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"""
A fairly generic script to produce plots that compare two or more Neo data sets.
Usage:
python comparison_plot.py <datafile1>, <datafile2>, etc.
"""
import argparse
import os
from datetime import datetime
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import numpy as np
import neo
from neo.io import get_io
from pyNN.utility.plotting import comparison_plot
def variable_names(segment):
return set(signal.name for signal in segment.analogsignals)
def plot_signal(panel, signal, index, colour='b', linewidth='1', label=''):
label = "%s (Neuron %d)" % (label, signal.array_annotations["channel_index"][index])
panel.plot(signal.times, signal[:, index], colour, linewidth=linewidth, label=label)
panel.set_ylabel("%s (%s)" % (signal.name, signal.units._dimensionality.string))
plt.setp(plt.gca().get_xticklabels(), visible=False)
def plot(datafiles, output_file, extra_annotation=None):
print(datafiles)
print(output_file)
# load data
blocks = [get_io(datafile).read_block() for datafile in datafiles]
# note: Neo needs a pretty printer that is not tied to IPython
# for block in blocks:
# print(block.describe())
# for now take only the first segment
segments = [block.segments[0] for block in blocks]
labels = [block.annotations['simulator'] for block in blocks]
# build annotations
script_name = blocks[0].annotations.get('script_name', '')
if script_name:
for block in blocks[1:]:
assert block.annotations['script_name'] == script_name
# also consider adding metadata to PNG file - see http://stackoverflow.com/questions/10532614/can-matplotlib-add-metadata-to-saved-figures
context = ["Generated by: %s" % __file__,
"Working directory: %s" % os.getcwd(),
"Timestamp: %s" % datetime.now().strftime("%Y-%m-%d %H:%M:%S%z"),
"Output file: %s" % output_file,
"Input file(s): %s" % "\n ".join(datafiles)]
if extra_annotation:
context.append(extra_annotation)
annotations = "\n".join(context)
# create and save plot
fig = comparison_plot(segments, labels, title=script_name,
annotations=annotations)
fig.save(output_file)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("datafiles", metavar="datafile", nargs="+",
help="a list of data files in a Neo-supported format")
parser.add_argument("-o", "--output-file", default="output.png",
help="output filename")
parser.add_argument("-a", "--annotation", help="additional annotation (optional)")
args = parser.parse_args()
plot(args.datafiles, output_file=args.output_file, extra_annotation=args.annotation)
if __name__ == "__main__":
main()
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