ASI RFVC Changes to be merged in Navigate #1099

Daniel-Buckelew · 2025-06-05T00:14:27Z

Bringing in the related RFVC things to parent Navigate. The PR says I'll be deleting a file from y'all's repository, but I do not believe that file exists, so hopefully that's not an issue.

…into asi_daq

Merge RFVC into DAQ for testing

This reverts commit f6f6864.

…ks...

…into asi_daq

…etagivan into asi_daq" This reverts commit e401072, reversing changes made to fa48620.

…SIDaq

Bringing all of the pieces into develop for packaging purposes

RFVC PR

…into rfvc_pr

Copilot

Pull Request Overview

This pull request integrates RFVC changes to support ASI devices within the Navigate codebase while removing deprecated implementations. Key changes include:

Addition of a new ASI Remote Focus module with updated waveform handling.
Minor type annotation improvements in the ASI Laser class.
Removal of the obsolete ASI Galvo module and corresponding documentation/configuration updates.
Updates to Tiger Controller command formatting for consistency.

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/navigate/model/devices/remote_focus/asi.py	Implements the new ASI Remote Focus driver and waveform methods.
src/navigate/model/devices/laser/asi.py	Fixes type annotation for the device_id parameter.
src/navigate/model/devices/galvo/asi.py	Deletes the obsolete ASI Galvo driver file.
src/navigate/model/devices/APIs/asi/asi_tiger_controller.py	Updates Tiger Controller commands (e.g., SA_waveform and SAM) with revised command prefixes.
src/navigate/config/configuration_database.py	Adds configuration support for ASI devices including an axis widget field.
docs/source/02_user_guide/01_supported_hardware/remote_focus.rst	Updates documentation to include ASI hardware details and configuration examples.

Comments suppressed due to low confidence (1)

src/navigate/model/devices/galvo/asi.py:1

Ensure that any dependencies or references to the deleted ASI Galvo module are removed from the codebase to prevent broken references.

# Copyright (c) 2021-2024  The University of Texas Southwestern Medical Center.

Copilot · 2025-06-05T02:32:38Z

src/navigate/model/devices/remote_focus/asi.py

+                if temp == "-" or temp == ".":
+                    waveform_constants["remote_focus_constants"][imaging_mode][zoom][
+                        laser
+                    ]["amplitude"] = "1000"
+
+                amplitude = float(
+                    waveform_constants["remote_focus_constants"][imaging_mode][zoom][
+                        laser
+                    ]["amplitude"]
+                )
+
+                # Validation for when user puts a '-' in spinbox
+                temp = waveform_constants["remote_focus_constants"][imaging_mode][zoom][
+                    laser
+                ]["offset"]
+                if temp == "-" or temp == ".":
+                    waveform_constants["remote_focus_constants"][imaging_mode][zoom][
+                        laser
+                    ]["offset"] = "0"
+
+                remote_focus_offset = float(
+                    waveform_constants["remote_focus_constants"][imaging_mode][zoom][
+                        laser
+                    ]["offset"]
+                )


Consider storing numeric constants as numbers rather than as strings in waveform_constants (e.g., using 1000 instead of "1000") to reduce the need for type conversion and improve clarity.

Suggested change

if temp == "-" or temp == ".":

waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["amplitude"] = "1000"

amplitude = float(

waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["amplitude"]

)

# Validation for when user puts a '-' in spinbox

temp = waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["offset"]

if temp == "-" or temp == ".":

waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["offset"] = "0"

remote_focus_offset = float(

waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["offset"]

)

if temp in ["-", "."]:

waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["amplitude"] = 1000

amplitude = waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["amplitude"]

# Validation for when user puts a '-' in spinbox

temp = waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["offset"]

if temp in ["-", "."]:

waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["offset"] = 0

remote_focus_offset = waveform_constants["remote_focus_constants"][imaging_mode][zoom][

laser

]["offset"]

Copilot · 2025-06-05T02:32:38Z

src/navigate/model/devices/APIs/asi/asi_tiger_controller.py

        """

        "Verify if this is for synchronous or asynchronous"
-        self.send_command(f"SAP {axis}={waveform}")
+        print(f"Period (ms): {frequency}")


Remove or replace the debug print statement with proper logging to avoid unintended console output in production.

Suggested change

print(f"Period (ms): {frequency}")

logging.debug(f"Period (ms): {frequency}")

Adopt recommended change to log this information, not print it to the console.

AdvancedImagingUTSW · 2025-06-05T12:55:46Z

src/navigate/model/devices/APIs/asi/asi_tiger_controller.py

@@ -1013,28 +1013,49 @@ def logic_card_off(self, axis : str):
        self.send_command(f'6 CCA Z=0\r')
        self.read_response()

-    def SA_waveform(self, axis:str, waveform=0, amplitude=1000, offset=500):
+    def logic_cell_on(self, axis : str):


Add numpydoc commenting

AdvancedImagingUTSW · 2025-06-05T12:57:37Z

src/navigate/model/devices/galvo/asi.py

-
-                elif self.galvo_waveform == "sine":
-                    frequency=galvo_frequency
-                    amplitude=galvo_amplitude


The ASI galvo does not support these waveforms, or does it?

Yes, we support sine waves.

AdvancedImagingUTSW

Only minor changes requested. See line comments.

EashaS and others added 30 commits March 20, 2025 23:29

Create asi.py

1ba1a81

adds ramp wave to rfvc

0150f56

class init for asidaq

a3d2e4e

Update asi_tiger_controller.py

11ee2c3

Update asi.py

07046df

Update asi.py

51d4559

Update asi.py

074cba4

prepare acquisition

a17aae7

Update asi.py

2ac3ec1

Merge branch 'asi_daq' of https://github.com/Daniel-Buckelew/etagivan …

2fe12a9

…into asi_daq

adds triangle wave

90e0004

sends the correct SAP command for the ramp wave

5e0d2dc

adds setup loop to API and adds close and turn off functions

1f8c3f0

fixed setup loop

e2864e0

create_analog_outputs

76b6e1b

Merge branch 'asi_daq' of https://github.com/Daniel-Buckelew/etagivan …

bc549eb

…into asi_daq

Merge branch 'asi_daq' into victoria/rfvc

adb6f9b

Merge pull request #10 from Daniel-Buckelew/victoria/rfvc

1e13f82

Merge RFVC into DAQ for testing

logic_Cell_on cmds

2240a65

Changes made to make things functions

71e3975

Maybe this improves things.

3a6aeb1

Update asi.py

a285c3d

The Navigate crashing error is resolved.

7db8435

The awkward cahnges to try and make stuff work.

b7a0f84

start daq calls start device

f6f6864

Revert "start daq calls start device"

6290ca6

This reverts commit f6f6864.

DAQ now effectively runs as another serial device. Hopefully this wor…

fa48620

…ks...

Merge branch 'asi_daq' of https://github.com/Daniel-Buckelew/etagivan …

e401072

…into asi_daq

Revert "Merge branch 'asi_daq' of https://github.com/Daniel-Buckelew/…

fb8c165

…etagivan into asi_daq" This reverts commit e401072, reversing changes made to fa48620.

Removing unnecessary catch

c3ba1bf

joelaugustine099 and others added 21 commits May 7, 2025 21:29

doesn't pass period to setup control loop

9895647

cleaned up some code, commented, pulled camera and rfvc delays into A…

a628c3e

…SIDaq

Adding camera delay and rfvc delay to workable features

518434d

Reordering the TTL in the hardcode.

9d6f110

Making things fast as heck

f7b246d

Making things fast pt. 2

fa47761

Maybe this did something?

39596bd

Final touches to fix minor bugs in frequency etc.

43ea873

Axis from config

e493c14

Tweaknig the galvo assignment to work more correctly.

0e49218

Merge pull request #16 from Daniel-Buckelew/asi_daq

7986977

Bringing all of the pieces into develop for packaging purposes

rfvc documentation and comments

b0a9378

Merge pull request #17 from Daniel-Buckelew/rfvc_pr

f1d3f2f

RFVC PR

added info to config database and fixed documentation

be425bc

Merge branch 'rfvc_pr' of https://github.com/Daniel-Buckelew/etagivan …

55df284

…into rfvc_pr

added some information to documentation

b9853d2

Packaging adjustment

81eacf1

More packaging adjustments

0e86e05

Removing Galvo for it's own pull request

a5d94fa

Pulling in the changes from the Laser PR

7a826e2

Removing DAQ text and reorganizing some things

683edfe

Daniel-Buckelew requested a review from AdvancedImagingUTSW June 5, 2025 00:14

AdvancedImagingUTSW requested a review from Copilot June 5, 2025 02:32

Copilot AI reviewed Jun 5, 2025

View reviewed changes

AdvancedImagingUTSW reviewed Jun 5, 2025

View reviewed changes

AdvancedImagingUTSW requested changes Jun 5, 2025

View reviewed changes

AdvancedImagingUTSW mentioned this pull request Jun 11, 2025

ASI Galvo Integration #1100

Open

Merge branch 'develop' into rfvc_pr

1c78126

joelaugustine099 requested a review from annie-xd-wang June 26, 2025 20:38

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ASI RFVC Changes to be merged in Navigate #1099

ASI RFVC Changes to be merged in Navigate #1099

Daniel-Buckelew commented Jun 5, 2025

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	print(f"Period (ms): {frequency}")
	logging.debug(f"Period (ms): {frequency}")

ASI RFVC Changes to be merged in Navigate #1099

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ASI RFVC Changes to be merged in Navigate #1099

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Pull Request Overview

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