def cmpLogRecords(msg, expected):
strStream = StringIO()
sHandler = logging.StreamHandler(strStream)
log.addHandler(sHandler)
log.info(msg)
log.removeHandler(sHandler)
got = strStream.getvalue()
assert got == ("%s\n" % expected), (got, expected)
def __init__(self, script):
# Setup error handling stuff first so any errors during driver loading
# or the main bits gets handled correctly.
global tty6Handler
sys.excepthook = lambda type, value, tb: \
exception.handleException(self, (type, value, tb),
traceInDetails=False)
try:
# The scui uses logging to write out user-visible output so we need
# another logger for tty6 (which stdout is redirected to by
# weasel.py).
tty6Handler = logging.StreamHandler(sys.stdout)
tty6Handler.setFormatter(formatterForHuman)
tty6Handler.setLevel(LOGLEVEL_HUMAN)
log.addHandler(tty6Handler)
except IOError:
#Could not open for writing. Probably not the root user
pass
self._execute(script)
def __init__(self, script):
# Setup error handling stuff first so any errors during driver loading
# or the main bits gets handled correctly.
global tty6Handler
sys.excepthook = lambda type, value, tb: \
exception.handleException(self, (type, value, tb),
traceInDetails=False)
try:
# The scui uses logging to write out user-visible output so we need
# another logger for tty6 (which stdout is redirected to by
# weasel.py).
tty6Handler = logging.StreamHandler(sys.stdout)
tty6Handler.setFormatter(formatterForHuman)
tty6Handler.setLevel(LOGLEVEL_HUMAN)
log.addHandler(tty6Handler)
except IOError:
#Could not open for writing. Probably not the root user
pass
self._execute(script)
#!/usr/bin/python
"""Generator for various formats from a CSV list of IP / hostnames / aliases."""
import sys
import argparse
import os
import pprint
try:
from log import log
except ImportError:
import logging
log = logging.getLogger()
log.addHandler(logging.StreamHandler())
class HostsInfo(object):
"""Host info class, keeping hostnames, IP addresses, groups and so on."""
def __init__(self, infile):
self.hosts = dict()
self.groups = dict()
log.debug("Initializing hosts object from file '%s'.", infile)
self.parse_hostsfile(infile)
log.debug("Done initializing hosts object.")
def parse_line(self, line):
"""Split a single line into its tokens (IP, name, aliases, hosts)."""
sys.argv[i] = arg.replace('--', '-')
parser = argparse.ArgumentParser(description=__doc__, epilog=epi)
add = parser.add_argument # shorthand to improve readability
add("--mosaiclog", metavar='FILE', required=True,
help='FluoView "MATL_Mosaic.log" XML file with stage positions')
add("--templates", required=False,
help='path containing the "templates/" subdirectory')
add("--dry-run", action="store_true", dest="dryrun", default=False,
help="print generated macro but don't run stitcher")
add("--verbose", action="count", default=0)
try:
args = parser.parse_args()
except IOError as err:
parser.error(str(err))
return args
# only run if we're called explicitly from the commandline or as a plugin from
# Fiji's menu, this allows being imported in the Jython console for testing
# and debugging purposes:
if (__name__ == '__main__'):
ijlogger = IJLogHandler()
log.addHandler(ijlogger)
log.warn("FluoView OIF / OIB stitcher (%s)." % imcf.VERSION)
log.warn("Arguments (sys.argv): %s" % sys.argv)
if (len(sys.argv) > 0):
sys.exit(main_noninteractive())
else:
main_interactive()