Merge pull request #163 from MouseLand/dev

Add saccade loading & plotting

Author: Atika-Syeda

.github/workflows/test_and_deploy.yml

@@ -90,4 +90,4 @@ jobs:
         run: |
           git tag
           python setup.py sdist bdist_wheel
-          twine upload dist/*
+          twine upload dist/*

facemap/gui/gui.py

@@ -30,9 +30,9 @@
     QStatusBar,
     QToolButton,
     QWidget,
+    QGraphicsItemGroup
 )
 from scipy.stats import skew, zscore
-
 from facemap import process, roi, utils
 from facemap.gui import (
     guiparts,
@@ -265,6 +265,7 @@ def __init__(
         self.cframe = 0
         self.traces1 = None
         self.traces2 = None
+        self.saccade_data = None
 
         ## Pose plot
         self.pose_scatterplot = pg.ScatterPlotItem(hover=True)
@@ -939,6 +940,7 @@ def reset(self):
         self.keypoints_vtick = None
         self.svd_plot_vtick = None
         self.neural_win = None
+        self.saccade_data = None
 
     def pupil_sigma_change(self):
         self.pupil_sigma = float(self.sigma_box.text())
@@ -1286,7 +1288,9 @@ def process_ROIs(self):
             savepath = self.save_path
         else:
             savepath = None
-        if self.motSVD_checkbox.isChecked() or self.movSVD_checkbox.isChecked():
+        print("Checking if ROIs are set")
+        if self.motSVD_checkbox.isChecked() or self.movSVD_checkbox.isChecked() or len(self.ROIs) > 0:
+            print("Processing ROIs")
             savename = process.run(
                 self.filenames, GUIobject=QtWidgets, parent=self, savepath=savepath
             )
@@ -2009,9 +2013,59 @@ def plot_trace(self, wplot, proctype, wroi, color, keypoints_group_selected=None
                 pen=pg.mkPen(color=(255, 255, 255), width=2, movable=True),
             )
             selected_plot.addItem(self.keypoints_vtick)
+        if self.saccade_data is not None:
+            self.plot_saccade_data()
         selected_plot.setLimits(xMin=0, xMax=self.nframes)
         return tr
 
+    def plot_saccade_data(self):
+        """
+        Plot saccade data on the SVD traces plot as a single toggleable item.
+        """
+        if self.saccade_data is not None:
+            # Extract saccade data
+            saccade = self.saccade_data['Saccade'][0, 0].squeeze()
+
+            # Check if saccade data matches the number of frames
+            if saccade.shape[0] != self.nframes:
+                print("Saccade data shape does not match the number of frames.")
+                return
+
+            # Find start and end indices for saccades
+            sac_start_idx = np.where(np.diff(saccade) == 1)[0] + 1
+            sac_end_idx = np.where(np.diff(saccade) == -1)[0] + 1
+
+            # Remove any existing saccade overlays to avoid duplication
+            if hasattr(self, 'saccade_vspan_items') and self.saccade_vspan_items:
+                for item in self.saccade_vspan_items:
+                    self.svd_traces_plot.removeItem(item)
+
+            # Create a list to store the saccade region items
+            self.saccade_vspan_items = []
+
+            # Add vertical spans for each saccade
+            for start, end in zip(sac_start_idx, sac_end_idx):
+                if start < end and end < self.nframes:
+                    # Create a LinearRegionItem for the saccade
+                    vspan = pg.LinearRegionItem(
+                        values=(start, end),  # Start and end positions
+                        brush=pg.mkBrush(255, 255, 255, 50),  # Semi-transparent white
+                        movable=False,  # Non-movable
+                    )
+
+                    # Add the region to the plot
+                    self.svd_traces_plot.addItem(vspan)
+
+                    # Keep track of added items for later removal
+                    self.saccade_vspan_items.append(vspan)
+        else:
+            print("No saccade data available.")
+
+    def toggle_saccade_vspans(self, show):
+        # Toggles visibility of the saccade vspans group
+        if hasattr(self, 'saccade_vspan_group'):  # Check if the group exists
+            self.saccade_vspan_group.setVisible(show)
+
     def on_click_svd_plot(self, event):
         """
         Update vtick position of svd plot when user clicks

facemap/gui/io.py

@@ -354,6 +354,24 @@ def load_movies(parent, filelist=None):
             parent.load_keypoints_from_videodir()
     return good
 
+def load_saccade(parent):
+    path = QFileDialog.getOpenFileName(parent, "Select a file", filter="MAT (*.mat)")
+    # Check if path exists
+    if path[0]:
+        try:
+            import scipy.io
+
+            saccade_data = scipy.io.loadmat(path[0])
+            parent.saccade_data = saccade_data['eye_movement_data']
+            parent.update_status_bar("Saccade data loaded")
+            parent.plot_saccade_data()
+        except Exception as e:
+            msg = QMessageBox(parent)
+            msg.setIcon(QMessageBox.Icon.Warning)
+            msg.setText("Error loading saccade data: " + str(e))
+            msg.setStandardButtons(QMessageBox.StandardButton.Ok)
+            msg.exec_()
+
 
 def load_npy_file(parent, allow_mat=False):
     # Open a file dialog to select a folder

facemap/gui/menus.py

@@ -23,6 +23,11 @@ def mainmenu(parent):
     load_proc.triggered.connect(lambda: io.open_proc(parent))
     parent.addAction(load_proc)
 
+    # Load saccade data
+    load_saccade = QAction("Load saccade data", parent)
+    load_saccade.triggered.connect(lambda: io.load_saccade(parent))
+    parent.addAction(load_saccade)
+
     # Set output folder
     set_output_folder = QAction("Set output folder", parent)
     set_output_folder.setShortcut("Ctrl+S")
@@ -95,6 +100,7 @@ def mainmenu(parent):
     file_menu.addAction(open_file)
     file_menu.addAction(open_folder)
     file_menu.addAction(load_proc)
+    file_menu.addAction(load_saccade)
     file_menu.addAction(set_output_folder)
 
     pose_menu = main_menu.addMenu("Pose")