Generalize get_binning and fix low-hanging mypy issues (#110)

* All configs have `default_binning` so define `get_binning` in `CameraBase`

* Fix 15 low-hanging mypy warning, mostly `(int, int)` -> `Tuple[int, int]`

* Avoid an expensive microscope call if possible

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

* Remove `CameraGatan2.get_binning` override of `CameraBase`

---------

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

Author: Baharis

src/instamatic/camera/camera_base.py

@@ -1,9 +1,9 @@
 from __future__ import annotations
 
 from abc import ABC, abstractmethod
-from typing import List, Tuple
+from typing import List, Optional, Tuple
 
-from numpy import ndarray
+import numpy as np
 
 from instamatic import config
 
@@ -37,33 +37,45 @@ def release_connection(self):
         pass
 
     @abstractmethod
-    def get_image(self, exposure: float = None, binsize: int = None, **kwargs) -> ndarray:
+    def get_image(
+        self,
+        exposure: Optional[float] = None,
+        binsize: Optional[int] = None,
+        **kwargs,
+    ) -> np.ndarray:
         pass
 
     def get_movie(
-        self, n_frames: int, exposure: float = None, binsize: int = None, **kwargs
-    ) -> List[ndarray]:
+        self,
+        n_frames: int,
+        exposure: Optional[float] = None,
+        binsize: Optional[int] = None,
+        **kwargs,
+    ) -> List[np.ndarray]:
         """Basic implementation, subclasses should override with appropriate
         optimization."""
         return [
             self.get_image(exposure=exposure, binsize=binsize, **kwargs)
             for _ in range(n_frames)
         ]
 
-    def __enter__(self):
+    def __enter__(self) -> CameraBase:
         self.establish_connection()
         return self
 
-    def __exit__(self, kind, value, traceback):
+    def __exit__(self, kind, value, traceback) -> None:
         self.release_connection()
 
+    def get_binning(self) -> int:
+        return self.default_binsize
+
     def get_camera_dimensions(self) -> Tuple[int, int]:
         return self.dimensions
 
     def get_name(self) -> str:
         return self.name
 
-    def load_defaults(self):
+    def load_defaults(self) -> None:
         if self.name != config.settings.camera:
             config.load_camera_config(camera_name=self.name)
         for key, val in config.camera.mapping.items():

src/instamatic/camera/camera_client.py

@@ -5,6 +5,7 @@
 import subprocess as sp
 import time
 from functools import wraps
+from typing import Dict
 
 import numpy as np
 
@@ -79,7 +80,7 @@ def __init__(
         )
         print('Use shared memory:', self.use_shared_memory)
 
-        self.buffers = {}
+        self.buffers: Dict[str, np.ndarray] = {}
         self.shms = {}
 
         self._init_dict()

src/instamatic/camera/camera_emmenu.py

@@ -4,6 +4,7 @@
 import logging
 import time
 from pathlib import Path
+from typing import Tuple
 
 import comtypes.client
 import numpy as np
@@ -347,19 +348,19 @@ def get_image_data_by_index(self, img_index: int, drc_index: int = None) -> 'np.
 
         return np.array(arr)
 
-    def get_camera_dimensions(self) -> (int, int):
+    def get_camera_dimensions(self) -> Tuple[int, int]:
         """Get the maximum dimensions reported by the camera."""
         # cfg = self.get_current_config()
         # return cfg.DimensionX, cfg.DimensionY
         return self._cam.RealSizeX, self._cam.RealSizeY
         # return self._cam.MaximumSizeX, self._cam.MaximumSizeY
 
-    def get_image_dimensions(self) -> (int, int):
+    def get_image_dimensions(self) -> Tuple[int, int]:
         """Get the dimensions of the image."""
         binning = self.get_binning()
         return int(self._cam.RealSizeX / binning), int(self._cam.RealSizeY / binning)
 
-    def get_physical_pixelsize(self) -> (int, int):
+    def get_physical_pixelsize(self) -> Tuple[int, int]:
         """Returns the physical pixel size of the camera nanometers."""
         return self._cam.PixelSizeX, self._cam.PixelSizeY
 

src/instamatic/camera/camera_gatan.py

@@ -18,6 +18,7 @@
     create_unicode_buffer,
 )
 from pathlib import Path
+from typing import Tuple
 
 import numpy as np
 
@@ -214,7 +215,7 @@ def is_camera_info_available(self) -> bool:
         """Return the status of the camera."""
         return self._isCameraInfoAvailable()
 
-    def get_camera_dimensions(self) -> (int, int):
+    def get_camera_dimensions(self) -> Tuple[int, int]:
         """Return the dimensions reported by the camera."""
         pnWidth = c_int(0)
         pnHeight = c_int(0)

src/instamatic/camera/camera_gatan2.py

@@ -5,6 +5,7 @@
 import sys
 import time
 from pathlib import Path
+from typing import Tuple
 
 import numpy as np
 
@@ -44,21 +45,16 @@ def get_dm_version(self) -> str:
         """Get the version number of DM."""
         return self.g.GetDMVersion()
 
-    def get_image_dimensions(self) -> (int, int):
+    def get_image_dimensions(self) -> Tuple[int, int]:
         """Get the dimensions of the image."""
         binning = self.get_binning()
         dim_x, dim_y = self.get_camera_dimensions()
         return int(dim_x / binning), int(dim_y / binning)
 
-    def get_physical_pixelsize(self) -> (int, int):
+    def get_physical_pixelsize(self) -> Tuple[int, int]:
         """Returns the physical pixel size of the camera nanometers."""
         raise NotImplementedError
 
-    def get_binning(self) -> int:
-        """Returns the binning corresponding to the currently selected camera
-        config."""
-        raise NotImplementedError
-
     def get_camera_name(self) -> str:
         """Get the name reported by the camera."""
         return self.name

src/instamatic/camera/camera_merlin.py

@@ -29,7 +29,7 @@
 import logging
 import socket
 import time
-from typing import Any, List
+from typing import Any, List, Tuple
 
 import numpy as np
 
@@ -337,7 +337,7 @@ def get_movie(self, n_frames: int, exposure: float = None, **kwargs) -> List[np.
 
         return data
 
-    def get_image_dimensions(self) -> (int, int):
+    def get_image_dimensions(self) -> Tuple[int, int]:
         """Get the binned dimensions reported by the camera."""
         binning = self.get_binning()
         dim_x, dim_y = self.get_camera_dimensions()

src/instamatic/camera/camera_serval.py

@@ -3,6 +3,7 @@
 import atexit
 import logging
 from pathlib import Path
+from typing import Tuple
 
 import numpy as np
 from serval_toolkit.camera import Camera as ServalCamera
@@ -92,7 +93,7 @@ def get_movie(self, n_frames, exposure=None, binsize=None, **kwargs):
 
         return arr
 
-    def get_image_dimensions(self) -> (int, int):
+    def get_image_dimensions(self) -> Tuple[int, int]:
         """Get the binned dimensions reported by the camera."""
         binning = self.get_binning()
         dim_x, dim_y = self.get_camera_dimensions()

src/instamatic/camera/camera_simu.py

@@ -3,6 +3,7 @@
 import atexit
 import logging
 import time
+from typing import List, Optional, Tuple
 
 import numpy as np
 
@@ -66,7 +67,14 @@ def get_image(self, exposure=None, binsize=None, **kwargs) -> np.ndarray:
 
         return arr
 
-    def get_movie(self, n_frames, *, exposure: float = None, binsize: int = None, **kwargs):
+    def get_movie(
+        self,
+        n_frames: int,
+        *,
+        exposure: Optional[float] = None,
+        binsize: Optional[int] = None,
+        **kwargs,
+    ) -> List[np.ndarray]:
         """Movie acquisition routine. If the exposure and binsize are not
         given, the default values are read from the config file.
 
@@ -93,7 +101,7 @@ def is_camera_info_available(self) -> bool:
         """Check if the camera is available."""
         return True
 
-    def get_image_dimensions(self) -> (int, int):
+    def get_image_dimensions(self) -> Tuple[int, int]:
         """Get the binned dimensions reported by the camera."""
         binning = self.get_binning()
         dim_x, dim_y = self.get_camera_dimensions()
@@ -170,9 +178,6 @@ def get_exposure(self) -> int:
     def get_timestamps(self, start_index, end_index):
         return list(range(20))
 
-    def get_binning(self):
-        return self.default_binsize
-
     def write_tiffs(
         self, start_index: int, stop_index: int, path: str, clear_buffer=True
     ) -> None:

src/instamatic/microscope/components/stage.py

@@ -283,6 +283,10 @@ def set_xy_with_backlash_correction(
             delay between movements in seconds to allow the stage to settle
         """
         wait = True
+        if (x is None) or (y is None):
+            current_x, current_y = self.xy
+            x = current_x if x is None else x
+            y = current_y if y is None else y
         self.set(x=x - step, y=y - step)
         if settle_delay:
             time.sleep(settle_delay)

src/instamatic/microscope/microscope.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from typing import Optional
+
 from instamatic import config
 from instamatic.microscope.base import MicroscopeBase
 
@@ -32,7 +34,7 @@ def get_microscope_class(interface: str) -> 'type[MicroscopeBase]':
     return cls
 
 
-def get_microscope(name: str = None, use_server: bool = False) -> MicroscopeBase:
+def get_microscope(name: Optional[str] = None, use_server: bool = False) -> MicroscopeBase:
     """Generic class to load microscope interface class.
 
     name: str