0 
import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import find_peaks
import pdb

The objective of the code is to plot a graph using the data and show the different peaks. Then Annotating the peak values of each peak.

Data 

X:-241, Y:-31, Z:17, T:73823
X:-241, Y:-31, Z:17, T:73952
X:-240, Y:-30, Z:26, T:74073
X:-240, Y:-30, Z:26, T:74191
X:-240, Y:-30, Z:26, T:74312
X:-240, Y:-32, Z:39, T:74432
X:-240, Y:-32, Z:39, T:74549
X:-240, Y:-32, Z:39, T:74668
X:-239, Y:-21, Z:12, T:74785
X:-239, Y:-21, Z:12, T:74904
X:-239, Y:-21, Z:12, T:75022
X:-246, Y:15, Z:18, T:75142
X:-246, Y:15, Z:18, T:75260
X:-246, Y:15, Z:18, T:75378
X:-250, Y:19, Z:14, T:75498
X:-250, Y:19, Z:14, T:75615
X:-250, Y:19, Z:14, T:75732
X:-239, Y:-5, Z:27, T:75854
X:-239, Y:-5, Z:27, T:75972
X:-239, Y:-5, Z:27, T:76102
X:-236, Y:-19, Z:46, T:76240
X:-236, Y:-19, Z:46, T:76369
X:-236, Y:-19, Z:46, T:76489
X:-235, Y:-14, Z:32, T:76610
X:-235, Y:-14, Z:32, T:76727
X:-235, Y:-14, Z:32, T:76845
X:-244, Y:-16, Z:22, T:76963
X:-244, Y:-16, Z:22, T:77081
X:-244, Y:-16, Z:22, T:77201
X:-220, Y:-25, Z:-3, T:77346
X:-220, Y:-25, Z:-3, T:77464
X:-220, Y:-25, Z:-3, T:77580
X:-229, Y:24, Z:2, T:77699
X:-229, Y:24, Z:2, T:77814
X:-229, Y:24, Z:2, T:77934
X:-248, Y:-20, Z:0, T:78052
X:-248, Y:-20, Z:0, T:78171
X:-248, Y:-20, Z:0, T:78288
X:-242, Y:-15, Z:-35, T:78515
X:-242, Y:-15, Z:-35, T:78630
X:-242, Y:-15, Z:-35, T:78747
X:-235, Y:-12, Z:-63, T:78865
X:-235, Y:-12, Z:-63, T:78982
X:-235, Y:-12, Z:-63, T:79102
X:-226, Y:-35, Z:-145, T:79221
X:-226, Y:-35, Z:-145, T:79340
X:-226, Y:-35, Z:-145, T:79461
X:-205, Y:-47, Z:-156, T:79582
X:-205, Y:-47, Z:-156, T:79702
X:-205, Y:-47, Z:-156, T:79821
X:-208, Y:-39, Z:-149, T:79940
X:-208, Y:-39, Z:-149, T:80061
X:-208, Y:-39, Z:-149, T:80181
X:-235, Y:-16, Z:-99, T:80304
X:-235, Y:-16, Z:-99, T:80432
X:-235, Y:-16, Z:-99, T:80657
X:-247, Y:-10, Z:12, T:80774
X:-247, Y:-10, Z:12, T:80890
X:-247, Y:-10, Z:12, T:81008
X:-242, Y:-1, Z:2, T:81127
X:-242, Y:-1, Z:2, T:81246
X:-242, Y:-1, Z:2, T:81363
X:-239, Y:-8, Z:15, T:81483
X:-239, Y:-8, Z:15, T:81600
X:-239, Y:-8, Z:15, T:81720
X:-241, Y:-13, Z:-11, T:81841
X:-241, Y:-13, Z:-11, T:81958
X:-241, Y:-13, Z:-11, T:82076
X:-242, Y:-5, Z:-37, T:82198
X:-242, Y:-5, Z:-37, T:82315
X:-242, Y:-5, Z:-37, T:82435
X:-215, Y:-43, Z:-128, T:82554
X:-215, Y:-43, Z:-128, T:82699
X:-215, Y:-43, Z:-128, T:82829
X:-207, Y:-48, Z:-153, T:82952
X:-207, Y:-48, Z:-153, T:83072
X:-207, Y:-48, Z:-153, T:83191
X:-198, Y:-37, Z:-166, T:83315
X:-198, Y:-37, Z:-166, T:83453
X:-198, Y:-37, Z:-166, T:83572
X:-218, Y:-33, Z:-134, T:83694
X:-218, Y:-33, Z:-134, T:83812
X:-218, Y:-33, Z:-134, T:83932
X:-228, Y:-15, Z:-80, T:84047
X:-228, Y:-15, Z:-80, T:84166
X:-228, Y:-15, Z:-80, T:84288
X:-243, Y:-8, Z:-4, T:84407
X:-243, Y:-8, Z:-4, T:84524
X:-243, Y:-8, Z:-4, T:84640
X:-238, Y:-4, Z:2, T:84756
X:-238, Y:-4, Z:2, T:84872
X:-238, Y:-4, Z:2, T:84994
X:-252, Y:-7, Z:-16, T:85136
X:-252, Y:-7, Z:-16, T:85265
X:-252, Y:-7, Z:-16, T:85385
X:-243, Y:-3, Z:-28, T:85504
X:-243, Y:-3, Z:-28, T:85618
X:-243, Y:-3, Z:-28, T:85739
X:-241, Y:-3, Z:-48, T:85858
X:-241, Y:-3, Z:-48, T:85975
X:-241, Y:-3, Z:-48, T:86094
X:-231, Y:-15, Z:-112, T:86216
X:-231, Y:-15, Z:-112, T:86334
X:-231, Y:-15, Z:-112, T:86453
X:-210, Y:-43, Z:-150, T:86573
X:-210, Y:-43, Z:-150, T:86691
X:-210, Y:-43, Z:-150, T:86811
X:-193, Y:-58, Z:-169, T:86933
X:-193, Y:-58, Z:-169, T:87051
X:-193, Y:-58, Z:-169, T:87171
X:-182, Y:-27, Z:-179, T:87305
X:-182, Y:-27, Z:-179, T:87435
X:-182, Y:-27, Z:-179, T:87566
X:-212, Y:-19, Z:-136, T:87686
X:-212, Y:-19, Z:-136, T:87803
X:-212, Y:-19, Z:-136, T:87920
X:-233, Y:-25, Z:-83, T:88040
X:-233, Y:-25, Z:-83, T:88160
X:-233, Y:-25, Z:-83, T:88278
X:-243, Y:-16, Z:-31, T:88396
X:-243, Y:-16, Z:-31, T:88510
X:-243, Y:-16, Z:-31, T:88625
X:-244, Y:-13, Z:-27, T:88744
X:-244, Y:-13, Z:-27, T:88860
X:-244, Y:-13, Z:-27, T:88978
X:-243, Y:-15, Z:-51, T:89099
X:-243, Y:-15, Z:-51, T:89218
X:-243, Y:-15, Z:-51, T:89338
X:-228, Y:-27, Z:-78, T:89472
X:-228, Y:-27, Z:-78, T:89601
X:-228, Y:-27, Z:-78, T:89746
X:-223, Y:-24, Z:-114, T:89876
X:-223, Y:-24, Z:-114, T:89995
X:-223, Y:-24, Z:-114, T:90115
X:-205, Y:-42, Z:-141, T:90236
X:-205, Y:-42, Z:-141, T:90354
X:-205, Y:-42, Z:-141, T:90474
X:-199, Y:-67, Z:-153, T:90595
X:-199, Y:-67, Z:-153, T:90713
X:-199, Y:-67, Z:-153, T:90833
X:-202, Y:-53, Z:-152, T:90951
X:-202, Y:-53, Z:-152, T:91069
X:-202, Y:-53, Z:-152, T:91191
X:-224, Y:-41, Z:-135, T:91312
X:-224, Y:-41, Z:-135, T:91431
X:-224, Y:-41, Z:-135, T:91549
X:-229, Y:-29, Z:-91, T:91669
X:-229, Y:-29, Z:-91, T:91789
X:-229, Y:-29, Z:-91, T:91923
X:-242, Y:-8, Z:-2, T:92066
X:-242, Y:-8, Z:-2, T:92184
X:-242, Y:-8, Z:-2, T:92302
X:-233, Y:-12, Z:-5, T:92420
X:-233, Y:-12, Z:-5, T:92534
X:-233, Y:-12, Z:-5, T:92654
X:-246, Y:-1, Z:-4, T:92773
X:-246, Y:-1, Z:-4, T:92892
X:-246, Y:-1, Z:-4, T:93010
X:-242, Y:-9, Z:-23, T:93130
X:-242, Y:-9, Z:-23, T:93251
X:-242, Y:-9, Z:-23, T:93370
X:-237, Y:-19, Z:-46, T:93491
X:-237, Y:-19, Z:-46, T:93608
X:-237, Y:-19, Z:-46, T:93727
X:-213, Y:-23, Z:-95, T:93849
X:-213, Y:-23, Z:-95, T:93966
X:-213, Y:-23, Z:-95, T:94112
X:-207, Y:-36, Z:-151, T:94241
X:-207, Y:-36, Z:-151, T:94359
X:-207, Y:-36, Z:-151, T:94480
X:-199, Y:-49, Z:-162, T:94600
X:-199, Y:-49, Z:-162, T:94721
X:-199, Y:-49, Z:-162, T:94840
X:-203, Y:-36, Z:-146, T:94961
X:-203, Y:-36, Z:-146, T:95082
X:-203, Y:-36, Z:-146, T:95202
X:-222, Y:-28, Z:-124, T:95324
X:-222, Y:-28, Z:-124, T:95439
X:-222, Y:-28, Z:-124, T:95583
X:-244, Y:2, Z:-53, T:95700
X:-244, Y:2, Z:-53, T:95817
X:-244, Y:2, Z:-53, T:95935
X:-237, Y:-5, Z:-9, T:96055
X:-237, Y:-5, Z:-9, T:96171
X:-237, Y:-5, Z:-9, T:96301
X:-239, Y:-2, Z:1, T:96439
X:-239, Y:-2, Z:1, T:96568
X:-239, Y:-2, Z:1, T:96685
X:-243, Y:-4, Z:2, T:96805
X:-243, Y:-4, Z:2, T:96919
X:-243, Y:-4, Z:2, T:97037
X:-246, Y:-3, Z:-16, T:97159
X:-246, Y:-3, Z:-16, T:97276
X:-246, Y:-3, Z:-16, T:97395
X:-239, Y:-8, Z:-42, T:97513
X:-239, Y:-8, Z:-42, T:97631
X:-239, Y:-8, Z:-42, T:97752
X:-221, Y:-10, Z:-115, T:97871
X:-221, Y:-10, Z:-115, T:97990
X:-221, Y:-10, Z:-115, T:98109
X:-219, Y:-25, Z:-145, T:98230
X:-219, Y:-25, Z:-145, T:98350
X:-219, Y:-25, Z:-145, T:98468
X:-202, Y:-31, Z:-172, T:98589
X:-202, Y:-31, Z:-172, T:98736
X:-202, Y:-31, Z:-172, T:98865
X:-214, Y:-34, Z:-144, T:98985
X:-214, Y:-34, Z:-144, T:99101
X:-214, Y:-34, Z:-144, T:99223
X:-224, Y:-24, Z:-116, T:99342
X:-224, Y:-24, Z:-116, T:99460
X:-224, Y:-24, Z:-116, T:99579
X:-232, Y:2, Z:-50, T:99699
X:-232, Y:2, Z:-50, T:99818
X:-232, Y:2, Z:-50, T:99936
X:-241, Y:-4, Z:-22, T:100056
X:-241, Y:-4, Z:-22, T:100175
X:-241, Y:-4, Z:-22, T:100293
X:-240, Y:4, Z:-2, T:100414
X:-240, Y:4, Z:-2, T:100532
X:-240, Y:4, Z:-2, T:100648
X:-241, Y:3, Z:1, T:100768
X:-241, Y:3, Z:1, T:100895
X:-241, Y:3, Z:1, T:101029
X:-243, Y:1, Z:-16, T:101160
X:-243, Y:1, Z:-16, T:101278
X:-243, Y:1, Z:-16, T:101399
X:-239, Y:-2, Z:-36, T:101518
X:-239, Y:-2, Z:-36, T:101661
X:-239, Y:-2, Z:-36, T:101780
X:-228, Y:-12, Z:-71, T:101901
X:-228, Y:-12, Z:-71, T:102019
X:-228, Y:-12, Z:-71, T:102138
X:-224, Y:-23, Z:-118, T:102260
X:-224, Y:-23, Z:-118, T:102378
X:-224, Y:-23, Z:-118, T:102498
X:-209, Y:-2, Z:-161, T:102617
X:-209, Y:-2, Z:-161, T:102735
X:-209, Y:-2, Z:-161, T:102855
X:-206, Y:-3, Z:-150, T:102974
X:-206, Y:-3, Z:-150, T:103088
X:-206, Y:-3, Z:-150, T:103216
X:-218, Y:0, Z:-142, T:103355
X:-218, Y:0, Z:-142, T:103469
X:-218, Y:0, Z:-142, T:103581
X:-226, Y:-17, Z:-118, T:103700
X:-226, Y:-17, Z:-118, T:103814
X:-226, Y:-17, Z:-118, T:103931
X:-242, Y:4, Z:-40, T:104054
X:-242, Y:4, Z:-40, T:104171
X:-242, Y:4, Z:-40, T:104292
X:-242, Y:4, Z:-22, T:104410
X:-242, Y:4, Z:-22, T:104523
X:-242, Y:4, Z:-22, T:104642
X:-240, Y:5, Z:-3, T:104762
X:-240, Y:5, Z:-3, T:104879
X:-240, Y:5, Z:-3, T:104993
X:-244, Y:-2, Z:-6, T:105111
X:-244, Y:-2, Z:-6, T:105231
X:-244, Y:-2, Z:-6, T:105361
X:-244, Y:1, Z:-10, T:105497
X:-244, Y:1, Z:-10, T:105623
X:-244, Y:1, Z:-10, T:105744
X:-244, Y:-4, Z:-34, T:105865
X:-244, Y:-4, Z:-34, T:105981
X:-244, Y:-4, Z:-34, T:106101
X:-231, Y:-1, Z:-63, T:106222
X:-231, Y:-1, Z:-63, T:106341
X:-231, Y:-1, Z:-63, T:106462
X:-222, Y:-11, Z:-116, T:106580
X:-222, Y:-11, Z:-116, T:106698
X:-222, Y:-11, Z:-116, T:106818
X:-219, Y:-15, Z:-144, T:106938
X:-219, Y:-15, Z:-144, T:107058
X:-219, Y:-15, Z:-144, T:107174
X:-204, Y:-6, Z:-150, T:107297
X:-204, Y:-6, Z:-150, T:107410
X:-204, Y:-6, Z:-150, T:107528
X:-196, Y:-5, Z:-163, T:107665
X:-196, Y:-5, Z:-163, T:107802
X:-196, Y:-5, Z:-163, T:107935
X:-214, Y:-2, Z:-153, T:108066
X:-214, Y:-2, Z:-153, T:108186
X:-214, Y:-2, Z:-153, T:108306
X:-223, Y:-12, Z:-123, T:108422
X:-223, Y:-12, Z:-123, T:108544
X:-223, Y:-12, Z:-123, T:108661
X:-230, Y:7, Z:-52, T:108783
X:-230, Y:7, Z:-52, T:108900
X:-230, Y:7, Z:-52, T:109019
X:-241, Y:9, Z:-25, T:109139
X:-241, Y:9, Z:-25, T:109258
X:-241, Y:9, Z:-25, T:109375
X:-245, Y:4, Z:-12, T:109496
X:-245, Y:4, Z:-12, T:109612
X:-245, Y:4, Z:-12, T:109732
X:-242, Y:3, Z:-6, T:109852
X:-242, Y:3, Z:-6, T:109968
X:-242, Y:3, Z:-6, T:110098
X:-239, Y:-4, Z:-35, T:110243
X:-239, Y:-4, Z:-35, T:110362
X:-239, Y:-4, Z:-35, T:110484
X:-235, Y:6, Z:-65, T:110606
X:-235, Y:6, Z:-65, T:110722
X:-235, Y:6, Z:-65, T:110840
X:-215, Y:-14, Z:-117, T:110962
X:-215, Y:-14, Z:-117, T:111081
X:-215, Y:-14, Z:-117, T:111204
X:-224, Y:7, Z:-146, T:111324
X:-224, Y:7, Z:-146, T:111441
X:-224, Y:7, Z:-146, T:111561
X:-209, Y:-6, Z:-149, T:111679
X:-209, Y:-6, Z:-149, T:111799
X:-209, Y:-6, Z:-149, T:111919
X:-219, Y:-8, Z:-140, T:112038
X:-219, Y:-8, Z:-140, T:112157
X:-219, Y:-8, Z:-140, T:112274
X:-226, Y:-3, Z:-116, T:112405
X:-226, Y:-3, Z:-116, T:112540
X:-226, Y:-3, Z:-116, T:112669
X:-233, Y:2, Z:-76, T:112792
X:-233, Y:2, Z:-76, T:112909
X:-233, Y:2, Z:-76, T:113028
X:-237, Y:7, Z:-35, T:113148
X:-237, Y:7, Z:-35, T:113266
X:-237, Y:7, Z:-35, T:113386
X:-242, Y:5, Z:-15, T:113504
X:-242, Y:5, Z:-15, T:113624
X:-242, Y:5, Z:-15, T:113764
X:-244, Y:5, Z:-3, T:113884
X:-244, Y:5, Z:-3, T:113999
X:-244, Y:5, Z:-3, T:114118
X:-242, Y:3, Z:-7, T:114239
X:-242, Y:3, Z:-7, T:114357
X:-242, Y:3, Z:-7, T:114473
X:-241, Y:0, Z:-30, T:114595
X:-241, Y:0, Z:-30, T:114720
X:-241, Y:0, Z:-30, T:114867
X:-227, Y:-13, Z:-95, T:114989
X:-227, Y:-13, Z:-95, T:115104
X:-227, Y:-13, Z:-95, T:115224
X:-212, Y:-5, Z:-114, T:115343
X:-212, Y:-5, Z:-114, T:115462
X:-212, Y:-5, Z:-114, T:115579
X:-215, Y:-6, Z:-145, T:115701
X:-215, Y:-6, Z:-145, T:115819
X:-215, Y:-6, Z:-145, T:115937
X:-210, Y:5, Z:-142, T:116059
X:-210, Y:5, Z:-142, T:116176
X:-210, Y:5, Z:-142, T:116296
X:-222, Y:-19, Z:-145, T:116415
X:-222, Y:-19, Z:-145, T:116534
X:-222, Y:-19, Z:-145, T:116655
X:-231, Y:6, Z:-119, T:116775
X:-231, Y:6, Z:-119, T:116894
X:-231, Y:6, Z:-119, T:117023

Code for import:

file = open("Data1r2.txt", 'r')
lines = file.readlines()
file.close()

t = []
z = []
y = []
x = []

for line in lines:

parts = line.split(", ")
if len(parts) > 3:
    column1 = parts[3].split(':')
    column2 = column1[1]

    column3 = parts[2].split(':')
    column4 = column3[1]

    column5 = parts[1].split(':')
    column6 = column5[1]

    column7 = parts[0].split(':')
    column8 = column7[1]

    T = column2[0:len(column2)]
    Z = column4[0:len(column4)]
    Y = column6[0:len(column6)]
    X = column8[0:len(column8)]

   # pdb.set_trace()

    T1 = float(T)
    t.append(T1)

    Z1 = float(Z)
    z.append(Z1)

    Y1 = float(Y)
    y.append(Y1)

    X1 = float(X)
    x.append(X1)

fig = plt.figure()
ax = fig.add_subplot(111)

This part of the code is for the peak detection for my highest peak.

zz = np.array(z)  
peaks, _ = find_peaks(zz, height = -50 )
plt.plot(zz)
plt.plot(peaks, zz[peaks],'o')
plt.plot(np.zeros_like(x), "--", color="gray")

This part im trying to annotate the highest peak value. The problem now is when i run it it will show 2 graph instead of 1. it suppose to be the same 1 graph but showing the peaks and annotate the peak values.

Picture of the 2 graphs

Picture of the other graph

line, = ax.plot(t, z)

ymax = max(z)
xpos = z.index(ymax)
xmax = t[xpos]


text= "x={:.1f}, y={:.1f}".format(xmax, ymax)
ax.annotate(text, xy=(xmax, ymax), xytext=(xmax, ymax),
        arrowprops=dict(facecolor='black', shrink=0.05),
        )

 ax.set_ylim(-150,100)
#ax.set_xlim(70000,110000)

plt.legend()
plt.show()
Improve this question
2
  • 1
    Do not add subplot if you dont want 2 graphs. Commented Sep 10, 2018 at 7:41
  • what should i replace it with? since i still need to define ax Commented Sep 10, 2018 at 7:53

1 Answer 1

Reset to default
1

Your "2-graph-problem" is, that you first plot y-values just over their indices, which go from 0 to len(zz):

plt.plot(zz)

and

plt.plot(peaks, zz[peaks],'o')

But the second plot is done over t, which is somewhere around 80000:

ax.plot(t, z)

and for the annotation, you also take care of the t-range:

xmax = t[xpos]
ax.annotate(text, xy=(xmax, ymax), xytext=(xmax, ymax), ...

So the solution for this would be to just decide wether to plot over indices or over t, but do not mix them up.

However:

Frankly spoken, there are more problems in your code than this. Mainly e.g. if I may say that your data import is very uncommon and because of not being very straight forward, it's hard not to loose orientation in there.

I'd suggest to use either a common approach like

t = []
z = []
y = []
x = []

with open("Data1r2.txt", 'r') as f:
    for line in f:
        parts = line.split(", ")
        x.append(float(parts[0][2:]))   # in case there are floats in your data
        y.append(float(parts[1][2:]))   # otherwise you should cast to int
        z.append(float(parts[2][2:]))
        t.append(float(parts[3][2:]))

or use a library like pandas, which is capable of importing almost everything.
Anyway, if you would please not post images of your data, but post them as text, there would be an even better chance to test if a suggestion of how to deal with your data works or not.

EDIT: supplemental for a start with pandas:

import pandas as pd

Your import would look like:

df = pd.read_table('Data1r2.txt', sep='[XYZT:,\s]+', names=['X', 'Y', 'Z', 'T'], usecols=[1,2,3,4], index_col=3, engine='python')

where

  • sep='[XYZT:,\s]+' describes the separators with a regex term (a sequence of length 1 or longer which consists of XYZ:, or space)
  • names is the kwarg for telling the column names if the file does not have a header
  • usecols is for choosing only certain columns. Here [1,2,3,4] says take all columns except the first (would be index 0) because each row starts with a separator, so there is an empty column on the left
  • index_col provides the possibility to use one column as index. You can delete this, if you want T to be a data column as the others and rather have a simple counting index. Just a matter of taste and how you'd like to deal with the data later
  • engine='python' is needed for regex type separator definitions

The structure of the resulting pandas dataframe can be seen with

    df.head()

which prints the first 5 lines:

    Out: 
             X   Y   Z
    T                 
    73823 -241 -31  17
    73952 -241 -31  17
    74073 -240 -30  26
    74191 -240 -30  26
    74312 -240 -30  26

Now you can play around. Just have a look at the docs. Either simply plot directly e.g.:

df.plot()

or use your now neatly structured data for plotting via matplotlib e.g.:

plt.plot(df['T'], df['X'], 'rx', label='X')
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8 Comments

Numpy has a couple of ok data import routines as well
i have added the data but its all together when i pasted not sure if its ok.
Yes, you should treat it the same like code. I.e. select it and press Ctrl + k, so that it is indented. Additionally you can replace the image of the data with the text version, as this is the idea behind it. Just have a look at the last edit, I made these changes for you this time.
plt.plot(zz) plt.plot(peaks, zz[peaks],'o') ,, how do i get this to plot over t instead of starting from 0? so that my 2 graphs will be 1 instead?
Did you read the syntax of matplotlib's plot? plot(y) creates a graph of y over its indices, plot(x, y) creates a graph of y over x, provided they have the same length. Hence, plotting zz over t would be realised by plt.plot(t, zz)
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