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'''
By Ben Schneider
Simple python wrapper for Gnuplot
Thanks to steview2000 for suggesting to separate processes,
jrbrearley for help with debugging in python 3.4+
Special Thanks to ddip!
This code was rewritten according to ddipp's suggestions resulting in
a cleaner and better code and finnaly giving accesss to gnuplot returns
thus allowing the use of the gnuplot fit function.
Also thanks to all the others who commented gave inputs and suggestions.
Example:
from PyGnuplot import gp
import numpy as np
X = np.arange(10)
Y = np.sin(X/(2*np.pi))
Z = Y**2.0
fig1 = gp()
fig1.save([X,Y,Z]) # saves data into tmp.dat
fig1.c('plot "tmp.dat" u 1:2 w lp) # send 'plot instructions to gnuplot'
fig1.c('replot "tmp.dat" u 1:3' w lp)
fig1.pdf('myfigure.pdf') # outputs pdf file
'''
import sys
from subprocess import PIPE, Popen
from threading import Thread
from time import sleep
try:
from queue import Queue, Empty # Python 3.x
except ImportError:
from Queue import Queue, Empty # Python 2.x
ON_POSIX = 'posix' in sys.builtin_module_names
class gp(object):
"""PyGnuplot object figure
example:
pi = f1.a('print pi')
"""
def __init__(self, gnuplot_address='gnuplot'):
# also also initialize with gnuplot_address = r"C:\Program Files\gnuplot\bin\gnuplot.exe"
self.gnuplot_address=gnuplot_address
''' open pipe with gnuplot '''
self.p = Popen([gnuplot_address], stdin=PIPE, stderr=PIPE, stdout=PIPE,
bufsize=1, close_fds=ON_POSIX,
shell=False, universal_newlines=True)
self.q_err = Queue()
self.t_err = Thread(target=self.enqueue_std,
args=(self.p.stderr, self.q_err))
self.t_err.daemon = True # thread dies with the program
self.t_err.start()
self.q_out = Queue()
self.t_out = Thread(target=self.enqueue_std,
args=(self.p.stdout, self.q_out))
self.t_out.daemon = True # thread dies with the program
self.t_out.start()
self.r() # clear return buffer
self.default_term = str(*self.a('print GPVAL_TERM'))
def enqueue_std(self, out, queue):
''' used to setup the queues for the return buffers'''
for line in iter(out.readline, ''):
queue.put(line)
out.close()
def c(self, command):
''' send a command to gnuplot.
this does not check for responses
>>> w('plot sin(x)') # only send a command to gnuplot'''
self.p.stdin.write(command + '\n') # \n 'send return in python 2.7'
self.p.stdin.flush() # send the command in python 3.4+
def r(self, vtype=str, timeout=0.05):
''' read line without blocking, also clears the buffer.
>>> r() # read response from gnuplot'''
lines = []
while True:
try:
line = self.q_err.get(timeout=timeout) # or .get_nowait()
lines.append(vtype(line.strip()))
except Empty:
break
return lines
def a(self, command='', vtype=str, timeout=0.05):
''' ask gnuplot (write and get answer)
>>> a('print pi')
'''
self.c(command)
sleep(0.01) # wait 10ms for gnuplot
return self.r(vtype, timeout)
def m_str(self, data, delimiter=' '):
''' turn data into string format
this string format can be used when sending data to gnuplot
usually via: plot "-" u 1:2 w lp'''
xy = list(zip(*data))
ascii_st = ''
for i in xy:
for j in i:
ascii_st += str(j) + delimiter
ascii_st += '\n'
return ascii_st
def plot(self, data, com='plot "-" u 1:2 w lp'):
''' quick plot data in gnuplot
it basically pipes the data to gnuplot and plots it
default plot :
com = "plot "-" u 1:2 w lp"
'''
str_data = self.m_str(data)
self.c(com)
self.c(str_data+'e') # add end character to plot string
return self.r()
def fit(self, data, func='y(x)=a + b*x', via='a,b', limit=1e-9, filename='tmp.dat', wait=1):
'''simple quick way to fit with gnuplot
this fit function temporarily stores the data in a file.
Inputs:
func : fitting function y(x) or f(x,y) or ...
via : space separated variables to fit
data : data set to fit
filename : location where it can temporarily store its data
wait : timing in s on how long to wait for the fit results
Outputs:
fit results in same order as via is defined
report generated by gnuplot
'''
self.save(data, filename=filename)
func_name = func.split('=')[0]
self.c(func) # 'y(x)=a+b*x'
self.c('set fit limit '+str(limit))
self.c('fit ' + func_name + ' "' + filename + '" via ' + via)
sleep(wait) # wait until fitting is done
report = self.a() # if no report is returned maybe increase the wait time here
return self.get_variables(via), report
def fit2d(self, data, func='y(x)=a + b*x', via='a,b', limit=1e-9):
'''simple quick way to fit with gnuplot
Inputs:
func : fitting function y(x) or f(x,y) or ...
via : space separated variables to fit
data : data set to fit
Outputs:
fit results in same order as via is defined
report generated by gnuplot
'''
str_data = self.m_str(data)
func_name = func.split('=')[0]
self.c(func) # 'y(x)=a+b*x'
self.c('set fit limit '+str(limit))
self.c('fit ' + func_name + ' "-" via ' + via)
report = self.a(str_data+'e')
return self.get_variables(via), report
def get_variables(self, via):
'''
returns values stored in gnuplot as given by via
Inputs:
via : for example via = 'a b c d e'
Outputs:
results in same order as via is given
'''
vals = via.split(',')
ret = []
for i in vals:
r = self.a('print ' + i)
try:
r = float(r[0]) # hard coded conversion if possible
except ValueError:
pass
ret.append(r)
return ret
def save(self, data, filename='tmp.dat', delimiter=' '):
'''
saves numbers arrays and text into filename (default = 'tmp.dat)
(assumes equal sizes and 2D data sets)
>>> s(data, filename='tmp.dat') # overwrites/creates tmp.dat
'''
with open(filename, 'w') as f:
filestr = self.m_str(data, delimiter=delimiter)
f.write(filestr)
f.close() # write the rest and close
def empty_plot(self):
self.c('plot [][-1:1] 1/0 t""')
def ps(self, filename='tmp.ps', width=14, height=9, fontsize=12):
'''Script to make gnuplot print into a postscript file
>>> ps(filename='myfigure.ps') # overwrites/creates myfigure.ps
'''
self.c('set term postscript size '
+ str(width) + 'cm, '
+ str(height) + 'cm color solid '
+ str(fontsize) + " font 'Calibri';")
self.c('set out "' + filename + '";replot;')
self.c('set term ' + self.default_term + ';replot')
return self.r()
def pdf(self, filename='tmp.pdf', width=8.8, height=6, fontscale=0.5):
'''Script to make gnuplot print into a pdf file
>>> pdf(filename='myfigure.pdf') # overwrites/creates myfigure.pdf
'''
self.c('set term pdfcairo fontscale '
+ str(fontscale) + 'size '
+ str(width) + 'cm, '
+ str(height) + "cm;")
self.c('set out "' + filename + '";replot;')
self.c('set term ' + self.default_term + '; replot')
return self.r() # clear buffer
def quit(self):
aa = self.a('exit') # close gnuplot
self.p.kill() # kill pipe
return aa
if __name__ == '__main__':
# test functionality
import numpy as np
f1 = gp()
x = np.linspace(0, 20, 1001)
yn = np.random.randn(1001)/10
y = np.sin(x)
data = [x, y+yn]
func = 'y(x) = a + b*cos(x + c)'
(a, b, c), report = f1.fit(data, func, via='a,b,c', limit=1e-9)
f1.save(data, "tmp.dat")
f1.a('plot "tmp.dat" w lp')
f1.a('replot y(x)')
dat_s = f1.m_str([x, y], delimiter='\t')
print()
print("fitting function is: " + func)
print("fit report:")
for line in report:
print(line)
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