maspack.image.dicom

Class DicomReader

java.lang.Object

maspack.image.dicom.DicomReader

public class DicomReader
extends java.lang.Object

Reads DICOM files and folders, creating DicomSlices and populating a DicomImage

Author:

Antonio

Constructor Summary

Constructors

Constructor and Description
DicomReader()

Method Summary

Modifier and Type	Method and Description
void	addImageDecoder(DicomImageDecoder decoder) Add a custom image decoder, the new decoder taking priority over existing ones if multiple decoders can handle a given DICOM file
void	addImageDecoderFirst(DicomImageDecoder decoder) Add a custom image decoder, the new decoder taking priority over existing ones if multiple decoders can handle a given DICOM file
void	addImageDecoderLast(DicomImageDecoder decoder) Add a custom image decoder, the new decoder will be the last to try, prioritizing existing decoders if multiple can handle a given DICOM file
java.util.ArrayList<java.io.File>	getAllFiles(java.io.File root, java.util.regex.Pattern filePattern, boolean recursive)
DicomImage	read(DicomImage im, java.util.List<java.io.File> files) Populates a DicomImage based on a given list of DICOM files.
DicomImage	read(DicomImage im, java.util.List<java.io.File> files, int temporalPosition) Populates a DicomImage based on a given list of DICOM files.
DicomImage	read(DicomImage im, java.lang.String directory) Populates a DicomImage based on a given directory containing DICOM files and a file pattern to restrict files to load.
DicomImage	read(DicomImage im, java.lang.String directory, java.util.regex.Pattern filePattern, boolean checkSubdirectories) Populates a DicomImage based on a given directory containing DICOM files and a file pattern to restrict files to load.
DicomImage	read(DicomImage im, java.lang.String directory, java.util.regex.Pattern filePattern, boolean checkSubdirectories, int temporalPosition) Populates a DicomImage based on a given directory containing DICOM files and a file pattern to restrict files to load.
DicomHeader	readHeader(IntHolder lastTagId, BinaryFileInputStream in, java.lang.String sourceName) Reads a header from a single input stream (e.g.
DicomSlice[]	readSlices(java.lang.String sliceTitle, java.io.File file) Reads a slice or set of slices from a single input stream (e.g.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DicomReader

public DicomReader()

Method Detail

addImageDecoder

public void addImageDecoder(DicomImageDecoder decoder)

Add a custom image decoder, the new decoder taking priority over existing ones if multiple decoders can handle a given DICOM file

Parameters:

decoder - decoder to add

addImageDecoderFirst

public void addImageDecoderFirst(DicomImageDecoder decoder)

Add a custom image decoder, the new decoder taking priority over existing ones if multiple decoders can handle a given DICOM file

Parameters:

decoder - decoder to add

addImageDecoderLast

public void addImageDecoderLast(DicomImageDecoder decoder)

Add a custom image decoder, the new decoder will be the last to try, prioritizing existing decoders if multiple can handle a given DICOM file

Parameters:

decoder - decoder to add

read

public DicomImage read(DicomImage im,
                       java.lang.String directory)
                throws java.io.IOException

Populates a DicomImage based on a given directory containing DICOM files and a file pattern to restrict files to load.

Parameters:

im - DICOM image to populate, or null to generate a new image

directory - directory from which to load files

Returns:

the populated DICOM image

Throws:

java.io.IOException - if there is an error reading a DICOM file

read

public DicomImage read(DicomImage im,
                       java.lang.String directory,
                       java.util.regex.Pattern filePattern,
                       boolean checkSubdirectories)
                throws java.io.IOException

Populates a DicomImage based on a given directory containing DICOM files and a file pattern to restrict files to load.

Parameters:

im - DICOM image to populate, or null to generate a new image

directory - directory from which to load files

filePattern - regular expression pattern for accepting files to load. The pattern is applied to the full absolute file names of files found. If null, all files are accepted.

checkSubdirectories - whether to recursively search sub-directories for matching files

Returns:

the populated DICOM image

Throws:

java.io.IOException - if there is an error reading a DICOM file

read

public DicomImage read(DicomImage im,
                       java.lang.String directory,
                       java.util.regex.Pattern filePattern,
                       boolean checkSubdirectories,
                       int temporalPosition)
                throws java.io.IOException

Populates a DicomImage based on a given directory containing DICOM files and a file pattern to restrict files to load. This allows the specification of a temporal position of the slice.

Parameters:

im - DICOM image to populate, or null to generate a new image

directory - directory from which to load files

filePattern - regular expression pattern for accepting files to load. The pattern is applied to the full absolute file names of files found. If null, all files are accepted.

checkSubdirectories - whether to recursively search sub-directories for matching files

temporalPosition - temporal index of slice (identifies stack). If negative, a temporal position will be extracted from each slice's header information. If positive or zero, the temporal position will be manually assigned.

Returns:

the populated DICOM image

Throws:

java.io.IOException - if there is an error reading a DICOM file

read

public DicomImage read(DicomImage im,
                       java.util.List<java.io.File> files)
                throws java.io.IOException

Populates a DicomImage based on a given list of DICOM files.

Parameters:

im - image to populate (null to generate new image)

files - list of DICOM files

Returns:

the populated DICOM image

Throws:

java.io.IOException - if there is a read failure

read

public DicomImage read(DicomImage im,
                       java.util.List<java.io.File> files,
                       int temporalPosition)
                throws java.io.IOException

Populates a DicomImage based on a given list of DICOM files.

Parameters:

im - image to populate (null to generate new image)

files - list of DICOM files

temporalPosition - temporal index

Returns:

the populated DICOM image

Throws:

java.io.IOException - if there is a read failure

getAllFiles

public java.util.ArrayList<java.io.File> getAllFiles(java.io.File root,
                                                     java.util.regex.Pattern filePattern,
                                                     boolean recursive)

readSlices

public DicomSlice[] readSlices(java.lang.String sliceTitle,
                               java.io.File file)
                        throws java.io.IOException

Reads a slice or set of slices from a single input stream (e.g. from a file).

Parameters:

sliceTitle - title to assign slice

file - input file

Returns:

the slice(s) (since a single file may represent multiple slices)

Throws:

java.io.IOException - if there is a read failure

readHeader

public DicomHeader readHeader(IntHolder lastTagId,
                              BinaryFileInputStream in,
                              java.lang.String sourceName)
                       throws java.io.IOException

Reads a header from a single input stream (e.g. from a file).

Parameters:

lastTagId - if non-null, stores the last tagId read from the stream

in - input stream

sourceName - name of the stream source, for error messages

Returns:

the header

Throws:

java.io.IOException - if there is a read failure