ch-plot-intensity-file

#!/usr/bin/env python

import os
import sys
import argparse

class HelpfulParser(argparse.ArgumentParser):
    def error(self, message):
        self.print_help(sys.stderr)
        sys.stderr.write('error: %s\n' % message)
        sys.exit(2)

parser = HelpfulParser()
parser.add_argument('filename')
parser.add_argument('-d', action='store_true', help='detrend using simple_detrender')

args = parser.parse_args()
input_filename = args.filename
input_basename = os.path.basename(input_filename)
input_dirname = os.path.dirname(input_filename)

output_basename = ('detrended_' if args.d else 'raw_')

for suffix in [ '.h5', '.hdf5' ]:
    if input_basename.endswith(suffix):
        output_basename += input_basename[:-len(suffix)]
        output_stem = os.path.join(input_dirname, output_basename)
        break
else:
    print >>sys.stderr, "ch-plot-intensity-file: expected filename '%s' to end with either .h5 or .hdf5" % input_filename
    sys.exit(1)

try:
    import rf_pipelines
except ImportError:
    print >>sys.stderr, "ch-plot-intensity-file: Couldn't import rf_pipelines.  Maybe you need to install it?  (https://github.com/kmsmith137/rf_pipelines)"
    sys.exit(1)

s = rf_pipelines.chime_stream_from_filename(input_filename)
t = rf_pipelines.plotter_transform(output_stem, img_nfreq=512, img_nt=1536, downsample_nt=16)
tlist = [ rf_pipelines.simple_detrender(1024), t ] if args.d else [ t ]

s.run(tlist)