AmiraMeshLoader¶

class io.loaders.AmiraMeshLoader¶

Bases: io.loaders.BaseImageLoader

AMIRAMESHLOADER - Loader for Amira Mesh (.am) files, based on io.loaders.BaseImageLoader base class.

This loader implements the legacy Amira Mesh reader from getImageMetadata.m and getImages.m as a standalone loader class.

It uses the existing helper functions: - getAmiraMeshHeader.m - amiraMesh2bitmap.m - ib_amiraImportGui.m (optional, used for custom binning / section selection)

Constructor Summary

AmiraMeshLoader(options)¶

AMIRAMESHLOADER - Constructor for AmiraMeshLoader class.

Syntax:

loader = io.loaders.AmiraMeshLoader(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 AmiraMeshLoader class

Example 1 - create loader with default options:

loader = io.loaders.AmiraMeshLoader();

Method Summary

loadImages(files, imginfo, options)¶

LOADIMAGES - Load image data from Amira Mesh files.

Syntax:

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

This method calls amiraMesh2bitmap() and stores the returned data into the MIB image array.

Input Arguments:

• files - structure array from loadMetadata

• 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

  • Format - HDF5 format type ('matlab.hdf5' or 'bdv.hdf5')

  • Levels - number of pyramid levels (for BDV only)

  • ReturnedLevel - selected pyramid level (for BDV only)

  • pixSize - struct with pixel sizes: .x, .y, .z, .t, .units, .tunits

  • other format-specific metadata fields

• options - (optional) struct for image loading

Output Arguments:

• img - loaded image dataset

• imginfo - updated dictionary

Example 1 - load images from Amira Mesh file:

loader = io.loaders.AmiraMeshLoader();
[imginfo, files] = loader.loadMetadata({'dataset.am'}, options);
[img, imginfo] = loader.loadImages(files, imginfo, options);

loadMetadata(filenames, options)¶

LOADMETADATA - Load metadata for Amira Mesh files.

Syntax:

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

This method reads the Amira Mesh header and populates: - files structure array (dimensions, class, binning options) - imginfo dictionary (format metadata) - pixSize structure (voxel sizes)

Input Arguments:

• filenames - cell array with filenames of Amira Mesh files

• options - (optional) struct with fields:

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

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

  • Font - [struct] font settings for dialogs

  • ParentFigure - parent figure handle for uiprogressdlg

Output Arguments:

• imginfo - dictionary with image metadata, including pixSize structure

• files - structure array with file information

Example 1 - load metadata from Amira Mesh file:

loader = io.loaders.AmiraMeshLoader();
filenames = {'dataset.am'};
[imginfo, files] = loader.loadMetadata(filenames, options);