I want to load a csv file in a matrix using matlab.
I used the following code:
formatSpec = ['%*f', repmat('%f',1,20)];
fid = fopen(filename);
X = textscan(fid, formatSpec, 'Delimiter', ',', 'CollectOutput', 1);
fclose(fid);
X = X{1};
The csv file has 1000 rows and 21 columns.
However, the matrix X generated has 2000 columns and 20 columns.
I tried using different delimiters like '\t' or '\n', but it doesn't change.
When I displayed X, I noticed that it displayed the correct csv file but with extra rows of zeros every 2 rows.
I also tried adding the 'HeaderLines' parameters:
`X = textscan(fid, formatSpec1, 'Delimiter', '\n', 'CollectOutput', 1, 'HeaderLines', 1);`
but this time, the result is an empty matrix.
Am I missing something?
EDIT: #horchler
I could read with no problem the 'test.csv' file.
There is no extra comma at the end of each row. I generated my csv file with a python script: I read the rows of another csv file, modified these (selecting some of them and doing arithmetic operations on them) and wrote the new rows on another csv file. In order to do this, I converted each element of the first csv file into floats...
New Edit:
Reading the textscan documentation more carefully, I think the problem is that my input file is neither a textfile nor a str, but a file containing floats
EDIT: three lines from the file
0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,1,0,0,0,2
1,-0.3834323,-1.92452324171,-1.2453254094,0.43455627857,-0.24571121,0.4340657,1,1,0,0,0,0.3517396202,1,0,0,0.3558122164,0.2936975319,0.4105696144,0,1,0
-0.78676,-1.09767,0.765554578,0.76579043,0.76,1,0,0,323124.235998,1,0,0,0,1,0,0,1,0,0,0,2
How about using regex ?
X=[];
fid = fopen(filename);
while 1
fl = fgetl(fid);
if ~ischar(fl), break, end
r =regexp(fl,'([-]*\d+[.]*\d*)','match');
r=r(1:21); % because your line 2nd is somehow having 22 elements,
% all lines must have same # elements or an error will be thrown
% Error: CAT arguments dimensions are not consistent.
X=[X;r];
end
fclose(fid);
Using csvread to read a csv file seems a good option. However, I also tend to read csv files with textscan as files are sometimes badly written. Having more options to read them is therefore necessary.
I face a reading problem like yours when I think the file is written a certain way but it is actually written another way. To debug it I use fgetl and print, for each line read, both the output of fgetl and its double version (see the example below). Examining the double version, you may find which character causes a problem.
In your case, I would first look at multiple occurrences of delimiters (',' and '\t') and , in 'textscan', I would activate the option 'MultipleDelimsAsOne' (while turning off 'CollectOutput').
fid = fopen(filename);
tline = fgetl(fid);
while ischar(tline)
disp(tline);
double(tline)
pause;
tline = fgetl(fid);
end
fclose(fid);
Related
I have a huge .txt file and parts of which I want to parse (using text scan), say I have 10000 line data and a part which starts at line 300, the part also has a header of 10 lines say,how can I skip the first 300 lines(not using header function of text scan of course as I then wont be able to get my actual 10 line header) or is there a way in which I can jump to line 300 and start text scan from there as if 301 line was the first line.
So, assuming your data is generated by the following (since you have not mentioned how it's formatted in your question):
fid = fopen('datafile.txt', 'w');
for i=1:300
fprintf(fid, 'ignore%d\n', i);
end
for i=301:310
fprintf(fid, 'header%d\n', i);
end
for i=311:10000
fprintf(fid, '%d\n', i);
end
fclose(fid);
You can read the data by first using fgetl to advance to the 300th line, then using textscan twice to get the header info and the data. Basically, the thing to remember is that textscan works starting from the place where fid is pointing. So, if it's pointing to the 301st line, it'll start scanning from there. So, here's the code to read the file above, starting from line 301:
fid = fopen('datafile.txt', 'r');
for i=1:300
fgetl(fid);
end
scannedHeader = textscan(fid, '%s', 10);
scannedData = textscan(fid, '%d');
fclose(fid);
NB: if the data is always the same format, you can use ftell to know where to skip to exactly then use fseek to go to that offset.
I'm trying to analyze a very large file using textscan in MATLAB. The file in question is about 12 GB in size and contains about 250 million lines with seven (floating) numbers in each (delimited by a whitespace); because this obviously would not fit into the RAM of my desktop, I'm using the approach suggested in the MATLAB documentation (i.e. loading and analyzing a smaller block of the file at a time. According to the documentation this should allow for processing "arbitrarily large delimited text file[s]"). This only allows me to scan about 43% of the file, after which textscan starts returning empty cells (despite there still being data left to scan in the file).
To debug, I attempted to go to several positions in the file using the fseek function, for example like this:
fileInfo = dir(fileName);
fid = fileopen(fileName);
fseek(fid, floor(fileInfo.bytes/10), 'bof');
textscan(fid,'%f %f %f %f %f %f %f','Delimiter',' ');
I'm assuming that the way I'm using fseek here moves the position indicator to about 10% of my file. (I'm aware this doesn't necessarily mean the indicator is at the beginning of a line, but if I run textscan twice I get a satisfactory answer.) Now, if I substitute fileInfo.bytes/10 by fileInfo.bytes/2 (i.e. moving it to about 50% of the file) everything breaks down and textscan only returns an empty 1x7 cell.
I looked at the file using a text editor for large files, and this shows that the entire file looks fine, and that there should be no reason for textscan to be confused. The only possible explanation that I can think of is that something goes wrong on a much deeper level that I have little understanding of. Any suggestions would be greatly appreciated!
EDIT
The relevant part of my code used to look like this:
while ~feof(fid)
data = textscan(fid, FormatString, nLines, 'Delimiter', ' '); %// Read nLines
%// do some stuff
end
First I tried fixing it using ftell and fseek as suggested by Hoki below. This gave exactly the same error as I got before: MATLAB was unable to read in more than approximately 43% of the file. Then I tried using the HeaderLines solution (also suggested below), like this:
i = 0;
while ~feof(fid)
frewind(fid)
data = textscan(fid, FormatString, nLines, 'Delimiter',' ', 'HeaderLines', i*nLines);
%// do some stuff
i = i + 1;
end
This seems to read in the data without producing errors; it is, however, incredibly slow.
I'm not entirely sure I understand what HeaderLines does in this context, but it seems to make textscan completely ignore everything that comes before the specified line. This doesn't seem to happen when using textscan in the "appropriate" way (either with or without ftell and fseek): in both cases it tries to continue from its last position, but to no avail because of some reason I don't understand yet.
fseek a pointer in a file is only good when you know precisely where (or by how many bytes) you want to move the cursor. It is very useful for binary files when you just want to skip some records of known length. But on a text file it is more dangerous and confusing than anything (unless you are absolutely sure that each line is the same size and each element on the line is at the same exact place/column, but that doesn't happen often).
There are several ways to read a text file block by block:
1) Use the HeaderLines option
To simply skip a block of lines on a text file, you can use the HeaderLines parameter of textscan, so for example:
readFormat = '%f %f %f %f %f %f %f' ; %// read format specifier
nLines = 10000 ; %// number of line to read per block
fileInfo = dir(fileName);
%// read FIRST block
fid = fileopen(fileName);
M = textscan(fid, readFormat, nLines,'Delimiter',' '); %// read the first 10000 lines
fclose(fid)
%// Now do something with your "M" data
Then when you want to read the second block:
%// later read the SECOND block:
fid = fileopen(fileName);
M = textscan(fid, readFormat, nLines,'Delimiter',' ','HeaderLines', nLines); %// read lines 10001 to 20000
fclose(fid)
And if you have many blocks, for the Nth block, just adapt:
%// and then for the Nth BLOCK block:
fid = fileopen(fileName);
M = textscan(fid, readFormat, nLines,'Delimiter',' ','HeaderLines', (N-1)*nLines);
fclose(fid)
If necessary (if you have many blocks), just code this last version in a loop.
Note that this is good if you close your file after each block reading (so the file pointer will start at the beginning of the file when you open it again). Closing the file after reading a block of data is safer if your processing might take a long time or may error out (you don't want to have files which remain open too long or loose the fid if you crash).
2) Read by block (without closing the file)
If the processing of the block is quick and safe enough so you're sure it won't bomb out, you could afford to not close the file. In this case, the textscan file pointer will stay where you stopped, so you could also :
read a block (do not close the file): M = textscan(fid, readFormat, nLines)
Process it then save your result (and release memory)
read the next block with the same call: M = textscan(fid, readFormat, nLines)
In this case you wouldn't need the headerlines parameter because textscan will resume reading exactly where it stopped.
3) use ftell and fseek
Lastly, you could use fseek to start reading the file at the precise position you want, but in this case I recommend using it in conjunction with ftell.
ftell will return the current position in an open file, so use that to know at which position you stop reading last, then use fseek the next time to go straight at this position. Something like:
%// read FIRST block
fid = fileopen(fileName);
M = textscan(fid, readFormat, nLines,'Delimiter',' ');
lastPosition = ftell(fid) ;
fclose(fid)
%// do some stuff
%// then read another block:
fid = fileopen(fileName);
fseek( fid , 'bof' , lastPosition ) ;
M = textscan(fid, readFormat, nLines,'Delimiter',' ');
lastPosition = ftell(fid) ;
fclose(fid)
%// and so on ...
I am trying to read a csv file use textscan. The fields are seperated with ',' . I used the following code, but it only read in one line of data into the matrix W.
I also tried dlmread(), it got the number of fields wrong.
The file is contructed under linux, matlab is under linux.
file_id = fopen('H:\data\overlapmatrices\cos.mat.10');
W = textscan(file_id, '%f', 'delimiter', ',' , 'EndOfLine', '\r\n');
fclose(file_id);
clear file_id;
you might wanna try csvread, it should do the trick.
or you could alway do something dirty like
fid = fopen( filename );
tline = fgetl(fid);
while ischar(tline) %or some other check
%sscanf(tline...
tline = fgetl(fid);
end
The problem could be in how the end of line is represented in the file (see also this article on Wikipedia). While \r\n (the combination of a carriage return and a newline character) is common on Windows, \n (just the newline character) is the standard on Linux and other Unix systems.
But as ben is saying, csvread might be an easier way how to read the file.
I have a .tsv file that I wish to open in MATLAB, however I am having several problems with this.
I have tried the following
fid = fopen('data.tsv');
C = textscan(fid, ['%s' repmat('%f',1,8)], 'HeaderLines', 1);
fclose(fid);
and got some weird values that had nothing to do with my file. I also tried:
data = dlmread('data.tsv', '\t');
and got this
Error using dlmread (line 139)
Mismatch between file and format string.
Trouble reading number from file (row 1u, field 1u) ==> Participant Assessment
Experiment Block Trial
Answer Reaction Timestamp Free Response\n
Is there some way I can get it to ignore the header, or am I doing it totally wrong?
With dlmread you can specify where to start reading in the file. This is one of the few times that MATLAB indexing begins at 0 - [0,0] is the first row, first column. Therefore, to ignore the first row (containing your header):
data = dlmread('data.tsv','\t', 1, 0);
This will only work if all the values (other than the header lines you skip) are numeric.
Your example with textscan also looks fine to me (provided that the format supplied is correct and there is indeed only one header line). C will be a cell array; to obtain the data from each column use C{n} where n is the column number.
Rather than skipping the header line, it's sometimes useful to just read it in to a separate value:
fid = fopen('data.tsv');
C_header = textscan(fid, '%s',9);
C = textscan(fid, ['%s' repmat('%f',1,8)]);
fclose(fid);
What is the equivalent of fgel and fgets in MATLAB for reading one column at a time (not a line) from a text file?
You cannot avoid reading the file. However, if your dataset is large, you can tell MATLAB to ignore the irrelevant parts while reading the file.
For instance, if your columns are space delimited, and you want to read the floating-point numbers in the first column, you can try the following:
fid = fopen('input.txt');
C = textscan(fid, '%f %*[^\n]');
C = C{:};
fclose(fid);
This still reads the entire file, but stores only the first column in memory.