I am working with an epilepsy EEG dataset (https://archive.physionet.org/pn6/chbmit/). In this dataset, there is a small text file (appendix .edf.seizures) that denote start and end time (e.g. [2951 3030] maybe they are integers but I am not sure) of seizure.
I am having trouble reading this file into matlab. Using the following code:
file = '/{filename}.edf.seizures';
fscanf(fopen(file,'r'),'c');
I get following output:
' Xü## time resolution: 256 ìÿÿÿÿ ì ³ ì > '
I tried all other encoding types other than 'c' but they gave empty strings. Can anyone help me get the right encoding to read the file? Any ideas are appreciated. Thanks.
Related
I have been trying in vain for days to do one seemingly simple thing--I want to read data from a .txt file that looks like this:
0.221351321
0.151351321
0.235165165
8.2254546 E-7
into Matlab. I've been able to load the data in the .txt file as a column vector using the fscanf command, like so:
U=fscanf(FileID, '%e')
provided that I go through the file first and remove the space before the 'E' wherever scientific notation occurs in the data set.
Since I have to generate a large number of such sets, it would be impractical to have to do a search-and-replace for every .txt file.
Is there a way for matlab to read the data as it appears, as in the above example (with the space preceding 'E'), and put it into a column vector?
For anyone who knows PARI-GP, an alternate fix would be to have the output devoid of spaces in the first place--but so far I haven't found a way to erase the space before 'E' in scientific notation, and I can't predict if a number in scientific notation will appear or not in the data set.
Thank you!
Thank you all for your help, I have found a solution. There is a way to eliminate the space from PARI-GP, so that the output .txt file has no spaces to begin with. I had the output set to "prettymatrix". One needs to enter the following:
? \o{0}
to change the output to "Raw," which eliminates the space before the "E" in scientific notation.
Thanks again for your help.
A simple way, may not be the best, is to read line by line, remove the space and convert back to floating point number.
For example,
x = []
tline = fgetl(FileID);
while ischar(tline)
x = [x str2num(tline(find(~isspace(tline))))]
tline = fgetl(FileID);
end
One liner:
data = str2double(strsplit(strrep(fileread('filename.txt'),' ',''), '\n'));
strrep removes all the spaces, strsplit takes each line as a separate string, and str2double coverts the strings to numbers.
I need to read text files into Matlab. In the text files there are numbers like 5.875489^*-6, which is indeed 0.000005875489. Matlab cannot read this format and since there are too many files, I cannot change the format in all the files manually. So, I wonder if there is any tips to make Matlab reading the files as they are?
Any help and guide is highly appreciated.
Marilla.
As pointed out by #vu1p3n0x, it would probably be easier to replace ^* by e using a replace-all. Alternatively, if that is unpractical, you could read in the the mantissa and exponent separately and perform the exponentiation in Matlab:
Raw = textscan(fid, '%f^*%f');
Result = Raw{1}.*10.^Raw{2};
I have the m-file on generating all the graphs in .fig I need with a for loop, but I don't know how to extract the array data to csv, txt or ascii format (16-bit).
imagesc(x,y,C); %C is the data I want to extract
%m and n are variables created inside the for loop
I have tried dlmwrite and save, but I failed and could not fix the problem.
So I want to convert fig into csv, txt or ascii format instead.
filename_B=strcat(MM,'_profile'); %MM is a variable created inside the for loop
dlmwrite(filename_B.txt,squeeze(Data_time(:,m,n,:)),''); %Data_time is C
save(filename_B, squeeze(Data_time(:,m,n,:)),'-ascii','-double');
I have also tried csvwrite
filename_B=strcat(MM,'_profile');
csvwrite(filename_B.txt, squeeze(Data_time(:,m,n,:)));
but there is an error message, "??? Attempt to reference field of non-structure array."
It would be better if I could just extract the data directly to the desirable format without first producing fig then convert.
For confidential issue, I can't provide the whole script, but I will try my best to explain my problem.
Many thanks!
I have large .bin files (10GB 60GB) that I want to import to MATLAB; each binary file represents the output of two sensors, thus there are too columns of data. Here is a more manageable sized example of my data.
You will notice that there is a .txt version of the data; I need to upload the .bin files directly to MATLAB, I can't use the .txt version because it takes hours to convert with larger files.
The problem I have is that the .bin file has header information that I can't seem to interpret properly, and thus I cannot extract the data in MATLAB every time I try I seem to get gibberish values.
This is all the information I have about the binary header:
Loading Labview Binary Data into Matlab
LabVIEW Data Logger: Binary Header File Format
Any help/advice would be much appreciated I have been trying to solve this problem for days now.
P.S. Someone has already written a function to solve this problem but it does not seem to work with my binary data (could be something to do with the dimensions/size of my data): http://www.mathworks.co.uk/matlabcentral/fileexchange/27195-load-labview-binary-data
Below is the code that I am using to import my data, I believe that that d1 and d2 are the dimensions of my binary data. D2 is probably incorrect for the example file in the dropbox because it has been truncated.
The problem I have is that the code extracts my data and I know it is correct because I can check it with the .txt file (also in the drop box) however there are seaming random bad values between the good data points. These bad values result from the following strings following strings: "NI_ChannelName", "Sensor A", "Sensor B", "NI_UnitDescription", and "Volts" scatted throughout the binary file.
clear all
clc
fname = 'RTL5_57.bin';
fid = fopen(fname,'r','ieee-be');
d1 = fread(fid,4);
trash=fread(fid,2,'double');
d2 = fread(fid,4);
trash=fread(fid,1,'double');
data=fread(fid,'double');
I suppose you will need to change the data-format. See Matlab help.
https://decibel.ni.com/content/docs/DOC-39038
Scope:
1) Write a binary file in matlab and read into labview. 2) Write a binary file in labview and read into matlab.
Background:
IMPORTANT:
You must know (3) things about the binary data in the file before you can read the data:
1) what binary format (precision) was used to store the data
2) the exact number of values in the file to read.
3) Endianness
There is no row or column in binary files. Think of a long row/or a long column that needs to be mapped to a 2D array.
Resources on data in binary format.
http://cse.unl.edu/~sincovec/Matlab/Lesson%2024/Binary/CS211%20Lesson%2024%20-%20Binary%20File%20Input-Output.htm
My raw CSV file looks like the 1st pic. And I wants to use Matlab read it into the format as the 2rd pic. I have over 1000 the same kind of CSV files, it will be painful if I do it by copy/paste. How can I do this? Any examples?
raw data:
output data:
First thing to realize is that a .csv file has a very simple format. Your above file is actually a plain text file with the following text on each line:
id,A001
height
a1,a2,a3
3,4,5
3,4,5
6,7,5
weight
a1,a2,a3
4,4,5
5,4,6
i6,7,5
So it is not all that hard for you to write your own parser in Matlab. You want to use commands like
fid = fopen('filename.csv','r');
L = fgetl(fid); % get a text line from the file
commas = find(L==','); % find where the commas are in the line
n1 = str2num(L(1:commas(1)-1); % convert the first comma-delimited number on line L
fidout - fopen('myfile.csv','w');
Lout = [ L(commas(2)+1:commas(3)-1) ', a1, a1'];
fwrite(fidout,Lout); % write a line out to the output file
fclose all; % close all open files.
It will seem slow at first reading the various values in to various variables, and then arranging them to write out the way you want them written out to your output file. But once you get rolling it will go pretty fast and you will find yourself with a pretty good understanding of what is in files, and you will know first hand what is involved in writing something like texscan.m or csvwrite.m and so on.
Good luck!