fable.python
Class FabioFile

java.lang.Object
  fable.python.FabioFile

All Implemented Interfaces:

java.lang.Comparable<java.lang.Object>, java.util.EventListener, org.eclipse.jface.util.IPropertyChangeListener

public class FabioFile
extends java.lang.Object
implements java.lang.Comparable<java.lang.Object>, org.eclipse.jface.util.IPropertyChangeListener

The FabioFile class is used to read files using the Python fabio package. It uses the Jep interpreter to call Python. It can be used in multi-threaded Java environments. Different thread should supply their own Jep interpreter. The image data is stored in a cache so that the last N images will be read from the cache and not from disk. This will be reflected in the time to read i.e. it will be zero. The cache size can be increased in function of the memory available. It is currently set to 20 i.e. 20*16 MB.

Author:

Andy Gotz + Gaelle Suchet

Field Summary

boolean	headerRead
boolean	imageRead

Constructor Summary

FabioFile(java.lang.String _fullFileName)
Create a FabioFile object which be able to read Fabio files via the fabio Python module.

Method Summary

void	acquire()
void	addHeaderInfo(java.lang.String key, java.lang.String value) Add new key in header info
void	addIndex(int index) Gaelle : add a sample Vector index for this fabioFile
int	compareTo(java.lang.Object other)
int	compareTo(java.lang.String key, java.lang.Object other)
int	getBytesPerPixel()
java.lang.String	getFileName() return short file name i.e.
java.lang.String	getFileNumber()
boolean	getFlag()
java.lang.String	getFullFilename()
java.lang.String	getFullFileName()
int	getHeight() get image height
float[]	getImageAsFloat() Return image as floating pint array
float[]	getImageAsFloat(FableJep jep) Return image as floating pint array
int[]	getImageAsInt() return image as int by converting the float image to int, do not keep the image in memory
java.lang.String[]	getKeys()
java.util.Vector<java.lang.String>	getKeysAsListedInHeader()
float	getMaximum() return maximum value in image
float	getMean() return mean value in image
float	getMinimum() return minimum value in image
java.lang.String	getStems() 8 janv.
long	getTimeToReadImage() get time to read image in ms
java.lang.String	getValue(java.lang.String key)
int	getWidth() get image width
void	loadHeader() Load only the header and not the image.
void	loadHeader(FableJep fableJep) Load only the header and not the image.
void	propertyChange(org.eclipse.jface.util.PropertyChangeEvent event)
void	readImage() read image into memory
void	readImageAsFloat() read image as float into memory
void	readImageAsFloat(FableJep fableJep) read image as float into memory
void	release()
void	setFlag(boolean b)
void	setFullFileName(java.lang.String fullfilename) Set the fullfilename of fabio file if different from header
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

headerRead

public boolean headerRead

imageRead

public boolean imageRead

Constructor Detail

FabioFile

public FabioFile(java.lang.String _fullFileName)
          throws FabioFileException

Create a FabioFile object which be able to read Fabio files via the fabio Python module.

Parameters:

fileName -

Throws:

FabioFileException

Method Detail

acquire

public void acquire()

release

public void release()

setFullFileName

public void setFullFileName(java.lang.String fullfilename)

Set the fullfilename of fabio file if different from header

Parameters:

fullfilename -

getFullFileName

public java.lang.String getFullFileName()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

loadHeader

public void loadHeader()
                throws FabioFileException

Load only the header and not the image. loadHeader() uses the python fabio module to read the header.

Throws:

FabioFileException

java.lang.Throwable

loadHeader

public void loadHeader(FableJep fableJep)
                throws FabioFileException

Load only the header and not the image. loadHeader() uses the python fabio module to read the header. Use the jep interpreter provided by the callee. This is needed for reading headers in multithreaded environments.

Throws:

FabioFileException

addHeaderInfo

public void addHeaderInfo(java.lang.String key,
                          java.lang.String value)

Add new key in header info

getKeys

public java.lang.String[] getKeys()
                           throws FabioFileException,
                                  java.lang.Throwable

Returns:

Fabio header keys

Throws:

FabioFileException

java.lang.Throwable

getKeysAsListedInHeader

public java.util.Vector<java.lang.String> getKeysAsListedInHeader()
                                                           throws FabioFileException,
                                                                  java.lang.Throwable

Returns:

a vector of EDF Header Keys

Throws:

FabioFileException

java.lang.Throwable

getValue

public java.lang.String getValue(java.lang.String key)
                          throws FabioFileException

Parameters:

key - the header key

Returns:

the value of the key header

Throws:

FabioFileException

java.lang.Throwable

addIndex

public void addIndex(int index)

Gaelle : add a sample Vector index for this fabioFile

Parameters:

index - index in sample vector file

getFullFilename

public java.lang.String getFullFilename()

getFileName

public java.lang.String getFileName()

return short file name i.e. without the path

Returns:

short file name

getTimeToReadImage

public long getTimeToReadImage()

get time to read image in ms

Returns:

time to took to read image and make a copy

getStems

public java.lang.String getStems()

8 janv. 08

Returns:

fabio file stem name

getFileNumber

public java.lang.String getFileNumber()

Returns:

file number, even for bruker format //TODO test with bruker files

getWidth

public int getWidth()
             throws java.lang.Throwable

get image width

Returns:

image width

Throws:

java.lang.Throwable

getHeight

public int getHeight()
              throws java.lang.Throwable

get image height

Returns:

image height

Throws:

java.lang.Throwable

getBytesPerPixel

public int getBytesPerPixel()

readImage

public void readImage()
               throws java.lang.Throwable

read image into memory

Throws:

java.lang.Throwable

readImageAsFloat

public void readImageAsFloat()
                      throws java.lang.Throwable

read image as float into memory

Throws:

java.lang.Throwable

readImageAsFloat

public void readImageAsFloat(FableJep fableJep)
                      throws java.lang.Throwable

read image as float into memory

Throws:

java.lang.Throwable

getImageAsFloat

public float[] getImageAsFloat()
                        throws java.lang.Throwable

Return image as floating pint array

Returns:

image as floating point array

Throws:

java.lang.Throwable

getImageAsFloat

public float[] getImageAsFloat(FableJep jep)

Return image as floating pint array

Returns:

image as floating point array

getImageAsInt

public int[] getImageAsInt()
                    throws java.lang.Throwable

return image as int by converting the float image to int, do not keep the image in memory

Returns:

image as integer array

Throws:

java.lang.Throwable

getMinimum

public float getMinimum()
                 throws java.lang.Throwable

return minimum value in image

Returns:

image minimum

Throws:

java.lang.Throwable

getMaximum

public float getMaximum()
                 throws java.lang.Throwable

return maximum value in image

Returns:

image maximum

Throws:

java.lang.Throwable

getMean

public float getMean()
              throws java.lang.Throwable

return mean value in image

Returns:

image mean

Throws:

java.lang.Throwable

setFlag

public void setFlag(boolean b)

getFlag

public boolean getFlag()

compareTo

public int compareTo(java.lang.Object other)

Specified by:

compareTo in interface java.lang.Comparable<java.lang.Object>

compareTo

public int compareTo(java.lang.String key,
                     java.lang.Object other)

Parameters:

key - the key used to sort

other - the fableFile

Returns:

0 if equal, 1 if keyValue for other is greater than this,-1 if otherValue

propertyChange

public void propertyChange(org.eclipse.jface.util.PropertyChangeEvent event)

Specified by:

propertyChange in interface org.eclipse.jface.util.IPropertyChangeListener