Stage control bug in MM2.0 gamma and workaround

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Stage control bug in MM2.0 gamma and workaround

Daniel Dickinson
I am seeing a bug in MM2.0 gamma where a special character (in my case '.') in the configuration file name will prevent the stage control dialog from opening.  When I click on the stage control button, nothing happens; no window appears. 

The core log shows the following error:
2019-12-31T11:24:18.412949 tid16456 [IFO,App] java.lang.ArrayIndexOutOfBoundsException: -1
2019-12-31T11:24:18.413947 tid16456 [IFO,App]   at org.micromanager.internal.dialogs.StageControlFrame.initialize(StageControlFrame.java:227)

Inspection of the code suggests that the error actually arises in line 169 of StageControlFrame.java.  A special character in the config file name apparently causes 
169      int nrZPanels = settings_.getInteger(NRZPANELS + sysConfigFile, nrZDrives);

to return 0, resulting in the array index in 
227      plusButtons_[nrZPanels-1].setVisible(true);

to evaluate as -1 and triggering the error. 

A straightforward workaround for the moment is to avoid special characters in the config file name (for example, don't copy your v1.4 config file and name it My_Config_File_2.0.cfg, as I did).  Perhaps the developers could add this bit of user-proofing as a low-priority item on the todo list. 

Dan Dickinson 
UT Austin


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Re: Stage control bug in MM2.0 gamma and workaround

Nico Stuurman-2
Hi Daniel,
> I am seeing a bug in MM2.0 gamma where a special character (in my case
> '.') in the configuration file name will prevent the stage control
> dialog from opening.  When I click on the stage control button,
> nothing happens; no window appears.

Thanks for the detailed bug description and spending the effort to find
the source of the problem!

Regretfully, I could not reproduce the issue on my Mac development
machine.  I guess that you found this on Windows?  I'll try it on that
platform later, but in the mean time added a check that should at least
work around the issue:

https://github.com/nicost/micro-manager/commit/c1ca249888db4fc21c643491bdbdca4bbdaeeb1a

Best,


Nico



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Re: Stage control bug in MM2.0 gamma and workaround

严程
Hi, All
     I have develop a new adapter for our camera, the live and snap are all ok. But the Multi-Dimen Acquisition function has some problem.
     When I click the Acquire button in the Multi-Dimen Acquisition dialog, the prompted preview window has no image but still showing "Waiting for image..."
     Can someone help me? Thanks


严程
 
Date: 2020-01-03 03:53
Subject: Re: [micro-manager-general] Stage control bug in MM2.0 gamma and workaround
Hi Daniel,
> I am seeing a bug in MM2.0 gamma where a special character (in my case
> '.') in the configuration file name will prevent the stage control
> dialog from opening.  When I click on the stage control button,
> nothing happens; no window appears.
 
Thanks for the detailed bug description and spending the effort to find
the source of the problem!
 
Regretfully, I could not reproduce the issue on my Mac development
machine.  I guess that you found this on Windows?  I'll try it on that
platform later, but in the mean time added a check that should at least
work around the issue:
 
https://github.com/nicost/micro-manager/commit/c1ca249888db4fc21c643491bdbdca4bbdaeeb1a
 
Best,
 
 
Nico
 
 
 
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Re: New camera adapter not working in MDA

Nico Stuurman-2
On 1/2/20 4:13 PM, 严程 wrote:
>      I have develop a new adapter for our camera, the live and snap
> are all ok. But the Multi-Dimen Acquisition function has some problem.
>      When I click the Acquire button in the Multi-Dimen Acquisition
> dialog, the prompted preview window has no image but still showing
> "Waiting for image..."

Enable debug logging (Tools > Options), and check the Corelog file for
indications of what may be happening.  Alternatively, use Help > Report
a Problem.. to generate information that may document the issue.
Also, try various settings for the MDA (for instance, only select Time
points, and ask for 2 time points 2 seconds apart with a much smaller
exposure time).

Best,


Nico



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Re: Stage control bug in MM2.0 gamma and workaround

Daniel Dickinson
In reply to this post by Nico Stuurman-2
Hi Nico,
Yes, this was on Windows 10.
Thanks,
Dan
From: Nico Stuurman <[hidden email]>
Sent: Thursday, January 2, 2020 2:53:49 PM
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] Stage control bug in MM2.0 gamma and workaround
 
Hi Daniel,
> I am seeing a bug in MM2.0 gamma where a special character (in my case
> '.') in the configuration file name will prevent the stage control
> dialog from opening.  When I click on the stage control button,
> nothing happens; no window appears.

Thanks for the detailed bug description and spending the effort to find
the source of the problem!

Regretfully, I could not reproduce the issue on my Mac development
machine.  I guess that you found this on Windows?  I'll try it on that
platform later, but in the mean time added a check that should at least
work around the issue:

https://github.com/nicost/micro-manager/commit/c1ca249888db4fc21c643491bdbdca4bbdaeeb1a

Best,


Nico



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[hidden email]
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