automatically load DICOM stack from folder

[Tony Shepherd]

Hi,
I would like my plugin to open a DICOM image into a stack, just like from the menu "file .. import sequence.." when the folder is known, where all the files (slices) are.
The code would look something like:
 
ImagePlus thisDicom = IJ.load("path-to-folder", "DICOM")
or
ImagePlus thisDicom = IJ.loadDicom("path-to-folder")
 
Can I do this (even if it means downloading a class library and using 'import newLibrary.*;' at the head of the plugin) ?    

[ctrueden]

Hi Tony,

I would like my plugin to open a DICOM image into a stack, just like from
> the menu "file .. import sequence.." when the folder is known, where all the
> files (slices) are.
>

If your DICOM files are numbered, you can do this using the Bio-Formats
Importer plugin API. Try something like:

import loci.plugins.BF;
import loci.plugins.in.ImporterOptions;
...
ImporterOptions options = new ImporterOptions();
options.setGroupFiles(true);
options.setId(oneOfTheDicomFiles);
ImagePlus thisDicom = BF.openImagePlus(options)[0];

The "setGroupFiles(true)" command instructs Bio-Formats to attempt to group
files in the same folder based on numbering.

You will need loci_tools.jar in your classpath for this to compile.

HTH,
Curtis

On Tue, Mar 22, 2011 at 4:39 AM, Tony Shepherd
<[hidden email]>wrote:

> Hi,
> I would like my plugin to open a DICOM image into a stack, just like from
> the menu "file .. import sequence.." when the folder is known, where all the
> files (slices) are.
> The code would look something like:
>
> ImagePlus thisDicom = IJ.load("path-to-folder", "DICOM")
> or
> ImagePlus thisDicom = IJ.loadDicom("path-to-folder")
>
> Can I do this (even if it means downloading a class library and using
> 'import newLibrary.*;' at the head of the plugin) ?
>

[Rasband, Wayne (NIH/NIMH) [E]]

On Mar 22, 2011, at 5:39 AM, Tony Shepherd wrote:

> Hi,
> I would like my plugin to open a DICOM image into a stack, just like from the menu "file .. import sequence.." when the folder is known, where all the files (slices) are.
> The code would look something like:
>
> ImagePlus thisDicom = IJ.load("path-to-folder", "DICOM")
> or
> ImagePlus thisDicom = IJ.loadDicom("path-to-folder")
>
> Can I do this (even if it means downloading a class library and using 'import newLibrary.*;' at the head of the plugin) ?

You can use

   ImagePlus imp = FolderOpener.open("path-to-folder");

if you upgrade to the 1.45e daily build by using the Help>Update ImageJ command and selecting "daily build" from the drop down menu.

-wayne

[Thomson Neil (EAST KENT HOSPITALS UNIVERSITY NHS FOUNDATION TRUST)]

Have you tried the Dicom Import/Export plugin (http://www.iftm.de/telemedizin/dcmimex.htm)? It supports multiple-slice import from a normal folder as well as DICOMDIR format.


Neil Thomson,
Nuclear Medicine Physics Section,
Medical Physics,
Kent and Canterbury Hospital,
UK. CT1 3NG
[phone]
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Tony Shepherd [[hidden email]]
Sent: 22 March 2011 09:39
To: [hidden email]
Subject: automatically load DICOM stack from folder

Hi,
I would like my plugin to open a DICOM image into a stack, just like from the menu "file .. import sequence.." when the folder is known, where all the files (slices) are.
The code would look something like:

ImagePlus thisDicom = IJ.load("path-to-folder", "DICOM")
or
ImagePlus thisDicom = IJ.loadDicom("path-to-folder")

Can I do this (even if it means downloading a class library and using 'import newLibrary.*;' at the head of the plugin) ?

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