IOFunctions (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.spim.io.IOFunctions

```
public class IOFunctions
extends Object
```

Field Summary

Fields
Modifier and Type Field and Description

static boolean printIJLog

Fields
Modifier and Type	Field and Description
`static boolean`	`printIJLog`

Constructor Summary

Constructors
Modifier Constructor and Description

protected IOFunctions()
Never instantiate this class, it contains only static methods

Constructors
Modifier	Constructor and Description
`protected`	`IOFunctions()` Never instantiate this class, it contains only static methods

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static AffineModel3D`	`getModelFromFile(File file)`
`static ProgressWriter`	`getProgressWriter()`
`static String`	`getShortName(String fileName)`
`static SPIMConfiguration`	`initSPIMProcessing()`
`static SPIMConfiguration`	`initSPIMProcessing(String configFile, String spimConfigFile)`
`static void`	`printErr()`
`static void`	`printErr(Object object)`
`static void`	`printErr(String string)`
`static void`	`printErrSafe()`
`static void`	`printErrSafe(Object object)`
`static void`	`printErrSafe(String string)`
`static void`	`println()`
`static void`	`println(Object object)`
`static void`	`println(String string)`
`static void`	`printlnSafe()`
`static void`	`printlnSafe(Object object)`
`static void`	`printlnSafe(String string)`
`static void`	`printlnTS()`
`static void`	`printlnTS(Object object)`
`static void`	`printlnTS(String string)`
`static boolean`	`readDim(ViewDataBeads view, String directory)`
`static ArrayList<Nucleus>`	`readNuclei(ViewDataBeads view, String directory, NucleiConfiguration nConf)`
`static boolean`	`readNucleiCorrespondences(ViewDataBeads view, String directory)`
`static boolean`	`readNucleiCorrespondences(ViewDataBeads view, String directory, boolean removePreviousEntries)`
`static boolean`	`readRegistration(ViewDataBeads view, String fileName)`
`static boolean`	`readSegmentation(ViewDataBeads view, String directory, SPIMConfiguration conf)`
`static void`	`reWriteRegistrationFile(File file, AffineModel3D newModel, AffineModel3D oldModel, AffineModel3D preConcatenated)`
`static boolean`	`writeDim(ViewDataBeads view, String directory)`
`static boolean`	`writeNuclei(ViewDataBeads view, Collection<Nucleus> nuclei, String directory)`
`static boolean`	`writeNucleiCorrespondences(ViewDataBeads view, String directory)`
`static boolean`	`writeRegistration(ViewDataBeads view, String directory)`
`static boolean`	`writeRegistration(ViewDataBeads view, String directory, String extension)`
`static boolean`	`writeSegmentation(ArrayList<Bead> beads, int[] imgSize, String viewName, int viewID, String directory)`
`static boolean`	`writeSegmentation(ViewDataBeads view, String directory)`

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

Field Detail
- printIJLog
```
public static boolean printIJLog
```

Constructor Detail
- IOFunctions
```
protected IOFunctions()
```
  Never instantiate this class, it contains only static methods

Method Detail

printlnTS
```
public static void printlnTS()
```

printlnTS

public static void printlnTS(Object object)

printlnTS

public static void printlnTS(String string)

println
```
public static void println()
```

println

public static void println(Object object)

println

public static void println(String string)

printErr
```
public static void printErr()
```

printErr

public static void printErr(Object object)

printErr

public static void printErr(String string)

getProgressWriter

public static ProgressWriter getProgressWriter()

printlnSafe
```
public static void printlnSafe()
```

printlnSafe

public static void printlnSafe(Object object)

printlnSafe

public static void printlnSafe(String string)

printErrSafe
```
public static void printErrSafe()
```

printErrSafe

public static void printErrSafe(Object object)

printErrSafe

public static void printErrSafe(String string)

initSPIMProcessing

public static SPIMConfiguration initSPIMProcessing()

initSPIMProcessing

public static SPIMConfiguration initSPIMProcessing(String configFile,
                                                   String spimConfigFile)

getShortName

public static String getShortName(String fileName)

writeNuclei

public static boolean writeNuclei(ViewDataBeads view,
                                  Collection<Nucleus> nuclei,
                                  String directory)

readNuclei

public static ArrayList<Nucleus> readNuclei(ViewDataBeads view,
                                            String directory,
                                            NucleiConfiguration nConf)

writeNucleiCorrespondences

public static boolean writeNucleiCorrespondences(ViewDataBeads view,
                                                 String directory)

readNucleiCorrespondences

public static boolean readNucleiCorrespondences(ViewDataBeads view,
                                                String directory)

readNucleiCorrespondences

public static boolean readNucleiCorrespondences(ViewDataBeads view,
                                                String directory,
                                                boolean removePreviousEntries)

writeSegmentation

public static boolean writeSegmentation(ViewDataBeads view,
                                        String directory)

writeSegmentation

public static boolean writeSegmentation(ArrayList<Bead> beads,
                                        int[] imgSize,
                                        String viewName,
                                        int viewID,
                                        String directory)

readSegmentation

public static boolean readSegmentation(ViewDataBeads view,
                                       String directory,
                                       SPIMConfiguration conf)

writeDim

public static boolean writeDim(ViewDataBeads view,
                               String directory)

readDim

public static boolean readDim(ViewDataBeads view,
                              String directory)

writeRegistration

public static boolean writeRegistration(ViewDataBeads view,
                                        String directory)

writeRegistration

public static boolean writeRegistration(ViewDataBeads view,
                                        String directory,
                                        String extension)

readRegistration

public static boolean readRegistration(ViewDataBeads view,
                                       String fileName)

reWriteRegistrationFile

public static void reWriteRegistrationFile(File file,
                                           AffineModel3D newModel,
                                           AffineModel3D oldModel,
                                           AffineModel3D preConcatenated)

getModelFromFile

public static AffineModel3D getModelFromFile(File file)

Class IOFunctions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

printIJLog

Constructor Detail

IOFunctions

Method Detail

printlnTS

printlnTS

printlnTS

println

println

println

printErr

printErr

printErr

getProgressWriter

printlnSafe

printlnSafe

printlnSafe

printErrSafe

printErrSafe

printErrSafe

initSPIMProcessing

initSPIMProcessing

getShortName

writeNuclei

readNuclei

writeNucleiCorrespondences

readNucleiCorrespondences

readNucleiCorrespondences

writeSegmentation

writeSegmentation

readSegmentation

writeDim

readDim

writeRegistration

writeRegistration

readRegistration

reWriteRegistrationFile

getModelFromFile