preparation for 1.5.1

src/shared/flaresbasewidget.py

@@ -239,6 +239,55 @@ class FullClickComboBox(QComboBox):
         return super().eventFilter(obj, event)
 
 
+
+from PySide6.QtWidgets import QWidget, QHBoxLayout, QLineEdit, QPushButton, QFileDialog
+from PySide6.QtCore import Signal
+
+class FilePickerWidget(QWidget):
+    # This custom signal lets our container mimic a standard QLineEdit
+    textChanged = Signal(str)
+
+    def __init__(self, default_val="", file_filter="JSON Files (*.json);;All Files (*)", parent=None):
+        super().__init__(parent)
+        
+        # Inline layout to hold line edit and button side-by-side
+        layout = QHBoxLayout(self)
+        layout.setContentsMargins(0, 0, 0, 0)
+        layout.setSpacing(5)
+        
+        self.line_edit = QLineEdit()
+        self.line_edit.setText(str(default_val))
+        self.line_edit.setPlaceholderText("Select file path...")
+        # Forward internal text updates out through our custom component signal
+        self.line_edit.textChanged.connect(self.textChanged.emit)
+        
+        self.browse_btn = QPushButton("Browse...")
+        self.browse_btn.clicked.connect(self.open_file_dialog)
+        
+        layout.addWidget(self.line_edit)
+        layout.addWidget(self.browse_btn)
+        
+        self.file_filter = file_filter
+
+    def open_file_dialog(self):
+        # Open PySide6 native file browser
+        file_path, _ = QFileDialog.getOpenFileName(
+            self, 
+            "Select Configuration File", 
+            self.line_edit.text(), 
+            self.file_filter
+        )
+        if file_path:
+            self.line_edit.setText(file_path)
+
+    # Mimic standard text getter/setter behaviors so parent systems remain unbothered
+    def text(self):
+        return self.line_edit.text()
+
+    def setText(self, text):
+        self.line_edit.setText(text)
+
+
 class ParamSection(QWidget):
     """
     A widget section that dynamically creates labeled input fields from parameter metadata.
@@ -339,9 +388,15 @@ class ParamSection(QWidget):
                 else:
                     widget.setValue(15) # Default fallback
                 widget.valueChanged.connect(lambda val, p=param["name"]: self.check_if_changed(p, val))
+            elif param["type"] == "json_file":
+                # Create our custom dual-element compound layout widget
+                widget = FilePickerWidget(default_val=default_val, file_filter="JSON Files (*.json)")
+                # Your existing tracking signals connect seamlessly!
+                widget.textChanged.connect(lambda val, p=param["name"]: self.check_if_changed(p, val))
             else: 
                 widget = QLineEdit()
                 widget.setText(str(default_val))
+                widget.textChanged.connect(lambda val, p=param["name"]: self.check_if_changed(p, val))
 
             if "depends_on" in param:
                 self.dependencies.append({
@@ -567,6 +622,8 @@ class ParamSection(QWidget):
                     values[name] = range(widget.value())
                 else:
                     values[name] = range(15) # Fallback
+            elif expected_type == "json_file":
+                values[name] = widget.text()
             else:
                 raw_text = widget.text()
                 try:
@@ -1236,7 +1293,7 @@ class CrossGroupUIMixin:
 
         return file_paths
     
-    def get_common_request_data(self, parameterized_indexes):
+    def get_common_request_data(self, parameterized_indexes, json_location=None, contrast_dfs=None):
         selected_event = self.event_dropdown.currentText()
         if selected_event == "<None Selected>":
             selected_event = None
@@ -1274,6 +1331,65 @@ class CrossGroupUIMixin:
             if idx in parameterized_indexes
         }
 
+        dynamic_rois = []
+        
+        # 1. Check for the JSON file and parse ROI names
+        if os.path.exists(json_location):
+            try:
+                with open(json_location, 'r', encoding='utf-8') as f:
+                    regions_data = json.load(f)
+                    
+                    # Extract "name" from each region under "regions_of_interest"
+                    regions_list = regions_data.get("regions_of_interest", [])
+                    dynamic_rois = [region["name"] for region in regions_list if "name" in region]
+                    
+            except Exception as e:
+                # Safe log if JSON is corrupted or unreadable
+                print(f"Error reading ROI configurations from {json_location}: {e}")
+                
+        # Fallback to prevent UI crashes if JSON file doesn't exist or is empty
+        if not dynamic_rois:
+            dynamic_rois = ["Option 1", "Option 2"]
+
+        dynamic_contrasts = []
+        if contrast_dfs:
+            contrast_set = set()
+            for fp in all_selected_paths:
+                # Get the contrasts dictionary associated with this file path
+                file_contrasts = contrast_dfs.get(fp, {})
+                for contrast_name in file_contrasts.keys():
+                    # If no event is selected, display all contrasts.
+                    # If an event is selected, only keep contrasts containing the event name as a substring.
+                    if selected_event is None or selected_event in contrast_name:
+                        contrast_set.add(contrast_name)
+                        
+            # Sort them cleanly for the UI
+            dynamic_contrasts = sorted(list(contrast_set))
+
+        # 2. Loop through the active parameters needing input and intercept 'roi_a' and 'roi_b'
+        for idx, params_list in indexes_needing_params.items():
+            for param_info in params_list:
+                if param_info["key"] == "roi_a":
+                    # Inject options list dynamically
+                    param_info["options"] = dynamic_rois
+                    # Default to the very first item
+                    param_info["default"] = dynamic_rois[0] if dynamic_rois else ""
+
+                elif param_info["key"] == "roi_b":
+                    # Inject the same options list
+                    param_info["options"] = dynamic_rois
+                    # Default to the first item not taken (index 1), with safety fallbacks
+                    if len(dynamic_rois) > 1:
+                        param_info["default"] = dynamic_rois[1]
+                    elif len(dynamic_rois) == 1:
+                        param_info["default"] = dynamic_rois[0]
+                    else:
+                        param_info["default"] = ""
+
+                elif param_info["key"] == "contrast_name":
+                    param_info["options"] = dynamic_contrasts
+                    param_info["default"] = dynamic_contrasts[0] if dynamic_contrasts else ""
+
         param_values = {}
         if indexes_needing_params:
             dialog = ParameterInputDialog(indexes_needing_params, parent=self)

src/shared/shareddata.py

@@ -43,9 +43,9 @@ PIPELINE_STAGES = [
     "Design Matrix",
     "General Linear Model",
     "Generate GLM Results",
-    "Generate Channel Significance",
-    "Generate Channel, Region of Interest, and Contrast Results",
-    "Compute Contrast Results",
+    "Generate Channel Results",
+    "Generate Region of Interest Results",
+    "Generate Contrast Results",
     "Finishing Up"
 ]