ImreadLoader¶

class io.loaders.ImreadLoader¶

Bases: io.loaders.BaseImageLoader

IMREADLOADER - Loader for standard MATLAB image formats using imread, based on.

io.loaders.BaseImageLoader base class

This loader handles standard image formats that can be read using MATLAB’s built-in imread function (TIF, TIFF, PNG, JPEG, BMP, GIF, etc.). It supports multi-page TIF files, pyramidal TIF images, custom region loading, and pixel size extraction from metadata.

Constructor Summary

ImreadLoader(options)¶

IMREADLOADER - Constructor for ImreadLoader class.

Syntax:

loader = io.loaders.ImreadLoader(options)

Input Arguments:

• options - (optional) struct with fields:

  • waitbar - [logical] show or not the waitbar; default: false

  • mibPath - [char] path to MIB directory

  • customSections - [logical] load custom sections only; default: false

  • customSectionsSettings - [struct] custom section parameters

  • imgStretch - [logical] stretch uint32 images to uint16; default: false

  • silentMode - [logical] do not ask user questions; default: false

  • verbose - [logical] show timing information; default: false

  • Font - [struct] font settings for dialogs

  • ParentFigure - handle of the main MIB window (parent for uiprogressdlg)

Output Arguments:

• obj - instance of the ImreadLoader class

Example 1 - create loader with options:

options.waitbar = true;
options.mibPath = 'c:\mib';
loader = io.loaders.ImreadLoader(options);

Method Summary

loadImages(files, imginfo, options)¶

LOADIMAGES - Load image data for standard image files.

Syntax:

[img, imginfo] = obj.loadImages(files, imginfo, options)

This method loads actual image data using imread for standard MATLAB image formats. It supports multi-page TIF files, pyramidal images, custom region loading (PixelRegion), GIF conversion, and dimension mismatch handling with background filling.

Input Arguments:

• files - structure array from loadMetadata with file information:

  • filename - [char] full filename

  • objecttype - [char] type of the image loader 'imread'

  • extension - [char] file extension with dot (e.g., '.jpg')

  • height - [numeric] image height

  • width - [numeric] image width

  • color - [numeric] number of color channels

  • noLayers - [numeric] number of image layers/frames

  • time - [numeric] number of image frames

  • imgClass - [char] image class ('uint8', 'uint16', 'uint32')

  • level - [numeric] pyramid level (optional)

  • xMin, xMax, yMin, yMax - [numeric] region coordinates (optional)

  • zMin, zMax - [numeric] slice range (optional)

  • xyStep - [numeric] XY step for binning (optional)

  • backgroundColor - [numeric] background color value (optional)

• imginfo - dictionary from loadMetadata with image metadata

• options - (optional) struct with fields:

  • waitbar - [logical] show or not the waitbar; default: true

  • imgStretch - [logical] stretch uint32 to uint16; default: true

  • silentMode - [logical] do not ask user questions; default: false

Output Arguments:

• img - loaded image dataset [height, width, depth, color, time]

• imginfo - updated dictionary with final metadata:

  • Height - final image height

  • Width - final image width

  • Depth - final number of slices

  • Time - number of time points

  • ColorType - color type

  • ColorTable - colormap for indexed images (optional)

Example 1 - load images from standard image file:

loader = io.loaders.ImreadLoader();
options.waitbar = true;
[imginfo, files] = loader.loadMetadata({'image.tif'}, options);
[img, imginfo] = loader.loadImages(files, imginfo, options);
fprintf('Loaded image size: %s\n', mat2str(size(img)));

loadMetadata(filenames, options)¶

LOADMETADATA - Load metadata for standard image files.

Syntax:

[imginfo, files] = obj.loadMetadata(filenames, options)

This method extracts image metadata using imfinfo for standard MATLAB-readable image formats. It handles pyramidal TIF detection, pixel size extraction from various formats (Amira, Zeiss, Fibics), and custom section parameters.

Input Arguments:

• filenames - cell array with filenames of images

• options - (optional) struct with fields:

  • waitbar - [logical] show or not the waitbar; default: false

  • customSections - [logical] load part of the dataset; default: false

  • customSectionsSettings - [struct] custom section settings

  • xMin - [numeric] min X coordinate

  • xMax - [numeric] max X coordinate

  • yMin - [numeric] min Y coordinate

  • yMax - [numeric] max Y coordinate

  • zMin - [numeric] min Z coordinate (slice)

  • zMax - [numeric] max Z coordinate (slice)

  • xyStep - [numeric] XY binning step

  • mibPath - [char] path to MIB directory

  • ParentFigure - handle to the parent window for progress dialog

  • Font - [struct] font settings for dialogs

  • BioFormatsIndices - [numeric] level index for pyramidal TIF

Output Arguments:

• imginfo - dictionary with image metadata containing fields:

  • Height - image height in pixels

  • Width - image width in pixels

  • Colors - number of color channels

  • Depth - number of z-slices

  • Time - number of time points

  • imgClass - image class (uint8, uint16, etc.)

  • ColorType - 'grayscale', 'truecolor', or 'indexed'

  • ImageDescription - description with BoundingBox info

  • other format-specific metadata fields

• files - structure array with file information for each file:

  • filename - [char] full filename

  • objecttype - [char] type of the image loader 'imread'

  • extension - [char] file extension, including the leading dot

  • height - [numeric] image height

  • width - [numeric] image width

  • color - [numeric] number of color channels

  • noLayers - [numeric] number of image frames

  • time - [numeric] number of time points

  • imgClass - [char] image class ('uint8', 'uint16', 'uint32', 'single')

  • level - [numeric] pyramid level (for pyramidal TIF)

  • levelMagScale - [numeric] magnification scale factor

  • xMin, xMax, yMin, yMax - [numeric] region coordinates

  • xyStep - [numeric] XY step for binning

Example 1 - load metadata from standard image files:

loader = io.loaders.ImreadLoader();
options.waitbar = true;
filenames = {'image1.tif', 'image2.tif'};
[imginfo, files] = loader.loadMetadata(filenames, options);
fprintf('Image size: %d x %d x %d\n', imginfo{"Width"}, imginfo{"Height"}, imginfo{"Depth"});