public class QParams extends Object
This class exists for compatibility purposes. Allows reading old files. There is also child class QParamsEsxhanger that is based on new file format. Because QParams is strongly integrated with QuimP it has been left.
BOAState.BOAp
Modifier and Type | Field and Description |
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double |
cortexWidth
The cortex width.
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double |
finalShrink
Shrink value.
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File[] |
fluTiffs
This field is set by direct call from ANA.
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static int |
NEW_QUIMP
The Constant NEW_QUIMP.
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static int |
OLD_QUIMP
The Constant OLD_QUIMP.
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protected int |
paramFormat
Indicates format of data file.
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static int |
QUIMP_11
The Constant QUIMP_11.
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protected File |
statsQP
The stats QP.
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Constructor and Description |
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QParams()
Instantiates a new q params.
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QParams(File p)
Read basic information from paQP file such as its name and path.
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Modifier and Type | Method and Description |
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File[] |
findParamFiles()
Traverse through current directory looking for paQP files.
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int |
getBlowup()
getBlowup.
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File |
getConvexFile()
getConvexFile name.
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File |
getCoordFile()
getCoordFile name.
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int |
getEndFrame()
getEndFrame.
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String |
getFileName()
Get the name of parameter file but without extension.
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File[] |
getFluFiles()
Get names of flu files.
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double |
getFrameInterval()
getFrameInterval.
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double |
getImageScale()
getImageScale.
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File |
getMotilityFile()
getMotilityFile name.
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double |
getNodeRes()
getNodeRes.
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File |
getOriginFile()
getOriginFile name.
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File |
getParamFile()
Get name of parameter file with extension (paQP).
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int |
getParamFormat()
Return loaded format.
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String |
getPath()
getPath.
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Path |
getPathasPath()
getPathasPath.
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File |
getSegImageFile()
Get name of BOA loaded image.
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File |
getSnakeQP()
Get snQP file name.
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int |
getStartFrame()
getStartFrame.
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File |
getStatsQP()
Get stats file name.
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File |
getxmapFile()
Get x coord map file.
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File |
getymapFile()
Get y coord map file.
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protected void |
guessOtherFileNames()
Generate names and handles of files associated with paQP that will be created in result of
analysis.
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boolean |
isEcmmHasRun()
Check if ECMM was run.
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void |
readParams()
Read the paQP file specified by paramFile
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void |
setBlowup(int blowup)
setBlowup.
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void |
setConvexFile(File convexFile)
setConvexFile name.
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void |
setCoordFile(File coordFile)
setCoordFile name.
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void |
setEndFrame(int endFrame)
setEndFrame.
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void |
setFrameInterval(double frameInterval)
setFrameInterval.
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void |
setImageScale(double imageScale)
setImageScale.
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void |
setMotilityFile(File motilityFile)
setMotilityFile name.
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void |
setNodeRes(double nodeRes)
setNodeRes.
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void |
setOriginFile(File originFile)
setOriginFile name.
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void |
setParamFile(File paramFile)
Set name of parameter file.
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void |
setSegImageFile(File segImageFile)
Set name of BOA loaded image.
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void |
setSnakeQP(File snakeQP)
Set snQP file name.
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void |
setStartFrame(int startFrame)
setStartFrame.
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void |
setStatsQP(File statsQP)
Set stats file name.
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void |
setxmapFile(File xmapFile)
Set x coord map file.
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void |
setymapFile(File ymapFile)
Set y coord map file.
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boolean |
verifyEcmminpsnQP()
Verify if ECMM was run on snQP file.
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void |
writeParams()
Write params.
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public static final int OLD_QUIMP
public static final int QUIMP_11
public static final int NEW_QUIMP
protected int paramFormat
protected File statsQP
public File[] fluTiffs
ANAp
public double finalShrink
public double cortexWidth
public QParams()
public QParams(File p)
p
- paQP file, should contain underscored cell number and absolute path.public boolean isEcmmHasRun()
public File getParamFile()
getPath()
public void setParamFile(File paramFile)
paramFile
- the paramFile to set. Extension will be removed.public String getFileName()
QParamsQconf
and should be added when
creating only this object QParams(File).public String getPath()
public Path getPathasPath()
getParamFile()
public double getNodeRes()
public void setNodeRes(double nodeRes)
nodeRes
- the nodeRes to setpublic int getBlowup()
public void setBlowup(int blowup)
blowup
- the blowup to setpublic double getImageScale()
public void setImageScale(double imageScale)
imageScale
- the imageScale to setpublic double getFrameInterval()
public void setFrameInterval(double frameInterval)
frameInterval
- the frameInterval to setpublic int getStartFrame()
public void setStartFrame(int startFrame)
startFrame
- the startFrame to setpublic int getEndFrame()
public void setEndFrame(int endFrame)
endFrame
- the endFrame to setpublic File getSnakeQP()
public void setSnakeQP(File snakeQP)
snakeQP
- the snakeQP to setpublic File getStatsQP()
public File[] getFluFiles()
public void setStatsQP(File statsQP)
statsQP
- the statsQP to setpublic File getSegImageFile()
public void setSegImageFile(File segImageFile)
segImageFile
- the segImageFile to setpublic File getConvexFile()
public void setConvexFile(File convexFile)
convexFile
- the convexFile to setpublic File getCoordFile()
public void setCoordFile(File coordFile)
coordFile
- the coordFile to setpublic File getMotilityFile()
public void setMotilityFile(File motilityFile)
motilityFile
- the motilityFile to setpublic File getOriginFile()
public void setOriginFile(File originFile)
originFile
- the originFile to setpublic File getxmapFile()
public void setxmapFile(File xmapFile)
xmapFile
- the xmapFile to setpublic File getymapFile()
public void setymapFile(File ymapFile)
ymapFile
- the ymapFile to setpublic int getParamFormat()
public void readParams() throws QuimpException
See QParams(File)
. Create handles to files stored as names in paQP. Read
segmentation parameters.
QuimpException
- on wrong file that can not be interpreted or read.IllegalStateException
- if input file is emptypublic void writeParams() throws IOException
IOException
- Signals that an I/O exception has occurred.public File[] findParamFiles()
Remarks
Current paQP file (that passed to QParams(File)) is not counted.
protected void guessOtherFileNames()
public boolean verifyEcmminpsnQP() throws IOException
snQP file contains ECMM string in first line after ECMM.
IOException
- on errorCopyright © 2002–2019 Department of Computer Science, Warwick University. All rights reserved.