Montage Builder

The MontageBuilder class creates montages from time series images. It arranges frames from a time series (with optional channel information) into a grid or linear layout, with flexible options for frame selection, arrangement, and preprocessing.

Constructor

MontageBuilder(Context context)

Creates a new builder for creating montages.

Parameters:

context: The SciJava context

Methods

Source Configuration

Method	Description
`setSource(ImgPlus<?> imgPlus)`	Set the source image to use for building the montage. Parameters: `imgPlus` - The source image Returns: This builder for method chaining

Layout Configuration

Method	Description
`setSpacing(int spacing)`	Set spacing between frames in the montage. Parameters: `spacing` - The spacing in pixels Returns: This builder for method chaining
`setHorizontalLayout(boolean horizontal)`	Set the layout orientation. Parameters: `horizontal` - True for horizontal layout (left to right), false for vertical (top to bottom) Returns: This builder for method chaining
`setColumns(int columns)`	Set the number of columns for grid layout. If not set or set to -1, frames will be arranged in a single row or column based on the layout orientation. Parameters: `columns` - Number of columns Returns: This builder for method chaining

Time Range Configuration

Method	Description
`setMinT(int minT)`	Set the minimum time point to include. Parameters: `minT` - The minimum time point Returns: This builder for method chaining
`setMaxT(int maxT)`	Set the maximum time point to include. Parameters: `maxT` - The maximum time point Returns: This builder for method chaining

Frame Reduction Methods

Method	Description
`skipFrames(int skipFactor)`	Set the frame reduction method to skip frames. This will include only every Nth frame in the montage. Parameters: `skipFactor` - Include every Nth frame (e.g., 5 means include frames 0, 5, 10, etc.) Returns: This builder for method chaining
`averageFrames(int groupSize)`	Set the frame reduction method to average frames. This will average groups of N frames to create each montage frame. Parameters: `groupSize` - Number of frames to average together Returns: This builder for method chaining
`sumFrames(int groupSize)`	Set the frame reduction method to sum frames. This will sum groups of N frames to create each montage frame. Parameters: `groupSize` - Number of frames to sum together Returns: This builder for method chaining
`useAllFrames()`	Reset frame reduction to use all frames without reduction. Returns: This builder for method chaining

Frame Processing

Method	Description
`setVerticalReflection(boolean reflect)`	Enable or disable vertical reflection (flipping) of the frames. Parameters: `reflect` - True to vertically reflect frames, false for normal orientation Returns: This builder for method chaining
`setHorizontalReflection(boolean reflect)`	Enable or disable horizontal reflection (flipping) of the frames. Parameters: `reflect` - True to horizontally reflect frames, false for normal orientation Returns: This builder for method chaining
`medianFilter(int radius)`	Set the filter method to median filter for all channels. Parameters: `radius` - The radius of the median filter Returns: This builder for method chaining
`medianFilter(int radius, int channel)`	Set the filter method to median filter for a specific channel. Parameters: `radius` - The radius of the median filter, `channel` - The channel number (1-based) Returns: This builder for method chaining
`gaussianFilter(double sigma)`	Set the filter method to Gaussian filter for all channels. Parameters: `sigma` - The sigma value for the Gaussian filter Returns: This builder for method chaining
`gaussianFilter(double sigma, int channel)`	Set the filter method to Gaussian filter for a specific channel. Parameters: `sigma` - The sigma value for the Gaussian filter, `channel` - The channel number (1-based) Returns: This builder for method chaining
`tophatFilter(int radius)`	Set the filter method to top-hat filter for all channels. Parameters: `radius` - The radius of the top-hat filter Returns: This builder for method chaining
`tophatFilter(int radius, int channel)`	Set the filter method to top-hat filter for a specific channel. Parameters: `radius` - The radius of the top-hat filter, `channel` - The channel number (1-based) Returns: This builder for method chaining
`clearChannelFilters()`	Clear all channel-specific filters and reset to global filtering mode. Returns: This builder for method chaining
`threads(int numThreads)`	Set the number of threads to use for filter operations. Parameters: `numThreads` - The number of threads Returns: This builder for method chaining
`interpolation(double factor)`	Enable interpolation to increase resolution. Parameters: `factor` - The factor by which to increase resolution Returns: This builder for method chaining

Building the Montage

Method	Description
`build()`	Builds the montage. Returns: A `Dataset` containing the montage
`getMontage()`	Get the built montage (same as returned by `build()`). Returns: The `Dataset` containing the montage

Enums

FrameReductionMethod

Value	Description
`NONE`	Use all frames
`SKIP`	Skip frames (e.g., every Nth frame)
`AVERAGE`	Average groups of frames
`SUM`	Sum groups of frames

ImageFilterMethod

Value	Description
`NONE`	No filter
`MEDIAN`	Median filter
`GAUSSIAN`	Gaussian filter
`TOPHAT`	Top-hat filter

Example Usage

// Create the builder
MontageBuilder montageBuilder = new MontageBuilder(context);

// Configure and build
Dataset montage = montageBuilder
    .setSource(imgPlus)
    .setMinT(0)
    .setMaxT(49)
    .setSpacing(5)
    .setHorizontalLayout(true)
    .setColumns(5)
    .skipFrames(2)
    .tophatFilter(2)
    .setVerticalReflection(false)
    .build();

Implementation Details

The MontageBuilder class processes a time series image to create a montage. It can apply various filters from the MarsKymographUtils class before arranging the frames. The montage can be arranged in horizontal or vertical layouts, or in a grid with a specified number of columns. Frame reduction methods can be used to include only a subset of frames, or to combine frames through averaging or summing.

Channel-Specific Filtering

The builder supports both global filtering (applied to all channels) and channel-specific filtering. When channel-specific filters are used, the global filter is automatically disabled. Channel filters are applied independently to each specified channel, allowing for different processing of different channels in multi-channel images.

Nested Classes

ChannelFilterConfig

A static nested class that stores filter configuration for individual channels:

method: The ImageFilterMethod to apply
size: The filter size parameter (radius for median/top-hat, sigma for Gaussian)