Multi-tracking in FastADT experiment (#145)

* Allow server cameras to be streamable by removing precaution checks

* Unify interface, naming between get_microscope/camera(_class)

* Remove unused _init_attr_dict/get_attrs from microscope client/server

* Do not force server-side attributes to be callable, use them first: these 3 lines took ~3h

* EAFP: Allow camera to call functions whether they are registered or not

* EAFP: Allow camera to call unregistered functions - fixes server cameras

* Remove unnecessary print debug statement

* Add **streamable** description to `config.md` documentation

* Encapsulate FastADT paths in separate prop/method

* Add new TrackingArtist to be used with plotting multi-runs

* Working multi-tracking FastADT frame! Still needs polish

* Change `ClickEvent` to dataclass, implement `ClickEvent.xy`

* Optimize clicking logic in FastADT experiment

* Streamline the `calibrate_beamshift_live` function

* Streamline `CalibBeamShift.plot`

* Improvements to `CalibBeamShift` readability (WIP)

* Add option to calibrate beamshift with vsp

* Fix errors, add beam center

* Switch calibration output format from pickle to yaml

* Allow delay during calibrate beamshift

* Add necessary reflections to fix plotting

* Final tweaks

* Make the yaml produced by CalibBeamShift human-readable

* Update src/instamatic/calibrate/calibrate_beamshift.py

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>

* Update src/instamatic/calibrate/calibrate_beamshift.py

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>

* Minor post-review type-hint improvements + ruff

* Add `instamatic.utils.iterating` with `sawtooth` iterating function

* Make the `click_dispatcher:ClickEvent.xy` a property

* Rephrase `VideoStreamProcessor.temporary` using `blocked` context

* Fix the bug where canceling FastADT did not remove its elements

* Fix the bug where colors of crystal tracking repeated after 10

* Remove debug message

* Attempt to generalize collecting, revert as needed

* Fix: rotation speed for negative target pace is negative, rounds to 0

* Rename tracking "mode" to "algo"; if continuous, track w/ movie

* Generalize FastADT run collection (+fix resulting bugs)

* Revert change: use stills for continuous tracking

* Minor fixes and code quality improvements

* Clean, remove unused code

* Fix tracking failing for beam not in the center at alignment

* Fix Run.__str__, clean up code, method, call order

* Log all behavior in two separate message windows.

* Fix ignore msg1,2 variables in headless FastADT experiment

* Update in tests `tracking_mode` -> `tracking_algo`

* Add estimated time required dialog in FastADT message 2

* Display which experiment is being collected in multi-expt

* Display which experiment is being collected in multi-expt

* Trace variables only after everything was defined to avoid Exceptions

* Fix: leaving input empty even temporarily caused exception

---------

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>

Author: Baharis

docs/gui.md

@@ -181,8 +181,8 @@ For optimum performance, the FastADT frame uses three separate TEM setting which
 **Diffraction exposure (s)**  
 : The time taken to collect each diffraction image in seconds. In the `continuous` mode it will additionally dictate the rotation speed.
 
-**Tracking mode**
-: Dictates whether `none` or `manual` tracking is to be performed at the start of the experiment.
+**Tracking algorithm**
+: Dictates whether `none` or `manual` tracking algorithm is to be performed at the start of the experiment to determine pathing.
 
 **Tracking step (deg)**
 : The target spacing between angles at which subsequent tracking images are collected within the tracking series in degrees.

src/instamatic/calibrate/calibrate_beamshift.py

@@ -57,12 +57,12 @@ class CalibBeamShift:
     def __repr__(self):
         return f'CalibBeamShift(transform=\n{self.transform},\n   reference_shift=\n{self.reference_shift},\n   reference_pixel=\n{self.reference_pixel})'
 
-    def beamshift_to_pixelcoord(self, beamshift: Sequence[float, float]) -> Vector2:
+    def beamshift_to_pixelcoord(self, beamshift: Sequence[float]) -> Vector2:
         """Converts from beamshift x,y to pixel coordinates."""
         r_i = np.linalg.inv(self.transform)
         return np.dot(self.reference_shift - np.array(beamshift), r_i) + self.reference_pixel
 
-    def pixelcoord_to_beamshift(self, pixelcoord: Sequence[float, float]) -> Vector2:
+    def pixelcoord_to_beamshift(self, pixelcoord: Sequence[float]) -> Vector2:
         """Converts from pixel coordinates to beamshift x,y."""
         pc = np.array(pixelcoord)
         return self.reference_shift - np.dot(pc - self.reference_pixel, self.transform)

src/instamatic/calibrate/calibrate_stage_rotation.py

@@ -137,7 +137,7 @@ def speed_time_to_span(self, speed: float, time: float) -> float:
 
     def plan_rotation(self, target_pace: float) -> RotationPlan:
         """Given target pace in sec / deg, find nearest pace, speed, delay."""
-        target_speed = self.alpha_pace / target_pace  # exact speed setting needed
+        target_speed = abs(self.alpha_pace / target_pace)  # exact speed setting needed
         nearest_speed = self.speed_options.nearest(target_speed)  # nearest setting
         nearest_pace = self.alpha_pace / nearest_speed  # nearest in sec/deg
         total_delay = self.alpha_windup / nearest_speed + self.delay

src/instamatic/camera/videostream.py

@@ -160,6 +160,10 @@ def unblock(self):
     def blocked(self):
         yield
 
+    @contextmanager
+    def unblocked(self):
+        yield
+
 
 class LiveVideoStream(VideoStream):
     """Handle the continuous stream of incoming data from the ImageGrabber."""
@@ -237,6 +241,17 @@ def blocked(self):
             if not was_set_before:
                 self.grabber.continuousCollectionEvent.clear()
 
+    @contextmanager
+    def unblocked(self):
+        """Clear `continuousCollectionEvent` in the statement scope only."""
+        was_set_before = self.grabber.continuousCollectionEvent.is_set()
+        try:
+            self.grabber.continuousCollectionEvent.clear()
+            yield
+        finally:
+            if was_set_before:
+                self.grabber.continuousCollectionEvent.set()
+
     def show_stream(self):
         from instamatic.gui import videostream_frame