Re: [micro-manager-general] Matlab Configuration - CMMCore Object
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Re: [micro-manager-general] Matlab Configuration - CMMCore Object
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From: Kiana Go <gok...@be...> - 2018-07-21 01:22:38
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Hi Kyle,
Got it to work. I had to close all the software, turn the camera off,
disconnect and reconnect the usb to the computer, turn the camera on, wait
about 10 seconds, and when I loaded the configuration, everything worked
fine!
However, I am wondering if Micro-Manager can stream in a webcam video
(using the standard UVC protocol)?
Much Appreciated,
Kiana Go
On Fri, Jul 20, 2018 at 4:51 PM, Kiana Go <gok...@be...> wrote:
> Hi Kyle,
>
> It's fine! I got the stage to load! However, now, the camera will not
> load. However, I was able to load the XY Stage, Z Stage, and Andor SDK3
> camera perfectly into a configuration file. However, I used the XYStage,
> ZStage, and Camera through matlab. Now when I try to reload the same
> configuration, the camera will not load. For matlab, all I did was move the
> stage and use: snapImage, img= getImage, and reshape(img, 2048, 2048). The
> following is the core log and includes the error:
>
> 2018-07-20T16:40:15.168729 tid10480 [IFO,App] User has been prompted to
> reproduce problem
> 2018-07-20T16:40:21.798640 tid10480 [dbg,Core] Will set Core property:
> Initialize = 0
> 2018-07-20T16:40:21.798640 tid10480 [dbg,Core] Will unload all devices
> 2018-07-20T16:40:21.798640 tid10480 [IFO,Core] Did unload all devices
> 2018-07-20T16:40:21.798640 tid10480 [dbg,App] Notification for Device:
> Core Property: Initialize changed to value: 0 ignored since the system is
> still loading
> 2018-07-20T16:40:21.798640 tid10480 [dbg,Core] Did set Core property:
> Initialize = 0
> 2018-07-20T16:40:21.798640 tid10480 [dbg,Core] Will load device COM5 from
> SerialManager
> 2018-07-20T16:40:21.798640 tid10480 [IFO,Core] Did load device COM5 from
> SerialManager; label = COM5
> 2018-07-20T16:40:21.798640 tid10480 [dbg,Core] Will load device Andor
> sCMOS Camera from AndorSDK3
> 2018-07-20T16:40:21.826639 tid10480 [IFO,Core] Did load device Andor sCMOS
> Camera from AndorSDK3; label = Camera
> 2018-07-20T16:40:21.826639 tid10480 [dbg,Core] Will load device XYStage
> from Prior
> 2018-07-20T16:40:21.828639 tid10480 [IFO,Core] Did load device XYStage
> from Prior; label = XYStage
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core] Will load device ZStage
> from Prior
> 2018-07-20T16:40:21.828639 tid10480 [IFO,Core] Did load device ZStage from
> Prior; label = ZStage
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:XYStage] Will set
> property "Port" to "COM5"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:XYStage] Did set
> property "Port" to "COM5"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:ZStage] Will set
> property "Port" to "COM5"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:ZStage] Did set property
> "Port" to "COM5"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "AnswerTimeout" to "500.0000"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "AnswerTimeout" to "500.0000"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "BaudRate" to "9600"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "BaudRate" to "9600"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "DataBits" to "8"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "DataBits" to "8"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "DelayBetweenCharsMs" to "0.0000"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "DelayBetweenCharsMs" to "0.0000"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "Handshaking" to "Off"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "Handshaking" to "Off"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "Parity" to "None"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "Parity" to "None"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "StopBits" to "1"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "StopBits" to "1"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Will set property
> "Verbose" to "1"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core:dev:COM5] Did set property
> "Verbose" to "1"
> 2018-07-20T16:40:21.828639 tid10480 [dbg,Core] Will set Core property:
> Initialize = 1
> 2018-07-20T16:40:21.828639 tid10480 [IFO,Core] Will initialize 4 devices
> 2018-07-20T16:40:21.828639 tid10480 [IFO,Core] Will initialize device COM5
> 2018-07-20T16:40:21.830639 tid10480 [dbg,dev:COM5] Attempting to set flow
> of COM5 to none
> 2018-07-20T16:40:21.832639 tid10480 [dbg,dev:COM5] Attempting to set
> parity of COM5 to none
> 2018-07-20T16:40:21.832639 tid10480 [dbg,dev:COM5] Attempting to set
> stopBits of COM5 to 1
> 2018-07-20T16:40:21.834639 tid10480 [dbg,dev:COM5] Attempting to set
> dataBits of COM5 to 8
> 2018-07-20T16:40:21.834639 tid10480 [IFO,Core] Did initialize device COM5
> 2018-07-20T16:40:21.834639 tid10480 [IFO,Core] Will initialize device
> Camera
> 2018-07-20T16:40:21.838639 tid10480 [IFO,dev:Camera]
> Exception[AT_ERR_CONNECTION] thrown: Error Connecting / Disconnecting
> Hardware
> 2018-07-20T16:40:21.838639 tid10480 [ERR,Core:dev:Camera] Error in device
> "Camera": Unable to communicate with the device. (35)
> 2018-07-20T16:40:21.838639 tid10480 [IFO,Core] Unloading all devices after
> failure to load system configuration
> 2018-07-20T16:40:21.838639 tid10480 [dbg,Core] Will unload all devices
> 2018-07-20T16:40:22.042639 tid10480 [IFO,Core] Did unload all devices
> 2018-07-20T16:40:22.042639 tid10480 [IFO,Core] Now rethrowing original
> error from system configuration loading
> 2018-07-20T16:40:22.044639 tid10480 [IFO,App] Failed to load hardware
> configuation
> [ ] java.lang.Exception: Line
> 29: Property,Core,Initialize,1
> [ ] Error in device "Camera":
> Unable to communicate with the device. (35)
> [ ]
> [ ] in
> Thread[AWT-EventQueue-0,6,main]
> [ ] at
> mmcorej.MMCoreJJNI.CMMCore_loadSystemConfiguration(Native Method)
> [ ] at mmcorej.CMMCore.
> loadSystemConfiguration(CMMCore.java:366)
> [ ] at
> org.micromanager.MMStudio.loadSystemConfiguration(MMStudio.java:1730)
> [ ] at
> org.micromanager.MMStudio.setSysConfigFile(MMStudio.java:962)
> [ ] at org.micromanager.menus.
> ToolsMenu.loadConfiguration(ToolsMenu.java:227)
> [ ] at org.micromanager.menus.
> ToolsMenu.access$400(ToolsMenu.java:28)
> [ ] at org.micromanager.menus.
> ToolsMenu$11.run(ToolsMenu.java:163)
> [ ] at org.micromanager.utils.
> GUIUtils$3.actionPerformed(GUIUtils.java:361)
> [ ] at
> javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
> [ ] at
> javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> [ ] at javax.swing.
> DefaultButtonModel.fireActionPerformed(Unknown Source)
> [ ] at javax.swing.
> DefaultButtonModel.setPressed(Unknown Source)
> [ ] at
> javax.swing.AbstractButton.doClick(Unknown Source)
> [ ] at javax.swing.plaf.basic.
> BasicMenuItemUI.doClick(Unknown Source)
> [ ] at javax.swing.plaf.basic.
> BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
> [ ] at
> java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
> [ ] at java.awt.Component.processMouseEvent(Unknown
> Source)
> [ ] at javax.swing.JComponent.processMouseEvent(Unknown
> Source)
> [ ] at java.awt.Component.processEvent(Unknown
> Source)
> [ ] at java.awt.Container.processEvent(Unknown
> Source)
> [ ] at java.awt.Component.dispatchEventImpl(Unknown
> Source)
> [ ] at java.awt.Container.dispatchEventImpl(Unknown
> Source)
> [ ] at java.awt.Component.dispatchEvent(Unknown
> Source)
> [ ] at java.awt.
> LightweightDispatcher.retargetMouseEvent(Unknown Source)
> [ ] at java.awt.
> LightweightDispatcher.processMouseEvent(Unknown Source)
> [ ] at java.awt.
> LightweightDispatcher.dispatchEvent(Unknown Source)
> [ ] at java.awt.Container.dispatchEventImpl(Unknown
> Source)
> [ ] at java.awt.Window.dispatchEventImpl(Unknown
> Source)
> [ ] at java.awt.Component.dispatchEvent(Unknown
> Source)
> [ ] at java.awt.EventQueue.dispatchEventImpl(Unknown
> Source)
> [ ] at
> java.awt.EventQueue.access$000(Unknown Source)
> [ ] at
> java.awt.EventQueue$1.run(Unknown Source)
> [ ] at
> java.awt.EventQueue$1.run(Unknown Source)
> [ ] at java.security.
> AccessController.doPrivileged(Native Method)
> [ ] at java.security.
> AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> [ ] at java.security.
> AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> [ ] at
> java.awt.EventQueue$2.run(Unknown Source)
> [ ] at
> java.awt.EventQueue$2.run(Unknown Source)
> [ ] at java.security.
> AccessController.doPrivileged(Native Method)
> [ ] at java.security.
> AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> [ ] at java.awt.EventQueue.dispatchEvent(Unknown
> Source)
> [ ] at
> java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
> [ ] at
> java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
> [ ] at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> [ ] at
> java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> [ ] at
> java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> [ ] at
> java.awt.EventDispatchThread.run(Unknown Source)
> 2018-07-20T16:40:23.326639 tid10480 [IFO,App] Updating GUI; config pad =
> true; from cache = false
> 2018-07-20T16:40:23.326639 tid10480 [IFO,App] Rebuilding config group table
> 2018-07-20T16:40:23.326639 tid10480 [IFO,App] Finished rebuilding config
> group table
> 2018-07-20T16:40:23.326639 tid10480 [dbg,Core] Will update system state
> cache
> 2018-07-20T16:40:23.326639 tid10480 [IFO,Core] Did update system state
> cache
> 2018-07-20T16:40:23.328638 tid10480 [IFO,App] Finished updating GUI
> 2018-07-20T16:40:23.328638 tid10480 [IFO,App] Updating GUI; config pad =
> true; from cache = false
> 2018-07-20T16:40:23.328638 tid10480 [IFO,App] Rebuilding config group table
> 2018-07-20T16:40:23.328638 tid10480 [IFO,App] Finished rebuilding config
> group table
> 2018-07-20T16:40:23.328638 tid10480 [dbg,Core] Will update system state
> cache
> 2018-07-20T16:40:23.328638 tid10480 [IFO,Core] Did update system state
> cache
> 2018-07-20T16:40:23.330638 tid10480 [IFO,App] Finished updating GUI
> 2018-07-20T16:40:25.956635 tid10480 [IFO,App] User has stopped log capture
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] ***** BEGIN Problem Report
> System Info (incremental) *****
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] Total physical memory
> (caveats apply if JVM is 32-bit): 68630441984 (63.9 GiB)
> [ ] Committed virtual memory
> size: 1246478336 (1.2 GiB)
> [ ] Free physical memory (may be
> meaningless if JVM is 32-bit): 63417466880 (59.1 GiB)
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] JVM heap memory usage: used =
> 139647464 (133.2 MiB); committed = 1027735552 (980.1 MiB); max = 1864171520
> (1.7 GiB)
> [ ] JVM non-heap memory usage:
> used = 59994976 (57.2 MiB); committed = 60489728 (57.7 MiB); max =
> 136314880 (130.0 MiB)
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] All Java threads:
> [ ] id 2 ("Reference Handler"):
> WAITING
> [ ] id 3 ("Finalizer"): WAITING
> [ ] id 4 ("Signal Dispatcher"):
> RUNNABLE
> [ ] id 5 ("Attach Listener"):
> RUNNABLE
> [ ] id 10 ("Java2D Disposer"):
> WAITING
> [ ] id 11 ("AWT-Shutdown"):
> WAITING
> [ ] id 12 ("AWT-Windows"):
> RUNNABLE
> [ ] id 15 ("AWT-EventQueue-0"):
> RUNNABLE
> [ ] id 18 ("DestroyJavaVM"):
> RUNNABLE
> [ ] id 20 ("TimerQueue"):
> TIMED_WAITING
> [ ] id 21 ("EDTHangLogger
> timer"): TIMED_WAITING
> [ ] id 23 ("D3D Screen
> Updater"): TIMED_WAITING
> [ ] id 24 ("Thread-5"):
> TIMED_WAITING
> [ ] id 25 ("BeanShell
> interpreter"): TIMED_WAITING
> [ ] id 30
> ("SwingWorker-pool-4-thread-1"): WAITING
> [ ] id 33 ("Swing-Shell"):
> WAITING
> [ ] id 39
> ("SwingWorker-pool-4-thread-2"): RUNNABLE
> [ ] (End all Java threads)
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] Deadlocked Java threads: none
> detected
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] MMCore version: MMCore
> version 8.7.1
> [ ] Circular buffer size (MB):
> 5120
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] Core property cache ("system
> state cache") contents:
> [ ] Core/AutoFocus =
> [ ] Core/AutoShutter = 1
> [ ] Core/Camera =
> [ ] Core/ChannelGroup =
> [ ] Core/Focus =
> [ ] Core/Galvo =
> [ ] Core/ImageProcessor =
> [ ] Core/Initialize = 1
> [ ] Core/SLM =
> [ ] Core/Shutter =
> [ ] Core/TimeoutMs = 5000
> [ ] Core/XYStage =
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] ***** END Problem Report
> System Info (incremental) *****
> 2018-07-20T16:40:25.960635 tid3636 [IFO,App] Problem Report: End of log
> capture
> 2018-07-20T16:40:25.960635 tid3636 [IFO,LogManager] Removing secondary log
> file C:\Users\Linda Liu\MMProblemReport\CoreLogCapture.txt
> ***** END Captured Log *****
>
>
> I am not sure why the camera will not load anymore. Any help would be
> appreciated.
>
> Much Appreciated,
> Kiana Go
>
>
> On Fri, Jul 20, 2018 at 12:11 AM, Kyle Douglass <kyl...@gm...
> > wrote:
>
>> Hi Kiana Go,
>>
>>
>> On Fri, Jul 13, 2018 at 2:02 AM, Kiana Go <gok...@be...>
>> wrote:
>>>
>>> >>import mmcorej.*;
>>> >> mmc= CMMCore;
>>> >> mmc.loadDevice("Port", "SerialManager", "COM5");
>>> >> mmc.initializeDevice("Port");
>>> >> mmc.loadDevice("ZStage", "Prior", "ZStage");
>>>
>>> The ZStage is connected to serial port COM5. The ZStage also works
>>> fine through Micro-Manager and its own software controller. Thus, it is
>>> connected. There seems to be a problem with matlab's interface with
>>> Micro-Manager to recognize and configure the ZStage.
>>> For reference, I am using Prior's ZStage. I am also using the
>>> ProScan III controller. Not sure why the ZStage will not initialize and
>>> move when given the appropriate methods.
>>>
>>
>> I'm sorry for the late reply; I've been a bit busy lately.
>>
>> I do not have much experience with loading devices from MATLAB, so I
>> might be wrong about this. At first glance, it looks like you're trying to
>> assign two devices to COM5, which to me seems like the most likely source
>> of the problem.
>>
>> I don't think that you need to assign a SerialManager device to COM5,
>> since this is a device adapter for general serial port communications. I
>> think you're getting an error when you run the line
>> mmc.loadDevice("ZStage", "Prior", "ZStage"); because the SerialManager is
>> already assigned to the same COM port.
>>
>> When you tested this in the Micro-Manager GUI, did you also add a
>> SerialManager device adapter to your configuration at COM5, or only the
>> Prior stage?
>>
>> Best regards,
>> Kyle
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
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>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>
>
>
> --
> Class of 2021
>
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Class of 2021
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