new saving format again

changelog.md

@@ -1,7 +1,9 @@
 # Version 1.4.0
 
-- This is potentially a save-changing release due to changes in how file paths are stored. Please update your project files to ensure compatibility
+- This is potentially a save-changing release due to changes in how file paths and parameters are stored. Please update your project files to ensure compatibility
 - It is still possible to load older saves by enabling 'Incompatible Save Bypass' from the Preferences menu, but your mileage may vary
+- AGE, GENDER, GROUP, loaded files, and all the parameters on the right side of the screen can now be saved before any data has been processed
+- If the values fail to load, they will fallback to the previous logic of retreiving these values after processing has occured. Fixes [Issue 66](https://git.research.dezeeuw.ca/tyler/flares/issues/66)
 - Added new parameters to the right side of the screen: MAX_SHIFT, T_MIN, T_MAX. Fixes [Issue 69](https://git.research.dezeeuw.ca/tyler/flares/issues/69)
 - Added feedback when clicking an analysis option that opens up a new window. Fixes [Issue 20](https://git.research.dezeeuw.ca/tyler/flares/issues/20)
 - Fixed an issue where projects can not be saved to a different drive letter on windows. Fixes [Issue 71](https://git.research.dezeeuw.ca/tyler/flares/issues/71)

main.py

@@ -1812,6 +1812,19 @@ class ParamSection(QWidget):
 
         self.update_dependencies()
 
+
+    def has_any_changes(self):
+        """Returns True if any parameter in this section differs from its default."""
+        for name, info in self.widgets.items():
+            default = info["default"]
+            
+            current_val = self.get_param_values().get(name)
+            
+            if str(current_val) != str(default):
+                return True
+        return False
+    
+
     def check_if_changed(self, param_name, current_value):
         """Toggles bold font on the label if the value differs from default."""
         info = self.widgets.get(param_name)
@@ -4581,7 +4594,22 @@ class MainApplication(QMainWindow):
         self.missing_events_bypass = False
         self.analysis_clearing_bypass = False
 
-        self.metadata_cache = {}  # { "file_path": {metadata_dict} }
+
+        # Initialization to ensure that saving can occur
+        self.raw_haemo_dict = {}         # Processed Hemodynamic data
+        self.config_dict = {}            # Analysis parameters/settings
+        self.epochs_dict = {}            # Timing/Event data
+        self.cha_dict = {}               # Channel configurations
+        self.contrast_results_dict = {}  # Statistical results
+        self.df_ind_dict = {}            # Individual dataframes
+        self.design_matrix_dict = {}     # GLM Design matrices
+        self.valid_dict = {}             # Quality control/Validity flags
+        self.fig_bytes_dict = {}         # Cached plot images (serialized)
+        self.file_metadata = {}          # AGE, GENDER, GROUP
+        self.metadata_cache = {}         # Internal file/path information metadata cache
+        self.bubble_widgets = {}         # References to the UI "Bubble" objects
+        self.current_file = None         # Tracks the currently selected absolute path
+
         self.metadata_processed.connect(self._safe_ui_update)
 
         self.files_total = 0        # total number of files to process
@@ -4609,9 +4637,6 @@ class MainApplication(QMainWindow):
         self.last_clicked_bubble = None
         self.installEventFilter(self)
 
-        self.file_metadata = {}
-        self.current_file = None
-
         # Start local pending update check thread
         self.local_check_thread = LocalPendingUpdateCheckThread(CURRENT_VERSION, self.platform_suffix, PLATFORM_NAME, APP_NAME)
         self.local_check_thread.pending_update_found.connect(self.updater.on_pending_update_found)
@@ -5088,48 +5113,62 @@ class MainApplication(QMainWindow):
 
 
     # TODO: Is this needed?
-    def open_multiple_folders_dialog(self):
+    # def open_multiple_folders_dialog(self):
-        while True:
+    #     while True:
-            folder_path = QFileDialog.getExistingDirectory(self, "Select Folder")
+    #         folder_path = QFileDialog.getExistingDirectory(self, "Select Folder")
-            if not folder_path:
+    #         if not folder_path:
-                break
-            
-            snirf_files = [str(f) for f in Path(folder_path).glob("*.snirf")]
-
-            if not hasattr(self, 'selected_paths'):
-                self.selected_paths = []
-            
-            for file_path in snirf_files:
-                if file_path not in self.selected_paths:
-                    self.selected_paths.append(file_path)
-
-            self.show_files_as_bubbles(folder_path)
-            
-            # for section_widget in self.param_sections:
-            #     if hasattr(section_widget, 'update_annotation_dropdown_from_loaded_files'):
-            #         if "REMOVE_EVENTS" in section_widget.widgets:
-            #             section_widget.update_annotation_dropdown_from_loaded_files(self.bubble_widgets, self.button1)
     #             break
-            # else:
+            
-            #     print("[MainWindow] Could not find ParamSection with 'REMOVE_EVENTS' widget")
+    #         snirf_files = [str(f) for f in Path(folder_path).glob("*.snirf")]
+
+    #         if not hasattr(self, 'selected_paths'):
+    #             self.selected_paths = []
+            
+    #         for file_path in snirf_files:
+    #             if file_path not in self.selected_paths:
+    #                 self.selected_paths.append(file_path)
+
+    #         self.show_files_as_bubbles(folder_path)
+            
+    #         # for section_widget in self.param_sections:
+    #         #     if hasattr(section_widget, 'update_annotation_dropdown_from_loaded_files'):
+    #         #         if "REMOVE_EVENTS" in section_widget.widgets:
+    #         #             section_widget.update_annotation_dropdown_from_loaded_files(self.bubble_widgets, self.button1)
+    #         #             break
+    #         # else:
+    #         #     print("[MainWindow] Could not find ParamSection with 'REMOVE_EVENTS' widget")
         
 
-            # Ask if the user wants to add another
+    #         # Ask if the user wants to add another
-            more = QMessageBox.question(
+    #         more = QMessageBox.question(
-                self,
+    #             self,
-                "Add Another?",
+    #             "Add Another?",
-                "Do you want to select another folder?",
+    #             "Do you want to select another folder?",
-                QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
+    #             QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
-            )
+    #         )
-            if more == QMessageBox.StandardButton.No:
+    #         if more == QMessageBox.StandardButton.No:
-                break
+    #             break
             
-        self.button1.setVisible(True)
+    #     self.button1.setVisible(True)
 
 
     def save_project(self, onCrash=False):
 
-        if not getattr(self, 'raw_haemo_dict', None):
+        if hasattr(self, 'current_file') and self.current_file:
+            self.file_metadata[self.current_file] = {
+                key: field.text().strip() for key, field in self.meta_fields.items()
+            }
+
+        has_metadata = any(
+            any(val for val in meta.values()) 
+            for meta in self.file_metadata.values()
+        )
+        has_param_changes = any(section.has_any_changes() for section in self.param_sections)
+
+        # Check if there is processed data
+        has_processed_data = bool(getattr(self, 'raw_haemo_dict', None))
+
+        if not (has_processed_data or has_metadata or has_param_changes):
             if not onCrash: # Don't show popups during a crash/autosave
                 QMessageBox.warning(
                     self, 
@@ -5138,6 +5177,11 @@ class MainApplication(QMainWindow):
                 )
             return
         
+        if hasattr(self, 'current_file') and self.current_file:
+            self.file_metadata[self.current_file] = {
+                key: field.text() for key, field in self.meta_fields.items()
+            }
+
         if not onCrash:
             filename, _ = QFileDialog.getSaveFileName(
                 self, "Save Project", "", "FLARE Project (*.flare)"
@@ -5179,6 +5223,19 @@ class MainApplication(QMainWindow):
             
             print(rel_metadata)
 
+            rel_file_params = {
+                self._get_safe_path(f_path, project_dir): meta 
+                for f_path, meta in self.file_metadata.items()
+            }
+
+
+            current_params = self.get_all_current_ui_params()
+            
+            # fallback - if UI reading fails, try the first processed file's config
+            if not current_params and self.config_dict:
+                first_file = next(iter(self.config_dict.keys()))
+                current_params = self.config_dict[first_file]  
+
             version = CURRENT_VERSION
             project_data = {
                 "version": version,
@@ -5186,10 +5243,12 @@ class MainApplication(QMainWindow):
                 "progress_states": progress_states,
                 "raw_haemo_dict": self.raw_haemo_dict,
                 "file_metadata": rel_metadata,
+                "file_parameters": rel_file_params,
                 "config_dict": self.config_dict,
                 "epochs_dict": self.epochs_dict,
                 "fig_bytes_dict": self.fig_bytes_dict,
                 "cha_dict": self.cha_dict,
+                "current_ui_params": current_params,
                 "contrast_results_dict": self.contrast_results_dict,
                 "df_ind_dict": self.df_ind_dict,
                 "design_matrix_dict": self.design_matrix_dict,
@@ -5257,7 +5316,8 @@ class MainApplication(QMainWindow):
             # Check for potentially broken saves
             checks = [
                 ("version", "<=1.1.7"),
-                ("file_metadata", "<=1.2.2")
+                ("file_metadata", "<=1.2.2"),
+                ("file_params", "<=1.3.0")
             ]
 
             for key, ver_str in checks:
@@ -5289,7 +5349,9 @@ class MainApplication(QMainWindow):
             project_dir = Path(filename).parent
 
             saved_cache = data.get("file_metadata", {})
+            raw_params = data.get("file_parameters", {})
             self.metadata_cache = {}
+            self.file_metadata = {}
             
             for rel_path, meta_content in saved_cache.items():
                 abs_path = str((project_dir / Path(rel_path)).resolve())
@@ -5307,29 +5369,43 @@ class MainApplication(QMainWindow):
 
             self.show_files_as_bubbles_from_list(file_list, progress_states, filename)
 
-            for file_path, config in self.config_dict.items():
+            for rel_path in data["file_list"]:
-                # Only store AGE, GENDER, GROUP
+                abs_path = str((project_dir / Path(rel_path)).resolve())
-                self.file_metadata[file_path] = {
+                
-                    key: str(config.get(key, ""))  # convert to str for QLineEdit
+                if rel_path in raw_params:
-                    for key in ["AGE", "GENDER", "GROUP"]
+                    # Scenario A: New format found
+                    self.file_metadata[abs_path] = raw_params[rel_path]
+                elif abs_path in self.config_dict:
+                    # Scenario B: Fallback to old config_dict
+                    old_cfg = self.config_dict[abs_path]
+                    self.file_metadata[abs_path] = {
+                        "AGE": str(old_cfg.get("AGE", "")),
+                        "GENDER": str(old_cfg.get("GENDER", "")),
+                        "GROUP": str(old_cfg.get("GROUP", ""))
                     }
+                else:
+                    # Scenario C: Empty default
+                    self.file_metadata[abs_path] = {"AGE": "", "GENDER": "", "GROUP": ""}
 
-            if self.config_dict:
+            if file_list:
-                first_file = next(iter(self.config_dict.keys()))
+                self.current_file = file_list[0]
-                self.current_file = first_file
-
-                # Update meta fields (AGE/GENDER/GROUP)
-                for key, field in self.meta_fields.items():
-                    field.setText(self.file_metadata[first_file][key])
                 self.right_column_widget.show()
                 
-                # Restore all other constants to the parameter sections
+                # Update Metadata fields (Age/Gender/Group) for the selected file
-                first_config = self.config_dict[first_file]
+                curr_meta = self.file_metadata.get(self.current_file, {"AGE": "", "GENDER": "", "GROUP": ""})
-                self.restore_sections_from_config(first_config)
+                for key, field in self.meta_fields.items():
+                    field.setText(curr_meta.get(key, ""))
 
-            # Re-enable buttons
+            if "current_ui_params" in data:
-            # self.button1.setVisible(True)
+                self.restore_sections_from_config(data["current_ui_params"])
-            self.button3.setVisible(True)
+            
+            elif self.config_dict:
+                first_file = next(iter(self.config_dict.keys()))
+                self.restore_sections_from_config(self.config_dict[first_file])
+
+            has_data = bool(self.raw_haemo_dict)
+            self.button1.setVisible(not has_data)
+            self.button3.setVisible(has_data)
 
             QMessageBox.information(self, "Loaded", f"Project loaded from:\n{filename}")
 
@@ -5384,57 +5460,68 @@ class MainApplication(QMainWindow):
                 section_widget.update_dependencies()
 
 
+    # def show_files_as_bubbles(self, folder_paths):
 
-    def show_files_as_bubbles(self, folder_paths):
+    #     if isinstance(folder_paths, str):
+    #         folder_paths = [folder_paths]
 
-        if isinstance(folder_paths, str):
+    #     # Clear previous bubbles
-            folder_paths = [folder_paths]
+    #     # while self.bubble_layout.count():
+    #     #     item = self.bubble_layout.takeAt(0)
+    #     #     widget = item.widget()
+    #     #     if widget:
+    #     #         widget.deleteLater()
 
-        # Clear previous bubbles
+    #     temp_bubble = ProgressBubble("Test Bubble", "")  # A dummy bubble for measurement
-        # while self.bubble_layout.count():
+    #     temp_bubble.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy. Preferred)
-        #     item = self.bubble_layout.takeAt(0)
+    #     # temp_bubble.setAttribute(Qt.WA_OpaquePaintEvent)  # Improve rendering?
-        #     widget = item.widget()
+    #     temp_bubble.adjustSize()  # Adjust size after the widget is created
-        #     if widget:
+    #     bubble_width = temp_bubble.width()  # Get the actual width of a bubble
-        #         widget.deleteLater()
+    #     available_width = self.bubble_container.width()
 
-        temp_bubble = ProgressBubble("Test Bubble", "")  # A dummy bubble for measurement
+    #     cols = max(1, available_width // bubble_width)  # Ensure at least 1 column
-        temp_bubble.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy. Preferred)
-        # temp_bubble.setAttribute(Qt.WA_OpaquePaintEvent)  # Improve rendering?
-        temp_bubble.adjustSize()  # Adjust size after the widget is created
-        bubble_width = temp_bubble.width()  # Get the actual width of a bubble
-        available_width = self.bubble_container.width()
 
-        cols = max(1, available_width // bubble_width)  # Ensure at least 1 column
+    #     index = 0
+    #     if not hasattr(self, 'selected_paths'):
+    #         self.selected_paths = []
             
-        index = 0
+    #     for folder_path in folder_paths:
-        if not hasattr(self, 'selected_paths'):
+    #         if not os.path.isdir(folder_path):
-            self.selected_paths = []
+    #             continue
 
-        for folder_path in folder_paths:
+    #         snirf_files = [str(f) for f in Path(folder_path).glob("*.snirf")]
-            if not os.path.isdir(folder_path):
-                continue
 
-            snirf_files = [str(f) for f in Path(folder_path).glob("*.snirf")]
+    #         for full_path in snirf_files:
                 
-            for full_path in snirf_files:
+    #             display_name = f"{os.path.basename(folder_path)} / {os.path.basename(full_path)}"
+    #             bubble = ProgressBubble(display_name, full_path)
+    #             bubble.set_loading_state(True)
+    #             bubble.setCursor(Qt.CursorShape.WaitCursor)
 
-                display_name = f"{os.path.basename(folder_path)} / {os.path.basename(full_path)}"
+    #             self.bubble_widgets[full_path] = bubble
-                bubble = ProgressBubble(display_name, full_path)
-                bubble.set_loading_state(True)
-                bubble.setCursor(Qt.CursorShape.WaitCursor)
 
-                self.bubble_widgets[full_path] = bubble
+    #             if full_path not in self.selected_paths:
+    #                 self.selected_paths.append(full_path)
 
-                if full_path not in self.selected_paths:
+    #             row = index // cols
-                    self.selected_paths.append(full_path)
+    #             col = index % cols
+    #             self.bubble_layout.addWidget(bubble, row, col)
+    #             index += 1
 
-                row = index // cols
+    #     self.statusBar().showMessage(f"{index} file(s) loaded from: {', '.join(folder_paths)}")
-                col = index % cols
-                self.bubble_layout.addWidget(bubble, row, col)
-                index += 1
-
-        self.statusBar().showMessage(f"{index} file(s) loaded from: {', '.join(folder_paths)}")
 
+    def get_all_current_ui_params(self):
+        """Gathers current values from all UI widgets across all sections."""
+        current_ui_config = {}
+        try:
+            for section in self.param_sections:
+                # This calls the get_param_values() method you shared earlier
+                section_values = section.get_param_values()
+                current_ui_config.update(section_values)
+            return current_ui_config
+        except Exception as e:
+            print(f"Error reading UI parameters: {e}")
+            return None
         
     def show_files_as_bubbles_from_list(self, file_list, progress_states=None, filenames=None):
         if not hasattr(self, 'file_executor') or self.file_executor is None: