Merge branch 'main' into FastADT_squashed

# Conflicts:
#	src/instamatic/_collections.py
#	src/instamatic/experiments/fast_adt/experiment.py

Author: Baharis

pyproject.toml

@@ -12,6 +12,9 @@ requires-python = ">=3.9"
 authors = [
 	{name = "Stef Smeets", email = "s.smeets@esciencecenter.nl"},
 ]
+maintainers = [
+    {name = "Daniel Mariusz Tchoń", email = "tchon@fzu.cz"}
+]
 keywords = [
     "electron-crystallography",
     "electron-microscopy",

readme.md

@@ -73,37 +73,7 @@ Alternatively, some of the methods implemented in `Instamatic` are described in:
 
 - S. Smeets, X. Zou, and W. Wan, [Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials](http://dx.doi.org/10.1107/S1600576718009500), J. Appl. Cryst. (2018). 51, 1262–1273
 
-## Source Code Structure
-
-* **`demos/`** - Jupyter demo notebooks
-* **`docs/`** - Documentation
-* **`src/`** - Source code for instamatic
-* **`src/instamatic/`**
-  * **`calibrate/`** - Tools for calibration
-  * **`camera/`** - Camera interaction code
-  * **`config/`** - Configuration management
-  * **`experiments/`** - Specific data collection routines
-  * **`formats/`** - Image formats and other IO
-  * **`gui/`** - GUI code
-  * **`microscope/`** - Microscope interaction code
-  * **`neural_network/`** - Crystal quality prediction
-  * **`processing/`** - Data processing tools
-  * **`server/`** - Manages interprocess/network communication
-  * **`utils/`** - Helpful utilities
-  * **`acquire_at_items.py`** - Stage movement/data acquisition engine
-  * **`admin.py`** - Check for administrator
-  * **`banner.py`** - Appropriately annoying thank you message
-  * **`browser.py`** - Montage browsing class
-  * **`controller.py`** - Main instrument interaction code
-  * **`exceptions.py`** - Internal exceptions
-  * **`goniotool.py`** - Goniotool (JEOL) interaction code
-  * **`gridmontage.py`** - Grid montage data collection code
-  * **`image_utils.py`** - Image transformation routines
-  * **`imreg.py`** - Image registration (cross correlation)
-  * **`io.py`** - Some io-related scripts
-  * **`main.py`** - Main entry point
-  * **`montage.py`** - Image stitching
-  * **`navigation.py`** - Optimize navigation paths
-  * **`tools.py`** - Collection of functions used throughout the code
-* **`scripts/`** - Helpful scripts
-* **`pyproject.toml`** - Dependency/build system declaration
+## Maintenance
+
+- 2025-now: [@Baharis](https://github.com/Baharis)
+- 2015-2025: [@stefsmeets](https://github.com/stefsmeets)

src/instamatic/experiments/fast_adt/experiment.py

@@ -385,26 +385,20 @@ def enqueue_still_steps(self, run: Run) -> None:
                 self.steps_queue.put(step)
         self.steps_queue.put(None)
 
-    def collect_continuous(self, run) -> None:
+    def collect_continuous(self, run: Run) -> None:
         """Collect a series of scans at angles/exposure specified in `run`"""
         self.msg('Collecting scans from {} to {} degree'.format(*run.scope))
         images, metas = [], []
         if run.has_beam_delta_information:
             run.calculate_beamshifts(self.ctrl, self.beamshift)
-
-        # this part correctly finds the closest possible speed settings for expt
-        detector_dead_time = self.get_dead_time(run.exposure)
-        time_for_one_frame = run.exposure + detector_dead_time
-        rot_calib = self.get_stage_rotation()
-        rot_plan = rot_calib.plan_rotation(time_for_one_frame / run.osc_angle)
-        run.exposure = abs(rot_plan.pace * run.osc_angle) - detector_dead_time
+        rot_speed, run.exposure = self.determine_rotation_speed_and_exposure(run)
 
         self.ctrl.stage.a = float(run.table.loc[0, 'alpha'])
-        with self.ctrl.stage.rotation_speed(speed=rot_plan.speed):
+        with self.ctrl.stage.rotation_speed(speed=rot_speed):
             with self.ctrl.beam.unblanked(delay=0.2):
                 movie = self.ctrl.get_movie(n_frames=len(run.table) - 1, exposure=run.exposure)
                 a = float(run.table.iloc[-1].loc['alpha'])
-                self.ctrl.stage.set_with_speed(a=a, speed=rot_plan.speed, wait=False)
+                self.ctrl.stage.set_with_speed(a=a, speed=rot_speed, wait=False)
                 for step, (image, header) in zip(run.steps, movie):
                     if run.has_beam_delta_information:
                         self.ctrl.beamshift.set(step.beamshift_x, step.beamshift_y)
@@ -415,6 +409,15 @@ def collect_continuous(self, run) -> None:
             self.run.table['meta'] = metas
         self.msg('Collected scans from {} to {} degree'.format(*run.scope))
 
+    def determine_rotation_speed_and_exposure(self, run: Run) -> tuple[float, float]:
+        """Closest possible speed setting & exposure considering dead time."""
+        detector_dead_time = self.get_dead_time(run.exposure)
+        time_for_one_frame = run.exposure + detector_dead_time
+        rot_calib = self.get_stage_rotation()
+        rot_plan = rot_calib.plan_rotation(time_for_one_frame / run.osc_angle)
+        exposure = abs(rot_plan.pace * run.osc_angle) - detector_dead_time
+        return rot_plan.speed, exposure
+
     def finalize(self) -> None:
         self.msg(f'Saving experiment in: {self.path}')
         rotation_axis = config.camera.camera_rotation_vs_stage_xy