506b449f4d
- pytest - use pathlib - series as part of the path: path/PosN - summary only shows some available metadata - allow dict in Imread[dict(c=c, z=z, t=t)] - bfread in different process so the user can start another jvm - deal with multiple images (series/positions) in czi files - use jpype instead of javabridge/bioformats - poetry for install
51 lines
1.7 KiB
Python
51 lines
1.7 KiB
Python
from pathlib import Path
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try:
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class JVM:
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""" There can be only one java virtual machine per python process,
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so this is a singleton class to manage the jvm.
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"""
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_instance = None
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vm_started = False
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vm_killed = False
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success = True
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def __new__(cls, *args):
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if cls._instance is None:
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cls._instance = object.__new__(cls)
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return cls._instance
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def __init__(self, classpath=None):
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if not self.vm_started and not self.vm_killed:
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if classpath is None:
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classpath = [str(Path(__file__).parent / 'jars' / '*')]
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import jpype
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jpype.startJVM(classpath=classpath)
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import jpype.imports
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from loci.common import DebugTools
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from loci.formats import ImageReader
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from loci.formats import ChannelSeparator
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from loci.formats import FormatTools
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from loci.formats import MetadataTools
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DebugTools.setRootLevel("ERROR")
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self.vm_started = True
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self.image_reader = ImageReader
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self.channel_separator = ChannelSeparator
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self.format_tools = FormatTools
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self.metadata_tools = MetadataTools
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if self.vm_killed:
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raise Exception('The JVM was killed before, and cannot be restarted in this Python process.')
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def kill_vm(self):
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if self.vm_started and not self.vm_killed:
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import jpype
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jpype.shutdownJVM()
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self.vm_started = False
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self.vm_killed = True
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except ImportError:
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JVM = None
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