public class BioformatConverter extends BatchDialog implements org.scijava.command.Command
The plugin gives the option to have an OME dataset with either all the metdata in each tiff header, or using a companion xml file.
In the later case, the companion contains most of the metadata and the tiff headers only a reference to the companion.
The companion must have the extension .companion.ome (enforced by the plugin). The companion filename can be adapted, here it is named after the dataset directory.
java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityTypejava.awt.Window.AccessibleAWTWindow, java.awt.Window.TypefilenameFilter, headless, imageDirectory, labelChannels, labelSubposition, labelTimepoint, labelZ, listChannels, listSubPositions, listTimepoints, listWells, listZslices, nColumns, nGroupCheckboxes, nRows, plate, rowSelectionCheckboxescheckbox, choice, defaultChoiceIndexes, defaultStrings, defaultText, defaultValues, numberField, radioButtonGroups, slider, stringField, textArea1, textArea2, theLabel| Constructor and Description |
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BioformatConverter(acquifer.core.im.FilenameFilter filenameFilter,
int versionIM)
Construct a converter from a filename filter (to pick the right images and extract metadata) and a Microscope (ex: IM03/IM04)
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| Modifier and Type | Method and Description |
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void |
run() |
boolean |
validateInputs()
Check values entered in the dialog, to make sure they make sense (no negative...).
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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, textValueChangedaddButton, addComponent, addComponent, addDirectoryField, addDirectoryField, addDirectoryOrFileField, addDirectoryOrFileField, addFileField, addFileField, addImage, addImage, addImage, addImageChoice, addStringField, createImageIcon, getConstraints, getNextImage, keyPressed, keyReleased, keyTypedaddCheckbox, 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, windowOpenedaddNotify, getAccessibleContext, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, paramString, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, setVisible, show, toBackaddPropertyChangeListener, 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, toFrontadd, 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, validateTreeaction, 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, transferFocusUpCyclepublic BioformatConverter(acquifer.core.im.FilenameFilter filenameFilter,
int versionIM)
filenameFilter - public boolean validateInputs()
BatchDialogvalidateInputs in class BatchDialogpublic void run()
run in interface Runnable