loci.formats.itk

Class ITKBridgePipes

java.lang.Object

loci.formats.itk.ITKBridgePipes

public class ITKBridgePipes
extends Object

ITKBridgePipes is a Java console application that listens for "commands" on stdin and issues results on stdout. It is used by the pipes version of the ITK Bio-Formats plugin to read image files.

Source code:

Trac, Gitweb

Author:

Mark Hiner, Curtis Rueden

Constructor Summary

Constructors

Constructor and Description
ITKBridgePipes()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canRead(String filePath) Tests whether the given file path can be parsed by Bio-Formats.
boolean	canWrite(String filePath) Tests whether the given file path can be written by Bio-Formats.
boolean	executeCommand(String commandLine) Executes the given command line.
boolean	exit()
static void	main(String[] args)
boolean	read(String filePath, int xBegin, int xEnd, int yBegin, int yEnd, int zBegin, int zEnd, int tBegin, int tEnd, int cBegin, int cEnd) Reads image pixels from the given file path, dumping the resultant binary stream to stdout.
boolean	readImageInfo(String filePath) Reads image metadata from the given file path, dumping the resultant values to stdout in a specific order (which we have not documented here because we are lazy).
void	waitForInput() Enters an input loop, waiting for commands, until EOF is reached.
boolean	write(String fileName, ColorModel cm, int byteOrder, int dims, int dimx, int dimy, int dimz, int dimt, int dimc, double pSizeX, double pSizeY, double pSizeZ, double pSizeT, double pSizeC, int pixelType, int rgbCCount, int xStart, int yStart, int zStart, int cStart, int tStart, int xCount, int yCount, int zCount, int cCount, int tCount)

Methods inherited from class java.lang.Object

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

Constructor Detail

ITKBridgePipes

public ITKBridgePipes()

Method Detail

waitForInput

public void waitForInput()
                  throws FormatException,
                         IOException

Enters an input loop, waiting for commands, until EOF is reached.

Throws:

FormatException

IOException

executeCommand

public boolean executeCommand(String commandLine)
                       throws FormatException,
                              IOException

Executes the given command line. The following commands are supported:

• info
- Dumps image metadata
• read
- Dumps image pixels
• canRead
- Tests whether the given file path can be parsed

Throws:

FormatException

IOException

readImageInfo

public boolean readImageInfo(String filePath)
                      throws FormatException,
                             IOException

Reads image metadata from the given file path, dumping the resultant values to stdout in a specific order (which we have not documented here because we are lazy).

Parameters:

filePath - a path to a file on disk, or a hash token for an initialized reader (beginning with "hash:") as given by a call to "info" earlier.

Throws:

FormatException

IOException

read

public boolean read(String filePath,
           int xBegin,
           int xEnd,
           int yBegin,
           int yEnd,
           int zBegin,
           int zEnd,
           int tBegin,
           int tEnd,
           int cBegin,
           int cEnd)
             throws FormatException,
                    IOException

Reads image pixels from the given file path, dumping the resultant binary stream to stdout.

Parameters:

filePath - a path to a file on disk, or a hash token for an initialized reader (beginning with "hash:") as given by a call to "info" earlier. Using a hash token eliminates the need to initialize the file a second time with a fresh reader object. Regardless, after reading the file, the reader closes the file handle, and invalidates its hash token.

Throws:

FormatException

IOException

write

public boolean write(String fileName,
            ColorModel cm,
            int byteOrder,
            int dims,
            int dimx,
            int dimy,
            int dimz,
            int dimt,
            int dimc,
            double pSizeX,
            double pSizeY,
            double pSizeZ,
            double pSizeT,
            double pSizeC,
            int pixelType,
            int rgbCCount,
            int xStart,
            int yStart,
            int zStart,
            int cStart,
            int tStart,
            int xCount,
            int yCount,
            int zCount,
            int cCount,
            int tCount)
              throws IOException,
                     FormatException

Throws:

IOException

FormatException

canRead

public boolean canRead(String filePath)
                throws FormatException,
                       IOException

Tests whether the given file path can be parsed by Bio-Formats.

Throws:

FormatException

IOException

canWrite

public boolean canWrite(String filePath)
                 throws FormatException,
                        IOException

Tests whether the given file path can be written by Bio-Formats.

Throws:

FormatException

IOException

exit

public boolean exit()
             throws FormatException,
                    IOException

Throws:

FormatException

IOException

main

public static void main(String[] args)
                 throws FormatException,
                        IOException

Throws:

FormatException

IOException