I am reading in a .txt-file using importdata:
MC_file = importdata('D:\Simon\Dropbox\SGM\Gigerwald\Results\Multi_SGM_10000.txt');
Data = MC_file.data
Header = MC_file.colheaders
which gives me a struct-variable with the header and the data-body:
data = 10000x52 double
colheaders = 1x52 cell
Now i'd like to change the data, i.e. add some columns to the end of the file and then print the file again with the same header + 5 new columns.
The body can be printed easily using dlmwrite(), e.g. like this:
dlmwrite('SGM.txt',Data,'precision',8,'delimiter','\t','newline','pc','-append')
...but how do I print the header into the file, of which I have a array of cells? I've seen this, but since I end up with 57 columns hard-coding is not an option...
The solution is attainable using repmat. Assuming that your file is tab separated, you can use:
NUM_COLS = 57;
A=cellstr(num2str((1:NUM_COLS)'))';
fid=fopen('newfile.txt','w');
fprintf(fid,repmat('%s\t ',[1,NUM_COLS]),A{:});
fclose(fid);
The result can be previewed with:
sprintf(repmat('%s\t ',[1,NUM_COLS]),A{:})
Related
I was trying to read a csv file with ezread https://de.mathworks.com/matlabcentral/fileexchange/11026-ezread and I get the following problem:
Error using textscan
The second input must be a format character vector containing at least one >specifier or a literal field.
Error in ezread (line 66)
data = textscan(fid,format_str,'delimiter',file_delim,'headerlines',1);
I call the function as follows:
tmpName = '/path/file.csv';
structRead = ezread(tmpName, 'r');
I have checked if tmpName is correct with isfile(), so it is a correct path.
First two rows of my file have the following format:
a,b,c,d
1,2,e,f
Do you know where the problem could be ?
Instead ezread, you should use importdata. However it will not recognize separation on comma ,. So you need to add extra line:
tmpName = importdata('/path/file.csv');
structRead = split(a, ',')
The result is:
2×4 cell array
{'a'} {'b'} {'c'} {'d'}
{'1'} {'2'} {'e'} {'f'}
I have a deco.csv file and I only want to extract B1 to K1 (20 columns of the first rows), i.e. Deco_0001 to Deco_0020.
I first make a pre-allocation:
names = string(20,1);
and what I want is when calling S(1), it gives Deco_0001; when calling S(20), it gives Deco_0020.
I have read through textscan but I do not know how to specify the range is first row and running from column 2 to column 21 of the csv file.
Also, I want save the names individually but what I have tried just save the first line in only one cell:
fid=fopen('deco.csv');
C=textscan(fid, '%s',1);
fclose(fid);
Thanks!
It's not very elegant, but this should work for you:
fid=fopen('deco.csv');
C=textscan(fid, '%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s',1,'Delimiter',',');
fclose(fid);
S = cell(20,1);
for ii = 1:20
S{ii} = C{ii+1};
end
I have a series of DICOM Images which I want to anonymize, I found few Matlab codes and some programs which do the job, but none of them export a .txt file of removed personal information. I was wondering if there is a function which can also save removed personal information of a DICOM images in .txt format for features uses. Also, I am trying to create a table which shows the corresponding new images ID to their real name.(subjects real name = personal-information-removed image ID)
Any thoughts?
Thanks for considering my request!
I'm guessing you only want to output to your text file the fields that are changed by anonymization (either modified, removed, or added). First, you may want to modify some dicomanon options to reduce the number of changes, in particular passing the arguments 'WritePrivate', true to ensure private extensions are kept.
First, you can perform the anonymization, saving structures of pre- and post-anonymization metadata using dicominfo:
preAnonData = dicominfo('input_file.dcm');
dicomanon('input_file.dcm', 'output_file.dcm', 'WritePrivate', true);
postAnonData = dicominfo('output_file.dcm');
Then you can use fieldnames and setdiff to find fields that are removed or added by anonymization, and add them to the post-anonymization or pre-anonymization data, respectively, with a nan value as a place holder:
preFields = fieldnames(preAnonData);
postFields = fieldnames(postAnonData);
removedFields = setdiff(preFields, postFields);
for iField = 1:numel(removedFields)
postAnonData.(removedFields{iField}) = nan;
end
addedFields = setdiff(postFields, preFields);
for iField = 1:numel(addedFields)
preAnonData.(addedFields{iField}) = nan;
end
It will also be helpful to use orderfields so that both data structures have the same ordering for their field names:
postAnonData = orderfields(postAnonData, preAnonData);
Finally, now that each structure has the same fields in the same order we can use struct2cell to convert their field data to a cell array and use cellfun and isequal to find any fields that have been modified by the anonymization:
allFields = fieldnames(preAnonData);
preAnonCell = struct2cell(preAnonData);
postAnonCell = struct2cell(postAnonData);
index = ~cellfun(#isequal, preAnonCell, postAnonCell);
modFields = allFields(index);
Now you can create a table of the changes like so:
T = table(modFields, preAnonCell(index), postAnonCell(index), ...
'VariableNames', {'Field', 'PreAnon', 'PostAnon'});
And you could use writetable to easily output the table data to a text file:
writetable(T, 'anonymized_data.txt');
Note, however, that if any of the fields in the table contain vectors or structures of data, the formatting of your output file may look a little funky (i.e. lots of columns, most of them empty, except for those few fields).
One way to do this is to store the tags before and after anonymisation and use these to write your text file. In Matlab, dicominfo() will read the tags into a structure:
% Get tags before anonymization
tags_before = dicominfo(file_in);
% Anoymize
dicomanon(file_in, file_out); % Need to set tags values where required
% Get tags after anonymization
tags_after = dicominfo(file_out);
% Do something with the two structures
disp(['Patient ID:', tags_before.PatientID ' -> ' tags_after.PatientID]);
disp(['Date of Birth:', tags_before.PatientBirthDate ' -> ' tags_after.PatientBirthDate]);
disp(['Family Name:', tags_before.PatientName.FamilyName ' -> ' tags_after.PatientName.FamilyName]);
You can then write out the before/after fields into a text file. You'd need to modify dicomanon() to choose your own values for the removed fields, since by default they are set to empty.
how do I insert a string into a csv file in matlab. i used this code to write some data and create my csv file:
and here is the output of the code:
I'm trying to insert some text in the first 2 columns before the numerical data..
thanks in advance :)
There are several approaches are possible here.
Let's take a look at some of them:
If you need to add string to your csv file.
For example, I create some csv file like your:
q = [1 2 3 4 5 6 7];
csvwrite('csvlist4.csv',q,2,0);
All troubles is to add some string to csv - it's because we need to combine numeric and text data. There are no good functions for it in Matlab except low levels:
c = 'some big text';
fid = fopen('csvlist4.csv','r+');
fprintf(fid,c);
How it works: the data in csv is an array. I put data in 3rd row, so first and second is an empty but they have ','. When you use fprintf it will replace this , with your text. So if text is too long it will overwrite your data.
How to avoid this?
Easiest way - is to do it with help of xlswrite function. For your example:
txt = cell(size(Q))
txt{1} = 'this is your text'
X = [txt; num2cell(Q)]
xlswrite('new.xlsx',X)
Result:
Important moment here: number of cell for text must be the same as your data. But I filled with the text only first cell in my example.
And the one more way: read csv file, modify it's data and write to csv:
csvwrite('csvlist4.csv',a,2,0);
m = csvread('csvlist4.csv');
fid = fopen('csvlist4.csv','w');
c = 'your text'
fprintf(fid, c); fprintf(fid, '\n');
fclose(fid);
dlmwrite('csvlist4.csv', m(3:end,:), '-append');
Of course you can use cell array instead c and so on and so on.
Hope it helps!
The following code generates a similar dataset to what I am currently working with:
clear all
a = rand(131400,12);
DateTime=datestr(datenum('2011-01-01 00:01','yyyy-mm-dd HH:MM'):4/(60*24):...
datenum('2011-12-31 23:57','yyyy-mm-dd HH:MM'),...
'yyyy-mm-dd HH:MM');
DateTime=cellstr(DateTime);
header={'DateTime','temp1','temp2','temp4','temp7','temp10',...
'temp13','temp16','temp19','temp22','temp25','temp30','temp35'};
I'm trying to convert the outputs into one variable (called 'Data'), i.e. have header as the first row (1,:), 'DateTime' starting from row 2 (2:end,1) and running through each row, and finally having 'a' as the data (2:end,2:end) if that makes sense. So, 'DateTime' and 'header' are used as the heading for the rows and column respectively. Following this I need to save this into a tab delimited text file.
I hope I've been clear in expressing what I'm attempting.
An easy way, but might be not the fastest:
Data = [header; DateTime, num2cell(a)];
filename = 'test.txt';
dlmwrite(filename,1); %# no create text file, not Excel
xlswrite(filename,Data);
UPDATE:
It appears that xlswrite actually changes the format of DateTime values even if it writes to a text file. If the format is important here is the better and actually faster way:
filename = 'test.txt';
out = [DateTime, num2cell(a)];
out = out'; %# our cell array will be printed by columns, so we have to transpose
fid = fopen(filename,'wt');
%# printing header
fprintf(fid,'%s\t',header{1:end-1});
fprintf(fid,'%s\n',header{end});
%# printing the data
fprintf(fid,['%s\t', repmat('%f\t',1,size(a,2)-1) '%f\n'], out{:});
fclose(fid);