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!
Related
I am trying to load a file in Matlab. But I am a bit confused about the best way to do it.
The file has 3 columns and looks like the screenshot below:
This file I can load very quickly by doing load('c').
However, I had to add 2 NaNs on the bottom row.
The original file actually looks like the file below:
Now if I do load('c') on the file below I get the error:
Error using load
Unable to read file 'c'. Input must be a MAT-file or an ASCII file containing numeric
data with same number of columns in each row.
Of course I can use ImportData to import this file, but it is just soooo slow to import it.
Any suggestions?
You should be able to use c = readtable('c'). This should automatically change the empty entries to "NaN" by default, but if not, there is a way to set that in the options.
If I have a file that is tricky to import (prior to readtable()...that made things a lot easier in the last few years), I will often use the Import Data tool (if its a really big file you can make a mock-up of the complicated file so it loads faster) then change all the import settings as I would want it, then where the green check says "Import Selection" use the black drop down arrow to select "Generate Function." This will give you the coded way of setting everything up to get the file in just the way you want it.
load() is better suited for reading in previously saved '.mat' files that were created in Matlab.
Here's a low-level approach, which might be faster than other methods:
filename = 'c'; % name of the file
N = 3; % number of columns
fid = fopen(filename, 'r'); % open file for reading
x = fscanf(fid, '%f'); % read all values as a column vector
fclose(fid); % close file
x = [x; NaN(N-mod(numel(x)-1,N)-1, 1)]; % include NaN's to make length a multiple of N
x = reshape(x, N, []).'; % reshape to N columns in row-major order
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.
What I have
A txt file like:
D091B
E7E1F
20823
...
What I need
To read them and store them like char, just as they are in the file: N (don't knot how many) lines, with its 5 characters (5 columns) at each one.
What have I tried
fichero = fopen('PS.txt','r');
sizeDatos = [[] 5]; % Several Options, read below
resultados=fscanf(fichero, '%s', sizeDatos); % Here too
fclose(fichero);
I've tried with the snippet above, to read my txt file. However, I didn't manage to get it. Most I've obtained is, using:
sizeDatos = [1 Inf];
So I got all my hex characters into an array, with no spaces.
As you can see, I've tried several optios changing fscanf size parameter, as well as trying to say into the format chain that it should recognize new lines by using \n for example. None of them have worked for me.
Any idea about how can I get it? I've readed fscanf page from documentation, but it didn't inspire me to make anything different.
One possible solution is using textscan and convert it to a cell array.
fileId = fopen('PS.txt');
C = textscan(fileId, '%s');
Now to show the content of cell you can use
celldisp(C)
Or you can convert it to other types.
Don't forget to close your file after using it.
Ok, so I'm struggling with the most mundane of things I have a space delimited text file with a header in the first row and a row per observation and I'd like to open that file in matlab. If I do this in R I have no problem at all, it'll create the most basic matrix and voila!
But MATLAB seems to be annoying with this...
Example of the text file:
"picFile" "subjCode" "gender"
"train_1" 504 "m"
etc.
Can I get something like a matrix at all? I would then like to have MATLAB pull out some data by doing data(1,2) for example.
What would be the simplest way to do this?
It seems like having to write a loop using f-type functions is just a waste of time...
If you have a sufficiently new version of Matlab (R2013b+, I believe), you can use readtable, which is very much like how R does it:
T = readtable('data.txt','Delimiter',' ')
There are many functions for manipulating tables and converting back and forth between them and other data types such as cell arrays.
There are some other options in the data import and export section of the Statistics toolbox that should work in older versions of Matlab:
tblread: output in terms of separate variables for strings and numbers
caseread: output in terms of a char array
tdfread: output in terms of a struct
Alternatively, textscan should be able to accomplish what you need and probably will be the fastest:
fid = fopen('data.txt');
header = textscan(fid,'%s',3); % Optionally save header names
C = textscan(fid,'%s%d%s','HeaderLines',1); % Read data skipping header
fclose(fid); % Don't forget to close file
C{:}
Found a way to solve my problem.
Because I don't have the latest version of MATLAB and cannot use readable which would be the preferred option I ended up doing using textread and specifying the format of each column.
Tedious but maybe the "simplest" way I could find:
[picFile subCode gender]=textread('data.txt', '%s %f %s', 'headerlines',1);
T=[picFile(:) subCode(:) gender(:)]
The textscan solution by #horchler seems pretty similar. Thanks!
I have decided to use memmapfile because my data (typically 30Gb to 60Gb) is too big to fit in a computer's memory.
My data files consist two columns of data that correspond to the outputs of two sensors and I have them in both .bin and .txt formats.
m=memmapfile('G:\E-Stress Research\Data\2013-12-18\LD101_3\EPS/LD101_3.bin','format','int32')
m.data(1)
I used the above code to memory map my data to a variable "m" but I have no idea what data format to use (int8', 'int16', 'int32', 'int64','uint8', 'uint16', 'uint32', 'uint64', 'single', and 'double').
In fact I tried all of the data formats listed that MATLAB supports, but when I used the m.data(index number) I never get a pair of numbers (2 columns of data) which is what I expected, also the number will be different depending on the format I used.
If anyone has experience with memmapfile please help me.
Here are some smaller versions of my data files so people can understand how my data is structured:
cheers
James
memmapfile is designed for reading binary files, that's why you are having trouble with your text file. The data in there is characters, so you'll have to read them as characters and then parse them into numbers. More on that below.
The binary file appears to contain more than just a stream of floating point values written in binary format. I see identifiers (strings) and other things in the file as well. Your only hope of reading that is to contact the manufacturer of the device that created the binary file and ask them about how to read in such files. There'll probably be an SDK, or at least a description of the format. You might want to look into this as the floating point numbers in your text file might be truncated, i.e., you have lost precision compared to directly reading the binary representation of the floats.
Ok, so how to read your file with memmapfile? This post provides some hints.
So first we open your file as 'uint8' (note there is no 'char' option, so as a workaround we read the content of the file into a datatype of the same size):
m = memmapfile('RTL5_57.txt','Format','uint8'); % uint8 is default, you could leave that off
We can render the data read in as uint8 as characters by casting it to char:
c = char(m.Data(1:19)).' % read the first three lines. NB: transpose just for getting nice output, don't use it in your code
c =
0.398516 0.063440
0.399611 0.063284
0.398985 0.061253
As each line in your file has the same length (2*8 chars for the numbers, 1 tab and 2 chars for newline = 19 chars), we can read N lines from the file by reading N*19 values. So m.Data(1:19) gets you the first line, m.Data(20:38), the second line, and m.Data(20:57) the second and third lines. Read as much as you want at once.
Then we'll have to parse the read-in data into floating point numbers:
f = sscanf(c,'%f')
f =
0.3985
0.0634
0.3996
0.0633
0.3990
0.0613
All that's left now is to reshape them into your two column format
d = reshape(f,2,[]).'
d =
0.3985 0.0634
0.3996 0.0633
0.3990 0.0613
Easier ways than using memmapfile:
You don't need to use memmapfile to solve your problem, and I think it makes things more complicated. You can simply use fopen followed by fread:
fid = fopen('RTL5_57.txt');
c = fread(fid,Nlines*19,'*char');
% now sscanf and reshape as above
% NB: one can read the values the text file directly with f = fscanf(fid,'%f',Nlines*19).
% However, in testing, I have found calling fread followed by sscanf to be faster
% which will make a significant difference when reading such large files.
Using this you can read Nlines pairs of values at a time, process them and simply call fread again to read the next Nlines. fread remembers where it is in the file (as does fscanf), so simply use same call to get next lines. Its thus easy to write a loop to process the whole file, testing with feof(fid) if you are at the end of the file.
An even easier way is suggested here: use textscan. To slightly adapt their example code:
Nlines = 10000;
% describe the format of the data
% for more information, see the textscan reference page
format = '%f\t%f';
fid = fopen('RTL5_57.txt');
while ~feof(fid)
C = textscan(fid, format, Nlines, 'CollectOutput', true);
d = C{1}; % immediately clear C at this point if you need the memory!
% process d
end
fclose(fid);
Note again however that the fread followed by sscanf will be fastest. Note however that the fread method would die as soon as there is one line in the text file that doesn't exactly match your format. textscan is forgiving of whitespace changes on the other hand and thus more robust.