large-image-converter 1.35.0

Converter for Large Image.

Convert a variety of images into the most efficient format for Large Image.

Geospatial files are converted into cloud-optimized geotiff via gdal_translate. Single-image non-geospatial files are converted into pyramidal tiff files via pyvips. Multi-image tiff files are converted into tiff files with multiple pyramidal tiff images and have a custom image description to store frame details.

Some files can be read via the various tile sources in large_image without conversion but are inefficient (for example, uncompressed data in nd2 files). Converting these files will result in more efficient data access.

Installation

To install via pip with custom-built wheels:

pip install large-image-converter[sources] --find-links https://girder.github.io/large_image_wheels

The [sources] extra requirement is optional. When specified, all of the default large-image tile sources are installed for additional metadata extraction and format support.

Requirements

If the custom-built wheels do not cover your platform, or you want to use different versions of tools, you can install the prerequisites manually. For full functionality, the following packages and libraries are needed:

• GDAL 3.1.0 or greater, including the command-line tools and the python library

• libtiff, including the command-line tools

• libvips

Additionally, the various tile sources for large_image can be used to read input files to extract and preserve metadata and to read files that can’t be read via libvips or GDAL. The requirements of those sources need to be installed.

Usage

Command Line

In the simplest use, an image can be converted via:

large_image_converter <source path>

An output image will be generated in the same directory as the source image.

The full list of options can be obtained via:

large_image_converter --help

From Python

The convert function contains all of the main functionality:

from large_image_converter import convert

convert(<source path>)

# See the options
print(convert.__doc__)

From Girder

The converter is installed by default when girder-large-image is installed. It relies on Girder Worker to actually run the conversion.

The conversion task can be reached via the user interface on the item details pages, via the createImageItem method on the ImageItem model, or via the POST item/{itemId}/tiles endpoint.

Limitations and Future Development

There are some limitations that may be improved with additional development.

• For some multi-image files, such as OME Tiff files that cannot be read by an existing large_image tile source, the specific channel, z-value, or time step is not converted to readily usable metadata.

• Whether the original file is stored in a lossy or lossless format is not always determined. If unknown, the output defaults to lossless, which may be needlessly large.