From a150689f6cddaa2027a14f364280d55263b847cf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Mon, 10 Nov 2025 20:25:42 +0100
Subject: [PATCH 01/18] Add a crude implementation to control beamshift with
 RMB (for FEI cRED)

---
 src/instamatic/gui/base_module.py |  1 +
 src/instamatic/gui/cred_frame.py  |  3 ++-
 src/instamatic/gui/ctrl_frame.py  | 36 +++++++++++++++++++++++++++++++
 src/instamatic/gui/gui.py         |  2 ++
 4 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/src/instamatic/gui/base_module.py b/src/instamatic/gui/base_module.py
index 29f97f01..cadbf6e0 100644
--- a/src/instamatic/gui/base_module.py
+++ b/src/instamatic/gui/base_module.py
@@ -39,3 +39,4 @@ class HasQMixin:
     """Asserts module.q remains reserved for DataCollectionController.q."""
 
     q: Queue
+    app: None
diff --git a/src/instamatic/gui/cred_frame.py b/src/instamatic/gui/cred_frame.py
index 65748ae9..0ed94612 100644
--- a/src/instamatic/gui/cred_frame.py
+++ b/src/instamatic/gui/cred_frame.py
@@ -8,7 +8,7 @@
 
 from .base_module import BaseModule, HasQMixin
 
-ENABLE_FOOTFREE_OPTION = False
+ENABLE_FOOTFREE_OPTION = True
 
 
 class ExperimentalcRED(LabelFrame, HasQMixin):
@@ -175,6 +175,7 @@ def init_vars(self):
         self.var_exposure_time_image = DoubleVar(value=0.01)
 
         self.var_footfree_rotate_to = DoubleVar(value=65.0)
+        self.var_footfree_rotate_speed = DoubleVar(value=0.0)
         self.var_toggle_footfree = BooleanVar(value=False)
         self.mode = 'regular'
 
diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index 139fea0d..094f1c85 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -8,6 +8,9 @@
 from typing import Dict
 
 from instamatic import config
+from instamatic.calibrate import CalibBeamShift
+from instamatic.calibrate.filenames import CALIB_BEAMSHIFT
+from instamatic.gui.click_dispatcher import ClickEvent, MouseButton
 from instamatic.utils.spinbox import Spinbox
 
 from .base_module import BaseModule, HasQMixin
@@ -44,6 +47,9 @@ def __init__(self, parent):
         self.o_mode = OptionMenu(frame, self.var_mode, modes[0], *modes, command=self.set_mode)
         self.o_mode.grid(row=8, column=1, sticky='EW')
 
+        self.rmb_beam = Checkbutton(frame, text='Move beam w/ RMB', variable=self.var_rmb_beam)
+        self.rmb_beam.grid(row=8, column=3)
+
         frame.pack(side='top', fill='x', padx=10, pady=10)
 
         frame = Frame(self)
@@ -212,6 +218,8 @@ def init_vars(self):
         self.var_diff_defocus_on = BooleanVar(value=False)
 
         self.var_stage_wait = BooleanVar(value=True)
+        self.var_rmb_beam = BooleanVar(value=False)
+        self.var_rmb_beam.trace_add('write', self.toggle_rmb_beam)
 
     def set_mode(self, event=None):
         self.ctrl.mode.set(self.var_mode.get())
@@ -301,6 +309,34 @@ def toggle_alpha_wobbler(self):
             if self.wobble_stop_event:
                 self.wobble_stop_event.set()
 
+    def toggle_rmb_beam(self, _name, _index, _mode) -> None:
+        """If self.var_rmb_beam, move beam using Right Mouse Button."""
+
+        try:
+            if not hasattr(self, 'calib_beamshift'):
+                path = self.app.get_module('io').get_experiment_directory().parent / 'calib'
+                print(path / CALIB_BEAMSHIFT)
+                self.calib_beamshift = CalibBeamShift.from_file(path / CALIB_BEAMSHIFT)
+                print(self.calib_beamshift)
+        except OSError:
+            print('No calibration :(')
+            # self.var_rmb_beam.set(False)
+            return
+
+        def _cb(click: ClickEvent) -> None:
+            if click.button == MouseButton.RIGHT:
+                bs = self.calib_beamshift.pixelcoord_to_beamshift((click.y, click.x))
+                self.ctrl.beamshift.set(*bs)
+            print(f'Beam shift at {self.ctrl.beamshift.get()}')
+
+        if self.var_rmb_beam.get():
+            d = self.app.get_module('stream').click_dispatcher
+            n = 'rmb_beam'
+            self.click_listener = c if (c := d.listeners.get(n)) else d.add_listener(n, _cb)
+            self.click_listener.active = True
+        else:
+            self.click_listener.active = False
+
     def stage_stop(self):
         self.q.put(('ctrl', {'task': 'stage.stop'}))
 
diff --git a/src/instamatic/gui/gui.py b/src/instamatic/gui/gui.py
index 3b7a4ccf..c5790504 100644
--- a/src/instamatic/gui/gui.py
+++ b/src/instamatic/gui/gui.py
@@ -43,6 +43,8 @@ def __init__(self, ctrl=None, stream=None, beam_ctrl=None, app=None, log=None):
         for module in self.app.modules.values():
             if 'q' in get_type_hints(module.__class__):
                 module.q = getattr(module, 'q', self.q)
+            if 'app' in get_type_hints(module.__class__):
+                module.app = getattr(module, 'app', self.app)
 
         self.exitEvent = threading.Event()
         atexit.register(self.exitEvent.set)

From 24a369a7949f3efbeecafd501ece6a137e316834 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Tue, 11 Nov 2025 12:49:05 +0100
Subject: [PATCH 02/18] Add a crude implementation to control stage opsition
 with LMB

---
 src/instamatic/gui/ctrl_frame.py | 50 +++++++++++++++++++++++++-------
 1 file changed, 40 insertions(+), 10 deletions(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index 094f1c85..7f903e9f 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -2,10 +2,10 @@
 
 import queue
 import threading
-from threading import Event
 from tkinter import *
 from tkinter.ttk import *
-from typing import Dict
+
+import numpy as np
 
 from instamatic import config
 from instamatic.calibrate import CalibBeamShift
@@ -47,9 +47,6 @@ def __init__(self, parent):
         self.o_mode = OptionMenu(frame, self.var_mode, modes[0], *modes, command=self.set_mode)
         self.o_mode.grid(row=8, column=1, sticky='EW')
 
-        self.rmb_beam = Checkbutton(frame, text='Move beam w/ RMB', variable=self.var_rmb_beam)
-        self.rmb_beam.grid(row=8, column=3)
-
         frame.pack(side='top', fill='x', padx=10, pady=10)
 
         frame = Frame(self)
@@ -80,6 +77,14 @@ def __init__(self, parent):
         )
         b_wobble.grid(row=4, column=2, sticky='W', columnspan=2)
 
+        text = 'Move stage with LMB'
+        self.lmb_stage = Checkbutton(frame, text=text, variable=self.var_lmb_stage)
+        self.lmb_stage.grid(row=1, column=3)
+
+        text = 'Move beam with RMB'
+        self.rmb_beam = Checkbutton(frame, text=text, variable=self.var_rmb_beam)
+        self.rmb_beam.grid(row=2, column=3)
+
         e_stage_x = Spinbox(frame, textvariable=self.var_stage_x, **stage)
         e_stage_x.grid(row=6, column=1, sticky='EW')
         e_stage_y = Spinbox(frame, textvariable=self.var_stage_y, **stage)
@@ -220,6 +225,8 @@ def init_vars(self):
         self.var_stage_wait = BooleanVar(value=True)
         self.var_rmb_beam = BooleanVar(value=False)
         self.var_rmb_beam.trace_add('write', self.toggle_rmb_beam)
+        self.var_lmb_stage = BooleanVar(value=False)
+        self.var_lmb_stage.trace_add('write', self.toggle_lmb_stage)
 
     def set_mode(self, event=None):
         self.ctrl.mode.set(self.var_mode.get())
@@ -309,6 +316,31 @@ def toggle_alpha_wobbler(self):
             if self.wobble_stop_event:
                 self.wobble_stop_event.set()
 
+    def toggle_lmb_stage(self, _name, _index, _mode):
+        """If self.var_lmb_stage, move stage using Left Mouse Button."""
+
+        try:
+            stage_matrix = self.ctrl.get_stagematrix()
+        except KeyError:
+            print('No calibration :<')
+            # self.var_lmb_stage.set(False)
+            return
+
+        def _cb(click: ClickEvent) -> None:
+            if click.button == MouseButton.LEFT:
+                cam_dim_x, cam_dim_y = self.ctrl.cam.get_camera_dimensions()
+                pixel_delta = np.array([click.y - cam_dim_y / 2, click.x - cam_dim_x / 2])
+                stage_shift = np.dot(pixel_delta, stage_matrix)
+                stage_x, stage_y = self.ctrl.stage.xy
+                self.ctrl.stage.set(x=stage_x + stage_shift[0], y=stage_y + stage_shift[1])
+            print(f'Stage position at {self.ctrl.stage.get()}')
+
+        if checked := self.var_lmb_stage.get():
+            d = self.app.get_module('stream').click_dispatcher
+            n = 'lmb_stage'
+            self.lmb_stage_cl = c if (c := d.listeners.get(n)) else d.add_listener(n, _cb)
+        self.lmb_stage_cl.active = checked
+
     def toggle_rmb_beam(self, _name, _index, _mode) -> None:
         """If self.var_rmb_beam, move beam using Right Mouse Button."""
 
@@ -329,13 +361,11 @@ def _cb(click: ClickEvent) -> None:
                 self.ctrl.beamshift.set(*bs)
             print(f'Beam shift at {self.ctrl.beamshift.get()}')
 
-        if self.var_rmb_beam.get():
+        if checked := self.var_rmb_beam.get():
             d = self.app.get_module('stream').click_dispatcher
             n = 'rmb_beam'
-            self.click_listener = c if (c := d.listeners.get(n)) else d.add_listener(n, _cb)
-            self.click_listener.active = True
-        else:
-            self.click_listener.active = False
+            self.rmb_beam_cl = c if (c := d.listeners.get(n)) else d.add_listener(n, _cb)
+        self.rmb_beam_cl.active = checked
 
     def stage_stop(self):
         self.q.put(('ctrl', {'task': 'stage.stop'}))

From 94fd7fbce6debe16d061e9b6a83c5c3578d2baa9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Tue, 11 Nov 2025 13:07:24 +0100
Subject: [PATCH 03/18] Allow rotation speed control even if goniotool is not
 available

---
 src/instamatic/gui/ctrl_frame.py | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index 7f903e9f..3f505a59d 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -10,6 +10,7 @@
 from instamatic import config
 from instamatic.calibrate import CalibBeamShift
 from instamatic.calibrate.filenames import CALIB_BEAMSHIFT
+from instamatic.exceptions import TEMCommunicationError
 from instamatic.gui.click_dispatcher import ClickEvent, MouseButton
 from instamatic.utils.spinbox import Spinbox
 
@@ -79,11 +80,11 @@ def __init__(self, parent):
 
         text = 'Move stage with LMB'
         self.lmb_stage = Checkbutton(frame, text=text, variable=self.var_lmb_stage)
-        self.lmb_stage.grid(row=1, column=3)
+        self.lmb_stage.grid(row=1, column=3, columnspan=3, sticky='W')
 
         text = 'Move beam with RMB'
         self.rmb_beam = Checkbutton(frame, text=text, variable=self.var_rmb_beam)
-        self.rmb_beam.grid(row=2, column=3)
+        self.rmb_beam.grid(row=2, column=3, columnspan=3, sticky='W')
 
         e_stage_x = Spinbox(frame, textvariable=self.var_stage_x, **stage)
         e_stage_x.grid(row=6, column=1, sticky='EW')
@@ -92,14 +93,14 @@ def __init__(self, parent):
         e_stage_z = Spinbox(frame, textvariable=self.var_stage_z, **stage)
         e_stage_z.grid(row=6, column=3, sticky='EW')
 
+        Label(frame, text='Rotation Speed', width=20).grid(row=5, column=0, sticky='W')
+        e_goniotool_tx = Spinbox(
+            frame, width=10, textvariable=self.var_goniotool_tx, from_=1, to=12, increment=1
+        )
+        e_goniotool_tx.grid(row=5, column=1, sticky='EW')
+        b_goniotool_set = Button(frame, text='Set', command=self.set_goniotool_tx)
+        b_goniotool_set.grid(row=5, column=2, sticky='EW')
         if config.settings.use_goniotool:
-            Label(frame, text='Rot. Speed', width=20).grid(row=5, column=0, sticky='W')
-            e_goniotool_tx = Spinbox(
-                frame, width=10, textvariable=self.var_goniotool_tx, from_=1, to=12, increment=1
-            )
-            e_goniotool_tx.grid(row=5, column=1, sticky='EW')
-            b_goniotool_set = Button(frame, text='Set', command=self.set_goniotool_tx)
-            b_goniotool_set.grid(row=5, column=2, sticky='W')
             b_goniotool_default = Button(
                 frame, text='Default', command=self.set_goniotool_tx_default
             )
@@ -272,7 +273,12 @@ def set_positive_angle(self):
     def set_goniotool_tx(self, event=None, value=None):
         if not value:
             value = self.var_goniotool_tx.get()
-        self.ctrl.stage.set_rotation_speed(value)
+        try:
+            self.ctrl.stage.set_rotation_speed(value)
+        except AttributeError:
+            print('This TEM does not implement `setRotationSpeed` method')
+        except TEMCommunicationError:
+            print('Could not connect to the stage rotation speed controller')
 
     def set_goniotool_tx_default(self, event=None):
         value = 12

From 5f5fac3e522063b0a9093df7fb79a84b80890f77 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Thu, 20 Nov 2025 15:47:19 +0100
Subject: [PATCH 04/18] Add more details, otherwise more difficult to reach, to
 pets input

---
 docs/config.md | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/docs/config.md b/docs/config.md
index 7de6f575..712e6145 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -258,7 +258,17 @@ This file holds the specifications of the camera. This file is must be located t
 **pets_prefix**
 : Arbitrary information to be added at the beginning of the `.pts` file created after an experiment. The prefix can include any [valid PETS2 input lines](http://pets.fzu.cz/download/pets2_manual.pdf). In the case of duplicate commands, prefix lines take precedence over hard-coded and suffix commands, and prevent the latter ones from being added. Additionally, this field can contain new python-style [replacement fields](https://pyformat.info/) which, if present among the `ImgConversion` instance attributes, will be filled automatically after each experiment (see the `pets_suffix` example). A typical `pets_prefix`, capable of overwriting the default detector specification output can look like this:
 ```yaml
-pets_prefix: "noiseparameters 4.2 0\nreflectionsize 8\ndetector asi"
+pets_prefix: |
+  # Measurement conditions:
+  # Start angle:               {start_angle:6.2f} deg
+  # Stop angle:                {stop_angle:6.2f} deg
+  # Step size:                 {osc_angle:6.2f} deg
+  # Exposure:                  {acquisition_time:6.3f} s
+  # Wave length:               {wavelength}
+  # Camera distance:           {distance}
+  noiseparameters 4.2 0
+  reflectionsize 8
+  detector asi
 ```
 
 **pets_suffix**

From 0ffc01f116c6101a1c702118a22e5c874b2202ba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Thu, 20 Nov 2025 16:05:56 +0100
Subject: [PATCH 05/18] Add some more examples to the pets prefix

---
 docs/config.md | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 712e6145..2996b5dd 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -256,16 +256,18 @@ This file holds the specifications of the camera. This file is must be located t
 ```
 
 **pets_prefix**
-: Arbitrary information to be added at the beginning of the `.pts` file created after an experiment. The prefix can include any [valid PETS2 input lines](http://pets.fzu.cz/download/pets2_manual.pdf). In the case of duplicate commands, prefix lines take precedence over hard-coded and suffix commands, and prevent the latter ones from being added. Additionally, this field can contain new python-style [replacement fields](https://pyformat.info/) which, if present among the `ImgConversion` instance attributes, will be filled automatically after each experiment (see the `pets_suffix` example). A typical `pets_prefix`, capable of overwriting the default detector specification output can look like this:
+: Arbitrary information to be added at the beginning of the `.pts` file created after an experiment. The prefix can include any [valid PETS2 input lines](http://pets.fzu.cz/download/pets2_manual.pdf). In the case of duplicate commands, prefix lines take precedence over hard-coded and suffix commands, and prevent the latter ones from being added. Additionally, this field can contain new python-style [replacement fields](https://pyformat.info/) which, if present among the `ImgConversion` instance attributes, will be filled automatically after each experiment. A typical `pets_prefix`, capable of overwriting the default detector specification output can look like this:
 ```yaml
 pets_prefix: |
-  # Measurement conditions:
+
+  # MEASUREMENT CONDITIONS:
   # Start angle:               {start_angle:6.2f} deg
-  # Stop angle:                {stop_angle:6.2f} deg
+  # End angle:                 {end_angle:6.2f} deg
   # Step size:                 {osc_angle:6.2f} deg
   # Exposure:                  {acquisition_time:6.3f} s
-  # Wave length:               {wavelength}
-  # Camera distance:           {distance}
+  # Wave length:      {wavelength:15.8g} A
+  # Camera distance:  {distance:15.8g} mm
+
   noiseparameters 4.2 0
   reflectionsize 8
   detector asi

From a73ed8fd1390ba5296e95ae5ce4baf016ecb67b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Fri, 21 Nov 2025 15:53:44 +0100
Subject: [PATCH 06/18] Videoframe instance needs no app kwarg anymore since it
 is class attribute now

---
 src/instamatic/gui/gui.py               | 4 ++--
 src/instamatic/gui/videostream_frame.py | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/instamatic/gui/gui.py b/src/instamatic/gui/gui.py
index c5790504..40d19489 100644
--- a/src/instamatic/gui/gui.py
+++ b/src/instamatic/gui/gui.py
@@ -138,11 +138,11 @@ def __init__(self, root, cam, modules: list = []):
         self.app = AppLoader()
 
         # the stream window is a special case, because it needs access
-        # to the cam module and the AppLoader itself
+        # to the cam module
         if cam:
             from .videostream_frame import module as stream_module
 
-            stream_module.set_kwargs(stream=cam, app=self.app)
+            stream_module.set_kwargs(stream=cam)
             modules.insert(0, stream_module)
 
         self.module_frame = Frame(root)
diff --git a/src/instamatic/gui/videostream_frame.py b/src/instamatic/gui/videostream_frame.py
index b4b4f45a..6e427225 100644
--- a/src/instamatic/gui/videostream_frame.py
+++ b/src/instamatic/gui/videostream_frame.py
@@ -26,13 +26,12 @@ class VideoStreamFrame(LabelFrame, HasQMixin):
     """GUI panel to continuously display the last frame streamed from the
     camera."""
 
-    def __init__(self, parent, stream, app=None):
+    def __init__(self, parent, stream):
         LabelFrame.__init__(self, parent, text='Stream')
 
         self.parent = parent
 
         self.stream = stream
-        self.app = app
 
         self.panel = None
 

From 0b94d82abd0da3d5dfc8b67dbe6a5265c0eca5e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Fri, 21 Nov 2025 16:01:51 +0100
Subject: [PATCH 07/18] Raname `HasQMixin` to `ModuleFrameMixin` to generalize
 it better

---
 src/instamatic/gui/autocred_frame.py         | 4 ++--
 src/instamatic/gui/base_module.py            | 4 ++--
 src/instamatic/gui/cred_fei_frame.py         | 4 ++--
 src/instamatic/gui/cred_frame.py             | 4 ++--
 src/instamatic/gui/cred_tvips_frame.py       | 4 ++--
 src/instamatic/gui/ctrl_frame.py             | 4 ++--
 src/instamatic/gui/debug_frame.py            | 4 ++--
 src/instamatic/gui/fast_adt_frame.py         | 4 ++--
 src/instamatic/gui/machine_learning_frame.py | 4 ++--
 src/instamatic/gui/red_frame.py              | 4 ++--
 src/instamatic/gui/sed_frame.py              | 4 ++--
 src/instamatic/gui/videostream_frame.py      | 4 ++--
 12 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/src/instamatic/gui/autocred_frame.py b/src/instamatic/gui/autocred_frame.py
index fecaa50b..718775a2 100644
--- a/src/instamatic/gui/autocred_frame.py
+++ b/src/instamatic/gui/autocred_frame.py
@@ -13,10 +13,10 @@
 from instamatic.calibrate import CalibBeamShift
 from instamatic.calibrate.filenames import *
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalautocRED(LabelFrame, HasQMixin):
+class ExperimentalautocRED(LabelFrame, ModuleFrameMixin):
     """Data collection protocol for SerialRED data collection on a high-speed
     Timepix camera using automated screening and crystal tracking.
 
diff --git a/src/instamatic/gui/base_module.py b/src/instamatic/gui/base_module.py
index cadbf6e0..aaa6a281 100644
--- a/src/instamatic/gui/base_module.py
+++ b/src/instamatic/gui/base_module.py
@@ -35,8 +35,8 @@ def initialize(self, parent):
         return frame
 
 
-class HasQMixin:
-    """Asserts module.q remains reserved for DataCollectionController.q."""
+class ModuleFrameMixin:
+    """Asserts some class attributes i.e. module.q, app remain reserved."""
 
     q: Queue
     app: None
diff --git a/src/instamatic/gui/cred_fei_frame.py b/src/instamatic/gui/cred_fei_frame.py
index d0fd8e9d..6fef0a23 100644
--- a/src/instamatic/gui/cred_fei_frame.py
+++ b/src/instamatic/gui/cred_fei_frame.py
@@ -5,10 +5,10 @@
 
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalcRED_FEI(LabelFrame, HasQMixin):
+class ExperimentalcRED_FEI(LabelFrame, ModuleFrameMixin):
     """Simple panel to assist cRED data collection (mainly rotation control) on
     a FEI microscope."""
 
diff --git a/src/instamatic/gui/cred_frame.py b/src/instamatic/gui/cred_frame.py
index 0ed94612..3438566e 100644
--- a/src/instamatic/gui/cred_frame.py
+++ b/src/instamatic/gui/cred_frame.py
@@ -6,12 +6,12 @@
 
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 ENABLE_FOOTFREE_OPTION = True
 
 
-class ExperimentalcRED(LabelFrame, HasQMixin):
+class ExperimentalcRED(LabelFrame, ModuleFrameMixin):
     """GUI panel for doing cRED experiments on a Timepix camera."""
 
     def __init__(self, parent):
diff --git a/src/instamatic/gui/cred_tvips_frame.py b/src/instamatic/gui/cred_tvips_frame.py
index b0aeac9a..dc7e20d0 100644
--- a/src/instamatic/gui/cred_tvips_frame.py
+++ b/src/instamatic/gui/cred_tvips_frame.py
@@ -9,12 +9,12 @@
 from instamatic import config
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 barrier = threading.Barrier(2, timeout=60)
 
 
-class ExperimentalTVIPS(LabelFrame, HasQMixin):
+class ExperimentalTVIPS(LabelFrame, ModuleFrameMixin):
     """GUI panel for doing cRED / SerialRED experiments on a TVIPS camera."""
 
     def __init__(self, parent):
diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index 3f505a59d..cb7ce2ae 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -14,10 +14,10 @@
 from instamatic.gui.click_dispatcher import ClickEvent, MouseButton
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalCtrl(LabelFrame, HasQMixin):
+class ExperimentalCtrl(LabelFrame, ModuleFrameMixin):
     """This panel holds some frequently used functions to control the electron
     microscope."""
 
diff --git a/src/instamatic/gui/debug_frame.py b/src/instamatic/gui/debug_frame.py
index 304c8197..293bf665 100644
--- a/src/instamatic/gui/debug_frame.py
+++ b/src/instamatic/gui/debug_frame.py
@@ -8,7 +8,7 @@
 
 from instamatic import config
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 scripts_drc = config.locations['scripts']
 
@@ -22,7 +22,7 @@
 VMPORT = config.settings.VM_server_port
 
 
-class DebugFrame(LabelFrame, HasQMixin):
+class DebugFrame(LabelFrame, ModuleFrameMixin):
     """GUI panel with advanced / debugging functions."""
 
     def __init__(self, parent):
diff --git a/src/instamatic/gui/fast_adt_frame.py b/src/instamatic/gui/fast_adt_frame.py
index 46638fbc..bfceb0e4 100644
--- a/src/instamatic/gui/fast_adt_frame.py
+++ b/src/instamatic/gui/fast_adt_frame.py
@@ -8,7 +8,7 @@
 from instamatic import controller
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 pad0 = {'sticky': 'EW', 'padx': 0, 'pady': 1}
 pad10 = {'sticky': 'EW', 'padx': 10, 'pady': 1}
@@ -82,7 +82,7 @@ def as_dict(self):
         return {n: v.get() for n, v in vars(self).items() if isinstance(v, Variable)}
 
 
-class ExperimentalFastADT(LabelFrame, HasQMixin):
+class ExperimentalFastADT(LabelFrame, ModuleFrameMixin):
     """GUI panel to perform selected FastADT-style (c)RED & PED experiments."""
 
     def __init__(self, parent):
diff --git a/src/instamatic/gui/machine_learning_frame.py b/src/instamatic/gui/machine_learning_frame.py
index 59fe9d6d..c7777e85 100644
--- a/src/instamatic/gui/machine_learning_frame.py
+++ b/src/instamatic/gui/machine_learning_frame.py
@@ -10,7 +10,7 @@
 
 from instamatic.formats import read_image
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 from .mpl_frame import ShowMatplotlibFig
 
 
@@ -25,7 +25,7 @@ def treeview_sort_column(tv, col, reverse):
     tv.heading(col, command=lambda: treeview_sort_column(tv, col, not reverse))
 
 
-class MachineLearningFrame(LabelFrame, HasQMixin):
+class MachineLearningFrame(LabelFrame, ModuleFrameMixin):
     """GUI Panel to read in the results from the machine learning algorithm to
     identify good/poor crystals based on their diffraction pattern."""
 
diff --git a/src/instamatic/gui/red_frame.py b/src/instamatic/gui/red_frame.py
index e3c0105f..ca6e64b9 100644
--- a/src/instamatic/gui/red_frame.py
+++ b/src/instamatic/gui/red_frame.py
@@ -5,10 +5,10 @@
 
 from instamatic.utils.spinbox import Spinbox
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 
-class ExperimentalRED(LabelFrame, HasQMixin):
+class ExperimentalRED(LabelFrame, ModuleFrameMixin):
     """GUI panel to perform a simple RED experiment using discrete rotation
     steps."""
 
diff --git a/src/instamatic/gui/sed_frame.py b/src/instamatic/gui/sed_frame.py
index 9f20fe6b..9fb9a41b 100644
--- a/src/instamatic/gui/sed_frame.py
+++ b/src/instamatic/gui/sed_frame.py
@@ -9,7 +9,7 @@
 from instamatic.calibrate import CalibDirectBeam
 from instamatic.calibrate.filenames import CALIB_BEAMSHIFT, CALIB_DIRECTBEAM
 
-from .base_module import BaseModule, HasQMixin
+from .base_module import BaseModule, ModuleFrameMixin
 
 # import matplotlib
 # matplotlib.use('TkAgg')
@@ -50,7 +50,7 @@
 Press <OK> to start"""
 
 
-class ExperimentalSED(LabelFrame, HasQMixin):
+class ExperimentalSED(LabelFrame, ModuleFrameMixin):
     """GUI panel to start a SerialED experiment."""
 
     def __init__(self, parent):
diff --git a/src/instamatic/gui/videostream_frame.py b/src/instamatic/gui/videostream_frame.py
index 6e427225..0ea39bb8 100644
--- a/src/instamatic/gui/videostream_frame.py
+++ b/src/instamatic/gui/videostream_frame.py
@@ -15,14 +15,14 @@
 
 from instamatic._typing import AnyPath
 from instamatic.formats import read_tiff, write_tiff
-from instamatic.gui.base_module import BaseModule, HasQMixin
+from instamatic.gui.base_module import BaseModule, ModuleFrameMixin
 from instamatic.gui.click_dispatcher import ClickDispatcher
 from instamatic.gui.videostream_processor import VideoStreamProcessor
 from instamatic.processing import apply_flatfield_correction
 from instamatic.utils.spinbox import Spinbox
 
 
-class VideoStreamFrame(LabelFrame, HasQMixin):
+class VideoStreamFrame(LabelFrame, ModuleFrameMixin):
     """GUI panel to continuously display the last frame streamed from the
     camera."""
 

From 621d954e434d71dddb6f836678554fb9299ff26c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Fri, 21 Nov 2025 16:05:32 +0100
Subject: [PATCH 08/18] `Any` is a significantly better type hint that `None`

---
 src/instamatic/gui/base_module.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/instamatic/gui/base_module.py b/src/instamatic/gui/base_module.py
index aaa6a281..971abf94 100644
--- a/src/instamatic/gui/base_module.py
+++ b/src/instamatic/gui/base_module.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from queue import Queue
+from typing import Any
 
 
 class BaseModule:
@@ -39,4 +40,4 @@ class ModuleFrameMixin:
     """Asserts some class attributes i.e. module.q, app remain reserved."""
 
     q: Queue
-    app: None
+    app: Any

From 8eeda49e6663d5feaaabba530900c5c7c4b0a0d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Fri, 21 Nov 2025 16:07:52 +0100
Subject: [PATCH 09/18] Do not change default `ENABLE_FOOTFREE_OPTION`

---
 src/instamatic/gui/cred_frame.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/instamatic/gui/cred_frame.py b/src/instamatic/gui/cred_frame.py
index 3438566e..802256a0 100644
--- a/src/instamatic/gui/cred_frame.py
+++ b/src/instamatic/gui/cred_frame.py
@@ -8,7 +8,7 @@
 
 from .base_module import BaseModule, ModuleFrameMixin
 
-ENABLE_FOOTFREE_OPTION = True
+ENABLE_FOOTFREE_OPTION = False
 
 
 class ExperimentalcRED(LabelFrame, ModuleFrameMixin):
@@ -175,7 +175,6 @@ def init_vars(self):
         self.var_exposure_time_image = DoubleVar(value=0.01)
 
         self.var_footfree_rotate_to = DoubleVar(value=65.0)
-        self.var_footfree_rotate_speed = DoubleVar(value=0.0)
         self.var_toggle_footfree = BooleanVar(value=False)
         self.mode = 'regular'
 

From 190d632c4d4f151e4679fb54c37ca1e5bbec0ed6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Fri, 21 Nov 2025 17:28:11 +0100
Subject: [PATCH 10/18] Improve lmb/rmb responsiveness, messages, GUI feedback

---
 src/instamatic/gui/click_dispatcher.py |  2 +
 src/instamatic/gui/ctrl_frame.py       | 89 +++++++++++++-------------
 2 files changed, 45 insertions(+), 46 deletions(-)

diff --git a/src/instamatic/gui/click_dispatcher.py b/src/instamatic/gui/click_dispatcher.py
index 7b430cb2..b07ec574 100644
--- a/src/instamatic/gui/click_dispatcher.py
+++ b/src/instamatic/gui/click_dispatcher.py
@@ -82,9 +82,11 @@ def add_listener(
         self,
         name: str,
         callback: Optional[Callable[[ClickEvent], None]] = None,
+        active: bool = False,
     ) -> ClickListener:
         """Convenience method that adds and returns a new `ClickListener`"""
         listener = ClickListener(name, callback)
+        listener.active = active
         self.listeners[name] = listener
         return listener
 
diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index cb7ce2ae..995262ba 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -81,10 +81,12 @@ def __init__(self, parent):
         text = 'Move stage with LMB'
         self.lmb_stage = Checkbutton(frame, text=text, variable=self.var_lmb_stage)
         self.lmb_stage.grid(row=1, column=3, columnspan=3, sticky='W')
+        self.var_lmb_stage.trace_add('write', self.toggle_lmb_stage)
 
         text = 'Move beam with RMB'
         self.rmb_beam = Checkbutton(frame, text=text, variable=self.var_rmb_beam)
         self.rmb_beam.grid(row=2, column=3, columnspan=3, sticky='W')
+        self.var_rmb_beam.trace_add('write', self.toggle_rmb_beam)
 
         e_stage_x = Spinbox(frame, textvariable=self.var_stage_x, **stage)
         e_stage_x.grid(row=6, column=1, sticky='EW')
@@ -224,10 +226,8 @@ def init_vars(self):
         self.var_diff_defocus_on = BooleanVar(value=False)
 
         self.var_stage_wait = BooleanVar(value=True)
-        self.var_rmb_beam = BooleanVar(value=False)
-        self.var_rmb_beam.trace_add('write', self.toggle_rmb_beam)
         self.var_lmb_stage = BooleanVar(value=False)
-        self.var_lmb_stage.trace_add('write', self.toggle_lmb_stage)
+        self.var_rmb_beam = BooleanVar(value=False)
 
     def set_mode(self, event=None):
         self.ctrl.mode.set(self.var_mode.get())
@@ -325,53 +325,50 @@ def toggle_alpha_wobbler(self):
     def toggle_lmb_stage(self, _name, _index, _mode):
         """If self.var_lmb_stage, move stage using Left Mouse Button."""
 
-        try:
-            stage_matrix = self.ctrl.get_stagematrix()
-        except KeyError:
-            print('No calibration :<')
-            # self.var_lmb_stage.set(False)
-            return
-
-        def _cb(click: ClickEvent) -> None:
-            if click.button == MouseButton.LEFT:
-                cam_dim_x, cam_dim_y = self.ctrl.cam.get_camera_dimensions()
-                pixel_delta = np.array([click.y - cam_dim_y / 2, click.x - cam_dim_x / 2])
-                stage_shift = np.dot(pixel_delta, stage_matrix)
-                stage_x, stage_y = self.ctrl.stage.xy
-                self.ctrl.stage.set(x=stage_x + stage_shift[0], y=stage_y + stage_shift[1])
-            print(f'Stage position at {self.ctrl.stage.get()}')
-
-        if checked := self.var_lmb_stage.get():
-            d = self.app.get_module('stream').click_dispatcher
-            n = 'lmb_stage'
-            self.lmb_stage_cl = c if (c := d.listeners.get(n)) else d.add_listener(n, _cb)
-        self.lmb_stage_cl.active = checked
+        d = self.app.get_module('stream').click_dispatcher
+        if self.var_lmb_stage.get():
+            try:
+                stage_matrix = self.ctrl.get_stagematrix()
+            except KeyError:
+                print('No stage matrix for current mode and magnification found.')
+                print('Run `instamatic.calibrate_stagematrix` to use this feature.')
+                self.var_lmb_stage.set(False)
+                return
+
+            def _callback(click: ClickEvent) -> None:
+                if click.button == MouseButton.LEFT:
+                    cam_dim_x, cam_dim_y = self.ctrl.cam.get_camera_dimensions()
+                    pixel_delta = np.array([click.y - cam_dim_y / 2, click.x - cam_dim_x / 2])
+                    stage_shift = np.dot(pixel_delta, stage_matrix)
+                    x, y = self.ctrl.stage.xy
+                    self.ctrl.stage.set(x=x + stage_shift[0], y=y + stage_shift[1])
+
+            d.add_listener('lmb_stage', _callback, active=True)
+        else:
+            d.listeners.pop('lmb_stage', None)
 
     def toggle_rmb_beam(self, _name, _index, _mode) -> None:
         """If self.var_rmb_beam, move beam using Right Mouse Button."""
 
-        try:
-            if not hasattr(self, 'calib_beamshift'):
-                path = self.app.get_module('io').get_experiment_directory().parent / 'calib'
-                print(path / CALIB_BEAMSHIFT)
-                self.calib_beamshift = CalibBeamShift.from_file(path / CALIB_BEAMSHIFT)
-                print(self.calib_beamshift)
-        except OSError:
-            print('No calibration :(')
-            # self.var_rmb_beam.set(False)
-            return
-
-        def _cb(click: ClickEvent) -> None:
-            if click.button == MouseButton.RIGHT:
-                bs = self.calib_beamshift.pixelcoord_to_beamshift((click.y, click.x))
-                self.ctrl.beamshift.set(*bs)
-            print(f'Beam shift at {self.ctrl.beamshift.get()}')
-
-        if checked := self.var_rmb_beam.get():
-            d = self.app.get_module('stream').click_dispatcher
-            n = 'rmb_beam'
-            self.rmb_beam_cl = c if (c := d.listeners.get(n)) else d.add_listener(n, _cb)
-        self.rmb_beam_cl.active = checked
+        d = self.app.get_module('stream').click_dispatcher
+        if self.var_rmb_beam.get():
+            path = self.app.get_module('io').get_experiment_directory().parent / 'calib'
+            try:
+                calib_beamshift = CalibBeamShift.from_file(path / CALIB_BEAMSHIFT)
+            except OSError:
+                print(f'No {CALIB_BEAMSHIFT} file in directory {path} found.')
+                print('Run `instamatic.calibrate_beamshift` there to use this feature.')
+                self.var_rmb_beam.set(False)
+                return
+
+            def _callback(click: ClickEvent) -> None:
+                if click.button == MouseButton.RIGHT:
+                    bs = calib_beamshift.pixelcoord_to_beamshift((click.y, click.x))
+                    self.ctrl.beamshift.set(*[float(b) for b in bs])
+
+            d.add_listener('rmb_beam', _callback, active=True)
+        else:
+            d.listeners.pop('rmb_beam', None)
 
     def stage_stop(self):
         self.q.put(('ctrl', {'task': 'stage.stop'}))

From 2f1d72674f3a5863aca5201cb9e17397f6572621 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Fri, 21 Nov 2025 17:32:53 +0100
Subject: [PATCH 11/18] After all, why would you ever want to disable the
 footfree option???

---
 src/instamatic/gui/cred_frame.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/instamatic/gui/cred_frame.py b/src/instamatic/gui/cred_frame.py
index 802256a0..b85b45aa 100644
--- a/src/instamatic/gui/cred_frame.py
+++ b/src/instamatic/gui/cred_frame.py
@@ -8,7 +8,7 @@
 
 from .base_module import BaseModule, ModuleFrameMixin
 
-ENABLE_FOOTFREE_OPTION = False
+ENABLE_FOOTFREE_OPTION = True
 
 
 class ExperimentalcRED(LabelFrame, ModuleFrameMixin):

From 9bfe76cbf5b64bd7f20365ed6606997c1f0286c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Fri, 21 Nov 2025 17:34:11 +0100
Subject: [PATCH 12/18] Change "Rotation Speed" to "Rotation speed" to align
 with other settings

---
 src/instamatic/gui/ctrl_frame.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index 995262ba..f0fcc1fb 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -95,7 +95,7 @@ def __init__(self, parent):
         e_stage_z = Spinbox(frame, textvariable=self.var_stage_z, **stage)
         e_stage_z.grid(row=6, column=3, sticky='EW')
 
-        Label(frame, text='Rotation Speed', width=20).grid(row=5, column=0, sticky='W')
+        Label(frame, text='Rotation speed', width=20).grid(row=5, column=0, sticky='W')
         e_goniotool_tx = Spinbox(
             frame, width=10, textvariable=self.var_goniotool_tx, from_=1, to=12, increment=1
         )

From d672d283178bf12c89d4c5eb5d6c515abe5bf0f7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Mon, 24 Nov 2025 11:45:03 +0100
Subject: [PATCH 13/18] Update src/instamatic/gui/ctrl_frame.py

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
---
 src/instamatic/gui/ctrl_frame.py | 39 ++++++++++++++++----------------
 1 file changed, 20 insertions(+), 19 deletions(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index f0fcc1fb..51551066 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -326,26 +326,27 @@ def toggle_lmb_stage(self, _name, _index, _mode):
         """If self.var_lmb_stage, move stage using Left Mouse Button."""
 
         d = self.app.get_module('stream').click_dispatcher
-        if self.var_lmb_stage.get():
-            try:
-                stage_matrix = self.ctrl.get_stagematrix()
-            except KeyError:
-                print('No stage matrix for current mode and magnification found.')
-                print('Run `instamatic.calibrate_stagematrix` to use this feature.')
-                self.var_lmb_stage.set(False)
-                return
-
-            def _callback(click: ClickEvent) -> None:
-                if click.button == MouseButton.LEFT:
-                    cam_dim_x, cam_dim_y = self.ctrl.cam.get_camera_dimensions()
-                    pixel_delta = np.array([click.y - cam_dim_y / 2, click.x - cam_dim_x / 2])
-                    stage_shift = np.dot(pixel_delta, stage_matrix)
-                    x, y = self.ctrl.stage.xy
-                    self.ctrl.stage.set(x=x + stage_shift[0], y=y + stage_shift[1])
-
-            d.add_listener('lmb_stage', _callback, active=True)
-        else:
+        if not self.var_lmb_stage.get():
             d.listeners.pop('lmb_stage', None)
+            return
+            
+        try:
+            stage_matrix = self.ctrl.get_stagematrix()
+        except KeyError:
+            print('No stage matrix for current mode and magnification found.')
+            print('Run `instamatic.calibrate_stagematrix` to use this feature.')
+            self.var_lmb_stage.set(False)
+            return
+
+        def _callback(click: ClickEvent) -> None:
+            if click.button == MouseButton.LEFT:
+                cam_dim_x, cam_dim_y = self.ctrl.cam.get_camera_dimensions()
+                pixel_delta = np.array([click.y - cam_dim_y / 2, click.x - cam_dim_x / 2])
+                stage_shift = np.dot(pixel_delta, stage_matrix)
+                x, y = self.ctrl.stage.xy
+                self.ctrl.stage.set(x=x + stage_shift[0], y=y + stage_shift[1])
+
+        d.add_listener('lmb_stage', _callback, active=True)
 
     def toggle_rmb_beam(self, _name, _index, _mode) -> None:
         """If self.var_rmb_beam, move beam using Right Mouse Button."""

From 08048e2d6cf132b3b9f956b0ce920ad41b382814 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Mon, 24 Nov 2025 11:45:23 +0100
Subject: [PATCH 14/18] Update src/instamatic/gui/ctrl_frame.py

Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
---
 src/instamatic/gui/ctrl_frame.py | 35 ++++++++++++++++----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index 51551066..d92063bb 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -352,24 +352,25 @@ def toggle_rmb_beam(self, _name, _index, _mode) -> None:
         """If self.var_rmb_beam, move beam using Right Mouse Button."""
 
         d = self.app.get_module('stream').click_dispatcher
-        if self.var_rmb_beam.get():
-            path = self.app.get_module('io').get_experiment_directory().parent / 'calib'
-            try:
-                calib_beamshift = CalibBeamShift.from_file(path / CALIB_BEAMSHIFT)
-            except OSError:
-                print(f'No {CALIB_BEAMSHIFT} file in directory {path} found.')
-                print('Run `instamatic.calibrate_beamshift` there to use this feature.')
-                self.var_rmb_beam.set(False)
-                return
-
-            def _callback(click: ClickEvent) -> None:
-                if click.button == MouseButton.RIGHT:
-                    bs = calib_beamshift.pixelcoord_to_beamshift((click.y, click.x))
-                    self.ctrl.beamshift.set(*[float(b) for b in bs])
-
-            d.add_listener('rmb_beam', _callback, active=True)
-        else:
+        if not self.var_rmb_beam.get():
             d.listeners.pop('rmb_beam', None)
+            return
+
+        path = self.app.get_module('io').get_experiment_directory().parent / 'calib'
+        try:
+            calib_beamshift = CalibBeamShift.from_file(path / CALIB_BEAMSHIFT)
+        except OSError:
+            print(f'No {CALIB_BEAMSHIFT} file in directory {path} found.')
+            print('Run `instamatic.calibrate_beamshift` there to use this feature.')
+            self.var_rmb_beam.set(False)
+            return
+
+        def _callback(click: ClickEvent) -> None:
+            if click.button == MouseButton.RIGHT:
+                bs = calib_beamshift.pixelcoord_to_beamshift((click.y, click.x))
+                self.ctrl.beamshift.set(*[float(b) for b in bs])
+
+        d.add_listener('rmb_beam', _callback, active=True)            
 
     def stage_stop(self):
         self.q.put(('ctrl', {'task': 'stage.stop'}))

From dc96cd05e363befadf7ae5a40de4e5f6c996bbaa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Mon, 24 Nov 2025 12:02:36 +0100
Subject: [PATCH 15/18] Make local config path reference more readable

---
 src/instamatic/gui/ctrl_frame.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index d92063bb..cfe7625b 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -329,7 +329,7 @@ def toggle_lmb_stage(self, _name, _index, _mode):
         if not self.var_lmb_stage.get():
             d.listeners.pop('lmb_stage', None)
             return
-            
+
         try:
             stage_matrix = self.ctrl.get_stagematrix()
         except KeyError:
@@ -356,7 +356,7 @@ def toggle_rmb_beam(self, _name, _index, _mode) -> None:
             d.listeners.pop('rmb_beam', None)
             return
 
-        path = self.app.get_module('io').get_experiment_directory().parent / 'calib'
+        path = self.app.get_module('io').get_working_directory() / 'calib'
         try:
             calib_beamshift = CalibBeamShift.from_file(path / CALIB_BEAMSHIFT)
         except OSError:
@@ -370,7 +370,7 @@ def _callback(click: ClickEvent) -> None:
                 bs = calib_beamshift.pixelcoord_to_beamshift((click.y, click.x))
                 self.ctrl.beamshift.set(*[float(b) for b in bs])
 
-        d.add_listener('rmb_beam', _callback, active=True)            
+        d.add_listener('rmb_beam', _callback, active=True)
 
     def stage_stop(self):
         self.q.put(('ctrl', {'task': 'stage.stop'}))

From 31c28ea309cf6b4a2988a23aefc7c428ab1fddb7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Mon, 24 Nov 2025 12:43:35 +0100
Subject: [PATCH 16/18] Implement `toggle_lmb_stage` fallback using
 `move_in_projection`

---
 src/instamatic/gui/ctrl_frame.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index cfe7625b..66a2e9ab 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -342,9 +342,8 @@ def _callback(click: ClickEvent) -> None:
             if click.button == MouseButton.LEFT:
                 cam_dim_x, cam_dim_y = self.ctrl.cam.get_camera_dimensions()
                 pixel_delta = np.array([click.y - cam_dim_y / 2, click.x - cam_dim_x / 2])
-                stage_shift = np.dot(pixel_delta, stage_matrix)
-                x, y = self.ctrl.stage.xy
-                self.ctrl.stage.set(x=x + stage_shift[0], y=y + stage_shift[1])
+                stage_delta = np.dot(pixel_delta, stage_matrix)
+                self.ctrl.stage.move_in_projection(*stage_delta)
 
         d.add_listener('lmb_stage', _callback, active=True)
 

From f639daba2b39f484a7c85828f402f2efa1b2235f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Mon, 24 Nov 2025 16:19:35 +0100
Subject: [PATCH 17/18] Implement fixes necessary to handle remote camera via
 server

---
 src/instamatic/camera/camera_client.py | 50 +++++++++++++-------------
 src/instamatic/server/cam_server.py    |  8 ++---
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/src/instamatic/camera/camera_client.py b/src/instamatic/camera/camera_client.py
index 6b320657..9f75314d 100644
--- a/src/instamatic/camera/camera_client.py
+++ b/src/instamatic/camera/camera_client.py
@@ -3,9 +3,9 @@
 import atexit
 import socket
 import subprocess as sp
+import threading
 import time
 from functools import wraps
-from typing import Dict
 
 import numpy as np
 
@@ -55,6 +55,7 @@ def __init__(
         self.name = name
         self.interface = interface
         self._bufsize = BUFSIZE
+        self._eval_lock = threading.Lock()
         self.verbose = False
 
         try:
@@ -79,7 +80,7 @@ def __init__(
         )
         print('Use shared memory:', self.use_shared_memory)
 
-        self.buffers: Dict[str, np.ndarray] = {}
+        self.buffers: dict[str, np.ndarray] = {}
         self.shms = {}
 
         self._attr_dct: dict = {}
@@ -122,36 +123,37 @@ def wrapper(*args, **kwargs):
 
     def _eval_dct(self, dct):
         """Takes approximately 0.2-0.3 ms per call if HOST=='localhost'."""
-        self.s.send(dumper(dct))
+        with self._eval_lock:
+            self.s.send(dumper(dct))
 
-        acquiring_image = dct['attr_name'] == 'get_image'
-        acquiring_movie = dct['attr_name'] == 'get_movie'
+            acquiring_image = dct['attr_name'] == 'get_image'
+            acquiring_movie = dct['attr_name'] == 'get_movie'
 
-        if acquiring_movie:
-            raise NotImplementedError('Acquiring movies over a socket is not supported.')
+            if acquiring_movie:
+                raise NotImplementedError('Acquiring movies over a socket is not supported.')
 
-        if acquiring_image and not self.use_shared_memory:
-            response = self.s.recv(self._imagebufsize)
-        else:
-            response = self.s.recv(self._bufsize)
+            if acquiring_image and not self.use_shared_memory:
+                response = self.s.recv(self._imagebufsize)
+            else:
+                response = self.s.recv(self._bufsize)
 
-        if response:
-            status, data = loader(response)
-        else:
-            raise RuntimeError(f'Received empty response when evaluating {dct=}')
+            if response:
+                status, data = loader(response)
+            else:
+                raise RuntimeError(f'Received empty response when evaluating {dct=}')
 
-        if self.use_shared_memory and acquiring_image:
-            data = self.get_data_from_shared_memory(**data)
+            if self.use_shared_memory and acquiring_image:
+                data = self.get_data_from_shared_memory(**data)
 
-        if status == 200:
-            return data
+            if status == 200:
+                return data
 
-        elif status == 500:
-            error_code, args = data
-            raise exception_list.get(error_code, TEMCommunicationError)(*args)
+            elif status == 500:
+                error_code, args = data
+                raise exception_list.get(error_code, TEMCommunicationError)(*args)
 
-        else:
-            raise ConnectionError(f'Unknown status code: {status}')
+            else:
+                raise ConnectionError(f'Unknown status code: {status}')
 
     def _init_dict(self):
         """Get list of functions and their doc strings from the uninitialized
diff --git a/src/instamatic/server/cam_server.py b/src/instamatic/server/cam_server.py
index 2d3c926f..290fbf70 100644
--- a/src/instamatic/server/cam_server.py
+++ b/src/instamatic/server/cam_server.py
@@ -2,7 +2,6 @@
 
 import datetime
 import logging
-import pickle
 import queue
 import socket
 import threading
@@ -12,10 +11,9 @@
 
 from instamatic import config
 from instamatic.camera import get_camera
+from instamatic.server.serializer import dumper, loader
 from instamatic.utils import high_precision_timers
 
-from .serializer import dumper, loader
-
 high_precision_timers.enable()
 
 if config.settings.cam_use_shared_memory:
@@ -174,13 +172,13 @@ def main():
 
 The host and port are defined in `config/settings.yaml`.
 
-The data sent over the socket is a pickled dictionary with the following elements:
+The data sent over the socket is a serialized dict with the following elements:
 
 - `attr_name`: Name of the function to call or attribute to return (str)
 - `args`: (Optional) List of arguments for the function (list)
 - `kwargs`: (Optiona) Dictionary of keyword arguments for the function (dict)
 
-The response is returned as a pickle object.
+The response is returned as a serialized object.
 """
 
     parser = argparse.ArgumentParser(

From c593bf49ebe0271492076169b176897a6552e753 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20Tcho=C5=84?= <dantch@onet.eu>
Date: Mon, 24 Nov 2025 18:05:55 +0100
Subject: [PATCH 18/18] Allow setting non-integer rotation speeds

---
 src/instamatic/gui/ctrl_frame.py                       | 2 +-
 src/instamatic/microscope/interface/jeol_microscope.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/instamatic/gui/ctrl_frame.py b/src/instamatic/gui/ctrl_frame.py
index 139fea0d..88befcc0 100644
--- a/src/instamatic/gui/ctrl_frame.py
+++ b/src/instamatic/gui/ctrl_frame.py
@@ -203,7 +203,7 @@ def init_vars(self):
         self.var_stage_y = IntVar(value=0)
         self.var_stage_z = IntVar(value=0)
 
-        self.var_goniotool_tx = IntVar(value=1)
+        self.var_goniotool_tx = DoubleVar(value=1)
 
         self.var_brightness = IntVar(value=65535)
         self.var_difffocus = IntVar(value=65535)
diff --git a/src/instamatic/microscope/interface/jeol_microscope.py b/src/instamatic/microscope/interface/jeol_microscope.py
index 76c9e90f..a5156264 100644
--- a/src/instamatic/microscope/interface/jeol_microscope.py
+++ b/src/instamatic/microscope/interface/jeol_microscope.py
@@ -384,7 +384,7 @@ def getRotationSpeed(self) -> int:
 
     def setRotationSpeed(self, value: int):
         if self.goniotool_available:
-            self.goniotool.set_rate(value)
+            self.goniotool.set_rate(int(value))
         else:
             raise TEMCommunicationError('Goniotool connection is not available.')