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

[Dr. Roman Grothausmann]

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
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# Author: Roman Grothausmann
File>Save As, "MHD/MHA ...", io.MetaImage_Writer
File>Save As, "MHD/MHA compressed ...", io.MetaImage_CWriter
File>Import, "MHD/MHA...", io.MetaImage_Reader

# Author: Stephan Saalfeld
File>Save As, "DF3 ...", io.Save_DF3
File>Import, "DF3...", io.Open_DF3

# Author: Stephan Preibisch
File>Import, "FIB-SEM ...", io.FIBSEM_Reader

# by Albert Cardona:
File>Import, "MRC Leginon ...", io.Open_MRC_Leginon
File>Import, "PDF ...", io.PDF_Viewer
File>Import, "Extract Images From PDF...", io.Extract_Images_From_PDF
File>Import, "DAT EMMENU ...", io.Open_DAT_EMMENU

# by Greg Jefferis
File>Import, "DM3 Reader...", io.DM3_Reader
File>Import, "TorstenRaw GZ Reader...", io.TorstenRaw_GZ_Reader
File>Import, "Nrrd ...", io.Nrrd_Reader
File>Save As, "Nrrd ... ", io.Nrrd_Writer

# by Johannes Schindelin
File>Import, "ICO...", io.ICO_Reader
File>Save As, "ICO ...", io.ICO_Writer
File>Import, "Icns...", io.Icns_Reader
File>Save As, "Icns ...", io.Icns_Writer
File>Import, "SVG...", io.SVG_Reader
File>Save As, "XPM ...", io.XPM_Writer
File>Import, "LSS16...", io.LSS16_Reader
File>Save As, "LSS16 ...", io.LSS16_Writer

# others:
File>Import, "IPLab Reader...", io.IPLab_Reader
File>Save As, "PDF ... ", io.PDF_Writer
File>Import, "Animated Gif...", io.Animated_Gif_Reader
File>Save As, "Animated Gif ... ", io.Gif_Stack_Writer
File>Save As, "EPS ...", io.Export_EPS
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