How to export images into DICOM in Java code??

[周鑫]

Hello Hacklaender,

I'm a developer working with ImageJ for quite a long time.

It was recently that I discovered ImageJ does not have a function like saveAsDicom,

and the only possibility seems to be using plugins such as dcmie or tudordicom......

Both plugins are quite big, with non-necessary code for my research project.

As dcmie requires less third-part dependency, I try to make it work for my project.

I red the Dcm_Export.java and FileExporter.java, but still has no idea about how to make it work.

Suppose that I have two variables, a ImagePlus "imp" which contains the images and a path "path" to save as.

Usually suing FileSaver, it can be done in two lines:

=====================================

  FileSaver fs = new FileSaver(imp);  
   fs.saveAsTiff(path);

=====================================

Now with Dcm_Export, I initialized an instance but did not find one function which deal with the export.

The FileExporter, on the other hand, requires 4 variables, which are not trivial to obtain from my point of view.

Could you give me a hand?

Best regards, Xin



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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi Xin,

for plugins that you can't call via their API, it is usually easiest to use 'IJ.run' to invoke them. Simply use the Plugins>Macros>Record (with the Record type set to Plugin) to see what the command should look like.  IJ.run has two versions, one where an ImagePlus can be specified [run(imp, command, options)], and one without the ImagePlus, where the current foreground image is used.

This should work with all plugins that appear in the menu and use standard ImageJ dialogs.

Michael
________________________________________________________________
On Aug 18, 2012, at 10:48, 周鑫 wrote:

> I'm a developer working with ImageJ for quite a long time.
>
> It was recently that I discovered ImageJ does not have a function like saveAsDicom,
> and the only possibility seems to be using plugins such as dcmie or tudordicom......
> Both plugins are quite big, with non-necessary code for my research project.
> As dcmie requires less third-part dependency, I try to make it work for my project.
> I red the Dcm_Export.java and FileExporter.java, but still has no idea about how to make it work.
> Suppose that I have two variables, a ImagePlus "imp" which contains the images and a path "path" to save as.
>
> Usually suing FileSaver, it can be done in two lines:
> =====================================
>  FileSaver fs = new FileSaver(imp);  
>   fs.saveAsTiff(path);
> =====================================
>
> Now with Dcm_Export, I initialized an instance but did not find one function which deal with the export.
> The FileExporter, on the other hand, requires 4 variables, which are not trivial to obtain from my point of view.
>
> Could you give me a hand?
>
> Best regards, Xin

... [show rest of quote]

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[Johannes Hermen]

Take a look at our DICOM Toolkit

http://www.santec.lu/project/dicom

it offers a DICOM Exporter class:

DicomExporter exporter = new DicomExporter();
File dcmFile = new File("/home/hermenj/jhermen.dcm");
ImagePlus ip = new ImagePlus("/home/hermenj/im0");
DicomObject dObj = exporter.createHeader(ip, true, true, true);
exporter.write(dObj, ip, dcmFile, true);


Greets
      Johannes



-----------------------------------------------------------------
Johannes Hermen  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  http://www.santec.tudor.lu
29, Avenue John F. Kennedy
L-1855 Luxembourg
-----------------------------------------------------------------



From: 周鑫 <[hidden email]>
To: <[hidden email]>,
Date: 18.08.2012 10:49
Subject: How to export images into DICOM in Java code??
Sent by: ImageJ Interest Group <[hidden email]>



Hello Hacklaender,

I'm a developer working with ImageJ for quite a long time.

It was recently that I discovered ImageJ does not have a function like
saveAsDicom,

and the only possibility seems to be using plugins such as dcmie or
tudordicom......

Both plugins are quite big, with non-necessary code for my research
project.

As dcmie requires less third-part dependency, I try to make it work for my
project.

I red the Dcm_Export.java and FileExporter.java, but still has no idea
about how to make it work.

Suppose that I have two variables, a ImagePlus "imp" which contains the
images and a path "path" to save as.

Usually suing FileSaver, it can be done in two lines:

=====================================

  FileSaver fs = new FileSaver(imp);
   fs.saveAsTiff(path);

=====================================

Now with Dcm_Export, I initialized an instance but did not find one
function which deal with the export.

The FileExporter, on the other hand, requires 4 variables, which are not
trivial to obtain from my point of view.

Could you give me a hand?

Best regards, Xin



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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[周鑫]

Hello Johannes,

Thank you so much. It works!!!! However, the tudor tookit is a big package.

In order to benefit the others, I list the only part that is necessary for DICOM export.

- 3 jars which are in the tudor tookit lib:

dcm4che-core-2.0.26.jar, dcm4che-iod-2.0.26.jar, slf4j-api-1.6.1.jar

- they two classes in src folder: DicomExporter.java and DicomHeader.java.

Finally, just use the code:

DicomExporter exporter = new DicomExporter();
File dcmFile = new File("/home/hermenj/jhermen.dcm");
ImagePlus ip = new ImagePlus("/home/hermenj/im0");
DicomObject dObj = exporter.createHeader(ip, true, true, true);
exporter.write(dObj, ip, dcmFile, true);


Best regards, Xin

> -----原始邮件-----
> 发件人: "Johannes Hermen" <[hidden email]>
> 发送时间: 2012年8月21日 星期二
> 收件人: [hidden email]
> 抄送:
> 主题: Re: How to export images into DICOM in Java code??
>
> Take a look at our DICOM Toolkit
>
> http://www.santec.lu/project/dicom
>
> it offers a DICOM Exporter class:
>
> DicomExporter exporter = new DicomExporter();
> File dcmFile = new File("/home/hermenj/jhermen.dcm");
> ImagePlus ip = new ImagePlus("/home/hermenj/im0");
> DicomObject dObj = exporter.createHeader(ip, true, true, true);
> exporter.write(dObj, ip, dcmFile, true);
>
>
> Greets
>       Johannes
>
>
>
> -----------------------------------------------------------------
> Johannes Hermen  -  Ingenieur de Recherche
> [hidden email]
> -----------------------------------------------------------------
> CRP Henri Tudor  http://www.santec.tudor.lu
> 29, Avenue John F. Kennedy
> L-1855 Luxembourg
> -----------------------------------------------------------------
>
>
>
> From: 周鑫 <[hidden email]>
> To: <[hidden email]>,
> Date: 18.08.2012 10:49
> Subject: How to export images into DICOM in Java code??
> Sent by: ImageJ Interest Group <[hidden email]>
>
>
>
> Hello Hacklaender,
>
> I'm a developer working with ImageJ for quite a long time.
>
> It was recently that I discovered ImageJ does not have a function like
> saveAsDicom,
>
> and the only possibility seems to be using plugins such as dcmie or
> tudordicom......
>
> Both plugins are quite big, with non-necessary code for my research
> project.
>
> As dcmie requires less third-part dependency, I try to make it work for my
> project.
>
> I red the Dcm_Export.java and FileExporter.java, but still has no idea
> about how to make it work.
>
> Suppose that I have two variables, a ImagePlus "imp" which contains the
> images and a path "path" to save as.
>
> Usually suing FileSaver, it can be done in two lines:
>
> =====================================
>
>   FileSaver fs = new FileSaver(imp);
>    fs.saveAsTiff(path);
>
> =====================================
>
> Now with Dcm_Export, I initialized an instance but did not find one
> function which deal with the export.
>
> The FileExporter, on the other hand, requires 4 variables, which are not
> trivial to obtain from my point of view.
>
> Could you give me a hand?
>
> Best regards, Xin
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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