changed the changelog

changelog.md

@@ -1,3 +1,14 @@
+# Version 1.1.4
+
+- Fixed some display text to now display the correct information
+- A new option under Analysis has been added to export the data from a specified participant as a csv file. Fixes [Issue 19](https://git.research.dezeeuw.ca/tyler/flares/issues/19), [Issue 27](https://git.research.dezeeuw.ca/tyler/flares/issues/27)
+- Added 2 new parameters - TIME_WINDOW_START and TIME_WINDOW_END. Fixes [Issue 29](https://git.research.dezeeuw.ca/tyler/flares/issues/29)
+- These parameters affect the visualization of the significance and contrast images but do not change the total time modeled underneath
+- Fixed the duration of annotations edited from a BORIS file from 0 seconds to their proper duration
+- Added the annotation information to each participant under their "File information" window
+- Fixed Macs not being able to save snirfs attempting to be updated from BORIS files, and in general the updated files not respecting the path chosen by the user
+
+
 # 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)
@@ -9,6 +20,7 @@
 - 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)
+- Fixed the description under "Update events in snirf file..."
 
 
 # Version 1.1.2

flares.py

@@ -134,6 +134,9 @@ SHORT_CHANNEL: bool
 
 REMOVE_EVENTS: list
 
+TIME_WINDOW_START: int
+TIME_WINDOW_END: int
+
 VERBOSITY = True
 
 # FIXME: Shouldn't need each ordering - just order it before checking
@@ -182,6 +185,8 @@ REQUIRED_KEYS: dict[str, Any] = {
     
     "SHORT_CHANNEL": bool,
     "REMOVE_EVENTS": list,
+    "TIME_WINDOW_START": int,
+    "TIME_WINDOW_END": int
     # "REJECT_PAIRS": bool,
     # "FORCE_DROP_ANNOTATIONS": list,
     # "FILTER_LOW_PASS": float,
@@ -3031,7 +3036,11 @@ def process_participant(file_path, progress_callback=None):
     contrast_dict = {}
 
     for condition in all_conditions:
-        delay_cols = [col for col in all_delay_cols if col.startswith(f"{condition}_delay_")]
+        delay_cols = [
+            col for col in all_delay_cols
+            if col.startswith(f"{condition}_delay_") and
+            TIME_WINDOW_START <= int(col.split("_delay_")[-1]) <= TIME_WINDOW_END
+        ]
 
         if not delay_cols:
             continue  # skip if no columns found (shouldn't happen?)

main.py

@@ -45,7 +45,7 @@ from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleVa
 from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
 
-CURRENT_VERSION = "1.0.1"
+CURRENT_VERSION = "1.0.0"
 
 API_URL = "https://git.research.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
 API_URL_SECONDARY = "https://git.research2.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
@@ -155,6 +155,8 @@ SECTIONS = [
     {
         "title": "General Linear Model",
         "params": [
+            {"name": "TIME_WINDOW_START", "default": "0", "type": int, "help": "Where to start averaging the fir model bins. Only affects the significance and contrast images."},
+            {"name": "TIME_WINDOW_END", "default": "15", "type": int, "help": "Where to end averaging the fir model bins. Only affects the significance and contrast images."},
             #{"name": "N_JOBS", "default": 1, "type": int, "help": "Number of jobs for GLM processing."},
         ]
     },
@@ -1016,64 +1018,94 @@ class UpdateEventsWindow(QWidget):
         try:
             raw = read_raw_snirf(snirf_path, preload=True)
 
-            # Build new Annotations from shifted BORIS events
             onsets = []
             durations = []
             descriptions = []
 
+            open_events = {}  # label -> list of start times
             label_counts = {}
 
             used_times = set()
-            
             sfreq = raw.info['sfreq']  # sampling frequency in Hz
             min_shift = 1.0 / sfreq
-            
             max_attempts = 10
 
             for event in boris_events:
                 if not isinstance(event, list) or len(event) < 3:
                     continue
 
-                orig_time = event[0]
-                desc = event[2]
+                event_time = event[0]
+                label = event[2]
 
-                # Count occurrences per event label
-                count = label_counts.get(desc, 0)
-                label_counts[desc] = count + 1
+                count = label_counts.get(label, 0) + 1
+                label_counts[label] = count
 
-                # Only use 1st, 3rd, 5th... (odd occurrences)
-                if (count % 2) == 0:
-                    shifted_time = orig_time + time_shift
+                if label not in open_events:
+                    open_events[label] = []
 
-                    # Ensure unique timestamp by checking and adjusting slightly
-                    adjusted_time = shifted_time
+                if count % 2 == 1:
+                    # Odd occurrence = start event
+                    open_events[label].append(event_time)
+                else:
+                    # Even occurrence = end event
+                    if open_events[label]:
+                        matched_start = open_events[label].pop(0)
+                        duration = event_time - matched_start
 
-                    # Try to find a unique timestamp
+                        if duration <= 0:
+                            print(f"Warning: Duration for {label} is non-positive ({duration}). Skipping.")
+                            continue
+
+                        shifted_start = matched_start + time_shift
+
+                        adjusted_time = shifted_start
                         attempts = 0
                         while round(adjusted_time, 6) in used_times and attempts < max_attempts:
                             adjusted_time += min_shift
                             attempts += 1
 
                         if attempts == max_attempts:
-                        print(f"Warning: Could not find unique timestamp for event '{desc}' at original time {orig_time:.3f}s. Skipping.")
-                        continue  # Skip problematic event
+                            print(f"Warning: Couldn't find unique time for {label} @ {matched_start}s. Skipping.")
+                            continue
 
                         adjusted_time = round(adjusted_time, 6)
                         used_times.add(adjusted_time)
 
-                    print(f"Applying event: {desc} @ {adjusted_time:.3f}s (original: {orig_time:.3f}s)")
+                        print(f"Adding event: {label} @ {adjusted_time:.3f}s for {duration:.3f}s")
 
+                        onsets.append(adjusted_time)
+                        durations.append(duration)
+                        descriptions.append(label)
+                    else:
+                        print(f"Warning: Unmatched end for label '{label}' at {event_time:.3f}s. Skipping.")
+
+            # Optionally warn about any unmatched starts left open
+            for label, starts in open_events.items():
+                for start_time in starts:
+                    shifted_start = start_time + time_shift
+
+                    adjusted_time = shifted_start
+                    attempts = 0
+                    while round(adjusted_time, 6) in used_times and attempts < max_attempts:
+                        adjusted_time += min_shift
+                        attempts += 1
+
+                    if attempts == max_attempts:
+                        print(f"Warning: Couldn't find unique time for unmatched start {label} @ {start_time}s. Skipping.")
+                        continue
+
+                    adjusted_time = round(adjusted_time, 6)
+                    used_times.add(adjusted_time)
+
+                    print(f"Warning: Unmatched start for label '{label}' at {start_time:.3f}s. Adding with duration 0.")
                     onsets.append(adjusted_time)
                     durations.append(0.0)
-                    descriptions.append(desc)
+                    descriptions.append(label)
 
             new_annotations = Annotations(onset=onsets, duration=durations, description=descriptions)
 
-            # Replace annotations in raw object
             raw.set_annotations(new_annotations)
-
-            # Write a new SNIRF file
-            write_raw_snirf(raw, suggested_name)
+            write_raw_snirf(raw, save_path)
 
             QMessageBox.information(self, "Success", "SNIRF file updated with aligned BORIS events.")
 
@@ -2197,7 +2229,7 @@ class ParticipantFoldChannelsWidget(QWidget):
         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(QLabel("This will cause the app to hang for ~30s/Participant!"))
         self.top_bar.addWidget(self.submit_button)
 
         self.scroll = QScrollArea()
@@ -2352,6 +2384,226 @@ class ParticipantFoldChannelsWidget(QWidget):
 
 
 
+class ExportDataAsCSVViewerWidget(QWidget):
+    def __init__(self, haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict):
+        super().__init__()
+        self.setWindowTitle("FLARES Export Data As CSV Viewer")
+        self.haemo_dict = haemo_dict
+        self.cha_dict = cha_dict
+        self.df_ind = df_ind
+        self.design_matrix = design_matrix
+        self.group = group
+        self.contrast_results_dict = contrast_results_dict
+        
+        # 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.participant_dropdown = self._create_multiselect_dropdown(self.participant_dropdown_items)
+        self.participant_dropdown.currentIndexChanged.connect(self.update_participant_dropdown_label)
+              
+        self.index_texts = [
+            "0 (Export Data to CSV)",
+            # "1 (second image)",
+            # "2 (third image)",
+            # "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.generate_and_save_csv)
+
+        self.top_bar.addWidget(QLabel("Participants:"))
+        self.top_bar.addWidget(self.participant_dropdown)
+        self.top_bar.addWidget(QLabel("Export Type:"))
+        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 _create_multiselect_dropdown(self, items):
+        combo = FullClickComboBox()
+        combo.setView(QListView())
+        model = QStandardItemModel()
+        combo.setModel(model)
+        combo.setEditable(True)
+        combo.lineEdit().setReadOnly(True)
+        combo.lineEdit().setPlaceholderText("Select...")
+
+
+        dummy_item = QStandardItem("<None Selected>")
+        dummy_item.setFlags(Qt.ItemIsEnabled)
+        model.appendRow(dummy_item)
+
+        toggle_item = QStandardItem("Toggle Select All")
+        toggle_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+        toggle_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+        model.appendRow(toggle_item)
+
+        for item in items:
+            standard_item = QStandardItem(item)
+            standard_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+            standard_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+            model.appendRow(standard_item)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+
+
+        def on_view_clicked(index):
+            item = model.itemFromIndex(index)
+            if item.isCheckable():
+                new_state = Qt.Checked if item.checkState() == Qt.Unchecked else Qt.Unchecked
+                item.setCheckState(new_state)
+
+        combo.view().pressed.connect(on_view_clicked)
+
+        self._updating_checkstates = False
+
+        def on_item_changed(item):
+            if self._updating_checkstates:
+                return
+            self._updating_checkstates = True
+
+            normal_items = [model.item(i) for i in range(2, model.rowCount())]  # skip dummy and toggle
+
+            if item == toggle_item:
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                if all_checked:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Unchecked)
+                    toggle_item.setCheckState(Qt.Unchecked)
+                else:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Checked)
+                    toggle_item.setCheckState(Qt.Checked)
+
+            elif item == dummy_item:
+                pass
+
+            else:
+                # When normal items change, update toggle item
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                toggle_item.setCheckState(Qt.Checked if all_checked else Qt.Unchecked)
+
+            # Update label text immediately after change
+            if combo == self.participant_dropdown:
+                self.update_participant_dropdown_label()
+            elif combo == self.image_index_dropdown:
+                self.update_image_index_dropdown_label()
+
+            self._updating_checkstates = False
+
+        model.itemChanged.connect(on_item_changed)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+        return combo
+    
+    def _get_checked_items(self, combo):
+        checked = []
+        model = combo.model()
+        for i in range(model.rowCount()):
+            item = model.item(i)
+            # Skip dummy and toggle items:
+            if item.text() in ("<None Selected>", "Toggle Select All"):
+                continue
+            if item.checkState() == Qt.Checked:
+                checked.append(item.text())
+        return checked
+
+    def update_participant_dropdown_label(self):
+        selected = self._get_checked_items(self.participant_dropdown)
+        if not selected:
+            self.participant_dropdown.lineEdit().setText("<None Selected>")
+        else:
+            # Extract just "Participant N" from "Participant N (filename)"
+            selected_short = [s.split(" ")[0] + " " + s.split(" ")[1] for s in selected]
+            self.participant_dropdown.lineEdit().setText(", ".join(selected_short))
+
+    def update_image_index_dropdown_label(self):
+        selected = self._get_checked_items(self.image_index_dropdown)
+        if not selected:
+            self.image_index_dropdown.lineEdit().setText("<None Selected>")
+        else:
+            # Only show the index part
+            index_labels = [s.split(" ")[0] for s in selected]
+            self.image_index_dropdown.lineEdit().setText(", ".join(index_labels))
+
+    def generate_and_save_csv(self):
+        
+        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)
+        ]
+
+        # Pass the necessary arguments to each method
+        for file_path in selected_file_paths:
+            haemo_obj = self.haemo_dict.get(file_path)
+
+            if haemo_obj is None:
+                continue
+
+            cha = self.cha_dict.get(file_path)
+
+            for idx in selected_indexes:
+                if idx == 0:
+                    try:
+                        suggested_name = f"{file_path}.csv"
+
+                        # Open save dialog
+                        save_path, _ = QFileDialog.getSaveFileName(
+                            self,
+                            "Save SNIRF File As",
+                            suggested_name,
+                            "CSV Files (*.csv)"
+                        )
+
+                        if not save_path:
+                            print("Save cancelled.")
+                            return
+
+                        if not save_path.lower().endswith(".csv"):
+                            save_path += ".csv"
+                        # Save the CSV here
+                        
+                        cha.to_csv(save_path)
+                        QMessageBox.information(self, "Success", "CSV file has been saved.")
+
+                    except Exception as e:
+                        QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
+
+
+                else:
+                    print(f"No method defined for index {idx}")
+
+
 class ClickableLabel(QLabel):
     def __init__(self, full_pixmap: QPixmap, thumbnail_pixmap: QPixmap):
         super().__init__()
@@ -3559,12 +3811,16 @@ class ViewerLauncherWidget(QWidget):
         btn5 = QPushButton("Open Cross Group Brain Viewer")
         btn5.clicked.connect(lambda: self.open_group_brain_viewer(haemo_dict, df_ind, design_matrix, group, contrast_results_dict))
         
+        btn6 = QPushButton("Open Export Data As CSV Viewer")
+        btn6.clicked.connect(lambda: self.open_export_data_as_csv_viewer(haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict))
+
 
         layout.addWidget(btn1)
         layout.addWidget(btn2)
         layout.addWidget(btn3)
         layout.addWidget(btn4)
         layout.addWidget(btn5)
+        layout.addWidget(btn6)
 
     def open_participant_viewer(self, haemo_dict, fig_bytes_dict):
         self.participant_viewer = ParticipantViewerWidget(haemo_dict, fig_bytes_dict)
@@ -3586,6 +3842,10 @@ class ViewerLauncherWidget(QWidget):
         self.participant_brain_viewer = GroupBrainViewerWidget(haemo_dict, df_ind, design_matrix, group, contrast_results_dict)
         self.participant_brain_viewer.show()
 
+    def open_export_data_as_csv_viewer(self, haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict):
+        self.export_data_as_csv_viewer = ExportDataAsCSVViewerWidget(haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict)
+        self.export_data_as_csv_viewer.show()
+
 
 class MainApplication(QMainWindow):
     """
@@ -4655,6 +4915,16 @@ class MainApplication(QMainWindow):
             else:
                 snirf_info['Digitization Points'] = "Not found"
                 
+            if raw.annotations is not None and len(raw.annotations) > 0:
+                annot_info = []
+                for onset, duration, desc in zip(raw.annotations.onset,
+                                                raw.annotations.duration,
+                                                raw.annotations.description):
+                    annot_info.append(f"Onset: {onset:.2f}s, Duration: {duration:.2f}s, Description: {desc}")
+                snirf_info['Annotations'] = annot_info
+            else:
+                snirf_info['Annotations'] = "No annotations found"
+                
             return snirf_info
         except:
             return None