Autofocus does not start (error 17)

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Autofocus does not start (error 17)

Abbas Shirinifard-2
Hi,

As described in the wiki I copied MMstartup.bsh to Micro-Manager folder, but when I try to start autofocus it throws "Error code 17: Can't find the device with the specified label". I saw in the Corelog file suggests another plugin (Call to installAutofocusPlugin in MMAcquisitionEngine received. This method has been deprecated. Use MMStudioMainFrame.
installAutofocusPlugin() instead.), but I can't find it. How can I fix this problem?

Thanks

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Re: Autofocus does not start (error 17)

Nico Stuurman-4
> As described in the wiki I copied MMstartup.bsh to Micro-Manager  
> folder, but when I try to start autofocus it throws "Error code 17:  
> Can't find the device with the specified label". I saw in the  
> Corelog file suggests another plugin (Call to installAutofocusPlugin  
> in MMAcquisitionEngine received. This method has been deprecated.  
> Use MMStudioMainFrame.
> installAutofocusPlugin() instead.), but I can't find it. How can I  
> fix this problem?

The relevant lines in my MMStartup.bsh are:

// load focusing module
response = gui.installAutofocusPlugin("Autofocus_");
mmc.logMessage(response);
response = gui.installAutofocusPlugin("AutofocusTB_");
mmc.logMessage(response);
response = gui.installAutofocusPlugin("AutofocusDuo_");
mmc.logMessage(response);

I though this was included in the latest release.  Let us know if this  
is not the case.

Best,

Nico


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Re: Autofocus does not start (error 17)

Abbas Shirinifard-2
In reply to this post by Abbas Shirinifard-2
Hi Nico,

The script in the wiki is not updated. (https://valelab.ucsf.edu/~nico/MMwiki/images/4/4e/MMStartup.bsh). I used the new script you sent and the autofocus plugins load, but still gives the same error message ("Error code 17:  Can't find the device with the specified label").

here is my CoreLog:

LOG(Thu Sep 10 2009 14:50:39.109000, 7360, 4528:): -------->>
LOG(Thu Sep 10 2009 14:50:39.109000, 7360, 4528:): Core session started on Thu Sep 10 2009 14:50:39.109000 by ashirini on BL-PHYS-D4T35S2
LOG(Thu Sep 10 2009 14:50:39.109000, 7360, 4528:): Debug logging disabled
LOG(Thu Sep 10 2009 14:50:39.109000, 7360, 4528:): Debug logging enabled
LOG(Thu Sep 10 2009 14:50:39.109000, 7360, 4528:): > MM Studio version: 1.3.40
LOG(Thu Sep 10 2009 14:50:39.109000, 7360, 4528:): > MMCore version 2.3.1
LOG(Thu Sep 10 2009 14:50:39.109000, 7360, 4528:): > Device API version 32, Module API version 4
DBG(7360, t:4528:) Circular buffer set to 25 MB.
LOG(Thu Sep 10 2009 14:50:41.140000, 7360, 4528:): All devices unloaded.
DBG(7360, t:4528:) Property set: device=Core, name=Initialize, value=0
LOG(Thu Sep 10 2009 14:50:41.140000, 7360, 4528:): Device COM3 loaded from SerialManager and labeled as COM3
LOG(Thu Sep 10 2009 14:50:41.140000, 7360, 4528:): Device LudlController loaded from Ludl and labeled as LudlController
LOG(Thu Sep 10 2009 14:50:41.140000, 7360, 4528:): Device XYStage loaded from Ludl and labeled as ludl-XYStage
LOG(Thu Sep 10 2009 14:50:41.140000, 7360, 4528:): Device ludl-XYStage set as xyStage.
LOG(Thu Sep 10 2009 14:50:41.156000, 7360, 4528:): Device Hamamatsu_DCAM loaded from Hamamatsu and labeled as Hamamatsu_DCAM
LOG(Thu Sep 10 2009 14:50:41.156000, 7360, 4528:): Device Hamamatsu_DCAM set as camera.
LOG(Thu Sep 10 2009 14:50:41.156000, 7360, 4528:): Device Stage loaded from Ludl and labeled as Z
DBG(7360, t:4528:) Property set: device=LudlController, name=Port, value=COM3
DBG(7360, t:4528:) Property set: device=Hamamatsu_DCAM, name=Slot, value=0
DBG(7360, t:4528:) Property set: device=Z, name=LudlSingleAxisName, value=B
DBG(7360, t:4528:) Property set: device=COM3, name=AnswerTimeout, value=2500.0000
DBG(7360, t:4528:) Property set: device=COM3, name=BaudRate, value=9600
DBG(7360, t:4528:) Property set: device=COM3, name=DelayBetweenCharsMs, value=0.0000
DBG(7360, t:4528:) Property set: device=COM3, name=Handshaking, value=Off
DBG(7360, t:4528:) Property set: device=COM3, name=Parity, value=None
DBG(7360, t:4528:) Property set: device=COM3, name=StopBits, value=2
LOG(Thu Sep 10 2009 14:50:41.156000, 7360, 4528:): Starting initialization sequence for 5 devices...
LOG(Thu Sep 10 2009 14:50:41.156000, 7360, 4528:): Device COM3 message: Serial port COM3 opened.

LOG(Thu Sep 10 2009 14:50:41.234000, 7360, 4528:): Device COM3 initialized.
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: VER

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: Version no. :      11.800   MAC6000 Interface with USB/ETH 
DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read:
:A
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: Rconfig

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: Configuration Report

Dev Addres   Label   Id   Description

    1       EMOT      X    X axis stage        MCMSE
    2       EMOT      Y    Y axis stage        MCMSE
    3       EMOT      B    B aux  motor        MCMSE

LOG(Thu Sep 10 2009 14:50:41.234000, 7360, 4528:): Device LudlController message: Configuration Report

Dev Addres   Label   Id   Description

    1       EMOT      X    X axis stage        MCMSE
    2       EMOT      Y    Y axis stage        MCMSE
    3       EMOT      B    B aux  motor        MCMSE

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: A
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: TRXDEL

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 0
LOG(Thu Sep 10 2009 14:50:41.250000, 7360, 4528:): Device LudlController initialized.
DBG(7360, t:4528:) Device COM3 debug message: Serial TX: 255 65

DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: ACCEL X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 4 4
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: SPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 18000 18000
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STSPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 5000 5000
LOG(Thu Sep 10 2009 14:50:41.328000, 7360, 4528:): Device ludl-XYStage initialized.
LOG(Thu Sep 10 2009 14:50:42.265000, 7360, 4528:): Device Hamamatsu_DCAM message: DCAM Module Version: 2.20.912.3153 (July 2009)
LOG(Thu Sep 10 2009 14:50:42.265000, 7360, 4528:): Device Hamamatsu_DCAM message: DCAM API Version: 2.20.912.3153 (July 2009)
LOG(Thu Sep 10 2009 14:50:42.921000, 7360, 4528:): Device Hamamatsu_DCAM message: Camera Model: Hamamatsu 1394 ORCA-ER
LOG(Thu Sep 10 2009 14:50:42.921000, 7360, 4528:): Device Hamamatsu_DCAM message: CameraID: S/N: 720753
LOG(Thu Sep 10 2009 14:50:42.921000, 7360, 4528:): Device Hamamatsu_DCAM message: Camera Version: 1.01.02.G
LOG(Thu Sep 10 2009 14:50:42.921000, 7360, 4528:): Device Hamamatsu_DCAM message: Driver version: 9.14.12
LOG(Thu Sep 10 2009 14:50:42.921000, 7360, 4528:): Device Hamamatsu_DCAM message: ScanMode works
DBG(7360, t:4528:) Device Hamamatsu_DCAM debug message: Triggermode found: 32
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Device Hamamatsu_DCAM initialized.
DBG(7360, t:4528:) Device COM3 debug message: Serial TX: 255 65

LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Device Z initialized.
DBG(7360, t:4528:) Property set: device=Core, name=Initialize, value=1
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Camera device set to Hamamatsu_DCAM
DBG(7360, t:4528:) Property set: device=Core, name=Camera, value=Hamamatsu_DCAM
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Focus device set to Z
DBG(7360, t:4528:) Property set: device=Core, name=Focus, value=Z
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Auto shutter OFF.
DBG(7360, t:4528:) Property set: device=Core, name=AutoShutter, value=0
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Image acquisition synchronized with ludl-XYStage
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Image acquisition synchronized with LudlController
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Image acquisition synchronized with Z
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Resolution ID Res0: for device ludl-XYStage defined as Acceleration=4.0000
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Pixel size 0.400000 um set for resolution ID: Res0
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Resolution ID Res0: for device ludl-XYStage defined as Speed=1800.0000
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Pixel size 0.400000 um set for resolution ID: Res0
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Resolution ID Res0: for device ludl-XYStage defined as StartSpeed=500.0000
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Pixel size 0.400000 um set for resolution ID: Res0
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Resolution ID Res0: for device ludl-XYStage defined as StepSize=0.1000
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Pixel size 0.400000 um set for resolution ID: Res0
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Resolution ID Res0: for device ludl-XYStage defined as TransposeMirrorX=1
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Pixel size 0.400000 um set for resolution ID: Res0
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Resolution ID Res0: for device ludl-XYStage defined as TransposeMirrorY=0
LOG(Thu Sep 10 2009 14:50:43.218000, 7360, 4528:): Pixel size 0.400000 um set for resolution ID: Res0
DBG(7360, t:4528:) Waiting for device COM3...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device LudlController...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device ludl-XYStage...
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS X

DBG(7360, t:4528:) Device ludl-XYStage debug message: Starting read in XY-Stage Busy
DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device ludl-XYStage debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS Y

DBG(7360, t:4528:) Device ludl-XYStage debug message: Starting read in XY-Stage Busy
DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device ludl-XYStage debug message: Tried reading 2 times, and finally read 1 chars
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device Hamamatsu_DCAM...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device Z...
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS B

DBG(7360, t:4528:) Device Z debug message: Starting read in Stage Busy

DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device Z debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: TRXDEL

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 0
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: ACCEL X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 4 4
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: SPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 18000 18000
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STSPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 5000 5000
DBG(7360, t:4528:) Device Hamamatsu_DCAM debug message: Triggermode found: 32
LOG(Thu Sep 10 2009 14:50:43.328000, 7360, 4528:): System state cache updated.
LOG(Thu Sep 10 2009 14:50:44.015000, 7360, 4528:): > Autofocus_ module loaded.
LOG(Thu Sep 10 2009 14:50:44.062000, 7360, 4528:): > AutofocusTB_ module loaded.
LOG(Thu Sep 10 2009 14:50:44.109000, 7360, 4528:): > AutofocusDuo_ module loaded.
LOG(Thu Sep 10 2009 14:50:44.140000, 7360, 4528:): > Autofocus_ module loaded.
LOG(Thu Sep 10 2009 14:50:44.140000, 7360, 4528:): > AutofocusTB_ module loaded.
LOG(Thu Sep 10 2009 14:50:44.156000, 7360, 4528:): > AutofocusDuo_ module loaded.
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: ACCEL X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 4 4
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: SPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 18000 18000
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STSPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 5000 5000
LOG(Thu Sep 10 2009 14:50:44.328000, 7360, 4528:): > com.imaging100x.tracker.TrackerControl module loaded.
LOG(Thu Sep 10 2009 14:50:44.328000, 7360, 4528:): > Startup script finished.
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: ACCEL X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 4 4
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: SPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 18000 18000
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STSPEED X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 5000 5000
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: WHERE B

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A -5129
LOG(Thu Sep 10 2009 14:50:45.078000, 7360, 4528:): Device Z message: B GetPosition() -512.9
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: WHERE X Y

DBG(7360, t:4528:) Device COM3 debug message:  Port: COM3.Read: :A 250060 80275
DBG(7360, t:4528:) Waiting for device COM3...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device LudlController...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device ludl-XYStage...
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS X

DBG(7360, t:4528:) Device ludl-XYStage debug message: Starting read in XY-Stage Busy
DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device ludl-XYStage debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS Y

DBG(7360, t:4528:) Device ludl-XYStage debug message: Starting read in XY-Stage Busy
DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device ludl-XYStage debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device Hamamatsu_DCAM...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device Z...
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS B

DBG(7360, t:4528:) Device Z debug message: Starting read in Stage Busy

DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device Z debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Finished waiting.
LOG(Thu Sep 10 2009 14:53:53.984000, 7360, 4528:): Error occured. Device core. Can't find the device with the specified label.

DBG(7360, t:4528:) Waiting for device COM3...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device LudlController...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device ludl-XYStage...
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS X

DBG(7360, t:4528:) Device ludl-XYStage debug message: Starting read in XY-Stage Busy
DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device ludl-XYStage debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS Y

DBG(7360, t:4528:) Device ludl-XYStage debug message: Starting read in XY-Stage Busy
DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device ludl-XYStage debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device Hamamatsu_DCAM...
DBG(7360, t:4528:) Finished waiting.
DBG(7360, t:4528:) Waiting for device Z...
DBG(7360, t:4528:) Device COM3 debug message: Serial port COM3 wrote: STATUS B

DBG(7360, t:4528:) Device Z debug message: Starting read in Stage Busy

DBG(7360, t:4528:) Device COM3 debug message: Serial RX: N [78 ]

DBG(7360, t:4528:) Device Z debug message: Tried reading 1 times, and finally read 1 chars
DBG(7360, t:4528:) Finished waiting.
LOG(Thu Sep 10 2009 14:54:07.156000, 7360, 4528:): Device COM3 message: Serial port COM3 closed.

LOG(Thu Sep 10 2009 14:54:07.156000, 7360, 4528:): Device COM3 message: Serial port COM3 closed.

LOG(Thu Sep 10 2009 14:54:07.156000, 7360, 4528:): All devices unloaded.
LOG(Thu Sep 10 2009 14:54:07.156000, 7360, 4528:): System reset at Thu Sep 10 2009 14:54:07.156000.


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Re: Autofocus does not start (error 17)

Nico Stuurman-4
Hi Abbas,

The script in the wiki is not updated. (https://valelab.ucsf.edu/~nico/MMwiki/images/4/4e/MMStartup.bsh).

The wiki has not yet been updated with information about the new autofocussing mechanism that we are using.  MMStartup.bsh is included in the distribution and will by default load three different Java-based autofocus methods.  You will see these when you click on the "tool" icon under Autofocus in the main panel.

I used the new script you sent and the autofocus plugins load, but still gives the same error message ("Error code 17:  Can't find the device with the specified label").

The "standard" autofocussing mechnaism (JAF(H&P)) uses a default shutter device, a default Focus drive, and a default camera.  If any of these are not set in your configuration file, you will get the error message you describe.  

Best,

Nico


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