Error in device "Scope": (error message unavailable)(10012)

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Error in device "Scope": (error message unavailable)(10012)

StevenF
Hello Micromanager community!

I have been experiencing some issues in the loading config step so here is
my "bug report"!

*What is my setup?*
- Windows10
- micromanager v2.0gamma1_20190424
- hardware/mm config  InBio_gamma.cfg
<http://micro-manager.3463995.n2.nabble.com/file/t396958/InBio_gamma.cfg>  
   - Leica DMI8

*What is happening?*
I have been experiencing configuration loading errors :
Error in device "Scope": (error message unavailable)(10012)
I have experienced this error before but for some reason it's becoming more
and more frequent lately (coincides with me switching from micromanager
v2.0beta3_20171106 to micromanager v2.0gamma1_20190424).
This error is very annoying and messes with our experiment setup flow as we
use micromanager to do the setup and the use then the python wrapper to do
the actual acquisition. This error will often prevent me from loading the
config from my script or even subsequent gui launches.

After investigation it seems the error is coming from my FocusDrive device
for some reason.
tests_scope_error.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/tests_scope_error.txt>  
in this text file i go through all the things i thought would trigger this
error and it seems it's a Z(Focus drive) issue. (more details in the text
file)
if you look through what i did you can clearly see when my z is below 1106µm
then i will never get this error and if the z is over 1107µm this error pops
up.
Also it seems this error can by "brute forced through"(meaning it will
appear but if i relaunch enough it goes away) if i switch to a 2.0beta
version i was using before.

here are some core logs, the first being a normal one and the second is one
with the error:
CoreLog20190522T112100_pid15716.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190522T112100_pid15716.txt>  
CoreLog20190522T111725_pid7832.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190522T111725_pid7832.txt>  

I am a bit stuck and i'm not sure what to do to solve this.

Thanks,

Steven



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Re: Error in device "Scope": (error message unavailable)(10012)

Stuurman, Nico
On 5/22/19 4:12 AM, StevenF wrote:

> Hello Micromanager community!
>
> I have been experiencing some issues in the loading config step so here is
> my "bug report"!
>
> *What is my setup?*
> - Windows10
> - micromanager v2.0gamma1_20190424
> - hardware/mm config  InBio_gamma.cfg
> - Leica DMI8
Please note that the LeicaDMI adapter was written long before there was
a DMI8, and that code was certainly not tested with that stand.
Experiences of others are welcome!

> here are some core logs, the first being a normal one and the second is one
> with the error:
> CoreLog20190522T112100_pid15716.txt
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__micro-2Dmanager.3463995.n2.nabble.com_file_t396958_CoreLog20190522T112100-5Fpid15716.txt&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=gADOT008SBKZWVlKIG83utVhnZRWP0WVxZRmssolXS8&s=UqRAqUj6t8VM3HPzJMSK1CCSCuyF4usb0g9ybRzVf4c&e=>
> CoreLog20190522T111725_pid7832.txt
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__micro-2Dmanager.3463995.n2.nabble.com_file_t396958_CoreLog20190522T111725-5Fpid7832.txt&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=gADOT008SBKZWVlKIG83utVhnZRWP0WVxZRmssolXS8&s=bBXDdX-jGOna--IygRy9eZlFCYRgpv4jWbbPBIZexEc&e=>

There is an interesting difference.  In the second log, your Leica DMI
is extremely chatty.  First, MM waits for about 1000 characters (to
empty the serial port), then starts sending messages.  After the second
message, the Leica sends a more or less random "$48023 10665.9500\r",
which completely confuses Micro-Manager (all answer/responds are out of
sync afterwards).  The code could do a better job interpreting the
messages returning from the microscope, but in teh short term, it would
be nice to figure out why your scope is so chatty, and politely ask it
to be quiet for a while.


Best,

Nico

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Re: Error in device "Scope": (error message unavailable)(10012)

Chon U Chan
Just a random thought, the trash message that confuses MMG, namely
"$48023 10667.7000\r" and "$48023 10665.9500\r", starts with a dollar
sign and ends with a carriar return, which doesn't appear elsewhere.
Also, the scope response seems correct otherwise. May be a quick fix
is to add a line to filter out messages with this pattern? You might
even start with the keyword "$48023".

Regards,

Chon

On Wed, 22 May 2019 at 12:58, Stuurman, Nico <[hidden email]> wrote:

>
> On 5/22/19 4:12 AM, StevenF wrote:
> > Hello Micromanager community!
> >
> > I have been experiencing some issues in the loading config step so here is
> > my "bug report"!
> >
> > *What is my setup?*
> > - Windows10
> > - micromanager v2.0gamma1_20190424
> > - hardware/mm config  InBio_gamma.cfg
> > - Leica DMI8
> Please note that the LeicaDMI adapter was written long before there was
> a DMI8, and that code was certainly not tested with that stand.
> Experiences of others are welcome!
>
> > here are some core logs, the first being a normal one and the second is one
> > with the error:
> > CoreLog20190522T112100_pid15716.txt
> > <https://urldefense.proofpoint.com/v2/url?u=http-3A__micro-2Dmanager.3463995.n2.nabble.com_file_t396958_CoreLog20190522T112100-5Fpid15716.txt&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=gADOT008SBKZWVlKIG83utVhnZRWP0WVxZRmssolXS8&s=UqRAqUj6t8VM3HPzJMSK1CCSCuyF4usb0g9ybRzVf4c&e=>
> > CoreLog20190522T111725_pid7832.txt
> > <https://urldefense.proofpoint.com/v2/url?u=http-3A__micro-2Dmanager.3463995.n2.nabble.com_file_t396958_CoreLog20190522T111725-5Fpid7832.txt&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=gADOT008SBKZWVlKIG83utVhnZRWP0WVxZRmssolXS8&s=bBXDdX-jGOna--IygRy9eZlFCYRgpv4jWbbPBIZexEc&e=>
>
> There is an interesting difference.  In the second log, your Leica DMI
> is extremely chatty.  First, MM waits for about 1000 characters (to
> empty the serial port), then starts sending messages.  After the second
> message, the Leica sends a more or less random "$48023 10665.9500\r",
> which completely confuses Micro-Manager (all answer/responds are out of
> sync afterwards).  The code could do a better job interpreting the
> messages returning from the microscope, but in teh short term, it would
> be nice to figure out why your scope is so chatty, and politely ask it
> to be quiet for a while.
>
>
> Best,
>
> Nico
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: Error in device "Scope": (error message unavailable)(10012)

Stuurman, Nico

> On 5/22/19 4:12 AM, StevenF wrote:
>>> Hello Micromanager community!
>>>
>>> I have been experiencing some issues in the loading config step so here is
>>> my "bug report"!
>>>
>>> *What is my setup?*
>>> - Windows10
>>> - micromanager v2.0gamma1_20190424
>>> - hardware/mm config  InBio_gamma.cfg
>>> - Leica DMI8
>> Please note that the LeicaDMI adapter was written long before there was
>> a DMI8, and that code was certainly not tested with that stand.
>> Experiences of others are welcome!
>>
>>> here are some core logs, the first being a normal one and the second is one
>>> with the error:
>>> CoreLog20190522T112100_pid15716.txt
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__micro-2Dmanager.3463995.n2.nabble.com_file_t396958_CoreLog20190522T112100-5Fpid15716.txt&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=gADOT008SBKZWVlKIG83utVhnZRWP0WVxZRmssolXS8&s=UqRAqUj6t8VM3HPzJMSK1CCSCuyF4usb0g9ybRzVf4c&e=>
>>> CoreLog20190522T111725_pid7832.txt
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__micro-2Dmanager.3463995.n2.nabble.com_file_t396958_CoreLog20190522T111725-5Fpid7832.txt&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=gADOT008SBKZWVlKIG83utVhnZRWP0WVxZRmssolXS8&s=bBXDdX-jGOna--IygRy9eZlFCYRgpv4jWbbPBIZexEc&e=>
>> There is an interesting difference.  In the second log, your Leica DMI
>> is extremely chatty.  First, MM waits for about 1000 characters (to
>> empty the serial port), then starts sending messages.  After the second
>> message, the Leica sends a more or less random "$48023 10665.9500\r",
>> which completely confuses Micro-Manager (all answer/responds are out of
>> sync afterwards).  The code could do a better job interpreting the
>> messages returning from the microscope, but in teh short term, it would
>> be nice to figure out why your scope is so chatty, and politely ask it
>> to be quiet for a while.

On 5/22/19 2:44 PM, Chon U Chan wrote:
> Just a random thought, the trash message that confuses MMG, namely
> "$48023 10667.7000\r" and "$48023 10665.9500\r", starts with a dollar
> sign and ends with a carriar return, which doesn't appear elsewhere.
> Also, the scope response seems correct otherwise. May be a quick fix
> is to add a line to filter out messages with this pattern? You might
> even start with the keyword "$48023".

If this is repeatable trash this may work.  Trash tends to be random...

Best,


Nico


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Re: Error in device "Scope": (error message unavailable)(10012)

StevenF
So yeah i can supply more logs of the crash but it indeed seems that this
long string is always present when the crash occurs!

no crash:
CoreLog20190425T172057_pid14984.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190425T172057_pid14984.txt>  
CoreLog20190425T173725_pid2004.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190425T173725_pid2004.txt>  
CoreLog20190425T173826_pid7784.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190425T173826_pid7784.txt>  

crash:
CoreLog20190425T173926_pid15252.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190425T173926_pid15252.txt>  
CoreLog20190425T174030_pid9516.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190425T174030_pid9516.txt>  
CoreLog20190425T174304_pid10948.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190425T174304_pid10948.txt>  

so it seems this very long line doesn't appear(or it does but later on after
the loading) in the log when it loads correctly but is always present when
it crahses!

i checked and they all do seem to follow this type of pattern :
0774.4500
$48023 10772.7700
$48023 10774.2900
$48023 10773.7200
$48023 10773.2700
$48023 10774.1000
$48023 10774.9100
$48023 10774.3200
$48023 10775.0100
$48023 10775.5400
$48023 10774.3200
$48023 10773.5500
$48023 10774.4700
$48023 10773.8900
...

the first line has no $(probably i would guess that it's a similar line from
the rest just cut, and the subsequent lines have the same format but it's
not always $48023.

thanks for being so reactive! If you need anymore details or testing let me
know!

Steven





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Re: Error in device "Scope": (error message unavailable)(10012)

Stuurman, Nico
On 5/23/19 1:07 AM, StevenF wrote:

> So yeah i can supply more logs of the crash but it indeed seems that this
> long string is always present when the crash occurs!
>
>
> i checked and they all do seem to follow this type of pattern :
> 0774.4500
> $48023 10772.7700
> $48023 10774.2900
> $48023 10773.7200
> $48023 10773.2700
> $48023 10774.1000
> $48023 10774.9100
> $48023 10774.3200
> $48023 10775.0100
> $48023 10775.5400
> $48023 10774.3200
> $48023 10773.5500
> $48023 10774.4700
> $48023 10773.8900
> ...
>
> the first line has no $(probably i would guess that it's a similar line from
> the rest just cut, and the subsequent lines have the same format but it's
> not always $48023.


48 is the code for the AFC (Automated focus controller?).   48 023 is
the command to get the "current edge position".  So, the question is why
your microscope wants to report these.  The documentation says that the
default after switching on the microscope is to not report the "current
edge position".

Does it help to power cycle the microscope before starting up
Micro-Manager?

Micro-Manager (after successful initialization) tells the microscope to
start reporting changes in the "current edge position", so it does make
sense that it continues to do so when you "restart" Micro-Manager.  By
setting your Z-value to a certain height, you apparently generate a lot
of these ACF events.  I see some place in the code where we could
potentially check for the correct answer, and possibly read another
message (especially, line 788 of LeicaDMInterface.cpp could be made to
read another line from the serial port rather than continue the loop),
but without access to a scope it is a bit too scary to change the code.
The "$" sign apparently indicates an event (i.e., a message that is not
an answer to a request, but an update about events that happened).  It
would be OK to read those away in that code, but it is a bit hard to
make these changes without actual access to a microscope (would be nice
if they had an emulator like the Zeiss one!).

Best,



Nico




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Re: Error in device "Scope": (error message unavailable)(10012)

StevenF
Stuurman, Nico wrote

> 48 is the code for the AFC (Automated focus controller?).   48 023 is
> the command to get the "current edge position".  So, the question is why
> your microscope wants to report these.  The documentation says that the
> default after switching on the microscope is to not report the "current
> edge position".
>
> Does it help to power cycle the microscope before starting up
> Micro-Manager?
>
> Micro-Manager (after successful initialization) tells the microscope to
> start reporting changes in the "current edge position", so it does make
> sense that it continues to do so when you "restart" Micro-Manager.  By
> setting your Z-value to a certain height, you apparently generate a lot
> of these ACF events.  I see some place in the code where we could
> potentially check for the correct answer, and possibly read another
> message (especially, line 788 of LeicaDMInterface.cpp could be made to
> read another line from the serial port rather than continue the loop),
> but without access to a scope it is a bit too scary to change the code.
> The "$" sign apparently indicates an event (i.e., a message that is not
> an answer to a request, but an update about events that happened).  It
> would be OK to read those away in that code, but it is a bit hard to
> make these changes without actual access to a microscope (would be nice
> if they had an emulator like the Zeiss one!).


Yes restarting the Microscope helps. The only way of making this error go
away in the gamma version i am using is either reduce the height or reboot
the microscope. But this will only work once and resume showing the error.
Since you said the message is coming from the AFC (Adaptive Focus Control) i
checked whether turning it off helps and yes indeed it also makes the error
go away! I will incorporate turning the AFC off before loading the
configuration in my experiment flow although it's a far from from ideal
solution.  

I understand your hesitancy. If you see a quick fix you could send me some
bit of code my way and i could try it locally?
Either that maybe i could try and contact Leica?
What do you think is the best solution ?

Thanks again,

Best,

Steven

 



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Re: Error in device "Scope": (error message unavailable)(10012)

Stuurman, Nico
On 5/24/19 1:57 AM, StevenF wrote:

> Stuurman, Nico wrote
>> 48 is the code for the AFC (Automated focus controller?).   48 023 is
>> the command to get the "current edge position".  So, the question is why
>> your microscope wants to report these.  The documentation says that the
>> default after switching on the microscope is to not report the "current
>> edge position".
>>
>> Does it help to power cycle the microscope before starting up
>> Micro-Manager?
> Yes restarting the Microscope helps. The only way of making this error go
> away in the gamma version i am using is either reduce the height or reboot
> the microscope. But this will only work once and resume showing the error.

That makes sense.

> Since you said the message is coming from the AFC (Adaptive Focus Control) i
> checked whether turning it off helps and yes indeed it also makes the error
> go away! I will incorporate turning the AFC off before loading the
> configuration in my experiment flow although it's a far from from ideal
> solution.

Great!
> I understand your hesitancy. If you see a quick fix you could send me some
> bit of code my way and i could try it locally?

I just pushed a few changes into the DMI adapter (r17057) that should
stop the AFC from reporting updates to the computer when you unload the
configuration file.  the changes should be in tonight's build of 1.4 and
2.0-gamma.  Please test (preferably with and without the AFC on), and
let me know if everything works as expected.

Best,

Nico




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Re: Error in device "Scope": (error message unavailable)(10012)

StevenF
Stuurman, Nico wrote
> I just pushed a few changes into the DMI adapter (r17057) that should
> stop the AFC from reporting updates to the computer when you unload the
> configuration file.  the changes should be in tonight's build of 1.4 and
> 2.0-gamma.  Please test (preferably with and without the AFC on), and
> let me know if everything works as expected.

Thanks Nico for working on this!
So i downloaded the latest gamma nightly and just did some tests and
unfortunately it seems its didn't solve the issue.
I did tests with AFC off and AFC on and it's the same behavior as before
although there is a new error that pops up every other config loading which
is linked to the Il-Turret apparently. AFC off works fine and no loading
issue.
Here are some CoreLogs:
no issue:
CoreLog20190527T144808_pid13412.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144808_pid13412.txt>  
CoreLog20190527T144735_pid10352.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144735_pid10352.txt>  
CoreLog20190527T144704_pid13164.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144704_pid13164.txt>  
scope & il-turret error:
CoreLog20190527T144543_pid10696.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144543_pid10696.txt>  
CoreLog20190527T144459_pid13572.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144459_pid13572.txt>  
CoreLog20190527T144433_pid11136.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144433_pid11136.txt>  
CoreLog20190527T144134_pid14356.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144134_pid14356.txt>  
CoreLog20190527T144102_pid10892.txt
<http://micro-manager.3463995.n2.nabble.com/file/t396958/CoreLog20190527T144102_pid10892.txt>  

Thanks again Nico,

Steven




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Re: Error in device "Scope": (error message unavailable)(10012)

Stuurman, Nico
On 5/27/19 5:57 AM, StevenF wrote:
> Stuurman, Nico wrote
>> I just pushed a few changes into the DMI adapter (r17057) that should
>> stop the AFC from reporting updates to the computer when you unload the
>> configuration file.  the changes should be in tonight's build of 1.4 and
>> 2.0-gamma.  Please test (preferably with and without the AFC on), and
>> let me know if everything works as expected.
>
> So i downloaded the latest gamma nightly and just did some tests and
> unfortunately it seems its didn't solve the issue.

Interesting.  I do not see the code sending the message to the AFC to
stop reporting its status.

I am not sure why, and it is impossible to figure this out without
access to the microscope system itself.  However, I moved the code to
the AFC Shutdown function, so you can test again.  Basically, you should
look for the message:

SetCommand -> 48003 0 0 0 0 0 0 0 0 0\r

when you unload the configuration file.  If that is there, the AFC should stop reporting its state.

B.t.w., 1 working Corelog and 1 that does not work is plenty for me...

Best,


Nico




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Re: Error in device "Scope": (error message unavailable)(10012)

StevenF
Hey Nico,

It seems the issue has been fixed indeed! I looked for the message in the
Corelogs and did find it. I ran a few dozen tests and so far so good :)!


Stuurman, Nico wrote
> B.t.w., 1 working Corelog and 1 that does not work is plenty for me...

Noted!

Thanks Nico for all the help!

Best,

Steven



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Re: Error in device "Scope": (error message unavailable)(10012)

StevenF
In reply to this post by Stuurman, Nico
So i did some testing this morning and it seems the problem has been fixed
indeed. I did also look through the corelogs and indeed found the
"SetCommand -> 48003 0 0 0 0 0 0 0 0 0\r" message!


Stuurman, Nico wrote
> B.t.w., 1 working Corelog and 1 that does not work is plenty for me...

Noted!

Thanks for the help Nico,

Best,

Steven

ps: i swore i had sent the message already but after more than an hour its
not delivered so if the previous one comes through later because of Nabble
issues my bad!



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Re: Error in device "Scope": (error message unavailable)(10012)

Stuurman, Nico
In reply to this post by StevenF
On 5/29/19 2:45 AM, StevenF wrote:

> It seems the issue has been fixed indeed!

Awesome, great to hear!

The code could possibly stop all devices from sending messages, but that
does not seem very clear to me.  The nicest thing would be to read out
what messages are being send on startup, and then set things back to
what they were on shutdown.  In any case, glad it now works!

Best,



Nico



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