continuation of the rewrite

src/analysis/crossgroupbrainimage.py

@@ -64,7 +64,7 @@ class CrossGroupBrainImageWidget(CrossGroupUIMixin, FlaresBaseWidget):
         self.setup_cross_group_ui(["0 (Contrast Image)"])
 
 
-    def proccess_request(self):
+    def process_request(self):
               
         request = self.get_common_request_data(PARAMETERIZED_INDEXES)
         if request is None:

src/analysis/intergroupfunctionalconnectivity.py

@@ -1,171 +1,58 @@
 """
-Filename: groupfunctionalconnectivity.py
+Filename: intergroupfunctionalconnectivity.py
-Description: Group functional connectivity analysis window for FLARES
+Description: Logic for the Inter-Group Functional Connectivity analysis window
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
-import os
+# External library imports
+from PySide6.QtWidgets import QMessageBox
 
-from PySide6.QtWidgets import QComboBox, QDialog, QGridLayout, QHBoxLayout, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel, QMessageBox
+from flares import run_group_functional_connectivity
-from PySide6.QtCore import QSize
+from src.shared.flaresbasewidget import InterGroupUIMixin, FlaresBaseWidget
-
-from src.shared.flaresbasewidget import FlaresBaseWidget, ParameterInputDialog
 from src.shared.shareddata import APP_NAME
 
 
-class GroupFunctionalConnectivityWidget(FlaresBaseWidget):
+PARAMETERIZED_INDEXES = {
+    0: [
+        {
+            "key": "n_lines",
+            "label": "<Description>",
+            "default": "20",
+            "type": int,
+        },
+        {
+            "key": "vmin",
+            "label": "<Description>",
+            "default": "0.9",
+            "type": float,
+        },
+    ],
+}
+
+
+
+class InterGroupFunctionalConnectivityWidget(InterGroupUIMixin, FlaresBaseWidget):
     def __init__(self, haemo_dict, group, config_dict):
-        super().__init__("GroupFunctionalConnectivityWidget")
+        super().__init__("InterGroupFunctionalConnectivity")
-        self.setWindowTitle(f"Group Functional Connectivity Viewer [BETA] - {APP_NAME.upper()}")
+        self.setWindowTitle(f"Inter-Group Functional Connectivity Viewer [BETA] - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.group = group
         self.config_dict = config_dict
-        self.show_all_events = True
-        self._updating_checkstates = False
 
         QMessageBox.warning(self, f"Warning - {APP_NAME.upper()}", f"Functional Connectivity is still in development and the results should currently be taken with a grain of salt. "
                     "By clicking OK, you accept that the images generated may not be factual.")
 
-        
+        self.setup_inter_group_ui(["0 (Betas)",])
-        # Create mappings: file_path -> participant label and dropdown display text
-        self.participant_map = {}  # file_path -> "Participant 1"
-        self.participant_dropdown_items = []  # "Participant 1 (filename)"
-
-        for i, file_path in enumerate(self.haemo_dict.keys(), start=1):
-            short_label = f"Participant {i}"
-            display_label = f"{short_label} ({os.path.basename(file_path)})"
-            self.participant_map[file_path] = short_label
-            self.participant_dropdown_items.append(display_label)
-
-        self.layout = QVBoxLayout(self)
-        self.top_bar = QHBoxLayout()
-        self.layout.addLayout(self.top_bar)
-
-        self.group_to_paths = {}
-        for file_path, group_name in self.group.items():
-            self.group_to_paths.setdefault(group_name, []).append(file_path)
-
-        self.group_names = sorted(self.group_to_paths.keys())
-
-        self.group_dropdown = QComboBox()
-        self.group_dropdown.addItem("<None Selected>")
-        self.group_dropdown.addItems(self.group_names)
-        self.group_dropdown.setCurrentIndex(0)
-        self.group_dropdown.currentIndexChanged.connect(self.update_participant_list_for_group)
-
-        self.participant_dropdown = self._create_multiselect_dropdown(self.participant_dropdown_items)
-        self.participant_dropdown.currentIndexChanged.connect(self.update_participant_dropdown_label)
-        self.participant_dropdown.setEnabled(False)
-
-        self.event_dropdown = QComboBox()
-        self.event_dropdown.addItem("<None Selected>")
-
-        self.index_texts = [
-            "0 (Betas)",
-            #"1 (Significance)",
-            #"2 (Brain Activity Visualization)",
-            # "3 (fourth image)",
-            ]
-
-        self.image_index_dropdown = self._create_multiselect_dropdown(self.index_texts)
-        self.image_index_dropdown.currentIndexChanged.connect(self.update_image_index_dropdown_label)
-
-        self.submit_button = QPushButton("Submit")
-        self.submit_button.clicked.connect(self.show_brain_images)
-
-        self.top_bar.addWidget(QLabel("Group:"))
-        self.top_bar.addWidget(self.group_dropdown)
-        self.top_bar.addWidget(QLabel("Participants:"))
-        self.top_bar.addWidget(self.participant_dropdown)
-        self.top_bar.addWidget(QLabel("Event:"))
-        self.top_bar.addWidget(self.event_dropdown)
-        self.top_bar.addWidget(QLabel("Image Indexes:"))
-        self.top_bar.addWidget(self.image_index_dropdown)
-        self.top_bar.addWidget(self.submit_button)
-
-        self.scroll = QScrollArea()
-        self.scroll.setWidgetResizable(True)
-        self.scroll_content = QWidget()
-        self.grid_layout = QGridLayout(self.scroll_content)
-        self.scroll.setWidget(self.scroll_content)
-        self.layout.addWidget(self.scroll)
-
-        self.thumb_size = QSize(280, 180)
-        self.showMaximized()
 
 
-    def show_brain_images(self):
+    def process_request(self):
-        import flares as flares
+        request = self.get_common_request_data(PARAMETERIZED_INDEXES)
-
+        if request is None:
-        selected_event = self.event_dropdown.currentText()
-        if selected_event == "<None Selected>":
-            selected_event = None
-
-        selected_display_names = self._get_checked_items(self.participant_dropdown)
-        selected_file_paths = []
-        for display_name in selected_display_names:
-            for fp, short_label in self.participant_map.items():
-                expected_display = f"{short_label} ({os.path.basename(fp)})"
-                if display_name == expected_display:
-                    selected_file_paths.append(fp)
-                    break
-
-        if selected_event:
-            valid_paths = []
-            for fp in selected_file_paths:
-                raw = self.haemo_dict.get(fp)
-                # Check if this participant actually has the event in their annotations
-                if raw is not None and hasattr(raw, "annotations"):
-                    if selected_event in raw.annotations.description:
-                        valid_paths.append(fp)
-            
-            selected_file_paths = valid_paths
-
-        selected_indexes = [
-            int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
-        ]
-
-        if not selected_file_paths:
-            print("No participants selected.")
             return
 
-        # Only keep indexes 0 and 1 that need parameters
+        (selected_event, selected_file_paths, selected_indexes, param_values,) = request     
-        parameterized_indexes = {
-            0: [
-                {
-                    "key": "n_lines",
-                    "label": "<Description>",
-                    "default": "20",
-                    "type": int,
-                },
-                {
-                    "key": "vmin",
-                    "label": "<Description>",
-                    "default": "0.9",
-                    "type": float,
-                },
-            ],
-        }
-
-        # Inject full_text from index_texts
-        for idx, params_list in parameterized_indexes.items():
-            full_text = self.index_texts[idx] if idx < len(self.index_texts) else f"{idx} (No label found)"
-            for param_info in params_list:
-                param_info["full_text"] = full_text
-
-        indexes_needing_params = {idx: parameterized_indexes[idx] for idx in selected_indexes if idx in parameterized_indexes}
-
-        param_values = {}
-        if indexes_needing_params:
-            dialog = ParameterInputDialog(indexes_needing_params, parent=self)
-            if dialog.exec_() == QDialog.Accepted:
-                param_values = dialog.get_values()
-                if param_values is None:
-                    return
-            else:
-                return
             
         for idx in selected_indexes:
             if idx == 0:
@@ -176,13 +63,7 @@ class GroupFunctionalConnectivityWidget(FlaresBaseWidget):
                 if n_lines is None or vmin is None:
                     print(f"Missing parameters for index {idx}, skipping.")
                     continue
-                flares.run_group_functional_connectivity(self.haemo_dict, self.config_dict, selected_file_paths, selected_event, 50, 0.5)            
+                run_group_functional_connectivity(self.haemo_dict, self.config_dict, selected_file_paths, selected_event, 50, 0.5)            
-            elif idx == 1:
-                pass
-            elif idx == 2:
-                pass
-            elif idx == 3:
-                pass
 
             else:
                 print(f"No method defined for index {idx}")

src/analysis/participantbrain.py

@@ -58,7 +58,7 @@ PARAMETERIZED_INDEXES = {
 
 class ParticipantBrainViewerWidget(ParticipantUIMixin, FlaresBaseWidget):
     def __init__(self, haemo_dict, cha_dict):
-        super().__init__("ParticipantBrainViewer")
+        super().__init__("ParticipantBrain")
         self.setWindowTitle(f"Participant Brain Viewer - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.cha_dict = cha_dict

src/analysis/participantfoldchannels.py

@@ -1,6 +1,6 @@
 """
 Filename: participantfoldchannels.py
-Description: Participant fOLD channels analysis window for FLARES
+Description: Logic for the Participant fOLD Channels analysis window
 
 Author: Tyler de Zeeuw
 License: GPL-3.0

src/analysis/participantfunctionalconnectivity.py

@@ -1,183 +1,103 @@
 """
 Filename: participantfunctionalconnectivity.py
-Description: Participant functional connectivity analysis window for FLARES
+Description: Logic for the Participant Functional Connectivity analysis window
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
-import os
+# External library imports
+from PySide6.QtWidgets import QMessageBox
 
-from PySide6.QtWidgets import QComboBox, QDialog, QGridLayout, QHBoxLayout, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel, QMessageBox
+from flares import functional_connectivity_betas, functional_connectivity_envelope, functional_connectivity_spectral_epochs, functional_connectivity_spectral_time
-from PySide6.QtCore import QSize
+from src.shared.flaresbasewidget import ParticipantUIMixin, FlaresBaseWidget
-
-from src.shared.flaresbasewidget import FlaresBaseWidget, ParameterInputDialog
 from src.shared.shareddata import APP_NAME
 
 
-class ParticipantFunctionalConnectivityWidget(FlaresBaseWidget):
+PARAMETERIZED_INDEXES = {
+    0: [
+        {
+            "key": "n_lines",
+            "label": "<Description>",
+            "default": "20",
+            "type": int,
+        },
+        {
+            "key": "vmin",
+            "label": "<Description>",
+            "default": "0.9",
+            "type": float,
+        },
+    ],
+    1: [
+        {
+            "key": "n_lines",
+            "label": "<Description>",
+            "default": "20",
+            "type": int,
+        },
+        {
+            "key": "vmin",
+            "label": "<Description>",
+            "default": "0.9",
+            "type": float,
+        },
+        
+    ],
+    2: [
+        {
+            "key": "n_lines",
+            "label": "<Description>",
+            "default": "20",
+            "type": int,
+        },
+        {
+            "key": "vmin",
+            "label": "<Description>",
+            "default": "0.9",
+            "type": float,
+        },
+        
+    ],
+    3: [
+        {
+            "key": "n_lines",
+            "label": "<Description>",
+            "default": "20",
+            "type": int,
+        },
+        {
+            "key": "vmin",
+            "label": "<Description>",
+            "default": "0.9",
+            "type": float,
+        },
+        
+    ],
+}
+
+
+
+class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidget):
     def __init__(self, haemo_dict, epochs_dict):
-        super().__init__("FunctionalConnectivityWidget")
+        super().__init__("ParticipantFunctionalConnectivity")
-        self.setWindowTitle(f"Functional Connectivity Viewer [BETA] - {APP_NAME.upper()}")
+        self.setWindowTitle(f"Participant Functional Connectivity Viewer [BETA] - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.epochs_dict = epochs_dict
 
         QMessageBox.warning(self, f"Warning - {APP_NAME.upper()}", f"Functional Connectivity is still in development and the results should currently be taken with a grain of salt. "
                             "By clicking OK, you accept that the images generated may not be factual.")
 
-        # Create mappings: file_path -> participant label and dropdown display text
+        self.setup_participant_ui(["0 (Spectral Connectivity Epochs)", "1 (Envelope Correlation)", "2 (Betas)", "3 (Spectral Connectivity Epochs)",])
-        self.participant_map = {}  # file_path -> "Participant 1"
-        self.participant_dropdown_items = []  # "Participant 1 (filename)"
-
-        for i, file_path in enumerate(self.haemo_dict.keys(), start=1):
-            short_label = f"Participant {i}"
-            display_label = f"{short_label} ({os.path.basename(file_path)})"
-            self.participant_map[file_path] = short_label
-            self.participant_dropdown_items.append(display_label)
-
-        self.layout = QVBoxLayout(self)
-        self.top_bar = QHBoxLayout()
-        self.layout.addLayout(self.top_bar)
-
-        self.participant_dropdown = self._create_multiselect_dropdown(self.participant_dropdown_items)
-        self.participant_dropdown.currentIndexChanged.connect(self.update_participant_dropdown_label)
-
-        self.event_dropdown = QComboBox()
-        self.event_dropdown.addItem("<None Selected>")
 
 
-        self.index_texts = [
-            "0 (Spectral Connectivity Epochs)",
-            "1 (Envelope Correlation)",
-            "2 (Betas)",
-            "3 (Spectral Connectivity Epochs)",
-            ]
 
-        self.image_index_dropdown = self._create_multiselect_dropdown(self.index_texts)
+    def process_request(self):
-        self.image_index_dropdown.currentIndexChanged.connect(self.update_image_index_dropdown_label)
+        request = self.get_common_request_data(PARAMETERIZED_INDEXES)
+        if request is None:
+            return
 
-        self.submit_button = QPushButton("Submit")
+        (selected_event, selected_file_paths, selected_indexes, param_values,) = request  
-        self.submit_button.clicked.connect(self.show_brain_images)
-
-        self.top_bar.addWidget(QLabel("Participants:"))
-        self.top_bar.addWidget(self.participant_dropdown)
-        self.top_bar.addWidget(QLabel("Event:"))
-        self.top_bar.addWidget(self.event_dropdown)
-        self.top_bar.addWidget(QLabel("Image Indexes:"))
-        self.top_bar.addWidget(self.image_index_dropdown)
-        self.top_bar.addWidget(self.submit_button)
-
-        self.scroll = QScrollArea()
-        self.scroll.setWidgetResizable(True)
-        self.scroll_content = QWidget()
-        self.grid_layout = QGridLayout(self.scroll_content)
-        self.scroll.setWidget(self.scroll_content)
-        self.layout.addWidget(self.scroll)
-
-        self.thumb_size = QSize(280, 180)
-        self.showMaximized()
-
-
-    def show_brain_images(self):
-        import flares as flares
-
-        selected_event = self.event_dropdown.currentText()
-        if selected_event == "<None Selected>":
-            selected_event = None
-
-        selected_display_names = self._get_checked_items(self.participant_dropdown)
-        selected_file_paths = []
-        for display_name in selected_display_names:
-            for fp, short_label in self.participant_map.items():
-                expected_display = f"{short_label} ({os.path.basename(fp)})"
-                if display_name == expected_display:
-                    selected_file_paths.append(fp)
-                    break
-
-        selected_indexes = [
-            int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
-        ]
-
-
-        parameterized_indexes = {
-            0: [
-                {
-                    "key": "n_lines",
-                    "label": "<Description>",
-                    "default": "20",
-                    "type": int,
-                },
-                {
-                    "key": "vmin",
-                    "label": "<Description>",
-                    "default": "0.9",
-                    "type": float,
-                },
-            ],
-            1: [
-                {
-                    "key": "n_lines",
-                    "label": "<Description>",
-                    "default": "20",
-                    "type": int,
-                },
-                {
-                    "key": "vmin",
-                    "label": "<Description>",
-                    "default": "0.9",
-                    "type": float,
-                },
-             
-            ],
-            2: [
-                {
-                    "key": "n_lines",
-                    "label": "<Description>",
-                    "default": "20",
-                    "type": int,
-                },
-                {
-                    "key": "vmin",
-                    "label": "<Description>",
-                    "default": "0.9",
-                    "type": float,
-                },
-             
-            ],
-            3: [
-                {
-                    "key": "n_lines",
-                    "label": "<Description>",
-                    "default": "20",
-                    "type": int,
-                },
-                {
-                    "key": "vmin",
-                    "label": "<Description>",
-                    "default": "0.9",
-                    "type": float,
-                },
-             
-            ],
-        }
-
-        # Inject full_text from index_texts
-        for idx, params_list in parameterized_indexes.items():
-            full_text = self.index_texts[idx] if idx < len(self.index_texts) else f"{idx} (No label found)"
-            for param_info in params_list:
-                param_info["full_text"] = full_text
-
-        indexes_needing_params = {idx: parameterized_indexes[idx] for idx in selected_indexes if idx in parameterized_indexes}
-
-        param_values = {}
-        if indexes_needing_params:
-            dialog = ParameterInputDialog(indexes_needing_params, parent=self)
-            if dialog.exec_() == QDialog.Accepted:
-                param_values = dialog.get_values()
-                if param_values is None:
-                    return
-            else:
-                return
 
         # Pass the necessary arguments to each method
         for file_path in selected_file_paths:
@@ -204,7 +124,7 @@ class ParticipantFunctionalConnectivityWidget(FlaresBaseWidget):
                     if n_lines is None or vmin is None:
                         print(f"Missing parameters for index {idx}, skipping.")
                         continue
-                    flares.functional_connectivity_spectral_epochs(epochs_obj, n_lines, vmin)
+                    functional_connectivity_spectral_epochs(epochs_obj, n_lines, vmin)
 
                 elif idx == 1:
                     params = param_values.get(idx, {})
@@ -214,7 +134,7 @@ class ParticipantFunctionalConnectivityWidget(FlaresBaseWidget):
                     if n_lines is None or vmin is None:
                         print(f"Missing parameters for index {idx}, skipping.")
                         continue
-                    flares.functional_connectivity_envelope(epochs_obj, n_lines, vmin)
+                    functional_connectivity_envelope(epochs_obj, n_lines, vmin)
                     
                 elif idx == 2:
                     params = param_values.get(idx, {})
@@ -224,7 +144,7 @@ class ParticipantFunctionalConnectivityWidget(FlaresBaseWidget):
                     if n_lines is None or vmin is None:
                         print(f"Missing parameters for index {idx}, skipping.")
                         continue
-                    flares.functional_connectivity_betas(haemo_obj, n_lines, vmin, selected_event)
+                    functional_connectivity_betas(haemo_obj, n_lines, vmin, selected_event)
 
                 elif idx == 3:
                     params = param_values.get(idx, {})
@@ -234,7 +154,7 @@ class ParticipantFunctionalConnectivityWidget(FlaresBaseWidget):
                     if n_lines is None or vmin is None:
                         print(f"Missing parameters for index {idx}, skipping.")
                         continue
-                    flares.functional_connectivity_spectral_time(epochs_obj, n_lines, vmin)
+                    functional_connectivity_spectral_time(epochs_obj, n_lines, vmin)
 
                 else:
                     print(f"No method defined for index {idx}")

src/analysis/participantimage.py

@@ -1,15 +1,17 @@
 """
-Filename: participant.py
+Filename: participantimage.py
-Description: Participant analysis window for FLARES
+Description: Logic for the Participant Image analysis window
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
+# Built-in Imports
 import os
 from pathlib import Path
 from datetime import datetime
 
+# External library imports
 from PySide6.QtWidgets import QGridLayout, QHBoxLayout, QMessageBox, QPushButton, QScrollArea, QWidget, QVBoxLayout, QLabel
 from PySide6.QtCore import Qt, QSize
 from PySide6.QtGui import QPixmap
@@ -22,7 +24,7 @@ class ParticipantImageViewerWidget(FlaresBaseWidget):
     def __init__(self, haemo_dict, fig_bytes_dict):
         super().__init__("ParticipantImage")
         self.setAttribute(Qt.WidgetAttribute.WA_DeleteOnClose)
-        self.setWindowTitle(f"Participant Viewer - {APP_NAME.upper()}")
+        self.setWindowTitle(f"Participant Image Viewer - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.fig_bytes_dict = fig_bytes_dict
 
@@ -36,9 +38,9 @@ class ParticipantImageViewerWidget(FlaresBaseWidget):
             self.participant_map[file_path] = short_label
             self.participant_dropdown_items.append(display_label)
 
-        self.layout = QVBoxLayout(self)
+        self.main_layout = QVBoxLayout(self)
         self.top_bar = QHBoxLayout()
-        self.layout.addLayout(self.top_bar)
+        self.main_layout.addLayout(self.top_bar)
 
         self.participant_dropdown = self._create_multiselect_dropdown(self.participant_dropdown_items)
         self.participant_dropdown.currentIndexChanged.connect(self.update_participant_dropdown_label)
@@ -58,12 +60,12 @@ class ParticipantImageViewerWidget(FlaresBaseWidget):
         self.top_bar.addWidget(self.image_index_dropdown)
         self.top_bar.addWidget(self.submit_button)
 
-        self.scroll = QScrollArea()
+        self.scroll_area = QScrollArea()
-        self.scroll.setWidgetResizable(True)
+        self.scroll_area.setWidgetResizable(True)
         self.scroll_content = QWidget()
         self.grid_layout = QGridLayout(self.scroll_content)
-        self.scroll.setWidget(self.scroll_content)
+        self.scroll_area.setWidget(self.scroll_content)
-        self.layout.addWidget(self.scroll)
+        self.main_layout.addWidget(self.scroll_area)
 
         self.thumb_size = QSize(280, 180)
 

src/shared/flaresbasewidget.py

@@ -1108,7 +1108,7 @@ class CrossGroupUIMixin:
 
 
         self.submit_button = QPushButton("Submit")
-        self.submit_button.clicked.connect(self.proccess_request)
+        self.submit_button.clicked.connect(self.process_request)
 
 
         self.top_bar.addWidget(QLabel("Group A:"))