Configuration Options

Some functionality of large_image is controlled through configuration parameters. These can be read or set via python using functions in the large_image.config module, getConfig and setConfig.

Configuration parameters:

  • logger: a Python logger. Most log messages are sent here.

  • logprint: a Python logger. Messages about available tilesources are sent here.

  • cache_backend: either python (the default) or memcached, specifying where tiles are cached. If memcached is not available for any reason, the python cache is used instead.

  • cache_python_memory_portion: If tiles are cached in python, the cache is sized so that it is expected to use less than 1 / (cache_python_memory_portion) of the available memory. This is an integer.

  • cache_memcached_url: If tiles are cached in memcached, the url or list of urls where the memcached server is located. Default ‘127.0.0.1’.

  • cache_memcached_username: A username for the memcached server. Default None.

  • cache_memcached_password: A password for the memcached server. Default None.

  • cache_tilesource_memory_portion: Tilesources are cached on open so that subsequent accesses can be faster. These use file handles and memory. This limits the maximum based on a memory estimation and using no more than 1 / (cache_tilesource_memory_portion) of the available memory.

  • cache_tilesource_maximum: If this is non-zero, this further limits the number of tilesources than can be cached to this value.

  • max_small_image_size: The PIL tilesource is used for small images if they are no more than this many pixels along their maximum dimension.

  • source_bioformats_ignored_names, source_pil_ignored_names, source_vips_ignored_names: Some tile sources can read some files that are better read by other tilesources. Since reading these files is suboptimal, these tile sources have a setting that, by default, ignores files without extensions or with particular extensions. This setting is a Python regular expressions. For bioformats this defaults to r'(^[!.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi))$'.

Configuration from Python

As an example, configuration parameters can be set via python code like:

import large_image

large_image.config.setConfig('max_small_image_size', 8192)

Configuration within the Girder Plugin

For the Girder plugin, these can also be set in the girder.cfg file in a large_image section. For example:

[large_image]
# cache_backend, used for caching tiles, is either "memcached" or "python"
cache_backend = "python"
# 'python' cache can use 1/(val) of the available memory
cache_python_memory_portion = 32
# 'memcached' cache backend can specify the memcached server.
# cache_memcached_url may be a list
cache_memcached_url = "127.0.0.1"
cache_memcached_username = None
cache_memcached_password = None
# The tilesource cache uses the lesser of a value based on available file
# handles, the memory portion, and the maximum (if not 0)
cache_tilesource_memory_portion = 8
cache_tilesource_maximum = 0
# The PIL tilesource won't read images larger than the max small images size
max_small_image_size = 4096
# The bioformats tilesource won't read files that end in a comma-separated
# list of extensions
source_bioformats_ignored_extensions = '.jpg,.jpeg,.jpe,.png,.tif,.tiff,.ndpi'

Logging from Python

The log levels can be adjusted in the standard Python manner:

import logging
import large_image

logger = logging.getLogger('large_image')
logger.setLevel(logging.CRITICAL)

Alternately, a different logger can be specified via setConfig in the logger and logprint settings:

import logging
import large_image

logger = logging.getLogger(__name__)
large_image.config.setConfig('logger', logger)
large_image.config.setConfig('logprint', logger)