Line/Ridge Detection Plugin

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Line/Ridge Detection Plugin

jumpfunky
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

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Re: Line/Ridge Detection Plugin

Jan Eglinger
Dear Thorsten,

On 10.12.14 17:30, Thorsten Wagner wrote:
> 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

Thanks for contributing! This plugin seems to be a very useful addition.

>
> In the next days I will add a google code repository.

May I suggest that you put the code on github.com? All the ImageJ and
Fiji projects are hosted there as well.

https://github.com/imagej
https://github.com/fiji

>
> Any suggestions or bug reports are welcome.
>

To make it easier for *users*, I'd also suggest that you create an
update site for your plugin, so users can install it with a single
mouse-click by activating your update site.
For details, see:
http://fiji.sc/How_to_set_up_and_populate_an_update_site

Cheers,
Jan

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Re: Line/Ridge Detection Plugin

Michael Schmid
In reply to this post by jumpfunky
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

--
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Re: Line/Ridge Detection Plugin

jumpfunky
Dear Michael,

it also works with ImageJ. But you have to copy the apache commons lang
3 jar into the plugins/jars directory:
https://commons.apache.org/proper/commons-lang/

Cheers,
Thorsten


Am Mittwoch, den 10.12.2014, 18:29 +0100 schrieb Michael Schmid:

> 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

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Re: Line/Ridge Detection Plugin

ctrueden
In reply to this post by Michael Schmid
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
>

--
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Re: Line/Ridge Detection Plugin

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

--
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Re: Line/Ridge Detection Plugin

jumpfunky
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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Re: Line/Ridge Detection Plugin

Glen MacDonald-2
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
(206) 616-4156
[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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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Re: Line/Ridge Detection Plugin

jumpfunky
Sorry, my fault! I've uploaded a corrupted jar file.

The latest version should work.

Cheers,
Thorsten

Am Mittwoch, den 10.12.2014, 12:25 -0800 schrieb Glen MacDonald:

> 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
> (206) 616-4156
> [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
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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Re: Line/Ridge Detection Plugin

jumpfunky
In reply to this post by Glen MacDonald-2
Dear Glen,

I've now resolved the bug in the stack processing and also a bug in the
preview mode.

The user also gets informed when the LUT is inverted and the LUT will be
reset.

Today I will create a GitHub repository and upload the code. I will also
add the plugin to Biomedgroup update site.

Cheers,
Thorsten

Am Mittwoch, den 10.12.2014, 12:25 -0800 schrieb Glen MacDonald:

> 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
> (206) 616-4156
> [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
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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