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bioformats_jar

License PyPI Python Version CI

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