large-image 1.27.5.dev71__tar.gz → 1.30.7.dev10__tar.gz

large_image-1.30.7.dev10/PKG-INFO

@@ -0,0 +1,312 @@
+Metadata-Version: 2.1
+Name: large-image
+Version: 1.30.7.dev10
+Summary: Python modules to work with large, multiresolution images.
+Home-page: https://github.com/girder/large_image
+Author: Kitware, Inc.
+Author-email: kitware@kitware.com
+License: Apache Software License 2.0
+Keywords: large_image
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: cachetools
+Requires-Dist: palettable
+Requires-Dist: Pillow
+Requires-Dist: numpy
+Requires-Dist: typing-extensions
+Provides-Extra: memcached
+Requires-Dist: pylibmc>=1.5.1; platform_system != "Windows" and extra == "memcached"
+Provides-Extra: redis
+Requires-Dist: redis>=4.5.5; extra == "redis"
+Provides-Extra: converter
+Requires-Dist: large-image-converter>=1.30.7.dev10; extra == "converter"
+Provides-Extra: colormaps
+Requires-Dist: matplotlib; extra == "colormaps"
+Requires-Dist: tol_colors; extra == "colormaps"
+Provides-Extra: tiledoutput
+Requires-Dist: pyvips; extra == "tiledoutput"
+Provides-Extra: performance
+Requires-Dist: psutil>=4.2.0; extra == "performance"
+Requires-Dist: simplejpeg; extra == "performance"
+Provides-Extra: bioformats
+Requires-Dist: large-image-source-bioformats>=1.30.7.dev10; extra == "bioformats"
+Provides-Extra: deepzoom
+Requires-Dist: large-image-source-deepzoom>=1.30.7.dev10; extra == "deepzoom"
+Provides-Extra: dicom
+Requires-Dist: large-image-source-dicom>=1.30.7.dev10; extra == "dicom"
+Provides-Extra: dummy
+Requires-Dist: large-image-source-dummy>=1.30.7.dev10; extra == "dummy"
+Provides-Extra: gdal
+Requires-Dist: large-image-source-gdal>=1.30.7.dev10; extra == "gdal"
+Provides-Extra: mapnik
+Requires-Dist: large-image-source-mapnik>=1.30.7.dev10; extra == "mapnik"
+Provides-Extra: multi
+Requires-Dist: large-image-source-multi>=1.30.7.dev10; extra == "multi"
+Provides-Extra: nd2
+Requires-Dist: large-image-source-nd2>=1.30.7.dev10; extra == "nd2"
+Provides-Extra: ometiff
+Requires-Dist: large-image-source-ometiff>=1.30.7.dev10; extra == "ometiff"
+Provides-Extra: openjpeg
+Requires-Dist: large-image-source-openjpeg>=1.30.7.dev10; extra == "openjpeg"
+Provides-Extra: openslide
+Requires-Dist: large-image-source-openslide>=1.30.7.dev10; extra == "openslide"
+Provides-Extra: pil
+Requires-Dist: large-image-source-pil>=1.30.7.dev10; extra == "pil"
+Provides-Extra: rasterio
+Requires-Dist: large-image-source-rasterio>=1.30.7.dev10; extra == "rasterio"
+Provides-Extra: test
+Requires-Dist: large-image-source-test>=1.30.7.dev10; extra == "test"
+Provides-Extra: tiff
+Requires-Dist: large-image-source-tiff>=1.30.7.dev10; extra == "tiff"
+Provides-Extra: tifffile
+Requires-Dist: large-image-source-tifffile>=1.30.7.dev10; extra == "tifffile"
+Provides-Extra: vips
+Requires-Dist: large-image-source-vips>=1.30.7.dev10; extra == "vips"
+Provides-Extra: zarr
+Requires-Dist: large-image-source-zarr>=1.30.7.dev10; extra == "zarr"
+Provides-Extra: sources
+Requires-Dist: large-image-source-mapnik>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-vips>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-test>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-tifffile>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-bioformats>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-ometiff>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-dummy>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-gdal>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-deepzoom>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-openslide>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-tiff>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-zarr>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-nd2>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-rasterio>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-openjpeg>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-multi>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-dicom>=1.30.7.dev10; extra == "sources"
+Requires-Dist: large-image-source-pil>=1.30.7.dev10; extra == "sources"
+Provides-Extra: all
+Requires-Dist: pyvips; extra == "all"
+Requires-Dist: large-image-source-mapnik>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-tifffile>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-test>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-bioformats>=1.30.7.dev10; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: large-image-source-gdal>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-tiff>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-deepzoom>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-openslide>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-tiff[all]>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-multi[all]>=1.30.7.dev10; extra == "all"
+Requires-Dist: tol_colors; extra == "all"
+Requires-Dist: large-image-source-multi>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-pil>=1.30.7.dev10; extra == "all"
+Requires-Dist: pylibmc>=1.5.1; platform_system != "Windows" and extra == "all"
+Requires-Dist: large-image-source-vips>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-rasterio[all]>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-pil[all]>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-ometiff>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-dummy>=1.30.7.dev10; extra == "all"
+Requires-Dist: redis>=4.5.5; extra == "all"
+Requires-Dist: psutil>=4.2.0; extra == "all"
+Requires-Dist: simplejpeg; extra == "all"
+Requires-Dist: large-image-converter>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-zarr>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-nd2>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-rasterio>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-openjpeg>=1.30.7.dev10; extra == "all"
+Requires-Dist: large-image-source-dicom>=1.30.7.dev10; extra == "all"
+Provides-Extra: common
+Requires-Dist: large-image-source-rasterio[all]>=1.30.7.dev10; extra == "common"
+Requires-Dist: large-image-source-tifffile>=1.30.7.dev10; extra == "common"
+Requires-Dist: large-image-source-test>=1.30.7.dev10; extra == "common"
+Requires-Dist: large-image-source-pil[all]>=1.30.7.dev10; extra == "common"
+Requires-Dist: matplotlib; extra == "common"
+Requires-Dist: psutil>=4.2.0; extra == "common"
+Requires-Dist: large-image-source-deepzoom>=1.30.7.dev10; extra == "common"
+Requires-Dist: large-image-source-openslide>=1.30.7.dev10; extra == "common"
+Requires-Dist: large-image-source-zarr>=1.30.7.dev10; extra == "common"
+Requires-Dist: simplejpeg; extra == "common"
+Requires-Dist: tol_colors; extra == "common"
+Requires-Dist: large-image-source-nd2>=1.30.7.dev10; extra == "common"
+Requires-Dist: large-image-source-multi>=1.30.7.dev10; extra == "common"
+Requires-Dist: large-image-source-dicom>=1.30.7.dev10; extra == "common"
+
+Large Image
+===========
+
+|build-status| |codecov-io| |license-badge| |doi-badge| |pypi-badge|
+
+.. |build-status| image:: https://img.shields.io/circleci/build/github/girder/large_image.svg
+    :target: https://circleci.com/gh/girder/large_image
+    :alt: Build Status
+
+.. |license-badge| image:: https://img.shields.io/badge/license-Apache%202-blue.svg
+    :target: https://raw.githubusercontent.com/girder/large_image/master/LICENSE
+    :alt: License
+
+.. |codecov-io| image:: https://img.shields.io/codecov/c/github/girder/large_image.svg
+   :target: https://codecov.io/github/girder/large_image?branch=master
+   :alt: codecov.io
+
+.. |doi-badge| image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4723355-blue.svg
+   :target: https://zenodo.org/badge/latestdoi/45569214
+
+.. |pypi-badge| image:: https://img.shields.io/pypi/v/large-image.svg?logo=python&logoColor=white
+   :target: https://pypi.org/project/large-image/
+
+*Python modules to work with large, multiresolution images.*
+
+Large Image is developed and maintained by the Data & Analytics group at `Kitware, Inc. <https://kitware.com>`_ for processing large geospatial and medical images. This provides the backbone for several of our image analysis platforms including `Resonant GeoData <https://github.com/ResonantGeoData/ResonantGeoData>`_, `HistomicsUI <https://github.com/DigitalSlideArchive/HistomicsUI>`_, and `the Digital Slide Archive <https://digitalslidearchive.github.io/digital_slide_archive/>`_.
+
+
+Highlights
+----------
+
+- Tile serving made easy
+- Supports a wide variety of geospatial and medical image formats
+- Convert to tiled Cloud Optimized (Geo)Tiffs (also known as pyramidal tiffs)
+- Python methods for retiling or accessing regions of images efficiently
+- Options for restyling tiles, such as dynamically applying color and band transform
+
+
+Installation
+------------
+
+In addition to installing the base ``large-image`` package, you'll need at least one tile source which corresponds to your target file format(s) (a ``large-image-source-xxx`` package).   You can install everything from the main project with one of these commands:
+
+Pip
+~~~
+
+Install common tile sources on linux, OSX, or Windows::
+
+    pip install large-image[common]
+
+Install all tile sources on linux::
+
+    pip install large-image[all] --find-links https://girder.github.io/large_image_wheels
+
+When using large-image with an instance of `Girder`_, 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
+
+
+Conda
+~~~~~
+
+Conda makes dependency management a bit easier if not on Linux. The base module, converter module, and two of the source modules are available on conda-forge. You can install the following::
+
+    conda install -c conda-forge large-image
+    conda install -c conda-forge large-image-source-gdal
+    conda install -c conda-forge large-image-source-tiff
+    conda install -c conda-forge large-image-converter
+
+
+Docker Image
+~~~~~~~~~~~~
+
+Included in this repository’s packages is a pre-built Docker image that has all
+of the dependencies to read any supported image format.
+
+This is particularly useful if you do not want to install some of the heavier
+dependencies like GDAL on your system or want a dedicated and isolated
+environment for working with large images.
+
+To use, pull the image and run it by mounting a local volume where the
+imagery is stored::
+
+    docker pull ghcr.io/girder/large_image:latest
+    docker run -v /path/to/images:/opt/images ghcr.io/girder/large_image:latest
+
+
+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.  For instance, you can do ``pip install large-image[tiff]``.  There are additional extras_require options:
+
+  - ``sources``: all of the tile sources in the repository, a specific source name (e.g., ``tiff``)
+
+  - ``memcached``: use memcached for tile caching
+
+  - ``converter``: include the converter module
+
+  - ``colormaps``: use matplotlib for named color palettes used in styles
+
+  - ``tiledoutput``: support for emitting large regions as tiled tiffs
+
+  - ``performance``: include optional modules that can improve performance
+
+  - ``common``: all of the tile sources and above packages that will install directly from pypi without other external libraries on linux, OSX, and Windows.
+
+  - ``all``: for all of the above
+
+- ``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.
+  You can specify extras_require of ``jp2k`` to include modules to allow output to JPEG2000 compression, ``sources`` to include all sources, ``stats`` to include modules to allow computing compression noise statistics, ``geospatial`` to include support for converting geospatial sources, or ``all`` for all of the optional extras_require.
+
+- Tile sources:
+
+  - ``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-dicom``: A tile source for reading DICOM Whole Slide Images (WSI).
+
+  - ``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-multi``: A tile source for compositing other tile sources into a single multi-frame source.
+
+  - ``large-image-source-nd2``: A tile source for reading nd2 (NIS Element) images.
+
+  - ``large-image-source-ometiff``: A tile source using the tiff library that can handle most multi-frame OMETiff files that are compliant with the specification.
+
+  - ``large-image-source-openjpeg``: A tile source using the Glymur library to read jp2 (JPEG 2000) files.
+
+  - ``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-pil``: A tile source for small images via the Python Imaging Library (Pillow). By default, the maximum size is 4096, but the maximum size can be configured.
+
+  - ``large-image-source-tiff``: A tile source for reading pyramidal tiff files in common compression formats.
+
+  - ``large-image-source-tifffile``: A tile source using the tifffile library that can handle a wide variety of tiff-like files.
+
+  - ``large-image-source-vips``: A tile source for reading any files handled by libvips.  This also can be used for writing tiled images from numpy arrays (up to 4 dimensions).
+
+  - ``large-image-source-zarr``: A tile source using the zarr library that can handle OME-Zarr (OME-NGFF) files as well as some other zarr files. This can also be used for writing N-dimensional tiled images from numpy arrays. Written images can be saved as any supported format.
+
+  - ``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. This is an absolutely minimal implementation of a tile source used for testing. If you want to create a custom tile source, start with this implementation.
+
+
+As a `Girder`_ plugin, ``large-image`` adds end points to access all of the image formats it can read both to get metadata and to act as a tile server.
+In the Girder UI, ``large-image`` shows images on item pages, and can show thumbnails in item lists when browsing folders.
+There is also cache management to balance memory use and speed of response in Girder when ``large-image`` is used as a tile server.
+
+Most tile sources can be used with Girder Large Image.  You can specify an extras_require of ``girder`` to install the following packages:
+
+  - ``girder-large-image``: Large Image as a Girder 3.x plugin.
+    You can install ``large-image[tasks]`` to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.
+
+  - ``girder-large-image-annotation``: Adds models to the Girder database for supporting annotating large images.  These annotations can be rendered on images. Annotations can include polygons, points, image overlays, and other types. Each annotation can have a label and metadata.
+
+  - ``large-image-tasks``: A utility for running the converter via Girder Worker.
+    You can specify an extras_require of ``girder`` to include modules needed to work with the Girder remote worker or ``worker`` to include modules needed on the remote side of the Girder remote worker.  If neither is specified, some conversion tasks can be run using Girder local jobs.
+
+
+
+.. _Girder: https://girder.readthedocs.io/en/latest/

{large-image-1.27.5.dev71 → large_image-1.30.7.dev10}/README.rst

@@ -15,7 +15,7 @@ Large Image
    :target: https://codecov.io/github/girder/large_image?branch=master
    :alt: codecov.io
 
-.. |doi-badge| image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4723355-blue
+.. |doi-badge| image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4723355-blue.svg
    :target: https://zenodo.org/badge/latestdoi/45569214
 
 .. |pypi-badge| image:: https://img.shields.io/pypi/v/large-image.svg?logo=python&logoColor=white
@@ -39,7 +39,7 @@ Highlights
 Installation
 ------------
 
-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:
+In addition to installing the base ``large-image`` package, you'll need at least one tile source which corresponds to your target file format(s) (a ``large-image-source-xxx`` package).   You can install everything from the main project with one of these commands:
 
 Pip
 ~~~
@@ -52,7 +52,7 @@ Install all tile sources on linux::
 
     pip install large-image[all] --find-links https://girder.github.io/large_image_wheels
 
-Install all tile sources and all Girder plugins on linux::
+When using large-image with an instance of `Girder`_, 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
 
@@ -60,8 +60,9 @@ Install all tile sources and all Girder plugins on linux::
 Conda
 ~~~~~
 
-Conda makes dependency management a bit easier if not on Linux. Some of the source modules are available on conda-forge. You can install the following::
+Conda makes dependency management a bit easier if not on Linux. The base module, converter module, and two of the source modules are available on conda-forge. You can install the following::
 
+    conda install -c conda-forge large-image
     conda install -c conda-forge large-image-source-gdal
     conda install -c conda-forge large-image-source-tiff
     conda install -c conda-forge large-image-converter
@@ -118,7 +119,7 @@ Large Image consists of several Python modules designed to work together.  These
 
   - ``large-image-source-deepzoom``: A tile source for reading Deepzoom tiles.
 
-  - ``large-image-source-dicom``: A tile source for reading DICOM WSI images.
+  - ``large-image-source-dicom``: A tile source for reading DICOM Whole Slide Images (WSI).
 
   - ``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.
 
@@ -128,62 +129,41 @@ Large Image consists of several Python modules designed to work together.  These
 
   - ``large-image-source-nd2``: A tile source for reading nd2 (NIS Element) images.
 
-  - ``large-image-source-ometiff``: A tile source using the tiff library that can handle some multi-frame OMETiff files.
+  - ``large-image-source-ometiff``: A tile source using the tiff library that can handle most multi-frame OMETiff files that are compliant with the specification.
 
   - ``large-image-source-openjpeg``: A tile source using the Glymur library to read jp2 (JPEG 2000) files.
 
   - ``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-pil``: A tile source for small images via the Python Imaging Library (Pillow).
+  - ``large-image-source-pil``: A tile source for small images via the Python Imaging Library (Pillow). By default, the maximum size is 4096, but the maximum size can be configured.
 
   - ``large-image-source-tiff``: A tile source for reading pyramidal tiff files in common compression formats.
 
   - ``large-image-source-tifffile``: A tile source using the tifffile library that can handle a wide variety of tiff-like files.
 
-  - ``large-image-source-vips``: A tile source for reading any files handled by libvips.  This also can be used for writing tiled images from numpy arrays.
+  - ``large-image-source-vips``: A tile source for reading any files handled by libvips.  This also can be used for writing tiled images from numpy arrays (up to 4 dimensions).
 
-  - ``large-image-source-zarr``: A tile source using the zarr library that can handle OME-Zarr (OME-NGFF) files as well as some other zarr files.
+  - ``large-image-source-zarr``: A tile source using the zarr library that can handle OME-Zarr (OME-NGFF) files as well as some other zarr files. This can also be used for writing N-dimensional tiled images from numpy arrays. Written images can be saved as any supported format.
 
   - ``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.
+  - ``large-image-source-dummy``: A tile source that does nothing. This is an absolutely minimal implementation of a tile source used for testing. If you want to create a custom tile source, start with this implementation.
 
-  Most tile sources can be used with girder-large-image.  You can specific an extras_require of ``girder`` to include ``girder-large-image`` with the source.
 
-- As a Girder plugin:
+As a `Girder`_ plugin, ``large-image`` adds end points to access all of the image formats it can read both to get metadata and to act as a tile server.
+In the Girder UI, ``large-image`` shows images on item pages, and can show thumbnails in item lists when browsing folders.
+There is also cache management to balance memory use and speed of response in Girder when ``large-image`` is used as a tile server.
 
-  - ``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.
+Most tile sources can be used with Girder Large Image.  You can specify an extras_require of ``girder`` to install the following packages:
 
-  - ``girder-large-image-annotation``: Annotations for large images as a Girder_ 3.x plugin.
+  - ``girder-large-image``: Large Image as a Girder 3.x plugin.
+    You can install ``large-image[tasks]`` to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.
+
+  - ``girder-large-image-annotation``: Adds models to the Girder database for supporting annotating large images.  These annotations can be rendered on images. Annotations can include polygons, points, image overlays, and other types. Each annotation can have a label and metadata.
 
   - ``large-image-tasks``: A utility for running the converter via Girder Worker.
     You can specify an extras_require of ``girder`` to include modules needed to work with the Girder remote worker or ``worker`` to include modules needed on the remote side of the Girder remote worker.  If neither is specified, some conversion tasks can be run using Girder local jobs.
 
 
-Developer Installation
-----------------------
-
-To install all packages from source, clone the repository::
-
-    git clone https://github.com/girder/large_image.git
-    cd large_image
-
-Install all packages and dependencies::
-
-    pip install -e . -r requirements-dev.txt
-
-If you aren't developing with Girder 3, you can skip installing those components.  Use ``requirements-dev-core.txt`` instead of ``requirements-dev.txt``::
-
-    pip install -e . -r requirements-dev-core.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
-
 
-.. _Girder: https://github.com/girder/girder
+.. _Girder: https://girder.readthedocs.io/en/latest/

large-image-1.27.5.dev71/docs/index.rst → large_image-1.30.7.dev10/docs/api_index.rst

@@ -1,21 +1,12 @@
-.. large_image documentation master file, created by
-   sphinx-quickstart on Tue Dec 31 14:43:10 2019.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root ``toctree`` directive.
-
-.. include:: ../README.rst
+API Documentation
+=======================
 
+The following pages are generated from module source code.
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Contents:
 
-   tilesource_options
-   example_usage
-   config_options
-   image_conversion
-   formats
-   upgrade
    _build/large_image/modules
    _build/large_image_source_bioformats/modules
    _build/large_image_source_deepzoom/modules
@@ -24,7 +15,6 @@
    _build/large_image_source_gdal/modules
    _build/large_image_source_mapnik/modules
    _build/large_image_source_multi/modules
-   multi_source_specification
    _build/large_image_source_nd2/modules
    _build/large_image_source_ometiff/modules
    _build/large_image_source_openjpeg/modules
@@ -38,18 +28,3 @@
    _build/large_image_source_zarr/modules
    _build/large_image_converter/modules
    _build/large_image_tasks/modules
-   _build/girder_large_image/modules
-   girder_config_options
-   _build/girder_large_image_annotation/modules
-   girder_annotation_config_options
-   annotations
-   caching
-   notebooks
-   development
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`

large_image-1.30.7.dev10/docs/caching.rst

@@ -0,0 +1,21 @@
+Caching in Large Image
+======================
+
+There are two main caches in large_image in addition to caching done on the operating system level.  These are:
+
+- Tile Cache: The tile cache stores individual images and/or numpy arrays for each tile processed.
+
+  - May be stored in the python process memory or memcached.  Other cache backends can also be added.
+  - The cache key is a hash that includes the tile source, tile location within the source, format and compression, and style.
+  - If memcached is used, cached tiles can be shared across multiple processes.
+  - Tiles are often bigger than what memcached was optimized for, so memcached needs to be set to allow larger values.
+  - Cached tiles can include original as-read data as well as styled or transformed data.  Tiles can be synthesized for sources that are missing specific resolutions; these are also cached.
+  - If using memcached, memcached determines how much memory is used (and what machine it is stored on).  If using the python process, memory is limited to a fraction of total memory as reported by psutils.
+
+- Tile Source Cache: The source cache stores file handles, parsed metadata, and other values to optimize reading a specific large image.
+
+  - Always stored in the python process memory (not shared between processes).
+  - Memory use is wildly different depending on tile source; an estimate is based on sample files and then the maximum number of sources that should be tiled is based on a frame of total memory as reported by psutils and this estimate.
+  - The cache key includes the tile source, default tile format, and style.
+  - File handles and other metadata are shared if sources only differ in style (for example if ICC color correction is applied in one and not in another).
+  - Because file handles are shared across sources that only differ in style, if a source implements a custom ``__del__`` operator, it needs to check if it is the unstyled source.

{large-image-1.27.5.dev71 → large_image-1.30.7.dev10}/docs/conf.py

@@ -13,8 +13,6 @@
 import os
 import sys
 
-import sphinx_rtd_theme
-
 docs_dir = os.path.dirname(__file__)
 sys.path.insert(0, os.path.abspath(os.path.join(docs_dir, '..', '..')))
 
@@ -53,7 +51,7 @@ templates_path = ['_templates']
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build/**.ipynb', '**.ipynb_checkpoints']
+exclude_patterns = ['_build/**.ipynb', '**.ipynb_checkpoints', 'format_table.rst']
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -62,7 +60,6 @@ exclude_patterns = ['_build/**.ipynb', '**.ipynb_checkpoints']
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 pygments_style = 'sphinx'
 
@@ -72,6 +69,9 @@ pygments_style = 'sphinx'
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['static']
 html_css_files = ['custom.css']
+html_favicon = 'static/K.png'
+html_permalinks = True
+html_permalinks_icon = '&#128279'
 
 autoclass_content = 'both'