Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

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Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

André Lampe
Hi everybody!

I tried to to get our Andor Clara working while there is also an Andor iXon present. But I do not think that the iXon is the Problem.

In the Hardware Configuration Wizard at Step 4 clicking on "next", while just trying to add the Clara. I got this Error-message: "Error in device Andor: Error code 20066 (4e62 hex)."

We wanted to switch from WinXP(32bit) to 7(64bit) and simultaneously switch from MM 1.3.something to MM 1.4.7. With MM 1.3 it is no Problem to run the Clara with the iXon still present and there is no error. We run the setup for about a year like this: One CFG for Clara and one CFG for iXon and it works fine.

I tried different SDKs from Andor. The latest (32 and 64bit) and those which came with the Clara. Win7 recognizes the camera properly with each of those drivers from within the SDK. I also tried changing to several versions of the "atmcd64d.dll" in the MM directory as it is mentioned on the MM homepage. I know, this was meant to be for the Error 22, but just to be sure. It changed nothing.

I searched the mailing list and several other resources. I hope someone here has an idea. I am a little bit lost.

Kind regards, André Lampe
André Lampe, Dipl.-Phys.
FU Berlin, BioChemPharm
Laboratory of Membrane Biochemistry and molecular cell biology
AG Haucke
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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Nico Stuurman
Administrator
Hi André,

> I tried to to get our Andor Clara working while there is also an Andor iXon present.

> In the Hardware Configuration Wizard at Step 4 clicking on "next", while just trying to add the Clara. I got this Error-message: "Error in device Andor: Error code 20066 (4e62 hex)."

That error means: "DRV_P1INVALID" (whatever that means!).  Can you generate a "Trouble Report" (under the "Help") menu so that we get a full log of what happens?

Is anyone else successfully running a Clara in Micro-Manager?

There have been several changes to the Andor adapter code since 1.3 and it is well possible that one of them makes assumptions that are only try for the iXon.  Your logs will help us pinpoint what is going on.

Best,

Nico



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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Karl Bellve-3


On Fri, Feb 10, 2012 at 11:10 AM, Nico Stuurman <[hidden email]> wrote:

There have been several changes to the Andor adapter code since 1.3 and it is well possible that one of them makes assumptions that are only try for the iXon.  Your logs will help us pinpoint what is going on.

Best,

Nico



We have one system with an Andor Clara running with an older 1.4.* uManager and I did run across that error last week when I changed to a new Andor system libraries (libandor.so.2.91.30001.0). I did try to upgrade to the latest nightly to see if that fixed the issue but ran into uManager compile errors. Since the system wanted to be used immediately, I downgraded to libandor.so.2.90.30004.0 and got everything working.

I have since compiled the latest uManager on the system and I will test it out maybe next week.

libandor.so.2.91.30001.0 should have the cooling issue fixed for Clara cameras so I definitely want to move to it.


--
Cheers,

Karl Bellvé
Biomedical Imaging Group
University of Massachusetts Medical School


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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

André Lampe
Thanks for the replies. The Logs have been sent to Nico.

If there is anything more I can do, just say so.

Cheers, André
André Lampe, Dipl.-Phys.
FU Berlin, BioChemPharm
Laboratory of Membrane Biochemistry and molecular cell biology
AG Haucke
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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Karl Bellve-3

sigh...making it hard to figure this issue out with the Andor Clara and the their latest driver...

Using uManager 1.4.7 I downloaded and was able to compile a few weeks ago. It told me that it needed ImageJ 1.4.6e. Only 1.4.5 is available at http://rsbweb.nih.gov/ij/download.html

However, ImageJ was able to update itself by using a menu to 1.4.6e..., which I did.

Running uManager brings me to:
Searching for /usr/local/lib/micro-manager/libmmgr_dal_Andor.so.0
#
# An unexpected error has been detected by Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fa07497e519, pid=6947, tid=140327146141440
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (11.0-b15 mixed mode linux-amd64)
# Problematic frame:
# C  [libMMCoreJ_wrap.so+0x7f519]  _ZN14CPluginManager14GetSystemErrorERSs+0x1b
#
# An error report file with more information is saved as:
# /usr/local/ImageJ/hs_err_pid6947.log
#
# If you would like to submit a bug report, please visit:


ok, crashes...when it tried to load the andor library.

Did a SVN update to version uManager 8726 to see if that fixed the issue...

and it doesn't compile....

pukes on Gaussian.jar

svn update on ../3rdpartypublic/

Improves the situation with much less errors. 

javac -source 1.5 -target 1.5 -sourcepath .:. -classpath /storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/ij.jar:/usr/share/java/bsh.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/commons-math-2.0.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/swing-layout-1.0.4.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/jfreechart-1.0.13.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/jcommon-1.0.16.jar:../bin/MMCoreJ.jar:../mmstudio/MMJ_.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/TSFProto.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/gproto.jar:. ./Gaussian/source/GaussianTrack_.java ./Gaussian/source/edu/valelab/GaussianFit/*.java -d build
./Gaussian/source/edu/valelab/GaussianFit/DataCollectionForm.java:57: package valelab does not exist

import valelab.LocalWeightedMean;
              ^
./Gaussian/source/edu/valelab/GaussianFit/DataCollectionForm.java:75: cannot find symbol
symbol  : class LocalWeightedMean
location: class edu.valelab.GaussianFit.DataCollectionForm
   private static LocalWeightedMean lwm_;
                  ^
./Gaussian/source/edu/valelab/GaussianFit/DataCollectionForm.java:553: cannot find symbol
symbol  : class LocalWeightedMean
location: class edu.valelab.GaussianFit.DataCollectionForm
         lwm_ = new LocalWeightedMean(2, points);
                    ^
Note: ./Gaussian/source/edu/valelab/GaussianFit/FitAllThread.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
3 errors
make[1]: *** [Gaussian.jar] Error 1
make[1]: Leaving directory `/mnt/mizar/VolGroup03-LogVol00/kdb/projects/svn/micromanager2/trunk/plugins'
make: *** [all-recursive] Error 1

moved to an older revision before Gaussian is added..
svn update -r 8708

That compiles...
installs...
cashes..
Error: org.micromanager.browser.Data_Browser fails to implement static String tooltipDescription.
LOG(2012-02-13T15:12:01.327760, 29635, 140549100615424:): > Error: org.micromanager.imageflipper.TaggedImageFlipper fails to implement static String tooltipDescription.
#
# An unexpected error has been detected by Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fd42298a4d9, pid=29635, tid=140549100615424
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (11.0-b15 mixed mode linux-amd64)
# Problematic frame:
# C  [libMMCoreJ_wrap.so+0x7f4d9]  _ZN14CPluginManager14GetSystemErrorERSs+0x1b
#
# An error report file with more information is saved as:
# /usr/local/ImageJ/hs_err_pid29635.log
#
# If you would like to submit a bug report, please visit:
#
./run: line 5: 29635 Aborted                 (core dumped) ./jre/bin/java -Xmx2048m -Djava.library.path="/usr/local/cuda/lib64/:/usr/lib64/micro-manager/" -cp ij.jar ij.ImageJ

oh well...maybe an even older revision?

No closer in solving this Andor Clara bug...maybe I will wait until the Gaussian compiles properly.  I would like to be working with the latest uManager before I look for the Andor issue.



--
Cheers,

Karl Bellvé
Biomedical Imaging Group
University of Massachusetts Medical School

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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Nico Stuurman
Administrator

On Feb 13, 2012, at 12:26 PM, Karl Bellve wrote:

> sigh...making it hard to figure this issue out with the Andor Clara and the their latest driver...
> javac -source 1.5 -target 1.5 -sourcepath .:. -classpath /storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/ij.jar:/usr/share/java/bsh.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/commons-math-2.0.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/swing-layout-1.0.4.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/jfreechart-1.0.13.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/jcommon-1.0.16.jar:../bin/MMCoreJ.jar:../mmstudio/MMJ_.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/TSFProto.jar:/storage/big1/kdb/projects/svn/micromanager2/trunk/../3rdpartypublic/classext/gproto.jar:. ./Gaussian/source/GaussianTrack_.java ./Gaussian/source/edu/valelab/GaussianFit/*.java -d build
> ./Gaussian/source/edu/valelab/GaussianFit/DataCollectionForm.java:57: package valelab does not exist
>
> import valelab.LocalWeightedMean;

Should be fixed now.

> That compiles...
> installs...
> cashes..
> Error: org.micromanager.browser.Data_Browser fails to implement static String tooltipDescription.
> LOG(2012-02-13T15:12:01.327760, 29635, 140549100615424:): > Error: org.micromanager.imageflipper.TaggedImageFlipper fails to implement static String tooltipDescription.
> #
> # An unexpected error has been detected by Java Runtime Environment:
> #
> #  SIGSEGV (0xb) at pc=0x00007fd42298a4d9, pid=29635, tid=140549100615424
> #
> # Java VM: Java HotSpot(TM) 64-Bit Server VM (11.0-b15 mixed mode linux-amd64)
> # Problematic frame:
> # C  [libMMCoreJ_wrap.so+0x7f4d9]  _ZN14CPluginManager14GetSystemErrorERSs+0x1b

You may want to try a make clean before running make.  

Best,

Nico


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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Karl Bellve-3
In reply to this post by Karl Bellve-3
I haven't updated and run uManager since all talk and changes with pluginManager.cpp but I had to drop off RTLD_NOLOAD from (PluginManager.cpp):

if (strcmp (shortName, "Andor") == 0)
         mode = RTLD_LAZY | RTLD_LOCAL;

The andor library fails to load at line (unlike all the other libraries)
HDEVMODULE hMod = dlopen(name.c_str(), RTLD_NOLOAD | mode);

But loads at line:
 hMod = dlopen(name.c_str(), RTLD_NODELETE | mode);

RTLD_NOLOAD, just like RTLD_NOW, doesn't work with the Andor library. 

Back to the Clara issue. I can reproduce the Clara error with the libandor.so.2.91.30001.0

EPROM: 0
COF File: 0
Driver: 0.0
DLL: 2.91

LOG(2012-02-13T16:23:46.536315, 17983, 140472409585408:): Error occured. Device Clara. Error in device Clara: Error code 20066 (4e62 hex).

This is the area of the code that is causing the error:

        nRet = SetAllowedValues("Pre-Amp-Gain", PreAmpGains_);
        nRet = SetProperty("Pre-Amp-Gain", PreAmpGains_[PreAmpGains_.size()-1].c_str());
        PreAmpGain_ = PreAmpGains_[numPreAmpGain-1];
        if(numPreAmpGain > 1)
        {
            ret = SetPreAmpGain(numPreAmpGain-1);
             if (ret != DRV_SUCCESS)
                return ret;
        }


If you skip SetPreAmpGain(numPreAmpGain-1);, then uManager is able to load the andor driver, but can't successfully take an image. 

This points to an incompatibility with the uManager Andor Device Adapter and the Andor Library. I don't think I can fix myself since I only have the source code to the former.

More tomorrow.

--
Cheers,

Karl Bellvé
Biomedical Imaging Group
University of Massachusetts Medical School


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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Nico Stuurman
Administrator

On Feb 13, 2012, at 2:03 PM, Karl Bellve wrote:

I haven't updated and run uManager since all talk and changes with pluginManager.cpp but I had to drop off RTLD_NOLOAD from (PluginManager.cpp):

if (strcmp (shortName, "Andor") == 0)
         mode = RTLD_LAZY | RTLD_LOCAL;

I committed that change.  Let me know of any issues.

Back to the Clara issue. I can reproduce the Clara error with the libandor.so.2.91.30001.0

EPROM: 0
COF File: 0
Driver: 0.0
DLL: 2.91

LOG(2012-02-13T16:23:46.536315, 17983, 140472409585408:): Error occured. Device Clara. Error in device Clara: Error code 20066 (4e62 hex).

This is the area of the code that is causing the error:

        nRet = SetAllowedValues("Pre-Amp-Gain", PreAmpGains_);
        nRet = SetProperty("Pre-Amp-Gain", PreAmpGains_[PreAmpGains_.size()-1].c_str());
        PreAmpGain_ = PreAmpGains_[numPreAmpGain-1];
        if(numPreAmpGain > 1)
        {
            ret = SetPreAmpGain(numPreAmpGain-1);
             if (ret != DRV_SUCCESS)
                return ret;
        }


If you skip SetPreAmpGain(numPreAmpGain-1);, then uManager is able to load the andor driver, but can't successfully take an image. 

Hmm.  It looks like the driver says that there is at least one pre-amp gain, but then when the code tries to set it it fails?

Best,

Nico


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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Karl Bellve-3


On Tue, Feb 14, 2012 at 12:08 AM, Nico Stuurman <[hidden email]> wrote:

On Feb 13, 2012, at 2:03 PM, Karl Bellve wrote:

I haven't updated and run uManager since all talk and changes with pluginManager.cpp but I had to drop off RTLD_NOLOAD from (PluginManager.cpp):

if (strcmp (shortName, "Andor") == 0)
         mode = RTLD_LAZY | RTLD_LOCAL;

I committed that change.  Let me know of any issues.


Works great. Latest nightly compiles and installs fine on Fedora 13.
 

Hmm.  It looks like the driver says that there is at least one pre-amp gain, but then when the code tries to set it it fails?

Best,




WORKS:
GetNumberPreAmpGains(&numPreAmpGain); returns 0 with libandor.so.2.90.30004.0


FAILS:
GetNumberPreAmpGains(&numPreAmpGain); returns 3 with libandor.so.2.91.30001.0

Above activates a bunch of code.

if  I force numPreAmpGain = 0 right after GetNumberPreAmpGains(&numPreAmpGain), then libandor.so.2.91.30001.0 works

This is an Andor issue and I don't know enough why one driver sets the number of PreAmpGains = 0 and the newer one sets it to 3 and croaks.

On the other hand, libandor.so.2.91.30001.0 allows you to set the CCD temperature below 0 for the Clara! Major fix! Too bad no one can make use of it...



--
Cheers,

Karl Bellvé
Biomedical Imaging Group
University of Massachusetts Medical School


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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Felipe Martínez-Pastor
Hi,
Which Java (JDK/JRE) are you using to compile and run on Fedora?
Cheers,
Felipe

El 14/02/12 15:39, Karl Bellve escribió:

> On Tue, Feb 14, 2012 at 12:08 AM, Nico Stuurman<[hidden email]>  wrote:
>
>>
>> On Feb 13, 2012, at 2:03 PM, Karl Bellve wrote:
>>
>> I haven't updated and run uManager since all talk and changes with
>> pluginManager.cpp but I had to drop off RTLD_NOLOAD from
>> (PluginManager.cpp):
>>
>> if (strcmp (shortName, "Andor") == 0)
>>           mode = RTLD_LAZY | RTLD_LOCAL;
>>
>>
>> I committed that change.  Let me know of any issues.
>>
>>
> Works great. Latest nightly compiles and installs fine on Fedora 13.
>
>


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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Karl Bellve-3


2012/2/14 Felipe Martínez-Pastor <[hidden email]>
Hi,
Which Java (JDK/JRE) are you using to compile and run on Fedora?
Cheers,
Felipe


jre-1.6.0_26-fcs.x86_64 from Sun
 
--
Cheers,

Karl Bellvé
Biomedical Imaging Group
University of Massachusetts Medical School

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Re: Problems with Andor Clara and MM 1.4.7 (Error code 20066 (4e62hex))

Pariksheet Nanda
In reply to this post by Karl Bellve-3
On Fri, Feb 10, 2012 at 11:44 AM, Karl Bellve <[hidden email]> wrote:
> libandor.so.2.91.30001.0 should have the cooling issue fixed for Clara
> cameras so I definitely want to move to it.

The Clara full cooling works (down to -55 C) with Micro-Manager-1.4.10
(svn rev 9309) and Andor Linux SDK 2.94.30006.0 from my test:
http://i.imgur.com/dM1IC.png

> Cheers,
> Karl Bellvé

Pariksheet

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