Some properties don't get saved

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Some properties don't get saved

nanthony
I have noticed that some device properties don't seem to get saved and so I
need to set them manually every time that I start up micromanager.

I have noticed this for the `Gain` setting of the PICAM device adapter as
well as for the `Transpose` settings of the Hamamatsu adapter.

I have additionally noticed that the transpose settings of the Hammamatsu
adapter don't seem to do anything.



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Re: Some properties don't get saved

nanthony
After taking a closer look at the device adapter it appears that even though
the `gain` setting is saved and loaded properly, the adapter then goes
through a bunch of logic to select a gain value based on the readout speed
and output port.

I am still very curious why the hammatsu transpose doesn't work. The source
code doesn't appear to be available.



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Re: Some properties don't get saved

Stuurman, Nico
In reply to this post by nanthony
Hi Nick,
> I have noticed that some device properties don't seem to get saved and so I
> need to set them manually every time that I start up micromanager.
>
> I have noticed this for the `Gain` setting of the PICAM device adapter as
> well as for the `Transpose` settings of the Hamamatsu adapter.

MM does not "save" device property settings (and never has).  Some
devices may save settings, but there is nothing in MM to guarantee that
a property will have the same value on restart.

If you want a property to have a certain value when starting MM, use the
"System" > "Startup" group.
> I have additionally noticed that the transpose settings of the Hammamatsu
> adapter don't seem to do anything.

The "Transpose" settings are inherited by all camera device adapters
(unless they do work to avoid it).  They do not change anything in the
image itself, however, they define how stage movement should be related
to camera orientation.  See:
https://micro-manager.org/wiki/Coordinates_and_Directionality.

In MM 2.0 gamma, a simplified affine transform is stored with the pixel
size definition.  Use of the "Transpose" settings should be phased out,
and the affine transform should be used for the relation between stage
movement and camera orientation.

Best,


Nico


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Re: Some properties don't get saved

nanthony
Nico Stuurman-2 wrote

> MM does not "save" device property settings (and never has).  Some
> devices may save settings, but there is nothing in MM to guarantee that
> a property will have the same value on restart.
>
> The "Transpose" settings are inherited by all camera device adapters
> (unless they do work to avoid it).  They do not change anything in the
> image itself, however, they define how stage movement should be related
> to camera orientation.  See:
> https://micro-manager.org/wiki/Coordinates_and_Directionality.
>
> In MM 2.0 gamma, a simplified affine transform is stored with the pixel
> size definition.  Use of the "Transpose" settings should be phased out,
> and the affine transform should be used for the relation between stage
> movement and camera orientation.

Thanks for the clarification. I'll set up a system startup in the
configuration.

I'll look into the affine transform. I know that this is present in Beta but
maybe it isn't actually used. I've never had a problem with the grid creator
but I have been using square camera sensors. I recently tried doing an
acquisition with a 720x960 camera and found that the grid creator had the
axes swapped, this resulted in having too much overlap along one direction
while having a gap in the other direction.




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Re: Some properties don't get saved

Stuurman, Nico
On 10/17/18 11:03 AM, nanthony wrote:

> Nico Stuurman-2 wrote
>> In MM 2.0 gamma, a simplified affine transform is stored with the pixel
>> size definition.  Use of the "Transpose" settings should be phased out,
>> and the affine transform should be used for the relation between stage
>> movement and camera orientation.
> I'll look into the affine transform. I know that this is present in Beta but
> maybe it isn't actually used. I've never had a problem with the grid creator
> but I have been using square camera sensors. I recently tried doing an
> acquisition with a 720x960 camera and found that the grid creator had the
> axes swapped, this resulted in having too much overlap along one direction
> while having a gap in the other direction.

The Grid Creator code
(org.micromanager.internal.positionlist.TileCreatorDlg.java) blissfully
ignores camera orientation.  It should look at the current affine
transform (which can be obtained from the code) and take it into
account.  Not totally trivial to get that code right.

Best,


Nico


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Re: Some properties don't get saved

nanthony
Nico Stuurman-2 wrote
> The Grid Creator code
> (org.micromanager.internal.positionlist.TileCreatorDlg.java) blissfully
> ignores camera orientation.  It should look at the current affine
> transform (which can be obtained from the code) and take it into
> account.  Not totally trivial to get that code right.

I can take a look at implementing this into the grid creator. Is there
somewhere in the code that could serve as an example of how to properly get
and apply the affine transform?



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Re: Some properties don't get saved

Stuurman, Nico

>> The Grid Creator code
>> (org.micromanager.internal.positionlist.TileCreatorDlg.java) blissfully
>> ignores camera orientation.  It should look at the current affine
>> transform (which can be obtained from the code) and take it into
>> account.  Not totally trivial to get that code right.
> I can take a look at implementing this into the grid creator. Is there
> somewhere in the code that could serve as an example of how to properly get
> and apply the affine transform?

Great!  The SlideExplorer plugin uses the affine transform, look at
org.micromanager.slideexplorer.Hub and
org.micromanager.slidexplorer.Controller.  Probably even better is the
CenterAndDragListener (org.manager.internal.navigation).


Best,

Nico




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