Re: Line/Ridge Detection Plugin

Posted by Glen MacDonald-2 on Dec 10, 2014; 8:25pm
URL: http://imagej.273.s1.nabble.com/Line-Ridge-Detection-Plugin-tp5010878p5010887.html

Thorsten, thanks for this plugin.   However, the latest version is producing an Exception message.  The prior version was sometimes running, sometimes giving a much longer error message.  Image was an 8-bit stack, 149x135x21.  
Pasted from Exception window:
*********************
(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49m; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.5; 264MB of 3151MB (8%)
 
java.lang.Error: Unresolved compilation problem:
        The method detect_lines(float[], long, long, Contours, MutableLong, double, double, double, long, boolean, boolean, boolean, Junctions) from the type Position refers to the missing type MutableLong

        at de.biomedical_imaging.ij.steger.Lines_.get_lines(Lines_.java:438)
        at de.biomedical_imaging.ij.steger.Lines_.run(Lines_.java:401)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
        at ij.plugin.filter.PlugInFilterRunner.processStack(PlugInFilterRunner.java:193)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:144)
        at ij.IJ.runUserPlugIn(IJ.java:204)
        at ij.IJ.runPlugIn(IJ.java:166)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:695)
***********************

regards,
Glen MacDonald
        Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
        Cellular Morphology Core
Center on Human Development and Disability
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]







On Dec 10, 2014, at 11:32 AM, Thorsten Wagner <[hidden email]> wrote:

> Dear Michael,
>
> I've now updated the plugin and it automatically checks whether the
> commons-lang3 is installed:
>
> try {
>    Class.forName("org.apache.commons.lang3.mutable.MutableLong");
> }
> catch (ClassNotFoundException exception) {
>    IJ.error("Please install apache-commons-lang 3", "It seems that
> the apache-commons-lang 3 library is not installed on your system. \n "
>     + "Download the jar file under
> https://commons.apache.org/proper/commons-lang/ and copy it to
> plugins/jars");
>    return DONE;
> }
>
> Cheers,
> Thorsten
>
>
> Am Mittwoch, den 10.12.2014, 19:43 +0100 schrieb Michael Schmid:
>> Hi Curtis,
>>
>> the problem is solved with adding the apache commons lang 3 jar file, as suggested by Thorsten.
>>
>> Nevertheless, thank you for pointing me to the code where the prefix is stripped! So, in case of a exception, IJ retries with the package name stripped off, and that retry gave the misleading error message.
>>
>> Michael
>> ________________________________________________________________
>> On Dec 10, 2014, at 19:18, Curtis Rueden wrote:
>>
>>> Hi Michael,
>>>
>>>> Plugin or class not found: "biomedical_imaging.ij.steger.Lines_"
>>>>
>>>> Strangely, it first shows the dialog, so it has found the main class
>>>> already. Also the path in the error message is without the preceding
>>>> 'de.', which is in the plugins.config and the path inside the jar.
>>>> Any ideas?
>>>
>>> I can't comment on why the plugin isn't working as expected, but I do know
>>> the lack of "de." prefix is due to how ImageJ 1.x tries to strip package
>>> names from plugins:
>>>
>>> https://github.com/imagej/ImageJA/blob/v1.49m/src/main/java/ij/IJ.java#L210-L223
>>>
>>> Regards,
>>> Curtis
>>>
>>> On Wed, Dec 10, 2014 at 11:29 AM, Michael Schmid <[hidden email]>
>>> wrote:
>>>
>>>> Hi Thorsten,
>>>>
>>>> is this plugin also meant for plain ImageJ (not Fiji)?
>>>> When trying to run it with plain ImageJ 1.49n8 (the current daily build)
>>>> on Mac OS X 10.6.8 (Java 1.6), upon pressing 'OK' I get an error:
>>>>
>>>> Plugin or class not found: "biomedical_imaging.ij.steger.Lines_"
>>>>
>>>> Strangely, it first shows the dialog, so it has found the main class
>>>> already. Also the path in the error message is without the preceding 'de.',
>>>> which is in the plugins.config and the path inside the jar. Any ideas?
>>>>
>>>> Michael
>>>> ________________________________________________________________
>>>> On Dec 10, 2014, at 17:30, Thorsten Wagner wrote:
>>>>
>>>>> Dear list,
>>>>>
>>>>> please find our new ridge detection plugin which implements a well known
>>>>> algorithm (however, we could not find an fiji/imagej implementation):
>>>>>
>>>>> http://fiji.sc/Ridge_Detection
>>>>>
>>>>> In the next days I will add a google code repository.
>>>>>
>>>>> Any suggestions or bug reports are welcome.
>>>>>
>>>>> --
>>>>> Kind regards
>>>>>
>>>>> Thorsten Wagner, M.Sc.
>>>>> Biomedical Imaging Group
>>>>> University of Applied Sciences and Arts Dortmund
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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