Fix PR111 and RED frame bugs (#114)

* Move `instamatic.typing` to `typing_` to avoid import conflicts

* `MediaGrabber`: fix bug: `get_media` cleared `continuousCollectionEvent`

* Fix RED frame logging

* `instamatic.typing_`: rename to `_typing`

Author: Baharis

src/instamatic/typing.py src/instamatic/_typing.pysrc/instamatic/typing.py renamed to src/instamatic/_typing.py

@@ -2,6 +2,7 @@
 
 import atexit
 import threading
+from contextlib import contextmanager
 from dataclasses import dataclass
 from typing import List, Optional, Union
 
@@ -162,16 +163,15 @@ def get_movie(self, n_frames: int, exposure=None, binsize=None):
         return self._get_media(request)
 
     def _get_media(self, request: MediaRequest) -> Union[np.ndarray, List[np.ndarray]]:
-        self.block()  # Stop the passive collection during request acquisition
-        self.grabber.request = request
-        self.grabber.acquireInitiateEvent.set()
-        self.grabber.acquireCompleteEvent.wait()
-        with self.grabber.lock:
-            media = self.requested_media
-            self.requested_media = None
-        self.grabber.request = None
-        self.grabber.acquireCompleteEvent.clear()
-        self.unblock()  # Resume the passive collection
+        with self.blocked():  # Stop the passive collection during request acquisition
+            self.grabber.request = request
+            self.grabber.acquireInitiateEvent.set()
+            self.grabber.acquireCompleteEvent.wait()
+            with self.grabber.lock:
+                media = self.requested_media
+                self.requested_media = None
+            self.grabber.request = None
+            self.grabber.acquireCompleteEvent.clear()
         return media
 
     def update_frametime(self, frametime):
@@ -187,6 +187,15 @@ def block(self):
     def unblock(self):
         self.grabber.continuousCollectionEvent.clear()
 
+    @contextmanager
+    def blocked(self):
+        """Set `continuousCollectionEvent` within the statement scope only."""
+        was_set_before = self.grabber.continuousCollectionEvent.is_set()
+        self.grabber.continuousCollectionEvent.set()
+        yield
+        if not was_set_before:
+            self.grabber.continuousCollectionEvent.clear()
+
     def continuous_collection(self, exposure=0.1, n=100, callback=None):
         """Function to continuously collect data Blocks the videostream while
         collecting data, and only shows collected images.

src/instamatic/camera/videostream.py

@@ -129,7 +129,7 @@ def start_collection(self, exposure_time: float, tilt_range: float, stepsize: fl
             )
 
         self.logger.info(
-            'Data collected from {start_angle:.2f} degree to {end_angle:.2f} degree (camera length: {camera_length} mm).'
+            f'Data collected from {start_angle:.2f} degree to {end_angle:.2f} degree (camera length: {self.camera_length} mm).'
         )
 
         self.current_angle = angle

src/instamatic/experiments/red/experiment.py

@@ -139,10 +139,10 @@ def get_params(self, task=None):
 
 
 def acquire_data_RED(controller, **kwargs):
-    controller.log.info('Start RED experiment')
     from instamatic.experiments import RED
 
     task = kwargs['task']
+    controller.log.info(task.title() + ' RED experiment')
 
     exposure_time = kwargs['exposure_time']
     tilt_range = kwargs['tilt_range']

src/instamatic/gui/red_frame.py

@@ -3,8 +3,8 @@
 from abc import ABC, abstractmethod
 from typing import Optional, Tuple
 
+from instamatic._typing import float_deg, int_nm
 from instamatic.microscope.utils import StagePositionTuple
-from instamatic.typing import float_deg, int_nm
 
 
 class MicroscopeBase(ABC):

src/instamatic/microscope/base.py

@@ -6,9 +6,9 @@
 
 import numpy as np
 
+from instamatic._typing import float_deg, int_nm
 from instamatic.microscope.base import MicroscopeBase
 from instamatic.microscope.utils import StagePositionTuple
-from instamatic.typing import float_deg, int_nm
 
 
 class Stage:

src/instamatic/microscope/components/stage.py

@@ -9,10 +9,10 @@
 from numpy import pi
 
 from instamatic import config
+from instamatic._typing import float_deg, int_nm
 from instamatic.exceptions import FEIValueError, TEMCommunicationError
 from instamatic.microscope.base import MicroscopeBase
 from instamatic.microscope.utils import StagePositionTuple
-from instamatic.typing import float_deg, int_nm
 
 logger = logging.getLogger(__name__)
 

src/instamatic/microscope/interface/fei_microscope.py

@@ -9,10 +9,10 @@
 import comtypes.client
 
 from instamatic import config
+from instamatic._typing import float_deg, int_nm
 from instamatic.exceptions import FEIValueError, TEMCommunicationError
 from instamatic.microscope.base import MicroscopeBase
 from instamatic.microscope.utils import StagePositionTuple
-from instamatic.typing import float_deg, int_nm
 
 logger = logging.getLogger(__name__)
 

src/instamatic/microscope/interface/fei_simu_microscope.py

@@ -8,10 +8,10 @@
 import comtypes.client
 
 from instamatic import config
+from instamatic._typing import float_deg, int_nm
 from instamatic.exceptions import JEOLValueError, TEMCommunicationError, TEMValueError
 from instamatic.microscope.base import MicroscopeBase
 from instamatic.microscope.utils import StagePositionTuple
-from instamatic.typing import float_deg, int_nm
 
 logger = logging.getLogger(__name__)
 

src/instamatic/microscope/interface/jeol_microscope.py

@@ -5,10 +5,10 @@
 from typing import Optional, Tuple
 
 from instamatic import config
+from instamatic._typing import float_deg, int_nm
 from instamatic.exceptions import TEMValueError
 from instamatic.microscope.base import MicroscopeBase
 from instamatic.microscope.utils import StagePositionTuple
-from instamatic.typing import float_deg, int_nm
 
 NTRLMAPPING = {
     'GUN1': 0,