Application defaults (utils.defaults)¶

utils.defaults.addToJavaClasspath(classpath, directory)¶

ADDTOJAVACLASSPATH - Add JAR files from a directory to the MATLAB Java classpath.

Syntax:

addToJavaClasspath(classpath, directory)

Scans directory for *.jar files and appends any that are not already in classpath using javaaddpath.

Input Arguments:

• classpath - [cell of char] current Java classpath entries (from javaclasspath)

• directory - [char] full path to the directory containing JAR files

Usage:

Example 1 - add BioFormats JARs during MIB startup

addToJavaClasspath(javaclasspath, fullfile(mibPath, 'jars'));

utils.defaults.generateDefaultPalette(paletteName, colorsNo, randomSeed)¶

GENERATEDEFAULTPALETTE - Generate a colour palette by name and number of colours.

Syntax:

palette = generateDefaultPalette(paletteName, colorsNo)
palette = generateDefaultPalette(paletteName, colorsNo, randomSeed)
[palette, cancelled] = generateDefaultPalette(paletteName, colorsNo, randomSeed)

Input Arguments:

• paletteName - [char] name of the palette to generate; supported values:

  • 'Default, 6 colors'

  • 'Distinct colors, 20 colors'

  • 'Qualitative (Monte Carlo->Half Baked), 3-12 colors'

  • 'Diverging (Merlot->Chardonnay), 3-11 colors'

  • 'Grayscale'

  • … and others defined in the function body

• colorsNo - [numeric] number of required colour channels (default: 6)

• randomSeed - (optional) seed for the 'Random Colors' palette; when omitted or empty a dialog asking for the seed is displayed. Provide a numeric value for a reproducible palette, or 'shuffle' to seed the generator from the system clock without showing the dialog

Output Arguments:

• palette - [numeric] matrix [colorId, [R G B]] with values in range 0-1; empty when the palette could not be generated, i.e. when colorsNo exceeds what the named scheme provides, or when the seed dialog was cancelled

• cancelled - [logical] true only when the user dismissed the random seed dialog. Callers must test this before reporting an empty palette as a failure, otherwise a plain cancel is shown as an error

Usage:

Example 1 - generate a 3-colour default palette

palette = utils.defaults.generateDefaultPalette('Default, 6 colors', 3);

Example 2 - generate 10 random colours without the seed dialog

palette = utils.defaults.generateDefaultPalette('Random Colors', 10, 'shuffle');

utils.defaults.generateKeyShortcuts()¶

GENERATEKEYSHORTCUTS - Generate KeyShortcuts structure with default key shortcuts.

Syntax:

KeyShortcuts = generateKeyShortcuts()

Output Arguments:

• KeyShortcuts - structure with default keyboard shortcut bindings used by MIB

Usage:

Example 1 - generate default key shortcuts

KeyShortcuts = utils.defaults.generateKeyShortcuts();

utils.defaults.generateLUT(noColorChannels)¶

GENERATELUT - Generate default LUT table for color channels.

Syntax:

lut = generateLUT(noColorChannels)

The first 3 color channels are Red, Green, Blue; others are generated using Hue shifts.

Input Arguments:

• noColorChannels - [numeric] required number of color channels; pass [] to get 3 colors (Red, Green, Blue)

Output Arguments:

• lut - [numeric] matrix with default LUT for color channels, lut(colorChannel, [R G B]) in range 0-1

Usage:

Example 1 - get the default colour scheme for 5 colour channels

lut = utils.defaults.generateLUT(5);

utils.defaults.generatePreferences()¶

GENERATEPREFERENCES - Generate the default MIB preferences structure.

Syntax:

Prefs = generatePreferences()

Output Arguments:

• Prefs - struct containing all MIB application preferences

These defaults are also the reference for the JSON override file: its values are coerced back to the class and shape of the default here, see models.MibModel.initializePreferences(). When adding a setting with a restricted set of values, describe it in preferenceComments of models.MibModel.saveOverridePreferences(), which writes the _comment entries of that file.

Usage:

Example 1 - initialise preferences at startup

obj.mibModel.preferences = utils.defaults.generatePreferences();

utils.defaults.generateSessionSettings()¶

GENERATESESSIONSETTINGS - Generate the default MIB session settings structure.

Syntax:

sessionSettings = generateSessionSettings()

Input Arguments:

• mibPath - path to MIB installation directory

Output Arguments:

• sessionSettings - struct with default session settings for MIB

Usage:

Example 1 - initialise session settings at startup

obj.mibModel.sessionSettings = utils.defaults.generateSessionSettings();

utils.defaults.initializePixSize(~)¶

INITIALIZEPIXSIZE - Initialize the pixSize structure with default voxel dimensions.

Syntax:

pixSize = initializePixSize()

Physical units default to micrometres; temporal units to seconds.

Output Arguments:

• pixSize - struct with default voxel dimensions:

  • .x - [numeric] pixel width (default: 1)

  • .y - [numeric] pixel height (default: 1)

  • .z - [numeric] slice thickness (default: 1)

  • .units - [char] physical units (default: 'um')

  • .t - [numeric] time between frames (default: 1)

  • .tunits - [char] time units (default: 's')

Usage:

Example 1 - create and customise a pixSize struct

pixSize = utils.defaults.initializePixSize();
pixSize.x = 0.065;
pixSize.units = 'um';