Implement SimuMicroscope stage speed and generalize motion calibration

src/instamatic/calibrate/calibrate_stage_motion.py

@@ -183,7 +183,7 @@ def plot(self, sst: Optional[Sequence[SpanSpeedTime]] = None) -> None:
                 spans = [s.span for s in sst if s.speed == speed]
                 times = [s.time for s in sst if s.speed == speed]
                 ax.plot(spans, times, fmt, color=color)
-            label = f'Speed setting {speed:.2f}'
+            label = f'Speed setting {speed:.2f}' if speed else 'Default speed'
             handles.append(Line2D([], [], color=color, marker='o', label=label))
 
         ax.set_xlabel(f'Motion span [{self._span_units}]')

src/instamatic/calibrate/calibrate_stage_rotation.py

@@ -2,6 +2,7 @@
 
 import argparse
 import logging
+from contextlib import nullcontext
 from dataclasses import dataclass
 from textwrap import dedent
 from time import perf_counter
@@ -71,7 +72,8 @@ def calibrate_stage_rotation_live(
     spans: `Optional[Sequence[float]]`
         Alpha rotations whose speed will be measured. Default: range(1, 11, 1).
     speeds: `Optional[Sequence[Union[float, int]]]`
-        Spead range to measure. Default: range(1, 13, 1) or range(.1, 1.1, .1).
+        Spead range to measure. Default: range(1, 13, 1) or range(.1, 1.1, .1),
+        or [None, None, None], 3 runs without setting speed if it's not possible
     mode: `Literal['auto', 'limited', 'listed']`
         Determines the way speed settings restrictions are set in calib file.
     outdir: `str` or None
@@ -91,6 +93,10 @@ def calibrate_stage_rotation_live(
     except AssertionError:  # or any other raised if speed can't be set
         speeds_default = np.linspace(0.01, 0.2, num=20)
         speed_options = FEI_ROTATION_SPEED_OPTIONS
+    except (AttributeError, ConnectionError, TypeError):
+        log('TEM does not support setting with speed, assuming default = 1.')
+        speeds_default: Sequence[Speed] = [None, None, None]  # no translation w/ speed
+        speed_options = None
     else:
         speeds_default = np.arange(1, 13, step=1)
         speed_options = JEOL_ROTATION_SPEED_OPTIONS
@@ -101,16 +107,20 @@ def calibrate_stage_rotation_live(
     elif mode == 'listed':
         speed_options = NumericDomain(options=sorted(speeds_))
 
+    try:
+        starting_stage_speed = ctrl.stage.get_rotation_speed()
+    except (AttributeError, ConnectionError, TypeError):
+        starting_stage_speed = None
+
     calib_points: list[SpanSpeedTime] = []
     starting_stage_alpha = ctrl.stage.a
-    starting_stage_speed = ctrl.stage.get_rotation_speed()
     ctrl.cam.block()
     try:
         n_calib_points = len(speeds_) * len(spans_array)
         log(f'Calibrating a-axis rotation speed based on {n_calib_points} points.')
         with tqdm(total=n_calib_points) as progress_bar:
             for speed in speeds_:
-                with ctrl.stage.rotation_speed(speed=float(speed)):
+                with ctrl.stage.rotation_speed(float(speed)) if speed else nullcontext():
                     ctrl.stage.a = 0.0
                     for target, span in zip(alpha_targets, spans_array):
                         t1 = perf_counter()
@@ -120,7 +130,8 @@ def calibrate_stage_rotation_live(
                         progress_bar.update(1)
     finally:
         ctrl.stage.set(a=starting_stage_alpha)
-        ctrl.stage.set_rotation_speed(starting_stage_speed)
+        if starting_stage_speed is not None:
+            ctrl.stage.set_rotation_speed(starting_stage_speed)
         ctrl.cam.unblock()
 
     c = CalibStageRotation.from_data(calib_points)
@@ -149,7 +160,8 @@ def main_entry() -> None:
 
     h = """Comma-delimited list of speed settings to calibrate for.
     Default: "0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0" or
-    "1 2 3 4 5 6 7 8 9 10 11 12", whichever is accepted by the microscope."""
+    "1 2 3 4 5 6 7 8 9 10 11 12", whichever is accepted by the microscope. "-s"
+    with no values forces 3 rounds using "set" instead of "set_with_speed"."""
     h = dedent(h.strip())
     parser.add_argument('-s', '--speeds', type=float, default=None, nargs='*', help=h)
 
@@ -169,8 +181,11 @@ def main_entry() -> None:
     parser.add_argument('--plot', action=argparse.BooleanOptionalAction, default=True, help=h)
 
     kwargs = vars(parser.parse_args())
-    if kwargs['speeds'] is not None and all(v.is_integer() for v in kwargs['speeds']):
-        kwargs['speeds'] = [int(v) for v in kwargs['speeds']]
+    if kwargs['speeds'] is not None:
+        if all(v.is_integer() for v in kwargs['speeds']):
+            kwargs['speeds'] = [int(v) for v in kwargs['speeds']]
+        if not kwargs['speeds']:
+            kwargs['speeds'] = [None, None, None]
 
     from instamatic import controller
 

src/instamatic/calibrate/calibrate_stage_translation.py

@@ -99,7 +99,8 @@ def calibrate_stage_translation_live(
     spans: `Optional[Sequence[float]]`
         Translations that will be timed. Default: 10_000 to 100_000 every 10_000
     speeds: `Optional[Sequence[Union[float, int]]]`
-        All speed settings used for calibration. Default: 0.1 to 1.0 every 0.1.
+        All speed settings used for calibration. Default: 0.1 to 1.0 every 0.1,
+        or [None, None, None], 3 runs without setting speed if it's not possible
     axis: `Literal['x', 'y', 'z']`
         Axis the speed of which is to be calibrated. Default: 'x'.
     mode: `Literal['auto', 'limited', 'listed']`
@@ -118,7 +119,7 @@ def calibrate_stage_translation_live(
     stage0: StagePositionTuple = ctrl.stage.get()
     try:
         ctrl.stage.set_with_speed(*stage0)
-    except KeyError:
+    except TypeError:
         log('TEM does not support setting with speed, assuming default = 1.')
         speeds_default: Sequence[Speed] = [None, None, None]  # no translation w/ speed
         speed_options = None
@@ -180,8 +181,9 @@ def main_entry() -> None:
     h += 'Default: "10000 20000 30000 40000 50000 60000 70000 80000 90000 100000".'
     parser.add_argument('-x', '--spans', type=int, default=None, nargs='*', help=h)
 
-    h = 'Comma-delimited list of speed settings to calibrate for.'
-    h += 'Default: "0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0".'
+    h = 'Comma-delimited list of speed settings to calibrate for. '
+    h += 'Default: "0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0". '
+    h += '"-s" with no values forces 3 rounds using "set" instead of "set_with_speed".'
     parser.add_argument('-s', '--speeds', type=float, default=None, nargs='*', help=h)
 
     h = 'Axis whose translation speed should be calibrated, x, y, or z. Default: x'
@@ -204,8 +206,11 @@ def main_entry() -> None:
     parser.add_argument('--plot', action=argparse.BooleanOptionalAction, default=True, help=h)
 
     kwargs = vars(parser.parse_args())
-    if kwargs['speeds'] is not None and all(v.is_integer() for v in kwargs['speeds']):
-        kwargs['speeds'] = [int(v) for v in kwargs['speeds']]
+    if kwargs['speeds'] is not None:
+        if all(v.is_integer() for v in kwargs['speeds']):
+            kwargs['speeds'] = [int(v) for v in kwargs['speeds']]
+        if not kwargs['speeds']:
+            kwargs['speeds'] = [None, None, None]
 
     from instamatic import controller
 

src/instamatic/camera/camera_client.py

@@ -127,7 +127,7 @@ def _eval_dct(self, dct):
         with self._eval_lock:
             self.s.send(dumper(dct))
 
-            acquiring_image = dct['attr_name'] in {'get_image', 'get_movie', '__gen_next__'}
+            acquiring_image = dct['attr_name'] in {'get_image', '__gen_next__'}
 
             if acquiring_image and not self.use_shared_memory:
                 response = self.s.recv(self._imagebufsize)
@@ -139,7 +139,7 @@ def _eval_dct(self, dct):
             else:
                 raise RuntimeError(f'Received empty response when evaluating {dct=}')
 
-            if self.use_shared_memory and acquiring_image:
+            if self.use_shared_memory and acquiring_image and data:
                 data = self.get_data_from_shared_memory(**data)
 
             if status == 200:
@@ -196,7 +196,7 @@ def get_data_from_shared_memory(self, name: str, shape: tuple, dtype: str, **kwa
             print(f'Retrieve data from buffer `{name}`')
 
         buffer = self.buffers[name]
-        data = buffer[:]
+        data = buffer[:].copy()
 
         return data
 

src/instamatic/microscope/interface/simu_microscope.py

@@ -2,7 +2,8 @@
 
 import random
 import time
-from typing import Optional, Tuple
+from contextlib import contextmanager, nullcontext
+from typing import Literal, Optional, Tuple
 
 from instamatic import config
 from instamatic._typing import float_deg, int_nm
@@ -126,7 +127,7 @@ def __init__(self, name: str = 'simulate'):
                 speed = 20.0  # degree / sec
                 current = random.randint(-40, 40)
             elif key in ('x', 'y'):
-                speed = 1_000_000.0  # nm / sec
+                speed = 100_000.0  # nm / sec
                 current = random.randint(-100000, 100000)
             elif key == 'z':
                 speed = 100_000.0  # nm / sec
@@ -199,6 +200,19 @@ def _StagePositionGetter(self, var: str) -> float:
 
         return ret
 
+    @contextmanager
+    def _speed_setting(self, key: Literal['a', 'b', 'x', 'y', 'z'], value: int):
+        previous_setting = self._stage_dict[key]['speed_setting']
+        previous_speed = self._stage_dict[key]['speed']
+        speed_base = {'x': 100_000, 'y': 100_000, 'z': 100_000, 'a': 20, 'b': 20}
+        try:
+            self._stage_dict[key]['speed_setting'] = value
+            self._stage_dict[key]['speed'] = speed_base[key] * value / 12
+            yield
+        finally:
+            self._stage_dict[key]['speed_setting'] = previous_setting
+            self._stage_dict[key]['speed'] = previous_speed
+
     @property
     def StagePosition_a(self):
         return self._StagePositionGetter('a')
@@ -438,26 +452,33 @@ def setStagePosition(
         wait: bool = True,
     ) -> None:
         if z is not None:
-            self.setStageZ(z, wait=wait)
+            with nullcontext() if speed is None else self._speed_setting('z', speed):
+                self.setStageZ(z, wait=wait)
         if a is not None:
-            self.setStageA(a, wait=wait)
+            with nullcontext() if speed is None else self._speed_setting('a', speed):
+                self.setStageA(a, wait=wait)
         if b is not None:
-            self.setStageB(b, wait=wait)
+            with nullcontext() if speed is None else self._speed_setting('b', speed):
+                self.setStageB(b, wait=wait)
 
         if (x is not None) and (y is not None):
-            self.setStageXY(x=x, y=y, wait=wait)
+            with nullcontext() if speed is None else self._speed_setting('x', speed):
+                with nullcontext() if speed is None else self._speed_setting('y', speed):
+                    self.setStageXY(x=x, y=y, wait=wait)
         else:
             if x is not None:
-                self.setStageX(x, wait=wait)
+                with nullcontext() if speed is None else self._speed_setting('x', speed):
+                    self.setStageX(x, wait=wait)
             if y is not None:
-                self.setStageY(y, wait=wait)
+                with nullcontext() if speed is None else self._speed_setting('y', speed):
+                    self.setStageY(y, wait=wait)
 
     def getRotationSpeed(self) -> int:
         return self._stage_dict['a']['speed_setting']
 
     def setRotationSpeed(self, value: int):
         self._stage_dict['a']['speed_setting'] = value
-        self._stage_dict['a']['speed'] = 10.0 * (value / 12)
+        self._stage_dict['a']['speed'] = 20.0 * (value / 12)
 
     def getFunctionMode(self) -> str:
         """Mag1, mag2, lowmag, samag, diff."""