de.unihalle.informatik.MiToBo.apps.scratchAssay
Class ScratchAssayAnalyzer
java.lang.Object
de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
- All Implemented Interfaces:
- de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator
@ALDAOperator(genericExecutionMode=ALL,
level=APPLICATION,
allowBatchMode=false)
public class ScratchAssayAnalyzer
- extends MTBOperator
class for analyzing the scratch area in several scratch assay images
- Author:
- glass
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
completeDAG, name, portHashAccess, verbose, versionProvider |
Method Summary |
void |
isSilent(boolean silent)
should results be saved without user interaction |
private MTBTableModel |
makeTable(java.util.Vector<java.lang.String> scratchFiles,
java.util.Vector<java.lang.Double> scratchAreas,
java.util.Vector<java.lang.Double> totalAreas,
double refArea,
java.util.Vector<java.lang.Integer> numIterations,
java.util.Vector<java.lang.Long> runtimes)
create results table |
void |
operate()
|
private MTBImage |
readImage(java.lang.String path)
|
void |
setSVMFile(java.lang.String path)
sets the path to a svm model file used for classification |
private void |
writeImage(MTBImage img,
java.lang.String path)
writes the given image to a file with the specified path |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
deserializeFromXmlFile, fieldContained, getALDPortHashAccessKey, getConstructionMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, isConfigured, parametersToXmlObject, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, runOp, runOp, runOp, serializeToXmlFile, setConstructionMode, setName, setParameter, setParametersFromXml, setParametersFromXml, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory, writeParametersToXml |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
deltaX
@Parameter(label="pixel length, x-direction",
required=false,
direction=IN,
supplemental=false,
description="pixel length in x-direction",
dataIOOrder=5)
private java.lang.Double deltaX
deltaY
@Parameter(label="pixel length, y-direction",
required=false,
direction=IN,
supplemental=false,
description="pixel length in y-direction",
dataIOOrder=6)
private java.lang.Double deltaY
doBatch
@Parameter(label="batch mode",
required=false,
direction=IN,
supplemental=false,
description="should all image files in the given directory be analyzed",
mode=STANDARD,
dataIOOrder=2)
private java.lang.Boolean doBatch
entropyFilterSize
@Parameter(label="entropy filter size",
required=true,
direction=IN,
supplemental=false,
description="size of entropy filter mask",
mode=STANDARD,
dataIOOrder=3)
private java.lang.Integer entropyFilterSize
fileName
@Parameter(label="first image file",
required=true,
direction=IN,
supplemental=false,
description="name of the first scratch assay image",
mode=STANDARD,
dataIOOrder=0)
private de.unihalle.informatik.Alida.datatypes.ALDFileString fileName
isHorizontal
private java.lang.Boolean isHorizontal
maxIter
@Parameter(label="maximum iterations",
required=false,
direction=IN,
supplemental=false,
description="maximum number of iterations for level set segmentation",
mode=ADVANCED,
dataIOOrder=0)
private java.lang.Integer maxIter
noCheck
@Parameter(label="don\'t check for scratch presence",
required=false,
direction=IN,
supplemental=false,
description="don\'t check for scratch presence prior to segmentation",
mode=STANDARD,
dataIOOrder=1)
private java.lang.Boolean noCheck
orientation
@Parameter(label="scratch orientation",
required=true,
direction=IN,
supplemental=false,
description="is scratch horizontally or vertically oriented",
mode=STANDARD,
dataIOOrder=1)
private ScratchAssayAnalyzer.ScratchOrientation orientation
resultsTable
@Parameter(label="results table",
required=true,
direction=OUT,
supplemental=false,
description="table containing the resulting values")
private MTBTableModel resultsTable
sigma
@Parameter(label="\u03c3",
required=true,
direction=IN,
supplemental=false,
description="standard deviation of gauss filter",
mode=STANDARD,
dataIOOrder=2)
private java.lang.Integer sigma
silent
@Parameter(label="silent",
required=false,
direction=IN,
supplemental=false,
description="should results be stored automatically",
mode=STANDARD)
private java.lang.Boolean silent
svmFile
@Parameter(label="external svm file",
required=false,
direction=IN,
supplemental=false,
description="absolute path to external svm model file",
mode=ADVANCED,
dataIOOrder=4)
private de.unihalle.informatik.Alida.datatypes.ALDFileString svmFile
unitXY
@Parameter(label="unit x/y",
required=false,
direction=IN,
supplemental=false,
description="unit x/y",
dataIOOrder=7)
private java.lang.String unitXY
useExternalSVM
@Parameter(label="use external svm file",
required=false,
direction=IN,
supplemental=false,
description="should an external svm file be used for classification",
mode=ADVANCED,
dataIOOrder=3)
private java.lang.Boolean useExternalSVM
ScratchAssayAnalyzer
public ScratchAssayAnalyzer()
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
ScratchAssayAnalyzer
public ScratchAssayAnalyzer(java.lang.String fileName,
int sigma,
int entropyFilterSize,
boolean isHorizontal,
boolean noCheck,
boolean doBatch,
int maxIter)
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Parameters:
fileName
- name of the first scratch assay imagesigma
- standard deviation of gauss filterentropyFilterSize
- size of entropy filter maskisHorizontal
- is scratch horizontally oriented (assumed to be vertically oriented else)noCheck
- should scratch present not be checkeddoBatch
- should all image files in the given directory be analyzedmaxIter
- maximum number of iterations for level set segmentation
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
isSilent
public void isSilent(boolean silent)
- should results be saved without user interaction
- Parameters:
silent
-
makeTable
private MTBTableModel makeTable(java.util.Vector<java.lang.String> scratchFiles,
java.util.Vector<java.lang.Double> scratchAreas,
java.util.Vector<java.lang.Double> totalAreas,
double refArea,
java.util.Vector<java.lang.Integer> numIterations,
java.util.Vector<java.lang.Long> runtimes)
- create results table
- Parameters:
scratchFiles
- scratchAreas
- totalAreas
- refArea
-
- Returns:
- table containing the results
operate
public void operate()
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- Specified by:
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
readImage
private MTBImage readImage(java.lang.String path)
- Parameters:
path
-
- Returns:
- image read from given path (if it points to a valid image)
setSVMFile
public void setSVMFile(java.lang.String path)
- sets the path to a svm model file used for classification
- Parameters:
path
-
writeImage
private void writeImage(MTBImage img,
java.lang.String path)
- writes the given image to a file with the specified path
- Parameters:
img
- MTBImage to savepath
- absolute path for storing