Series_Labeler (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- Series_Labeler

All Implemented Interfaces:

DialogListener, ij.ImageListener, ij.plugin.filter.ExtendedPlugInFilter, ij.plugin.filter.PlugInFilter
```
public class Series_Labeler
extends Object
implements ij.plugin.filter.ExtendedPlugInFilter, DialogListener, ij.ImageListener
```
This plugin is inspired by the Time_Stamper plugins from ImageJ and from Tony Collins' plugin collection at macbiophotonics. It aims to combine all the functionality of both plugins and refine and enhance the functionality for instance by adding the preview functionality suggested by Michael Weber. Series Labeler is not a drop in replacement for Time Stamper, since it does not do hyperstacks or macro recording. Series Labeler handles any kind of stack, t, z or c (eg spectral series).

Author:

Dan White and Tom Kazimiers

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected class`	`Series_Labeler.AbstractStampFormat` A class representing a supported label format It relates supported format units/suffixes to a format name.
`protected class`	`Series_Labeler.CustomLabelFormat` Represents a label format that is essentially the same as a decimal format, but allows custom suffixes.
`protected class`	`Series_Labeler.DecimalLabelFormat` Represents a decimal label format, e.
`protected class`	`Series_Labeler.DigitalLabelFormat` Represents a digital label format, e.
`protected class`	`Series_Labeler.ExtendedFonts` This class extends Fonts so we can listen to the changes in the imageJ fonts GUI that we reuse for font settings and update the preview accordingly.
`protected class`	`Series_Labeler.FontPropertiesPanel` Class for a panel containing several font manipulation items.
`protected class`	`Series_Labeler.StackType` A class representing a type of stack.
`protected class`	`Series_Labeler.TimeStackType`
`protected class`	`Series_Labeler.ZStackType`

Field Summary

Fields
Modifier and Type	Field and Description
`protected static boolean`	`antiAliasedText`
`protected static boolean`	`backgroundEnabled`
`protected boolean`	`canceled`
`protected static String`	`chosenSuffix`
`protected int`	`currentSlice`
`protected static int`	`CUSTOM`
`protected static String`	`customFormat`
`protected static boolean`	`customIntervalEntered`
`protected Panel`	`customLabelFormatPanel`
`protected static String`	`customSuffix`
`protected Panel`	`customSuffixPanel`
`protected static boolean`	`customUnitSelected`
`protected static int`	`decimalPlaces`
`protected Panel`	`decimalPlacesPanel`
`protected static int`	`first`
`protected int`	`flags`
`protected static Font`	`font`
`protected Panel`	`fontPropertiesContainer`
`protected Choice`	`formatsComboBox`
`protected int`	`frame`
`protected static int`	`frameMask`
`protected GenericDialog`	`gd`
`protected Panel`	`generalSettingsContainer`
`protected ij.ImagePlus`	`imp`
`protected static double`	`interval`
`protected TextField`	`intervalTextField`
`protected Choice`	`labelUnitsComboBox`
`protected Panel`	`labelUnitsPanel`
`protected static int`	`last`
`protected Panel`	`locationFontContainer`
`protected static int`	`locationPreset`
`protected Choice`	`locationPresetsComboBox`
`protected static String[]`	`locations`
`protected TextField`	`locationXTextField`
`protected TextField`	`locationYTextField`
`protected static int`	`LOWER_LEFT`
`protected static int`	`LOWER_RIGHT`
`protected ij.plugin.filter.PlugInFilterRunner`	`pluginFilterRunner`
`protected static String`	`PREF_KEY`
`protected boolean`	`preview`
`protected boolean`	`previewCheckState`
`protected static Series_Labeler.AbstractStampFormat`	`selectedFormat`
`protected static Series_Labeler.StackType`	`selectedStackType`
`protected Series_Labeler.AbstractStampFormat[]`	`spectralFormats`
`protected Series_Labeler.StackType[]`	`stackTypes`
`protected static double`	`start`
`protected Panel`	`startStopIntervalsContainer`
`protected TextField`	`suffixTextField`
`protected Series_Labeler.AbstractStampFormat[]`	`timeFormats`
`protected Panel`	`unitsFormattingContainer`
`protected static int`	`UPPER_LEFT`
`protected static int`	`UPPER_RIGHT`
`protected static int`	`x`
`protected static int`	`y`
`protected Series_Labeler.AbstractStampFormat[]`	`zFormats`

Fields inherited from interface ij.plugin.filter.ExtendedPlugInFilter
KEEP_PREVIEW

Fields inherited from interface ij.plugin.filter.PlugInFilter
CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, NO_UNDO_RESET, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors
Constructor and Description

Series_Labeler()

Constructors
Constructor and Description
`Series_Labeler()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`addPanelIntoDialog(Panel container)` The container Panel is added to the generic dialog.
`protected void`	`addPanelsToDialog(Panel container, Panel[] panels)` Adds different Panels to a container Panel.
`protected String[]`	`convertFormatsToStrings(Series_Labeler.AbstractStampFormat[] formats)` Creates a string array out of the names of the available formats.
`protected String[]`	`convertStackTypesToStrings(Series_Labeler.StackType[] types)` Creates a string array out of the names of the available formats.
`protected Panel`	`createComboBoxPanel(String labelText, String[] values, int defaultIndex)` drop down selection with a text label
`protected Panel`	`createComboBoxPanel(String labelText, String[] values, int defaultIndex, int labelWidth, int comboboxWidth)` generate gd drop down selections for use in a different container later
`protected Panel`	`createContainerPanel(int height, String label)` container panel for gui items to be put in, with a border.
`protected Panel`	`createContainerPanel(int height, String label, boolean border)` container panel for gui items to be put in.
`protected Component`	`createMessage(String labelText)` generate gd message for use in a different container later.
`protected Panel`	`createNumericFieldPanel(String labelText, double defaultValue, int digits)` A numeric field for the GUI
`protected Panel`	`createNumericFieldPanel(String labelText, double defaultValue, int digits, int labelWidth, int textFieldWidth)` Generates gd awt numeric fields for use in a different container later
`protected Panel`	`createTextFieldPanel(String labelText, String defaultText)` This is a text field panel for use in the GUI
`protected Panel`	`createTextFieldPanel(String labelText, String defaultText, int labelWidth, int textFieldWidth)` Generates gd awt string fields for use in a different container later
`boolean`	`dialogItemChanged(GenericDialog gd, AWTEvent e)` This method deals with changes the user makes in the GUI
`void`	`imageClosed(ij.ImagePlus imp)`
`void`	`imageOpened(ij.ImagePlus imp)`
`void`	`imageUpdated(ij.ImagePlus imp)`
`void`	`run(ij.process.ImageProcessor ip)` Run the plug-in on the ip object, which is the ImageProcessor object associated with the open/selected image.
`protected void`	`selectCustomFormat()` A method for selecting the custom unit format of the currently selected stack type.
`void`	`setNPasses(int nPasses)` This is part of the preview functionality.
`int`	`setup(String arg, ij.ImagePlus imp)` Setup the plug-in and tell ImageJ it needs to work on a stack by returning the flags
`int`	`showDialog(ij.ImagePlus imp, String command, ij.plugin.filter.PlugInFilterRunner pfr)` Make the GUI for the plug-in, with fields to fill all the variables we need.
`protected void`	`updatePreview()` Updates the label preview.
`protected void`	`updateUI()` Shows and Hides relevant GUI components, based on the current state of the selected label format.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PREF_KEY
```
protected static String PREF_KEY
```

x
```
protected static int x
```

y
```
protected static int y
```

font
```
protected static Font font
```

start
```
protected static double start
```

interval
```
protected static double interval
```

customSuffix
```
protected static String customSuffix
```

chosenSuffix
```
protected static String chosenSuffix
```

decimalPlaces
```
protected static int decimalPlaces
```

customFormat
```
protected static String customFormat
```

antiAliasedText

protected static boolean antiAliasedText

first
```
protected static int first
```

last
```
protected static int last
```

frameMask
```
protected static int frameMask
```

backgroundEnabled

protected static boolean backgroundEnabled

selectedFormat

protected static Series_Labeler.AbstractStampFormat selectedFormat

selectedStackType

protected static Series_Labeler.StackType selectedStackType

locationPreset
```
protected static int locationPreset
```

imp
```
protected ij.ImagePlus imp
```

canceled
```
protected boolean canceled
```

preview
```
protected boolean preview
```

previewCheckState
```
protected boolean previewCheckState
```

frame
```
protected int frame
```

currentSlice
```
protected int currentSlice
```

pluginFilterRunner

protected ij.plugin.filter.PlugInFilterRunner pluginFilterRunner

flags
```
protected int flags
```

gd
```
protected GenericDialog gd
```

locations

protected static final String[] locations

UPPER_RIGHT
```
protected static final int UPPER_RIGHT
```
See Also:

Constant Field Values

LOWER_RIGHT
```
protected static final int LOWER_RIGHT
```
See Also:

Constant Field Values

LOWER_LEFT
```
protected static final int LOWER_LEFT
```
See Also:

Constant Field Values

UPPER_LEFT
```
protected static final int UPPER_LEFT
```
See Also:

Constant Field Values

CUSTOM
```
protected static final int CUSTOM
```
See Also:

Constant Field Values

timeFormats

protected final Series_Labeler.AbstractStampFormat[] timeFormats

zFormats

protected final Series_Labeler.AbstractStampFormat[] zFormats

spectralFormats

protected final Series_Labeler.AbstractStampFormat[] spectralFormats

stackTypes

protected final Series_Labeler.StackType[] stackTypes

labelUnitsComboBox
```
protected Choice labelUnitsComboBox
```

formatsComboBox
```
protected Choice formatsComboBox
```

locationPresetsComboBox

protected Choice locationPresetsComboBox

generalSettingsContainer

protected Panel generalSettingsContainer

unitsFormattingContainer

protected Panel unitsFormattingContainer

startStopIntervalsContainer

protected Panel startStopIntervalsContainer

locationFontContainer
```
protected Panel locationFontContainer
```

fontPropertiesContainer

protected Panel fontPropertiesContainer

locationXTextField
```
protected TextField locationXTextField
```

locationYTextField
```
protected TextField locationYTextField
```

intervalTextField
```
protected TextField intervalTextField
```

suffixTextField
```
protected TextField suffixTextField
```

labelUnitsPanel
```
protected Panel labelUnitsPanel
```

customSuffixPanel
```
protected Panel customSuffixPanel
```

customLabelFormatPanel
```
protected Panel customLabelFormatPanel
```

decimalPlacesPanel
```
protected Panel decimalPlacesPanel
```

customIntervalEntered

protected static boolean customIntervalEntered

customUnitSelected

protected static boolean customUnitSelected

Constructor Detail
- Series_Labeler
```
public Series_Labeler()
```

Method Detail

setup
```
public int setup(String arg,
                 ij.ImagePlus imp)
```
Setup the plug-in and tell ImageJ it needs to work on a stack by returning the flags

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

showDialog
```
public int showDialog(ij.ImagePlus imp,
                      String command,
                      ij.plugin.filter.PlugInFilterRunner pfr)
```
Make the GUI for the plug-in, with fields to fill all the variables we need. We use ExtendedPluginFilter, so first argument is imp not ip.

Specified by:

showDialog in interface ij.plugin.filter.ExtendedPlugInFilter

setNPasses
```
public void setNPasses(int nPasses)
```
This is part of the preview functionality. Informs the filter of the number of calls of run(ip) that will follow. The argument nPasses is worked out by the plug-in runner.

Specified by:

setNPasses in interface ij.plugin.filter.ExtendedPlugInFilter

run
```
public void run(ij.process.ImageProcessor ip)
```
Run the plug-in on the ip object, which is the ImageProcessor object associated with the open/selected image. but remember that showDialog method is run before this in ExtendedPluginFilter

Specified by:

run in interface ij.plugin.filter.PlugInFilter

createContainerPanel

protected Panel createContainerPanel(int height,
                                     String label,
                                     boolean border)

container panel for gui items to be put in.

createContainerPanel

protected Panel createContainerPanel(int height,
                                     String label)

container panel for gui items to be put in, with a border.

createComboBoxPanel

protected Panel createComboBoxPanel(String labelText,
                                    String[] values,
                                    int defaultIndex)

drop down selection with a text label

createComboBoxPanel

protected Panel createComboBoxPanel(String labelText,
                                    String[] values,
                                    int defaultIndex,
                                    int labelWidth,
                                    int comboboxWidth)

generate gd drop down selections for use in a different container later

createMessage
```
protected Component createMessage(String labelText)
```
generate gd message for use in a different container later.

createTextFieldPanel

protected Panel createTextFieldPanel(String labelText,
                                     String defaultText)

This is a text field panel for use in the GUI

createTextFieldPanel

protected Panel createTextFieldPanel(String labelText,
                                     String defaultText,
                                     int labelWidth,
                                     int textFieldWidth)

Generates gd awt string fields for use in a different container later

createNumericFieldPanel

protected Panel createNumericFieldPanel(String labelText,
                                        double defaultValue,
                                        int digits)

A numeric field for the GUI

createNumericFieldPanel

protected Panel createNumericFieldPanel(String labelText,
                                        double defaultValue,
                                        int digits,
                                        int labelWidth,
                                        int textFieldWidth)

Generates gd awt numeric fields for use in a different container later

selectCustomFormat
```
protected void selectCustomFormat()
```
A method for selecting the custom unit format of the currently selected stack type.

addPanelsToDialog

protected void addPanelsToDialog(Panel container,
                                 Panel[] panels)

Adds different Panels to a container Panel. Moreover the container Panel is added to the generic dialog.

addPanelIntoDialog
```
protected void addPanelIntoDialog(Panel container)
```
The container Panel is added to the generic dialog.

updatePreview
```
protected void updatePreview()
```
Updates the label preview.

updateUI
```
protected void updateUI()
```
Shows and Hides relevant GUI components, based on the current state of the selected label format.

dialogItemChanged

public boolean dialogItemChanged(GenericDialog gd,
                                 AWTEvent e)

This method deals with changes the user makes in the GUI

Specified by:: dialogItemChanged in interface DialogListener

imageClosed
```
public void imageClosed(ij.ImagePlus imp)
```
Specified by:

imageClosed in interface ij.ImageListener

imageOpened
```
public void imageOpened(ij.ImagePlus imp)
```
Specified by:

imageOpened in interface ij.ImageListener

imageUpdated
```
public void imageUpdated(ij.ImagePlus imp)
```
Specified by:

imageUpdated in interface ij.ImageListener

convertFormatsToStrings

protected String[] convertFormatsToStrings(Series_Labeler.AbstractStampFormat[] formats)

Creates a string array out of the names of the available formats.

convertStackTypesToStrings
```
protected String[] convertStackTypesToStrings(Series_Labeler.StackType[] types)
```
Creates a string array out of the names of the available formats.

Class Series_Labeler

Nested Class Summary

Field Summary

Fields inherited from interface ij.plugin.filter.ExtendedPlugInFilter

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

PREF_KEY

x

y

font

start

interval

customSuffix

chosenSuffix

decimalPlaces

customFormat

antiAliasedText

first

last

frameMask

backgroundEnabled

selectedFormat

selectedStackType

locationPreset

imp

canceled

preview

previewCheckState

frame

currentSlice

pluginFilterRunner

flags

gd

locations

UPPER_RIGHT

LOWER_RIGHT

LOWER_LEFT

UPPER_LEFT

CUSTOM

timeFormats

zFormats

spectralFormats

stackTypes

labelUnitsComboBox

formatsComboBox

locationPresetsComboBox

generalSettingsContainer

unitsFormattingContainer

startStopIntervalsContainer

locationFontContainer

fontPropertiesContainer

locationXTextField

locationYTextField

intervalTextField

suffixTextField

labelUnitsPanel

customSuffixPanel

customLabelFormatPanel

decimalPlacesPanel

customIntervalEntered

customUnitSelected

Constructor Detail

Series_Labeler

Method Detail

setup

showDialog

setNPasses

run

createContainerPanel

createContainerPanel

createComboBoxPanel

createComboBoxPanel

createMessage

createTextFieldPanel

createTextFieldPanel

createNumericFieldPanel

createNumericFieldPanel