Convert the contents of columns containing numeric text to numbers - matlab

I have a csv file that consists of text or number. But some columns are corrupted as seen in the image below("<<"K.O). When I open the csv file via Matlab (without importing), it converts them to number and define undefined values such as "<<"K.O as NaN as I wanted. But when I read the file via script I wrote:
opts = detectImportOptions(filedir);
table = readtable(filedir,opts);
It reads them as char arrays. Since I have many different csv files (columns are different), I want to do it automatically rather than using textscan(since it requires file format and my file format is different for each csv file). Is there any way to convert the contents of columns containing numeric text to numbers automatically?

As far as I can understand from your comments, this is what you are actually looking for:
for i = 1:numel(files)
file = fullfile(folder,files(i).name));
opts = detectImportOptions(file);
idx = strcmp(opts.VariableNames,'Grade');
if (any(idx))
opts.VariableTypes(idx) = {'double'};
end
tabs(i) = readtable(file,opts);
end

Assuming you have your data stored in a table, you can attempt to convert each column of character arrays to numeric values using str2double. Any values that don't convert to a numeric value (empty entries, words, non-numeric strings, etc.) will be converted to NaN.
Since you want to do the conversions automatically, we'll have to make one key assumption: any column that converts to all NaN values should remain unchanged. In such a case, the data was likely either all non-convertable character arrays, or already numeric. Given that assumption, this generic conversion could be applied to any table T:
for varName = T.Properties.VariableNames
numData = str2double(T.(varName{1}));
if ~all(isnan(numData))
T.(varName{1}) = numData;
end
end
As a test, the following sample data:
T = table((1:5).', {'Y'; 'N'; 'Y'; 'Y'; 'N'}, {'pi'; ''; '1.4e5'; '1'; 'A'});
T =
Var1 Var2 Var3
____ ____ _______
1 'Y' 'pi'
2 'N' ''
3 'Y' '1.4e5'
4 'Y' '1'
5 'N' 'A'
Will be converted to the following by the above code:
T =
Var1 Var2 Var3
____ ____ ______
1 'Y' NaN
2 'N' NaN
3 'Y' 140000
4 'Y' 1
5 'N' NaN

Related

MATLAB / Octave - how to parse CSV file with numbers and strings that contain commas

I have a CSV file that has 20 columns. Some of the columns have number values, others have text values, and the text ones may or may not contain commas.
CSV content example:
column1, column2, column3, column4
"text value 1", 123, "text, with a comma", 25
"another, comma", 456, "other text", 78
I'm using textscan function, but I'm getting the most buggy and weird behavior. With some arguments, it reads all the values in only one column, sometimgs it repeats columns, and most of the things I've tried lead to the commas being incorrectly interpreted as column separators (despite text being enclosed in double quotes). That is, I've tried specifying 'delimiter' argument, and also including literals in the format specification, to no avail.
What's the correct way of invoking textscan to deal with a CSV file as the example above? I'm looking for a solution that runs both on MATLAB and on Octave (or, if that's not possible, the equivalent solution in each one).
For GNU Octave, using io package
pkg load io
c = csv2cell ("jota.csv")
gives
c =
{
[1,1] = column1
[2,1] = text value 1
[3,1] = another, comma
[1,2] = column2
[2,2] = 123
[3,2] = 456
[1,3] = column3
[2,3] = text, with a comma
[3,3] = other text
[1,4] = column4
[2,4] = 25
[3,4] = 78
}
btw, you should explicitly mention if the solution should run on GNU Octave, Matlab or both
First, read the column headers using the format '%s' four times:
fileID = fopen(filename);
C_text = textscan(fileID,'%s', 4,'Delimiter',',');
Then use the conversion specifier, %q to read the text enclosed by double quotation marks ("):
C = textscan(fileID,'%q %d %q %d','Delimiter',',');
fclose(fileID);
(This works for reading your sample data on Octave. It should work on MATLAB, too.)
Edit: removed redundant fopen.

joining arrays in Matlab and writing to file using dlmwrite( ) adds extra space

I am generating 2500 values in Matlab in format (time,heart_rate, resp_rate) by using below code
numberOfSeconds = 2500;
time = 1:numberOfSeconds;
newTime = transpose(time);
number0 = size(newTime, 1)
% generating heart rates
heart_rate = 50 +(70-50) * rand (numberOfSeconds,1);
intHeartRate = int64(heart_rate);
number1 = size(intHeartRate, 1)
% hist(heart_rate)
% generating resp rates
resp_rate = 50 +(70-50) * rand (numberOfSeconds,1);
intRespRate = int64(resp_rate);
number2 = size(intRespRate, 1)
% hist(heart_rate)
% joining time and sensor data
joinedStream = strcat(num2str(newTime),{','},num2str(intHeartRate),{','},num2str(intRespRate))
dlmwrite('/Users/amar/Desktop/geenrated/rate.txt', joinedStream,'delimiter','');
The data shown in the console is alright, but when I save this data to a .txt file, it contains extra spaces in beginning. Hence I am not able to parse the .txt file to generate input stream. Please help
Replace the last two lines of your code with the following. No need to use strcat if you want a CSV output file.
dlmwrite('/Users/amar/Desktop/geenrated/rate.txt', [newTime intHeartRate intRespRate]);
π‘‡β„Žπ‘’ π‘ π‘œπ‘™π‘’π‘‘π‘–π‘œπ‘› 𝑠𝑒𝑔𝑔𝑒𝑠𝑑𝑒𝑑 𝑏𝑦 π‘ƒπΎπ‘œ 𝑖𝑠 π‘‘β„Žπ‘’ π‘ π‘–π‘šπ‘π‘™π‘’π‘ π‘‘ π‘“π‘œπ‘Ÿ π‘¦π‘œπ‘’π‘Ÿ π‘π‘Žπ‘ π‘’. π‘‡β„Žπ‘–π‘  π‘Žπ‘›π‘ π‘€π‘’π‘Ÿ 𝑒π‘₯π‘π‘™π‘Žπ‘–π‘›π‘  π‘€β„Žπ‘¦ π‘¦π‘œπ‘’ 𝑔𝑒𝑑 π‘‘β„Žπ‘’ 𝑒𝑛𝑒π‘₯𝑝𝑒𝑐𝑑𝑒𝑑 π‘œπ‘’π‘‘π‘π‘’π‘‘.
The data written in the file is exactly what is shown in the console.
>> joinedStream(1) %The exact output will differ since 'rand' is used
ans =
cell
' 1,60,63'
num2str basically converts a matrix into a character array. Hence number of characters in its each row must be same. So for each column of the original matrix, the row with the maximum number of characters is set as a standard for all the rows with less characters and the deficiency is filled by spaces. Columns are separated by 2 spaces. Take a look at the following smaller example to understand:
>> num2str([44, 42314; 4, 1212421])
ans =
2Γ—11 char array
'44 42314'
' 4 1212421'

How do I read comma separated values from a .txt file in MATLAB using textscan()?

I have a .txt file with rows consisting of three elements, a word and two numbers, separated by commas.
For example:
a,142,5
aa,3,0
abb,5,0
ability,3,0
about,2,0
I want to read the file and put the words in one variable, the first numbers in another, and the second numbers in another but I am having trouble with textscan.
This is what I have so far:
File = [LOCAL_DIR 'filetoread.txt'];
FID_File = fopen(File,'r');
[words,var1,var2] = textscan(File,'%s %f %f','Delimiter',',');
fclose(FID_File);
I can't seem to figure out how to use a delimiter with textscan.
horchler is indeed correct. You first need to open up the file with fopen which provides a file ID / pointer to the actual file. You'd then use this with textscan. Also, you really only need one output variable because each "column" will be placed as a separate column in a cell array once you use textscan. You also need to specify the delimiter to be the , character because that's what is being used to separate between columns. This is done by using the Delimiter option in textscan and you specify the , character as the delimiter character. You'd then close the file after you're done using fclose.
As such, you just do this:
File = [LOCAL_DIR 'filetoread.txt'];
f = fopen(File, 'r');
C = textscan(f, '%s%f%f', 'Delimiter', ',');
fclose(f);
Take note that the formatting string has no spaces because the delimiter flag will take care of that work. Don't add any spaces. C will contain a cell array of columns. Now if you want to split up the columns into separate variables, just access the right cells:
names = C{1};
num1 = C{2};
num2 = C{3};
These are what the variables look like now by putting the text you provided in your post to a file called filetoread.txt:
>> names
names =
'a'
'aa'
'abb'
'ability'
'about'
>> num1
num1 =
142
3
5
3
2
>> num2
num2 =
5
0
0
0
0
Take note that names is a cell array of names, so accessing the right name is done by simply doing n = names{ii}; where ii is the name you want to access. You'd access the values in the other two variables using the normal indexing notation (i.e. n = num1(ii); or n = num2(ii);).

read complicated format .txt file into Matlab

I have a txt file that I want to read into Matlab. Data format is like below:
term2 2015-07-31-15_58_25_612 [0.9934343, 0.3423043, 0.2343433, 0.2342323]
term0 2015-07-31-15_58_25_620 [12]
term3 2015-07-31-15_58_25_625 [2.3333, 3.4444, 4.5555]
...
How can I read these data in the following way?
name = [term2 term0 term3] or namenum = [2 0 3]
time = [2015-07-31-15_58_25_612 2015-07-31-15_58_25_620 2015-07-31-15_58_25_625]
data = {[0.9934343, 0.3423043, 0.2343433, 0.2342323], [12], [2.3333, 3.4444, 4.5555]}
I tried to use textscan in this way 'term%d %s [%f, %f...]', but for the last data part I cannot specify the length because they are different. Then how can I read it? My Matlab version is R2012b.
Thanks a lot in advance if anyone could help!
There may be a way to do that in one single pass, but for me these kind of problems are easier to sort with a 2 pass approach.
Pass 1: Read all the columns with a constant format according to their type (string, integer, etc ...) and read the non constant part in a separate column which will be processed in second pass.
Pass 2: Process your irregular column according to its specificities.
In a case with your sample data, it looks like this:
%% // read file
fid = fopen('Test.txt','r') ;
M = textscan( fid , 'term%d %s %*c %[^]] %*[^\n]' ) ;
fclose(fid) ;
%% // dispatch data into variables
name = M{1,1} ;
time = M{1,2} ;
data = cellfun( #(s) textscan(s,'%f',Inf,'Delimiter',',') , M{1,3} ) ;
What happened:
The first textscan instruction reads the full file. In the format specifier:
term%d read the integer after the literal expression 'term'.
%s read a string representing the date.
%*c ignore one character (to ignore the character '[').
%[^]] read everything (as a string) until it finds the character ']'.
%*[^\n] ignore everything until the next newline ('\n') character. (to not capture the last ']'.
After that, the first 2 columns are easily dispatched into their own variable. The 3rd column of the result cell array M contains strings of different lengths containing different number of floating point number. We use cellfun in combination with another textscan to read the numbers in each cell and return a cell array containing double:
Bonus:
If you want your time to be a numeric value as well (instead of a string), use the following extension of the code:
%% // read file
fid = fopen('Test.txt','r') ;
M = textscan( fid , 'term%d %f-%f-%f-%f_%f_%f_%f %*c %[^]] %*[^\n]' ) ;
fclose(fid) ;
%% // dispatch data
name = M{1,1} ;
time_vec = cell2mat( M(1,2:7) ) ;
time_ms = M{1,8} ./ (24*3600*1000) ; %// take care of the millisecond separatly as they are not handled by "datenum"
time = datenum( time_vec ) + time_ms ;
data = cellfun( #(s) textscan(s,'%f',Inf,'Delimiter',',') , M{1,end} ) ;
This will give you an array time with a Matlab time serial number (often easier to use than strings). To show you the serial number still represent the right time:
>> datestr(time,'yyyy-mm-dd HH:MM:SS.FFF')
ans =
2015-07-31 15:58:25.612
2015-07-31 15:58:25.620
2015-07-31 15:58:25.625
For comlicated string parsing situations like such it is best to use regexp. In this case assuming you have the data in file data.txt the following code should do what you are looking for:
txt = fileread('data.txt')
tokens = regexp(txt,'term(\d+)\s(\S*)\s\[(.*)\]','tokens','dotexceptnewline')
% Convert namenum to numeric type
namenum = cellfun(#(x)str2double(x{1}),tokens)
% Get time stamps from the second row of all the tokens
time = cellfun(#(x)x{2},tokens,'UniformOutput',false);
% Split the numbers in the third column
data = cellfun(#(x)str2double(strsplit(x{3},',')),tokens,'UniformOutput',false)

Creating an array from an str concatenation Matlab

Hello I have these two vectors
Q = [1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4]
and
Year = [2000,2000,2000,2000,2001,2001,2001,2001,2002.....]
and I would like to concatenate them into one single array Time
Time = [20001,20002,20003,20004,20010....]
Or
Time= {'2000Q1', '2000Q2', '2000Q3', '2000Q4', '2001Q1'....}
So far I tried with this code
m = zeros(136,1)
for i=1:136
m(i,1)= strcat(Q(i),Year(i));
end
And Matlab outputed me this:
Subscripted assignment dimension mismatch.
Help pls ?
If your vectors Year and Q have the same number of elements, you do not need a loop, just transpose them (or just make sure they are in column), then concatenate with the [] operator:
Time = [ num2str(Year.') num2str(Q.') ] ;
will give you:
20001
20002
20003
20004
20011
...
And if you want the 'Q' character, insert it in the expression:
Time = [ num2str(Year.') repmat('Q',length(Q),1) num2str(Q.') ]
Will give you:
2000Q1
2000Q2
2000Q3
2000Q4
2001Q1
...
This will be a char array, if you want a cell array, use cellstr on the same expression:
time = cellstr( [num2str(Year.') repmat('Q',length(Q),1) num2str(Q.')] ) ;
To obtain strings:
strtrim(mat2cell(num2str([Year(:) Q(:) ],'%i%i'), ones(1,numel(Q))));
Explanation:
Concat both numeric vectors as two columns (using [...])
Convert to char array, where each row is the concatenation of two numbers (using num2str with sprintf-like format specifiers). It is assumed that all numbers are integers (if not, change the format specifiers). This may introduce unwanted spaces if not all the concatenated numbers have the same number of digits.
Convert to a cell array, putting each row in a different cell (using mat2cell).
Remove whitespaces in each cell (using strtrim)
To obtain numbers: apply str2double to the above:
str2double(strtrim(mat2cell(num2str([Year(:) Q(:) ],'%i%i'), ones(1,numel(Q)))));
Or compute directly
10.^ceil(max(log10(Q)))*Year + Q;
You can use arrayfun
If you want your output in string format (with a 'Q' in the middle) then use sprintf to format the string
Time = arrayfun( #(y,q) sprintf('%dQ%d', y, q ), Year, Q, 'uni', 0 );
Resulting with a cellarray
Time =
'2000Q1' '2000Q2' '2000Q3' '2000Q4' '2001Q1' '2001Q2' '2001Q3'...
Alternatively, if you skip the 'Q' you can save each number in an array
Time = arrayfun( #(y,q) y*10+q, Year, Q )
Resulting with a regular array
Time =
20001 20002 20003 20004 20011 20012 20013 ...
Thats because you are initializing m to zeros(136,1) and then trying to save a full string into the first value. and obviously a double cannot hold a string.
I give you 2 options, but I favor the first one.
1.- you can just use cell arrays, so your code converts into:
m = cell(136,1)
for ii=1:136
m{ii}= strcat(Q(ii),Year(ii));
end
and then m will be: m{1}='2000Q1';
2.- Or if you know that your strings will ALWAYS be the same size (in your case it lokos like they are always 6) you can:
m = zeros(136,strsize)
for ii=1:136
m(ii,:)= strcat(Q(ii),Year(ii));
end
and then m will be: m(1,:)= [ 50 48 48 48 81 49 ] wich translated do ASCII will be 2000Q1