828 save waveform constants with acquisition and generate method to load it #841

AdvancedImagingUTSW · 2024-03-08T02:58:18Z

Annie, this could use a close look. Sriya led the charge on these code changes, and her branch combined two different issues: #828 and #804

For #828, she had a hard time getting the waveform popup to repopulate with new values, once she loaded a new waveform constants file. I dabbled with it, and then resorted to something that may not be ideal; I now destroy the waveform popup window, delete the waveform popup controller, and then launch a new popup and controller. To make it less annoying, The new popup shows up where the old one was.

For #804, we will need to change things to accommodate all of the work you did overhauling the camera timing.

Pushing changes so that I can jump on the machine. Co-Authored-By: Sriya Veerapaneni <78429510+Sriya-235@users.noreply.github.com>

@annie-xd-wang

Hey! So I made some changes to the menu_controller.py to save and load waveform_constants files. This allows us to save the waveform constants for experiments and load the same constants for future experiments. This commit also includes changes that @annie-xd-wang made to waveforms.py to align the wave.

Removed hot keys from menu controller. Now saves the waveform constants with the data. Only thing remaining is to have the popup GUI automatically populated with the new parameters.

Updated the documentation to show the updated file menu. Also added few lines about the load and save waveform constants option in the documentation. Replaced the menu_file.png image with a new image of the file menu.

…-acquisition-and-generate-method-to-load-it

AdvancedImagingUTSW · 2024-03-08T03:03:30Z

src/navigate/controller/sub_controllers/menu_controller.py

        #: str: Feature list file name.
        self.feature_list_file_name = "feature_lists.yaml"

+        #: waveform_popup_controller: Waveform Popup Controller.
+        # self.parent_controller.waveform_popup_controller = None
+


Perhaps we should delete these commented lines.

AdvancedImagingUTSW · 2024-03-08T03:05:08Z

src/navigate/model/devices/APIs/hamamatsu/HamamatsuAPI.py

-    "internal_line_interval": 4208720,  # 0x00403850, R/W, sec,
-    # "INTERNAL LINE INTERVAL"
+    "internal_line_interval": 4208720,  # 0x00403850, R/W, sec,    "INTERNAL LINE INTERVAL"
+    "internal_line_speed": 4208704,  # 0x00403840, R/W, m/sec,    "INTERNAL LINE SPEED"


Important changes, presumably.

The modifications to camera functions originate from the commits in PR #808.

AdvancedImagingUTSW · 2024-03-08T03:05:47Z

src/navigate/model/devices/camera/camera_base.py

-        #: int: Maximum image width
-        self.max_image_width = 2048
-        #: int: Maximum image height
-        self.max_image_height = 2048


More important stuff.

AdvancedImagingUTSW · 2024-03-08T03:06:11Z

src/navigate/model/devices/camera/camera_base.py

-        self.camera_parameters["x_pixels"] = self.max_image_width
-        self.camera_parameters["y_pixels"] = self.max_image_height
+        self.y_pixels = 2048
+        self.camera_parameters["x_pixels"] = 2048


Hard coding

AdvancedImagingUTSW · 2024-03-08T03:07:17Z

src/navigate/model/devices/camera/camera_hamamatsu.py

@@ -43,10 +43,11 @@
 logger = logging.getLogger(p)


-class HamamatsuOrca(CameraBase):


I assume that most of these changes can be ignored. I take responsibility for this, and I'm sorry.

AdvancedImagingUTSW · 2024-03-08T03:08:07Z

src/navigate/model/devices/daq/daq_ni.py

@@ -264,6 +266,9 @@ def create_analog_output_tasks(self, channel_key):
        """
        self.n_sample = int(self.sample_rate * self.sweep_times[channel_key])
        max_sample = self.n_sample * self.waveform_expand_num
+        print("max_sample", max_sample)


Delete print statements.

AdvancedImagingUTSW · 2024-03-08T03:08:34Z

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

@@ -188,7 +188,7 @@ def adjust(self, exposure_times, sweep_times):
                elif self.galvo_waveform == "halfsaw":
                    new_wave = sawtooth(
                        sample_rate=self.sample_rate,
-                        sweep_time=self.sweep_time,
+                        sweep_time= self.sweep_time,


Uniform spacing

AdvancedImagingUTSW · 2024-03-08T03:09:16Z

src/navigate/model/microscope.py

@@ -405,13 +405,18 @@ def prepare_acquisition(self):
        sensor_mode = self.configuration["experiment"]["CameraParameters"][
            "sensor_mode"
        ]
+
+        print('sensor_mode', sensor_mode)
+


Delete print statement

…ion-and-generate-method-to-load-it

codecov · 2024-03-12T22:56:27Z

Codecov Report

Attention: Patch coverage is 33.33333% with 26 lines in your changes are missing coverage. Please review.

Project coverage is 54.32%. Comparing base (c1c0d11) to head (b4aeb15).

Files	Patch %	Lines
src/navigate/model/waveforms.py	7.69%	12 Missing ⚠️
...gate/controller/sub_controllers/menu_controller.py	21.42%	11 Missing ⚠️
...te/model/devices/remote_focus/remote_focus_base.py	71.42%	2 Missing ⚠️
src/navigate/controller/controller.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #841      +/-   ##
===========================================
- Coverage    54.33%   54.32%   -0.02%     
===========================================
  Files          154      154              
  Lines        17444    17478      +34     
===========================================
+ Hits          9479     9495      +16     
- Misses        7965     7983      +18

Flag	Coverage Δ
unittests	`54.32% <33.33%> (-0.02%)`	⬇️

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annie-xd-wang

We can test bidirectional acquisition on a machine now.

AdvancedImagingUTSW · 2024-03-13T02:16:53Z

src/navigate/controller/sub_controllers/menu_controller.py

+        )
+
+        if hasattr(self.parent_controller, "waveform_popup_controller"):
+            self.parent_controller.waveform_popup_controller.populate_experiment_values(


Much nicer.

AdvancedImagingUTSW · 2024-03-13T02:20:02Z

Will test first thing tomorrow. But everything looks great.

AdvancedImagingUTSW and others added 10 commits January 25, 2024 10:07

Quick update

55ba0b3

Pushing changes so that I can jump on the machine. Co-Authored-By: Sriya Veerapaneni <78429510+Sriya-235@users.noreply.github.com>

temporary changes

942c6f0

Pre-merge

34afd1f

Merge branch 'fix_exposure_time_error' into triangle_wave_v1

19291ae

Hot keys + Save With Data

42ee19c

Removed hot keys from menu controller. Now saves the waveform constants with the data. Only thing remaining is to have the popup GUI automatically populated with the new parameters.

Merge branch 'develop' into triangle_wave_v1

d7b75e0

Updating documentation

912529a

Updated the documentation to show the updated file menu. Also added few lines about the load and save waveform constants option in the documentation. Replaced the menu_file.png image with a new image of the file menu.

Merge branch 'triangle_wave_v1' into 828-save-waveform-constants-with…

bc946d3

…-acquisition-and-generate-method-to-load-it

Destroy and Recreate Waveform Popup Window

96c107e

AdvancedImagingUTSW requested a review from annie-xd-wang March 8, 2024 02:58

This was linked to issues Mar 8, 2024

Save Waveform Constants with Acquisition and Generate Method to Load it #828

Closed

Implement and test bidirectional ASLM #239

Closed

AdvancedImagingUTSW commented Mar 8, 2024

View reviewed changes

annie-xd-wang added 7 commits March 12, 2024 08:39

Merge branch 'develop' into 828-save-waveform-constants-with-acquisit…

824c7bd

…ion-and-generate-method-to-load-it

update waveform constants popup values

0f28154

test populating waveform constants

87db915

remove prints

028f740

clean up

8b40fcd

update triangle waveform calculation

d9a2c23

update tests

b4aeb15

annie-xd-wang approved these changes Mar 12, 2024

View reviewed changes

AdvancedImagingUTSW commented Mar 13, 2024

View reviewed changes

AdvancedImagingUTSW merged commit 2872042 into develop Mar 13, 2024
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828 save waveform constants with acquisition and generate method to load it #841

828 save waveform constants with acquisition and generate method to load it #841

AdvancedImagingUTSW commented Mar 8, 2024

AdvancedImagingUTSW Mar 8, 2024

annie-xd-wang Mar 12, 2024

AdvancedImagingUTSW Mar 8, 2024

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AdvancedImagingUTSW Mar 13, 2024

AdvancedImagingUTSW commented Mar 13, 2024

		@@ -43,10 +43,11 @@
		logger = logging.getLogger(p)


		class HamamatsuOrca(CameraBase):

828 save waveform constants with acquisition and generate method to load it #841

828 save waveform constants with acquisition and generate method to load it #841

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AdvancedImagingUTSW commented Mar 8, 2024

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codecov bot commented Mar 12, 2024

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AdvancedImagingUTSW commented Mar 13, 2024