bioformats_jar

May 27, 2022 ยท View on GitHub

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deprecated

This package is deprecated. You should use scyjava to download and import jars. The functionality in this package can be accomplished using scyjava as follows:

import jpype
import scyjava

scyjava.config.endpoints.append('ome:formats-gpl:6.7.0')
scyjava.start_jvm()
loci = jpype.JPackage("loci")
loci.common.DebugTools.setRootLevel("ERROR")

This package remains only for packages that already depend on it.

usage

from bioformats_jar import get_loci, set_loci_log_level

# start the JVM and get the loci module
loci = get_loci()

# optionally:
set_loci_log_level("DEBUG")  # by default "ERROR"

The following environment variables can also be used:

  • BIOFORMATS_VERSION - version of bioformats to use. by default "LATEST"
  • BIOFORMATS_LOG_LEVEL - logging level for loci tools. by default "ERROR"
  • BIOFORMATS_LICENSE - license version of bioformats to use. must be either "gpl" or "bsd". By default "gpl"

see also:

install

pip install bioformats-jar

conda install -c conda-forge bioformats-jar