| CBZip2InputStream |
An input stream that decompresses from the BZip2 format (without the file
header chars) to be read as any other stream.
|
| CBZip2OutputStream |
An output stream that compresses into the BZip2 format (without the file
header chars) into another stream.
|
| CBZip2OutputStream.StackElem |
|
| CRC |
A simple class the hold and calculate the CRC for sanity checking
of the data.
|
| DelimitedRandomAccessFile |
This class is a random access file that has an internal delimiter for fast
processing of text files.
|
| DicomDictionary |
This class reads a text file that lists all the tags that the DICOM file reader will need to know about.
|
| DTIParameters |
Object to store parameters in the ModelImage acquired from DWI image file or ImageInfo DTI tab
|
| FileAfni |
Afni file format.
|
| FileAnalyze |
The class reads and writes Analyze Version 7.5.x files.
|
| FileAvi |
AVI file writer and reader.
|
| FileBase |
FileBase is an abstract class that has many methods that support the reading/writing of files.
|
| FileBFLOAT |
|
| FileBioRad |
Reads BioRaD pic file format.
|
| FileBMP |
|
| FileBRUKER |
Reads a BRUKER file by first reading in the d3proc header file or if the d3proc header file is not\
present the visu_pars file, second the reco header file, third the acqp file in the
same directory or up one or two two parent directories, then the method file,l and finally the 2dseq binary file.
|
| FileCheshire |
The class reads Cheshire file images.
|
| FileCheshireVOI |
Addresses and lengths are always contained in 4 bytes.
|
| FileCOR |
FreeSurfer COR files are used to store 3 dimensional unsigned byte data.
|
| FileCZI |
File written using Zeiss Release Version 1.1 for ZEN 2012
|
| FileDataProvenance |
|
| FileDeleter |
Class to safely delete a file using a looped thread.
|
| FileDicom |
This class reads and writes DICOM files.
|
| FileDicomBase |
FileDICOMBase is an class that supports the reading/writing of DICOM files.
|
| FileDicomJPEG |
Class that reads a lossless compressed JPEG file.
|
| FileDicomKey |
FileDicomKey goes along with FileDicomTag - it is the key into the hashtable that corresponds to a tag.
|
| FileDicomSQ |
This is a class for reading in a DICOM sequence tag.
|
| FileDicomSQItem |
A table containing dicom tags.
|
| FileDicomTag |
This class holds all the important information about each DICOM tag.
|
| FileDicomTagInfo |
Information about a DICOM tag, stored in the DicomDictionary table once for each DICOM tag.
|
| FileDicomTagTable |
A table containing dicom tags.
|
| FileDM3 |
Some of this code is derived from DM3_Reader.java in ImageJ.
|
| FileFits |
Some of this code is derived from FITS.java in ImageJ.
|
| FileGESigna4X |
Fixed format header
Image data is not compressed
Image data fixed offset 14336 bytes
Data General host
The image files are of fixed layout, described here as a series of 256 by 16
bit word blocks (512 bytes), blocks numbered from 0.
|
| FileGESigna5X |
Reads both GE Neducak Systems MR 5X and LX.
|
| FileHistoLUT |
HistoLUT reader/writer.
|
| FileICS |
Reference: 1.
|
| FileImageXML |
File class for reading/writing Image.XML file headers and their associated images.
|
| FileInfoAfni |
This structures contains the information that describes how an Afni image is stored on disk.
|
| FileInfoAnalyze |
This structures contains the information that describes how an analyze image is stored on disk.
|
| FileInfoAvi |
This structures contains the information that describes how an Avi image is stored on disk.
|
| FileInfoBase |
This structure contains the basic information that describes how the image is stored on disk.
|
| FileInfoBFLOAT |
|
| FileInfoBioRad |
This structures contains the information that describes how a Biorad image is stored on disk.
|
| FileInfoBMP |
File info storage container.
|
| FileInfoBRUKER |
File information related to the Bruker/Biospin scanner format.
|
| FileInfoCheshire |
This structures contains the information that describes how an analyze image is stored on disk.
|
| FileInfoCOR |
File info storage container.
|
| FileInfoCZI |
File info storage container.
|
| FileInfoDicom |
This class contains DICOM header information.
|
| FileInfoDM3 |
This structures contains the information that describes how a DM3 image is stored on disk.
|
| FileInfoFits |
This structures contains the information that describes how a Fits image is stored on disk.
|
| FileInfoGESigna4X |
This structures contains the information that describes how a GE Signa 5X image is stored on disk.
|
| FileInfoGESigna5X |
This structures contains the information that describes how a GE Signa 5X image is stored on disk.
|
| FileInfoICS |
This structures contains the information that describes how an ICS image is stored on disk.
|
| FileInfoImageXML |
This structure contains the information that describes how an XML image is stored on disk.
|
| FileInfoImageXML.Investigator |
Title: Investigator
|
| FileInfoInterfile |
This structures contains the information that describes how an Interfile image is stored on disk.
|
| FileInfoJP2 |
This structures contains the information that describes how a JP2 compressed image of 3D medical image is stored on disk.
|
| FileInfoJSON |
This structures contains the information that describes how a Fits image is stored on disk.
|
| FileInfoLattice |
This structure contains the information that describes how a Lattice image is stored on disk.
|
| FileInfoLIFF |
File info storage container.
|
| FileInfoLSM |
This structures contains the information that describes how a LSM image is stored on disk.
|
| FileInfoMagnetomVision |
This structures contains the information that describes how a Siemens MagnetomVision image is stored on disk.
|
| FileInfoMATLAB |
File info storage container.
|
| FileInfoMedVision |
This structure contains the information that describes how an MedVision image is stored on disk, as well as header
information.
|
| FileInfoMetaImage |
This structures contains the information that describes how a MetaImage image is stored on disk.
|
| FileInfoMGH |
|
| FileInfoMicroCat |
This structures contains the information that describes how.
|
| FileInfoMinc |
This class holds all the file information for a MINC file.
|
| FileInfoMincHDF |
|
| FileInfoMRC |
This structures contains the information that describes how a MRC image is stored on disk.
|
| FileInfoNIFTI |
This structures contains the information that describes how a NIFTI image is stored on disk.
|
| FileInfoNRRD |
|
| FileInfoOME |
Title:
|
| FileInfoPARREC |
Created by IntelliJ IDEA.
|
| FileInfoPGM |
|
| FileInfoPPM |
|
| FileInfoRaw |
This structure contains the information that describes how a RAW image is stored on disk.
|
| FileInfoSiemensText |
|
| FileInfoSPAR |
|
| FileInfoSPM |
This structures contains the information that describes how an SPM image is stored on disk.
|
| FileInfoSTK |
This structures contains the information that describes how a STK image is stored on disk.
|
| FileInfoSurfaceRefXML |
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
|
| FileInfoSurfaceXML |
This structure contains the information that describes how an XML surface (see surface.xsd and FileSurfaceXML.java)
is stored on disk.
|
| FileInfoSVS |
This structures contains the information that describes how a SVS image is stored on disk.
|
| FileInfoTiff |
This structures contains the information that describes how a Tiff image is stored on disk.
|
| FileInfoTMG |
This structures contains the information that describes how a TMG image is stored on disk.
|
| FileInfoTrackVis |
|
| FileInfoVista |
File Info Vista
|
| FileInfoXML |
Abstract base clase contains the information that contains the shared information for XML images and XML surfaces.
|
| FileInfoZVI |
File info storage container.
|
| FileInterfile |
|
| FileIO |
This class controls the file input/output of most formats that MIPAV supports, including tiff, raw, analyze, DICOM,
and Medvision.
|
| FileIO.LinkedComparator |
|
| FileIO.LinkedNum |
|
| FileJP2 |
Jpeg2K reader/ writer for 3D images.
|
| FileJPEG2000 |
|
| FileJSON |
|
| FileLIFF |
|
| FileLSM |
Reads Zeiss LSM 510 image files - an extension of the TIFF format.
|
| FileMagnetomVision |
Class that reads Siemens Magnetom Vision files.
|
| FileMap |
Special for Benes.
|
| FileMATLAB |
|
| FileMedVision |
The class reads MedVision files that have been saved as MAC bin files.
|
| FileMetaImage |
|
| FileMGH |
The class reads MGH files.
|
| FileMicroCat |
|
| FileMinc |
The MINC file format is built on top of NetCDF.
|
| FileMincAttElem |
This class represents a MINC atrribute element.
|
| FileMincDimElem |
This class represents a MINC dimension element.
|
| FileMincHDF |
HDF5 based reader/writer for MINC 2.0
Currently, for the image max and image min nodes: in the case of 3d images in which 1 image min and 1 image max is to
be written out per slice, the dimorder is hardcoded to zspace.
|
| FileMincVarElem |
This class represents a MINC variable element.
|
| FileMRC |
Comments from David Mastronarde:
I am not familiar with the latest standards for MRC files, but typically the extra header information has been used
to save information about each section in the file.
|
| FilenameSorter |
DOCUMENT ME!
|
| FileNIFTI |
The class reads and writes NIFTI files.
|
| FileNRRD |
|
| FileOME |
DOCUMENT ME!
|
| FilePackBit |
The class reads and writes packed bit files for tiff formatted images (including STK).
|
| FilePaintBitmap |
|
| FilePARREC |
The class reads and writes PAR/REC files.
|
| FilePGM |
|
| FilePolylineVOIXML |
|
| FilePPM |
|
| FileRaw |
The class reads and writes raw files of all data types: boolean, byte, short, int, long, float, and double.
|
| FileRawChunk |
The class reads and writes raw files of all data types: boolean, byte, short, int, long, float, and double.
|
| FileSiemensText |
|
| FileSpar |
Reads a spar/sdat file.
|
| FileSPM |
The class reads and writes SPM files.
|
| FileSTK |
The MetaMorph Stack (STK) file format is derived from the TIFF format.
|
| FileSurfaceGiftiXML |
Inherits from FileXML, reads SurfaceRef.XML files based on the "surfaceref.xsd" file.
|
| FileSurfaceRefXML |
Inherits from FileXML, reads SurfaceRef.XML files based on the "surfaceref.xsd" file.
|
| FileSurfaceVTKXML |
This class facilitates reading and writing vtk xml
|
| FileSurfaceXML |
Inherits from FileXML, reads Surface.XML files based on the "surface.xsd" file.
|
| FileSVS |
Tagged Image File Format (TIFF 6.0) reader/ writer.
|
| FileTiff |
Tagged Image File Format (TIFF 6.0) reader/ writer.
|
| FileTMG |
DOCUMENT ME!
|
| FileTrackVis |
Reads a .trk track file as a MIPAV mask image.
|
| FileTypeInfo |
This class stores information about a file type, including the type description (i.e., 'NRRD') and allowed extensions
(i.e., '.nrrd,.nhdr').
|
| FileTypeTable |
|
| FileUtility |
Constants and static methods which relate to file input, output or processing.
|
| FileUtility.nameSliceComparator |
|
| FileUtility.nameSliceItem |
|
| FileVista |
|
| FileVOI |
VOI reader/writer.
|
| FileWriteOptions |
This structure contains information to direct file writing.
|
| FileXML |
Abstract base class for reading/writing .XML file headers.
|
| FileZVI |
Documentation used was the ZVI Format Specification V 2.0.5 - August, 2010.
|
| libjpeg |
Ported from C to Java by William Gandler
LEGAL ISSUES
============
In plain English:
1.
|
| libjpeg_IDCT |
Ported from C to Java by William Gandler
LEGAL ISSUES
============
In plain English:
1.
|
| MetadataExtractor |
|
| MetadataExtractor.BplistReader |
A limited-functionality binary property list (BPLIST) utility.
|
| MetadataExtractor.BplistReader.PropertyListResults |
|
| MetadataExtractor.BplistReader.Trailer |
A data structure to hold the BPLIST trailer data.
|
| MetadataExtractor.FileUtil |
A series of utility methods for working with the file system.
|
| MetadataExtractor.JpegSegmentReader |
Performs read functions of JPEG files, returning specific file segments.
|
| MetadataExtractor.PhotographicConversions |
Contains helper methods that perform photographic conversions.
|
| MetadataExtractor.StringUtil |
|
| MetadataExtractorTest |
|
| NDARWriteData |
|
| PrivateDicomDictionary |
Note does not use hashtable since two Private keys can have same hashcode.
|
| PrivateFileDicomKey |
Associates a FileDicomKey with a particular publisher to denote the source of the FileDicomKey.
|
| RawImageInfo |
Class designed to hold pre-loaded information for opening RAW images.
|
| TIFFLZWDecoder |
A class for performing LZW decoding.
|
| XMLErrorHandler |
Error handler to report errors and warnings from the XML parser.
|
| XMLParameter |
Title: Parameter
|
| XMLPSet |
Title: PSet
|