java.lang.Object
- adams.data.io.input.foss.FossHelper

```
public class FossHelper
extends Object
```
Helper for handling Foss cal files. Info used here is from studying .cal files with hex editor. Has been tested on many .cal files, but no guarantees.

Author:

dale

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class FossHelper.FossFields
Stores non-spectral data for a row.

Field Summary

Fields
Modifier and Type	Field	Description
`protected static int`	`count_offset`	number of Rows in this file.
`protected static int`	`datapoint_offset`	number of nir wavelengths.
`protected static int`	`deleted_offset`	number of Rows in this file.
`protected static int`	`head_end`	data header end.
`protected int`	`m_count`	number of (non deleted) spectra.
`protected int`	`m_deleted`	number of deleted rows in this file.
`protected int`	`m_num_points`	number of spectral data points.
`protected int`	`m_ref_count`	number of reference values per spectra.
`protected List<String>`	`m_ref_names`	reference names.
`protected int`	`m_spectra_head_size`	size of spectrum header (static).
`protected int`	`m_spectra_size`	size of spectra data.
`protected int`	`m_spectra_tail_size`	size of spectrum tail (static).
`protected static int`	`Npps_offset`
`protected static int`	`NSeg_offset`
`protected static int`	`reference_count`
`protected static int`	`reference_name_num`
`protected static int`	`reference_name_width`
`protected static int`	`reference_offset`
`protected static int`	`Wave_offset`
`protected static int`	`WaveType_offset`

Constructor Summary

Constructors
Constructor Description

FossHelper(byte[] bytes)
Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`byte2UByte(byte by)`	Convert byte to unsigned byte.
`protected long`	`convertToLong(byte[] b, int offset)`	Convert 4 bytes to long.
`int`	`countDeleted()`	How many deleted rows?
`int`	`getBlockSize()`	Get block size of a row in bytes.
`int`	`getCount()`	Number of non-deleted rows.
`FossHelper.FossFields`	`getFields(int i)`	Get the non-spectral data for a given row.
`int`	`getNumDatapoints()`	Number of spectral data points.
`int`	`getNumSegments()`	get number of segments
`int`	`getRefCount()`	number of reference values.
`List<String>`	`getReferenceNames()`	Get names of references.
`float[]`	`getRefForRow(int i)`	Get reference values for a row.
`int`	`getRefOffsetForRow(int i)`	Get start of reference for given row.
`double[]`	`getSegmentEnd()`
`double[]`	`getSegmentInc()`
`int[]`	`getSegmentLengths()`
`double[]`	`getSegmentStart()`
`int`	`getSegmentsType()`	Get segment type (00=TILFIL, 01=EQLSPC, 02=FILFIL, 03=SINSPA
`protected int`	`getSpectraBlockSize()`	Get size of the spectral data block.
`double[]`	`getSpectraForRow(int i)`	Get spectrum of row.
`int`	`getSpectraOffsetForRow(int i)`	Get start of spectrum for given row.
`int`	`getTotal()`	Total number of rows, including deleted rows.
`double[]`	`getWavenumbers()`
`protected String`	`getZeroTerminatedString(int offset)`	Build string until reaching zero termination.
`protected long`	`longFrom2Bytes(byte[] b, int offset)`	Get long from 2 bytes LSByte first.
`static void`	`main(String[] args)`	Test.
`boolean`	`processHeader()`	Process the data from the cal file header.

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

- Field Detail
  - count_offset
```
protected static int count_offset
```
    number of Rows in this file.
  - deleted_offset
```
protected static int deleted_offset
```
    number of Rows in this file.
  - datapoint_offset
```
protected static int datapoint_offset
```
    number of nir wavelengths.
  - reference_count
```
protected static int reference_count
```
  - reference_offset
```
protected static int reference_offset
```
  - reference_name_width
```
protected static int reference_name_width
```
  - reference_name_num
```
protected static int reference_name_num
```
  - NSeg_offset
```
protected static int NSeg_offset
```
  - Npps_offset
```
protected static int Npps_offset
```
  - WaveType_offset
```
protected static int WaveType_offset
```
  - Wave_offset
```
protected static int Wave_offset
```
  - head_end
```
protected static int head_end
```
    data header end.
  - m_count
```
protected int m_count
```
    number of (non deleted) spectra.
  - m_num_points
```
protected int m_num_points
```
    number of spectral data points.
  - m_ref_names
```
protected List<String> m_ref_names
```
    reference names.
  - m_ref_count
```
protected int m_ref_count
```
    number of reference values per spectra.
  - m_spectra_head_size
```
protected int m_spectra_head_size
```
    size of spectrum header (static).
  - m_spectra_size
```
protected int m_spectra_size
```
    size of spectra data.
  - m_spectra_tail_size
```
protected int m_spectra_tail_size
```
    size of spectrum tail (static).
  - m_deleted
```
protected int m_deleted
```
    number of deleted rows in this file.
- Constructor Detail
  - FossHelper
```
public FossHelper(byte[] bytes)
```
    Constructor.
    
    Parameters:
    
    bytes - byte array of cal file
- Method Detail
  - getFields
```
public FossHelper.FossFields getFields(int i)
```
    Get the non-spectral data for a given row.
    
    Parameters:
    
    i - row number
    
    Returns:
  - getSpectraForRow
```
public double[] getSpectraForRow(int i)
```
    Get spectrum of row.
    
    Parameters:
    
    i - row num
    
    Returns:
    
    spectrum as array
  - getRefForRow
```
public float[] getRefForRow(int i)
```
    Get reference values for a row. Sorted as per getRefNames()
    
    Parameters:
    
    i - row num
    
    Returns:
    
    array of reference values
  - getBlockSize
```
public int getBlockSize()
```
    Get block size of a row in bytes.
    
    Returns:
    
    size of all data for a row
  - getSpectraBlockSize
```
protected int getSpectraBlockSize()
```
    Get size of the spectral data block. (taking account of padding)
    
    Returns:
    
    size of the spectral data block
  - getSpectraOffsetForRow
```
public int getSpectraOffsetForRow(int i)
```
    Get start of spectrum for given row.
    
    Parameters:
    
    i - row number
    
    Returns:
    
    spectrum start
  - getRefOffsetForRow
```
public int getRefOffsetForRow(int i)
```
    Get start of reference for given row.
    
    Parameters:
    
    i - row number
    
    Returns:
    
    ref values start
  - processHeader
```
public boolean processHeader()
```
    Process the data from the cal file header.
    
    Returns:
    
    true
  - getTotal
```
public int getTotal()
```
    Total number of rows, including deleted rows.
    
    Returns:
    
    total num rows
  - countDeleted
```
public int countDeleted()
```
    How many deleted rows?
    
    Returns:
    
    deleted rows?
  - getRefCount
```
public int getRefCount()
```
    number of reference values.
    
    Returns:
    
    ref count
  - getSegmentsType
```
public int getSegmentsType()
```
    Get segment type (00=TILFIL, 01=EQLSPC, 02=FILFIL, 03=SINSPA
    
    Returns:
    
    type
  - getNumSegments
```
public int getNumSegments()
```
    get number of segments
    
    Returns:
    
    num segments
  - getSegmentLengths
```
public int[] getSegmentLengths()
```
  - getSegmentStart
```
public double[] getSegmentStart()
```
  - getSegmentInc
```
public double[] getSegmentInc()
```
  - getSegmentEnd
```
public double[] getSegmentEnd()
```
  - getWavenumbers
```
public double[] getWavenumbers()
```
  - getReferenceNames
```
public List<String> getReferenceNames()
```
    Get names of references.
    
    Returns:
    
    reference names
  - getZeroTerminatedString
```
protected String getZeroTerminatedString(int offset)
```
    Build string until reaching zero termination.
    
    Parameters:
    
    offset - pos in file to start
    
    Returns:
    
    string
  - getCount
```
public int getCount()
```
    Number of non-deleted rows.
    
    Returns:
    
    num rows
  - getNumDatapoints
```
public int getNumDatapoints()
```
    Number of spectral data points.
    
    Returns:
    
    num data points
  - byte2UByte
```
protected int byte2UByte(byte by)
```
    Convert byte to unsigned byte.
    
    Parameters:
    
    by - byte
    
    Returns:
    
    unsigned byte
  - convertToLong
```
protected long convertToLong(byte[] b,
                             int offset)
```
    Convert 4 bytes to long. LSByte first.
    
    Parameters:
    
    b - byte array
    
    offset - starting pos
    
    Returns:
    
    long
  - longFrom2Bytes
```
protected long longFrom2Bytes(byte[] b,
                              int offset)
```
    Get long from 2 bytes LSByte first.
    
    Parameters:
    
    b - byte array
    
    offset - start in array
    
    Returns:
    
    long
  - main
```
public static void main(String[] args)
                 throws Exception
```
    Test. arg0 cal filename
    
    Parameters:
    
    args - commandline arguments
    
    Throws:
    
    Exception - if somethin goes wrong

Class FossHelper

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

count_offset

deleted_offset

datapoint_offset

reference_count

reference_offset

reference_name_width

reference_name_num

NSeg_offset

Npps_offset

WaveType_offset

Wave_offset

head_end

m_count

m_num_points

m_ref_names

m_ref_count

m_spectra_head_size

m_spectra_size

m_spectra_tail_size

m_deleted

Constructor Detail

FossHelper

Method Detail

getFields

getSpectraForRow

getRefForRow

getBlockSize

getSpectraBlockSize

getSpectraOffsetForRow

getRefOffsetForRow

processHeader

getTotal

countDeleted

getRefCount

getSegmentsType

getNumSegments

getSegmentLengths

getSegmentStart

getSegmentInc

getSegmentEnd

getWavenumbers

getReferenceNames

getZeroTerminatedString

getCount

getNumDatapoints

byte2UByte

convertToLong

longFrom2Bytes

main