[ITK] [ITK-users] Extensions to the MetaImage (MHDs) IO-plugin to support compression and MHAs

[Williams, Norman K]

This is a good thing to submit to ITK proper; it would require conversion
to C++, though.

On 7/28/14, 9:23 AM, "Dr. Roman Grothausmann"
<grothausmann.roman at mh-hannover.de> wrote:

>Dear mailing list members,
>
>
>I've extended the MetaImage (used by e.g. ITK/VTK)  IO-plugin from Kang
>Li
>(http://www.kangli.org/code/MetaImage_Reader_Writer.html) to also support
>compression and local data storage, i.e. MHAs. The MetaImage
>Reader/Writer from
>(http://ij-plugins.sourceforge.net/plugins/3d-io/) seems not to support
>this
>either.
>Reading and writing in Fiji was tested with MHDs and MHAs created/read by
>ITK-4.5.1. While the plugin handles files bigger than 4GB correctly, (for
>unknown reasons my) ITK seems to have problems with MHDs/MHAs bigger than
>4GB
>(in general).
>The plugin does not check whether the size of the compressed data is
>correct,
>ITK however does. If the header lacks an entry of CompressedDataSize, ITK
>throws
>an error when reading/loading such a file. If the size specified with
>CompressedDataSize is too big, ITK just issues a warning. This was used
>as a
>workaround because I did not find an easy way in Java to put the correct
>value
>for CompressedDataSize without using extra temporary files (which might
>be quite
>big).
>
>Attached are the modified files (java-files, plugins.config and a
>repacked
>IO_-2.0.0-SNAPSHOT.jar).
>A modified HandleExtraFileTypes.java (based on:
>https://github.com/fiji/IO/blob/master/src/main/java/HandleExtraFileTypes.
>java)
>is also included.
>Togehter with the modified Plugin it allows opening MHDs and MHAs
>directly.
>
>
>The repacked IO_-2.0.0-SNAPSHOT.jar was generated with:
>
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_Reader.java
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_Writer.java
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. MetaImage_CWriter.java
>
>javac -cp /opt/fiji/Fiji.app/jars/ij-1.48a.jar:. HandleExtraFileTypes.java
>
>The compiled Class-files were moved to a subfolder named io/:
>ExtendedFileOpener.class  MetaImage_CWriter.class  MetaImage_Writer.class
>ExtendedFileSaver.class   MetaImage_Reader.class
>ReplacingInputStream.class
>
>And then included/replaced with zip:
>zip -r IO_-2.0.0-SNAPSHOT.jar plugins.config HandleExtraFileTypes.class
>io/
>
>Feel free to add these extensions to the Plugin-Page or the ImageJ/Fiji
>repository.
>Any suggestions concerning improvements are very welcome.
>
>
>Many thanks for ImageJ/Fiji and the initial Metaimage IO-plugin.
>Roman
>
>
>--
>Dr. Roman Grothausmann
>
>Tomographie und Digitale Bildverarbeitung
>Tomography and Digital Image Analysis
>
>Institut für Funktionelle und Angewandte Anatomie, OE 4120
>Medizinische Hochschule Hannover
>Carl-Neuberg-Str. 1
>D-30625 Hannover
>
>Tel. +49 511 532-9574
>
>
>
>======================================================================
>A potentially unsafe attachment has been removed from this email
>message. See http://its.uiowa.edu/support/article/100806 for further
>information.
>
>Removed attachment name(s):
>IO_-2.0.0-SNAPSHOT.jar
>======================================================================
>



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