def convert(path):
headerList = [] # used to generate one csv file for folder
tmpPath, enclosingFolder = os.path.split(path)
with javabridge.vm(run_headless=True, class_path=bioformats.JARS):
# turn off logging, see:
# ./bStack_env/lib/python3.7/site-packages/bioformats/log4j.py
log4j = javabridge.JClassWrapper("loci.common.Log4jTools")
log4j.enableLogging()
log4j.setRootLevel("WARN")
# build a list of oir header dictionaries
for file in sorted(os.listdir(path)):
if file.startswith('.'):
continue
if file.endswith('.oir'):
filePath = os.path.join(path, file)
myStack = bStack(filePath)
myStack.loadHeader()
myStack.header.prettyPrint() # print to command line
headerList.append(myStack.header.header
) # used to generate one csv file for folder
# save the .txt file
baseFileName = os.path.basename(file)
baseFileName, ext = baseFileName.split('.')
textFilePath = os.path.join(path, baseFileName + '.txt')
with open(textFilePath, 'w') as textFile:
textFile.write(myStack.header.getMetaData())
#
# generate one file with one row for each oir header
if len(headerList) > 0:
outFilePath = os.path.join(path, enclosingFolder + '.csv')
with open(outFilePath, 'w') as outFile:
print('saving file:', outFilePath)
for idx, header in enumerate(headerList):
if idx == 0:
columnNames = ''
for k, v in header.items():
columnNames += k + ','
outFile.write(columnNames + '\n')
for k, v in header.items():
outFile.write(str(v) + ',')
outFile.write('\n')
def main():
sys.modules["javabridge"] = importlib.import_module("jt.javabridge")
sys.modules["javabridge.__about__"] = importlib.import_module("jt.javabridge.__about__")
sys.modules["javabridge.jutil"] = importlib.import_module("jt.javabridge.jutil")
sys.modules["javabridge.locate"] = importlib.import_module("jt.javabridge.locate")
sys.modules["javabridge.wrappers"] = importlib.import_module("jt.javabridge.wrappers")
print("Running testsuite", "\n", file=sys.stderr)
import javabridge as jb
with jb.vm(class_path=[os.path.join(test_java, "classes")] + jb.JARS,
max_heap_size="512M"):
tests = test_suite(sys.argv[1:] or None)
result = unittest.TextTestRunner(verbosity=2).run(tests)
sys.exit(0 if result.wasSuccessful() else 1)
import os
import javabridge
with javabridge.vm(run_headless=True):
print(
javabridge.run_script(
'java.lang.String.format("Hello, %s!", greetee);',
dict(greetee='world')))
#!/usr/bin/env python
"""demo_nogui.py - show how to start the Javabridge without a GUI
python-javabridge is licensed under the BSD license. See the
accompanying file LICENSE for details.
Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2013 Broad Institute
All rights reserved.
"""
import os
import javabridge
with javabridge.vm(run_headless=True):
print javabridge.run_script('java.lang.String.format("Hello, %s!", greetee);', dict(greetee="world"))
import bioformats
print('bioformats.JARS:', bioformats.JARS)
#from bimpy import bStack
import bimpy
if __name__ == '__main__':
startSeconds = time.time()
path = sys.argv[1]
print('bConvertOir', path)
with javabridge.vm(
run_headless=True,
class_path=bioformats.JARS
):
log4j = javabridge.JClassWrapper("loci.common.Log4jTools")
log4j.enableLogging()
log4j.setRootLevel("WARN")
myStack = bimpy.bStack.bStack(path)
savePath = myStack.convert_getSaveFile(channelNumber=1)
if os.path.isfile(savePath):
print('bConvertOir did not convert, destination file exists', savePath)
else:
myStack.convert()