Opening pdf files in ImageJ

[Mario Faretta]

Dear all,
is there any way using Imagej to open pdf files?
Thanks for the help
Mario

--
Mario Faretta
Department of Experimental Oncology
European Institute of Oncology
c/o IFOM-IEO Campus for Oncogenomics
via Adamello 16
20139 Milan
Italy
Phone: ++39-02574303054
email: [hidden email]
http://www.ifom-ieo-campus.it



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[Fabrice Senger]

Mario Faretta a écrit :
> Dear all,
> is there any way using Imagej to open pdf files?
> Thanks for the help
> Mario
>
>  
http://pacific.mpi-cbg.de/wiki/index.php/Category:Plugins

Category E :

Extract Images From PDF...

Cheers ,

Fabrice.

--
Senger Fabrice

[dscho]

Hi,

On Fri, 10 Jul 2009, Mario Faretta wrote:

> is there any way using Imagej to open pdf files?

We have something in IO_.jar in Fiji which relies on jpedal to open PDF
files.  (Fiji can be downloaded from http://pacific.mpi-cbg.de/)

Ciao,
Dscho

[Aryeh Weiss]

Senger Fabrice wrote:

> Mario Faretta a écrit :
>> Dear all,
>> is there any way using Imagej to open pdf files?
>> Thanks for the help
>> Mario
>>
>>  
> http://pacific.mpi-cbg.de/wiki/index.php/Category:Plugins
>
> Category E :
>
> Extract Images From PDF...
>
> Cheers ,
>
> Fabrice.

I downloaded the source, and compiled using compile and run. To make it
compile, I had to name the source Extract_Images_From_PDF.java (it
downloads as src-plugins_IO__io_Extract_Images_From_PDF)

However, when I run it following apparently successful compilation, I
get the following error:

Plugin or class not found: "Extract_Images_From_PDF"
(java.lang.NoClassDefFoundError: Extract_Images_From_PDF (wrong name:
io/Extract_Images_From_PDF))

What have I done wrong?

--aryeh

--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[dscho]

Hi,

On Fri, 10 Jul 2009, Aryeh Weiss wrote:

> Senger Fabrice wrote:
> > Mario Faretta a écrit :
> > > Dear all,
> > > is there any way using Imagej to open pdf files?
> > > Thanks for the help
> > > Mario
> > >
> > >  
> > http://pacific.mpi-cbg.de/wiki/index.php/Category:Plugins
> >
> > Category E :
> >
> > Extract Images From PDF...
> >
> > Cheers ,
> >
> > Fabrice.
>
> I downloaded the source, and compiled using compile and run. To make it
> compile, I had to name the source Extract_Images_From_PDF.java (it downloads
> as src-plugins_IO__io_Extract_Images_From_PDF)
>
> However, when I run it following apparently successful compilation, I get the
> following error:
>
> Plugin or class not found: "Extract_Images_From_PDF"
> (java.lang.NoClassDefFoundError: Extract_Images_From_PDF (wrong name:
> io/Extract_Images_From_PDF))
>
> What have I done wrong?

You need to put it into the subdirectory io/ because the class says
"package io;" at the beginning.  Alternatively, you can remove that
statement and recompile.  Be advised that you really need the jpedal.jar
in your plugins folder (but I guess you have, because you could
successfully compile the class).

Ciao,
Dscho

[Michael Schmid]

Hi all,

this is great!
But you need a bit more than is obvious at first glance:

The JPedal jar file from
   http://www.jpedal.org/download/lgpl/jpedal_lgpl.jar
This should go into the java classpath; on the Macintosh I moved it  
into /Library/Java/Extensions

The PDF_Viewer from
   http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?
p=fiji.git;a=blob;f=src-plugins/IO_/io/PDF_Viewer.java;hb=HEAD
   (Click on "PDF_Viewer.java")

and finally as stated, Extract_Images_From_PDF.java
   http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?
p=fiji.git;a=blob;f=src-plugins/IO_/io/
Extract_Images_From_PDF.java;hb=HEAD

Even with everything in folder .../ImageJ/plugins/io, it did not work  
for me; I had to remove the 'package io' statements from both java  
files for 'Compile and Run'

Extract_Images_From_PDF works flawlessly.
PDF_Viewer alone always gives me an Error:  
java.lang.NullPointerException in the log window (unfortunately  
without any trace information).

Michael
________________________________________________________________

On 10 Jul 2009, at 15:53, Senger Fabrice wrote:

> Mario Faretta a écrit :
>> Dear all,
>> is there any way using Imagej to open pdf files?
>> Thanks for the help
>> Mario
>>
>>
> http://pacific.mpi-cbg.de/wiki/index.php/Category:Plugins
>
> Category E :
>
> Extract Images From PDF...
>
> Cheers ,
>
> Fabrice.
>
> --
> Senger Fabrice

[Michael Schmid]

Hi All,

in the meanwhile I have also found the problem of the PDF_Viewer.java

In public ImagePlus open (String, int, int)
the sequence of commands should be changed:

     decoder.setDefaultDisplayFont("SansSerif");
     if (path.startsWith("http://")) decoder.openPdfFileFromURL(path);
     else decoder.openPdfFile(path);
     decoder.setPageParameters(scale, 1);

The setPageParameters throws a NullPointerException if called before  
the file or URL has been opened.

Michael
________________________________________________________________

On 10 Jul 2009, at 20:48, Michael Schmid wrote:

> Hi all,
>
> this is great!
> But you need a bit more than is obvious at first glance:
>
> The JPedal jar file from
>   http://www.jpedal.org/download/lgpl/jpedal_lgpl.jar
> This should go into the java classpath; on the Macintosh I moved it  
> into /Library/Java/Extensions
>
> The PDF_Viewer from
>   http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?
> p=fiji.git;a=blob;f=src-plugins/IO_/io/PDF_Viewer.java;hb=HEAD
>   (Click on "PDF_Viewer.java")
>
> and finally as stated, Extract_Images_From_PDF.java
>   http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?
> p=fiji.git;a=blob;f=src-plugins/IO_/io/
> Extract_Images_From_PDF.java;hb=HEAD
>
> Even with everything in folder .../ImageJ/plugins/io, it did not  
> work for me; I had to remove the 'package io' statements from both  
> java files for 'Compile and Run'
>
> Extract_Images_From_PDF works flawlessly.
> PDF_Viewer alone always gives me an Error:  
> java.lang.NullPointerException in the log window (unfortunately  
> without any trace information).
>
> Michael
> ________________________________________________________________
>
> On 10 Jul 2009, at 15:53, Senger Fabrice wrote:
>
>> Mario Faretta a écrit :
>>> Dear all,
>>> is there any way using Imagej to open pdf files?
>>> Thanks for the help
>>> Mario
>>>
>>>
>> http://pacific.mpi-cbg.de/wiki/index.php/Category:Plugins
>>
>> Category E :
>>
>> Extract Images From PDF...
>>
>> Cheers ,
>>
>> Fabrice.
>>
>> --
>> Senger Fabrice
>