I want to save data to files that have consecutive numbers in these file names within a for-loop.
first I have a function "SetConfeguration.m" in which I specifie the input directory and the file name as fields in a structure as below
StrConf.InputDirectory = 'C:/ElastixMatlab/elx_input';
StrConf.ParameterFilename = 'parameter.%d.txt';
the structure "StrConf" will be used as a parameter in the main function as below
ParameterFilename = fullfile(Conf.InputDirectory, Conf.ParameterFilename);
for Cpt = 1:NbParameterFiles
TmpParameterFilename = sprintf(ParameterFilename, Cpt - 1);
disp('ParameterFilename: '); disp(ParameterFilename);
end
I have the following error:
Warning: Invalid escape sequence appears in format string. See help sprintf for
valid escape sequences.
> In elxElastix at 153
In elxExampleStreet at 93
ParameterFilename :
C:\ElastixMatlab\elx_input\parameter.%d.txt
TmpParameterFilename :
C:
I think you forgot to call the structure StrConf to access the parameters
TmpParameterFilename = sprintf(StrConf.ParameterFilename, Cpt - 1);
disp('ParameterFilename: '); disp(StrConf.ParameterFilename);
Also, i suggest you to make a little change in the for loop, since it loops from 0 to n-1.
ParameterFilename = fullfile(Conf.InputDirectory, Conf.ParameterFilename);
for Cpt = 0:NbParameterFiles-1
TmpParameterFilename = sprintf(StrConf.ParameterFilename, Cpt);
disp('ParameterFilename: '); disp(StrConf.ParameterFilename);
end
This way you save an operation in every iteration, since you don't make the substraction of Cpt - 1, making your code a little bit more efficient.
You need to use sprintf before fullfile. The problem is that fullfile is normalizing your path separator from / used in your code, to \ which is the standard on Windows. But \ is also used for escape sequences which sprintf recognizes.
This will work better:
for Cpt = 1:NbParameterFiles
TmpParameterFilename = fullfile(Conf.InputDirectory, ...
sprintf(StrConf.ParameterFilename, Cpt - 1));
disp('ParameterFilename: '); TmpParameterFilename;
end
I think you want
TmpParamterFilename = sprinf('%s%d.txt',ParameterFilename, Cpt-1);
And then ParameterFilename wouldn't have .txt at the end.
Related
this question about matlab:
i'm running a loop and each iteration a new set of data is produced, and I want it to be saved in a new file each time. I also overwrite old files by changing the name. Looks like this:
name_each_iter = strrep(some_source,'.string.mat','string_new.(j).mat')
and what I#m struggling here is the iteration so that I obtain files:
...string_new.1.mat
...string_new.2.mat
etc.
I was trying with various combination of () [] {} as well as 'string_new.'j'.mat' (which gave syntax error)
How can it be done?
Strings are just vectors of characters. So if you want to iteratively create filenames here's an example of how you would do it:
for j = 1:10,
filename = ['string_new.' num2str(j) '.mat'];
disp(filename)
end
The above code will create the following output:
string_new.1.mat
string_new.2.mat
string_new.3.mat
string_new.4.mat
string_new.5.mat
string_new.6.mat
string_new.7.mat
string_new.8.mat
string_new.9.mat
string_new.10.mat
You could also generate all file names in advance using NUM2STR:
>> filenames = cellstr(num2str((1:10)','string_new.%02d.mat'))
filenames =
'string_new.01.mat'
'string_new.02.mat'
'string_new.03.mat'
'string_new.04.mat'
'string_new.05.mat'
'string_new.06.mat'
'string_new.07.mat'
'string_new.08.mat'
'string_new.09.mat'
'string_new.10.mat'
Now access the cell array contents as filenames{i} in each iteration
sprintf is very useful for this:
for ii=5:12
filename = sprintf('data_%02d.mat',ii)
end
this assigns the following strings to filename:
data_05.mat
data_06.mat
data_07.mat
data_08.mat
data_09.mat
data_10.mat
data_11.mat
data_12.mat
notice the zero padding. sprintf in general is useful if you want parameterized formatted strings.
For creating a name based of an already existing file, you can use regexp to detect the '_new.(number).mat' and change the string depending on what regexp finds:
original_filename = 'data.string.mat';
im = regexp(original_filename,'_new.\d+.mat')
if isempty(im) % original file, no _new.(j) detected
newname = [original_filename(1:end-4) '_new.1.mat'];
else
num = str2double(original_filename(im(end)+5:end-4));
newname = sprintf('%s_new.%d.mat',original_filename(1:im(end)-1),num+1);
end
This does exactly that, and produces:
data.string_new.1.mat
data.string_new.2.mat
data.string_new.3.mat
...
data.string_new.9.mat
data.string_new.10.mat
data.string_new.11.mat
when iterating the above function, starting with 'data.string.mat'
Loading a well formatted and delimited text file in Matlab is relatively simple, but I struggle with a text file that I have to read in. Sadly I can not change the structure of the source file, so I have to deal with what I have.
The basic file structure is:
123 180 (two integers, white space delimited)
1.5674e-8
.
.
(floating point numbers in column 1, column 2 empty)
.
.
100 4501 (another two integers)
5.3456e-4 (followed by even more floating point numbers)
.
.
.
.
45 String (A integer in column 1, string in column 2)
.
.
.
A simple
[data1,data2]=textread('filename.txt','%f %s', ...
'emptyvalue', NaN)
Does not work.
How can I properly filter the input data? All examples I found online and in the Matlab help so far deal with well structured data, so I am a bit lost at where to start.
As I have to read a whole bunch of those files >100 I rather not iterate trough every single line in every file. I hope there is a much faster approach.
EDIT:
I made a sample file available here: test.txt (google drive)
I've looked at the text file you supplied and tried to draw a few general conclusions -
When there are two integers on a line, the second integer corresponds to the number of rows following.
You always have (two integers (A, B) followed by "B" floats), repeated twice.
After that you have some free-form text (or at least, I couldn't deduce anything useful about the format after that).
This is a messy format so I doubt there are going to be any nice solutions. Some useful general principles are:
Use fgetl when you need to read a single line (it reads up to the next newline character)
Use textscan when it's possible to read multiple lines at once - it is much faster than reading a line at a time. It has many options for how to parse, which it is worth getting to know (I recommend typing doc textscan and reading the entire thing).
If in doubt, just read the lines in as strings and then analyse them in MATLAB.
With that in mine, here is a simple parser for your files. It will probably need some modifications as you are able to infer more about the structure of the files, but it is reasonably fast on the ~700 line test file you gave.
I've just given the variables dummy names like "a", "b", "floats" etc. You should change them to something more specific to your needs.
function output = readTestFile(filename)
fid = fopen(filename, 'r');
% Read the first line
line = '';
while isempty(line)
line = fgetl(fid);
end
nums = textscan(line, '%d %d', 'CollectOutput', 1);
a = nums{1}(1);
b = nums{1}(2);
% Read 'b' of the next lines:
contents = textscan(fid, '%f', b);
floats1 = contents{1};
% Read the next line:
line = '';
while isempty(line)
line = fgetl(fid);
end
nums = textscan(line, '%d %d', 'CollectOutput', 1);
c = nums{1}(1);
d = nums{1}(2);
% Read 'd' of the next lines:
contents = textscan(fid, '%f', d);
floats2 = contents{1};
% Read the rest:
rest = textscan(fid, '%s', 'Delimiter', '\n');
output.a = a;
output.b = b;
output.c = c;
output.d = d;
output.floats1 = floats1;
output.floats2 = floats2;
output.rest = rest{1};
end
You can read in the file line by line using the lower-level functions, then parse each line manually.
You open the file handle like in C
fid = fopen(filename);
Then you can read a line using fgetl
line = fgetl(fid);
String tokenize it on spaces is probably the best first pass, storing each piece in a cell array (because a matrix doesn't support ragged arrays)
colnum = 1;
while ~isempty(rem)
[token, rem] = strtok(rem, ' ');
entries{linenum, colnum} = token;
colnum = colnum + 1;
end
then you can wrap all of that inside another while loop to iterate over the lines
linenum = 1;
while ~feof(fid)
% getl, strtok, index bookkeeping as above
end
It's up to you whether it's best to parse the file as you read it or read it into a cell array first and then go over it afterwards.
Your cell entries are all going to be strings (char arrays), so you will need to use str2num to convert them to numbers. It does a good job of working out the format so that might be all you need.
I have file names stored as follows:
>> allFiles.name
ans =
k-120_knt-500_threshold-0.3_percent-34.57.csv
ans =
k-216_knt-22625_threshold-0.3_percent-33.33.csv
I wish to extract the 4 values from them and store in a cell.
data={};
for k =1:numel(allFiles)
data{k,1}=csvread(allFiles(k).name,1,0);
data{k,2}= %kvalue
data{k,3}= %kntvalue
data{k,4}=%threshold
data{k,5}=%percent
...
end
There's probably a regular expression that can be used to do this, but a simple piece of code would be
data={numel(allFiles),5};
for k =1:numel(allFiles)
data{k,1}=csvread(allFiles(k).name,1,0);
[~,name] = fileparts(allFiles(k).name);
dashIdx = strfind(name,'-'); % find location of dashes
usIdx = strfind(name,'_'); % find location of underscores
data{k,2}= str2double(name(dashIdx(1)+1:usIdx(1)-1)); %kvalue
data{k,3}= str2double(name(dashIdx(2)+1:usIdx(2)-1)); %kntvalue
data{k,4}= str2double(name(dashIdx(3)+1:usIdx(3)-1)); %threshold
data{k,5}= str2double(name(dashIdx(4)+1:end)); %percent
...
end
For efficiency, you might consider using a single matrix to store all the numeric data, and/or a structure (so that you can access the data by name rather than index).
You simply need to tokenize using strtok multiple times (there is more than 1 way to solve this). Someone has a handy matlab script somewhere on the web to tokenize strings into a cell array.
(1) Starting with:
filename = 'k-216_knt-22625_threshold-0.3_percent-33.33.csv'
Use strfind to prune out the extension
r = strfind(filename, '.csv')
filenameWithoutExtension = filename(1:r-1)
This leaves us with:
'k-216_knt-22625_threshold-0.3_percent-33.33'
(2) Then tokenize this:
'k-216_knt-22625_threshold-0.3_percent-33.33'
using '_' . You get the tokens:
'k-216'
'knt-22625'
'threshold-0.3'
'percent-33.33'
(3) Lastly, for each string, tokenize using using '-'. Each second string will be:
'216'
'22625'
'0.3'
'33.33'
And use str2num to convert.
Strategy: strsplit() + str2num().
data={};
for k =1:numel(allFiles)
data{k,1}=csvread(allFiles(k).name,1,0);
words = strsplit( allFiles(k).name(1:(end-4)), '_' );
data{k,2} = str2num(words{1}(2:end));
data{k,3} = str2num(words{2}(4:end));
data{k,4} = str2num(words{3}(10:end));
data{k,5} = str2num(words{4}(8:end));
end
I have a data stored in below format, no delimeter and digit domain is {0,1}. With using octave, taking the digits and storing them in martix is reaised a problem for me. I have not managed below scnerio. So, How can I take those digits and store them on matrix as told at below?
Data in File, 32 x 32 digits
00000000000000000000000000000000
00000000001111110000000000000000
...
00000010000000100001000000000000
how to store data
matrix[1, 1:32] = 00000000000000000000000000000000
matrix[2, 1:32] = 00000000001111110000000000000000
. . .
matrix[32, 1:32] = 00000010000000100001000000000000
OR
matrix[1, 1:32] = 00000000000000000000000000000000
matrix[1, 33:64] = 00000000001111110000000000000000
. . .
matrix[1, 993:1024] = 00000010000000100001000000000000
One possible solution is to read the data as a string first:
octave> textread('foo.dat', '%s', 'headerlines', 2)
ans =
{
[1,1] = 00000000000000000000000000000000
[2,1] = 00000000001111110000000000000000
...
}
If these are binary representations of decimals, you may find bin2dec() useful.
This would do the trick (though I don't know how well that third input to fread and arrayfun work with Octave, tested this on Matlab):
fid = fopen('a.txt','rt');
str = fread(fid,inf,'char=>char');
st = fclose(fid);
qrn = str==10|str==13;
str(qrn) = [];
yourMat = reshape(arrayfun(#str2num,str),find(qrn,1)-1,[]).'
Assuming you don't have header lines, you can read the text in as a cell arrray of strings like so:
C = textread('names.txt', '%s');
Then, in general for all numbers from 0 to 9, you can transform this into a matrix like so:
M = vertcat(S{:})-'0';
If performance is an issue you can look into other ways to import the strings, but this should get the job done.
I have never used Matlab, but asuming it reads files the same way Octave does, and if using an external tool is OK, you could try replacing the characters to add a delimiter using a text editor. You could change every "0" to "0," and every "1" to "1," and then simply load the file.
(This would add a delimiter at the end of every line. In case that creates a problem, you could try replacing your text by pairs instead "00"->"0,0" "10" -> "1,0" and so on)
In case the file is too big for a normal editor, you might even try replacing the characters with sed:
sed -i 's/charactertoreplace/newcharacter/g' yourfile.txt
how I can read the following files using the for loop: (can the loop ignore the characters in filenames?)
abc-1.TXT
cde-2.TXT
ser-3.TXT
wsz-4.TXT
aqz-5.TXT
iop-6.TXT
What do I have to add at the beginning of this loop ??
for i = 1:1:6
nom_fichier = strcat(['MyFile\.......' num2str(i) '.TXT']);
You can avoid constructing the filenames by using the DIR command. For instance:
myfiles = dir('*.txt');
for i = 1:length(myfiles)
nom_fichier = myfiles(i).name;
...do processing here...
end
First of all, why would you use strcat here? This is, by itself, a SINGLE string. All concatenation has already been done by the brackets [].
['MyFile\.......' num2str(i) '.TXT']
Next, I'm not certain what is your question here. Is it how to load in the data? If the files are simply delimited numbers, with the same number of them on each line, then load will suffice to load them in, or perhaps you may need textread.
My guess is you do not know how to build the main part of of the file name. You might do it this way:
Names = {'abc' 'cde 'ser' 'wsz' 'aqz' 'iop'};
for i = 1:6
fn = ['MyFile',filesep,Names{i},'-',num2str(i),'.TXT'];
data = load(fn);
% do other stuff ...
end
If you don't want to create a variable with the names by typing them in, then use dir, perhaps like this to create a list of text file names:
Names = dir('MyFile\*.TXT');