Package net.preibisch.mvrecon.headless.definedataset

Class MultipageTiffReader

java.lang.Object

net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

public class MultipageTiffReader
extends Object

Adapted version from the MicroManager codebase that supports the new diSPIM related tags and multiple-file reading.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	MultipageTiffReader.IFDData
class	MultipageTiffReader.IFDEntry

Field Summary

Fields

Modifier and Type	Field	Description
protected List<String>	angleNames
protected boolean	applyAxis
static final char	BITS_PER_SAMPLE
protected double	calX
protected double	calY
protected double	calZ
protected List<String>	channelNames
static final int	COMMENTS_HEADER
static final int	COMMENTS_OFFSET_HEADER
static final int	DISPLAY_SETTINGS_HEADER
static final int	DISPLAY_SETTINGS_OFFSET_HEADER
static final char	IMAGE_DESCRIPTION
static final int	INDEX_MAP_HEADER
static final int	INDEX_MAP_OFFSET_HEADER
static String	lastDisplayedFile
static final char	MM_METADATA
protected double[]	rotAxis
static final char	SAMPLES_PER_PIXEL
static final char	STRIP_BYTE_COUNTS
static final char	STRIP_OFFSETS
static final int	SUMMARY_MD_HEADER
protected String	unit

Constructor Summary

Constructors

Constructor	Description
MultipageTiffReader(File file)

Method Summary

Modifier and Type	Method	Description
boolean	applyAxis()
String	calUnit()
double	calX()
double	calY()
double	calZ()
String	channelName(int channelId)
void	close()
int	depth()
static String	generateLabel(int channel, int slice, int frame, int position)
Set<String>	getIndexKeys()
String	getPixelType()
HashMap<String,Object>	getSummaryMetadata()
int	height()
int	interleavedId(int channelId, int angleId)
static void	main(String[] args)
int	numAngles()
int	numChannels()
int	numChannelsAndAngles()
int	numPositions()
int	numTimepoints()
protected HashMap<String,Object>	parseJSONSimple(String json)
ImgLib2Temp.Pair<Object,HashMap<String,Object>>	readImage(String label)
String	rotationAngle(int angleId)
double[]	rotationAxis()
int	rotationAxisIndex()
String	rotationAxisName()
void	setAngleNames(List<String> names)
void	setApplyAxis(boolean apply)
void	setCalUnit(String unit)
void	setCalX(double cal)
void	setCalY(double cal)
void	setCalZ(double cal)
void	setChannelNames(List<String> names)
void	setRotAxis(double[] axis)
int	width()

Methods inherited from class java.lang.Object

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

Field Details

INDEX_MAP_HEADER

public static final int INDEX_MAP_HEADER

See Also:

• Constant Field Values

DISPLAY_SETTINGS_OFFSET_HEADER

public static final int DISPLAY_SETTINGS_OFFSET_HEADER

See Also:

• Constant Field Values

DISPLAY_SETTINGS_HEADER

public static final int DISPLAY_SETTINGS_HEADER

See Also:

• Constant Field Values

INDEX_MAP_OFFSET_HEADER

public static final int INDEX_MAP_OFFSET_HEADER

See Also:

• Constant Field Values

SUMMARY_MD_HEADER

public static final int SUMMARY_MD_HEADER

See Also:

• Constant Field Values

COMMENTS_OFFSET_HEADER

public static final int COMMENTS_OFFSET_HEADER

See Also:

• Constant Field Values

COMMENTS_HEADER

public static final int COMMENTS_HEADER

See Also:

• Constant Field Values

BITS_PER_SAMPLE

public static final char BITS_PER_SAMPLE

See Also:

• Constant Field Values

STRIP_OFFSETS

public static final char STRIP_OFFSETS

See Also:

• Constant Field Values

SAMPLES_PER_PIXEL

public static final char SAMPLES_PER_PIXEL

See Also:

• Constant Field Values

STRIP_BYTE_COUNTS

public static final char STRIP_BYTE_COUNTS

See Also:

• Constant Field Values

IMAGE_DESCRIPTION

public static final char IMAGE_DESCRIPTION

See Also:

• Constant Field Values

MM_METADATA

public static final char MM_METADATA

See Also:

• Constant Field Values

lastDisplayedFile

public static String lastDisplayedFile

unit

protected String unit

calX

protected double calX

calY

protected double calY

calZ

protected double calZ

rotAxis

protected double[] rotAxis

applyAxis

protected boolean applyAxis

angleNames

protected List<String> angleNames

channelNames

protected List<String> channelNames

Constructor Details

MultipageTiffReader

public MultipageTiffReader(File file)
                    throws IOException

Throws:

IOException

Method Details

getPixelType

public String getPixelType()

setAngleNames

public void setAngleNames(List<String> names)

setChannelNames

public void setChannelNames(List<String> names)

getSummaryMetadata

public HashMap<String,Object> getSummaryMetadata()

readImage

public ImgLib2Temp.Pair<Object,HashMap<String,Object>> readImage(String label)

getIndexKeys

public Set<String> getIndexKeys()

parseJSONSimple

protected HashMap<String,Object> parseJSONSimple(String json)

generateLabel

public static String generateLabel(int channel,
 int slice,
 int frame,
 int position)

close

public void close()
           throws IOException

Throws:

IOException

setApplyAxis

public void setApplyAxis(boolean apply)

applyAxis

public boolean applyAxis()

setCalX

public void setCalX(double cal)

setCalY

public void setCalY(double cal)

setCalZ

public void setCalZ(double cal)

setCalUnit

public void setCalUnit(String unit)

width

public int width()

height

public int height()

depth

public int depth()

calX

public double calX()

calY

public double calY()

calZ

public double calZ()

calUnit

public String calUnit()

numTimepoints

public int numTimepoints()

numPositions

public int numPositions()

numChannelsAndAngles

public int numChannelsAndAngles()

numChannels

public int numChannels()

numAngles

public int numAngles()

rotationAngle

public String rotationAngle(int angleId)

interleavedId

public int interleavedId(int channelId,
 int angleId)

channelName

public String channelName(int channelId)

rotationAxisName

public String rotationAxisName()

rotationAxisIndex

public int rotationAxisIndex()

setRotAxis

public void setRotAxis(double[] axis)

rotationAxis

public double[] rotationAxis()

main

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

Throws:

IOException