Fiji starts with a warning log dialog

[Yili Zhao]

Hi,

  I download the latest Fiji continuous release win64 version, every time I start Fiji, it will come with a warning log dialog with these messages:

  2014-12-29 8:42:06 java.util.prefs.WindowsPreferences <init>

  Warning: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.

  After I running Fiji (ImageJ-win64.exe) as Administrator, there is no this warning log dialog with next Fiji starting.

  Is this problem related to Windows 7 UAC?

[Jayanta Bordoloi]

Same problem here....to add trouble whenever I open images they appear very dark and colors are completely distorted.

[Curtis Rueden]

Hi Yili,

> Warning: Could not open/create prefs root node Software\JavaSoft\Prefs

> at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.

Apparently, this is a general problem with the Java Preferences API on some versions of Windows. If you could find any further information on it via web searches, it would be most appreciated. While you can certainly avoid the issue by either A) running as Administrator once; or B) manually creating one or more registry keys in the right place, it would be best to avoid those annoying solutions in favor of a fix in the code.

So feel free to file an issue at:

https://github.com/scijava/scijava-common/issues

And file a PR with a fix if you are feeling ambitious.

The code which like triggers the issue is:

https://github.com/scijava/scijava-common/blob/scijava-common-2.36.0/src/main/java/org/scijava/prefs/DefaultPrefService.java#L539-L549

You can see that we always request user nodes, which means that administrator privileges are not supposed to be required...

Regards,

Curtis

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[Curtis Rueden]

Hi Jayanta,

> whenever I open images they appear very dark and colors are completely

> distorted.

Sounds like a separate issue from the one Yili reported.

What file format? Are you using Bio-Formats? (Do you see a "Bio-Formats Import Options" dialog pop up?) If so, do you have the "Autoscale" option checked?

What happens if you hit Shift+C to bring up the Brightness/Contrast dialog after the file opens and click the Auto button? If you have a composite image, you may need to move the C slider and press Auto at each channel position. Or manually set the display range for each channel using the Set button.

Regards,

Curtis

P.S. Further reading:

- http://imagej.net/Frequently_Asked_Questions#The_image_I_loaded_is_displayed_all_black.21_But_it_is_not_black.21

- http://imagej.net/IP_Principles

- http://imagej.net/Color_Image_Processing

- http://imagej.net/Image_Intensity_Processing

On Fri, Jan 2, 2015 at 6:02 PM, Jayanta Bordoloi <jkbor...@gmail.com> wrote:

[Mark Hiner]

Hi all,

Some discussion on the original topic from Yili in #fiji-devel today:

http://code.imagej.net/chatlogs/fiji-devel?times=prefix&start-date=2015-01-06&start-time=1446&end-date=2015-01-06&end-time=1508

Best,
Mark

[Yili Zhao]

Hi Curtis,

  I did a we search, and found the problem origin description:

  Root cause: In a Windows installation with Java 7 version 21 or later, the Windows Preferences classes in Oracle's JVM try to read from the Windows Registry key: HKEY_LOCAL_MACHINE\Software\JavaSoft\Prefs . Since the key has not been created by the Java installer (as was the case in previous versions of Java), these classes try to create them and fail due to insufficient privileges. This is displayed on the Java console as seen above in the warning message.

Workaround: This warning message can be safely ignored. But if you want to remove it completely the easiest workaround is starting HIPE at least once as administrator.

Side effects: The attempt to read this Registry key does not affect the behaviour of HIPE, since HIPE stores the user preferences in the CURRENT_USER hive of the Windows Registry.

So I think this problem is not related to Fiji. Instead, it is related to JDK 7 installer.

在 2015年1月6日星期二UTC+8上午6时11分37秒，Curtis Rueden写道：

[Curtis Rueden]

Hi Yili,

Thanks for the additional information.

While it might still be good to address this issue somehow, for the time being it is moot because I reverted the annoying stdout/stderr console logging. So at least people won't see that message on startup anymore, even though it is still happening.

Regards,

Curtis

P.S. For details see:

https://github.com/imagej/imagej-legacy/commit/3950a27d6b1bec66c3a3fb7c19137ff58981a729