acquifer.ij.im.plugins

Class Hyperstack_Maker

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

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_Macro, Hyperstack_Maker, Hyperstack_Maker, Hyperstack_Script

public class Hyperstack_Maker
extends BatchDialog
implements org.scijava.command.Command

Plugin to generate hyperstacks and/or Z-Projection of IM images provided an image directory and optional selection of dimensions.
Running the plugin will display a dialog to set the image directory and the selection of wells and dimensions.

The plugin (and subclasses of this plugin) can be called either via their menu entry, by calling Hyperstack_Maker.run("") (display the GUI) or by running the macro-recorded command ("preconfigured headless execution").
Macro-recording is automatically implemented thanks to the use of BatchDialog (a custom subclass of GenericDialog).

The generated hyperstack use VirtualStacks for efficient data-loading from disk.
The pixel size (Calibration) is automatically set according to the metadata in the filename, for images of original dimensions (2048 x 2048, to make sure no binning was done).
With Z-stack, the pixel size is also set for the Z-dimension. It is reported as the pixel depth, although it is NOT the depth-of-focus, but the spacing between slices.
The depth for the full stack volume is thus not as reported in Image > Show Info..., but the reported value - 1 pixel "depth".

With multiple channels, colour LUT are automatically associated to the corresponding microscope channel of the image.
Default colour LUTs are provided, but the mapping microscope channel<->LUT-colour can be customised either programmatically with setDefaultChannelsLut(String[]) or setChannelLut(int, String).
Or via the dedicated plugin in ACQUIFER > Settings > Set_Channel_Colors.py

Note about headless execution
While the plugin can be executed in headless mode, since displaying of images is not supported it has limited benefit. The saving of the projected images can be performed though.
The plugin can also be called via the command line without the --headless tag.
This works with the --ij2 --console --run myMacro.ijm for instance, but only for a single call.
This first call opens Fiji and will run the macro, eventually calling the plugin and showing the images.
Calling a second time the command in the same command prompt currently fails though, if the single instance listener option is on (Edit > Options > Misc).

TODO use a custom class WellStack like the PlateStack that would facilitate defining custom LUT...

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Hyperstack_Maker.DisplayMode Display mode for hyperstack with multiple channels.

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

Modifier and Type	Field and Description
protected static String[]	channelsLuts User-defined LUT names to use for the IM channels.
protected static double	displayMagnification Relative size of the image window displayed in Fiji in %.
protected acquifer.core.ImageSeries[]	groupedImageInfos
protected acquifer.core.im.MetadataParser	metadataParser
String[]	METHODS Set of projection method for the stack
protected ij.ImagePlus	proj Stack projection
protected String	projDir Where to save the projection if saveProjection is true
protected boolean	projectStack If yes or no the stack should be projected
protected String	projMethod The selected projection method as a string
protected static double	saturation Percentage of pixels that will be saturated when enhancing the contrast.
protected boolean	saveProjection If the projection should be saved
protected boolean	saveStack If yes or no, the stack should be saved.
protected boolean	showProjection Show stack projection (yes/no)
protected boolean	showProjectionTickbox If a tick box should be shown in the GUI to ask the user about yes/no project stack
protected boolean	showStack If yes or no the stack should be shown
protected ij.ImagePlus	stack Stack/hyperstack generated by the plugin at each iteration (each well).
protected String	stackDir Where the stack should be saved if saveStack is true.
protected int	startSlice
protected int	stopSlice
protected boolean	useCustomRange If a custom Z-slice range should be used for projection
protected boolean	useVirtual If VirtualStack should be used to display the stack.

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_Maker(String title, acquifer.core.im.FilenameFilter filenameFilter) Initialise the hyperstack maker plugin with the associated GUI window title, (ie IM03/4) metadataParser and fileUtils.

Method Summary

Modifier and Type	Method and Description
protected void	composeGUI() Compose the right panel of the plugin GUI.
static ij.gui.ImageWindow	createImageWindow(ij.ImagePlus imp, double magnification) Create an image window for the display of an image at a predefined display magnification (for ImageJ>=1.53i27).
boolean	executedOnce() Method called once in the run() method before loopBody(ImageSeries) is called for each stack.
static String[]	getChannelsLuts() Return the list of colours LUT associated to the microscope channels.
static String	getLutNameForChannel(int channel) Return the name of the color-LUT associated to a given microscope channel (between 1 and 6).
static String[]	getLuts() Returns the list of LUTs advised for the display of hyperstacks channels.
static ij.ImagePlus[]	groupAsHyperStacks(acquifer.core.Dataset dataset, acquifer.core.im.MetadataParser metadataParser) Make a list of hyperstacks from the ImageSeries contained in a dataset.
static boolean	isMultiDimensional(ij.ImagePlus stack) Return true if the stack has at least 2-dimension sliders.
static boolean	isOneDimensional(ij.ImagePlus imp) Check if an ImagePlus is a 1D dimensional stack (ie single dimension slider).
boolean	loopBody(acquifer.core.ImageSeries imageSeries) Define what is executed for each list of images representing a hyperstack.
static ij.ImagePlus	makeHyperStack(acquifer.core.ImageSeries imageSeries, acquifer.core.im.MetadataParser metadataParser) Create a hyperstack from an imageSeries adding pixel size read from the tiff header.
ij.ImagePlus	makeHyperStack(acquifer.core.im.Metadata[] subList) Deprecated. prefer makeHyperStack(ImageSeries, MetadataParser)
static ij.ImagePlus	makeHyperStack(String title, ij.VirtualStack vStack, int nChannels, int nZslices, int nTimepoints) Same as makeHyperStack(String, VirtualStack, int, int, int, DisplayMode) but uses the display mode set in preference (hyperstack.displayMode).
static ij.ImagePlus	makeHyperStack(String title, ij.VirtualStack vStack, int nChannels, int nZslices, int nTimepoints, Hyperstack_Maker.DisplayMode displayMode) Make a multi-dimensional hyperstack from a 1D virtual stack of disk-resident images.
static ij.VirtualStack	makeVirtualStack(acquifer.core.im.Metadata[] listImageInfos) Returns a 1D VirtualStack from a list of ImageInfos, for a given well and subposition.
void	readGuiInputs() Read the GUI inputs, in a macro-recordable way : storing them as fields of the class.
void	renameProjectedSlices(ij.ImagePlus stack, ij.ImagePlus proj, String projMethod, boolean useCustomRange, int firstSlice) When the result of the projection is a stack, rename the slice labels according to original stack.
static void	resetDisplayRange(ij.ImagePlus hyperstack) Auto-scale display range by histogram stretching, same as Process>Enhance Contrast or Image>Adjust>Brightness/Contrast.
void	run() Call the hyperstack plugin to generate hyperstacks from list of IM files.
static void	setChannelLut(int channel, String lutName) Set the Look Up Table (LUT) for a given channel of the microscope.
static void	setContrastSaturation(double percentSaturation) Set the saturation used to automatically enhance contrast of stacks generated with the plugin.
static void	setDefaultChannelsLut(String[] lutNames) Set the Look Up Tables used to rendered the IM channels in hyperstacks.
static void	setDefaultDisplayMagnification(double magnification) Set default magnification used by the hyperstack plugin for the display of new images.
static void	setDefaultSliderPositions(ij.ImagePlus imp) Set the slider position to the default values defined in settings
static void	setHyperStackDisplayMode(Hyperstack_Maker.DisplayMode mode) Set the default display mode for hyperstack when nChannels>1.
static void	setLUTs(ij.ImagePlus imp, Collection<Integer> setChannels) Apply the LUT defined in settings to the channels of the provided imp (for ImageJ>=1.53).
static void	showHyperStacks(acquifer.core.Dataset dataset, acquifer.core.im.MetadataParser metadataParser) Display the hyperstack(s) of a dataset.
static void	updateDisplayMagnification(ij.ImagePlus imp, double magnification) Set the magnification-level of an image already displayed.
static boolean	validateCustomRange(ij.ImagePlus stack, int start, int stop) Verify that the custom range for projection with a substack fits in the actual stack dimensions.
boolean	validateInputs() Check values entered in the dialog, to make sure they make sense (no negative...).

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

Field Detail

metadataParser

protected acquifer.core.im.MetadataParser metadataParser

groupedImageInfos

protected acquifer.core.ImageSeries[] groupedImageInfos

showStack

protected boolean showStack

If yes or no the stack should be shown

useVirtual

protected boolean useVirtual

If VirtualStack should be used to display the stack.
Faster but potential compatibility issues with macros (i.e need to duplicate).

saveStack

protected boolean saveStack

If yes or no, the stack should be saved.
If yes, it is saved in stackDir.

stackDir

protected String stackDir

Where the stack should be saved if saveStack is true.

projectStack

protected boolean projectStack

If yes or no the stack should be projected

showProjectionTickbox

protected boolean showProjectionTickbox

If a tick box should be shown in the GUI to ask the user about yes/no project stack

showProjection

protected boolean showProjection

Show stack projection (yes/no)

saveProjection

protected boolean saveProjection

If the projection should be saved

METHODS

public final String[] METHODS

Set of projection method for the stack

projMethod

protected String projMethod

The selected projection method as a string

useCustomRange

protected boolean useCustomRange

If a custom Z-slice range should be used for projection

startSlice

protected int startSlice

stopSlice

protected int stopSlice

projDir

protected String projDir

Where to save the projection if saveProjection is true

stack

protected ij.ImagePlus stack

Stack/hyperstack generated by the plugin at each iteration (each well).

proj

protected ij.ImagePlus proj

Stack projection

saturation

protected static double saturation

Percentage of pixels that will be saturated when enhancing the contrast.

displayMagnification

protected static double displayMagnification

Relative size of the image window displayed in Fiji in %.

channelsLuts

protected static String[] channelsLuts

User-defined LUT names to use for the IM channels.
The colors in this array are listed in order of the IM channels, from CO1 to CO6.
The process from IM channel to color LUT is : channel number > LUT name > colorModel = LUTLoader.getLut(name) > lut = LUT(colorModel) > imp.setLUT(lut)
.

Constructor Detail

Hyperstack_Maker

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

Initialise the hyperstack maker plugin with the associated GUI window title, (ie IM03/4) metadataParser and fileUtils.
The idea is that for different IM versions, one can simply extend this plugin, specifying the corresponding MetadataParser and FileUtils for the desired IM version.

Parameters:

filenameFilter - an instance of filenameFilter specific to the relevant IM version, used to keep only IM image files.

Method Detail

composeGUI

protected void composeGUI()

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

run

public void run()

Call the hyperstack plugin to generate hyperstacks from list of IM files.
1) display dialog and read values
2) Validate input values
3) Make group of images belonging to the same hyperstack
4) Loop over each of this group, calling loopBody(ImageSeries) for each of them.
By default loopBody(ImageSeries) makes a hyperstack and if selected a Z-projection and display them if selected.

Specified by:

run in interface Runnable

readGuiInputs

public void readGuiInputs()

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.

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 BatchDialog

Returns:

true if all inputs are valid, false otherwise.

executedOnce

public boolean executedOnce()

Method called once in the run() method before loopBody(ImageSeries) is called for each stack.
Returns true, if no issue, otherwise false to interrupt execution (ex: no images matching the GUI selection).
Overwriting this function can be useful to do action in additions to default before looping for every stack.

loopBody

public boolean loopBody(acquifer.core.ImageSeries imageSeries)

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 saveStack, showStack..

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.

makeVirtualStack

public static ij.VirtualStack makeVirtualStack(acquifer.core.im.Metadata[] listImageInfos)
                                        throws loci.formats.FormatException,
                                               IOException,
                                               IllegalArgumentException

Returns a 1D VirtualStack from a list of ImageInfos, for a given well and subposition.
The images should have the same width/height dimensions, and reside in the same directory.

Throws:

IOException

loci.formats.FormatException

IllegalArgumentException

makeHyperStack

public static ij.ImagePlus makeHyperStack(String title,
                                          ij.VirtualStack vStack,
                                          int nChannels,
                                          int nZslices,
                                          int nTimepoints,
                                          Hyperstack_Maker.DisplayMode displayMode)

Make a multi-dimensional hyperstack from a 1D virtual stack of disk-resident images.
The number of slices in the VirtualStack should match the dimensions of the hyperstack (nSlices == nChannels x nZslices x nTimepoints).
The slice order in the VirtualStack should also match the default dimensions order (czt).
Use resetDisplayRange(ImagePlus) after displaying the resulting hyperstack to auto-adjust the brightness for each channel.
This function also populates the FileInfo for the hyperstack such as the directory.. available by pressing "i" when the image is displayed.

Parameters:

title - title for the output ImagePlus

vStack -

nChannels - the number of channels in the resulting hyperstack

nZslices - the number of Z-slices in the resulting hyperstack

nTimepoints - the number of timepoints in the resulting hyperstack

displayMode - when nChannels>1, set the display mode to "grayscale", "color" (1 LUT/channel) or "composite" (1 LUT/channel and overlaid).

Returns:

an ImagePlus, which can be a hyperstack or a single image plane if nSlices=1.

makeHyperStack

public static ij.ImagePlus makeHyperStack(String title,
                                          ij.VirtualStack vStack,
                                          int nChannels,
                                          int nZslices,
                                          int nTimepoints)

Same as makeHyperStack(String, VirtualStack, int, int, int, DisplayMode) but uses the display mode set in preference (hyperstack.displayMode).
If the this preference does not exist yet, default to DisplayMode.COLOR.
Use resetDisplayRange(ImagePlus) after displaying the hyperstack to auto-adjust the brightness for each channel.

makeHyperStack

public static ij.ImagePlus makeHyperStack(acquifer.core.ImageSeries imageSeries,
                                          acquifer.core.im.MetadataParser metadataParser)
                                   throws IOException

Create a hyperstack from an imageSeries adding pixel size read from the tiff header.
The generated hyperstack uses the default display mode defined in preferences (GRAY or COMPOSITE).
Use resetDisplayRange(ImagePlus) after displaying the hyperstack to auto-adjust the brightness for each channel.

Parameters:

imageSeries - images forming a hyperstack

metadataParser - used to parse the pixel size from the image name

Throws:

IOException

makeHyperStack

@Deprecated
public ij.ImagePlus makeHyperStack(acquifer.core.im.Metadata[] subList)
                                         throws IllegalArgumentException,
                                                loci.formats.FormatException,
                                                IOException

Deprecated. prefer makeHyperStack(ImageSeries, MetadataParser)

Make a multi-dimensional hyperstack (as VirtualStack) from a list of Metadata.
The ImageInfos should be for a given well and subposition.
The images should have the same width/height dimensions and reside in the same directory.

Parameters:

subList -

Returns:

Throws:

IOException

loci.formats.FormatException

IllegalArgumentException

groupAsHyperStacks

public static ij.ImagePlus[] groupAsHyperStacks(acquifer.core.Dataset dataset,
                                                acquifer.core.im.MetadataParser metadataParser)

Make a list of hyperstacks from the ImageSeries contained in a dataset.
Tip : Use a DatasetBuilder to make a dataset with a specific set of dimensions.

Parameters:

dataset - a hyperstack will be generated for each ImageSeries in the dataset.

metadataParser - used to parse the pixel size from the image name.

showHyperStacks

public static void showHyperStacks(acquifer.core.Dataset dataset,
                                   acquifer.core.im.MetadataParser metadataParser)

Display the hyperstack(s) of a dataset.

isMultiDimensional

public static boolean isMultiDimensional(ij.ImagePlus stack)

Return true if the stack has at least 2-dimension sliders.
This function is different than ImagePlus.isHyperStack which also returns true for 1D multi-channels stack.

isOneDimensional

public static boolean isOneDimensional(ij.ImagePlus imp)

Check if an ImagePlus is a 1D dimensional stack (ie single dimension slider).

validateCustomRange

public static boolean validateCustomRange(ij.ImagePlus stack,
                                          int start,
                                          int stop)

Verify that the custom range for projection with a substack fits in the actual stack dimensions.

renameProjectedSlices

public void renameProjectedSlices(ij.ImagePlus stack,
                                  ij.ImagePlus proj,
                                  String projMethod,
                                  boolean useCustomRange,
                                  int firstSlice)

When the result of the projection is a stack, rename the slice labels according to original stack.
For projection of the Z-dimension, replace the SLXXX with SL + projection method ex: SLmax.
For projection of the time dimension, replace the LOXXX with LO + projection method.

setDefaultSliderPositions

public static void setDefaultSliderPositions(ij.ImagePlus imp)

Set the slider position to the default values defined in settings

setDefaultChannelsLut

public static void setDefaultChannelsLut(String[] lutNames)

Set the Look Up Tables used to rendered the IM channels in hyperstacks.
The list of LUTs should be ordered according to the microscope channels (CO1 to CO6).
{getLuts() returns a list of LUT names advised for channels, but any LUt in IJ.getLuts is actually supported.

Parameters:

lutNames - a list of colour names ex: ["Blue", "Red"...]. The number of colours should not exceed the number of channels (ie max 6).
If less than 6 LUT names are provided, only the first n channel colours are set.

setChannelLut

public static void setChannelLut(int channel,
                                 String lutName)

Set the Look Up Table (LUT) for a given channel of the microscope.
Use getLuts() to see the list of LUTs advised for rendering of channels (additional channels in IJ.getLuts are supported though).

Parameters:

channel - index of the microscope channel, between 1 and 6 (brightfield)

lutName - name (case sensitive) of a LUT to use for this channel, ex: "Red"

setLUTs

public static void setLUTs(ij.ImagePlus imp,
                           Collection<Integer> setChannels)

Apply the LUT defined in settings to the channels of the provided imp (for ImageJ>=1.53).
The LUT colours are applied according to the IM channels contained in this imp, mentioned by the argument setChannels.
IM channels are mapped to an imp (or hyperstack) channels in reverse order (CO6 to CO1).
Reminder: imp channels are only positional arguments (position of the slider along the channel dimension).

Parameters:

imp - hyperstack image for which to set custom LUT

setChannels - the IM channels contained in this imp. In the imp the IM channels are sorted in reverse order to have the brightfield channel in first position when present (CO6).

resetDisplayRange

public static void resetDisplayRange(ij.ImagePlus hyperstack)

Auto-scale display range by histogram stretching, same as Process>Enhance Contrast or Image>Adjust>Brightness/Contrast.
This method should be called once the image displayed.
It should not affect the pixel values, just the display range (ie reversible).
However in practice it sometimes normalizes the histogram to the full bit range.

NOTE : this function should work well with CompositeImage. It might not work with VirtualStacks as the ImageProcessor are reloaded from disk.

The code below sets the same display range for all slices of a given channel.
Using ContrastEnhancer.stretchHistogram will not work since we are using VirtualStacks by default, instead we use the center slice as reference and set the stack display range to it's min/max.

However, running Enhance Contrast after the hyperstack plugin might yield a slightly different result, either because useStackHistogram is set to false -> it will use the histogram for the current slice, not what is done here.
while for multi-channel stacks even with useStackHistogram, the result will be different because it will use the full stack
With multi-channel images, only the center Z-slice (or first Z-slice if only 1 Z-slice) should yield the same result than if done with the GUI.

getLuts

public static String[] getLuts()

Returns the list of LUTs advised for the display of hyperstacks channels.

getChannelsLuts

public static String[] getChannelsLuts()

Return the list of colours LUT associated to the microscope channels.

getLutNameForChannel

public static String getLutNameForChannel(int channel)

Return the name of the color-LUT associated to a given microscope channel (between 1 and 6).

setContrastSaturation

public static void setContrastSaturation(double percentSaturation)

Set the saturation used to automatically enhance contrast of stacks generated with the plugin.

Parameters:

percentSaturation - between 0 and 100

Throws:

IllegalArgumentException - if saturation is not between 0 and 100

createImageWindow

public static ij.gui.ImageWindow createImageWindow(ij.ImagePlus imp,
                                                   double magnification)

Create an image window for the display of an image at a predefined display magnification (for ImageJ>=1.53i27).
Don't call this function in headless mode.

Parameters:

imp - image for which to create a window

magnification - zoom level, e.g 0.5 for 50% (supported for ImageJ>=1.53i27)

updateDisplayMagnification

public static void updateDisplayMagnification(ij.ImagePlus imp,
                                              double magnification)

Set the magnification-level of an image already displayed.

Parameters:

imp - the image to resize

magnification - zoom factor (e.g 0.5 = 50%)

setDefaultDisplayMagnification

public static void setDefaultDisplayMagnification(double magnification)

Set default magnification used by the hyperstack plugin for the display of new images.

Parameters:

magnification - between 0 and 1 (ie 0.5 = 50%)

setHyperStackDisplayMode

public static void setHyperStackDisplayMode(Hyperstack_Maker.DisplayMode mode)

Set the default display mode for hyperstack when nChannels>1.
This is equivalent than Prefs.set("hyperstack.displayMode", mode) with mode = "grayscale", "color" or "composite"