Fix warnings (#102)

* Fix warnings for 3.12

* Fix deprecation warnings introduced in #99

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 = controller.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 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/experiments/cred/experiment.py

@@ -30,7 +30,7 @@ class Experiment(ExperimentBase):
     """Initialize continuous rotation electron diffraction experiment.
 
     ctrl:
-        Instance of instamatic.TEMController.TEMController
+        Instance of instamatic.controller.TEMController
     path:
         `str` or `pathlib.Path` object giving the path to save data at
     log:

src/instamatic/experiments/cred_gatan/experiment.py

@@ -20,7 +20,7 @@ class Experiment(ExperimentBase):
     rotation electron diffraction data.
 
     ctrl: `TEMController`
-        Instance of instamatic.TEMController.TEMController
+        Instance of instamatic.controller.TEMController
     path: str
         `str` or `pathlib.Path` object giving the path to save data at
     log: `logging.Logger`
@@ -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

@@ -163,7 +163,7 @@ class Experiment(ExperimentBase):
     rotation electron diffraction data.
 
     ctrl: `TEMController`
-        Instance of instamatic.TEMController.TEMController
+        Instance of instamatic.controller.TEMController
     path: str
         `str` or `pathlib.Path` object giving the path to save data at
     log: `logging.Logger`
@@ -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

@@ -18,7 +18,7 @@ class Experiment(ExperimentBase):
     """Initialize stepwise rotation electron diffraction experiment.
 
     ctrl:
-        Instance of instamatic.TEMController.TEMController
+        Instance of instamatic.controller.TEMController
     path:
         `str` or `pathlib.Path` object giving the path to save data at
     log:
@@ -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 controller
 
     try:
         params = json.load(open('params.json'))
@@ -628,7 +628,7 @@ def main():
     logging.captureWarnings(True)
     log = logging.getLogger(__name__)
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     exp = Experiment(ctrl, params, log=log)
     exp.report_status()

src/instamatic/formats/__init__.py

@@ -53,7 +53,7 @@ def write_tiff(fname: str, data, header: dict = None):
     fname = Path(fname).with_suffix('.tiff')
 
     with tifffile.TiffWriter(fname) as f:
-        f.save(data=data, software='instamatic', description=header)
+        f.write(data=data, software='instamatic', description=header)
 
 
 def read_tiff(fname: str) -> (np.array, dict):

src/instamatic/formats/mrc.py

@@ -599,11 +599,11 @@ def read_image(filename, index=None, cache=None, no_strict_mrc=False, force_volu
         else:
             d_len = h['nx'][0] * h['ny'][0]
         dtype = numpy.dtype(mrc2numpy[h['mode'][0]])
-        offset = 1024 + int(h['nsymbt']) + idx * d_len * dtype.itemsize
+        offset = 1024 + int(h['nsymbt'][0]) + idx * d_len * dtype.itemsize
         total = file_size(f)
         if total != (
             1024
-            + int(h['nsymbt'])
+            + int(h['nsymbt'][0])
             + int(h['nx'][0]) * int(h['ny'][0]) * int(h['nz'][0]) * dtype.itemsize
         ):
             raise util.InvalidHeaderException(
@@ -650,15 +650,14 @@ def reshape_data(out, h, index, count, force_volume=False):
     out : array
           Array with image information from the file
     """
-
     if index is None and int(h['nz'][0]) > 1 and (count == h['nx'][0] or force_volume):
         if h['mapc'][0] == 2 and h['mapr'][0] == 1:
             out = out.reshape((int(h['nx'][0]), int(h['ny'][0]), int(h['nz'][0])))
             for i in range(out.shape[2]):
                 out[:, :, i] = out[:, :, i].squeeze().T
         else:
             out = out.reshape((int(h['nx'][0]), int(h['ny'][0]), int(h['nz'][0])))
-    elif int(h['ny']) > 1:
+    elif int(h['ny'][0]) > 1:
         if h['mapc'][0] == 2 and h['mapr'][0] == 1:
             out = out.reshape((int(h['ny'][0]), int(h['nx'][0])))  # .transpose() # Test this!
         else:

src/instamatic/gridmontage.py

@@ -207,9 +207,9 @@ def plot(self):
 
 
 if __name__ == '__main__':
-    from instamatic import TEMController
+    from instamatic import controller
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.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/processing/flatfield.py

@@ -9,7 +9,7 @@
 import numpy as np
 from tqdm.auto import tqdm
 
-from instamatic import TEMController, config
+from instamatic import config, controller
 from instamatic.formats import *
 
 
@@ -234,7 +234,7 @@ def main_entry():
     args = options.args
 
     if options.collect:
-        ctrl = TEMController.initialize()
+        ctrl = controller.initialize()
         collect_flatfield(ctrl=ctrl, save_images=False)
         ctrl.close()
         exit()

src/instamatic/server/TEMServer_FEI.py

@@ -10,7 +10,7 @@
 import threading
 from socket import *
 
-from instamatic import TEMController, config
+from instamatic import config, controller
 
 HOST = config.settings.fei_server_host
 PORT = config.settings.fei_server_port
@@ -68,7 +68,7 @@ def main():
     logging.captureWarnings(True)
     log = logging.getLogger(__name__)
 
-    ctrl = TEMController.initialize()
+    ctrl = controller.initialize()
 
     s = socket(AF_INET, SOCK_STREAM)
     s.bind((HOST, PORT))

src/instamatic/server/tem_client.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from instamatic import config
-from instamatic.TEMController.microscope_client import MicroscopeClient
+from instamatic.microscope.client import MicroscopeClient
 
 microscope_id = config.microscope.name
 

src/instamatic/server/tem_server.py

@@ -10,7 +10,7 @@
 import traceback
 
 from instamatic import config
-from instamatic.TEMController import Microscope
+from instamatic.microscope import get_microscope
 
 from .serializer import dumper, loader
 
@@ -45,7 +45,7 @@ def __init__(self, log=None, q=None, name=None):
 
     def run(self):
         """Start the server thread."""
-        self.tem = Microscope(name=self._name, use_server=False)
+        self.tem = get_microscope(name=self._name, use_server=False)
         print(f'Initialized connection to microscope: {self.tem.name}')
 
         while True:

src/instamatic/tools.py

@@ -94,7 +94,7 @@ def find_peak_max(
     interpolate the pattern to get the peak maximum position with
     subpixel precision.
     """
-    y1 = ndimage.filters.gaussian_filter1d(arr, sigma)
+    y1 = ndimage.gaussian_filter1d(arr, sigma)
     c1 = np.argmax(y1)  # initial guess for beam center
 
     win_len = 2 * w + 1