public class RandomWalkModel extends AbstractPluginOptions
RandomWalkSegmentationPlugin_
,
RandomWalkView
,
RandomWalkOptions
Modifier and Type | Class and Description |
---|---|
static class |
RandomWalkModel.SeedSource
Possible sources of seeds.
|
Modifier and Type | Field and Description |
---|---|
double |
alev
alev parameter.
|
RandomWalkOptions |
algOptions
Parameters of Random Walk algorithm itself.
|
boolean |
estimateBackground
Estimate background if true.
|
double |
expandPower
ExpandPower parameter.
|
boolean |
hatFilter
true for HatFilter active.
|
boolean |
interFrameFilter
If true add extra filtering during applying
PropagateSeeds.Propagators.CONTOUR shrink method. |
int |
num
num parameter.
|
double |
scaleCurvDistDist
Range of averaging of curvature.
|
double |
scaleEqNormalsDist
If non zero, normals are set to direction of normal of node with smallest curvature (negative).
|
double |
scaleMagn
Maximal magnitude of scaling for regions with smallest curvature.
|
double |
scaleSigma
Scale sigma parameter.
|
PropagateSeeds.Propagators |
selectedShrinkMethod
Selected shrink algorithm.
|
boolean |
showPreview
true for showing preview.
|
boolean |
showProbMaps
true for showing probability maps.
|
boolean |
showSeeds
true for showing seeds.
|
double |
shrinkPower
ShrinkPower parameter.
|
int |
window
window parameter.
|
KEY, LOGGER, MAXITER, paramFile
Constructor and Description |
---|
RandomWalkModel()
Default constructor setting default parameters.
|
Modifier and Type | Method and Description |
---|---|
void |
afterSerialize()
This method is called after restoring object from JSON but before returning the object.
|
boolean |
equals(Object obj) |
String[] |
getFilteringMethods()
Get filtering methods supported by BinaryFilters class in form of String[].
|
ij.ImagePlus |
getOriginalImage()
Get original image from this object.
|
String |
getQconfFile()
Get qconffile field.
|
ij.ImagePlus |
getSeedImage()
Get seed image.
|
String[] |
getSeedSources()
Get seed sources defined in
RandomWalkModel.SeedSource . |
BinaryFilters.Filters |
getSelectedFilteringMethod()
Filtering getter.
|
BinaryFilters.Filters |
getSelectedFilteringPostMethod()
Post filtering getter.
|
RandomWalkModel.SeedSource |
getSelectedSeedSource()
SeedSource getter.
|
PropagateSeeds.Propagators |
getselectedShrinkMethod()
Shrink method getter.
|
String[] |
getShrinkMethods()
Get shrink methods supported by PropagateSeeds class in form of String[].
|
int |
hashCode() |
void |
setOriginalImage(ij.ImagePlus originalImage)
Set original image and update name field for serialisation.
|
void |
setQconfFile(String qconfFile)
Setter of qconffile filed.
|
void |
setSeedImage(ij.ImagePlus seedImage)
Set seed image and update name for serialisation.
|
void |
setSelectedFilteringMethod(BinaryFilters.Filters selectedFilteringMethod)
Filtering setter.
|
void |
setSelectedFilteringMethod(int selectedFilteringMethod)
Post filtering setter.
|
void |
setSelectedFilteringPostMethod(BinaryFilters.Filters selectedFilteringPostMethod)
Post filtering setter.
|
void |
setSelectedFilteringPostMethod(int selectedFilteringPostMethod)
Post filtering setter.
|
void |
setSelectedSeedSource(int selectedSeedSource)
SeedSource setter.
|
void |
setSelectedSeedSource(RandomWalkModel.SeedSource selectedSeedSource)
SeedSource setter.
|
void |
setselectedShrinkMethod(int selectedShrinkMethod)
Seed propagator setter.
|
void |
setselectedShrinkMethod(PropagateSeeds.Propagators selectedShrinkMethod)
Seed propagator setter.
|
String |
toString() |
beforeSerialize, deserialize, deserialize2Macro, escapeJsonMacro, removeSpacesMacro, serialize, serialize2Macro, unescapeJsonMacro
public RandomWalkOptions algOptions
RandomWalkSegmentation
public PropagateSeeds.Propagators selectedShrinkMethod
PropagateSeeds
public double shrinkPower
Number of erosions for generating next seed from previous one. Also number of pixels to shrink contour.
public double expandPower
Number of dilations for generating next seed from previous one. Also number of pixels to expand contour.
public double scaleSigma
Shape of Gaussian curve used to estimate magnitude of scaling related to local curvature.
public double scaleMagn
public double scaleEqNormalsDist
public double scaleCurvDistDist
public boolean estimateBackground
public boolean interFrameFilter
PropagateSeeds.Propagators.CONTOUR
shrink method.
By default none filtering is applied (use of TrackOutlinNoFilter
object. Otherwise
TrackOutline
is used.
TrackOutlinNoFilter
,
TrackOutline
,
PropagateSeeds.Contour.useFiltering
public boolean hatFilter
public double alev
public int num
public int window
public boolean showSeeds
public boolean showPreview
public boolean showProbMaps
public RandomWalkModel()
public String[] getShrinkMethods()
PropagateSeeds
,
RandomWalkSegmentationPlugin_.runPlugin()
public String[] getFilteringMethods()
BinaryFilters
,
RandomWalkSegmentation.run(Seeds)
,
RandomWalkSegmentation
public String[] getSeedSources()
RandomWalkModel.SeedSource
.RandomWalkModel.SeedSource
public ij.ImagePlus getOriginalImage()
If not available try to restore from remembered title searched among opened images. If it fails tries to load from disk.
public void setOriginalImage(ij.ImagePlus originalImage)
originalImage
- the originalImage to setpublic RandomWalkModel.SeedSource getSelectedSeedSource()
RandomWalkModel.SeedSource
public void setSelectedSeedSource(RandomWalkModel.SeedSource selectedSeedSource)
selectedSeedSource
- the selectedSeedSource to setpublic void setSelectedSeedSource(int selectedSeedSource)
selectedSeedSource
- index of SeedSource to set according to order returned by
getSeedSources()
public ij.ImagePlus getSeedImage()
It returns image from this object. If it is null it tries to get it from opened images or finally read from disk.
public void setSeedImage(ij.ImagePlus seedImage)
seedImage
- the seedImage to setpublic String getQconfFile()
public void setQconfFile(String qconfFile)
Replaces windows paths for Linux. required for proper call of GenerateMask_
from
RandomWalkSegmentationPlugin_.runPlugin()
qconfFile
- the qconfFile to setpublic PropagateSeeds.Propagators getselectedShrinkMethod()
PropagateSeeds.getPropagator(Propagators, boolean, ij.process.AutoThresholder.Method)
,
PropagateSeeds.Propagators
public void setselectedShrinkMethod(PropagateSeeds.Propagators selectedShrinkMethod)
selectedShrinkMethod
- the selectedFilteringMethod to setpublic void setselectedShrinkMethod(int selectedShrinkMethod)
selectedShrinkMethod
- index of shrink method respecting order returned by
getShrinkMethods()
public BinaryFilters.Filters getSelectedFilteringMethod()
BinaryFilters.getFilter(Filters)
,
BinaryFilters.Filters
public void setSelectedFilteringMethod(BinaryFilters.Filters selectedFilteringMethod)
selectedFilteringMethod
- the selectedFilteringMethod to setpublic void setSelectedFilteringMethod(int selectedFilteringMethod)
selectedFilteringMethod
- index of filter to set according to order returned by
getFilteringMethods()
public BinaryFilters.Filters getSelectedFilteringPostMethod()
BinaryFilters.getFilter(Filters)
,
BinaryFilters.Filters
public void setSelectedFilteringPostMethod(BinaryFilters.Filters selectedFilteringPostMethod)
selectedFilteringPostMethod
- the selectedFilteringPostMethod to setpublic void setSelectedFilteringPostMethod(int selectedFilteringPostMethod)
selectedFilteringPostMethod
- index of filter to set according to order returned by
getFilteringMethods()
public void afterSerialize() throws Exception
IQuimpSerialize
afterSerialize
in interface IQuimpSerialize
afterSerialize
in class AbstractPluginOptions
Exception
- from wrapped object in any problem. This is implementation dependentSerializer.load(String)
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