So i have an issue. I have two Scripts running one which is a CPU and Time logger of every second to record the CPU usage to a text file. The other is a Script that reads the text file into a graph but the graph is not a uniform axis and does not increase in units and i get the wrong output view.
Script1: logs PSU and time to txt file
import psutil import time
print(str(time.strftime("%H:%M:%S", time.localtime())) + ", " +
str(psutil.cpu_percent(interval=1)))
f = open("example.txt", "a+")
f.write(str(time.strftime("%H:%M:%S", time.localtime())) +
", " + str(psutil.cpu_percent(interval=1)) + " \n")
Program 2: plots to a graph
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib import style
style.use('fivethirtyeight')
fig = plt.figure() ax1 = fig.add_subplot(1,1,1)
def animate(i):
graph_data = open ('example.txt','r').read()
lines = graph_data.split('\n')
xs = []
ys = []
for line in lines:
if len(line) > 1:
x, y = line.split(',')
xs.append(x)
ys.append(y)
ax1.clear()
ax1.plot(xs, ys)
ani = animation.FuncAnimation(fig, animate, interval=1000) plt.show()
Script2 output
If this can be made into one Script then great but i am trying to learn the basics. I think it is a String issue with writing to txt files but dont know why a string would matter in a txt file.
I suppose that the string you need to write in the TXT o CSV file will be generated by (in CSV is much easier to read before):
import time
import psutil
import csv
num_measures = 10
with open("cpu_pcnt.csv", mode='w') as file:
for _ in range(num_measures):
str_time = time.strftime("%H:%M:%S")
cpu_pcnt = psutil.cpu_percent(interval=1)
str_data = f"{str_time},{cpu_pcnt}\n"
file.write(str_data)
Then, convert the time in datetime object to the plot and look to cast the pcu percent into float:
def animate(i):
xs = []
ys = []
with open("cpu_pcnt.csv") as file:
reader = csv.reader(file)
for line in reader:
xs.append(datetime.strptime(line[0], "%H:%M:%S"))
ys.append(float(line[1]))
ax1.clear()
ax1.plot(xs, ys)
Related
i am currently working on a hobby project and got stuck on annotations in Matplotlib.
I have 2 Python files, one which scrapes the current price of a stock from yahoo and the current time. This information is then written in an csv:
from yahoo_fin import stock_info as si
import csv
import random
import time
from datetime import datetime
fieldnames = ['MSFTPrice', 'CurrentTime']
with open('MSFT.csv', 'w') as csv_file:
csv_writer = csv.DictWriter(csv_file, delimiter=',', lineterminator='\n', fieldnames= fieldnames)
csv_writer.writeheader()
count = 0
while True:
with open('MSFT.csv', 'a') as csv_file:
csv_writer = csv.DictWriter(csv_file, delimiter=',', lineterminator='\n', fieldnames= fieldnames)
MSFTPrice = si.get_live_price("MSFT")
count += 1.0
now = datetime.now()
CurrentTime = now.strftime("%H:%M:%S")
info = {
"MSFTPrice": '%.2f' %MSFTPrice,
"CurrentTime": CurrentTime}
csv_writer.writerow(info)
print('%.2f'%MSFTPrice, CurrentTime)
time.sleep(1)
if count >= 10000:
break
So the second one is then reading those 2 values and then creates a live visualization with matplotlib:
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
plt.style.use('fivethirtyeight')
plt.style.use('dark_background')
def animate(i):
data = pd.read_csv('MSFT.csv')
x = data ["CurrentTime"]
y = data ["MSFTPrice"]
plt.cla()
plt.xlabel('Time')
plt.ylabel('Price')
plt.plot(x, y, color= 'green', linewidth=1.5)
plt.xticks(x[::300],fontsize= 12, rotation='horizontal')
for i,j in zip(x,y):
plt.annotate (str(j), xy = (i,j))
plt.tight_layout()
plt.grid(b=None)
ani = FuncAnimation(plt.gcf(), animate, interval=1000)
plt.tight_layout()
plt.show()
I want to annotate only the latest datapoint from the csv, but currently it annotate all datapoints. Here is a screenshot on how it looks now:
Plot
Hope you can help me :)
You can replace the following (which annotates all points in a loop):
for i,j in zip(x,y):
plt.annotate (str(j), xy = (i,j))
with the statement annotating the latest point (x[-1], y[-1]):
plt.annotate(str(y[-1]), xy=(x[-1], y[-1]))
I'm trying to measure distance between CA atoms in a particular PDB file. The output appears as it should in Spyder, but the written text file appears strange and I don't know how to search for what the output is because I honestly do not know what it is written in. Below is my code:
import sys
import os
from Bio.PDB.PDBParser import PDBParser
import numpy as np
import warnings
def plot(data):
# import matplotlib # matplotlib.use( 'Agg' )
import pylab
fig = pylab.figure()
ax = fig.add_subplot(111)
cax = ax.imshow(data, interpolation='nearest')
ax.set_title('Ca-Ca distance plot')
# Add colorbar, make sure to specify tick locations to match desired ticklabels
min = np.min(data)
max = np.max(data)
cbar = fig.colorbar(cax, ticks=[min, max])
cbar.set_ticks([min,max])
pylab.show()
# pylab.savefig( 'distmat.png', format='png' )
if __name__ == '__main__':
fnam = 'myfile.pdb'
if not os.path.exists(fnam):
print "file not found"
raise SystemExit
id = 'myfile'
warnings.simplefilter('ignore')
parser = PDBParser()
s = parser.get_structure(id, fnam)
chains = [c for c in s.get_chains()]
x = []
for r in chains[0]:
if 'CA' in r.child_dict:
ca = r.child_dict['CA']
x.append(ca.get_coord())
coords = np.array(x)
print (coords)
import scipy.spatial
data = scipy.spatial.distance.cdist(coords, coords, 'euclidean')
print data.shape
plot(data)
print(data)
with open('some file.txt', 'w') as f:
f.write(data)
f.close()
Below is part of the output. What is it and how do I fix it? Thank you for your help!:
‹ñ:(tO#m f\⁄l#cÿÖ∂r!#²«1pi"#ß!•=E6'#=∫;oÆ)#cQ¥Ë¢a(#O)[hÉû/#Æ$≠€781#‹∞'å©X1#x±Mjû+#…‘0™û¥)#Ø1”P/#·uùπ„,#SrÆ¡·˙%#-‰Ÿ^>Â*#QCy‘O/#B?˜+#͵øµÇ|'#e∫≤òÌÄ.#ú?1#Õú…È.#«wX˜¥,#´i¥Ç–è+#◊s°(¯%#βø¶·+#¨ÉSίz.#k`rÕ=C(#åܪÆ'#ï¯ÛU’.#kc÷é.#(¢·F£%*#óqÖîMµ0#Xö1Â
[
I'm trying to plot data from different text files.
I've had to manipulate data so I could construct the graphic that I desire for just one document. All other documents are in the same way. But I can't see how I can plot all in one panel. The code that I tried for the loop of all files was:
import numpy as np
import matplotlib.pyplot as plt
filenames=["b_10.txt","b_100.txt","b_500.txt","b_1000.txt"]
for i in filenames:
with open(i) as f:
data = f.read()
data = data.split('\n')
x = [row.split(' ')[0] for row in data]
y = [row.split(' ')[-1] for row in data]
x
a=list(map(str.strip, y))
trip_list = [item.strip('\tall\t') for item in y]
yy = np.array(trip_list[1:12])
yy
xx= np.array(x[21:32])
xx
fig = plt.figure()
plt.hold(True)
plt.ylabel('Precisão Interpolada')
plt.xlabel('Recall')
plt.plot(xx,yy,'-',label="Precisão Interpolada vs Recall")
plt.show()
It gave me an error:
ValueError: could not convert string to float:
and a blank panel
enter image description here
Here is my code so far:
with open(logfile,'rb') as f:
while True:
lines = sum(1 for line in f)
print lines
X = np.arange(lines)
data = []
for line in f:
a = line.split(',')
data.append(a[1][:-2])
print data
Y = np.array(data)
plt.ion()
graph = plt.plot(X,Y)[0]
graph.set_y_data(Y)
plt.plot(data)
plt.draw()
plt.pause(0.01)
Right now when I print data or Y, it prints an empty array. Then it complains about X not being the same dimension as Y of course. I wonder if perhaps this is because data is not filled quickly enough before the print command is called? But python is supposed to execute sequentially, right?
In any case, I think the logic itself here is probably at fault. This is my best guess - open the file, and while True, try and read everything in and send it into the plot for plot.draw to use. Then as the file is growing as log files do, the chart data and the chart itself will update. How can I ensure that this works?
Use matplotlibs animation features
You need to make an animation like this example.
Version updating the data
Create an empty plot first and update along the way:
import time
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
def read(logfile):
with open(logfile) as f:
data = []
while True:
line = f.readline()
time.sleep(0.1)
if line:
data.append(float(line.split(',')[1][:-2]))
yield data
def animate(values):
x = list(range(len(values)))
line.set_data(x, values)
ax.set_xlim(x[0], x[-1])
ax.set_ylim(min(values), max(values))
return line,
fig, ax = plt.subplots()
line, = ax.plot([])
ani = FuncAnimation(fig, animate, frames=read('log.txt'), interval=10)
plt.show()
Version creating a new plot each time
Less code, but works only for a few steps:
import time
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
def read(logfile):
with open(logfile) as f:
data = []
while True:
line = f.readline()
time.sleep(0.1)
if line:
data.append(float(line.split(',')[1][:-2]))
yield data
def animate(values):
line, = plt.plot(values, color='blue')
return line,
fig = plt.figure(figsize = (5,5))
ani = FuncAnimation(fig, animate, frames=read('log.txt'), interval=10)
plt.show()
Here is the plot I have currently:
The 'time' strings I import are like this: 08:12:46, so I would like to cut the zeros at the end, but I can't seem to find the problem. Also, is there a way to show the floats on the Y axis in the exponential format, which is the one I am importing from the csv?
I just started to look into matplotlib and numpy for work, so if you have some advice it would be fantastic.
Thank you in advance!
import numpy as np
import datetime as dt
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib import style
print(plt.style.available)
style.use('ggplot')
fig = plt.figure()
ax1 = fig.add_subplot(1,1,1)
def animate(i):
graph_data = open('C:\\Users\\arzuffi pc test\\Desktop\\VMI WIP - Copia (2)\\Cycle info\\_Current Cycle.csv','r').read()
#graph_data = open('C:\\Users\\arzuffi pc test\\Desktop\\Visual Machine Interface Alpha 1.4.3\\Cycle info\\_Current Cycle.csv','r').read()
lines = graph_data.split('\n')
xs = []
ys = []
skip = 0
for line in lines:
if skip < 7:
skip += 1
else:
if len(line) > 1:
time, cycle, pc, pd, co, hv, cr, ph, gd_volt, gd_amp, gd_power, eva_amp, eva_volt, p_rpm, p_amp, r1_rpm, r1_amp, r2_rpm, r2_amp, hmdso, gas, ahc, diff_l, diff_r = line.split(';')
#x, y = line.split(';')
print(time)
print(pc)
xs.append(dt.datetime.strptime(time,'%H:%M:%S'))#.date())
ys.append(pc)
#print(i)
#xs = matplotlib.dates.date2num(xs)
print(xs)
if len (xs) > 100:
xs = xs[-100:]
if len (ys) > 100:
ys = ys[-100:]
ax1.clear()
ax1.plot(xs, ys)
plt.gcf().autofmt_xdate()
ani = animation.FuncAnimation(fig, animate,interval = 1000)
plt.show()
these are the data:
You can specify the format to be used as follows:
xs = matplotlib.dates.date2num(xs) # You need to keep this line
hfmt = matplotlib.dates.DateFormatter('%H:%M:%S')
ax1.xaxis.set_major_formatter(hfmt)
ax1.plot(xs, ys) # You have this already
This would give you an output as follows: