Fix a few oversights in new workflow switching.

.vscode_shared/CistemDev/workspace.code-workspace

@@ -1,7 +1,7 @@
 {
     "folders": [
         {
-            "path": "../"
+            "path": "/workspaces/cisTEM"
         }
     ],
     "settings": {

regenerate_containers.sh

@@ -25,8 +25,8 @@ fi
 # somewhere near vscode 1.98 the devcontainers extension stopped recognizing softlinks to .devcontainer.json
 # this is acknowedged as a bug (https://github.com/microsoft/vscode-remote-release/issues/10536)
 # As a workaround we create a softlink to .devcontainer.json in the current directory
-mkdir -p .devcontainer.json
-cd  .devcontainer.json
+mkdir -p .devcontainer
+cd  .devcontainer
 if [[ ! -L .devcontainer.json ]] ; then
     ln -s ../.vscode/devcontainer.json .devcontainer.json
 fi

scripts/containers/top_image/Dockerfile

@@ -65,8 +65,7 @@ RUN if [[ "x${build_type}" != "xstatic" ]]; then echo "export LD_RUN_PATH=/opt/l
 # RUN ls /usr/local/cuda/lib64/lib*_static.a | grep -v cufft_static.a | while read a; do rm -rf /usr/local/cuda/lib64/$(basename $a); done && \
 #     rm -rf /usr/local/cuda/lib64/libcufft_static_nocallback.a
 
-
+RUN echo "set filename-display basename" > /home/cisTEMdev/.gdbinit
 
 USER cisTEMdev
 WORKDIR /home/cisTEMdev
-

src/gui/MainFrame.cpp

@@ -273,6 +273,7 @@ void MyMainFrame::ResetAllPanels( ) {
     picking_results_panel->Clear( );
     refine2d_results_panel->Clear( );
     refinement_results_panel->Clear( );
+    match_template_results_panel->Clear( );
 
     align_movies_panel->Reset( );
     findctf_panel->Reset( );
@@ -285,7 +286,6 @@ void MyMainFrame::ResetAllPanels( ) {
     generate_3d_panel->Reset( );
     sharpen_3d_panel->Reset( );
     match_template_panel->Reset( );
-    match_template_results_panel->Clear( );
     refine_template_panel->Reset( );
 
     DirtyEverything( );
@@ -338,9 +338,8 @@ void MyMainFrame::DirtyImageGroups( ) {
     picking_results_panel->group_combo_is_dirty = true;
 
     if ( current_workflow == "Template Matching" ) {
-        match_template_panel->group_combo_is_dirty         = true;
-        match_template_results_panel->group_combo_is_dirty = true;
-        refine_template_panel->group_combo_is_dirty        = true;
+        match_template_panel->group_combo_is_dirty  = true;
+        refine_template_panel->group_combo_is_dirty = true;
     }
 }
 
@@ -366,10 +365,11 @@ void MyMainFrame::DirtyTemplateMatchesPackages( ) {
 }
 
 void MyMainFrame::DirtyRefinements( ) {
-    refine_3d_panel->input_params_combo_is_dirty     = true;
-    refine_ctf_panel->input_params_combo_is_dirty    = true;
-    refinement_results_panel->input_params_are_dirty = true;
-    generate_3d_panel->input_params_combo_is_dirty   = true;
+    refine_3d_panel->input_params_combo_is_dirty       = true;
+    refine_ctf_panel->input_params_combo_is_dirty      = true;
+    refinement_results_panel->input_params_are_dirty   = true;
+    generate_3d_panel->input_params_combo_is_dirty     = true;
+    match_template_results_panel->group_combo_is_dirty = true;
 }
 
 void MyMainFrame::DirtyClassifications( ) {
@@ -695,8 +695,10 @@ void MyMainFrame::OpenProject(wxString project_filename) {
         //	current_project.database.AddCTFIcinessColumnIfNecessary();
         my_dialog->Update(8, "Opening project (loading Match Template Results...)");
 
+        // If this is in the if block, then by default it will never get filled as we default to Single Particle
+        match_template_results_panel->FillBasedOnSelectCommand("SELECT DISTINCT IMAGE_ASSET_ID FROM TEMPLATE_MATCH_LIST");
+
         if ( current_workflow == "Template Matching" ) {
-            match_template_results_panel->FillBasedOnSelectCommand("SELECT DISTINCT IMAGE_ASSET_ID FROM TEMPLATE_MATCH_LIST");
             my_dialog->Update(9, "Opening project (loading atomic coordinates assets...)");
             atomic_coordinates_asset_panel->ImportAllFromDatabase( );
             my_dialog->Update(10, "Opening project (loading Template Matches Packages...)");
@@ -739,6 +741,12 @@ void MyMainFrame::OpenProject(wxString project_filename) {
             }
             else {
                 current_workflow = current_project.database.ReturnSingleStringFromSelectCommand("select CURRENT_WORKFLOW from MASTER_SETTINGS");
+                // FIXME: this should never execute, but if somehow current_workflow is empty, log that it was and set a default.
+                //        This is a bandaid on something that is otherwise broken (we aren't storing the workflow somewhere properly)
+                if ( current_workflow.IsEmpty( ) ) {
+                    wxLogWarning("The current workflow returned empty from the database call; returning Single Particle as default to prevent errors.");
+                    current_workflow = "Single Particle";
+                }
             }
             current_project.database.RecordCurrentWorkflowInDB(current_workflow);
             SwitchWorkflowPanels(current_workflow);
@@ -978,6 +986,12 @@ void MyMainFrame::SwitchWorkflowPanels(const wxString& workflow_name) {
     actions_panel->Layout( );
     MenuBook->Layout( );
     Layout( );
+
+    // After creating the new panels, ensure they have correct dirty state
+    if ( current_project.is_open ) {
+        DirtyEverything( ); // This will set all panels to dirty state
+    }
+
     Thaw( );
 }
 

src/gui/MainFrame.h

@@ -102,8 +102,6 @@ class MyMainFrame : public MainFrame, public SocketCommunicator, public UpdatePr
     template <class FrameTypeFrom, class FrameTypeTo>
     void UpdateWorkflow(FrameTypeFrom* input_frame, FrameTypeTo* output_frame, wxString frame_name);
 
-    void SetSingleParticleWorkflow(bool triggered_by_gui_event = false);
-    void SetTemplateMatchingWorkflow(bool triggered_by_gui_event = false);
     void SwitchWorkflowPanels(const wxString& workflow_name);
 
     inline void ManuallyUpdateWorkflowMenuCheckBox( ) {

src/gui/workflows/SpaWorkflow.h

@@ -63,7 +63,7 @@ struct SpaWorkflowRegister {
             actions_panel->ActionsBook->AddPage(generate_3d_panel, "Generate 3D", false, 8);
             actions_panel->ActionsBook->AddPage(sharpen_3d_panel, "Sharpen 3D", false, 9);
 
-            return actions_panel;
+                return actions_panel;
         };
         // TODO: define a results panel function as well
         WorkflowRegistry::Instance( ).RegisterWorkflow(def);

src/gui/workflows/TmWorkflow.h

@@ -35,7 +35,6 @@ struct TmWorkflowRegister {
             actions_panel                    = static_cast<ActionsPanelParent*>(actions_panel_tm);
             align_movies_panel               = new MyAlignMoviesPanel(actions_panel->ActionsBook);
             findctf_panel                    = new MyFindCTFPanel(actions_panel->ActionsBook);
-            match_template_results_panel     = new MatchTemplateResultsPanel(actions_panel->ActionsBook);
             match_template_panel             = new MatchTemplatePanel(actions_panel->ActionsBook);
             refine_template_panel            = new RefineTemplatePanel(actions_panel->ActionsBook);
             generate_3d_panel                = new Generate3DPanel(actions_panel->ActionsBook);
@@ -49,7 +48,6 @@ struct TmWorkflowRegister {
             actions_panel->ActionsBook->AddPage(findctf_panel, "Find CTF", false, 1);
             actions_panel->ActionsBook->AddPage(match_template_panel, "Match Templates", false, 2);
             actions_panel->ActionsBook->AddPage(refine_template_panel, "Refine Template", false, 3);
-            actions_panel->ActionsBook->AddPage(match_template_results_panel, "MT Results", false, 2);
             actions_panel->ActionsBook->AddPage(generate_3d_panel, "Generate 3D", false, 4);
             actions_panel->ActionsBook->AddPage(sharpen_3d_panel, "Sharpen 3D", false, 5);
 

src/programs/projectx/projectx.cpp

@@ -25,8 +25,8 @@ RefineCTFPanel*       refine_ctf_panel;
 Generate3DPanel*      generate_3d_panel;
 Sharpen3DPanel*       sharpen_3d_panel;
 
-MyOverviewPanel*    overview_panel;
-ActionsPanelParent* actions_panel;
+MyOverviewPanel*           overview_panel;
+ActionsPanelParent*        actions_panel;
 AssetsPanel*               assets_panel;
 MyResultsPanel*            results_panel;
 SettingsPanel*             settings_panel;
@@ -141,17 +141,18 @@ bool MyGuiApp::OnInit( ) {
 
     refinement_package_asset_panel = new MyRefinementPackageAssetPanel(assets_panel->AssetsBook);
 
-	// See src/gui/workflows/SpaWorkflow.h for instantiation of the SPA workflow panels
+    // See src/gui/workflows/SpaWorkflow.h for instantiation of the SPA workflow panels
 
     actions_panel = static_cast<ActionsPanelParent*>(WorkflowRegistry::Instance( ).CreateActionsPanel("Single Particle", main_frame->MenuBook));
 
-    movie_results_panel      = new MyMovieAlignResultsPanel(results_panel->ResultsBook);
-    ctf_results_panel        = new MyFindCTFResultsPanel(results_panel->ResultsBook);
-    picking_results_panel    = new MyPickingResultsPanel(results_panel->ResultsBook);
-    refine2d_results_panel   = new Refine2DResultsPanel(results_panel->ResultsBook);
-    refinement_results_panel = new MyRefinementResultsPanel(results_panel->ResultsBook);
+    movie_results_panel          = new MyMovieAlignResultsPanel(results_panel->ResultsBook);
+    ctf_results_panel            = new MyFindCTFResultsPanel(results_panel->ResultsBook);
+    picking_results_panel        = new MyPickingResultsPanel(results_panel->ResultsBook);
+    refine2d_results_panel       = new Refine2DResultsPanel(results_panel->ResultsBook);
+    refinement_results_panel     = new MyRefinementResultsPanel(results_panel->ResultsBook);
+    match_template_results_panel = new MatchTemplateResultsPanel(results_panel->ResultsBook);
 
-	// See src/gui/workflows/TmWorkflow.h for instantiation of Template Matching workflow panels.
+    // See src/gui/workflows/TmWorkflow.h for instantiation of Template Matching workflow panels.
 
 #ifdef EXPERIMENTAL
     refine_template_dev_panel = new RefineTemplateDevPanel(experimental_panel->ExperimentalBook);
@@ -230,7 +231,7 @@ bool MyGuiApp::OnInit( ) {
 
     SettingsBookIconImages->Add(run_profiles_icon_bmp);
 
-	// See src/gui/workflows headers for assignment of wxImageList to Actions Panel
+    // See src/gui/workflows headers for assignment of wxImageList to Actions Panel
     main_frame->MenuBook->AssignImageList(MenuBookIconImages);
     assets_panel->AssetsBook->AssignImageList(AssetsBookIconImages);
     results_panel->ResultsBook->AssignImageList(ResultsBookIconImages);
@@ -259,13 +260,14 @@ bool MyGuiApp::OnInit( ) {
     assets_panel->AssetsBook->AddPage(volume_asset_panel, "3D Volumes", false, 3);
     assets_panel->AssetsBook->AddPage(refinement_package_asset_panel, "Refine Pkgs.", false, 4);
     assets_panel->AssetsBook->AddPage(atomic_coordinates_asset_panel, "Atomic Coordinates", false, 5);
-    assets_panel->AssetsBook->AddPage(template_matches_package_asset_panel, "MT Pkgs.", false, 4);
+    assets_panel->AssetsBook->AddPage(template_matches_package_asset_panel, "TM Pkgs.", false, 4); // re-using icon FIXME
 
     results_panel->ResultsBook->AddPage(movie_results_panel, "Align Movies", true, 0);
     results_panel->ResultsBook->AddPage(ctf_results_panel, "Find CTF", false, 1);
     results_panel->ResultsBook->AddPage(picking_results_panel, "Find Particles", false, 2);
     results_panel->ResultsBook->AddPage(refine2d_results_panel, "2D Classify", false, 3);
     results_panel->ResultsBook->AddPage(refinement_results_panel, "3D Refinement", false, 4);
+    results_panel->ResultsBook->AddPage(match_template_results_panel, "TM Results", false, 2); // re-using icon FIXME
 
     settings_panel->SettingsBook->AddPage(run_profiles_panel, "Run Profiles", true, 0);