Configuration (Bio-Formats API)

java.lang.Object
- loci.tests.testng.Configuration

public class Configuration
extends Object

Field Summary

Fields
Modifier and Type	Field and Description
`private static String`	`ACCESS_TIME`
`private static String`	`ALTERNATE_MD5`
`private static String`	`CHANNEL_COUNT`
`private static String`	`CHANNEL_NAME`
`private String`	`configFile`
`private IniTable`	`currentTable`
`private String`	`dataFile`
`private static String`	`DATE`
`private static String`	`DELTA_T`
`private static String`	`DESCRIPTION`
`private static String`	`DETECTOR`
`private static String`	`DIMENSION_ORDER`
`private static String`	`EMISSION_WAVELENGTH`
`private static String`	`EMISSION_WAVELENGTH_UNIT`
`private static String`	`EXCITATION_WAVELENGTH`
`private static String`	`EXCITATION_WAVELENGTH_UNIT`
`private static String`	`EXPOSURE_TIME`
`private static String`	`EXPOSURE_TIME_UNIT`
`private IniTable`	`globalTable`
`private static String`	`HAS_VALID_XML`
`private IniList`	`ini`
`private static String`	`IS_FALSE_COLOR`
`private static String`	`IS_INDEXED`
`private static String`	`IS_INTERLEAVED`
`private static String`	`IS_LITTLE_ENDIAN`
`private static String`	`IS_RGB`
`private static String`	`LIGHT_SOURCE`
`private static String`	`MD5`
`private static String`	`MEMORY`
`private static String`	`NAME`
`private static String`	`PHYSICAL_SIZE_X`
`private static String`	`PHYSICAL_SIZE_X_UNIT`
`private static String`	`PHYSICAL_SIZE_Y`
`private static String`	`PHYSICAL_SIZE_Y_UNIT`
`private static String`	`PHYSICAL_SIZE_Z`
`private static String`	`PHYSICAL_SIZE_Z_UNIT`
`private static String`	`PIXEL_TYPE`
`private static String`	`READER`
`private static String`	`SERIES`
`private static String`	`SERIES_COUNT`
`private static String`	`SIZE_C`
`private static String`	`SIZE_T`
`private static String`	`SIZE_X`
`private static String`	`SIZE_Y`
`private static String`	`SIZE_Z`
`private static String`	`TEST`
`private static String`	`THUMB_SIZE_X`
`private static String`	`THUMB_SIZE_Y`
`private static String`	`TILE_ALTERNATE_MD5`
`private static String`	`TILE_MD5`
`static int`	`TILE_SIZE`
`private static String`	`TIME_INCREMENT`
`private static String`	`TIME_INCREMENT_UNIT`
`private static String`	`X_POSITION`
`private static String`	`X_POSITION_UNIT`
`private static String`	`Y_POSITION`
`private static String`	`Y_POSITION_UNIT`
`private static String`	`Z_POSITION`
`private static String`	`Z_POSITION_UNIT`

Constructor Summary

Constructors
Constructor and Description

Configuration(IFormatReader reader, String configFile)

Configuration(String dataFile, String configFile)

Constructors
Constructor and Description
`Configuration(IFormatReader reader, String configFile)`
`Configuration(String dataFile, String configFile)`

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`doTest()`
`boolean`	`equals(Object o)`
`long`	`getAccessTimeMillis()`
`String`	`getAlternateMD5()`
`int`	`getChannelCount()`
`String`	`getChannelName(int channel)`
`String`	`getDate()`
`Double`	`getDeltaT(int plane)`
`String`	`getDetector(int channel)`
`String`	`getDimensionOrder()`
`Length`	`getEmissionWavelength(int channel)`
`Length`	`getExcitationWavelength(int channel)`
`Time`	`getExposureTime(int channel)`
`String`	`getFile()`
`String`	`getImageDescription()`
`String`	`getImageName()`
`IniList`	`getINI()`
`String`	`getLightSource(int channel)`
`String`	`getMD5()`
`int`	`getMemory()`
`Length`	`getPhysicalSizeX()`
`Length`	`getPhysicalSizeY()`
`Length`	`getPhysicalSizeZ()`
`String`	`getPixelType()`
`Double`	`getPositionX(int plane)`
`String`	`getPositionXUnit(int plane)`
`Double`	`getPositionY(int plane)`
`String`	`getPositionYUnit(int plane)`
`Double`	`getPositionZ(int plane)`
`String`	`getPositionZUnit(int plane)`
`String`	`getReader()`
`int`	`getSeriesCount()`
`int`	`getSizeC()`
`int`	`getSizeT()`
`int`	`getSizeX()`
`int`	`getSizeY()`
`int`	`getSizeZ()`
`int`	`getThumbSizeX()`
`int`	`getThumbSizeY()`
`String`	`getTileAlternateMD5()`
`String`	`getTileMD5()`
`Time`	`getTimeIncrement()`
`boolean`	`hasExposureTime(int channel)`
`int`	`hashCode()`
`boolean`	`hasImageDescription()`
`boolean`	`hasValidXML()`
`boolean`	`isFalseColor()`
`boolean`	`isIndexed()`
`boolean`	`isInterleaved()`
`boolean`	`isLittleEndian()`
`boolean`	`isRGB()`
`private void`	`populateINI(IFormatReader reader)`
`private void`	`pruneINI()`
`private void`	`putTableName(IniTable table, IFormatReader reader, String suffix)`
`void`	`saveToFile()`
`void`	`setSeries(int series)`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail

TILE_SIZE
```
public static final int TILE_SIZE
```
See Also:
Constant Field Values

ACCESS_TIME

private static final String ACCESS_TIME

See Also:: Constant Field Values

MEMORY
```
private static final String MEMORY
```
See Also:
Constant Field Values

TEST
```
private static final String TEST
```
See Also:
Constant Field Values

HAS_VALID_XML

private static final String HAS_VALID_XML

See Also:: Constant Field Values

READER
```
private static final String READER
```
See Also:
Constant Field Values

SERIES
```
private static final String SERIES
```
See Also:
Constant Field Values

SIZE_X
```
private static final String SIZE_X
```
See Also:
Constant Field Values

SIZE_Y
```
private static final String SIZE_Y
```
See Also:
Constant Field Values

SIZE_Z
```
private static final String SIZE_Z
```
See Also:
Constant Field Values

SIZE_C
```
private static final String SIZE_C
```
See Also:
Constant Field Values

SIZE_T
```
private static final String SIZE_T
```
See Also:
Constant Field Values

DIMENSION_ORDER

private static final String DIMENSION_ORDER

See Also:: Constant Field Values

IS_INDEXED
```
private static final String IS_INDEXED
```
See Also:
Constant Field Values

IS_INTERLEAVED

private static final String IS_INTERLEAVED

See Also:: Constant Field Values

IS_FALSE_COLOR

private static final String IS_FALSE_COLOR

See Also:: Constant Field Values

IS_RGB
```
private static final String IS_RGB
```
See Also:
Constant Field Values

THUMB_SIZE_X

private static final String THUMB_SIZE_X

See Also:: Constant Field Values

THUMB_SIZE_Y

private static final String THUMB_SIZE_Y

See Also:: Constant Field Values

PIXEL_TYPE
```
private static final String PIXEL_TYPE
```
See Also:
Constant Field Values

IS_LITTLE_ENDIAN

private static final String IS_LITTLE_ENDIAN

See Also:: Constant Field Values

MD5
```
private static final String MD5
```
See Also:
Constant Field Values

ALTERNATE_MD5

private static final String ALTERNATE_MD5

See Also:: Constant Field Values

TILE_MD5
```
private static final String TILE_MD5
```
See Also:
Constant Field Values

TILE_ALTERNATE_MD5

private static final String TILE_ALTERNATE_MD5

See Also:: Constant Field Values

PHYSICAL_SIZE_X

private static final String PHYSICAL_SIZE_X

See Also:: Constant Field Values

PHYSICAL_SIZE_X_UNIT

private static final String PHYSICAL_SIZE_X_UNIT

See Also:: Constant Field Values

PHYSICAL_SIZE_Y

private static final String PHYSICAL_SIZE_Y

See Also:: Constant Field Values

PHYSICAL_SIZE_Y_UNIT

private static final String PHYSICAL_SIZE_Y_UNIT

See Also:: Constant Field Values

PHYSICAL_SIZE_Z

private static final String PHYSICAL_SIZE_Z

See Also:: Constant Field Values

PHYSICAL_SIZE_Z_UNIT

private static final String PHYSICAL_SIZE_Z_UNIT

See Also:: Constant Field Values

TIME_INCREMENT

private static final String TIME_INCREMENT

See Also:: Constant Field Values

TIME_INCREMENT_UNIT

private static final String TIME_INCREMENT_UNIT

See Also:: Constant Field Values

LIGHT_SOURCE

private static final String LIGHT_SOURCE

See Also:: Constant Field Values

CHANNEL_NAME

private static final String CHANNEL_NAME

See Also:: Constant Field Values

EXPOSURE_TIME

private static final String EXPOSURE_TIME

See Also:: Constant Field Values

EXPOSURE_TIME_UNIT

private static final String EXPOSURE_TIME_UNIT

See Also:: Constant Field Values

EMISSION_WAVELENGTH

private static final String EMISSION_WAVELENGTH

See Also:: Constant Field Values

EMISSION_WAVELENGTH_UNIT

private static final String EMISSION_WAVELENGTH_UNIT

See Also:: Constant Field Values

EXCITATION_WAVELENGTH

private static final String EXCITATION_WAVELENGTH

See Also:: Constant Field Values

EXCITATION_WAVELENGTH_UNIT

private static final String EXCITATION_WAVELENGTH_UNIT

See Also:: Constant Field Values

DETECTOR
```
private static final String DETECTOR
```
See Also:
Constant Field Values

NAME
```
private static final String NAME
```
See Also:
Constant Field Values

DESCRIPTION

private static final String DESCRIPTION

See Also:: Constant Field Values

SERIES_COUNT

private static final String SERIES_COUNT

See Also:: Constant Field Values

CHANNEL_COUNT

private static final String CHANNEL_COUNT

See Also:: Constant Field Values

DATE
```
private static final String DATE
```
See Also:
Constant Field Values

DELTA_T
```
private static final String DELTA_T
```
See Also:
Constant Field Values

X_POSITION
```
private static final String X_POSITION
```
See Also:
Constant Field Values

X_POSITION_UNIT

private static final String X_POSITION_UNIT

See Also:: Constant Field Values

Y_POSITION
```
private static final String Y_POSITION
```
See Also:
Constant Field Values

Y_POSITION_UNIT

private static final String Y_POSITION_UNIT

See Also:: Constant Field Values

Z_POSITION
```
private static final String Z_POSITION
```
See Also:
Constant Field Values

Z_POSITION_UNIT

private static final String Z_POSITION_UNIT

See Also:: Constant Field Values

dataFile
```
private String dataFile
```

configFile
```
private String configFile
```

ini
```
private IniList ini
```

currentTable
```
private IniTable currentTable
```

globalTable
```
private IniTable globalTable
```

Constructor Detail

Configuration

public Configuration(String dataFile,
             String configFile)
              throws IOException

Throws:: IOException

Configuration

public Configuration(IFormatReader reader,
             String configFile)

Method Detail

getFile
```
public String getFile()
```

getAccessTimeMillis
```
public long getAccessTimeMillis()
```

getMemory
```
public int getMemory()
```

doTest
```
public boolean doTest()
```

hasValidXML
```
public boolean hasValidXML()
```

getReader
```
public String getReader()
```

getSeriesCount
```
public int getSeriesCount()
```

getSizeX
```
public int getSizeX()
```

getSizeY
```
public int getSizeY()
```

getSizeZ
```
public int getSizeZ()
```

getSizeC
```
public int getSizeC()
```

getSizeT
```
public int getSizeT()
```

getDimensionOrder
```
public String getDimensionOrder()
```

isInterleaved
```
public boolean isInterleaved()
```

isIndexed
```
public boolean isIndexed()
```

isFalseColor
```
public boolean isFalseColor()
```

isRGB
```
public boolean isRGB()
```

getThumbSizeX
```
public int getThumbSizeX()
```

getThumbSizeY
```
public int getThumbSizeY()
```

getPixelType
```
public String getPixelType()
```

isLittleEndian
```
public boolean isLittleEndian()
```

getMD5
```
public String getMD5()
```

getAlternateMD5
```
public String getAlternateMD5()
```

getTileMD5
```
public String getTileMD5()
```

getTileAlternateMD5
```
public String getTileAlternateMD5()
```

getPhysicalSizeX
```
public Length getPhysicalSizeX()
```

getPhysicalSizeY
```
public Length getPhysicalSizeY()
```

getPhysicalSizeZ
```
public Length getPhysicalSizeZ()
```

getTimeIncrement
```
public Time getTimeIncrement()
```

getChannelCount
```
public int getChannelCount()
```

getLightSource

public String getLightSource(int channel)

getChannelName

public String getChannelName(int channel)

hasExposureTime

public boolean hasExposureTime(int channel)

getExposureTime

public Time getExposureTime(int channel)

getDeltaT
```
public Double getDeltaT(int plane)
```

getPositionX

public Double getPositionX(int plane)

getPositionXUnit

public String getPositionXUnit(int plane)

getPositionY

public Double getPositionY(int plane)

getPositionYUnit

public String getPositionYUnit(int plane)

getPositionZ

public Double getPositionZ(int plane)

getPositionZUnit

public String getPositionZUnit(int plane)

getEmissionWavelength

public Length getEmissionWavelength(int channel)

getExcitationWavelength

public Length getExcitationWavelength(int channel)

getDetector

public String getDetector(int channel)

getImageName
```
public String getImageName()
```

hasImageDescription
```
public boolean hasImageDescription()
```

getImageDescription
```
public String getImageDescription()
```

getDate
```
public String getDate()
```

setSeries
```
public void setSeries(int series)
```

saveToFile

public void saveToFile()
                throws IOException

Throws:: IOException

getINI
```
public IniList getINI()
```

equals
```
public boolean equals(Object o)
```
Overrides:

equals in class Object

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class Object

populateINI

private void populateINI(IFormatReader reader)

putTableName

private void putTableName(IniTable table,
                IFormatReader reader,
                String suffix)

pruneINI
```
private void pruneINI()
```

Class Configuration

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TILE_SIZE

ACCESS_TIME

MEMORY

TEST

HAS_VALID_XML

READER

SERIES

SIZE_X

SIZE_Y

SIZE_Z

SIZE_C

SIZE_T

DIMENSION_ORDER

IS_INDEXED

IS_INTERLEAVED

IS_FALSE_COLOR

IS_RGB

THUMB_SIZE_X

THUMB_SIZE_Y

PIXEL_TYPE

IS_LITTLE_ENDIAN

MD5

ALTERNATE_MD5

TILE_MD5

TILE_ALTERNATE_MD5

PHYSICAL_SIZE_X

PHYSICAL_SIZE_X_UNIT

PHYSICAL_SIZE_Y

PHYSICAL_SIZE_Y_UNIT

PHYSICAL_SIZE_Z

PHYSICAL_SIZE_Z_UNIT

TIME_INCREMENT

TIME_INCREMENT_UNIT

LIGHT_SOURCE

CHANNEL_NAME

EXPOSURE_TIME

EXPOSURE_TIME_UNIT

EMISSION_WAVELENGTH

EMISSION_WAVELENGTH_UNIT

EXCITATION_WAVELENGTH

EXCITATION_WAVELENGTH_UNIT

DETECTOR

NAME

DESCRIPTION

SERIES_COUNT

CHANNEL_COUNT

DATE

DELTA_T

X_POSITION

X_POSITION_UNIT

Y_POSITION

Y_POSITION_UNIT

Z_POSITION

Z_POSITION_UNIT

dataFile

configFile

ini

currentTable

globalTable

Constructor Detail

Configuration

Configuration

Method Detail

getFile

getAccessTimeMillis

getMemory

doTest

hasValidXML

getReader

getSeriesCount

getSizeX

getSizeY

getSizeZ

getSizeC