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bioformats_jar.py
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bioformats_jar.py
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import os
from functools import lru_cache
from importlib.metadata import PackageNotFoundError, version
from typing import Any
import jpype
import scyjava
try:
__version__ = version("bioformats_jar")
except PackageNotFoundError:
__version__ = "uninstalled"
__all__ = [
"get_loci",
"set_loci_log_level",
"get_ome",
"loci",
"ome",
"__version__",
]
BIOFORMATS_VERSION = os.getenv("BIOFORMATS_VERSION", "LATEST")
BIOFORMATS_LICENSE = os.getenv("BIOFORMATS_LICENSE", "gpl")
assert BIOFORMATS_LICENSE in {
"gpl",
"bsd",
}, "BIOFORMATS_LICENSE env var must be either 'gpl' or 'bsd'"
LOG_LEVEL = os.getenv("BIOFORMATS_LOG_LEVEL", "ERROR")
scyjava.config.endpoints.append(
f"ome:formats-{BIOFORMATS_LICENSE}:{BIOFORMATS_VERSION}"
)
@lru_cache()
def get_loci(log_level: str = LOG_LEVEL):
"""Start JVM (if necessary) and get the `loci` module
Parameters
----------
log_level : str
the logging level for loci tools. by default "ERROR". Can also be set by
setting the 'BIOFORMATS_LOG_LEVEL' environment variable.
Returns
-------
loci
the loci module from bioformats_package.jar
"""
FormatTools = scyjava.jimport("loci.formats.FormatTools")
loci = jpype.JPackage("loci")
loci.common.DebugTools.setRootLevel(log_level)
loci.__version__ = FormatTools.VERSION
return loci
def set_loci_log_level(level):
"""Set loging level for loci tools."""
get_loci().common.DebugTools.setRootLevel(level)
@lru_cache()
def get_ome():
"""Start JVM (if necessary) and get the `ome` module"""
scyjava.start_jvm()
return jpype.JPackage("ome")
def __getattr__(name: str) -> Any:
if name == "loci":
return get_loci()
if name == "ome":
return get_ome()
raise AttributeError(f"module {__name__!r} has no attribute {name!r}")