FIBSEM_Reader (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.io.FIBSEM_Reader

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class FIBSEM_Reader
extends Object
implements ij.plugin.PlugIn
```
Opens the proprietary FIB-SEM format used at Janelia Farm

Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class FIBSEM_Reader.FIBSEMData

Nested Classes
Modifier and Type	Class and Description
`class`	`FIBSEM_Reader.FIBSEMData`

Field Summary

Fields
Modifier and Type	Field and Description
`static boolean`	`openAsFloat` Opens it either as: UnsignedShort with the range [0..65535] where 0 == -10 Volts and 65535 == +10 Volts (default) Float with a range from -10 Volts to +10 Volts Note, the voltage might be different in future versions, it is stored in FIBSEMData.detMin and FIBSEMData.detMax

Constructor Summary

Constructors
Constructor and Description

FIBSEM_Reader()

Constructors
Constructor and Description
`FIBSEM_Reader()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`FIBSEM_Reader.FIBSEMData`	`getHeader()`
`static int`	`getUnsignedByte(byte signedByte)`
`static long`	`getUnsignedInt(int signedInt)`
`static int`	`getUnsignedShort(short signedShort)`
`static boolean`	`isFIBSEM(File f)` Determines if the given file is a FIB-SEM file based on the magic number (first 4 bytes)
`static void`	`main(String[] args)`
`FIBSEM_Reader.FIBSEMData`	`parseHeader(FileInputStream file)` Parses the header and sets the `FileInputStream` to right location where the raw image data starts
`ij.ImagePlus`	`readFIBSEM(FIBSEM_Reader.FIBSEMData header, FileInputStream file, boolean openAsFloat)`
`void`	`run(String filename)`

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

- Field Detail
  - openAsFloat
```
public static boolean openAsFloat
```
    Opens it either as: UnsignedShort with the range [0..65535] where 0 == -10 Volts and 65535 == +10 Volts (default) Float with a range from -10 Volts to +10 Volts Note, the voltage might be different in future versions, it is stored in FIBSEMData.detMin and FIBSEMData.detMax
- Constructor Detail
  - FIBSEM_Reader
```
public FIBSEM_Reader()
```
- Method Detail
  - getHeader
```
public FIBSEM_Reader.FIBSEMData getHeader()
```
    Returns:
    
    - the header of the last opened FIB-SEM file
  - run
```
public void run(String filename)
```
    Specified by:
    
    run in interface ij.plugin.PlugIn
  - isFIBSEM
```
public static boolean isFIBSEM(File f)
```
    Determines if the given file is a FIB-SEM file based on the magic number (first 4 bytes)
    
    Parameters:
    
    f - - the File
    
    Returns:
  - readFIBSEM
```
public ij.ImagePlus readFIBSEM(FIBSEM_Reader.FIBSEMData header,
                               FileInputStream file,
                               boolean openAsFloat)
                        throws IOException
```
    Throws:
    
    IOException
  - parseHeader
```
public FIBSEM_Reader.FIBSEMData parseHeader(FileInputStream file)
                                     throws IOException
```
    Parses the header and sets the FileInputStream to right location where the raw image data starts
    
    Parameters:
    
    file - - the input file
    
    Returns:
    
    the FIBSEM_Reader.FIBSEMData that contains all meta-data or null if the magic number (file id) does not match
    
    Throws:
    
    IOException
  - getUnsignedInt
```
public static long getUnsignedInt(int signedInt)
```
  - getUnsignedShort
```
public static int getUnsignedShort(short signedShort)
```
  - getUnsignedByte
```
public static int getUnsignedByte(byte signedByte)
```
  - main
```
public static void main(String[] args)
```

Class FIBSEM_Reader

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

openAsFloat

Constructor Detail

FIBSEM_Reader

Method Detail

getHeader

run

isFIBSEM

readFIBSEM

parseHeader

getUnsignedInt

getUnsignedShort

getUnsignedByte

main