DataContainer (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.coloc.gadgets.DataContainer<T>

Type Parameters:

T -
```
public class DataContainer<T extends RealType<T>>
extends Object
```
The DataContainer keeps all the source data, jobName, pre-processing results and algorithm results that have been computed. It allows a ResultsHandler implementation to get most of its content and makes the source image and channel information available to a client.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class DataContainer.MaskType

Nested Classes
Modifier and Type	Class and Description
`static class`	`DataContainer.MaskType`

Field Summary

Fields
Modifier and Type Field and Description

String jobName

protected long[] maskBBOffset

protected long[] maskBBSize

protected DataContainer.MaskType maskType

Fields
Modifier and Type	Field and Description
`String`	`jobName`
`protected long[]`	`maskBBOffset`
`protected long[]`	`maskBBSize`
`protected DataContainer.MaskType`	`maskType`

Constructor Summary

Constructors
Constructor and Description
`DataContainer(RandomAccessibleInterval<T> src1, RandomAccessibleInterval<T> src2, int ch1, int ch2, String name1, String name2)` Creates a new `DataContainer` for a specific image channel combination.
`DataContainer(RandomAccessibleInterval<T> src1, RandomAccessibleInterval<T> src2, int ch1, int ch2, String name1, String name2, long[] offset, long[] size)` Creates a new `DataContainer` for a specific set of image and channel combination.
`DataContainer(RandomAccessibleInterval<T> src1, RandomAccessibleInterval<T> src2, int ch1, int ch2, String name1, String name2, RandomAccessibleInterval<T> mask, long[] offset, long[] size)` Creates a new `DataContainer` for a specific set of image and channel combination.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`adjustRoiOffset(long[] oldOffset, long[] newOffset, long[] dimensions)` Make sure that the ROI offset has the same dimensionality as the image.
`protected void`	`adjustRoiSize(long[] oldSize, long[] newSize, long[] dimensions, long[] offset)` Transforms a ROI size array to a dimensionality.
`protected void`	`calculateStatistics()`
`AutoThresholdRegression<T>`	`getAutoThreshold()`
`int`	`getCh1()`
`int`	`getCh2()`
`InputCheck<T>`	`getInputCheck()`
`double`	`getIntegralCh1()`
`double`	`getIntegralCh2()`
`String`	`getJobName()`
`RandomAccessibleInterval<BitType>`	`getMask()`
`long[]`	`getMaskBBOffset()`
`long[]`	`getMaskBBSize()`
`int`	`getMaskID()`
`DataContainer.MaskType`	`getMaskType()`
`double`	`getMaxCh1()`
`double`	`getMaxCh2()`
`double`	`getMeanCh1()`
`double`	`getMeanCh2()`
`double`	`getMinCh1()`
`double`	`getMinCh2()`
`String`	`getSourceCh1Name()`
`String`	`getSourceCh2Name()`
`RandomAccessibleInterval<T>`	`getSourceImage1()`
`String`	`getSourceImage1Name()`
`RandomAccessibleInterval<T>`	`getSourceImage2()`
`String`	`getSourceImage2Name()`
`Algorithm<T>`	`setAutoThreshold(AutoThresholdRegression<T> autoThreshold)`
`Algorithm<T>`	`setInputCheck(InputCheck<T> inputCheck)`

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

Field Detail

jobName
```
public String jobName
```

maskType

protected DataContainer.MaskType maskType

maskBBSize
```
protected long[] maskBBSize
```

maskBBOffset
```
protected long[] maskBBOffset
```

Constructor Detail
- DataContainer
```
public DataContainer(RandomAccessibleInterval<T> src1,
                     RandomAccessibleInterval<T> src2,
                     int ch1,
                     int ch2,
                     String name1,
                     String name2)
```
  Creates a new DataContainer for a specific image channel combination. We create default thresholds here that are the max and min of the data type of the source image channels.
  
  Parameters:
  
  src1 - The channel one image source
  
  src2 - The channel two image source
  
  ch1 - The channel one image channel
  
  ch2 - The channel two image channel
- DataContainer
```
public DataContainer(RandomAccessibleInterval<T> src1,
                     RandomAccessibleInterval<T> src2,
                     int ch1,
                     int ch2,
                     String name1,
                     String name2,
                     RandomAccessibleInterval<T> mask,
                     long[] offset,
                     long[] size)
              throws MissingPreconditionException
```
  Creates a new DataContainer for a specific set of image and channel combination. It will give access to the image according to the mask passed. It is expected that the mask is of the same size as an image slice. Default thresholds, min, max and mean will be set according to the mask as well.
  
  Parameters:
  
  src1 - The channel one image source
  
  src2 - The channel two image source
  
  ch1 - The channel one image channel
  
  ch2 - The channel two image channel
  
  mask - The mask to use
  
  offset - The offset of the ROI in each dimension
  
  size - The size of the ROI in each dimension
  
  Throws:
  
  MissingPreconditionException
- DataContainer
```
public DataContainer(RandomAccessibleInterval<T> src1,
                     RandomAccessibleInterval<T> src2,
                     int ch1,
                     int ch2,
                     String name1,
                     String name2,
                     long[] offset,
                     long[] size)
              throws MissingPreconditionException
```
  Creates a new DataContainer for a specific set of image and channel combination. It will give access to the image according to the region of interest (ROI) passed. Default thresholds, min, max and mean will be set according to the ROI as well.
  
  Parameters:
  
  src1 - The channel one image source
  
  src2 - The channel two image source
  
  ch1 - The channel one image channel
  
  ch2 - The channel two image channel
  
  offset - The offset of the ROI in each dimension
  
  size - The size of the ROI in each dimension
  
  Throws:
  
  MissingPreconditionException

Method Detail

calculateStatistics
```
protected void calculateStatistics()
```

adjustRoiOffset
```
protected void adjustRoiOffset(long[] oldOffset,
                               long[] newOffset,
                               long[] dimensions)
                        throws MissingPreconditionException
```
Make sure that the ROI offset has the same dimensionality as the image. The method fills it up with zeros if needed.

Parameters:

oldOffset - The offset with the original dimensionality

newOffset - The output array with the new dimensionality

dimensions - An array of the dimensions

Throws:

MissingPreconditionException

adjustRoiSize
```
protected void adjustRoiSize(long[] oldSize,
                             long[] newSize,
                             long[] dimensions,
                             long[] offset)
                      throws MissingPreconditionException
```
Transforms a ROI size array to a dimensionality. The method fill up with image (dimension - offset in that dimension) if needed.

Parameters:

oldSize - Size array of old dimensionality

newSize - Output size array of new dimensionality

dimensions - Dimensions representing the new dimensionality

offset - Offset of the new dimensionality

Throws:

MissingPreconditionException

getSourceImage1

public RandomAccessibleInterval<T> getSourceImage1()

getSourceImage2

public RandomAccessibleInterval<T> getSourceImage2()

getSourceImage1Name
```
public String getSourceImage1Name()
```

getSourceImage2Name
```
public String getSourceImage2Name()
```

getSourceCh1Name
```
public String getSourceCh1Name()
```

getSourceCh2Name
```
public String getSourceCh2Name()
```

getJobName
```
public String getJobName()
```

getMask

public RandomAccessibleInterval<BitType> getMask()

getMaskBBOffset
```
public long[] getMaskBBOffset()
```

getMaskBBSize
```
public long[] getMaskBBSize()
```

getMaskType

public DataContainer.MaskType getMaskType()

getMaskID
```
public int getMaskID()
```

getCh1
```
public int getCh1()
```

getCh2
```
public int getCh2()
```

getMeanCh1
```
public double getMeanCh1()
```

getMeanCh2
```
public double getMeanCh2()
```

getMinCh1
```
public double getMinCh1()
```

getMaxCh1
```
public double getMaxCh1()
```

getMinCh2
```
public double getMinCh2()
```

getMaxCh2
```
public double getMaxCh2()
```

getIntegralCh1
```
public double getIntegralCh1()
```

getIntegralCh2
```
public double getIntegralCh2()
```

getInputCheck
```
public InputCheck<T> getInputCheck()
```

setInputCheck

public Algorithm<T> setInputCheck(InputCheck<T> inputCheck)

getAutoThreshold

public AutoThresholdRegression<T> getAutoThreshold()

setAutoThreshold

public Algorithm<T> setAutoThreshold(AutoThresholdRegression<T> autoThreshold)

Class DataContainer<T extends RealType<T>>

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

jobName

maskType

maskBBSize

maskBBOffset

Constructor Detail

DataContainer

DataContainer

DataContainer

Method Detail

calculateStatistics

adjustRoiOffset

adjustRoiSize

getSourceImage1

getSourceImage2

getSourceImage1Name

getSourceImage2Name

getSourceCh1Name

getSourceCh2Name

getJobName

getMask

getMaskBBOffset

getMaskBBSize

getMaskType

getMaskID

getCh1

getCh2

getMeanCh1

getMeanCh2

getMinCh1

getMaxCh1

getMinCh2

getMaxCh2

getIntegralCh1

getIntegralCh2

getInputCheck

setInputCheck

getAutoThreshold

setAutoThreshold