Extract values from filenames - matlab

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

Related

Saving figure without providing filename [duplicate]

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'

addressing array in the function return

I would like to make the following code simpler.
files=dir('~/some*.txt');
numFiles=length(files);
for i = 1:numFiles
name=files(i).name;
name=strsplit(name,'.');
name=name{1};
name=strsplit(name, '_');
name=name(2);
name = str2num(name{1});
disp(name);
end
I am a begginer in Matlab, in general I would love something like:
name = str2num(strsplit(strsplit(files(i).name,'.')(1),'_')(2));
but matlab does not like this.
Another issue of the approach above is that matlab keeps giving cell type even for something like name(2) but this may be just the problem with my syntax.
Example file names:
3000_0_100ms.txt
3000_0_5s.txt
3000_110_5s.txt
...
Let's say I want to select all files ending in '5s' then I need to split them (after removing the extension) by '_' and return the second part, in the case of the three filenames above, that would be 0, 0, 110.
But I am in general curious how to do this simple operation in matlab without the complicated code that I have above.
Because your filenames follow a specific pattern, they're a prime candidate for a regular expression. While regular expressions can be confusing to learn at the outset they are very powerful tools.
Consider the following example, which pulls out all numbers that have both leading and trailing underscores:
filenames = {'3000_0_100ms.txt', '3000_0_5s.txt', '3000_110_5s.txt'};
strs = regexp(filenames, '(?<=\_)(\d+)(?=\_)', 'match');
strs = [strs{:}]; % Denest one layer of cells
nums = str2double(strs);
Which returns:
nums =
0 0 110
Being used here are what's called lookbehind (?<=...) and lookahead (?=...) operators. As their names suggest, they look in their respective directions related to the expression they're part of, (\d+) in our case, which looks for one or more digits. Though this approach requires more steps than the simple '\_(\d+)\_' expression, the latter requires you either utilize MATLAB's 'tokens' regex operator, which adds another layer of cells and that annoys me, or use the 'match' operator and strip the underscores from the match prior to converting to a numeric value.
Approach 2:
filenames = {'3000_0_100ms.txt', '3000_0_5s.txt', '3000_110_5s.txt'};
strs = regexp(filenames, '\_(\d+)\_', 'tokens');
strs = [strs{:}]; % Denest one layer of cells
strs = [strs{:}]; % Denest another layer of cells
nums = str2double(strs);
Approach 3:
filenames = {'3000_0_100ms.txt', '3000_0_5s.txt', '3000_110_5s.txt'};
strs = regexp(filenames, '\_(\d+)\_', 'match');
strs = [strs{:}]; % Denest one layer of cells
strs = regexprep(strs, '\_', '');
nums = str2double(strs);
You can use regexp to do a regular expression matching and obtain the numbers in the second place directly. This is an explanation of the regular expression I am using.
>>names = regexp({files(:).name},'\d*_(\d*)_\d*m?s\.txt$','tokens')
>>names = [names{:}]; % Get names out of their cells
>>names = [names{:}]; % Break cells one more time
>> nums = str2double(names); % Convert to double to obtain numbers

Function to split string in matlab and return second number

I have a string and I need two characters to be returned.
I tried with strsplit but the delimiter must be a string and I don't have any delimiters in my string. Instead, I always want to get the second number in my string. The number is always 2 digits.
Example: 001a02.jpg I use the fileparts function to delete the extension of the image (jpg), so I get this string: 001a02
The expected return value is 02
Another example: 001A43a . Return values: 43
Another one: 002A12. Return values: 12
All the filenames are in a matrix 1002x1. Maybe I can use textscan but in the second example, it gives "43a" as a result.
(Just so this question doesn't remain unanswered, here's a possible approach: )
One way to go about this uses splitting with regular expressions (MATLAB's strsplit which you mentioned):
str = '001a02.jpg';
C = strsplit(str,'[a-zA-Z.]','DelimiterType','RegularExpression');
Results in:
C =
'001' '02' ''
In older versions of MATLAB, before strsplit was introduced, similar functionality was achieved using regexp(...,'split').
If you want to learn more about regular expressions (abbreviated as "regex" or "regexp"), there are many online resources (JGI..)
In your case, if you only need to take the 5th and 6th characters from the string you could use:
D = str(5:6);
... and if you want to convert those into numbers you could use:
E = str2double(str(5:6));
If your number is always at a certain position in the string, you can simply index this position.
In the examples you gave, the number is always the 5th and 6th characters in the string.
filename = '002A12';
num = str2num(filename(5:6));
Otherwise, if the formating is more complex, you may want to use a regular expression. There is a similar question matlab - extracting numbers from (odd) string. Modifying the code found there you can do the following
all_num = regexp(filename, '\d+', 'match'); %Find all numbers in the filename
num = str2num(all_num{2}) %Convert second number from str

embed a number and extension in a variable file name

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.

How to read digits from file to matrix, no delimeter

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