Skip to main content

Girder Worker tasks for Large Image.

Project description

Large Image Build Status codecov.io License doi-badge

Python modules to work with large multiresolution images.

Quick Installation via pip

In addition to installing the large-image package, you’ll need at least one tile source (a large-image-source-xxx package). You can install everything from the main project with one of these commands:

  • Install all tile sources and all Girder plugins on linux: pip install large-image[all] girder-large-image-annotation[tasks] --find-links https://girder.github.io/large_image_wheels

  • Install all tile sources on linux: pip install large-image[all] --find-links https://girder.github.io/large_image_wheels

Modules

Large Image consists of several Python modules designed to work together. These include:

  • large-image: The core module. You can specify extras_require of the name of any tile source included with this repository, sources for all of the tile sources in the repository, memcached for using memcached for tile caching, or all for all of the tile sources and memcached.

  • large-image-converter: A utility for using pyvips and other libraries to convert images into pyramidal tiff files that can be read efficiently by large_image.

  • girder-large-image: Large Image as a Girder 3.x plugin. You can specify extras_require of tasks to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.

  • girder-large-image-annotation: Annotations for large images as a Girder 3.x plugin.

  • large-image-tasks: A utility for running the converter via Girder Worker.

  • Tile sources:

    • large-image-source-tiff: A tile source for reading pyramidal tiff files in common compression formats.

    • large-image-source-openslide: A tile source using the OpenSlide library. This works with svs, ndpi, Mirax, tiff, vms, and other file formats.

    • large-image-source-ometiff: A tile source using the tiff library that can handle some multi-frame OMETiff files.

    • large-image-source-pil: A tile source for small images via the Python Imaging Library (Pillow).

    • large-image-source-gdal: A tile source for reading geotiff files via GDAL. This handles source data with more complex transforms than the mapnik tile source.

    • large-image-source-mapnik: A tile source for reading geotiff and netcdf files via Mapnik and GDAL. This handles more vector issues than the gdal tile source.

    • large-image-source-openjpeg: A tile source using the Glymur library to read jp2 (JPEG 2000) files.

    • large-image-source-nd2: A tile source for reading nd2 (NIS Element) images.

    • large-image-source-bioformats: A tile source for reading any file handled by the Java Bioformats library.

    • large-image-source-deepzoom: A tile source for reading Deepzoom tiles.

    • large-image-source-test: A tile source that generates test tiles, including a simple fractal pattern. Useful for testing extreme zoom levels.

    • large-image-source-dummy: A tile source that does nothing.

    Most tile sources can be used with girder-large-image.

Installation

To install all packages from source:

  1. Clone the repository:

    git clone https://github.com/girder/large_image.git

    Change to the source directory:

    cd large_image

  2. Install all packages and dependencies:

    pip install -e . -r requirements-dev.txt

Tile source prerequisites

Many tile sources have complex prerequisites. These can be installed directly using your system’s package manager or from some prebuilt Python wheels for Linux. The prebuilt wheels are not official packages, but they can be used by instructing pip to use them by preference:

pip install -e . -r requirements-dev.txt --find-links https://girder.github.io/large_image_wheels

Migration from Girder 2 to Girder 3

If you are migrating a Girder 2 instance with Large Image to Girder 3, you need to do a one time database update. Specifically, one of the tile sources’ internal name changed.

Access the Girder Mongo database. The command for this in a simple installation is:

mongo girder

Update the tile source name by issuing the Mongo command:

db.item.updateMany({"largeImage.sourceName": "svs"}, {$set: {"largeImage.sourceName": "openslide"}})

Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

large-image-tasks-1.7.2.dev22.tar.gz (4.2 kB view details)

Uploaded Source

Built Distribution

large_image_tasks-1.7.2.dev22-py3-none-any.whl (6.3 kB view details)

Uploaded Python 3

File details

Details for the file large-image-tasks-1.7.2.dev22.tar.gz.

File metadata

  • Download URL: large-image-tasks-1.7.2.dev22.tar.gz
  • Upload date:
  • Size: 4.2 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.4.2 importlib_metadata/4.6.4 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.7.11

File hashes

Hashes for large-image-tasks-1.7.2.dev22.tar.gz
Algorithm Hash digest
SHA256 0d76a393636acbec59461b8d124a93cb0041a7f9845f3f807399769c473e149b
MD5 936fb692915d6b9e8d6d3cca1448bd67
BLAKE2b-256 4305ef5c88f5a6a75bda0bc4249d49cd4e71bdb1596c99535e1319f62ea49d3a

See more details on using hashes here.

Provenance

File details

Details for the file large_image_tasks-1.7.2.dev22-py3-none-any.whl.

File metadata

  • Download URL: large_image_tasks-1.7.2.dev22-py3-none-any.whl
  • Upload date:
  • Size: 6.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.4.2 importlib_metadata/4.6.4 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.7.11

File hashes

Hashes for large_image_tasks-1.7.2.dev22-py3-none-any.whl
Algorithm Hash digest
SHA256 8fb78490490d92346a8238f0a350787562409af4affd909ce8903dc1fc03d164
MD5 e2d7c2f1c38c7034b79a8804e5710973
BLAKE2b-256 498644a6da15c2f296d3dd323ef3e98ec7b069f9c5b36d3e57560d378f9368f8

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page