SPIMExperiment (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spimopener.SPIMExperiment

public class SPIMExperiment
extends Object

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`angleEnd`
`String[]`	`angles`
`int`	`angleStart`
`int`	`channelEnd`
`String[]`	`channels`
`int`	`channelStart`
`int`	`d`
`String`	`experimentName`
`static int`	`F`
`int`	`frameEnd`
`int`	`frameStart`
`static int`	`GAUSSIAN_STACK_FOCUSER`
`int`	`h`
`static int`	`MAX_PROJECTION`
`static int`	`MIN_PROJECTION`
`static int`	`NO_PROJECTION`
`String`	`pathFormatString`
`double`	`pd`
`double`	`ph`
`int`	`planeEnd`
`int`	`planeStart`
`double`	`pw`
`int`	`regionEnd`
`String[]`	`regions`
`int`	`regionStart`
`int`	`sampleEnd`
`String[]`	`samples`
`int`	`sampleStart`
`static int`	`T`
`int`	`timepointEnd`
`int`	`timepointStart`
`int`	`w`
`static int`	`X`
`static int`	`Y`
`static int`	`Z`

Constructor Summary

Constructors
Constructor and Description

SPIMExperiment(String xmlfile)

Constructors
Constructor and Description
`SPIMExperiment(String xmlfile)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`getPath(int sample, int timepoint, int region, int angle, int channel, int plane, int frame)`
`ij.ImagePlus`	`open(int sample, int tpMin, int tpMax, int region, int angle, int channel, int zMin, int zMax, int fMin, int fMax, int projectionMethod, boolean virtual)`
`ij.ImagePlus`	`open(int sample, int tpMin, int tpMax, int region, int angle, int channel, int zMin, int zMax, int fMin, int fMax, int yMin, int yMax, int xMin, int xMax, int projectionMethod, boolean virtual)`
`ij.ImagePlus`	`open(int sample, int tpMin, int tpMax, int region, int angle, int channel, int zMin, int zMax, int fMin, int fMax, int yMin, int yMax, int xMin, int xMax, int xDir, int yDir, int zDir, boolean virtual, int projectionMethod, int projectionDir)`
`ij.ImagePlus`	`open(int sample, int tpMin, int tpMax, int tpStep, int region, int angle, int channel, int zMin, int zMax, int zStep, int fMin, int fMax, int fStep, int yMin, int yMax, int yStep, int xMin, int xMax, int xStep, int xDir, int yDir, int zDir, boolean virtual, int projectionMethod, int projectionDir)`
`ij.ImagePlus`	`openNotProjected(int sample, int tpMin, int tpMax, int region, int angle, int channel, int zMin, int zMax, int fMin, int fMax, int yMin, int yMax, int xMin, int xMax, int xDir, int yDir, int zDir, boolean virtual)`
`ij.ImagePlus`	`openNotProjected(int sample, int tpMin, int tpMax, int region, int angle, int channel, int zMin, int zMax, int zStep, int fMin, int fMax, int yMin, int yMax, int xMin, int xMax, int xDir, int yDir, int zDir, boolean virtual)`
`ij.ImagePlus`	`openNotProjected(int sample, int tpMin, int tpMax, int tpStep, int region, int angle, int channel, int zMin, int zMax, int zStep, int fMin, int fMax, int fStep, int yMin, int yMax, int yStep, int xMin, int xMax, int xStep, int xDir, int yDir, int zDir, boolean virtual)`
`static ij.process.ImageProcessor`	`openRaw(String path, int w, int h)`
`static ij.process.ImageProcessor`	`openRaw(String path, int orgW, int orgH, int xMin, int xMax, int yMin, int yMax)`
`static void`	`saveRaw(ij.process.ImageProcessor ip, String path)`

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

Field Detail

X
```
public static final int X
```
See Also:

Constant Field Values

Y
```
public static final int Y
```
See Also:

Constant Field Values

F
```
public static final int F
```
See Also:

Constant Field Values

Z
```
public static final int Z
```
See Also:

Constant Field Values

T
```
public static final int T
```
See Also:

Constant Field Values

sampleStart
```
public final int sampleStart
```

sampleEnd
```
public final int sampleEnd
```

timepointStart
```
public final int timepointStart
```

timepointEnd
```
public final int timepointEnd
```

regionStart
```
public final int regionStart
```

regionEnd
```
public final int regionEnd
```

angleStart
```
public final int angleStart
```

angleEnd
```
public final int angleEnd
```

channelStart
```
public final int channelStart
```

channelEnd
```
public final int channelEnd
```

planeStart
```
public final int planeStart
```

planeEnd
```
public final int planeEnd
```

frameStart
```
public final int frameStart
```

frameEnd
```
public final int frameEnd
```

pathFormatString
```
public final String pathFormatString
```

pw
```
public final double pw
```

ph
```
public final double ph
```

pd
```
public final double pd
```

w
```
public final int w
```

h
```
public final int h
```

d
```
public final int d
```

samples
```
public final String[] samples
```

regions
```
public final String[] regions
```

angles
```
public final String[] angles
```

channels
```
public final String[] channels
```

experimentName
```
public final String experimentName
```

NO_PROJECTION
```
public static final int NO_PROJECTION
```
See Also:

Constant Field Values

MAX_PROJECTION
```
public static final int MAX_PROJECTION
```
See Also:

Constant Field Values

MIN_PROJECTION
```
public static final int MIN_PROJECTION
```
See Also:

Constant Field Values

GAUSSIAN_STACK_FOCUSER
```
public static final int GAUSSIAN_STACK_FOCUSER
```
See Also:

Constant Field Values

Constructor Detail
- SPIMExperiment
```
public SPIMExperiment(String xmlfile)
```

Method Detail

getPath

public String getPath(int sample,
                      int timepoint,
                      int region,
                      int angle,
                      int channel,
                      int plane,
                      int frame)

open

public ij.ImagePlus open(int sample,
                         int tpMin,
                         int tpMax,
                         int region,
                         int angle,
                         int channel,
                         int zMin,
                         int zMax,
                         int fMin,
                         int fMax,
                         int projectionMethod,
                         boolean virtual)

open

public ij.ImagePlus open(int sample,
                         int tpMin,
                         int tpMax,
                         int region,
                         int angle,
                         int channel,
                         int zMin,
                         int zMax,
                         int fMin,
                         int fMax,
                         int yMin,
                         int yMax,
                         int xMin,
                         int xMax,
                         int projectionMethod,
                         boolean virtual)

open

public ij.ImagePlus open(int sample,
                         int tpMin,
                         int tpMax,
                         int region,
                         int angle,
                         int channel,
                         int zMin,
                         int zMax,
                         int fMin,
                         int fMax,
                         int yMin,
                         int yMax,
                         int xMin,
                         int xMax,
                         int xDir,
                         int yDir,
                         int zDir,
                         boolean virtual,
                         int projectionMethod,
                         int projectionDir)

open

public ij.ImagePlus open(int sample,
                         int tpMin,
                         int tpMax,
                         int tpStep,
                         int region,
                         int angle,
                         int channel,
                         int zMin,
                         int zMax,
                         int zStep,
                         int fMin,
                         int fMax,
                         int fStep,
                         int yMin,
                         int yMax,
                         int yStep,
                         int xMin,
                         int xMax,
                         int xStep,
                         int xDir,
                         int yDir,
                         int zDir,
                         boolean virtual,
                         int projectionMethod,
                         int projectionDir)

openNotProjected

public ij.ImagePlus openNotProjected(int sample,
                                     int tpMin,
                                     int tpMax,
                                     int region,
                                     int angle,
                                     int channel,
                                     int zMin,
                                     int zMax,
                                     int fMin,
                                     int fMax,
                                     int yMin,
                                     int yMax,
                                     int xMin,
                                     int xMax,
                                     int xDir,
                                     int yDir,
                                     int zDir,
                                     boolean virtual)

openNotProjected

public ij.ImagePlus openNotProjected(int sample,
                                     int tpMin,
                                     int tpMax,
                                     int region,
                                     int angle,
                                     int channel,
                                     int zMin,
                                     int zMax,
                                     int zStep,
                                     int fMin,
                                     int fMax,
                                     int yMin,
                                     int yMax,
                                     int xMin,
                                     int xMax,
                                     int xDir,
                                     int yDir,
                                     int zDir,
                                     boolean virtual)

openNotProjected

public ij.ImagePlus openNotProjected(int sample,
                                     int tpMin,
                                     int tpMax,
                                     int tpStep,
                                     int region,
                                     int angle,
                                     int channel,
                                     int zMin,
                                     int zMax,
                                     int zStep,
                                     int fMin,
                                     int fMax,
                                     int fStep,
                                     int yMin,
                                     int yMax,
                                     int yStep,
                                     int xMin,
                                     int xMax,
                                     int xStep,
                                     int xDir,
                                     int yDir,
                                     int zDir,
                                     boolean virtual)

openRaw

public static ij.process.ImageProcessor openRaw(String path,
                                                int orgW,
                                                int orgH,
                                                int xMin,
                                                int xMax,
                                                int yMin,
                                                int yMax)

openRaw

public static ij.process.ImageProcessor openRaw(String path,
                                                int w,
                                                int h)

saveRaw

public static void saveRaw(ij.process.ImageProcessor ip,
                           String path)

Class SPIMExperiment

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

X

Y

F

Z

T

sampleStart

sampleEnd

timepointStart

timepointEnd

regionStart

regionEnd

angleStart

angleEnd

channelStart

channelEnd

planeStart

planeEnd

frameStart

frameEnd

pathFormatString

pw

ph

pd

w

h

d

samples

regions

angles

channels

experimentName

NO_PROJECTION

MAX_PROJECTION

MIN_PROJECTION

GAUSSIAN_STACK_FOCUSER

Constructor Detail

SPIMExperiment

Method Detail

getPath

open

open

open

open

openNotProjected

openNotProjected

openNotProjected

openRaw

openRaw

saveRaw