plot_PSEC4

#!/usr/bin/env python
import matplotlib.pyplot as plt
import bokeh.plotting as bkh
from bokeh.models import Range1d
from bokeh.models import HoverTool
import os
import datetime
import subprocess

def plot_PSEC(fname, oname=''):
	# takes a PSEC4 log file, reads it and plots it to a bokeh file. 
	#  <fname> = file to open and read
	#  <oname> = filename to write to. will be appended with '.html'
	# Returns:
	#  <p>     = bokeh plot object for further manipulation, if desired.
	if oname == '':
		oname = fname.strip('.txt')

	f = open(fname, 'r')

	# Samples is a list, and each sample contains
	#  a set of 6 lists which are the channels readings
	samples = []
	channels = [[],[],[],[],[],[]]
	t = [0.0]

	j = 0
	vmin = 0.
	vmax = 0.
	for line in f:
		if line[0] == '#':
			continue
		else:
			line = [float(x)*1000. for x in line.split()]
			t.append(t[-1]+0.1) # 100ps step size, or 0.1ns
			for i in range(6):
				channels[i].append(line[i])
				if line[i] > vmax:
					vmax = float(line[i])
				if line[i] < vmin:
					vmin = float(line[i])
			j += 1
		if j%256 == 0:
			samples.append(channels)
			channels = [[],[],[],[],[],[]]

	f.close() # REMOVE FOR THE MAIN VERSION

	print 'Read %d samples, in %d lines' % (len(samples), j)

	#recover the user inputted name so it can be applied to graphs and whatever
	stamp = oname.split('/')[-1].strip('.txt').strip('.html')
	oname = oname.strip('.html')+'.html'

	# output graph to a static HTML file
	print "saving to %s" % (oname)
	bkh.output_file(oname, title=stamp)

	#create plot object
	p = bkh.figure(plot_width=1000, title=stamp, x_axis_label='t-t0, ns', y_axis_label='Voltage, mV')

	# Read the channels from each sample into long lists for plotting
	channels = [[],[],[],[],[],[]]
	t = [0.0]
	for sample in samples:
		for channel, ochannel in zip(sample, channels):
			for data in channel:
				ochannel.append(data)
	for data in channels[0][1:]:
		t.append(t[-1]+0.1) # 0.1ns step size

	print 'Plotting...'
	# Plot the data
	cols = ['red', 'blue', 'orange', 'green', 'purple', 'black']
	i = 0
	data = []
	#add data to the plot object with ColumnDataSource
	# line = [<data structure>, <line colour>, <Channel ID>]
	for channel in channels:
		i += 1
		line = [bkh.ColumnDataSource(data=dict(
					x=t,
					y=channel),
					# column_names=['N', 'Voltage']
					),
				cols[i-1], # Line colour
				str(i)     # Channel Number
				]
		data.append(line)

	# plot data
	for line in data:
		p.line('x', 'y',  
			line_width=1,
			line_color=line[1], 
			legend=('Channel '+line[2]),
			source=line[0],
			# tools=['box_select', 'box_zoom', 'pan', 'xpan', 'wheel_zoom', 'undo', 'redo']
			)

	# Make data toggleable
	p.legend.location = "top_left"
	p.legend.click_policy="hide"

	# set ranges
	p.y_range = Range1d(1.1*vmin, 1.1*vmax)

	bkh.save(p)
	bkh.show(p)
	return p