de.unihalle.informatik.MiToBo.io.tools

Class ImageIOUtils

java.lang.Object

de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils

public class ImageIOUtils
extends Object

A class of utility functions used by the MiToBo's image-IO classes

Author:

Oliver Gress

Constructor Summary

Constructors

Constructor and Description
ImageIOUtils()

Method Summary

Modifier and Type	Method and Description
static HashMap<Integer,String>	availableCodecs(Class<? extends loci.formats.IFormatWriter> writerclass) Get available codecs of a specific writer class.
static HashMap<Integer,String>	availableQualities(Class<? extends loci.formats.IFormatWriter> writerclass) Get available qualities of a specific writer class.
static Integer	getKey(HashMap<Integer,String> hmap, String value) Obtain the key for a given value of a HashMap, if available.
static String	imgReadInfo(loci.formats.IFormatReader r) Create a string of image reading information
static String	imgWriteInfo(String filename, loci.formats.IFormatWriter w, int imgIdx) Create a string of image writing information
static ome.xml.model.enums.PixelType	omePixelType(MTBImage.MTBImageType type) Get the OME pixel type corresponding to the specified MTB image type
static void	physicalPixelSize_from_OME(ij.measure.Calibration cal, loci.formats.meta.IMetadata omemeta, int imageIdx) Set the calibration of an image from the OME meta data of image of index imageIdx
static void	physicalPixelSize_to_OME(ij.measure.Calibration cal, loci.formats.meta.IMetadata omemeta, int imageIdx) Set OME meta data for image of index imageIdx using information from a Calibration object.
static double	toMicrons(double val, String unit) Convert a value of given space unit to microns.
static double	toSeconds(double val, String unit) Convert a value of given time unit to seconds.

Methods inherited from class java.lang.Object

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

Constructor Detail

ImageIOUtils

public ImageIOUtils()

Method Detail

omePixelType

public static ome.xml.model.enums.PixelType omePixelType(MTBImage.MTBImageType type)

Get the OME pixel type corresponding to the specified MTB image type

Parameters:

type -

Returns:

OME pixel type

physicalPixelSize_to_OME

public static void physicalPixelSize_to_OME(ij.measure.Calibration cal,
                                            loci.formats.meta.IMetadata omemeta,
                                            int imageIdx)

Set OME meta data for image of index imageIdx using information from a Calibration object.

Parameters:

cal - Calibration object.

omemeta - OME object where to store calibration metadata.

imageIdx - Index of image.

toMicrons

public static double toMicrons(double val,
                               String unit)

Convert a value of given space unit to microns.

Parameters:

val - Value to convert.

unit - Source unit.

Returns:

Value in microns.

toSeconds

public static double toSeconds(double val,
                               String unit)

Convert a value of given time unit to seconds.

Parameters:

val -

unit -

Returns:

physicalPixelSize_from_OME

public static void physicalPixelSize_from_OME(ij.measure.Calibration cal,
                                              loci.formats.meta.IMetadata omemeta,
                                              int imageIdx)

Set the calibration of an image from the OME meta data of image of index imageIdx

Parameters:

cal -

omemeta -

imageIdx -

imgWriteInfo

public static String imgWriteInfo(String filename,
                                  loci.formats.IFormatWriter w,
                                  int imgIdx)

Create a string of image writing information

Parameters:

filename -

w -

imgIdx -

Returns:

imgReadInfo

public static String imgReadInfo(loci.formats.IFormatReader r)

Create a string of image reading information

Parameters:

r -

Returns:

availableCodecs

public static HashMap<Integer,String> availableCodecs(Class<? extends loci.formats.IFormatWriter> writerclass)

Get available codecs of a specific writer class. The returned HashMap contains the codec ID as key and corresponding to a key a String containing the codec's name.

Parameters:

writerclass -

Returns:

availableQualities

public static HashMap<Integer,String> availableQualities(Class<? extends loci.formats.IFormatWriter> writerclass)

Get available qualities of a specific writer class. The returned HashMap contains the quality ID as key and corresponding to a key a String containing the quality's name.

Parameters:

writerclass -

Returns:

getKey

public static Integer getKey(HashMap<Integer,String> hmap,
                             String value)

Obtain the key for a given value of a HashMap, if available. Otherwise null is returned

Parameters:

hmap -

value -

Returns: