def __init__(self, vars, decon, reml, loglevel=zlogger.logging.DEBUG, interp="lin", dry_run=False):
# todo: check vars has subject, func...
self.__dict__.update(**vars)
self.vars = vars
# create output
if dry_run is True:
log_fname = None
else:
log_fname = op.join(self.outputdir, "logs", "glm_subject.log")
os.mkdir(self.outputdir)
os.mkdir(op.join(self.outputdir, "logs"))
# create logger
self.slog = zlogger.getLogger("glm_%s" % self.subject, level=loglevel,
fname=log_fname)
# save args
self.tdecon = deepcopy(decon) # template
self.treml = deepcopy(reml) # template
self.interp = interp
self.dry_run = dry_run
return
def __init__(self, subject_list, config_file, interp="lin", cores=1, dry_run=False, verbosity=0, force=False):
# cores
os.putenv("OMP_NUM_THREADS", str(cores))
# config
self.opts = yaml.load(config_file)
# args
self.subject_list = subject_list
self.interp = interp
self.dry_run = dry_run
self.force = force
# logger
# note: there is one root logger self.log
# and one subject specific logger self.slog
if verbosity == 0:
self.loglevel = zlogger.logging.IMPORTANT
elif verbosity == 1:
self.loglevel = zlogger.logging.COMMAND_INFO
else:
self.loglevel = zlogger.logging.DEBUG
self.log = zlogger.getLogger("glm_root", level=self.loglevel)
# setup inputs/outputs and check basics
self._setup_and_check()
def __init__(self, verbosity, outdir, template_context={}, overwrite=False):
super(Reporter, self).__init__()
outdir = op.abspath(op.expanduser(outdir))
if op.isdir(outdir):
if overwrite:
shutil.rmtree(outdir)
else:
raise ReporterException("Output directory already exists")
os.mkdir(outdir)
self.outdir = outdir
os.mkdir(op.join(outdir, "logs"))
if self._logname is None:
raise Exception("You must set the _logname in the class")
logfile = op.join(op.join(outdir, "logs"), self._logname + ".log")
if verbosity == 0:
self.loglevel = zlogger.logging.IMPORTANT
elif verbosity == 1:
self.loglevel = zlogger.logging.COMMAND_INFO
else:
self.loglevel = zlogger.logging.DEBUG
self.log = zlogger.getLogger(self._logname, level=self.loglevel, fname=logfile,
allow_exceptions=True)
shutil.copytree(op.join(os.getenv("NISCRIPTS"), "etc", "css"),
op.join(outdir, "css"))
shutil.copytree(op.join(os.getenv("NISCRIPTS"), "etc", "js"),
op.join(outdir, "js"))
shutil.copytree(op.join(os.getenv("NISCRIPTS"), "etc", "images"),
op.join(outdir, "images"))
self._setTemplateContext(template_context)
self.env = Environment(loader=PackageLoader('report', 'templates'))
self.report = None
return
def create_logger(name, level, fname):
log = zlogger.getLogger(name, level, fname=fname, allow_exceptions=True)
return log
