public class ProtAnalysisOptions extends AbstractPluginOptions implements IQuimpSerialize
Modifier and Type | Class and Description |
---|---|
static class |
ProtAnalysisOptions.GradientType
Types of gradient points.
|
static class |
ProtAnalysisOptions.OutlinePlotTypes
Plot types supported by
TrackVisualisation.Stack.addOutlinesToImage(STmap, ProtAnalysisOptions) . |
Modifier and Type | Field and Description |
---|---|
MutableBoolean |
bnGradientPickActive
Indicate that pick point mode is on.
|
static int |
CH1
Channel for tables.
|
static int |
CH2
Channel for tables.
|
static int |
CH3
Channel for tables.
|
MutableBoolean |
chbAreaPlot
Plot map.
|
MutableBoolean |
chbCircPlot
Plot map.
|
MutableBoolean |
chbCortexAreaPlot
Plot 2D.
|
MutableBoolean |
chbCortexWidthPlot
Plot 2D.
|
MutableBoolean |
chbCytoAreaPlot
Plot 2D.
|
MutableBoolean |
chbDisplPlot
Plot map.
|
MutableBoolean |
chbDistPlot
Plot map.
|
MutableBoolean |
chbElongPlot
Plot map.
|
MutableBoolean |
chbFlattenStaticTrackImage
Whether to flatten static track.
|
MutableBoolean |
chbManCtfPlot
Plot 2D.
|
MutableBoolean |
chbMeanCtfPlot
Plot 2D.
|
MutableBoolean |
chbMeanCytoPlot
Plot 2D.
|
MutableBoolean |
chbMeanFluPlot
Plot 2D.
|
MutableBoolean |
chbNewImage
Whether to show tracks in new plot or in embedded in GUI.
|
MutableBoolean |
chbPerimPlot
Plot map.
|
MutableBoolean |
chbPersistencePlot
Plot map.
|
MutableBoolean |
chbShowPoint
Show tracked point on dynamic track.
|
MutableBoolean |
chbShowTrack
Show track on dynamic track.
|
MutableBoolean |
chbShowTrackMotility
Show tracks on motility map.
|
MutableBoolean |
chbSmoothTracks
Apply track smoothing.
|
MutableBoolean |
chbSpeedPlot
Plot map.
|
MutableBoolean |
chbTotalCtf2Plot
Plot 2D.
|
MutableBoolean |
chbTotalCytoPlot
Plot 2D.
|
MutableBoolean |
chbTotFluPlot
Plot 2D.
|
MutableBoolean |
chbXcentrPlot
Plot map.
|
MutableBoolean |
chbYcentrPlot
Plot map.
|
double |
circleRadius
Radius of circles plotted by tool.
|
double |
dropValue
Percentage of drop from maximum of motility map to consider point in tracking line.
|
Point2d |
gradientPoint
Gradient point for polar plot.
|
double |
noiseTolerance
Sensitivity of maximum detection.
|
static int |
PLOT_DYNAMIC
Vale for dynamic plot.
|
static int |
PLOT_STATIC
Vale for static plot.
|
MutableInt |
plotStaticDynamic
Plot dynamic or static plots.
|
static Color |
pointColor
Color of selected point on the outline when hoover the mouse.
|
static int |
pointSize
Size of the point when hoover.
|
static String |
roiPrefix
Prefix added to Roi in ROI Manager.
|
MutableBoolean |
saveTracks
Save tracks to csv file.
|
MutableInt |
selActiveCellMap
Cell used for generating maps.
|
MutableInt |
selActiveCellPlot
Cell used for generating plots.
|
MutableInt |
selActiveChannel
Active channel for plotting maps.
|
com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.OutlinesToImage |
selOutlineColoring
Hold configuration for plotting outlines of cells on stack of images.
|
static Color |
staticPointColor
Color of selected point.
|
static int |
staticPointSize
Size of the point when selected.
|
KEY, LOGGER, MAXITER, paramFile
Constructor and Description |
---|
ProtAnalysisOptions()
Instantiates a new prot analysis config.
|
Modifier and Type | Method and Description |
---|---|
void |
afterSerialize()
This method is called after restoring object from JSON but before returning the object.
|
void |
beforeSerialize()
This method is called just before JSON is generated.
|
deserialize, deserialize2Macro, escapeJsonMacro, removeSpacesMacro, serialize, serialize2Macro, unescapeJsonMacro
public static Color pointColor
public static Color staticPointColor
public static int staticPointSize
public static int pointSize
public static final String roiPrefix
public double circleRadius
public static final int PLOT_STATIC
plotStaticDynamic
,
Constant Field Valuespublic static final int PLOT_DYNAMIC
plotStaticDynamic
,
Constant Field Valuespublic static final int CH1
public static final int CH2
public static final int CH3
public MutableBoolean chbNewImage
public MutableBoolean chbFlattenStaticTrackImage
public MutableInt plotStaticDynamic
0 - static, 1 - dynamic
PLOT_DYNAMIC
,
PLOT_STATIC
public MutableBoolean chbSmoothTracks
public MutableBoolean chbShowPoint
public MutableBoolean chbShowTrack
public MutableBoolean chbShowTrackMotility
public MutableInt selActiveCellPlot
public MutableInt selActiveCellMap
public MutableInt selActiveChannel
public MutableBoolean chbXcentrPlot
public MutableBoolean chbYcentrPlot
public MutableBoolean chbDisplPlot
public MutableBoolean chbDistPlot
public MutableBoolean chbPersistencePlot
public MutableBoolean chbSpeedPlot
public MutableBoolean chbPerimPlot
public MutableBoolean chbElongPlot
public MutableBoolean chbCircPlot
public MutableBoolean chbAreaPlot
public MutableBoolean chbTotFluPlot
public MutableBoolean chbMeanFluPlot
public MutableBoolean chbCortexWidthPlot
public MutableBoolean chbCytoAreaPlot
public MutableBoolean chbTotalCytoPlot
public MutableBoolean chbMeanCtfPlot
public MutableBoolean chbMeanCytoPlot
public MutableBoolean chbCortexAreaPlot
public MutableBoolean chbTotalCtf2Plot
public MutableBoolean chbManCtfPlot
public com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.OutlinesToImage selOutlineColoring
ActionTrackPoints
public Point2d gradientPoint
public MutableBoolean bnGradientPickActive
public MutableBoolean saveTracks
Currently not available from UI. Maps are saved always under fixed name.
ActionTrackPoints
public double noiseTolerance
public double dropValue
public ProtAnalysisOptions()
public void beforeSerialize()
IQuimpSerialize
beforeSerialize
in interface IQuimpSerialize
beforeSerialize
in class AbstractPluginOptions
Serializer.save(String)
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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