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 00:18:29
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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
>
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