Package gda.device.detector.pco

Class PCOTomography

java.lang.Object

gda.factory.FindableBase

gda.device.detector.pco.PCOTomography

All Implemented Interfaces:

Findable, ITomographyDetector

@ServiceInterface(ITomographyDetector.class)
public class PCOTomography
extends FindableBase
implements ITomographyDetector

Tomography implementation for the PCO camera.

Constructor Summary

Constructors

Constructor	Description
PCOTomography()

Method Summary

Modifier and Type	Method	Description
void	abort()	This is called when the acquisition and any file capture activities need to be stopped.
void	acquireMJpeg(Double expTime, int binX, int binY, Double scale, Double offset)	The MJpeg streamer is set-up and made ready.
String	demandRaw(Double acqTime, String demandRawFilePath, String demandRawFileName, Boolean isHdf, Boolean isFlatFieldCorrectionRequired, Boolean demandWhileStreaming)
void	disableDarkSubtraction()	Request to disable the dark subtraction flag on the area detector.
void	disableFlatField()	Sets the flat field correction on the proc plug-ins of the detector to "disabled".
void	enableDarkSubtraction()	Request to enable the dark subtraction flag on the area detector.
void	enableFlatField()	Sets the flat field correction on the proc plug-ins of the detector to "enabled".
String	getDetectorName()
double	getMaxIntensity()
IPCODetector	getPcoDetector()
double	getProc1Scale()
Integer	getRoi1BinX()
Integer	getRoi2BinX()
String	getTiffFileName()
String	getTiffFilePath()
String	getTiffFileTemplate()
String	getTiffImageFileName()
void	initDetector()	Invoked to initialise the detector properties - in case of the PCO detector, an image needs to be taken so that the array values are passed to all the plugins.
boolean	isAcquiring()
boolean	isHdfFormat()
void	resetAfterTiltToInitialValues()	Reset the values of minY and maxY the initial values
void	resetAll()	In addition to its own resets, this method also calls reset on all plugins
void	resetFileFormat()	Resets only the file format
void	resumeAcquisition()	method called when acquisition is stopped to update exposure time - should continue where it left off
void	setExposureTime(double collectionTime)	Exposure time on the detector to be set when this method is invoked.
void	setExternalTriggered(Boolean val)	The PCO detector can be controlled using an external hardware trigger - however, for the tomography alignment it is important that this is set to false
void	setHdfFormat(boolean hdfFormat)	Sets the file saver format to hdf.
void	setMaxIntensity(double maxIntensity)
void	setOffsetAndScale(double offset, double scale)	Set offset and scale on the proc plugins of the detector.
void	setPcoDetector(IPCODetector pcoDetector)
void	setProc1Scale(double newScale)	Update the scale value on the proc1 plugin.
void	setProcScale(double factor)	Sets the proc scale factor to the given value
void	setRoi1ScalingDivisor(double divisor)	Set the scaling divisor on the ROI1
void	setTiffFileNumber(int fileNumber)	Sets the file number on the tiff plugin - this will be used when the plugin writes a tiff file the next time.
void	setupForTilt(int minY, int maxY, int minX, int maxX)	The tilt alignment is generally done on a known sample - the data that needs to be collected can be cropped on the y axis so that data processing can be relieved of memory issues.
void	setupHistoStatCollection(int binSize)	method invoked to call histogram stat collection
void	setupZoomMJpeg(Rectangle roi, Point bin)	This sets up the MJpeg streamer for the zoomed images.
void	setZoomRoiStart(Point roiStart)	Set roi2 roiStart to the values provided.
String	takeDark(int numberOfImages, double acqTime, String fileLocation, String fileName, String filePathTemplate)	This method is invoked when dark images need to be taken.
String	takeFlat(double acqTime, int numberOfImages, String fileLocation, String fileName, String filePathTemplate)	This method is invoked when a flat image needs to be taken

Methods inherited from class gda.factory.FindableBase

equals, getName, hashCode, setName

Methods inherited from class java.lang.Object

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

Methods inherited from interface gda.factory.Findable

getName, setName

Constructor Details

PCOTomography

public PCOTomography()

Method Details

getPcoDetector

public IPCODetector getPcoDetector()

setPcoDetector

public void setPcoDetector(IPCODetector pcoDetector)

setExposureTime

public void setExposureTime(double collectionTime)
                     throws Exception

Description copied from interface: ITomographyDetector

Exposure time on the detector to be set when this method is invoked.

Specified by:

setExposureTime in interface ITomographyDetector

Parameters:

collectionTime -

Throws:

Exception

acquireMJpeg

public void acquireMJpeg(Double expTime,
 int binX,
 int binY,
 Double scale,
 Double offset)
                  throws Exception

Description copied from interface: ITomographyDetector

The MJpeg streamer is set-up and made ready. The detector acquisition is started in "Continuous" mode. The proc scale factor is set on the proc plugin

Specified by:

acquireMJpeg in interface ITomographyDetector

Parameters:

expTime -

binX -

binY -

scale -

offset -

Throws:

Exception

resumeAcquisition

public void resumeAcquisition()
                       throws Exception

Description copied from interface: ITomographyDetector

method called when acquisition is stopped to update exposure time - should continue where it left off

Specified by:

resumeAcquisition in interface ITomographyDetector

Throws:

Exception

setZoomRoiStart

public void setZoomRoiStart(Point roiStart)
                     throws Exception

Description copied from interface: ITomographyDetector

Set roi2 roiStart to the values provided.

Specified by:

setZoomRoiStart in interface ITomographyDetector

Parameters:

roiStart -

Throws:

Exception

setupZoomMJpeg

public void setupZoomMJpeg(Rectangle roi,
 Point bin)
                    throws Exception

Description copied from interface: ITomographyDetector

This sets up the MJpeg streamer for the zoomed images. On the tomography alignment GUI the zoomed images are displayed on the right. The display ROI is set and the bin values are set.

Specified by:

setupZoomMJpeg in interface ITomographyDetector

Parameters:

roi -

bin -

Throws:

Exception

getRoi1BinX

public Integer getRoi1BinX()
                    throws Exception

Specified by:

getRoi1BinX in interface ITomographyDetector

Returns:

roi1BinX - the bin X value from the roi1 plugin of the detector.

Throws:

Exception

getRoi2BinX

public Integer getRoi2BinX()
                    throws Exception

Specified by:

getRoi2BinX in interface ITomographyDetector

Returns:

roi2BinX - the bin X value from the roi1 plugin of the detector.

Throws:

Exception

enableFlatField

public void enableFlatField()
                     throws Exception

Description copied from interface: ITomographyDetector

Sets the flat field correction on the proc plug-ins of the detector to "enabled".

Specified by:

enableFlatField in interface ITomographyDetector

Throws:

Exception

disableFlatField

public void disableFlatField()
                      throws Exception

Description copied from interface: ITomographyDetector

Sets the flat field correction on the proc plug-ins of the detector to "disabled".

Specified by:

disableFlatField in interface ITomographyDetector

Throws:

Exception

getTiffFilePath

public String getTiffFilePath()
                       throws Exception

Specified by:

getTiffFilePath in interface ITomographyDetector

Returns:

tillFilePath - the file location of the most recent tiff collected. The path is generally calculated using the location and the template.

Throws:

Exception

getTiffFileName

public String getTiffFileName()
                       throws Exception

Specified by:

getTiffFileName in interface ITomographyDetector

Returns:

tiff file name - the file name of the most recent tiff collected.

Throws:

Exception

getTiffFileTemplate

public String getTiffFileTemplate()
                           throws Exception

Specified by:

getTiffFileTemplate in interface ITomographyDetector

Returns:

tiff file template - the template for writing a tiff file.

Throws:

Exception

setTiffFileNumber

public void setTiffFileNumber(int fileNumber)
                       throws Exception

Description copied from interface: ITomographyDetector

Sets the file number on the tiff plugin - this will be used when the plugin writes a tiff file the next time.

Specified by:

setTiffFileNumber in interface ITomographyDetector

Parameters:

fileNumber -

Throws:

Exception

demandRaw

public String demandRaw(Double acqTime,
 String demandRawFilePath,
 String demandRawFileName,
 Boolean isHdf,
 Boolean isFlatFieldCorrectionRequired,
 Boolean demandWhileStreaming)
                 throws Exception

Specified by:

demandRaw in interface ITomographyDetector

Parameters:

acqTime - - the exposure time

demandRawFilePath - - the file path (folder) where the file needs to be saved - this is set on the tiff filepath

demandRawFileName - - the filename that needs to be set on the tiff plugin.

isHdf - - flag to say whether the file should be saved as a hdf or not.

isFlatFieldCorrectionRequired - - flag to say whether flat field correction is required or not.

demandWhileStreaming - - flag to say whether the demand raw must happen while the detector is in continuous streaming mode.

Returns:

fileName of the raw image - the complete file path of the file written by the file saver plugin of the detector.

Throws:

Exception

takeFlat

public String takeFlat(double acqTime,
 int numberOfImages,
 String fileLocation,
 String fileName,
 String filePathTemplate)
                throws Exception

Description copied from interface: ITomographyDetector

This method is invoked when a flat image needs to be taken

Specified by:

takeFlat in interface ITomographyDetector

Parameters:

acqTime - - exposure time to be set on the detector.

numberOfImages - - number of images to recurse through. Only the last should be saved to the file system.

fileLocation - - Filepath of the tiff file that is saved after a flat image is captured.

fileName - - file name of the tiff file that needs to be captured.

filePathTemplate - - template of the tiff file that needs to be saved.

Returns:

the file name that the flat is saved to - the full file name(filePath + filename) of the tiff file that is saved to the file system.

Throws:

Exception

getTiffImageFileName

public String getTiffImageFileName()
                            throws Exception

Specified by:

getTiffImageFileName in interface ITomographyDetector

Returns:

tiff image name depending on the os env of the ioc.

Throws:

Exception

takeDark

public String takeDark(int numberOfImages,
 double acqTime,
 String fileLocation,
 String fileName,
 String filePathTemplate)
                throws Exception

Description copied from interface: ITomographyDetector

This method is invoked when dark images need to be taken.

Specified by:

takeDark in interface ITomographyDetector

Parameters:

numberOfImages - - number of dark images to be taken.

acqTime - - exposure time at which the dark image should be captured.

Throws:

Exception

abort

public void abort()
           throws Exception

Description copied from interface: ITomographyDetector

This is called when the acquisition and any file capture activities need to be stopped.

Specified by:

abort in interface ITomographyDetector

Throws:

Exception

setHdfFormat

public void setHdfFormat(boolean hdfFormat)

Description copied from interface: ITomographyDetector

Sets the file saver format to hdf. The detector then delegates any file saving activity to the hdf plugin on the detector.

Specified by:

setHdfFormat in interface ITomographyDetector

Parameters:

hdfFormat -

resetFileFormat

public void resetFileFormat()
                     throws Exception

Description copied from interface: ITomographyDetector

Resets only the file format

Specified by:

resetFileFormat in interface ITomographyDetector

Throws:

Exception

isHdfFormat

public boolean isHdfFormat()

Specified by:

isHdfFormat in interface ITomographyDetector

Returns:

true if the file saving format is 'hdf'.

resetAll

public void resetAll()
              throws Exception

Description copied from interface: ITomographyDetector

In addition to its own resets, this method also calls reset on all plugins

Specified by:

resetAll in interface ITomographyDetector

Throws:

Exception

setupForTilt

public void setupForTilt(int minY,
 int maxY,
 int minX,
 int maxX)
                  throws Exception

Description copied from interface: ITomographyDetector

The tilt alignment is generally done on a known sample - the data that needs to be collected can be cropped on the y axis so that data processing can be relieved of memory issues.

Specified by:

setupForTilt in interface ITomographyDetector

Parameters:

minY - - the minimum y value

maxY - - the maximum y value

minX -

maxX -

Throws:

Exception

resetAfterTiltToInitialValues

public void resetAfterTiltToInitialValues()
                                   throws Exception

Description copied from interface: ITomographyDetector

Reset the values of minY and maxY the initial values

Specified by:

resetAfterTiltToInitialValues in interface ITomographyDetector

Throws:

Exception

setProcScale

public void setProcScale(double factor)
                  throws Exception

Description copied from interface: ITomographyDetector

Sets the proc scale factor to the given value

Specified by:

setProcScale in interface ITomographyDetector

Parameters:

factor - - value to which the proc scale should be set

Throws:

Exception

setRoi1ScalingDivisor

public void setRoi1ScalingDivisor(double divisor)
                           throws Exception

Description copied from interface: ITomographyDetector

Set the scaling divisor on the ROI1

Specified by:

setRoi1ScalingDivisor in interface ITomographyDetector

Parameters:

divisor -

Throws:

Exception

getMaxIntensity

public double getMaxIntensity()

setMaxIntensity

public void setMaxIntensity(double maxIntensity)

getDetectorName

public String getDetectorName()

Specified by:

getDetectorName in interface ITomographyDetector

Returns:

name - name of the detector.

isAcquiring

public boolean isAcquiring()
                    throws DeviceException

Specified by:

isAcquiring in interface ITomographyDetector

Returns:

true if the detector is busy; false otherwise.

Throws:

DeviceException

setExternalTriggered

public void setExternalTriggered(Boolean val)

Description copied from interface: ITomographyDetector

The PCO detector can be controlled using an external hardware trigger - however, for the tomography alignment it is important that this is set to false

Specified by:

setExternalTriggered in interface ITomographyDetector

Parameters:

val -

initDetector

public void initDetector()
                  throws Exception

Description copied from interface: ITomographyDetector

Invoked to initialise the detector properties - in case of the PCO detector, an image needs to be taken so that the array values are passed to all the plugins.

Specified by:

initDetector in interface ITomographyDetector

Throws:

Exception

disableDarkSubtraction

public void disableDarkSubtraction()
                            throws Exception

Description copied from interface: ITomographyDetector

Request to disable the dark subtraction flag on the area detector.

Specified by:

disableDarkSubtraction in interface ITomographyDetector

Throws:

Exception

enableDarkSubtraction

public void enableDarkSubtraction()
                           throws Exception

Description copied from interface: ITomographyDetector

Request to enable the dark subtraction flag on the area detector.

Specified by:

enableDarkSubtraction in interface ITomographyDetector

Throws:

Exception

getProc1Scale

public double getProc1Scale()
                     throws Exception

Specified by:

getProc1Scale in interface ITomographyDetector

Returns:

scale value from the proc1 plugin.

Throws:

Exception

setProc1Scale

public void setProc1Scale(double newScale)
                   throws Exception

Description copied from interface: ITomographyDetector

Update the scale value on the proc1 plugin.

Specified by:

setProc1Scale in interface ITomographyDetector

Parameters:

newScale -

Throws:

Exception

setOffsetAndScale

public void setOffsetAndScale(double offset,
 double scale)
                       throws Exception

Description copied from interface: ITomographyDetector

Set offset and scale on the proc plugins of the detector.

Specified by:

setOffsetAndScale in interface ITomographyDetector

Parameters:

offset -

scale -

Throws:

Exception

setupHistoStatCollection

public void setupHistoStatCollection(int binSize)
                              throws Exception

Description copied from interface: ITomographyDetector

method invoked to call histogram stat collection

Specified by:

setupHistoStatCollection in interface ITomographyDetector

Throws:

Exception