stage: integrate into the system (replace NavigationController) #48

ianohara · 2024-12-28T02:16:35Z

This replaces NavigationController with AbstractStage, and starts pulling apart the different pieces that depended on signals from afar in various pieces.

Still To Do:

Fix click to move
Test all the use cases we know are actually used in HW
Test all the sign issues that were uncovered and make sure it is all consistent now (eg: backlash direction, dz for acquisitions, etc)

ianohara · 2024-12-28T02:18:42Z

software/control/core/core.py

@@ -1610,1207 +1311,23 @@ def add_current_coords_to_focus_map(self):
        self.focus_map_coords.append((x,y,z))
        print(f"Added triple ({x},{y},{z}) to focus map")

-
-class MultiPointWorker(QObject):


It might make sense to move this back from core.multipoint.py just so we can see what actually changed, and then break core.py apart into pieces in multiple subsequent pr.

Perhaps it’s time to make this independent of pyqt (remove dependence on signaling, for example for updating the illumination and channel settings)?

ianohara · 2024-12-28T02:20:08Z

software/control/core/core.py

@@ -3785,122 +2285,6 @@ def scale_contrast_limits(self, target_dtype):
        self.acquisition_dtype = target_dtype


-class PlateReaderNavigationController(QObject):             # Not implemented for Prior stage


This was unused. ag PlateReaderNavigationController only showed this occurence.

Yes this obsolete and can be deleted.

ianohara · 2024-12-28T02:20:42Z

software/control/core/core.py

        # update the displacement measurement
        self.measure_displacement()

    def set_reference(self):
        # turn on the laser
        self.microcontroller.turn_on_AF_laser()
-        self.wait_till_operation_is_completed()
+        self.microcontroller.wait_till_operation_is_completed()
        # get laser spot location
        x,y = self._get_laser_spot_centroid()
        # turn off the laser
        self.microcontroller.turn_off_AF_laser()


Need to add the wait back here.

ianohara · 2024-12-28T02:21:18Z

software/control/gui.py

@@ -1,216 +0,0 @@
-# set QT_API environment variable


This was very broken, so delete it for now. We can restore it later.

software/control/gui_hcs.py

ianohara · 2024-12-28T02:22:26Z

software/control/gui_hcs.py

-            self.navigationController.signal_joystick_button_pressed.connect(self.trackingControlWidget.slot_joystick_button_pressed)
-        else:
-            self.navigationController.signal_joystick_button_pressed.connect(self.autofocusController.autofocus)
+        # TODO(imo): Fix joystick after removal of navigation controller


This TODO needs to be addressed before merge

Currently the joystick buttons are not implemented in the firmware. Previously joystick is connected directly to the microcontroller (arduino). Now it’s joystick -> teensy lc -> teensy 4.1 -> computer.

software/control/gui_hcs.py

ianohara · 2024-12-28T02:23:52Z

software/control/gui_malaria.py

This was broken already, so removing it for now. We can restore + fix it later.

We can remove this. The malaria “app” is now in Heguang’s repo.

ianohara · 2024-12-28T02:24:51Z

software/control/microcontroller.py

@@ -591,6 +591,11 @@ def analog_write_onboard_DAC(self,dac,value):
        cmd[4] = value & 0xff
        self.send_command(cmd)

+    def set_piezo_um(self, z_piezo_um):


It probably makes sense to move this here since it requires intricate knowledge of the micro dac setup. An alternative would be to figure out how to have AbstractStage handle this (eg: in its Z axis)

Yes we’ll need to think about how to deal with the different z stage options: stepper alone, stepper + piezo, direct drive stage alone (Dover Motion DOF-5 or PI V-308), piezo alone.

ianohara · 2024-12-28T02:26:03Z

software/control/navigation_prior.py

I think @hongquanli said this actually needs to work, but hopefully the way we'd do it is to just use a PriorStage instead of CephlaStage (and then everything should just work).

The only caveat is populating any special controls for the CephlaStage and PriorStage in the ui. For that, I think we are stuck doing isinstance checks for now.

ianohara · 2024-12-28T02:28:48Z

software/control/widgets.py

        self.add_components()
        self.setFrameStyle(QFrame.Panel | QFrame.Raised)

+        self.position_update_timer = QTimer()


This is one way to do position updates. It is nice because we only need to pass in pieces of the future Microscope API, and otherwise the widgets can be independent of each other.

An alternative, if we don't like the Timer/polling approach, is to define a standard collection of Signal that any Widget can assume exists and pass them as an init argument. Then each Widget can just connect itself to any of those signals if needed at init time, but doesn't need to be passed the entire machinery behind other Widgets.

software/control/widgets.py

This is starting work on the "X, Y, Z Motion stage" task in https://www.notion.so/cephla/Headless-Mode-and-Scripting-Design-1452dfbf6ae480c3b444ee0847f532a5 . This adds the `AbstractStage` concept, and implements the `CephlaStage`. It also adds basic simulated stage tests. See #48 for integration of this into the system.

…and use stage everywhere

…ration Feature/napari integration

ianohara commented Dec 28, 2024

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ianohara commented Dec 28, 2024

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ianohara commented Dec 28, 2024

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ianohara force-pushed the ian-use-stage branch from 093d1b7 to 52ee495 Compare December 28, 2024 23:29

ianohara force-pushed the ian-stage-breakout branch from 00ef16c to 359951c Compare December 28, 2024 23:29

ianohara added 15 commits December 30, 2024 12:39

interface: get rid of stage implementation details outside of stage, …

5646102

…and use stage everywhere

fix rebase issues

0e7989c

Address all the click + position update TODO

68dfb64

lots more updates to fix things

003e2ff

from hongquan, nav bar is no longer used. delete it

dac6cb9

fix flexible multi point widget construction

d5ad958

remove unused init arg

f3da65b

fix get_pos call

d20a67c

Fix rebase issue

69ff824

Fix rebase issue

16aa289

rebase errors, missed stage conversion

c0c021e

Fix click to move toggle

75f9a0d

more fixes

6e30b3e

throw from camera upon failure

cb117e2

pass stage to microscope

ea8ca50

ianohara added 3 commits December 30, 2024 12:39

home y, then x

0d70942

fix reference to non-existent config variable

971671e

elim nav controller from microscope

7a18115

ianohara force-pushed the ian-use-stage branch from 28e28d6 to 7a18115 Compare December 30, 2024 20:41

ianohara changed the base branch from ian-stage-breakout to master December 30, 2024 20:42

ianohara marked this pull request as ready for review December 30, 2024 20:42

ianohara merged commit 98f3f09 into master Dec 30, 2024
1 of 3 checks passed

beniroquai pushed a commit to beniroquai/octopi-research that referenced this pull request Jan 20, 2025

Merge pull request Cephla-Lab#48 from hongquanli/feature/napari-integ…

ad9de41

…ration Feature/napari integration

ianohara deleted the ian-use-stage branch February 4, 2025 00:33

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stage: integrate into the system (replace NavigationController) #48

stage: integrate into the system (replace NavigationController) #48

ianohara commented Dec 28, 2024

ianohara Dec 28, 2024

hongquanli Dec 29, 2024

ianohara Dec 28, 2024

hongquanli Dec 29, 2024

ianohara Dec 28, 2024

ianohara Dec 28, 2024

ianohara Dec 28, 2024

hongquanli Dec 29, 2024

ianohara Dec 28, 2024

hongquanli Dec 29, 2024

ianohara Dec 28, 2024

hongquanli Dec 29, 2024

ianohara Dec 28, 2024

ianohara Dec 28, 2024

		@@ -3785,122 +2285,6 @@ def scale_contrast_limits(self, target_dtype):
		self.acquisition_dtype = target_dtype


		class PlateReaderNavigationController(QObject): # Not implemented for Prior stage

stage: integrate into the system (replace NavigationController) #48

stage: integrate into the system (replace NavigationController) #48

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ianohara commented Dec 28, 2024

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