def main(args=None):
if args is None:
args = sys.argv[1:]
pargs = docopt(__doc__, args, version=version.description)
if pargs['-o']:
return acq_markers_output_file(pargs['<file>'], pargs['-o'])
else:
return acq_markers(pargs['<file>'], sys.stdout)
def main(args=None):
if args is None:
args = sys.argv[1:]
pargs = docopt(
__doc__,
args,
version=version.description)
if pargs['-o']:
return acq_markers_output_file(pargs['<file>'], pargs['-o'])
else:
return acq_markers(pargs['<file>'], sys.stdout)
def run(self):
pargs = docopt(__doc__, self.argv, version=version.description)
infile = pargs['<acq_file>']
channel_indexes = None
if pargs['--channel-indexes']:
channel_indexes = [
int(i) for i in pargs['--channel-indexes'].split(',')
]
data = bioread.read(infile, channel_indexes=channel_indexes)
mval = pargs['--missing-as']
if pargs['--outfile']:
with open(pargs['--outfile'], 'w') as f:
txtwriter.write_text(data, f, channel_indexes, mval)
else:
txtwriter.write_text(data, sys.stdout, channel_indexes, mval)
def run(self):
old_err = sys.stderr
sys.stderr = self.err
pargs = docopt(__doc__, self.argv, version=version.description)
try:
import scipy # noqa -- catch this error before matlabwriter
except:
sys.stderr.write("scipy is required for writing matlab files\n")
sys.exit(1)
infile = pargs['<acq_file>']
matfile = pargs['<mat_file>']
compress = pargs['--compress']
data = Reader.read(infile).datafile
MatlabWriter.write_file(data, matfile, compress=compress)
sys.stderr = old_err
def run(self):
pargs = docopt(
__doc__,
self.argv,
version=version.description)
infile = pargs['<acq_file>']
channel_indexes = None
if pargs['--channel-indexes']:
channel_indexes = [
int(i) for i in pargs['--channel-indexes'].split(',')]
data = bioread.read(infile, channel_indexes=channel_indexes)
mval = pargs['--missing-as']
if pargs['--outfile']:
with open(pargs['--outfile'], 'w') as f:
txtwriter.write_text(data, f, channel_indexes, mval)
else:
txtwriter.write_text(data, sys.stdout, channel_indexes, mval)
def run(self):
old_err = sys.stderr
sys.stderr = self.err
pargs = docopt(
__doc__,
self.argv,
version=version.description)
try:
import scipy # noqa -- catch this error before matlabwriter
except:
sys.stderr.write("scipy is required for writing matlab files\n")
sys.exit(1)
infile = pargs['<acq_file>']
matfile = pargs['<mat_file>']
compress = pargs['--compress']
data = Reader.read(infile).datafile
MatlabWriter.write_file(data, matfile, compress=compress)
sys.stderr = old_err
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
pargs = docopt(__doc__, argv, version=version.description)
if pargs['--verbose']:
logger.setLevel(logging.DEBUG)
br.logger.setLevel(logger.level)
logger.debug(pargs)
try:
comp_opts = COMPRESSION_OPTS[pargs['--compress']]
except KeyError:
logger.error("Unknown compression: {0}".format(pargs['--compress']))
sys.exit(1)
scale = False
try:
scale = SCALE_DATA[pargs['--values-as']]
except KeyError:
logger.error("Unknown values-as option: {}".format(
pargs['--values-as']))
make_hdf5(pargs['<acq_file>'], pargs['<hdf5_file>'], comp_opts, scale)
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
pargs = docopt(__doc__, argv, version=version.description)
if pargs['--verbose']:
logger.setLevel(logging.DEBUG)
br.logger.setLevel(logger.level)
logger.debug(pargs)
try:
comp_opts = COMPRESSION_OPTS[pargs['--compress']]
except KeyError:
logger.error("Unknown compression: {0}".format(pargs['--compress']))
sys.exit(1)
scale = False
try:
scale = SCALE_DATA[pargs['--values-as']]
except KeyError:
logger.error("Unknown values-as option: {}".format(
pargs['--values-as']))
make_hdf5(pargs['<acq_file>'], pargs['<hdf5_file>'], comp_opts, scale)
def run(self):
old_out = sys.stdout
old_err = sys.stderr
sys.stdout = self.out
sys.stderr = self.err
pargs = docopt(
__doc__,
self.argv,
version=version.description)
df = None
infile = pargs['<acq_file>']
try:
if infile == '-':
df = BytesIO(sys.stdin.read())
else:
df = open(infile, 'rb')
except:
sys.stderr.write("Error reading {0}\n".format(infile))
sys.exit(1)
self.reader = Reader(df)
try:
self.reader._read_headers()
except:
sys.stderr.write("Error reading headers!\n")
# Don't exit here; it'll still print what it can.
if pargs['--debug']:
self.__print_debug()
else:
self.__print_simple()
sys.stderr = old_err
sys.stdout = old_out
