Difference between revisions of "ITK/File Formats"

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ITK features a powerful plugin-based IO mechanism for reading and writing images, which is covered briefly in [[Plugin IO mechanisms]] and in detail in Chapter 7 (PDF page 219) of the [http://www.itk.org/ItkSoftwareGuide.pdf ITK Software Guide]. The discussion in [[Plugin IO mechanisms]] also discusses how new file formats can be added existing compiled applications!
Hahaha anto  yes actually i wtenad to begin by the basics  the code that we made in university was already doneand i wtenad to improve it .. ( on the code of university i already putted threads    to improve the code )anyway i wtenad to explain how to create a pixel from scratch in a bmp file and toshow how to make something better  cause i wasn't following this course as you remember
 
== File Formats and Pixel Types ==
 
The itk::Image<> class can be templated over virtually any pixel type, however not all file formats support all data types for reading and writing.  In some cases, it may be necessary to add an itk::CastImageFilter<> to convert the output to a pixel format appropriate for the target file.  It is important not to truncate the data by converting to a smaller type (ie. short -> char).  In this case, the itk::RescaleIntensityImageFilter<> can be used before casting.
 
The following table lists the built-in file format support against each data type:
 
* Analyze
char
unsigned char
short
unsigned short
int
unsigned int
float
double
RGB<unsigned char>
* BMP (2D only)
unsigned char
RGB<unsigned char>
* DICOM
float
char
unsigned char
short
unsigned short
RGB<char>
RGB<short>
* GDCM
unsigned char
char
unsigned short
short
unsigned int
int
double
* GE
???
* GIPL
binary
char
unsigned char
short
unsigned short
unsigned int
int
float
double
short
surface
polygon
* IPL
???
* JPEG (2D only)
unsigned char
* MetaImage (mhd): raw, compressed
char
unsigned char
short
unsigned short
  long
ulong
int
unsigned int
float
double
vector<>
Also supports reading and writing
  - itk's SpatialObjects (i.e., scenes containing ellipses, images, vessels, dti fiber tracks, etc)
  - Patient Meta Data (orientation, scan date, comments, modality, etc. - user extensible)
  - data stored in multiple files (e.g., a metaImage file could be a text file pointing to a series of
      2D images that are stacked to form the 3D metaImage).
Reference: http://www.itk.org/Wiki/MetaIO
* Nrrd (.nhdr, .nrrd): raw or gzip compressed
signed char
unsigned char
short
unsigned short
int
unsigned int
long long (on 64-bit platforms)
unsigned long long (on 64-bit platforms)
float
double
vector<>
Also supports reading and writing
  - all the pixel types in ImageIOBase, including DIFFUSIONTENSOR3D
  - MetaData dictionary, via mapping to key/value pairs
  - data from multiple files, using MetaIO conventions
[[Getting Started with the NRRD Format]]
 
[http://teem.sourceforge.net/nrrd/format.html NRRD format definition]
 
*PNG (2D)
  unsigned char
unsigned short
RGB
RGBA
* SiemensVision
???
* Stimulate
char
short
int
float
double
* TIFF (2D only)
unsigned char
unsigned short
RGB
* VTK
float
double
unsigned char
char
unsigned short
short
unsigned int
int
unsigned long
long
RGB
 
== Importing other file format ==
 
=== Movies as 3D images ===
 
From the Insight-User Amadeus:
 
I work exclusively in Linux and one can use mplayer - the mother of all
multimedia tools - to dump each frame in a movie clip. MPlayer understands
just about any format under the sun and can use just about any codec as
well. E.g. to dump each frame in an avi clip to a separate png image
 
mplayer -vo png movie.avi
 
To see to what other formats one can output the frames to,
 
mplayer -vo help
 
Then, the frames dumped by mplayer can be put together into a volume
using ImageSeriesReadWrite in InsightToolkit-2.0.0/Examples/IO/.
 
Of course, in Linux and other unixes the shell understands wildcards,
so with minor changes, it ImageSeriesReadWrite can be modified to work
like this:
 
ImageSeriesReadWrite frame*.png output.mha  # or e.g. output.mhd
 
The input frames need not have the names that the original
ImageSeriesReadWrite expects.
 
=== Converting unsupported 2D images to an ITK supported format ===
 
[http://www.imagemagick.org ImageMagick] supports conversion between over 90 (typically 2D) image formats as well as some basic image processing.  Operates from the command line on PCs and on *nix machines.
 
{{ITK/Template/Footer}}

Revision as of 17:16, 18 June 2012

Hahaha anto yes actually i wtenad to begin by the basics the code that we made in university was already doneand i wtenad to improve it .. ( on the code of university i already putted threads to improve the code )anyway i wtenad to explain how to create a pixel from scratch in a bmp file and toshow how to make something better cause i wasn't following this course as you remember