Add inheritance (#91)

* Add simple experiment base class

* Use pytest's `tmp_path` for IO testing

* Refactor format tests

* Properly separate read/write tests

* Add context manager for experiments

* Refactor experiment tests

* Microscope base class

* Sort alphabethically

* Use microscope base class; add type hints

* Base camera class proposal

* Add mock cameras for testing

* Run ruff

* Use the camera base class

* Add rudimentary camera tests

* Add type hints

* PR feedback; 3.7 compatibility

* Run pre-commit

Author: viljarjf

src/instamatic/TEMController/TEMController.py

@@ -1,15 +1,17 @@
 import time
 from collections import namedtuple
 from concurrent.futures import ThreadPoolExecutor
-from typing import Tuple
+from typing import Optional, Tuple
 
 import numpy as np
 
 from instamatic import config
 from instamatic.camera import Camera
+from instamatic.camera.camera_base import CameraBase
 from instamatic.exceptions import TEMControllerError
 from instamatic.formats import write_tiff
 from instamatic.image_utils import rotate_image
+from instamatic.TEMController.microscope_base import MicroscopeBase
 
 from .deflectors import *
 from .lenses import *
@@ -89,7 +91,7 @@ class TEMController:
     cam: Camera control object (see instamatic.camera) [optional]
     """
 
-    def __init__(self, tem, cam=None):
+    def __init__(self, tem: MicroscopeBase, cam: Optional[CameraBase] = None):
         super().__init__()
 
         self._executor = ThreadPoolExecutor(max_workers=1)
@@ -122,7 +124,7 @@ def __init__(self, tem, cam=None):
 
     def __repr__(self):
         return (f'Mode: {self.tem.getFunctionMode()}\n'
-                f'High tension: {self.high_tension/1000:.0f} kV\n'
+                f'High tension: {self.high_tension / 1000:.0f} kV\n'
                 f'Current density: {self.current_density:.2f} pA/cm2\n'
                 f'{self.gunshift}\n'
                 f'{self.guntilt}\n'
@@ -244,7 +246,7 @@ def run_script(self, script: str, verbose: bool = True) -> None:
         t1 = time.perf_counter()
 
         if verbose:
-            print(f'\nScript finished in {t1-t0:.4f} s')
+            print(f'\nScript finished in {t1 - t0:.4f} s')
 
     def get_stagematrix(self, binning: int = None, mag: int = None, mode: int = None):
         """Helper function to get the stage matrix from the config file. The

src/instamatic/TEMController/fei_microscope.py

@@ -7,6 +7,7 @@
 
 from instamatic import config
 from instamatic.exceptions import FEIValueError, TEMCommunicationError
+from instamatic.TEMController.microscope_base import MicroscopeBase
 
 logger = logging.getLogger(__name__)
 
@@ -45,7 +46,7 @@ def get_camera_length_mapping():
 CameraLengthMapping = get_camera_length_mapping()
 
 
-class FEIMicroscope:
+class FEIMicroscope(MicroscopeBase):
     """Python bindings to the FEI microscope using the COM interface."""
 
     def __init__(self, name='fei'):

src/instamatic/TEMController/fei_simu_microscope.py

@@ -7,6 +7,7 @@
 
 from instamatic import config
 from instamatic.exceptions import FEIValueError, TEMCommunicationError
+from instamatic.TEMController.microscope_base import MicroscopeBase
 
 logger = logging.getLogger(__name__)
 
@@ -17,7 +18,7 @@
 MAX = 1.0
 
 
-class FEISimuMicroscope:
+class FEISimuMicroscope(MicroscopeBase):
     """Python bindings to the FEI simulated microscope using the COM
     interface."""
 

src/instamatic/TEMController/jeol_microscope.py

@@ -7,6 +7,7 @@
 
 from instamatic import config
 from instamatic.exceptions import JEOLValueError, TEMCommunicationError, TEMValueError
+from instamatic.TEMController.microscope_base import MicroscopeBase
 
 logger = logging.getLogger(__name__)
 
@@ -45,7 +46,7 @@
 # Piezo stage seems to operate on a different level than standard XY
 
 
-class JeolMicroscope:
+class JeolMicroscope(MicroscopeBase):
     """Python bindings to the JEOL microscope using the COM interface."""
 
     def __init__(self, name: str = 'jeol'):

src/instamatic/TEMController/microscope.py

@@ -1,11 +1,12 @@
 from instamatic import config
+from instamatic.TEMController.microscope_base import MicroscopeBase
 
 default_tem_interface = config.microscope.interface
 
 __all__ = ['Microscope', 'get_tem']
 
 
-def get_tem(interface: str):
+def get_tem(interface: str) -> 'type[MicroscopeBase]':
     """Grab tem class with the specific 'interface'."""
     simulate = config.settings.simulate
 
@@ -28,7 +29,7 @@ def get_tem(interface: str):
     return cls
 
 
-def Microscope(name: str = None, use_server: bool = False):
+def Microscope(name: str = None, use_server: bool = False) -> MicroscopeBase:
     """Generic class to load microscope interface class.
 
     name: str

src/instamatic/TEMController/microscope_base.py

@@ -0,0 +1,176 @@
+from abc import ABC, abstractmethod
+from typing import Tuple
+
+
+class MicroscopeBase(ABC):
+    @abstractmethod
+    def getBeamShift(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getBeamTilt(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getBrightness(self) -> int:
+        pass
+
+    @abstractmethod
+    def getCondensorLensStigmator(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getCurrentDensity(self) -> float:
+        pass
+
+    @abstractmethod
+    def getDiffFocus(self, confirm_mode: bool) -> int:
+        pass
+
+    @abstractmethod
+    def getDiffShift(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getFunctionMode(self) -> str:
+        pass
+
+    @abstractmethod
+    def getGunShift(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getGunTilt(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getHTValue(self) -> float:
+        pass
+
+    @abstractmethod
+    def getImageShift1(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getImageShift2(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getIntermediateLensStigmator(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getMagnification(self) -> int:
+        pass
+
+    @abstractmethod
+    def getMagnificationAbsoluteIndex(self) -> int:
+        pass
+
+    @abstractmethod
+    def getMagnificationIndex(self) -> int:
+        pass
+
+    @abstractmethod
+    def getMagnificationRanges(self) -> dict:
+        pass
+
+    @abstractmethod
+    def getObjectiveLensStigmator(self) -> Tuple[int, int]:
+        pass
+
+    @abstractmethod
+    def getSpotSize(self) -> int:
+        pass
+
+    @abstractmethod
+    def getStagePosition(self) -> Tuple[int, int, int, int, int]:
+        pass
+
+    @abstractmethod
+    def isBeamBlanked(self) -> bool:
+        pass
+
+    @abstractmethod
+    def isStageMoving(self) -> bool:
+        pass
+
+    @abstractmethod
+    def release_connection(self) -> None:
+        pass
+
+    @abstractmethod
+    def setBeamBlank(self, mode: bool) -> None:
+        pass
+
+    @abstractmethod
+    def setBeamShift(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setBeamTilt(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setBrightness(self, value: int) -> None:
+        pass
+
+    @abstractmethod
+    def setCondensorLensStigmator(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setDiffFocus(self, value: int, confirm_mode: bool) -> None:
+        pass
+
+    @abstractmethod
+    def setDiffShift(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setFunctionMode(self, value: int) -> None:
+        pass
+
+    @abstractmethod
+    def setGunShift(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setGunTilt(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setImageShift1(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setImageShift2(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setIntermediateLensStigmator(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setMagnification(self, value: int) -> None:
+        pass
+
+    @abstractmethod
+    def setMagnificationIndex(self, index: int) -> None:
+        pass
+
+    @abstractmethod
+    def setObjectiveLensStigmator(self, x: int, y: int) -> None:
+        pass
+
+    @abstractmethod
+    def setSpotSize(self, value: int) -> None:
+        pass
+
+    @abstractmethod
+    def setStagePosition(self, x: int, y: int, z: int, a: int, b: int, wait: bool) -> None:
+        pass
+
+    @abstractmethod
+    def stopStage(self) -> None:
+        pass

src/instamatic/TEMController/simu_microscope.py

@@ -4,6 +4,7 @@
 
 from instamatic import config
 from instamatic.exceptions import TEMValueError
+from instamatic.TEMController.microscope_base import MicroscopeBase
 
 NTRLMAPPING = {
     'GUN1': 0,
@@ -30,7 +31,7 @@
 MIN = 0
 
 
-class SimuMicroscope:
+class SimuMicroscope(MicroscopeBase):
     """Simulates a microscope connection.
 
     Has the same variables as the real JEOL/FEI equivalents, but does

src/instamatic/camera/camera.py

@@ -24,7 +24,7 @@ def get_cam(interface: str = None):
     elif interface == 'gatansocket':
         from instamatic.camera.camera_gatan2 import CameraGatan2 as cam
     elif interface in ('timepix', 'pytimepix'):
-        from instamatic.camera import camera_timepix as cam
+        from instamatic.camera.camera_timepix import CameraTPX as cam
     elif interface in ('emmenu', 'tvips'):
         from instamatic.camera.camera_emmenu import CameraEMMENU as cam
     elif interface == 'serval':

src/instamatic/camera/camera_base.py

@@ -0,0 +1,71 @@
+from abc import ABC, abstractmethod
+from typing import List, Tuple
+
+from numpy import ndarray
+
+from instamatic import config
+
+
+class CameraBase(ABC):
+
+    # Set manually
+    name: str
+    streamable: bool
+
+    # Set by `load_defaults`
+    camera_rotation_vs_stage_xy: float
+    default_binsize: int
+    default_exposure: float
+    dimensions: Tuple[int, int]
+    interface: str
+    possible_binsizes: List[int]
+    stretch_amplitude: float
+    stretch_azimuth: float
+
+    @abstractmethod
+    def __init__(self, name: str):
+        self.name = name
+        self.load_defaults()
+
+    @abstractmethod
+    def establish_connection(self):
+        pass
+
+    @abstractmethod
+    def release_connection(self):
+        pass
+
+    @abstractmethod
+    def get_image(
+        self, exposure: float = None, binsize: int = None, **kwargs
+    ) -> ndarray:
+        pass
+
+    def get_movie(
+        self, n_frames: int, exposure: float = None, binsize: int = None, **kwargs
+    ) -> List[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):
+        self.establish_connection()
+        return self
+
+    def __exit__(self, kind, value, traceback):
+        self.release_connection()
+
+    def get_camera_dimensions(self) -> Tuple[int, int]:
+        return self.dimensions
+
+    def get_name(self) -> str:
+        return self.name
+
+    def load_defaults(self):
+        if self.name != config.settings.camera:
+            config.load_camera_config(camera_name=self.name)
+        for key, val in config.camera.mapping.items():
+            setattr(self, key, val)