,73 @@ bool DeepSSMCommand::execute(const optparse::Values& options, SharedCommandData&
   ProjectHandle project = std::make_shared<Project>();
   project->load(project_file);
 
-  DeepSSMJob job(project, DeepSSMJob::JobType::DeepSSM_PrepType);
+  PythonWorker python_worker;
+
+  auto wait_for_job = [&](auto job) {
+    // This lambda will block until the job is complete
+    while (!job->is_complete()) {
+      QCoreApplication::processEvents();
+      std::this_thread::sleep_for(std::chrono::milliseconds(100));
+      if (job->is_aborted()) {
+        return false;
+      }
+    }
+    return true;
+  };
 
   if (do_prep) {
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_PrepType);
     if (prep_step == "all") {
-      job.set_prep_step(DeepSSMJob::PrepStep::NOT_STARTED);
+      job->set_prep_step(DeepSSMJob::PrepStep::NOT_STARTED);
     } else if (prep_step == "groom_training") {
-      job.set_prep_step(DeepSSMJob::PrepStep::GROOM_TRAINING);
+      job->set_prep_step(DeepSSMJob::PrepStep::GROOM_TRAINING);
     } else if (prep_step == "optimize_training") {
-      job.set_prep_step(DeepSSMJob::PrepStep::OPTIMIZE_TRAINING);
+      job->set_prep_step(DeepSSMJob::PrepStep::OPTIMIZE_TRAINING);
     } else if (prep_step == "optimize_validation") {
-      job.set_prep_step(DeepSSMJob::PrepStep::OPTIMIZE_VALIDATION);
+      job->set_prep_step(DeepSSMJob::PrepStep::OPTIMIZE_VALIDATION);
     } else if (prep_step == "groom_images") {
-      job.set_prep_step(DeepSSMJob::PrepStep::GROOM_IMAGES);
+      job->set_prep_step(DeepSSMJob::PrepStep::GROOM_IMAGES);
     } else {
       SW_ERROR("Unknown prep step: {}", prep_step);
       return false;
     }
     std::cout << "Running DeepSSM preparation step...\n";
-    job.run_prep();
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM preparation step completed.\n";
   }
   if (do_augment) {
     std::cout << "Running DeepSSM data augmentation...\n";
-    job.run_augmentation();
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_AugmentationType);
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM data augmentation completed.\n";
   }
   if (do_train) {
     std::cout << "Running DeepSSM training...\n";
-    job.run_training();
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_TrainingType);
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM training completed.\n";
   }
   if (do_test) {
     std::cout << "Running DeepSSM testing...\n";
-    job.run_testing();
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_TestingType);
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM testing completed.\n";
   }
 
   project->save();
 
-  SW_ERROR("DeepSSM command is not implemented yet.");
   return false;
 }
 

Libs/Application/CMakeLists.txt

@@ -1,6 +1,8 @@
 SET(APPLICATION_MOC_HDRS
   DeepSSM/DeepSSMJob.h
   Job/Job.h
+  Job/PythonWorker.h
+  ShapeWorksVtkOutputWindow.h
 )
 
 qt5_wrap_cpp( APPLICATION_MOC_SRCS ${APPLICATION_MOC_HDRS} )
@@ -11,6 +13,8 @@ SET(Application_headers
 add_library(Application STATIC
   DeepSSM/DeepSSMJob.cpp
   Job/Job.cpp
+  Job/PythonWorker.cpp
+  ShapeWorksVtkOutputWindow.cpp
   ${APPLICATION_MOC_SRCS}
   )
 

Libs/Application/Job/Job.h

@@ -1,6 +1,7 @@
 #pragma once
 #include <QElapsedTimer>
 #include <QObject>
+#include <QSharedPointer>
 
 namespace shapeworks {
 
@@ -62,3 +63,6 @@ class Job : public QObject {
   QElapsedTimer timer_;
 };
 }  // namespace shapeworks
+
+
+Q_DECLARE_METATYPE(QSharedPointer<shapeworks::Job>);

Studio/Python/PythonWorker.cpp Libs/Application/Job/PythonWorker.cppStudio/Python/PythonWorker.cpp renamed to Libs/Application/Job/PythonWorker.cpp

@@ -7,15 +7,14 @@
 namespace py = pybind11;
 using namespace pybind11::literals;  // to bring in the `_a` literal
 
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
-#include <Python/PythonWorker.h>
-#include <Shape.h>
 
 #include <QFileInfo>
 #include <QMessageBox>
 #include <QProcess>
+#include <QThread>
 #include <iostream>
-#include <sstream>
 
 namespace shapeworks {
 
@@ -58,6 +57,8 @@ PYBIND11_EMBEDDED_MODULE(logger, m) {
 PythonWorker::PythonWorker() {
   python_logger_ = QSharedPointer<PythonLogger>::create();
 
+  qRegisterMetaType<QSharedPointer<Job>>("QSharedPointer<Job>");
+
   // create singular Python thread and move this object to the new thread
   thread_ = new QThread(this);
   moveToThread(thread_);
@@ -67,8 +68,10 @@ PythonWorker::PythonWorker() {
 //---------------------------------------------------------------------------
 PythonWorker::~PythonWorker() {
   end_python();
-  thread_->wait();
-  delete thread_;
+  if (thread_) {
+    thread_->wait();
+    delete thread_;
+  }
 }
 
 //---------------------------------------------------------------------------
@@ -109,6 +112,9 @@ void PythonWorker::run_job(QSharedPointer<Job> job) {
   QMetaObject::invokeMethod(this, "start_job", Qt::QueuedConnection, Q_ARG(QSharedPointer<Job>, job));
 }
 
+//---------------------------------------------------------------------------
+void PythonWorker::set_current_job(QSharedPointer<Job> job) { current_job_ = job; }
+
 //---------------------------------------------------------------------------
 bool PythonWorker::init() {
   std::string script = "install_shapeworks.sh";

Studio/Python/PythonWorker.h Libs/Application/Job/PythonWorker.hStudio/Python/PythonWorker.h renamed to Libs/Application/Job/PythonWorker.h

@@ -9,7 +9,7 @@
 
 // studio
 #include <Job/Job.h>
-#include <Visualization/ShapeWorksVtkOutputWindow.h>
+#include <Libs/Application/ShapeWorksVtkOutputWindow.h>
 
 namespace shapeworks {
 class PythonLogger;
@@ -26,6 +26,7 @@ class PythonWorker : public QObject {
   void set_vtk_output_window(vtkSmartPointer<ShapeWorksVtkOutputWindow> output_window);
 
   void run_job(QSharedPointer<Job> job);
+  void set_current_job(QSharedPointer<Job> job);
 
   void incoming_python_message(std::string message_string);
   void incoming_python_progress(double value, std::string message);
@@ -57,6 +58,6 @@ class PythonWorker : public QObject {
 
   QSharedPointer<Job> current_job_;
 
-  QThread* thread_;
+  QThread* thread_{nullptr};
 };
 }  // namespace shapeworks

…ualization/ShapeWorksVtkOutputWindow.cpp …pplication/ShapeWorksVtkOutputWindow.cppStudio/Visualization/ShapeWorksVtkOutputWindow.cpp renamed to Libs/Application/ShapeWorksVtkOutputWindow.cpp Studio/Visualization/ShapeWorksVtkOutputWindow.cpp renamed to Libs/Application/ShapeWorksVtkOutputWindow.cpp

@@ -11,8 +11,8 @@
 #include <Job/NetworkAnalysisJob.h>
 #include <Job/ParticleNormalEvaluationJob.h>
 #include <Job/StatsGroupLDAJob.h>
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
-#include <Python/PythonWorker.h>
 #include <QMeshWarper.h>
 #include <Shape.h>
 #include <StudioMesh.h>

…isualization/ShapeWorksVtkOutputWindow.h …/Application/ShapeWorksVtkOutputWindow.hStudio/Visualization/ShapeWorksVtkOutputWindow.h renamed to Libs/Application/ShapeWorksVtkOutputWindow.h Studio/Visualization/ShapeWorksVtkOutputWindow.h renamed to Libs/Application/ShapeWorksVtkOutputWindow.h

@@ -10,8 +10,8 @@
 #include <Interface/ShapeWorksStudioApp.h>
 #include <Interface/Style.h>
 #include <Job/GroupPvalueJob.h>
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
-#include <Python/PythonWorker.h>
 #include <QMeshWarper.h>
 #include <Shape.h>
 #include <StudioMesh.h>

Studio/Analysis/AnalysisTool.cpp

@@ -126,13 +126,6 @@ SET(STUDIO_GROOM_MOC_HDRS
   Groom/GroomTool.h
   )
 
-SET(STUDIO_PYTHON_SRCS
-  Python/PythonWorker.cpp
-  )
-SET(STUDIO_PYTHON_MOC_HDRS
-  Python/PythonWorker.h
-  )
-
 SET(STUDIO_OPTIMIZE_SRCS
   Optimize/OptimizeTool.cpp
   Optimize/QOptimize.cpp
@@ -228,14 +221,12 @@ SET(STUDIO_VISUALIZATION_SRCS
   Visualization/MeshSlice.cpp
   Visualization/Viewer.cpp
   Visualization/Visualizer.cpp
-  Visualization/ShapeWorksVtkOutputWindow.cpp
   Visualization/StudioHandleWidget.cpp
 )
 
 SET(STUDIO_VISUALIZATION_MOC_HDRS
   Visualization/Lightbox.h
   Visualization/ParticleColors.h
-  Visualization/ShapeWorksVtkOutputWindow.h
   Visualization/Visualizer.h
 )
 
@@ -246,7 +237,6 @@ SET(STUDIO_SRCS
   ${STUDIO_DEEPSSM_SRCS}
   ${STUDIO_MONAILABEL_SRCS}
   ${STUDIO_GROOM_SRCS}
-  ${STUDIO_PYTHON_SRCS}
   ${STUDIO_INTERFACE_SRCS}
   ${STUDIO_OPTIMIZE_SRCS}
   ${STUDIO_UTILS_SRCS}
@@ -260,7 +250,6 @@ SET(STUDIO_MOC_HDRS
   ${STUDIO_DEEPSSM_MOC_HDRS}
   ${STUDIO_MONAILABEL_MOC_HDRS}
   ${STUDIO_GROOM_MOC_HDRS}
-  ${STUDIO_PYTHON_MOC_HDRS}
   ${STUDIO_INTERFACE_MOC_HDRS}
   ${STUDIO_OPTIMIZE_MOC_HDRS}
   ${STUDIO_UTILS_MOC_HDRS}