bioformats_package.jar installer for scyjava
Project description
bioformats_jar
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:
- Bioformats Docs
- Javadocs with the loci API
install
pip install bioformats-jar
conda install -c conda-forge bioformats-jar
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