plot_correlated: add include_dead_time

The defaults ensure that this change is not breaking

changelog.md

@@ -2,10 +2,15 @@
 
 ## v1.3.2 | t.b.d.
 
+#### New features
+
+* Add option to `include_dead_time` to [`ImageStack.plot_correlated()`](https://lumicks-pylake.readthedocs.io/en/v1.3.0/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.plot_correlated) for `Scan` and `ImageStack`. This parameter defaults to `True`. 
+
 #### Bug fixes
 
 * Fixed a bug where the time indicator was off by one frame in [`ImageStack.plot_correlated()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.plot_correlated) and [`ImageStack.export_video()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.export_video).
 * Fixed a bug where the time between frames was incorrectly not excluded when calling [`ImageStack.frame_timestamp_ranges()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.frame_timestamp_ranges) with `include_dead_time=False`. Note that `Scan` and `Kymo` are not affected.
+* Fixed a bug where [`ImageStack.plot_correlated()`](https://lumicks-pylake.readthedocs.io/en/v1.3.0/_api/lumicks.pylake.ImageStack.html#lumicks.pylake.ImageStack.plot_correlated) was not excluding the dead time between frames.
 * Changed the `DateTime` tag on TIFFs exported with Pylake from `Scan` and `Kymo` objects. Before the change, the start and end of the scanning period in nanoseconds was stored. After the change, we store the starting timestamp of the frame, followed by the starting timestamp of the next frame to be consistent with data exported from Bluelake. The scanning time is stored in the field `Exposure time (ms)` on the Description tag.
 
 ## v1.3.1 | 2023-12-07

lumicks/pylake/image_stack.py

@@ -484,6 +484,7 @@ def plot_correlated(
         adjustment=no_adjustment,
         *,
         vertical=False,
+        include_dead_time=False,
         return_frame_setter=False,
     ):
         """Downsample channel on a frame by frame basis and plot the results. The downsampling
@@ -513,10 +514,12 @@ def plot_correlated(
             figure.
         adjustment : lk.ColorAdjustment
             Color adjustments to apply to the output image.
-        vertical : bool
-            Align plots vertically.
-        return_frame_setter : bool
-            Whether to return a handle that allows updating the plotted frame.
+        vertical : bool, optional
+            Align plots vertically, default: False.
+        include_dead_time : bool, optional
+            Include dead time between frames, default: False.
+        return_frame_setter : bool, optional
+            Whether to return a handle that allows updating the plotted frame, default: False.
 
         Note
         ----
@@ -543,7 +546,7 @@ def post_update(image_handle, image):
 
         frame_setter = plot_correlated(
             channel_slice=channel_slice,
-            frame_timestamps=self.frame_timestamp_ranges(),
+            frame_timestamps=self.frame_timestamp_ranges(include_dead_time=include_dead_time),
             get_plot_data=frame_grabber,
             title_factory=lambda frame: make_image_title(self, frame, show_name=False),
             frame=frame,

lumicks/pylake/scan.py

@@ -294,6 +294,7 @@ def plot_correlated(
         adjustment=no_adjustment,
         *,
         vertical=False,
+        include_dead_time=False,
         return_frame_setter=False,
     ):
         """Downsample channel on a frame by frame basis and plot the results. The downsampling
@@ -324,9 +325,11 @@ def plot_correlated(
             figure.
         adjustment : lk.ColorAdjustment
             Color adjustments to apply to the output image.
-        vertical : bool
+        vertical : bool, optional
             Align plots vertically.
-        return_frame_setter : bool
+        include_dead_time : bool, optional
+            Include dead time between scan frames.
+        return_frame_setter : bool, optional
             Whether to return a handle that allows updating the plotted frame.
 
         Examples
@@ -353,7 +356,7 @@ def post_update(image_handle, image):
         def title_factory(frame):
             return make_image_title(self, frame, show_name=False)
 
-        frame_timestamps = self.frame_timestamp_ranges()
+        frame_timestamps = self.frame_timestamp_ranges(include_dead_time=include_dead_time)
 
         frame_setter = plot_correlated(
             channel_slice,