loci.formats.tools

Class AmiraParameters

java.lang.Object

loci.formats.tools.AmiraParameters

public class AmiraParameters
extends java.lang.Object

AmiraParameters handles parsing and writing of AmiraMesh headers.

Author:

Gregory Jefferis jefferis at gmail.com, Johannes Schindelin johannes.schindelin at gmx.de

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ascii
protected char	c
protected int	column
int	depth
int	firstDataStream
int	height
protected loci.common.RandomAccessInputStream	in
boolean	littleEndian
private static org.slf4j.Logger	LOGGER
protected java.util.Map	map
int	nStreams
protected int	row
java.lang.String[]	streamNames
protected java.util.Map	streams
java.lang.String[]	streamTypes
int	width
double	x0
double	x1
double	y0
double	y1
double	z0
double	z1

Constructor Summary

Constructors

Constructor and Description
AmiraParameters(loci.common.RandomAccessInputStream inputStream)
AmiraParameters(java.lang.String path)

Method Summary

Modifier and Type	Method and Description
static java.lang.String	entryToString(java.lang.Object object, java.lang.String indent)
protected void	extractCoreMetaData()
java.util.Map	getMap()
java.util.Map	getStreams()
static void	main(java.lang.String[] args)
protected char	readByte()
protected java.lang.Double[]	readDoubleArray(int count)
protected void	readFile(loci.common.RandomAccessInputStream inputStream)
protected void	readFile(java.lang.String path)
protected java.lang.Integer[]	readIntArray()
protected java.lang.Integer[]	readIntArray(int count)
protected java.lang.String	readKey()
protected java.util.Map	readMap()
protected java.lang.Number	readNumber()
protected java.lang.Number[]	readNumberArray()
protected java.lang.String	readQuotedString()
protected void	readTopLevel()
protected void	skipComment()
protected void	skipWhiteSpace()
protected void	syntaxError(java.lang.String message)
java.lang.String	toString()
static java.lang.String	toString(java.util.Map map, java.lang.String indent)

Methods inherited from class java.lang.Object

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

Field Detail

width

public int width

height

public int height

depth

public int depth

firstDataStream

public int firstDataStream

x0

public double x0

y0

public double y0

z0

public double z0

x1

public double x1

y1

public double y1

z1

public double z1

littleEndian

public boolean littleEndian

ascii

public boolean ascii

nStreams

public int nStreams

streamNames

public java.lang.String[] streamNames

streamTypes

public java.lang.String[] streamTypes

in

protected transient loci.common.RandomAccessInputStream in

map

protected java.util.Map map

streams

protected java.util.Map streams

column

protected int column

row

protected int row

c

protected char c

LOGGER

private static final org.slf4j.Logger LOGGER

Constructor Detail

AmiraParameters

public AmiraParameters(java.lang.String path)
                throws FormatException

Throws:

FormatException

AmiraParameters

public AmiraParameters(loci.common.RandomAccessInputStream inputStream)
                throws FormatException,
                       java.io.IOException

Throws:

FormatException

java.io.IOException

Method Detail

readFile

protected void readFile(java.lang.String path)
                 throws FormatException

Throws:

FormatException

readFile

protected void readFile(loci.common.RandomAccessInputStream inputStream)
                 throws FormatException,
                        java.io.IOException

Throws:

FormatException

java.io.IOException

extractCoreMetaData

protected void extractCoreMetaData()
                            throws FormatException

Throws:

FormatException

syntaxError

protected void syntaxError(java.lang.String message)
                    throws FormatException

Throws:

FormatException

readTopLevel

protected void readTopLevel()
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.IOException

readByte

protected char readByte()
                 throws java.io.IOException

Throws:

java.io.IOException

skipComment

protected void skipComment()
                    throws java.io.IOException

Throws:

java.io.IOException

skipWhiteSpace

protected void skipWhiteSpace()
                       throws java.io.IOException

Throws:

java.io.IOException

readKey

protected java.lang.String readKey()
                            throws java.io.IOException

Throws:

java.io.IOException

readNumber

protected java.lang.Number readNumber()
                               throws FormatException,
                                      java.io.IOException

Throws:

FormatException

java.io.IOException

readIntArray

protected java.lang.Integer[] readIntArray()
                                    throws FormatException,
                                           java.io.IOException

Throws:

FormatException

java.io.IOException

readNumberArray

protected java.lang.Number[] readNumberArray()
                                      throws FormatException,
                                             java.io.IOException

Throws:

FormatException

java.io.IOException

readIntArray

protected java.lang.Integer[] readIntArray(int count)
                                    throws FormatException,
                                           java.io.IOException

Throws:

FormatException

java.io.IOException

readDoubleArray

protected java.lang.Double[] readDoubleArray(int count)
                                      throws FormatException,
                                             java.io.IOException

Throws:

FormatException

java.io.IOException

readQuotedString

protected java.lang.String readQuotedString()
                                     throws FormatException,
                                            java.io.IOException

Throws:

FormatException

java.io.IOException

readMap

protected java.util.Map readMap()
                         throws FormatException,
                                java.io.IOException

Throws:

FormatException

java.io.IOException

getMap

public java.util.Map getMap()

getStreams

public java.util.Map getStreams()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toString

public static java.lang.String toString(java.util.Map map,
                                        java.lang.String indent)
                                 throws FormatException

Throws:

FormatException

entryToString

public static java.lang.String entryToString(java.lang.Object object,
                                             java.lang.String indent)
                                      throws FormatException

Throws:

FormatException

main

public static void main(java.lang.String[] args)