Simulation with dependencies

pyproject.toml

@@ -88,6 +88,9 @@ publishing = [
     "wheel",
     "build",
 ]
+simulation = [
+    "diffsims",
+]
 
 [project.scripts]
 "instamatic" = "instamatic.main:main"

src/instamatic/calibrate/calibrate_beamshift.py

@@ -108,7 +108,7 @@ def plot(self, to_file=None, outdir=''):
 
     def center(self, ctrl):
         """Return beamshift values to center the beam in the frame."""
-        pixel_center = [val / 2.0 for val in ctrl.cam.get_image_dimensions()]
+        pixel_center = [val / 2.0 for val in ctrl.cam.get_camera_dimensions()]
 
         beamshift = self.pixelcoord_to_beamshift(pixel_center)
         if ctrl:

src/instamatic/camera/fakevideostream.py

@@ -51,7 +51,7 @@ def __getattr__(self, attrname):
     def get_image(self, exposure=None, binsize=None):
         frame = self.cam.get_image(exposure=exposure, binsize=binsize)
 
-        self.frame, scale = autoscale(frame, maxdim=self.display_dim)
+        # self.frame, scale = autoscale(frame, maxdim=self.display_dim)
 
         return frame
 

src/instamatic/controller.py

@@ -16,6 +16,7 @@
 from instamatic.microscope import components
 from instamatic.microscope.base import MicroscopeBase
 from instamatic.microscope.microscope import get_microscope
+from instamatic.simulation import get_simulation_instances
 
 _ctrl = None  # store reference of ctrl so it can be accessed without re-initializing
 
@@ -46,22 +47,25 @@ def initialize(
     ctrl : `TEMController`
         Return TEM control object
     """
-    print(f"Microscope: {tem_name}{' (server)' if use_tem_server else ''}")
-    tem = get_microscope(tem_name, use_server=use_tem_server)
-
-    if cam_name:
-        if use_cam_server:
-            cam_tag = ' (server)'
-        elif stream:
-            cam_tag = ' (stream)'
-        else:
-            cam_tag = ''
-
-        print(f'Camera    : {cam_name}{cam_tag}')
 
-        cam = Camera(cam_name, as_stream=stream, use_server=use_cam_server)
+    if tem_name == 'simulate' or cam_name == 'simulate':
+        cam, tem = get_simulation_instances()
     else:
-        cam = None
+        print(f"Microscope: {tem_name}{' (server)' if use_tem_server else ''}")
+        tem = get_microscope(tem_name, use_server=use_tem_server)
+        if cam_name:
+            if use_cam_server:
+                cam_tag = ' (server)'
+            elif stream:
+                cam_tag = ' (stream)'
+            else:
+                cam_tag = ''
+
+            print(f'Camera    : {cam_name}{cam_tag}')
+
+            cam = Camera(cam_name, as_stream=stream, use_server=use_cam_server)
+        else:
+            cam = None
 
     global _ctrl
     ctrl = _ctrl = TEMController(tem=tem, cam=cam)
@@ -384,11 +388,11 @@ def find_eucentric_height(
 
         def one_cycle(tilt: float = 5, sign=1) -> list:
             angle1 = -tilt * sign
-            self.stage.a = angle1
+            self.stage.set(a=angle1)
             img1 = self.get_rotated_image()
 
             angle2 = +tilt * sign
-            self.stage.a = angle2
+            self.stage.set(a=angle2)
             img2 = self.get_rotated_image()
 
             if sign < 1:
@@ -398,7 +402,7 @@ def one_cycle(tilt: float = 5, sign=1) -> list:
 
             return shift
 
-        self.stage.a = 0
+        self.stage.set(a=0)
         # self.stage.z = 0 # for testing
 
         zc = self.stage.z
@@ -410,7 +414,7 @@ def one_cycle(tilt: float = 5, sign=1) -> list:
         sign = 1
 
         for i, z in enumerate(zs):
-            self.stage.z = z
+            self.stage.set(z=z)
             if verbose:
                 print(f'z = {z:.1f} nm')
 
@@ -419,9 +423,7 @@ def one_cycle(tilt: float = 5, sign=1) -> list:
 
             sign *= -1
 
-        mean_shift = shifts[-1] + shifts[0]
-        mean_shift = mean_shift / np.linalg.norm(mean_shift)
-        ds = np.dot(shifts, mean_shift)
+        ds = np.sum(shifts, axis=1)
 
         p = np.polyfit(zs, ds, 1)  # linear fit
         alpha, beta = p
@@ -592,6 +594,35 @@ def get_rotated_image(self, exposure: float = None, binsize: int = None) -> np.n
 
         return arr
 
+    def get_rotated_raw_image(self, exposure: float = None, binsize: int = None) -> np.ndarray:
+        """Simplified function equivalent to `get_image` that returns the
+        rotated image array.
+
+        Parameters
+        ----------
+        exposure: float
+            Exposure time in seconds
+        binsize: int
+            Binning to use for the image, must be 1, 2, or 4, etc
+        mode : str
+            Magnification mode
+        mag : int
+            Magnification value
+
+        Returns
+        -------
+        arr : np.array
+            Image as 2D numpy array.
+        """
+
+        mag = self.magnification.value
+        mode = self.mode.get()
+
+        arr = self.get_raw_image(exposure=exposure, binsize=binsize)
+        arr = rotate_image(arr, mode=mode, mag=mag)
+
+        return arr
+
     def get_image(
         self,
         exposure: float = None,

src/instamatic/experiments/autocred/experiment.py

@@ -252,6 +252,8 @@ def __init__(
             except BaseException:
                 print('Is DIALS server running? Connection failed.')
                 self.s_c = 0
+        else:
+            self.s_c = 0
 
         if use_vm:
             self.s2 = socket.socket()
@@ -264,6 +266,12 @@ def __init__(
             except BaseException:
                 print('Is VM server running? Connection failed.')
                 self.s2_c = 0
+        else:
+            self.s2_c = 0
+
+    @property
+    def magnification(self) -> float:
+        return self.ctrl.magnification.value
 
     def image_cropper(self, img, window_size=0):
         crystal_pos, r = find_defocused_image_center(
@@ -1152,7 +1160,7 @@ def raster_scan(self):
             config.calibration['mag1']['pixelsize'][self.magnification] / 1000
         )  # nm -> um
         xdim, ydim = self.ctrl.cam.get_camera_dimensions()
-        box_x, box_y = self.pixelsize_mag1 * xdim, self.pixelsize_mag1 * ydim
+        box_x, box_y = pixelsize_mag1 * xdim, pixelsize_mag1 * ydim
 
         # Make negative to reflect config change 2019-07-03 to make omega more in line with other software
         rot_axis = -config.camera.camera_rotation_vs_stage_xy
@@ -1185,7 +1193,6 @@ def raster_scan(self):
                 try:
                     img, h = self.ctrl.get_image(exposure=self.expt, header_keys=None)
                     if img.mean() > 10:
-                        self.magnification = self.ctrl.magnification.value
                         crystal_positions = find_crystals_timepix(
                             img, self.magnification, spread=self.spread, offset=self.offset
                         )
@@ -1380,8 +1387,6 @@ def start_collection_point(self):
                 y=self.calib_beamshift.reference_shift[1],
             )
 
-            self.magnification = self.ctrl.magnification.value
-
             self.rotation_direction = self.eliminate_backlash_in_tiltx()
             img, h = self.ctrl.get_image(exposure=self.expt, header_keys=header_keys)
             # img, h = Experiment.apply_corrections(img, h)
@@ -1690,9 +1695,9 @@ def start_collection(self):
                 input(
                     'No z-height adjustment found. Please find an area with particles! Press Enter to continue auto adjustment of z height>>>'
                 )
-                x_zheight, y_zheight = center_z_height_HYMethod(
-                    self.ctrl, spread=self.spread, offset=self.offset
-                )
+                # x_zheight, y_zheight = center_z_height_HYMethod(
+                #     self.ctrl, spread=self.spread, offset=self.offset
+                # )
                 xpoint, ypoint, zpoint, aaa, bbb = self.ctrl.stage.get()
                 self.logger.info(
                     f'Stage position: x = {xpoint}, y = {ypoint}. Z height adjusted to {zpoint}. Tilt angle x {aaa} deg, Tilt angle y {bbb} deg'

src/instamatic/experiments/red/experiment.py

@@ -98,12 +98,12 @@ def start_collection(self, exposure_time: float, tilt_range: float, stepsize: fl
             ctrl.cam.block()
 
         # for i, a in enumerate(tilt_positions):
-        for i, angle in enumerate(tqdm(tilt_positions)):
-            ctrl.stage.a = angle
+        for i, angle in enumerate((tilt_positions)):
+            ctrl.stage.set(a=angle)
 
             j = i + self.offset
 
-            img, h = self.ctrl.get_image(exposure_time)
+            img, h = ctrl.get_image(exposure_time, header_keys='')
 
             self.buffer.append((j, img, h))
 

src/instamatic/gui/autocred_frame.py

@@ -385,8 +385,6 @@ def acquire_data_autocRED(controller, **kwargs):
     )
     cexp.start_collection()
 
-    stop_event.clear()
-    stop_event_experiment.clear()
     controller.log.info('Finish autocRED experiment')
 
 

src/instamatic/gui/ctrl_frame.py

@@ -50,6 +50,8 @@ def __init__(self, parent):
         frame.pack(side='top', fill='x', padx=10, pady=10)
 
         frame = Frame(self)
+        stage_reset_btn = Button(frame, text='Reset stage', command=self.reset_stage)
+        stage_reset_btn.grid(row=0, column=0, sticky='W')
 
         Label(frame, text='Angle (-)', width=20).grid(row=1, column=0, sticky='W')
         Label(frame, text='Angle (0)', width=20).grid(row=2, column=0, sticky='W')
@@ -161,6 +163,13 @@ def __init__(self, parent):
         )
         slider.grid(row=12, column=0, columnspan=3, sticky='EW')
 
+        # Magnification
+        Label(frame, text='Magnification', width=20).grid(row=14, column=0, sticky='W')
+        mag_inc_btn = Button(frame, text='+', command=self.increase_mag)
+        mag_inc_btn.grid(row=14, column=1)
+        mag_dec_btn = Button(frame, text='-', command=self.decrease_mag)
+        mag_dec_btn.grid(row=14, column=2)
+
         frame.pack(side='top', fill='x', padx=10, pady=10)
 
         frame = Frame(self)
@@ -228,6 +237,15 @@ def set_brightness(self, event=None):
     def get_brightness(self, event=None):
         self.var_brightness.set(self.ctrl.brightness.get())
 
+    def increase_mag(self):
+        self.ctrl.magnification.increase()
+
+    def decrease_mag(self):
+        self.ctrl.magnification.decrease()
+
+    def reset_stage(self):
+        self.ctrl.stage.set(0, 0, 0, 0, 0)
+
     def set_difffocus(self, event=None):
         self.var_difffocus.set(self.var_difffocus.get())
         self.q.put(('ctrl', {'task': 'difffocus.set', 'value': self.var_difffocus.get()}))

src/instamatic/microscope/microscope.py

@@ -19,7 +19,7 @@ def get_microscope_class(interface: str) -> 'type[MicroscopeBase]':
             raise PermissionError('Access to the TEM interface requires admin rights.')
 
     if simulate or interface == 'simulate':
-        from .interface.simu_microscope import SimuMicroscope as cls
+        from ..simulation.microscope import MicroscopeSimulation as cls
     elif interface == 'jeol':
         from .interface.jeol_microscope import JeolMicroscope as cls
     elif interface == 'fei':

src/instamatic/processing/find_crystals.py

@@ -82,7 +82,7 @@ def segment_crystals(img, r=101, offset=5, footprint=5, remove_carbon_lacing=Tru
     # remove carbon lines
     if remove_carbon_lacing:
         arr = morphology.remove_small_objects(arr, min_size=8 * 8, connectivity=0)
-        arr = morphology.remove_small_holes(arr, min_size=32 * 32, connectivity=0)
+        arr = morphology.remove_small_holes(arr, area_threshold=32 * 32, connectivity=0)
     arr = morphology.binary_dilation(arr, morphology.disk(footprint))  # dilation
 
     # get background pixels
@@ -227,7 +227,7 @@ def main_entry():
 
     for fn in args:
         img, h = read_image(fn)
-
+        print(h)
         crystals = find_crystals_timepix(img, h['exp_magnification'], plot=True)
 
         for crystal in crystals:

src/instamatic/simulation/__init__.py

@@ -0,0 +1,32 @@
+from __future__ import annotations
+
+from typing import Tuple
+
+from instamatic import config
+from instamatic.camera.camera_client import CamClient
+from instamatic.camera.fakevideostream import VideoStream
+from instamatic.microscope.client import MicroscopeClient
+from instamatic.simulation.camera import CameraSimulation
+from instamatic.simulation.microscope import MicroscopeSimulation
+
+
+def get_simulation_instances() -> Tuple[CameraSimulation, MicroscopeSimulation]:
+    """Initialize simulated camera and microscope.
+
+    Returns
+    -------
+    Tuple[CameraSimulation, MicroscopeSimulation]
+    """
+    tem = MicroscopeSimulation()
+    cam = CameraSimulation(tem=tem)
+    return cam, tem
+    if config.settings.use_tem_server:
+        tem = MicroscopeClient(interface='simulate')
+    else:
+        tem = MicroscopeSimulation()
+    if config.settings.use_cam_server:
+        cam = CamClient(name='simulate', interface=config.camera.interface)
+    else:
+        camsim = CameraSimulation(tem=tem)
+        cam = VideoStream(camsim)
+    return cam, tem