loci.formats.ome

Class OmeisImporter

java.lang.Object

loci.formats.ome.OmeisImporter

Deprecated.

The r2003fc classes are replaced by the ome.xml.model classes

@Deprecated
public class OmeisImporter
extends Object

A command line utility used by the OME Image Server (OMEIS) to interface with Bio-Formats.

Source code:

Trac, Gitweb

Author:

Curtis Rueden ctrueden at wisc.edu, Ilya Goldberg igg at nih.gov

Constructor Summary

Constructors

Constructor and Description
OmeisImporter() Deprecated.
OmeisImporter(boolean stitchFiles) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
int	finishPixels(int pixelsId) Deprecated. Instructs OMEIS to process the Pixels file corresponding to the given pixels ID.
Hashtable	getFileInfo(int fileId) Deprecated. Gets information about the file corresponding to the given file ID.
String	getLocalFilePath(int fileId) Deprecated. Gets path to original file corresponding to the given file ID.
String	getLocalPixelsPath(int pixelsId) Deprecated. Gets path to Pixels file corresponding to the given pixels ID.
String	getPixelsSHA1(int pixelsId) Deprecated. Gets SHA1 hash for the pixels corresponding to the given pixels ID.
void	importIds(int[] fileIds) Deprecated. Attempts to import the given file IDs using Bio-Formats, as a single group.
boolean	isLittleEndian() Deprecated. Gets whether the local system uses little-endian byte order.
static void	main(String[] args) Deprecated. Run ./omebf with a list of file IDs to import those IDs.
int	newPixels(int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int bytesPerPixel, boolean isSigned, boolean isFloat) Deprecated. Instructs OMEIS to construct a new Pixels object.
void	printVersion() Deprecated. Prints out the build date for the Bio-Formats OMEIS utility.
void	testIds(int[] fileIds) Deprecated. Tests whether Bio-Formats is potentially capable of importing the given file IDs.

Methods inherited from class java.lang.Object

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

Constructor Detail

OmeisImporter

public OmeisImporter()

Deprecated.

OmeisImporter

public OmeisImporter(boolean stitchFiles)

Deprecated.

Method Detail

printVersion

public void printVersion()

Deprecated.

Prints out the build date for the Bio-Formats OMEIS utility.

testIds

public void testIds(int[] fileIds)
             throws OmeisException,
                    FormatException,
                    IOException

Deprecated.

Tests whether Bio-Formats is potentially capable of importing the given file IDs. Outputs the IDs it can potentially import, one group per line, with elements of the each group separated by spaces.

Throws:

OmeisException

FormatException

IOException

importIds

public void importIds(int[] fileIds)
               throws OmeisException,
                      FormatException,
                      IOException

Deprecated.

Attempts to import the given file IDs using Bio-Formats, as a single group. Pixels are saved to the pixels file designated by OMEIS, and an OME-XML metadata block describing the successfully imported data is dumped to standard output.

Throws:

OmeisException

FormatException

IOException

getLocalFilePath

public String getLocalFilePath(int fileId)
                        throws OmeisException

Deprecated.

Gets path to original file corresponding to the given file ID.

Throws:

OmeisException

getFileInfo

public Hashtable getFileInfo(int fileId)
                      throws OmeisException

Deprecated.

Gets information about the file corresponding to the given file ID.

Returns:

hashtable containing the information as key/value pairs

Throws:

OmeisException

newPixels

public int newPixels(int sizeX,
            int sizeY,
            int sizeZ,
            int sizeC,
            int sizeT,
            int bytesPerPixel,
            boolean isSigned,
            boolean isFloat)
              throws OmeisException

Deprecated.

Instructs OMEIS to construct a new Pixels object.

Returns:

pixels ID of the newly created pixels

Throws:

OmeisException

isLittleEndian

public boolean isLittleEndian()
                       throws OmeisException

Deprecated.

Gets whether the local system uses little-endian byte order.

Throws:

OmeisException

getLocalPixelsPath

public String getLocalPixelsPath(int pixelsId)
                          throws OmeisException

Deprecated.

Gets path to Pixels file corresponding to the given pixels ID.

Throws:

OmeisException

finishPixels

public int finishPixels(int pixelsId)
                 throws OmeisException

Deprecated.

Instructs OMEIS to process the Pixels file corresponding to the given pixels ID.

Returns:

final (possibly changed) pixels ID of the processed pixels

Throws:

OmeisException

getPixelsSHA1

public String getPixelsSHA1(int pixelsId)
                     throws OmeisException

Deprecated.

Gets SHA1 hash for the pixels corresponding to the given pixels ID.

Throws:

OmeisException

main

public static void main(String[] args)

Deprecated.

Run ./omebf with a list of file IDs to import those IDs. Run with the -test flag to ask Bio-Formats whether it thinks it can import those files.