Using presets, certain Andor camera properties do not apply, unless preset is selected twice

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Using presets, certain Andor camera properties do not apply, unless preset is selected twice

Pariksheet Nanda
Hello,

The "Preamp", "VerticalClockVoltage" and "VerticalSpeed" settings of
an Andor iXon3 camera do not always get applied using presets.

I tried a few times to send the automated problem report by get the
error "There was a problem sending the report, please verify your
internet connection."
The university internet is probably blocking Micro-Manager since it
won't let me register either (connection timeout).


Summary:
Created pesets for the iXon3 camera.
*** Uploaded system configuration to
https://gist.github.com/3795223#file_system%202012_09_27.cfg ***
Settings from the "camera-mode" do not apply correctly as evidenced by
watching the Device Property Browser window, and also running a
Multi-D experiment.

Reproducible:  Always

Steps to reproduce:
1.  Open Device Property Browser to watch values of "Preamp",
"VerticalClockVoltage" and "Vertical Speed"
2.  Select any "camera-mode" preset
3.  Select any other "camera-mode" preset
4.  Setting for "VerticalClockVoltage", "VerticalSpeed" and "Preamp"
do not get updated correctly (per Device Property browser)
5.  Re-select the same preset chosen in step #3
5.  Settings update to expected values
6.  Edit preset and note that settings show up as expected

Expected behavior
Values of camera presets should update with one selection
Suspect fault is with how camera DeviceAdapter applies settings, since
Micro-Manager reads in correct values per step #6

Workaround:
Must select "camera-mode" preset twice

System:
Windows 7 (64-bit)
iXon3 897 (Serial# X-5921)
Dell Precision T1600

 --Pariksheet

PS:  Do you have a workaround for the Micro-Manager internet
connection being blocked?  What port does Micro-Manager use to
connect?  Maybe an ssh tunnel is needed here?

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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

Pariksheet Nanda
Forgot to mention I'm using MM 1.4.10 (64-bit)

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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

Pariksheet Nanda
Sorry, this was PEBKAC

If I click on "Refresh" in the Device Property Browser after selecting
a preset, the values then show as expected.
I was confused by seeing some of the values update when changing the
preset instead of all values updating, forgetting that the typical
behavior is for values not to update unless refreshed.

I'll show myself out...

Pariksheet

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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

Arthur D. Edelstein
Hi Pariksheet,

It might be possible for the Device/Property browser to update
automatically, using Micro-Manager's property cache. I think Nico was
looking into this before, so he might have a suggestion. I'm adding a
ticket:

https://valelab.ucsf.edu/trac/micromanager/ticket/639

Arthur


On Thu, Sep 27, 2012 at 3:30 PM, Pariksheet Nanda
<[hidden email]> wrote:

> Sorry, this was PEBKAC
>
> If I click on "Refresh" in the Device Property Browser after selecting
> a preset, the values then show as expected.
> I was confused by seeing some of the values update when changing the
> preset instead of all values updating, forgetting that the typical
> behavior is for values not to update unless refreshed.
>
> I'll show myself out...
>
> Pariksheet
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://ad.doubleclick.net/clk;258768047;13503038;j?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general

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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

Nico Stuurman
Administrator
> <[hidden email]> wrote:

>> If I click on "Refresh" in the Device Property Browser after selecting a preset, the values then show as expected. I was confused by seeing some of the values update when changing the preset instead of all values updating, forgetting that the typical behavior is for values not to update unless refreshed.

On Sep 28, 2012, at 11:03 AM, Arthur D. Edelstein wrote:

> It might be possible for the Device/Property browser to update automatically, using Micro-Manager's property cache. I think Nico was looking into this before, so he might have a suggestion.

Indeed, I reworked the Device/Property Browser such that it no longer communicates with the hardware three times in a row but rather only one time (it now updates the system cache first and then updates its values from the cache).  I also noted on a system here that not all properties are refreshed correctly automatically.  Great that you found a reproducible example of this problem using hardware that we have access to.  I'll look into this once I get back at UCSF.

Best,


Nico
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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

ed@esimaging.co.uk
Nico Stuurman wrote
> <[hidden email]> wrote:

>> If I click on "Refresh" in the Device Property Browser after selecting a preset, the values then show as expected. I was confused by seeing some of the values update when changing the preset instead of all values updating, forgetting that the typical behavior is for values not to update unless refreshed.

On Sep 28, 2012, at 11:03 AM, Arthur D. Edelstein wrote:

> It might be possible for the Device/Property browser to update automatically, using Micro-Manager's property cache. I think Nico was looking into this before, so he might have a suggestion.

Indeed, I reworked the Device/Property Browser such that it no longer communicates with the hardware three times in a row but rather only one time (it now updates the system cache first and then updates its values from the cache).  I also noted on a system here that not all properties are refreshed correctly automatically.  Great that you found a reproducible example of this problem using hardware that we have access to.  I'll look into this once I get back at UCSF.

Best,


Nico
Hi Nico,

We have a system with continuously variable zoom that works with MM, this discussion caught my interest since we've been looking into what MM does WRT checking magnification. Is it possible in the DAL to set a flag/otherwise let MM know that the magnification has changed and it should check?

It appears that the magnification is only checked when a new image window is opened (clicking snap with no image window always checks) but we'd like to be able to keep up to date with this lens. Can you possibly suggest anything that might help here?

Thanks,
Ed
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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

Nico Stuurman
Administrator
Hi Ed,

> We have a system with continuously variable zoom that works with MM, this discussion caught my interest since we've been looking into what MM does WRT checking magnification. Is it possible in the DAL to set a flag/otherwise let MM know that the magnification has changed and it should check?

What is "DAL"?

> It appears that the magnification is only checked when a new image window is opened (clicking snap with no image window always checks) but we'd like to
> be able to keep up to date with this lens. Can you possibly suggest anything that might help here?

The general mechanism that devices can use to tell the Micro-Manager GUI about changes in the device is through the calbback mechanism.  For instance, the device can call the "OnPropertyChanged" function.  This will cause the Core to update its cache with the new state of the property and will also cause it to update the pixel size (if this property was part of a pixel size configuration).

Regretfully, "Magnifier" devices do not yet have a callback to indicate a change in magnification.  It seems straigh-forward to implement so let us know whether this is what you had in mind.

Best,

Nico



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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

Arthur D. Edelstein
> What is "DAL"?

Device adapter library :)

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Re: Using presets, certain Andor camera properties do not apply, unless preset is selected twice

ed@esimaging.co.uk
In reply to this post by Nico Stuurman
Nico Stuurman wrote
Hi Ed,

The general mechanism that devices can use to tell the Micro-Manager GUI about changes in the device is through the calbback mechanism.  For instance, the device can call the "OnPropertyChanged" function.  This will cause the Core to update its cache with the new state of the property and will also cause it to update the pixel size (if this property was part of a pixel size configuration).

Regretfully, "Magnifier" devices do not yet have a callback to indicate a change in magnification.  It seems straigh-forward to implement so let us know whether this is what you had in mind.

Best,

Nico
Hi Nico,

Thanks - I think that the callback for magnification changed would be the best way to deal with this, since if we snap an image and then move the magnifier and snap again, the second image is still displayed using the scale of the first image.

This device has only a single pixel size value and only the camera (actually, grabber) resolution property affects this value.
The device adaptor runs a thread that keeps track of the magnification at all times now, and the GetMagnification function simply returns a cached value that the thread keeps up to date.

Thanks for your help!

Best,
Ed
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OnMagnificationChanged callback

ed@esimaging.co.uk
Nico Stuurman wrote
Hi Ed,

The general mechanism that devices can use to tell the Micro-Manager GUI about changes in the device is through the calbback mechanism.  For instance, the device can call the "OnPropertyChanged" function.  This will cause the Core to update its cache with the new state of the property and will also cause it to update the pixel size (if this property was part of a pixel size configuration).

Regretfully, "Magnifier" devices do not yet have a callback to indicate a change in magnification.  It seems straigh-forward to implement so let us know whether this is what you had in mind.

Best,

Nico
Hi MM team,

Please could you implement the callback for magnifier devices to notify the core when the magnification changes?

Thanks very much,

Wishing you all a merry Christmas too!
Ed
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Re: OnMagnificationChanged callback

Mark Tsuchida-2
Hi Ed,

On Fri, Dec 20, 2013 at 9:42 AM, [hidden email]
<[hidden email]> wrote:

> Nico Stuurman wrote
>> The general mechanism that devices can use to tell the Micro-Manager GUI
>> about changes in the device is through the calbback mechanism.  For
>> instance, the device can call the "OnPropertyChanged" function.  This will
>> cause the Core to update its cache with the new state of the property and
>> will also cause it to update the pixel size (if this property was part of
>> a pixel size configuration).
>>
>> Regretfully, "Magnifier" devices do not yet have a callback to indicate a
>> change in magnification.  It seems straigh-forward to implement so let us
>> know whether this is what you had in mind.
>
> Please could you implement the callback for magnifier devices to notify the
> core when the magnification changes?

It's now on my to-do list!

Happy Holidays,
Mark

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Re: OnMagnificationChanged callback

Nico Stuurman-2
>> Please could you implement the callback for magnifier devices to notify the
>> core when the magnification changes?
>
> It's now on my to-do list!

Just added that to the code.  There is now a OnMagnifierChanged callback.  Calling this will result in the Core figuring out the new magnification and sending the onPixelSizeChanged callback to the GUI.  This change let to the device interface version going from 54 to 55, so those of you working on their own device adapters should make sure to use tonight's build or later with the current source in the trunk.

Best,

Nico




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