fixes to build version 1.1.3

changelog.md

@@ -1,3 +1,22 @@
+# Version 1.1.3
+
+- Added back the ability to use the fOLD dataset. Fixes [Issue 23](https://git.research.dezeeuw.ca/tyler/flares/issues/23)
+- 5th option has been added under Analysis to get to fOLD channels per participant
+- Added an option to cancel the running process. Fixes [Issue 15](https://git.research.dezeeuw.ca/tyler/flares/issues/15)
+- Prevented graph images from showing when participants are being processed. Fixes [Issue 24](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+- Allow the option to remove all events of a type from all loaded snirfs. Fixes [Issue 25](https://git.research.dezeeuw.ca/tyler/flares/issues/25)
+- Added new icons in the menu bar
+- Added a terminal to interact with the app in a more command-like form
+- Currently the terminal has no functionality but some features for batch operations will be coming soon!
+- Inter-Group viewer now has the option to visualize the average response on the brain of all participants in the group. Fixes [Issue 26](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+
+
+# Version 1.1.2
+
+- Fixed incorrect colormaps being applied
+- Added functionality to utilize external event markers from a file. Fixes [Issue 6](https://git.research.dezeeuw.ca/tyler/flares/issues/6)
+
+
 # Version 1.1.1
 
 - Fixed the number of rectangles in the progress bar to 19

flares.py

@@ -1077,7 +1077,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
 
     # Plot drop log
     # TODO: Why show this if we never use epochs2?
-    fig_epochs_dropped = epochs2.plot_drop_log()
+    fig_epochs_dropped = epochs2.plot_drop_log(show=False)
     fig_epochs.append(("fig_epochs_dropped", fig_epochs_dropped))
 
     # Plot for each condition

icons/terminal_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M160-160q-33 0-56.5-23.5T80-240v-480q0-33 23.5-56.5T160-800h640q33 0 56.5 23.5T880-720v480q0 33-23.5 56.5T800-160H160Zm0-80h640v-400H160v400Zm140-40-56-56 103-104-104-104 57-56 160 160-160 160Zm180 0v-80h240v80H480Z"/></svg>

icons/upgrade_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M280-160v-80h400v80H280Zm160-160v-327L336-544l-56-56 200-200 200 200-56 56-104-103v327h-80Z"/></svg>

main.py

@@ -42,6 +42,7 @@ from PySide6.QtWidgets import (
 )
 from PySide6.QtCore import QThread, Signal, Qt, QTimer, QEvent, QSize
 from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleValidator, QPixmap, QStandardItemModel, QStandardItem
+from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
 
 CURRENT_VERSION = "1.0.1"
@@ -173,10 +174,10 @@ SECTIONS = [
 
 
 
-class CommandConsole(QWidget):
+class TerminalWindow(QWidget):
     def __init__(self, parent=None):
         super().__init__(parent, Qt.WindowType.Window)
-        self.setWindowTitle("Custom Console")
+        self.setWindowTitle("Terminal - FLARES")
 
         self.output_area = QTextEdit()
         self.output_area.setReadOnly(True)
@@ -189,10 +190,8 @@ class CommandConsole(QWidget):
         layout.addWidget(self.input_line)
         self.setLayout(layout)
 
-        # Define your commands
         self.commands = {
             "hello": self.cmd_hello,
-            "add": self.cmd_add,
             "help": self.cmd_help
         }
 
@@ -219,12 +218,9 @@ class CommandConsole(QWidget):
         else:
             self.output_area.append(f"[Unknown command] '{command_name}'")
 
-    # Example commands
-    def cmd_hello(self, *args):
-        return "Hello from the console!"
 
-    def cmd_add(self, a, b):
-        return f"Result: {int(a) + int(b)}"
+    def cmd_hello(self, *args):
+        return "Hello from the terminal!"
 
     def cmd_help(self, *args):
         return f"Available commands: {', '.join(self.commands.keys())}"
@@ -734,13 +730,12 @@ class UpdateEventsWindow(QWidget):
         self.description = QLabel()
         self.description.setTextFormat(Qt.TextFormat.RichText)
         self.description.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
-        self.description.setOpenExternalLinks(False) # Handle the click internally
+        self.description.setOpenExternalLinks(True)
             
-        self.description.setText("Some software when creating snirf files will insert a template of optode positions as the correct position of the optodes for the participant.<br>"
-        "This is rarely correct as each head differs slightly in shape or size, and a lot of calculations require the optodes to be in the correct location.<br>"
-        "Using a .txt file, we can update the positions in the snirf file to match those of a digitization system such as one from Polhemus or elsewhere.<br>"
-        "The .txt file should have the fiducials, detectors, and sources clearly labeled, followed by the x, y, and z coordinates seperated by a space.<br>"
-        "An example format of what a digitization text file should look like can be found <a href='custom_link'>by clicking here</a>.")
+        self.description.setText("The events that are present in a snirf file may not be the events that are to be studied and examined.<br>"
+        "Utilizing different software and video recordings, it is easy enough to see when an action actually occured in a file.<br>"
+        "The software <a href='https://www.boris.unito.it/'>BORIS</a> is used to add these events to video files, and these events can be applied to the snirf file <br>"
+        "selected below by selecting the correct BORIS observation and time syncing it to an event that it shares with the snirf file.")
 
         layout.addWidget(self.description)
 
@@ -1179,6 +1174,11 @@ class ProgressBubble(QWidget):
             else:
                 rect.setStyleSheet("background-color: white; border: 1px solid gray;")
                 
+    def mark_cancelled(self):
+        if 0 <= self.current_step < len(self.rects):
+            rect = self.rects[self.current_step]
+            rect.setStyleSheet("background-color: red; border: 1px solid gray;")
+
     def mousePressEvent(self, event):
         self.clicked.emit(self)
         super().mousePressEvent(event)
@@ -2191,12 +2191,13 @@ class ParticipantFoldChannelsWidget(QWidget):
         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.submit_button.clicked.connect(self.show_fold_images)
 
         self.top_bar.addWidget(QLabel("Participants:"))
         self.top_bar.addWidget(self.participant_dropdown)
         self.top_bar.addWidget(QLabel("Fold Type:"))
         self.top_bar.addWidget(self.image_index_dropdown)
+        self.top_bar.addWidget(QLabel("This will cause the app to hang for ~30s!"))
         self.top_bar.addWidget(self.submit_button)
 
         self.scroll = QScrollArea()
@@ -2316,7 +2317,7 @@ class ParticipantFoldChannelsWidget(QWidget):
             index_labels = [s.split(" ")[0] for s in selected]
             self.image_index_dropdown.lineEdit().setText(", ".join(index_labels))
 
-    def show_brain_images(self):
+    def show_fold_images(self):
         import flares
 
         selected_display_names = self._get_checked_items(self.participant_dropdown)
@@ -2332,42 +2333,6 @@ class ParticipantFoldChannelsWidget(QWidget):
             int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
         ]
 
-
-        parameterized_indexes = {
-            0: [
-                {
-                    "key": "show_optodes",
-                    "label": "Determine what is rendered above the brain. Valid values are 'sensors', 'labels', 'none', 'all'.",
-                    "default": "all",
-                    "type": str,
-                },
-                {
-                    "key": "show_brodmann",
-                    "label": "Show common brodmann areas on the brain.",
-                    "default": "True",
-                    "type": bool,
-                }
-            ],
-        }
-
-        # 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:
             haemo_obj = self.haemo_dict.get(file_path)
@@ -2380,14 +2345,6 @@ class ParticipantFoldChannelsWidget(QWidget):
             for idx in selected_indexes:
                 if idx == 0:
 
-                    params = param_values.get(idx, {})
-                    show_optodes = params.get("show_optodes", None)
-                    show_brodmann = params.get("show_brodmann", None)
-
-                    if show_optodes is None or show_brodmann is None:
-                        print(f"Missing parameters for index {idx}, skipping.")
-                        continue
-
                     flares.fold_channels(haemo_obj)
 
                 else:
@@ -2600,7 +2557,7 @@ class GroupViewerWidget(QWidget):
         self.index_texts = [
             "0 (GLM Results)",
             "1 (Significance)",
-            # "2 (third_image)",
+            "2 (Brain Activity Visualization)",
             # "3 (fourth image)",
             ]
 
@@ -2903,6 +2860,32 @@ class GroupViewerWidget(QWidget):
                     "type": float,
                 }
             ],
+            2: [
+                {
+                    "key": "show_optodes",
+                    "label": "Determine what is rendered above the brain. Valid values are 'sensors', 'labels', 'none', 'all'.",
+                    "default": "all",
+                    "type": str,
+                },
+                {
+                    "key": "t_or_theta",
+                    "label": "Specify if t values or theta values should be plotted. Valid values are 't', 'theta'",
+                    "default": "theta",
+                    "type": str,
+                },
+                {
+                    "key": "show_text",
+                    "label": "Display informative text on the top left corner. THIS DOES NOT WORK AND SHOULD BE LEFT AT FALSE",
+                    "default": "False",
+                    "type": bool,
+                },
+                {
+                    "key": "brain_bounds",
+                    "label": "Graph Upper/Lower Limit",
+                    "default": "1.0",
+                    "type": float,
+                }
+            ],
         }
 
         # Inject full_text from index_texts
@@ -2925,8 +2908,13 @@ class GroupViewerWidget(QWidget):
             
 
         all_cha = pd.DataFrame()
-        for fp in selected_file_paths:
-            cha_df = self.cha.get(fp)
+        for file_path in selected_file_paths:
+            haemo_obj = self.haemo_dict.get(file_path)
+
+            if haemo_obj is None:
+                continue
+            
+            cha_df = self.cha.get(file_path)
             if cha_df is not None:
                 all_cha = pd.concat([all_cha, cha_df], ignore_index=True)
 
@@ -2981,6 +2969,20 @@ class GroupViewerWidget(QWidget):
                 df_contrasts = pd.concat(all_contrasts, ignore_index=True)
                 flares.run_second_level_analysis(df_contrasts, p_haemo, p_val, graph_bounds)
 
+            elif idx == 2:
+                params = param_values.get(idx, {})
+                show_optodes = params.get("show_optodes", None)
+                t_or_theta = params.get("t_or_theta", None)
+                show_text = params.get("show_text", None)
+                brain_bounds = params.get("brain_bounds", None)
+
+                if show_optodes is None or t_or_theta is None or show_text is None or brain_bounds is None:
+                    print(f"Missing parameters for index {idx}, skipping.")
+                    continue
+
+                flares.brain_3d_visualization(haemo_obj, all_cha, selected_event, t_or_theta=t_or_theta, show_optodes=show_optodes, show_text=show_text, brain_bounds=brain_bounds)
+
+                
             elif idx == 3:
                 pass
 
@@ -3606,6 +3608,7 @@ class MainApplication(QMainWindow):
         self.param_sections = []
         self.folder_paths = []
         self.section_widget = None
+        self.first_run = True
 
         self.init_ui()
         self.create_menu_bar()
@@ -3834,8 +3837,8 @@ class MainApplication(QMainWindow):
         options_actions = [
             ("User Guide", "F1", self.user_guide, resource_path("icons/help_24dp_1F1F1F.svg")), 
             ("Check for Updates", "F5", self.manual_check_for_updates, resource_path("icons/update_24dp_1F1F1F.svg")),
-            ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/update_24dp_1F1F1F.svg")),
-            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/update_24dp_1F1F1F.svg")),
+            ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
+            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
             ("About", "F12", self.about_window, resource_path("icons/info_24dp_1F1F1F.svg"))
         ]
 
@@ -3846,9 +3849,7 @@ class MainApplication(QMainWindow):
 
         terminal_menu = menu_bar.addMenu("Terminal")
         terminal_actions = [
-            ("Cut", "Ctrl+X", self.terminal_gui, resource_path("icons/content_cut_24dp_1F1F1F.svg")),
-            ("Copy", "Ctrl+C", self.terminal_gui, resource_path("icons/content_copy_24dp_1F1F1F.svg")),
-            ("Paste", "Ctrl+V", self.terminal_gui, resource_path("icons/content_paste_24dp_1F1F1F.svg"))
+            ("New Terminal", "Ctrl+Alt+T", self.terminal_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
         ]
         for name, shortcut, slot, icon in terminal_actions:
             terminal_menu.addAction(make_action(name, shortcut, slot, icon=icon))
@@ -3875,6 +3876,8 @@ class MainApplication(QMainWindow):
 
     def clear_all(self):
         
+        self.cancel_task()
+        
         self.right_column_widget.hide()
         
         # Clear the bubble layout
@@ -3937,7 +3940,7 @@ class MainApplication(QMainWindow):
             
     def terminal_gui(self):
         if self.terminal is None or not self.terminal.isVisible():
-            self.terminal = CommandConsole(self)
+            self.terminal = TerminalWindow(self)
             self.terminal.show()
 
     def update_optode_positions(self):
@@ -4284,8 +4287,52 @@ class MainApplication(QMainWindow):
         return self.file_metadata
 
 
+    def cancel_task(self):
+        self.button1.clicked.disconnect(self.cancel_task)
+        self.button1.setText("Stopping...")
+
+        if hasattr(self, "result_process") and self.result_process.is_alive():
+            parent = psutil.Process(self.result_process.pid)
+            children = parent.children(recursive=True)
+            for child in children:
+                try:
+                    child.kill()
+                except psutil.NoSuchProcess:
+                    pass
+            self.result_process.terminate()
+            self.result_process.join()
+
+        if hasattr(self, "result_timer") and self.result_timer.isActive():
+            self.result_timer.stop()
+        
+        # if hasattr(self, "result_process") and self.result_process.is_alive():
+        #     self.result_process.terminate()  # Forcefully terminate the process
+        #     self.result_process.join()       # Wait for it to properly close
+
+        # # Stop the QTimer if running
+        # if hasattr(self, "result_timer") and self.result_timer.isActive():
+        #     self.result_timer.stop()
+        
+        for bubble in self.bubble_widgets.values():
+            bubble.mark_cancelled()
+
+        self.statusbar.showMessage("Processing cancelled.")
+        self.button1.clicked.connect(self.on_run_task)
+        self.button1.setText("Process")
+
+
     '''MODULE FILE'''
     def on_run_task(self):
+        
+        self.button1.clicked.disconnect(self.on_run_task)
+        self.button1.setText("Cancel")
+        self.button1.clicked.connect(self.cancel_task)
+        
+        if not self.first_run:
+            for bubble in self.bubble_widgets.values():
+                bubble.mark_cancelled()
+        self.first_run = False
+
         # Collect all selected snirf files in a flat list
         snirf_files = []
 
@@ -4813,7 +4860,7 @@ def resource_path(relative_path):
         # PyInstaller bundle path
         base_path = sys._MEIPASS
     else:
-        base_path = os.path.abspath(".")
+        base_path = os.path.dirname(os.path.abspath(__file__))
 
     return os.path.join(base_path, relative_path)