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 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