fable.python
Class Sample

java.lang.Object
  fable.python.Sample

public class Sample
extends java.lang.Object

Author:

SUCHET

Field Summary

boolean

headersRead

Constructor Summary

Sample()

Sample(java.lang.String path, java.io.File[] files)

Sample(java.lang.String experimentName, java.lang.String sampleName)

Sample(java.lang.String experimentName, java.lang.String sampleName, java.lang.String path)

Sample(java.lang.String experimentName, java.lang.String sampleName, java.lang.String directory, java.io.File[] filesInDir)

Sample(java.lang.String experimentName, java.lang.String sampleName, java.lang.String path, java.lang.String[] listFiles)

Method Summary

void	addCurrentFiles(java.lang.String[] newFiles) For preprocessor, to avoid invalid thread access
boolean	addFabioFile(FabioFile _fabioFile) 30 nov.
void	addFabioFiles(java.lang.String[] newFiles)
void	addHeaderValues(java.lang.String key, double[] values)
void	addPropertyChangeListener(org.eclipse.jface.util.IPropertyChangeListener listener) Register or remove listeners to sample changes
void	addSampleListener(ISampleListener pl)
void	fireSomeHeaderValuesLoaded() update plot every 10 files read
FabioFile	getCurrentFabioFile()
java.lang.String	getDirectoryName() fable.preprocessor fable.preprocessor.process Feb 12, 2007
java.lang.String	getDirectoryPath() fable.preprocessor fable.preprocessor.process Feb 14, 2007
java.util.Vector<FabioFile>	getFabioFiles() 26 sept.
java.lang.String[]	getFabioFilesToProcess(boolean flag) Get files to process with the filter and also a good size comparing to the dark and/or the flood
java.lang.String	getFileFormat()
java.lang.String[]	getFiles()
java.lang.String	getFilter()
java.util.Vector<FabioFile>	getFilteredfiles() 22 Jul 2007
int	getFirst()
double[]	getHeaderValues(java.lang.String key) used in Header plot
double[]	getHeaderValuesDiff(java.lang.String key) used in Header plot
java.lang.String[]	getKeys() Get keys for current file
int	getLast()
java.lang.String	getName()
java.lang.String	getNDigits()
java.lang.String	getParentDirectoryName() fable.preprocessor fable.preprocessor.process Feb 14, 2007
java.lang.String	getPeaksearchoutStem()
java.util.Vector<FabioFile>	getSortedFiles() This function is used to sort a vector of fabio files.
java.lang.String	getStem() This method init a file serie in python object.
boolean	hasFile() 26 sept.
boolean	isDirectory()
boolean	isShowInNavigator() 07/08/08 Gaelle since peaksearchSptView is speaking with imageviewer
boolean	isValide()
void	removeFabioFile(FabioFile f)
void	removeFileAt(int indice)
void	removeFiles()
void	removePropertyrChangeListener(org.eclipse.jface.util.IPropertyChangeListener listener)
void	removeSampleListener(ISampleListener pl)
void	setComparator(java.lang.String Key, int dir)
void	setCurrentFile(FabioFile fabio)
void	setCurrentFilesFromFabio()
void	setDirectory(boolean isDirectory)
void	setDirectoryName(java.lang.String name) fable.preprocessor fable.preprocessor.process Feb 12, 2007
void	setDirectoryPath(java.lang.String path) fable.preprocessor fable.preprocessor.process Feb 14, 2007
void	setFileFormat(java.lang.String format)
void	setFiles(java.lang.String[] _files)
void	setFilter(java.lang.String s_filter)
void	setFirst(int one)
void	setlast(int l)
void	setNDigits(java.lang.String val)
void	setParentDirectoryName(java.lang.String experiment) fable.preprocessor fable.preprocessor.process Feb 14, 2007
void	setPeaksearchOutfile(java.lang.String outfile)
void	setShowInNavigator(boolean showInNavigator) 07/08/08 Gaelle since peaksearchSptView is speaking with imageviewer
void	setStem(java.lang.String val)
void	setValide(boolean b)
java.lang.String	toString()
void	updateFabioFiles(java.io.File[] files) Update the list of FabioFiles by replacing the current list with the new list of file names.
void	updatefabioFiles(java.lang.String[] newFiles)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

headersRead

public boolean headersRead

Constructor Detail

Sample

public Sample(java.lang.String experimentName,
              java.lang.String sampleName,
              java.lang.String path,
              java.lang.String[] listFiles)
       throws FabioFileException

Throws:

FabioFileException

Sample

public Sample(java.lang.String experimentName,
              java.lang.String sampleName,
              java.lang.String path)

Sample

public Sample(java.lang.String experimentName,
              java.lang.String sampleName)

Sample

public Sample()

Sample

public Sample(java.lang.String path,
              java.io.File[] files)
       throws FabioFileException

Throws:

FabioFileException

Sample

public Sample(java.lang.String experimentName,
              java.lang.String sampleName,
              java.lang.String directory,
              java.io.File[] filesInDir)
       throws FabioFileException

Throws:

FabioFileException

Method Detail

addCurrentFiles

public void addCurrentFiles(java.lang.String[] newFiles)

For preprocessor, to avoid invalid thread access

addFabioFiles

public void addFabioFiles(java.lang.String[] newFiles)
                   throws FabioFileException

Throws:

FabioFileException

updatefabioFiles

public void updatefabioFiles(java.lang.String[] newFiles)
                      throws FabioFileException

Throws:

FabioFileException

addFabioFile

public boolean addFabioFile(FabioFile _fabioFile)
                     throws FabioFileException

30 nov. 07

Parameters:

fileName -

Throws:

FabioFileException - This method adds a fabio file to the vector fabiofiles

getKeys

public java.lang.String[] getKeys()
                           throws SampleException

Get keys for current file

Returns:

Throws:

SampleException

isValide

public boolean isValide()

Returns:

true if sample contains valid values (for example, if all files are ready to be processed with a dark and a flood that has the same dimension as files.

hasFile

public boolean hasFile()

26 sept. 07

Returns:

true if a file has been stored into sample at least

getParentDirectoryName

public java.lang.String getParentDirectoryName()

fable.preprocessor fable.preprocessor.process Feb 14, 2007

Returns:

the _Experiment

setParentDirectoryName

public void setParentDirectoryName(java.lang.String experiment)

fable.preprocessor fable.preprocessor.process Feb 14, 2007

Parameters:

experiment - the _Experiment to set

getDirectoryName

public java.lang.String getDirectoryName()

fable.preprocessor fable.preprocessor.process Feb 12, 2007

Returns:

the _name

setDirectoryName

public void setDirectoryName(java.lang.String name)

fable.preprocessor fable.preprocessor.process Feb 12, 2007

Parameters:

directoryName -

getDirectoryPath

public java.lang.String getDirectoryPath()

fable.preprocessor fable.preprocessor.process Feb 14, 2007

Returns:

the directoryPath

setDirectoryPath

public void setDirectoryPath(java.lang.String path)

fable.preprocessor fable.preprocessor.process Feb 14, 2007

Parameters:

path - the directoryPath to set

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getFabioFilesToProcess

public java.lang.String[] getFabioFilesToProcess(boolean flag)

Get files to process with the filter and also a good size comparing to the dark and/or the flood

Parameters:

flag -

Returns:

getFiles

public java.lang.String[] getFiles()

Returns:

A Tab with the names of the current files to process

setFiles

public void setFiles(java.lang.String[] _files)

Parameters:

_files - the current files to set. Warning : no fabio files loaded

setCurrentFilesFromFabio

public void setCurrentFilesFromFabio()

Parameters:

_files - the current files to set. Warning : no fabio files loaded

getFabioFiles

public java.util.Vector<FabioFile> getFabioFiles()

26 sept. 07

Returns:

a vector containing all edf files object

getFilteredfiles

public java.util.Vector<FabioFile> getFilteredfiles()

22 Jul 2007

Returns:

a vector containing filtered files

setComparator

public void setComparator(java.lang.String Key,
                          int dir)

getSortedFiles

public java.util.Vector<FabioFile> getSortedFiles()

This function is used to sort a vector of fabio files.

Returns:

a sorted vector of fabio files

addPropertyChangeListener

public void addPropertyChangeListener(org.eclipse.jface.util.IPropertyChangeListener listener)

Register or remove listeners to sample changes

removePropertyrChangeListener

public void removePropertyrChangeListener(org.eclipse.jface.util.IPropertyChangeListener listener)

removeFiles

public void removeFiles()

removeFileAt

public void removeFileAt(int indice)

removeFabioFile

public void removeFabioFile(FabioFile f)

setFilter

public void setFilter(java.lang.String s_filter)

fireSomeHeaderValuesLoaded

public void fireSomeHeaderValuesLoaded()

update plot every 10 files read

addSampleListener

public void addSampleListener(ISampleListener pl)

removeSampleListener

public void removeSampleListener(ISampleListener pl)

getName

public java.lang.String getName()

Returns:

stem of sample

getFirst

public int getFirst()

Returns:

the number of the first file

Throws:

FabioFileException

FabioFileException

setFirst

public void setFirst(int one)

setlast

public void setlast(int l)

getLast

public int getLast()

getFileFormat

public java.lang.String getFileFormat()

Returns:

the number of the last file

Throws:

FabioFileException

setFileFormat

public void setFileFormat(java.lang.String format)

setNDigits

public void setNDigits(java.lang.String val)

getNDigits

public java.lang.String getNDigits()

setPeaksearchOutfile

public void setPeaksearchOutfile(java.lang.String outfile)

getPeaksearchoutStem

public java.lang.String getPeaksearchoutStem()

getHeaderValues

public double[] getHeaderValues(java.lang.String key)
                         throws SampleException

used in Header plot

Parameters:

key - header key with number values. Except for the date.

Returns:

double[] all double values for this key for all fabio files in this sample

Throws:

SampleException

addHeaderValues

public void addHeaderValues(java.lang.String key,
                            double[] values)

getHeaderValuesDiff

public double[] getHeaderValuesDiff(java.lang.String key)
                             throws SampleException

used in Header plot

Parameters:

key - header key

Returns:

double[] all double values for this key for all fabio files in this sample

Throws:

SampleException

setCurrentFile

public void setCurrentFile(FabioFile fabio)

getCurrentFabioFile

public FabioFile getCurrentFabioFile()

isDirectory

public boolean isDirectory()

Returns:

true if files have been set to this sampl by selecting a directory.

setDirectory

public void setDirectory(boolean isDirectory)

Parameters:

isDirectory - true if files have been loaded from a folder. False if files have been selected from files menu.

getFilter

public java.lang.String getFilter()

isShowInNavigator

public boolean isShowInNavigator()

07/08/08 Gaelle since peaksearchSptView is speaking with imageviewer

Returns:

true if this sample must be shown in the navigator

setShowInNavigator

public void setShowInNavigator(boolean showInNavigator)

07/08/08 Gaelle since peaksearchSptView is speaking with imageviewer

Parameters:

showInNavigator - true if sample must be shown in sample navigator

setValide

public void setValide(boolean b)

getStem

public java.lang.String getStem()

This method init a file serie in python object. It is based on filteredfabio file.

Returns:

the stem taken from python code.

updateFabioFiles

public void updateFabioFiles(java.io.File[] files)
                      throws FabioFileException

Update the list of FabioFiles by replacing the current list with the new list of file names. For efficiency reasons reuse the existing FabioFile if exists in the old list.

Parameters:

Files - [] files - new list of files to replace existing list in Sample

Throws:

FabioFileException

setStem

public void setStem(java.lang.String val)

Parameters:

val - the stem to set to this file serie