net.sf.basedb.core
Class SpotImages

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.ChildItem<SpotImagesData>
          net.sf.basedb.core.SpotImages

All Implemented Interfaces:

AccessControlled, Identifiable

public class SpotImages
extends ChildItem<SpotImagesData>

Holds settings for creating small spot iamges from 1-3 image files and the raw data information for a single raw bioassay.

For performance and disk space reasons the spot images are placed NxN (N given by the NUM_SPOT_IMAGES constant) into JPEG files, which are put in a zip file.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2010-08-13 10:50:27 +0200 (Fri, 13 Aug 2010) $

Field Summary

static int	NUM_SPOT_IMAGES The number of spot images to place side by side in each file.
static Item	TYPE The type of item represented by this class.

Constructor Summary

SpotImages(SpotImagesData data)

Method Summary

private RenderedImage	convertTiffImage(RenderedImage image, byte[] conversionTable) Convert TIFF image from 16 bits to 8 bits if needed
void	createSpotImages(File spotImagesFile, int xScale, int yScale, int xOffset, int yOffset, int spotsize, float gamma, float quality, File redImageFile, File greenImageFile, File blueImageFile, ProgressReporter progress) Creates spot images with 8 bits per channel, from source images.
void	disconnectSpotImages() Disconnects the generated spot image file from this item.
File	getBlueImageFile() Get the file which was used for the blue channel in the spot images.
float	getGamma() Get the gamma correction value.
File	getGreenImageFile() Get the file which was used for the green channel in the spot images.
(package private) static SpotImages	getNew(DbControl dc, RawBioAssay rawBioAssay) Create a new Image item.
float	getQuality() Get the quality used for the jpeg compression.
RawBioAssay	getRawBioAssay() Get the raw bioassay the spot images belongs to.
File	getRedImageFile() Get the file which was used for the red channel in the spot images.
(package private) SharedData	getSharedParent() Get the shareable parent item of this child item.
SpotImage	getSpotImage(RawData data) Get a spot as a PNG image.
List<SpotImage>	getSpotImages(List<RawData> data) Get a list of spot PNG images from a list of RawData.
File	getSpotImagesFile() Get the file which holds the spot images.
int	getSpotsize() Get the size of the spots in pixels.
Item	getType() Get the type of item represented by the object.
int	getXOffset() Get the X-axis offset used to convert data coordinates to image pixel values: xPixel = (xData - xOffset) / xScale.
int	getXScale() Get the X-axis scale factor used to convert data coordinates to image pixel values: xPixel = (xData - xOffset) / xScale.
int	getYOffset() Get the Y-axis offset used to convert data coordinates to image pixel values: yPixel = (yData - yOffset) / yScale.
int	getYScale() Get the Y-axis scale factor used to convert data coordinates to image pixel values: yPixel = (yData - yOffset) / yScale.
private boolean	insideImage(float x, float y, int spotsize, int width, int height) Check if entire spot is inside the soure image.
private RenderedOp	loadTiffImage(File file, int band) Loads a TIFF file and returns a RenderedOp.
private RenderedOp	mergeColorImages() Merge the three color images into a single image.
private RenderedOp	rescaleColors(RenderedOp image, boolean red, boolean green, boolean blue) Rescale the colors of the images so we use the whole 16-bit color range.
private void	saveImage(ZipOutputStream zipFileStream, String fileName, RenderedImage image, float quality) Saving an image as jpeg and putting it in a zip file
private void	setBlueImageFile(File blueImageFile)
private void	setGamma(float gamma)
private void	setGreenImageFile(File greenImageFile)
private void	setQuality(float quality)
(package private) void	setRawBioAssay(RawBioAssay rawBioAssay) Set the raw bioassay the spot images belongs to.
private void	setRedImageFile(File redImageFile)
private void	setSpotsize(int spotsize)
private void	setXOffset(int xOffset)
private void	setXScale(int xScale)
private void	setYOffset(int yOffset)
private void	setYScale(int yScale)

Methods inherited from class net.sf.basedb.core.ChildItem

getPermissionForWriteDeleteAndCreate, getPluginPermissions, initPermissions

Methods inherited from class net.sf.basedb.core.BasicItem

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, toString, toTransferable, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.SPOTIMAGES, getType()

NUM_SPOT_IMAGES

public static final int NUM_SPOT_IMAGES

The number of spot images to place side by side in each file. Each file contains NxN spot images.

See Also:

Constant Field Values

Constructor Detail

SpotImages

SpotImages(SpotImagesData data)

Method Detail

getNew

static SpotImages getNew(DbControl dc,
                         RawBioAssay rawBioAssay)
                  throws BaseException

Create a new Image item.

Parameters:

dc - The DbControl which will be used for permission checking and database access

rawBioAssay - The RawBioAssay to create spot images for

Returns:

The new SpotImages item

Throws:

BaseException - If there is an error

See Also:

RawBioAssay.getSpotImages()

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Returns:

A value indicating the type of item

getSharedParent

SharedData getSharedParent()

Description copied from class: ChildItem

Get the shareable parent item of this child item. This is used by the ChildItem.initPermissions(int, int) method to calculate the logged in user's permissions for the child item.

Specified by:

getSharedParent in class ChildItem<SpotImagesData>

Returns:

The parent item

getRawBioAssay

public RawBioAssay getRawBioAssay()
                           throws PermissionDeniedException,
                                  BaseException

Get the raw bioassay the spot images belongs to.

Returns:

The RawBioAssay item

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission

BaseException - If there is another error

setRawBioAssay

void setRawBioAssay(RawBioAssay rawBioAssay)
              throws PermissionDeniedException,
                     InvalidDataException

Set the raw bioassay the spot images belongs to. Can only be set on a new item.

Throws:

InvalidDataException - If the raw bioassay is null

PermissionDeniedException

getXScale

public int getXScale()

Get the X-axis scale factor used to convert data coordinates to image pixel values: xPixel = (xData - xOffset) / xScale. The scale is always a positive integer.

setXScale

private void setXScale(int xScale)
                throws InvalidDataException

Throws:

InvalidDataException

getYScale

public int getYScale()

Get the Y-axis scale factor used to convert data coordinates to image pixel values: yPixel = (yData - yOffset) / yScale. The scale is always a positive integer.

setYScale

private void setYScale(int yScale)
                throws InvalidDataException

Throws:

InvalidDataException

getXOffset

public int getXOffset()

Get the X-axis offset used to convert data coordinates to image pixel values: xPixel = (xData - xOffset) / xScale. The offset may be positive or negative.

setXOffset

private void setXOffset(int xOffset)

getYOffset

public int getYOffset()

Get the Y-axis offset used to convert data coordinates to image pixel values: yPixel = (yData - yOffset) / yScale. The offset may be positive or negative.

setYOffset

private void setYOffset(int yOffset)

getSpotsize

public int getSpotsize()

Get the size of the spots in pixels. The size is a positive integer.

setSpotsize

private void setSpotsize(int spotsize)
                  throws InvalidDataException

Throws:

InvalidDataException

getQuality

public float getQuality()

Get the quality used for the jpeg compression. The quality is a number between 0.0 and 1.0, with 1.0 indicating highest quality.

setQuality

private void setQuality(float quality)
                 throws InvalidDataException

Throws:

InvalidDataException

getGamma

public float getGamma()

Get the gamma correction value. The value is always greater than or equal to 1.0.

setGamma

private void setGamma(float gamma)
               throws InvalidDataException

Throws:

InvalidDataException

getRedImageFile

public File getRedImageFile()
                     throws PermissionDeniedException,
                            BaseException

Get the file which was used for the red channel in the spot images.

Returns:

A file object or null if no file was used

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the file

BaseException - If there is another error

setRedImageFile

private void setRedImageFile(File redImageFile)
                      throws PermissionDeniedException

Throws:

PermissionDeniedException

getGreenImageFile

public File getGreenImageFile()
                       throws PermissionDeniedException,
                              BaseException

Get the file which was used for the green channel in the spot images.

Returns:

A file object or null if no file was used

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the file

BaseException - If there is another error

setGreenImageFile

private void setGreenImageFile(File greenImageFile)
                        throws PermissionDeniedException

Throws:

PermissionDeniedException

getBlueImageFile

public File getBlueImageFile()
                      throws PermissionDeniedException,
                             BaseException

Get the file which was used for the blue channel in the spot images.

Returns:

A file object or null if no file was used

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the file

BaseException - If there is another error

setBlueImageFile

private void setBlueImageFile(File blueImageFile)
                       throws PermissionDeniedException

Throws:

PermissionDeniedException

getSpotImagesFile

public File getSpotImagesFile()
                       throws PermissionDeniedException,
                              BaseException

Get the file which holds the spot images. The file is a zip file with a number of images each holding several spots.

Returns:

A file object or null if no file exists

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the file

BaseException - If there is another error

disconnectSpotImages

public void disconnectSpotImages()
                          throws PermissionDeniedException,
                                 BaseException

Disconnects the generated spot image file from this item. To delete the file you must also call the DbControl.deleteItem(BasicItem) method.

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

BaseException - If there is an error

createSpotImages

public void createSpotImages(File spotImagesFile,
                             int xScale,
                             int yScale,
                             int xOffset,
                             int yOffset,
                             int spotsize,
                             float gamma,
                             float quality,
                             File redImageFile,
                             File greenImageFile,
                             File blueImageFile,
                             ProgressReporter progress)
                      throws PermissionDeniedException,
                             InvalidDataException,
                             BaseException

Creates spot images with 8 bits per channel, from source images. The spot images is group together, 16x16, into larger images. The larger images are stored in a zip file.

Parameters:

spotImagesFile - The file which will hold the created zip file with the spot images. Any existing content will be replaced

xScale - X-axis scale factor from data values to pixel values, must be > 0

yScale - Y-axis scale factor from data values to pixel values, must be > 0

xOffset - X offset in data value, can be any value

yOffset - Y offset in data value, can be any value

spotsize - The size of the spot i pixels, must be > 0

gamma - Gamma correction value, must be > 1.0

quality - The JPEG compression qualtity, must be a value between 0.0 and 1.0

redImageFile - The file containing the image to be used for the red channel or null

greenImageFile - The file containing the image to be used for the green channel or null

blueImageFile - The file containing the image to be used for the blue channel or null

progress - A ProgressReporter object if the calling client is interested in the progress or null if not

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay or to the specified spot images file or doesn't have use permission for any of the image files

InvalidDataException - If the directory or file name is null or all image files are null, or any of the other values are out of range

ItemAlreadyExistsException - If a file with the same name already exists in the directory

BaseException - If there is another error

getSpotImage

public SpotImage getSpotImage(RawData data)
                       throws InvalidDataException,
                              ItemNotFoundException,
                              BaseException

Get a spot as a PNG image. It is returned as a SpotImage.

Parameters:

data - A RawData object representing the spot

Returns:

SpotImage as a PNG image

Throws:

InvalidDataException - If the data object is null

ItemNotFoundException - If a spot image for the position is not found

BaseException - If there is another error

getSpotImages

public List<SpotImage> getSpotImages(List<RawData> data)
                              throws InvalidDataException,
                                     ItemNotFoundException,
                                     PermissionDeniedException,
                                     BaseException

Get a list of spot PNG images from a list of RawData. It is returned as a list of SpotImage objects. The returned list will be mapped to the incomming list. If a spot image is not found, null will be put at its position in the list. That will make both list to always have the same size. It is more efficient having the list sorted by the RawData's position.

Parameters:

data - A list of RawData objects representing the spots

Returns:

List of SpotImage objects as PNG images

Throws:

InvalidDataException - If the list of data is null

ItemNotFoundException - If the file with the spot images is not found

PermissionDeniedException - If the logged in user doesn't have read permission for the file continaing the spot images

BaseException - If there is another error

mergeColorImages

private RenderedOp mergeColorImages()
                             throws BaseException

Merge the three color images into a single image. If any of the color files are missing an empty band will be used for that color.

Returns:

The merged image

Throws:

BaseException

rescaleColors

private RenderedOp rescaleColors(RenderedOp image,
                                 boolean red,
                                 boolean green,
                                 boolean blue)

Rescale the colors of the images so we use the whole 16-bit color range. The empty bands are not include in the calculation.

Parameters:

image - Image to rescale

red - TRUE if the red channel isn't empty and should be included in the calculation

green - TRUE if green red channel isn't empty and should be included in the calculation

blue - TRUE if the blue channel isn't empty and should be included in the calculation

Returns:

Rescaled image

loadTiffImage

private RenderedOp loadTiffImage(File file,
                                 int band)
                          throws BaseException

Loads a TIFF file and returns a RenderedOp.

Parameters:

file - A Base File object pointing to the image to be loaded

band - The index of the TIFF directory to load

Throws:

BaseException

convertTiffImage

private RenderedImage convertTiffImage(RenderedImage image,
                                       byte[] conversionTable)
                                throws BaseException

Convert TIFF image from 16 bits to 8 bits if needed

Parameters:

image - TIFF image to convert

conversionTable - Conversion table

Returns:

A RenderedOp object of the image

Throws:

BaseException - If there is an error

saveImage

private void saveImage(ZipOutputStream zipFileStream,
                       String fileName,
                       RenderedImage image,
                       float quality)
                throws IOException

Saving an image as jpeg and putting it in a zip file

Parameters:

zipFileStream - Destination stream to where the JPEG is saved to

fileName - The filename of the image

image - The image to be saved

quality - The quality setting of the JPEG image

Throws:

IOException

insideImage

private boolean insideImage(float x,
                            float y,
                            int spotsize,
                            int width,
                            int height)

Check if entire spot is inside the soure image.

Parameters:

x - Spot x coordinate

y - Spot y coordinate

spotsize - Spot width and height

width - Source image width

height - Source image height