acquifer.ij.im.plugins

Class Hyperstack_Script

Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

ij.gui.GenericDialog

fiji.util.gui.GenericDialogPlus

acquifer.ij.BatchDialog

acquifer.ij.im.plugins.Hyperstack_Maker

acquifer.ij.im.plugins.Hyperstack_Script

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.FocusListener, java.awt.event.ItemListener, java.awt.event.KeyListener, java.awt.event.TextListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, Serializable, Runnable, EventListener, javax.accessibility.Accessible, org.scijava.command.Command, org.scijava.plugin.SciJavaPlugin

Direct Known Subclasses:

Hyperstack_Script, Hyperstack_Script

public class Hyperstack_Script
extends Hyperstack_Maker

Hyperstack plugin with file input field for a custom script file to execute with the generated images.
Any Fiji scripting language is supported. The only condition is that the script uses 2 script parameters of the following names:
- #@ImagePlus stack
- #@ImagePlus proj
The plugin automatically passes the generated ImagePlus hyperstack to the script via the "stack" variable, and similarly for the hyperstack projection with the proj variable.
For macro-files, an additional condition is to display the images, which is automatically done if a file with ijm extension is provided.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class acquifer.ij.im.plugins.Hyperstack_Maker

Hyperstack_Maker.DisplayMode

Nested classes/interfaces inherited from class java.awt.Dialog

java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields inherited from class acquifer.ij.im.plugins.Hyperstack_Maker

channelsLuts, displayMagnification, groupedImageInfos, metadataParser, METHODS, proj, projDir, projectStack, projMethod, saturation, saveProjection, saveStack, showProjection, showProjectionTickbox, showStack, stack, stackDir, startSlice, stopSlice, useCustomRange, useVirtual

Fields inherited from class acquifer.ij.BatchDialog

filenameFilter, headless, imageDirectory, labelChannels, labelSubposition, labelTimepoint, labelZ, listChannels, listSubPositions, listTimepoints, listWells, listZslices, nColumns, nGroupCheckboxes, nRows, plate, rowSelectionCheckboxes

Fields inherited from class fiji.util.gui.GenericDialogPlus

windowIDs, windowTitles

Fields inherited from class ij.gui.GenericDialog

checkbox, choice, defaultChoiceIndexes, defaultStrings, defaultText, defaultValues, numberField, radioButtonGroups, slider, stringField, textArea1, textArea2, theLabel

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component

accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
Hyperstack_Script(String title, acquifer.core.im.FilenameFilter filenameFilter)

Method Summary

Modifier and Type	Method and Description
void	composeGUI() Compose the right panel of the plugin GUI.
boolean	loopBody(acquifer.core.ImageSeries imageSeries) Define what is executed for each list of images representing a hyperstack.
void	readGuiInputs() Read the GUI inputs, in a macro-recordable way : storing them as fields of the class.
boolean	validateInputs() Check values entered in the dialog, to make sure they make sense (no negative...).

Methods inherited from class acquifer.ij.im.plugins.Hyperstack_Maker

createImageWindow, executedOnce, getChannelsLuts, getLutNameForChannel, getLuts, groupAsHyperStacks, isMultiDimensional, isOneDimensional, makeHyperStack, makeHyperStack, makeHyperStack, makeHyperStack, makeVirtualStack, renameProjectedSlices, resetDisplayRange, run, setChannelLut, setContrastSaturation, setDefaultChannelsLut, setDefaultDisplayMagnification, setDefaultSliderPositions, setHyperStackDisplayMode, setLUTs, showHyperStacks, updateDisplayMagnification, validateCustomRange

Methods inherited from class acquifer.ij.BatchDialog

actionPerformed, addDefaultDirectoryInput, addMessageBold, convertToIntegerSet, createAndSetDefaultDirectory, escapePressed, getBoldFont, getChannels, getCheckboxesForColumn, getCheckboxGroup, getCurrentImageDirectory, getDefaultInputs, getFont, getHeaderCheckboxes, getImageDirectory, getMatchingDataset, getMatchingDataset, getMatchingDataset, getNextStringAsIntegers, getSavedWellCheckboxState, getSubpositions, getTimepoints, getWellCheckboxes, getWells, getZslice, itemStateChanged, readMacroContent, saveDefaultParameters, saveWellCheckboxState, setOKLabel, showDialog, textValueChanged

Methods inherited from class fiji.util.gui.GenericDialogPlus

addButton, addComponent, addComponent, addDirectoryField, addDirectoryField, addDirectoryOrFileField, addDirectoryOrFileField, addFileField, addFileField, addImage, addImage, addImage, addImageChoice, addStringField, createImageIcon, getConstraints, getNextImage, keyPressed, keyReleased, keyTyped

Methods inherited from class ij.gui.GenericDialog

addCheckbox, addCheckboxGroup, addCheckboxGroup, addChoice, addDialogListener, addEnumChoice, addHelp, addImage, addMessage, addMessage, addMessage, addNumericField, addNumericField, addNumericField, addPanel, addPanel, addPreviewCheckbox, addPreviewCheckbox, addRadioButtonGroup, addSlider, addSlider, addStringField, addTextAreas, addToSameRow, adjustmentValueChanged, centerDialog, dispose, enableYesNoCancel, enableYesNoCancel, focusGained, focusLost, getButtons, getCheckboxes, getChoices, getErrorMessage, getInsets, getInstance, getLabel, getMessage, getNextBoolean, getNextChoice, getNextChoiceIndex, getNextEnumChoice, getNextNumber, getNextRadioButton, getNextString, getNextText, getNumericFields, getPreviewCheckbox, getRadioButtonGroups, getSliders, getStringFields, getTextArea1, getTextArea2, getValue, hideCancelButton, invalidNumber, isMacro, isPreviewActive, paint, parseDouble, previewRunning, repaint, setCancelLabel, setDefaultString, setEchoChar, setFont, setHelpLabel, setInsets, setLocation, setSmartRecording, setup, wasCanceled, wasOKed, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.awt.Dialog

addNotify, getAccessibleContext, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, paramString, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, setVisible, show, toBack

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, postEvent, processEvent, processWindowEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, update, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Hyperstack_Script

public Hyperstack_Script(String title,
                         acquifer.core.im.FilenameFilter filenameFilter)

Method Detail

composeGUI

public void composeGUI()

Description copied from class: Hyperstack_Maker

Compose the right panel of the plugin GUI.
The function readGUIInputs should be adapted accordingly.

Overrides:

composeGUI in class Hyperstack_Maker

readGuiInputs

public void readGuiInputs()

Description copied from class: Hyperstack_Maker

Read the GUI inputs, in a macro-recordable way : storing them as fields of the class.
It also saves their value in persistence.
This method can be overwritten/extended in descendant classes to read additional GUI-elements.

Overrides:

readGuiInputs in class Hyperstack_Maker

validateInputs

public boolean validateInputs()

Description copied from class: BatchDialog

Check values entered in the dialog, to make sure they make sense (no negative...).
This method should be called after the dialog is OKed, as in plugins run() method.

Overrides:

validateInputs in class Hyperstack_Maker

Returns:

true if all inputs are valid, false otherwise.

loopBody

public boolean loopBody(acquifer.core.ImageSeries imageSeries)

Description copied from class: Hyperstack_Maker

Define what is executed for each list of images representing a hyperstack.
This method can be overwritten in descendant class to execute additional stuff for every stack.
By default, it will make the hyperstack and projection as well as save them, based on the values of the protected Hyperstack_Maker.saveStack, Hyperstack_Maker.showStack..

Overrides:

loopBody in class Hyperstack_Maker

Parameters:

imageSeries - list of images infos, for a specific well and sub-Position

Returns:

true if no issue, false to interrupt the plugin execution e.g if escape was pressed.