Add movie saving option

Author: pgleeson

Player.py

@@ -19,7 +19,7 @@ def __init__(
         mini=0,
         maxi=100,
         pos=(0.125, 0.92),
-        **kwargs
+        **kwargs,
     ):
         self.i = 0
         self.min = mini
@@ -37,7 +37,7 @@ def __init__(
             init_func=init_func,
             fargs=fargs,
             save_count=save_count,
-            **kwargs
+            **kwargs,
         )
 
     def play(self):
@@ -92,11 +92,11 @@ def setup(self, pos):
         fax = divider.append_axes("right", size="80%", pad=0.05)
         ofax = divider.append_axes("right", size="100%", pad=0.05)
         sliderax = divider.append_axes("right", size="500%", pad=0.07)
-        self.button_oneback = matplotlib.widgets.Button(playerax, label="$\u29CF$")
-        self.button_back = matplotlib.widgets.Button(bax, label="$\u25C0$")
-        self.button_stop = matplotlib.widgets.Button(sax, label="$\u25A0$")
-        self.button_forward = matplotlib.widgets.Button(fax, label="$\u25B6$")
-        self.button_oneforward = matplotlib.widgets.Button(ofax, label="$\u29D0$")
+        self.button_oneback = matplotlib.widgets.Button(playerax, label="$\u29cf$")
+        self.button_back = matplotlib.widgets.Button(bax, label="$\u25c0$")
+        self.button_stop = matplotlib.widgets.Button(sax, label="$\u25a0$")
+        self.button_forward = matplotlib.widgets.Button(fax, label="$\u25b6$")
+        self.button_oneforward = matplotlib.widgets.Button(ofax, label="$\u29d0$")
         self.button_oneback.on_clicked(self.onebackward)
         self.button_back.on_clicked(self.backward)
         self.button_stop.on_clicked(self.stop)

WormView.py

@@ -11,81 +11,111 @@
 midline_plot = None
 perimeter_plot = None
 
+
 def validate_file(file_path):
     if not os.path.exists(file_path):
         raise argparse.ArgumentTypeError(f"The file {file_path} does not exist.")
     if not os.path.isfile(file_path):
         raise argparse.ArgumentTypeError(f"{file_path} is not a valid file.")
     return file_path
 
+
 def get_perimeter(x, y, r):
     n_bar = x.shape[0]
     num_steps = x.shape[1]
 
     n_seg = int(n_bar - 1)
 
     # radii along the body of the worm
-    r_i = np.array([
-        r * abs(math.sin(math.acos(((i) - n_seg / 2.0) / (n_seg / 2.0 + 0.2))))
-        for i in range(n_bar)
-    ]).reshape(-1, 1)
+    r_i = np.array(
+        [
+            r * abs(math.sin(math.acos(((i) - n_seg / 2.0) / (n_seg / 2.0 + 0.2))))
+            for i in range(n_bar)
+        ]
+    ).reshape(-1, 1)
 
     diff_x = np.diff(x, axis=0)
     diff_y = np.diff(y, axis=0)
 
     arctan = np.arctan2(diff_x, -diff_y)
     d_arr = np.zeros((n_bar, num_steps))
 
-    d_mask = np.full((n_bar,num_steps), False)
-    arctan_diff = np.abs(np.diff(arctan, axis = 0)) > np.pi
-    d_mask[1:-1,:] = arctan_diff
-
+    d_mask = np.full((n_bar, num_steps), False)
+    arctan_diff = np.abs(np.diff(arctan, axis=0)) > np.pi
+    d_mask[1:-1, :] = arctan_diff
 
     # d of worm endpoints is based off of two points, whereas d of non-endpoints is based off of 3 (x, y) points
-    
+
     d_arr[:-1, :] = arctan
     d_arr[1:, :] = d_arr[1:, :] + arctan
     d_arr[1:-1, :] = d_arr[1:-1, :] / 2
-    d_arr = d_arr - np.pi*d_mask
-    dx = np.cos(d_arr)*r_i
-    dy = np.sin(d_arr)*r_i
-    
+    d_arr = d_arr - np.pi * d_mask
+    dx = np.cos(d_arr) * r_i
+    dy = np.sin(d_arr) * r_i
 
-    px = np.zeros((2*n_bar, x.shape[1]))
-    py = np.zeros((2*n_bar, x.shape[1]))
+    px = np.zeros((2 * n_bar, x.shape[1]))
+    py = np.zeros((2 * n_bar, x.shape[1]))
 
     px[:n_bar, :] = x - dx
-    px[n_bar:, :] = np.flipud(x + dx) # Make perimeter counter-clockwise
+    px[n_bar:, :] = np.flipud(x + dx)  # Make perimeter counter-clockwise
 
     py[:n_bar, :] = y - dy
-    py[n_bar:, :] = np.flipud(y + dy) # Make perimeter counter-clockwise
+    py[n_bar:, :] = np.flipud(y + dy)  # Make perimeter counter-clockwise
 
     return px, py
 
 
 def main():
-
-    # Default behavior is to use (px, py) if it exists, and if it doesn’t then automatically generate the perimeter from the midline. 
-    parser = argparse.ArgumentParser(description="Open a player for the worm behaviour.")
-    parser.add_argument('-f', '--wcon_file', type=validate_file, help='WCON file path', required=True )
-    parser.add_argument('-nogui', action='store_true', help="Just load file, don't show GUI")
-    parser.add_argument('-s', '--suppress_automatic_generation', action='store_true', help='Suppress the automatic generation of a perimeter which would be computed from the midline of the worm. If (px, py) is not specified in the WCON, a perimeter will not be shown.')
-    parser.add_argument('-i', '--ignore_wcon_perimeter', action='store_true', help='Ignore (px, py) values in the WCON. Instead, a perimeter is automatically generated based on the midline of the worm.')
-    parser.add_argument('-r', '--minor_radius', type=float, default=40e-3, help='Minor radius of the worm in millimeters (default: 40e-3)', required=False)
+    # Default behavior is to use (px, py) if it exists, and if it doesn’t then automatically generate the perimeter from the midline.
+    parser = argparse.ArgumentParser(
+        description="Open a player for the worm behaviour."
+    )
+    parser.add_argument(
+        "-f", "--wcon_file", type=validate_file, help="WCON file path", required=True
+    )
+    parser.add_argument(
+        "-nogui", action="store_true", help="Just load file, don't show GUI"
+    )
+    parser.add_argument(
+        "-s",
+        "--suppress_automatic_generation",
+        action="store_true",
+        help="Suppress the automatic generation of a perimeter which would be computed from the midline of the worm. If (px, py) is not specified in the WCON, a perimeter will not be shown.",
+    )
+    parser.add_argument(
+        "-i",
+        "--ignore_wcon_perimeter",
+        action="store_true",
+        help="Ignore (px, py) values in the WCON. Instead, a perimeter is automatically generated based on the midline of the worm.",
+    )
+    parser.add_argument(
+        "-r",
+        "--minor_radius",
+        type=float,
+        default=40e-3,
+        help="Minor radius of the worm in millimeters (default: 40e-3)",
+        required=False,
+    )
 
     args = parser.parse_args()
 
     fig, ax = plt.subplots()
     plt.get_current_fig_manager().set_window_title("WCON replay")
     ax.set_aspect("equal")
 
-    with open(args.wcon_file, 'r') as f:
+    with open(args.wcon_file, "r") as f:
         wcon = json.load(f)
-    
+
     if "@CelegansNeuromechanicalGaitModulation" in wcon:
-        center_x_arr = wcon["@CelegansNeuromechanicalGaitModulation"]["objects"]["circles"]["x"]
-        center_y_arr = wcon["@CelegansNeuromechanicalGaitModulation"]["objects"]["circles"]["y"]
-        radius_arr = wcon["@CelegansNeuromechanicalGaitModulation"]["objects"]["circles"]["r"]
+        center_x_arr = wcon["@CelegansNeuromechanicalGaitModulation"]["objects"][
+            "circles"
+        ]["x"]
+        center_y_arr = wcon["@CelegansNeuromechanicalGaitModulation"]["objects"][
+            "circles"
+        ]["y"]
+        radius_arr = wcon["@CelegansNeuromechanicalGaitModulation"]["objects"][
+            "circles"
+        ]["r"]
 
         for center_x, center_y, radius in zip(center_x_arr, center_y_arr, radius_arr):
             circle = plt.Circle((center_x, center_y), radius, color="b")
@@ -94,32 +124,35 @@ def main():
         print("No objects found")
 
         # Set the limits of the plot since we don't have any objects to help with autoscaling
-        
+
         ax.set_ylim([-1.5, 1.5])
 
     t = np.array(wcon["data"][0]["t"])
     x = np.array(wcon["data"][0]["x"]).T
     y = np.array(wcon["data"][0]["y"]).T
 
-    print(f"Range of time: {t[0]}->{t[0]}; x range: {x.max()}->{x.min()}; y range: {y.max()}->{y.min()}")
+    print(
+        f"Range of time: {t[0]}->{t[0]}; x range: {x.max()}->{x.min()}; y range: {y.max()}->{y.min()}"
+    )
     factor = 0.05
-    if abs(x.max()-x.min())>abs(y.max()-y.min()):
-        side = abs(x.max()-x.min())
-        ax.set_xlim([x.min()-side*factor, x.max()+side*factor])
-        mid = (y.max()+y.min())/2
-        ax.set_ylim([mid-side*(.5+factor), mid+side*(.5+factor)])
+    if abs(x.max() - x.min()) > abs(y.max() - y.min()):
+        side = abs(x.max() - x.min())
+        ax.set_xlim([x.min() - side * factor, x.max() + side * factor])
+        mid = (y.max() + y.min()) / 2
+        ax.set_ylim([mid - side * (0.5 + factor), mid + side * (0.5 + factor)])
     else:
-        side = abs(y.max()-y.min())
-        ax.set_ylim([y.min()-side*factor, y.max()+side*factor])
-        mid = (x.max()+x.min())/2
-        ax.set_xlim([mid-side*(.5+factor), mid+side*(.5+factor)])
-
+        side = abs(y.max() - y.min())
+        ax.set_ylim([y.min() - side * factor, y.max() + side * factor])
+        mid = (x.max() + x.min()) / 2
+        ax.set_xlim([mid - side * (0.5 + factor), mid + side * (0.5 + factor)])
 
     num_steps = t.size
 
     if "px" in wcon["data"][0] and "py" in wcon["data"][0]:
         if args.ignore_wcon_perimeter:
-            print("Ignoring (px, py) values in WCON file and computing perimeter from midline.")
+            print(
+                "Ignoring (px, py) values in WCON file and computing perimeter from midline."
+            )
             px, py = get_perimeter(x, y, args.minor_radius)
         else:
             print("Using (px, py) from WCON file")
@@ -142,23 +175,37 @@ def update(ti):
         print("Time step: %s, fract: %f, color: %s" % (ti, f, color))
 
         if midline_plot is None:
-            (midline_plot,) = ax.plot(x[:, ti], y[:, ti], color="g", label="t=%sms" % t[ti], linewidth=0.5)
+            (midline_plot,) = ax.plot(
+                x[:, ti], y[:, ti], color="g", label="t=%sms" % t[ti], linewidth=0.5
+            )
         else:
             midline_plot.set_data(x[:, ti], y[:, ti])
-        
+
         if px is not None and py is not None:
             if perimeter_plot is None:
-                (perimeter_plot,) = ax.plot(px[:, ti], py[:, ti], color="grey", linewidth=1)
+                (perimeter_plot,) = ax.plot(
+                    px[:, ti], py[:, ti], color="grey", linewidth=1
+                )
             else:
                 perimeter_plot.set_data(px[:, ti], py[:, ti])
 
-    ani = Player(fig, update, maxi=num_steps - 1)
+    anim = Player(fig, update, maxi=num_steps - 1)
 
-    # TODO WormViewCSV and WormViewWCON - should WormViewCSV just be the original WormView? That's what it initially did. 
-    # TODO Could take out Player and WormViewWCON into separate repo - Taking out Player could be ugly. It is quite coupled with WormView due to the update function. 
+    # TODO WormViewCSV and WormViewWCON - should WormViewCSV just be the original WormView? That's what it initially did.
+    # TODO Could take out Player and WormViewWCON into separate repo - Taking out Player could be ugly. It is quite coupled with WormView due to the update function.
 
     if not args.nogui:
         plt.show()
+    else:
+        print("GUI suppressed, exiting without showing %s." % anim)
+
+        from matplotlib.animation import FFMpegWriter
+
+        FFwriter = FFMpegWriter(fps=10)
+        mp4_file = args.wcon_file.replace(".wcon", ".mp4")
+        print(f"Saving animation to: {mp4_file}")
+        anim.save(mp4_file, writer=FFwriter)
+
 
 if __name__ == "__main__":
     sys.exit(main())