MultipageTiffReader (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spim.fiji.spimdata.imgloaders.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 and Description

class MultipageTiffReader.IFDData

class MultipageTiffReader.IFDEntry

Nested Classes
Modifier and Type	Class and Description
`class`	`MultipageTiffReader.IFDData`
`class`	`MultipageTiffReader.IFDEntry`

Field Summary

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

Constructor Summary

Constructors
Constructor and Description

MultipageTiffReader(File file)
This constructor is used for opening datasets that have already been saved

Constructors
Constructor and Description
`MultipageTiffReader(File file)` This constructor is used for opening datasets that have already been saved

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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)`
`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 Detail

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 Detail
- MultipageTiffReader
```
public MultipageTiffReader(File file)
                    throws IOException
```
  This constructor is used for opening datasets that have already been saved
  
  Throws:
  
  IOException

Method Detail

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 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

Class MultipageTiffReader

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

INDEX_MAP_HEADER

DISPLAY_SETTINGS_OFFSET_HEADER

DISPLAY_SETTINGS_HEADER

INDEX_MAP_OFFSET_HEADER

SUMMARY_MD_HEADER

COMMENTS_OFFSET_HEADER

COMMENTS_HEADER

BITS_PER_SAMPLE

STRIP_OFFSETS

SAMPLES_PER_PIXEL

STRIP_BYTE_COUNTS

IMAGE_DESCRIPTION

MM_METADATA

lastDisplayedFile

unit

calX

calY

calZ

rotAxis

applyAxis

angleNames

channelNames

Constructor Detail

MultipageTiffReader

Method Detail

getPixelType

setAngleNames

setChannelNames

getSummaryMetadata

readImage

getIndexKeys

parseJSONSimple

generateLabel

close

setApplyAxis

applyAxis

setCalX

setCalY

setCalZ

setCalUnit

width

height

depth

calX

calY

calZ

calUnit

numTimepoints

numPositions

numChannelsAndAngles

numChannels

numAngles

rotationAngle

interleavedId

channelName

rotationAxisName

rotationAxisIndex

setRotAxis

rotationAxis

main