I have a set of data in the following format, and I would like to import each block in order to analyze them with Matlab.
Emax=0.5/real
----------------------------------------------------------------------
4.9750557 14535
4.9825821 14522
4.990109 14511
4.9976354 14491
5.0051618 14481
5.0126886 14468
5.020215 14437
5.0277414 14418
5.0352678 14400
5.0427947 14372
5.0503211 14355
5.0578475 14339
5.0653744 14321
Emax=1/real
----------------------------------------------------------------------
24.965595 597544
24.973122 597543
24.980648 597543
24.988174 597542
24.995703 597542
25.003229 597542
I have modified this piece of code from MathWorks, but I think, I have problems dealing with the spaces between each column.
Each block of data consist of 3874 rows and is divided by a text (Emax=XX/real) and a line of ----, unfortunately is the only way the software export the data.
Here is one way to import the data:
% read file as a cell-array of lines
fid = fopen('file.dat', 'rt');
C = textscan(fid, '%s', 'Delimiter','');
C = C{1};
fclose(fid);
% remove separator lines
C(strncmp('---',C,3)) = [];
% location of section headers
headInd = [find(strncmp('Emax=', C, length('Emax='))) ; numel(C)+1];
% extract each section
num = numel(headInd)-1;
blocks = struct('header',cell(num,1), 'data',cell(num,1));
for i=1:num
% section header
blocks(i).header = C{headInd(i)};
% data
X = regexp(C(headInd(i)+1:headInd(i+1)-1), '\s+', 'split');
blocks(i).data = str2double(vertcat(X{:}));
end
The result is a structure array containing the data from each block:
>> blocks
blocks =
2x1 struct array with fields:
header
data
>> blocks(2)
ans =
header: 'Emax=1/real'
data: [6x2 double]
>> blocks(2).data(:,1)
ans =
24.9656
24.9731
24.9806
24.9882
24.9957
25.0032
This should work. I don't think textscan() will work with a file like this because of the breaks between blocks.
Essentially what this code does is loop through lines between blocks until it finds a line that matches the data format. The code is naive and assumes that the file will have exactly the number of blocks lines per block that you specify. If there were a fixed number of lines between blocks it would be a lot easier and you could remove the first inner loop and replace with just ~=fgets(fid) once for each line.
function block_data = readfile(in_file_name)
fid = fopen(in_file_name, 'r');
delimiter = ' ';
line_format = '%f %f';
n_cols = 2; % Number of numbers per line
block_length = 3874; % Number of lines per block
n_blocks = 2; % Total number of blocks in file
tline = fgets(fid);
line_data = cell2mat(textscan(tline,line_format,'delimiter',delimiter,'MultipleDelimsAsOne',1));
block_n = 0;
block_data = zeros(n_blocks,block_length,n_cols);
while ischar(tline) && block_n < n_blocks
block_n = block_n+1;
tline = fgets(fid);
if ischar(tline)
line_data = cell2mat(textscan(tline,line_format,'delimiter',delimiter,'MultipleDelimsAsOne',1));
end
while ischar(tline) && isempty(line_data)
tline = fgets(fid);
line_data = cell2mat(textscan(tline,line_format,'delimiter',delimiter,'MultipleDelimsAsOne',1));
end
line_n = 1;
while line_n <= block_length
block_data(block_n,line_n,:) = cell2mat(textscan(tline,line_format,'delimiter',delimiter,'MultipleDelimsAsOne',1));
tline = fgets(fid);
line_n = line_n+1;
end
end
fclose(fid)
Related
I have a csv file which consists of a N-by-M table.
in the first colum each row consists of 6 different numbers and I need to detect if any of the numbers is identical and then print a error message
This is how I thought it should be writte
valid=true(height(Information),1);
for i=1:height(Information),1;
if Information{i, 1} == Information{:, 1}
fprintf('Invalid number in line %d', i);
valid(i)=false;
end
end
use third output of unique and histcounts:
% generate two matrices, one with 2 identical elements
A1 = rand(3);
A1(end,1) = A1(1);
A2 = rand(3);
% check identical elements
[~,~,ic] = unique(A1(:,1),'stable');
identicalNumbers = any(histcounts(ic,max(ic)) > 1) % true
[~,~,ic] = unique(A2(:,1),'stable');
identicalNumbers = any(histcounts(ic,max(ic)) > 1) % false
Edit it can be done even simpler:
identicalNumbers = numel(ic) > max(ic)
First read the csv file in a matrix called A. then try the following code:
uniqueVals = unique( A(:,1) );% find unique values of col 1
[r c] = size(uniqueVals);% r determines the number of unique values in A(:,1)
[rr cc] = size(A);% rr is total number of values in A(:,1)
if (r~=rr)
disp('identical numbers detected');
end
I have modified my code. The below code detect the same numbers in the firs column and tells you the index:
A = randi (8,6)
uniqueVals = unique( A(:,1) );
[c r] = size(uniqueVals);
for i=1:c
[m n]= size(find(A(:,1) == uniqueVals(i)));
if m>1
disp('same values detected in rows: ')
find(A(:,1) == uniqueVals(i))
end
end
check the code and give me a feedback.
I have downloaded youe csv file in my local drive. run the code and select the csv file using the dialog box.
clear
clc
[file_name, mach_path] = uigetfile( ...
{'*.csv', 'All CSV (*.csv)'}, ...
'Select File');
% If "Cancel" is selected then return
if isequal([file_name,mach_path],[0,0])
return
% Otherwise construct the fullfilename and Check and load the file
else
fileName = fullfile(mach_path,file_name);
end
fid = fopen(fileName,'r'); %# Open the file
lineArray = cell(100,1); %# Preallocate a cell array (ideally slightly
%# larger than is needed)
lineIndex = 1; %# Index of cell to place the next line in
nextLine = fgetl(fid); %# Read the first line from the file
while ~isequal(nextLine,-1) %# Loop while not at the end of the file
lineArray{lineIndex} = nextLine; %# Add the line to the cell array
lineIndex = lineIndex+1; %# Increment the line index
nextLine = fgetl(fid); %# Read the next line from the file
end
fclose(fid); %# Close the file
lineArray = lineArray(1:lineIndex-1); %# Remove empty cells, if needed
for iLine = 1:lineIndex-1 %# Loop over lines
lineData = textscan(lineArray{iLine},'%s',... %# Read strings
'Delimiter',',');
lineData = lineData{1}; %# Remove cell encapsulation
if strcmp(lineArray{iLine}(end),',') %# Account for when the line
lineData{end+1} = ''; %# ends with a delimiter
end
lineArray(iLine,1:numel(lineData)) = lineData; %# Overwrite line data
end
A = lineArray;
uniqueVals = unique( A(:,1) );
[cc ~] = size(uniqueVals);
for i=1:cc
[mm ~]= size(find(ismember(A(:,1),uniqueVals(i))));
if mm>1
second = find(ismember(A(:,1),uniqueVals(i)));
disp('same value detected in rows: ')
disp(second(2));
A(second(2),:) = [];
disp(A);
end
end
I am trying to import every rows that starts with '//', I have tried to extract it with the script below. can anybody check my script please?
formatSpec = '//NFE=%f //ElapsedTime=%f //SBX=%f //DE=%f //PCX=%f //SPX=%f //UNDX=%f //UM=%f //Improvements=%f //Restarts=%f //PopulationSize=%f //ArchiveSize=%f //MutationIndex=%f %*f';
N=1
k = 0;
while ~feof(fileID)
k = k+1;
C = textscan(fileID,formatSpec,N,'CommentStyle','#','Delimiter','\n');
end
It is not clear to me how you want the output to look, but here is one possibilitiy:
fid = fopen(filename, 'rt');
dataset = textscan(fid, '%s', 'delimiter', '\n', 'headerlines', 0);
fclose(fid);
result = regexp(dataset{1}, '//([A-Za-z].*)=([0-9\.].*)', 'tokens');
result = result(cellfun(#(x) ~isempty(x), result));
result contains both the type, e.g. NFE or SBX, and the number (albeit in character format).
Is there a faster way to replace the third line of file by another one without using cell ?
I've used this code but it slows my programs, especially that my txt file is composed by more than 1000 lines
% Read txt into cell A
fid7 = fopen([handles.filenameproba],'r');
i = 1;
tline = fgetl(fid7);
A{i} = tline;
while ischar(tline)
i = i+1;
tline = fgetl(fid7);
A{i} = tline;
end
fclose(fid7);
% Change cell A
newval =...
A{3} = sprintf('StartExperiment:%s',num2str(newval);
% Write cell A into txt
fid7 = fopen([handles.filenameproba], 'w');
for i = 1:numel(A)
if A{i+1} == -1
fprintf(fid7,'%s', A{i});
break
else
fprintf(fid7,'%s\n', A{i});
end
end
fclose(fid7);
Thanks !
If performance is your primary concern, try this importdata approach to see if it's any faster -
f=importdata(handles.filenameproba,'')
f(3)={sprintf('StartExperiment:%s',num2str(newval))}
%%// Save the modified text file
fid1 = fopen(handles.filenameproba,'w');
for k = 1:numel(f)
fprintf(fid1,'%s\n',f{k});
end
fclose(fid1);
Cells are not your problem. Your problem is reading and writing one line at a time. Additionally, you are re-sizing your cell array at every iteration.
For the following problem, I created a test file with 10000 lines in it.
fileId = fopen('test.txt', 'w');
for i = 1:10000
fprintf(fileId, 'This is the %dth line.\n', i);
end
fclose(fileId);
I'm calling your method ranellMethod.
>> timeit(#ranellMethod)
ans =
0.5160
A better way to do it is to limit the number of read/write operations you have to do. Assuming your file is small enough, you can read the entire contents into memory at once. Perform your operations, and write everything at once.
function entireFileMethod()
fileName = 'test.txt';
fileId = fopen(fileName, 'r');
try
text = fread(fileId, '*char')'; %'
catch Me
fclose(fileId);
Me.rethrow();
end
fclose(fileId);
newLineInds = find(text == char(10));
newLine = sprintf('This is the new line. %1.*f', randi(10), rand);
newText = [text(1:newLineInds(2)), newLine, text(newLineInds(3):end)];
fileId = fopen(fileName, 'w');
try
fprintf(fileId, '%s', newText);
catch Me
fclose(fileId);
Me.rethrow();
end
fclose(fileId);
end
This function has one read operation, and one write operation:
>> timeit(#entireFileMethod)
ans =
0.0043
See Fastest Matlab file reading? for more detailed information about file IO in MATLAB
I've have a
function [Q,A] = load_test(filename) which is loading in a text file. I would like the function to skip empty lines, but i'm not sure how to do it.
I have tried to use
~isempty(x), ~ischar(x)
but I keep getting an error message. my code so far is:
fid = fopen(filename);
data = textscan(fid, '%s','delimiter','\n');
fclose(fid);
Q = cellfun(#(x) x(1:end-2), data{1}, 'uni',0);
A = cellfun(#(x) x(end) == 'T' || x(end) == 'F' && ~isempty(x),data{1});
what do I need to do ?
Code
%%// Your code
fid = fopen(filename);
data = textscan(fid, '%s','delimiter','\n')
fclose(fid);
%%// Additional code
%%// 1. Remove empty lines
c1 = ~cellfun(#isempty,data{:})
t1 = data{:,:}(c1,:)
%%// 2. Select only the lines that have F or T as end characters
lastInLine = regexp(t1,'.$','match','lineanchors') %%// Get the end characters
%%// Get a binary array of rows that have F or T at the end
c2 = strcmp(vertcat(lastInLine{:}),'F') | strcmp(vertcat(lastInLine{:}),'T')
%%// Finally select those rows/lines
data = {t1(c2,:)}
Please note that I am not sure if you still need Q and A.
I trying to do script to evalute my lab data into matlab, I have lots of txt files for many samples, each sample has 30 txt files. I did a function to get the data from these files and store them into a structure that contains data and labels.
I would like to know if it is possible to load all the 30 files using loop instead of line by line .
function s = try1(fn)
% adapt for other file format according to your needs
fid = fopen(fn);
s.data = [];
% skip first lines
for k=1:6
l = fgetl(fid);
% read header
a = regexp(l,',','split');
s.labels = a;
l = fgetl(fid);
k=0;
end
while( (l~=-1)&(k<130) )
l = l(1:end-1);
a = regexp(l,', ','split');
a = regexpre
p(a, ',','.');
s.data = [s.data; str2double(a(2:4))];
l = fgetl(fid);
k = k+1;
end
fclose(fid);
end
To do what you want with a data directory and processing each file in a loop you can use a combination of fullfile(...) and a loop. This will likely work:
dataDirectory = 'c:/myDirectory';
allFilesDir = dir(fullfile(dataDirectory , '*.txt'));
allFN = {allFilesDir.name}
% Or do this:
% allFN = {'file1.txt', 'file2.txt'};
result = [];
for ind = 1:length(allFN)
myFN = fullfile(dataDirectory, allFN{ind});
result(ind) = try1(myFN);
end
% Now get the mean:
myMean = mean([result.data])