Reorganize TEMController

src/instamatic/TEMController.py

@@ -0,0 +1,7 @@
+import warnings
+from instamatic.utils.deprecated import VisibleDeprecationWarning
+
+warnings.warn("The `TEMController` module is deprecated since version 2.0.6. Use the `controller`-module instead", VisibleDeprecationWarning)
+
+from instamatic.microscope import Microscope
+from instamatic.controller import get_instance, initialize

src/instamatic/calibrate/calibrate_beamshift.py

@@ -342,9 +342,9 @@ def main_entry():
     args = options.args
 
     if not args:
-        from instamatic import TEMController
+        from instamatic import controller
 
-        ctrl = TEMController.initialize()
+        ctrl = controller.initialize()
         calibrate_beamshift(ctrl=ctrl, save_images=True)
     else:
         center_fn = args[0]

src/instamatic/calibrate/calibrate_brightness.py

@@ -206,9 +206,9 @@ def main_entry():
     args = options.args
 
     if not args:
-        from instamatic import TEMController
+        from instamatic import controller
 
-        ctrl = TEMController.initialize()
+        ctrl = controller.initialize()
         calibrate_brightness(ctrl, save_images=True)
     else:
         calibrate_brightness(args)

src/instamatic/calibrate/calibrate_directbeam.py

@@ -393,9 +393,9 @@ def main_entry():
     if args:
         calibrate_directbeam(patterns=args)
     else:
-        from instamatic import TEMController
+        from instamatic import controller
 
-        ctrl = TEMController.initialize()
+        ctrl = controller.initialize()
         calibrate_directbeam(ctrl=ctrl)
 
 

src/instamatic/calibrate/calibrate_stage_lowmag.py

@@ -430,9 +430,9 @@ def main_entry():
     args = options.args
 
     if not args:
-        from instamatic import TEMController
+        from instamatic import controller
 
-        ctrl = TEMController.initialize()
+        ctrl = TEMtroller.initialize()
         calibrate_stage_lowmag(ctrl=ctrl, save_images=True)
     else:
         center_fn = args[0]

src/instamatic/calibrate/calibrate_stage_mag1.py

@@ -289,9 +289,9 @@ def main_entry():
     args = options.args
 
     if not args:
-        from instamatic import TEMController
+        from instamatic import controller
 
-        ctrl = TEMController.initialize()
+        ctrl = controller.initialize()
         calibrate_mag1(ctrl=ctrl, save_images=True)
     else:
         center_fn = args[0]

src/instamatic/calibrate/calibrate_stagematrix.py

@@ -528,9 +528,9 @@ def main_entry():
     mode = options.mode
     mags = options.mags
 
-    from instamatic import TEMController
+    from instamatic import controller
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     if not mode:
         mode = ctrl.mode.get()

src/instamatic/camera/camera.py

@@ -157,9 +157,9 @@ def main_entry():
 
     take_series = options.take_series
 
-    from instamatic import TEMController
+    from instamatic import controller
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     if take_series:
         i = 1

src/instamatic/config/autoconfig.py

@@ -126,15 +126,15 @@ def main():
         cam_name = None
 
     from instamatic.camera.camera import get_cam
-    from instamatic.TEMController.microscope import get_tem
-    from instamatic.TEMController.TEMController import TEMController
+    from instamatic.controller import TEMController
+    from instamatic.microscope.microscope import get_microscope_class
 
     if cam_connect:
         cam = get_cam(cam_name)() if cam_name else None
     else:
         cam = None
 
-    tem = get_tem(tem_name)()
+    tem = get_microscope_class(tem_name)()
 
     ctrl = TEMController(tem=tem, cam=cam)
 

src/instamatic/TEMController/TEMController.py → src/instamatic/controller.py

@@ -13,13 +13,9 @@
 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 *
-from .microscope import Microscope
-from .stage import *
-from .states import *
+from instamatic.microscope.base import MicroscopeBase
+from instamatic.microscope.components import *
+from instamatic.microscope.microscope import get_microscope
 
 _ctrl = None  # store reference of ctrl so it can be accessed without re-initializing
 
@@ -51,7 +47,7 @@ def initialize(
         Return TEM control object
     """
     print(f"Microscope: {tem_name}{' (server)' if use_tem_server else ''}")
-    tem = Microscope(tem_name, use_server=use_tem_server)
+    tem = get_microscope(tem_name, use_server=use_tem_server)
 
     if cam_name:
         if use_cam_server:

src/instamatic/experiments/cred_gatan/experiment.py

@@ -462,14 +462,14 @@ def log_stage_positions(self):
 
 
 if __name__ == '__main__':
-    from instamatic import TEMController
+    from instamatic import controller
     from instamatic.io import get_new_work_subdirectory
 
     print('Usage:')
     print(' 1. Start `insteadmatic_module.s` in DM')
     print(' 2. Run this script.')
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     time.sleep(1)
 

src/instamatic/experiments/cred_tvips/experiment.py

@@ -620,10 +620,10 @@ def log_stage_positions(self):
 
 
 if __name__ == '__main__':
-    from instamatic import TEMController
+    from instamatic import controller
     from instamatic.io import get_new_work_subdirectory
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     expdir = get_new_work_subdirectory()
     expdir.mkdir(exist_ok=True, parents=True)

src/instamatic/experiments/red/experiment.py

@@ -202,9 +202,9 @@ def teardown(self):
 
 
 def main():
-    from instamatic import TEMController
+    from instamatic import controller
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     import logging
 

src/instamatic/experiments/serialed/experiment.py

@@ -613,7 +613,7 @@ def main():
 
     options = parser.parse_args()
 
-    from instamatic import TEMController
+    from instamatic import microscope
 
     try:
         params = json.load(open('params.json'))

src/instamatic/gridmontage.py

@@ -207,9 +207,9 @@ def plot(self):
 
 
 if __name__ == '__main__':
-    from instamatic import TEMController
+    from instamatic import TEMtroller
 
-    ctrl = TEMController.initialize()
+    ctrl = TEMtroller.initialize()
     ctrl.mode.set('lowmag')
     ctrl.magnification.value = 100
 

src/instamatic/gui/cred_tvips_frame.py

@@ -193,9 +193,9 @@ def __init__(self, parent):
 
         frame.pack(side='bottom', fill='x', padx=10, pady=10)
 
-        from instamatic import TEMController
+        from instamatic import controller
 
-        self.ctrl = TEMController.get_instance()
+        self.ctrl = controller.get_instance()
 
     def init_vars(self):
         self.var_target_angle = DoubleVar(value=40.0)

src/instamatic/gui/ctrl_frame.py

@@ -187,9 +187,9 @@ def __init__(self, parent):
 
         frame.pack(side='top', fill='x', padx=10, pady=10)
 
-        from instamatic import TEMController
+        from instamatic import controller
 
-        self.ctrl = TEMController.get_instance()
+        self.ctrl = controller.get_instance()
 
     def init_vars(self):
         self.var_negative_angle = DoubleVar(value=-40)

src/instamatic/gui/defocus_button.py

@@ -3,7 +3,7 @@
 from tkinter import *
 from tkinter.ttk import *
 
-from instamatic import TEMController
+from instamatic import controller
 
 
 class DefocusButton(LabelFrame):
@@ -84,7 +84,7 @@ def main():
 
     options = parser.parse_args()
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     root = Tk()
     DefocusButton(root).pack(side='top', fill='both', expand=True, padx=10, pady=10)

src/instamatic/gui/gui.py

@@ -180,7 +180,7 @@ def start_gui(ctrl, log=None):
 
 
 if __name__ == '__main__':
-    from instamatic import TEMController
+    from instamatic import controller
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
     start_gui(ctrl)

src/instamatic/main.py

@@ -165,9 +165,9 @@ def main():
     log = logging.getLogger(__name__)
     log.info(f'Instamatic started: {repr(options.__dict__)}')
 
-    from instamatic import TEMController
+    from instamatic import controller
 
-    ctrl = TEMController.initialize(stream=True)
+    ctrl = controller.initialize(stream=True)
 
     if options.nav_file:
         from pyserialem import read_nav_file

src/instamatic/microscope/__init__.py

@@ -0,0 +1,3 @@
+from __future__ import annotations
+
+from .microscope import Microscope, get_microscope

src/instamatic/TEMController/microscope_client.py → src/instamatic/microscope/client.py

@@ -114,9 +114,9 @@ def _eval_dct(self, dct):
             raise ConnectionError(f'Unknown status code: {status}')
 
     def _init_dict(self):
-        from instamatic.TEMController.microscope import get_tem
+        from instamatic.microscope.microscope import get_microscope_class
 
-        tem = get_tem(interface=self.interface)
+        tem = get_microscope_class(interface=self.interface)
 
         self._dct = {
             key: value for key, value in tem.__dict__.items() if not key.startswith('_')

src/instamatic/microscope/components/__init__.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+from .deflectors import (
+    BeamShift,
+    BeamTilt,
+    DiffShift,
+    GunShift,
+    GunTilt,
+    ImageShift1,
+    ImageShift2,
+)
+from .lenses import Brightness, DiffFocus, Magnification
+from .stage import Stage
+from .states import Beam, Mode, Screen
+
+__all__ = [
+    'Beam',
+    'BeamShift',
+    'BeamTilt',
+    'Brightness',
+    'DiffFocus',
+    'DiffShift',
+    'GunShift',
+    'GunTilt',
+    'ImageShift1',
+    'ImageShift2',
+    'Magnification',
+    'Mode',
+    'Screen',
+    'Stage',
+]

src/instamatic/TEMController/fei_microscope.py → src/instamatic/microscope/interface/fei_microscope.py

@@ -9,7 +9,7 @@
 
 from instamatic import config
 from instamatic.exceptions import FEIValueError, TEMCommunicationError
-from instamatic.TEMController.microscope_base import MicroscopeBase
+from instamatic.microscope.base import MicroscopeBase
 
 logger = logging.getLogger(__name__)
 

src/instamatic/TEMController/fei_simu_microscope.py → src/instamatic/microscope/interface/fei_simu_microscope.py

@@ -9,7 +9,7 @@
 
 from instamatic import config
 from instamatic.exceptions import FEIValueError, TEMCommunicationError
-from instamatic.TEMController.microscope_base import MicroscopeBase
+from instamatic.microscope.base import MicroscopeBase
 
 logger = logging.getLogger(__name__)
 

src/instamatic/TEMController/jeol_microscope.py → src/instamatic/microscope/interface/jeol_microscope.py

@@ -9,7 +9,7 @@
 
 from instamatic import config
 from instamatic.exceptions import JEOLValueError, TEMCommunicationError, TEMValueError
-from instamatic.TEMController.microscope_base import MicroscopeBase
+from instamatic.microscope.base import MicroscopeBase
 
 logger = logging.getLogger(__name__)
 

src/instamatic/TEMController/simu_microscope.py → src/instamatic/microscope/interface/simu_microscope.py

@@ -6,7 +6,7 @@
 
 from instamatic import config
 from instamatic.exceptions import TEMValueError
-from instamatic.TEMController.microscope_base import MicroscopeBase
+from instamatic.microscope.base import MicroscopeBase
 
 NTRLMAPPING = {
     'GUN1': 0,