I would like to create a script in Matlab that can read data from a CSV file and plot it. My data looks something like:
Time BPM(HeartRate)
5:55:26 0
5:55:26 0
5:55:27 66
5:55:27 70
5:55:27 71
5:55:27 74
...
I would like to plot time on the x axis and BPM on the y axis. I have tried the following:
clear, clc;
ftoread = 'data.csv';
fid = fopen(ftoread);
y=data(:,1);
x=data(:,2);
plot(x,y);
xlabel('Time');
ylabel('Heart Rate');
title('Heart Rate Vs. Time');
Unfortunately, I am getting an error at y=data(:,1).
Why don't you use csvread instead?
data = csvread('data.csv');
x=data(:,1);
y=data(:,2);
% etc...
It looks like you're missing some steps. csvread or dlmread may not work well since you have a string and a number on each line. textscan should be fast and easy:
ftoread = 'data.csv';
fid = fopen(ftoread);
data = textscan(fid,'%s%f'); % Read in a string and a double
fclose(fid); % If you call fopen, make sure you also call fclose
x = data{1};
y = data{2};
You'll then may want to use functions like datestr and datenum to convert your time strings to other values. I believe that the even accept cell array (like x) as inputs.
Related
I have a file with float numbers( -1.22070E-02 -7.32420E-02 ) on two columns.
I want to read them and make a plot. Something like the examples here: https://www.mathworks.com/help/signal/examples/signal-generation-and-visualization.html.
After searching this is my code:
fid = fopen('sample_b.txt', 'r');
a = fscanf(fid, '%f %f', [2 inf]);
simin = a';
plot(simin(:,1),simin(:,2));
fclose(fid);
But this is the plot I get:
And when I display simin using 'disp(simin)' I see:
81.4724 90.5792
12.6987 91.3376
63.2359 9.7540
27.8498 54.6882
I do not understand why my program uses these 8 numbers. My file contains many numbers, but the first 8 are these:
-1.22070E-02 -7.32420E-02
1.22070E-02 0.197750
4.88280E-03 9.27730E-02
-4.39450E-02 3.41800E-02
If I use 'plot(a(:,1),a(:,2));' the plot is just a line.
Edit: my data represents and EEG signal.
I need to read data from a file and plot a graph with its data. The problem is:
(1) I can't change the format of data in the file
(2) The format contains information and characters that I don't know how to deal with.
Here is a part of the data file, it's in a txt format:
Estation;Date;Time;Temp1;Temp2;Pressure;
83743;01/01/2016;0000;31.9;25.3;1005.1;
83743;01/01/2016;1200;31.3;26.7;1005.7;
83743;01/01/2016;1800;33.1;25.4;1004.3;
83743;02/01/2016;0000;26.1;24.2;1008.6;
What I'm trying to do is to plot the Date and Time against Temp1 and Temp2, not worrying about Pressure. The first column can be neglected as well. How can I extract the Date, Time and Temps into and matrix so I can plot them? All I did so far was this:
fileID = fopen('teste.txt','r');
[A] = fscanf(fileID, ['%d' ';']);
fclose(fileID);
disp(A);
Which just reads the first value, 83743.
To build on m7913d's answer:
fileID = fopen('MyFile.txt','r');
A = fscanf(fileID, ['%s' ';']); % read the header line
B = fscanf(fileID, '%d;%d/%d/%d;%d;%f;%f;%f;', [8,inf]); % read all the data into B (the date is parsed into three columns)
fclose(fileID);
B = B.'; % transpose B
% C is just for verification, can be omitted
C = datetime([B(:,4:-1:2) B(:,5)/100zeros(numel(B(:,1)),2)],'InputFormat','yyyy-MM-dd HH:mm:ss');
D = datenum(C); % Get the date in a MATLAB usable format
Titles = strsplit(A,';'); % Get column names
figure;
hold on % hold the figure for multiple plots
plot(D,B(:,6),'r')
plot(D,B(:,7),'b')
datetick('x') % Set a date tick as axis
legend(Titles{4},Titles{5}); % uses titles for legend
note the parsing of the date into C: first is the date as given by you in dd-MM-yyyy format, which I flip to the official standard of yyyy-MM-dd, then your hour, which needs to be divided by 100, then a 0 for both minutes and seconds. You might need to rip those apart when you don't have exactly hourly data. Finally transform to a regular datenum, which MATLAB can use for processing.
Which results in:
You might want to play around with the datetick format, as it's got lots of options which might appeal to you.
fileID = fopen('input.txt','r');
[A] = fscanf(fileID, ['%s' ';']); % read the header line
[B] = fscanf(fileID, '%d;%d/%d/%d;%d;%f;%f;%f;', [8,inf]); % read all the data into B (the date is parsed into three columns)
fclose(fileID);
disp(B');
Note that %d reads an integer (not a double) and %f reads a floating point number.
See fscanf for more details.
Im trying to plot trajectories on matlab
My data file (try.txt) that has the trajectories looks like this:
NumofTrajectories
TrajID1 #ofPoints x y x y....
TrajID2 #ofPoints x y x y....
example:
7
0 23 898.6 673.0 859.1 669.9 813.7 667.8 776.8 664.0 739.8 662.1 699.9 654.7 664.5 649.6 625.3 645.5 588.2 640.6 552.3 634.2 516.6 628.2 477.2 624.3 442.1 613.6 406.7 603.4 369.5 599.8 332.7 594.1 297.4 585.2 258.6 583.7 224.1 573.1 191.2 556.8 152.7 554.0 115.1 546.0 79.6 535.8
1 8 481.4 624.9 445.9 596.3 374.5 573.9 354.2 541.0 334.2 508.9 327.6 474.1 324.6 437.5 324.2 390.3
2 24 151.6 570.8 188.3 556.5 225.1 547.7 257.9 529.4 292.9 509.8 326.8 496.8 356.2 476.0 391.2 463.3 423.7 447.9 455.7 431.8 489.2 416.0 524.3 405.3 560.0 395.9 595.8 385.6 632.8 376.1 671.5 372.0 706.9 361.8 742.3 347.3 778.0 334.5 820.5 336.5 856.5 325.0 894.5 309.5 946.1 309.9 990.5 287.0
3 3 594.2 580.4 566.6 544.3 544.9 509.4
4 5 281.8 661.9 266.8 623.4 246.2 576.4 229.7 541.0 220.9 498.4
5 2 563.6 511.3 532.5 479.7
6 5 571.9 617.7 525.6 576.4 481.0 551.9 456.8 524.2 419.7 474.0
I'm trying to plot this on matlab
my code is as follows:
clc;
clear;
%read the input
importfile('try.txt')
%See how many trajectorys there are convert to number
nTraj=str2num(cell2mat(textdata));
%loop over the trajectories
for i = 1:nTraj
disp(data(i,1));
%print the current trajectory number of points
disp(data(i,2));
%get the x-y coordinates of each trajectory
current_traj=data(i,2);
for j=1:current_traj
points=data(i,3:j*2+2);
end
%print the x-y coordinates of each trajectory
%disp(points);
%seperate the x-y coordinates of each trajectory
x=points(1:2:length(points)-1)
y=points(2:2:length(points))
xlabel('latitude');
ylabel('longitude');
plot(x,y,'r');
grid on ;
hold on;
end
And function importfile:
function importfile(fileToRead1)
%IMPORTFILE(FILETOREAD1)
% Imports data from the specified file
% FILETOREAD1: file to read
DELIMITER = ' ';
HEADERLINES = 1;
% Import the file
newData1 = importdata(fileToRead1, DELIMITER, HEADERLINES);
% Create new variables in the base workspace from those fields.
vars = fieldnames(newData1);
for i = 1:length(vars)
assignin('base', vars{i}, newData1.(vars{i}));
end
The code sometimes works and usually gives me an error say:
Index exceeds matrix dimensions.
Error in ==> plotTrajectory at 23
points=data(i,3:j*2+2);
Can someone explain the error and tell me how to fix it?
The trajectories in try.txt have different lengths. importdata will use the first line to determine the length of your data. If another line is the longest, this line will be split over several lines of your imported matrix. At least this is what debugging shows. I would suggest you use another method to read your file. For me dlmread works:
%read the input
data = dlmread('try.txt', ' ');
% remove header
data = data(2:end,:);
%See how many trajectorys there are convert to number
nTraj=size(data,1);
You can replace your first lines with this code and remove your importfilefunction.
I am trying to export data from Matlab in format that would be understood by another application... For that I need to change the NaN, Inf and -Inf strings (that Matlab prints by default for such values) to //m, //inf+ and //Inf-.
In general I DO KNOW how to accomplish this. I am asking how (and whether it is possible) to exploit one particular thing in Matlab. The actual question is located in the last paragraph.
There are two approaches that I have attempted (code bellow).
Use sprintf() on data and strrep() the output. This is done in line-by-line fashion in order to save memory. This solution takes almost 10 times more time than simple fprintf(). The advantage is that it has low memory overhead.
Same as option 1., but the translation is done on the whole data at once. This solution is way faster, but vulnerable to out of memory exception. My problem with this approach is that I do not want to unnecessarily duplicate the data.
Code:
rows = 50000
cols = 40
data = rand(rows, cols); % generate random matrix
data([1 3 8]) = NaN; % insert some NaN values
data([5 6 14]) = Inf; % insert some Inf values
data([4 2 12]) = -Inf; % insert some -Inf values
fid = fopen('data.txt', 'w'); %output file
%% 0) Write data using default fprintf
format = repmat('%g ', 1, cols);
tic
fprintf(fid, [format '\n'], data');
toc
%% 1) Using strrep, writing line by line
fprintf(fid, '\n');
tic
for i = 1:rows
fprintf(fid, '%s\n', strrep(strrep(strrep(sprintf(format, data(i, :)), 'NaN', '//m'), '-Inf', '//inf-'), 'Inf', '//inf+'));
end
toc
%% 2) Using strrep, writing all at once
fprintf(fid, '\n');
format = [format '\n'];
tic
fprintf(fid, '%s\n', strrep(strrep(strrep(sprintf(format, data'), 'NaN', '//m'), '-Inf', '//inf-'), 'Inf', '//inf+'));
toc
Output:
Elapsed time is 1.651089 seconds. % Regular fprintf()
Elapsed time is 11.529552 seconds. % Option 1
Elapsed time is 2.305582 seconds. % Option 2
Now to the question...
I am not satisfied with the memory overhead and time lost using my solutions in comparison with simple fprintf().
My rationale is that the 'NaN', 'Inf' and '-Inf' strings are simple data saved in some variable inside the *printf() or *2str() implementation. Is there any way to change their value at runtime?
For example in C# I would change the System.Globalization.CultureInfo.NumberFormat.NaNSymbol, etc. as explaind here.
In the limited case mentioned in comments that a number of (unknown, changing per data set) columns may be entirely NaN (or Inf, etc), but that there are not unwanted NaN values otherwise, another possibility is to check the first row of data, assemble a format string which writes the \\m strings directly, and use that while telling fprintf to ignore the columns that contain NaN or other unwanted values.
y = ~isnan(data(1,:)); % find all non-NaN
format = sprintf('%d ',y); % print a 1/0 string
format = strrep(format,'1','%g');
format = strrep(format,'0','//m');
fid = fopen('data.txt', 'w');
fprintf(fid, [format '\n'], data(:,y)'); %pass only the non-NaN data
fclose(fid);
By my check with two columns of NaN this fprintf is pretty much the same as your "regular" fprintf and quicker than the loop - not taking into account the initialisation step of producing format. It would be fiddlier to set it up to automatically produce the format string if you also have to take +/- Inf into account, but certainly possible. There is probably a cleaner way of producing format as well.
How it works:
You can pass in a subset of your data, and you can also insert any text you like into a format string, so if every row has the same desired "text" in the same spot (in this case NaN columns and our desired replacement for "NaN"), we can put the text we want in that spot and then just not pass those parts of the data to fprintf in the first place. A simpler example for trying out on the command line:
x = magic(5);
x(:,3)=NaN
sprintf('%d %d ihatethrees %d %d \n',x(:,[1,2,4,5])');
I want to read in a text file that contains some strings but mostly numbers. I want to be able to ignore the strings and only look at the numbers. I want to plot those values on a 3D plane. The data looks like this:
Tech4:<152.266724,173.189377,27.995975>
<117.880638,156.116531,27.999983>
<129.849899,59.195660,27.999983>
<249.321121,60.605404,27.999983>
<224.120361,139.072739,28.000668>
<171.188950,143.490921,56.933430>
<171.188950,143.490921,83.548088>
<171.188950,143.490921,27.999985>
I believe to read in a file is just:
File = textread('testFile.txt');
How can I only look at those values and then plot it.
Thanks!
fid = fopen([pathname,filename]);
tline = fgetl(fid);
CX = [];
CY = [];
CZ = [];
while ischar(tline)
% skip < and >
tline = substr(tline, 1, length(tline)-2)
% extract numbers
temp = textscan(tline,'%n%n%n', 'delimiter',',');
CX(end+1,:) = [temp(1)];
CY(end+1,:) = [temp(2)];
CZ(end+1,:) = [temp(3)];
tline = fgetl(fid);
end
fclose(fid);
and then plot it using
plot3(CX, CY, CZ)
function call.
Add the check for "Tech4:" at the beginning however...
I think you can also directly use textscan in a one-liner:
fid = fopen('testFile.txt');
data = textscan(fid,'%*s%f,%f,%f');
fclose(fid);
this loads the values from all rows with the specified format into the variable data.
no matlab around to test it out though.
fscanf is an option to, the same kind of parameters as textscan.
EDIT: typo, you want to detect floats (%f) of course, and not integers (%d)
EDIT2: got matlab and tested it out, this works here for your sample input ^^
fid = fopen('testFile.txt');
data = textscan(fid,'%*s%f%f%f','Delimiter',',<>')
fclose(fid);