Extract only numerical data from MATLAB from a text file into a matrix - matlab

Question

I have a code which is producing output files containing information about some mesh which I need to analyse using MATLAB.
The output files look like this.
Vertex 1 1.3 -2.1 0 {z=(1.3e+0 -2.1e+0) mu=(1.4e-3 2.0e-3) uv=(-0.6 0.4)}
Vertex 2 1.4 -2.1 0 {z=(1.4e+0 -2.1e+0) mu=(2.8e-3 1.5e-3) uv=(-0.6 0.4)}
Vertex 3 -1.9 1.9 0 {z=(-1.9e+0 1.9e+0) mu=(-8.9e-2 1.4e-1) uv=( 0.7 -0.2)}
.
.
.
I would like my MATLAB code to read in this data file and form a matrix containing all the numbers
in the order specified.
So e.g I would want the above 3 lines to be processed into the matrix
1 1.3 -2.1 0 1.3e+0 -2.1e+0 1.4e-3 2.0e-3 -0.6 0.4
2 1.4 -2.1 0 1.4e+0 -2.1e+0 2.8e-3 1.5e-3 -0.6 0.4
3 -1.9 1.9 0 -1.9e+0 1.9e+0 -8.9e-2 1.4e-1 0.7 -0.2
Is there some convenient MATLAB facility/command to do this?

Answer 1

I think you could use textscan for this:
Example date.txt:
Vertex 1 1.3 -2.1 0 {z=(1.3e+0 -2.1e+0) mu=(1.4e-3 2.0e-3) uv=(-0.6 0.4)}
Vertex 2 1.4 -2.1 0 {z=(1.4e+0 -2.1e+0) mu=(2.8e-3 1.5e-3) uv=(-0.6 0.4)}
Vertex 3 -1.9 1.9 0 {z=(-1.9e+0 1.9e+0) mu=(-8.9e-2 1.4e-1) uv=( 0.7 -0.2)}
Code:
fileID = fopen('data.txt');
C = textscan(fileID,'Vertex %f %f %f %f {z=(%f %f) mu=(%f %f) uv=(%f %f)}');
fclose(fileID);
mtxC = [C{:}];
Result:
mtxC =
1.0000 1.3000 -2.1000 0 1.3000 -2.1000 0.0014 0.0020 -0.6000 0.4000
2.0000 1.4000 -2.1000 0 1.4000 -2.1000 0.0028 0.0015 -0.6000 0.4000
3.0000 -1.9000 1.9000 0 -1.9000 1.9000 -0.0890 0.1400 0.7000 -0.2000

Answer 2

MATLAB Option (partly tested)
I had to do something similar with a CMM once and it was easy to do in Python (see below). You could use the MATLAB command regexp(text, expression) to match a regular expression that gets what you want. This will return string data though, which you can save to a data file and then load that data file, or convert to numbers using str2double.
To use this, you first have to get your data file into MATLAB as series of strings. You can do this with fgetl.
in_fid = fopen('my_input_file.txt', 'r');
out_fid = fopen('my_output_file.txt', 'w');
data = [];
line = fgetl(in_fid);
while ischar(line)
match = regexp(line, '[+-]?\d+\.?\d*e?[+-]?\d*', 'match'); % find all matches
% Write to text file
fprintf(out_fid, '%s\t', match); % write values to file with tabs between
fprintf(out_fid, '\n'); % write a new line to the file
% Or save to an array locally
data = [data; str2double(match)];
line = fgetl(in_fid); % grab the next line
end
fclose('all');
% If you wrote to a text file, retrieve the data
data = dlmread('my_output_file.txt', 'delimiter', '\t'); % not sure about this...
Note that this will not match numbers that begin with a decimal point with no preceding digit, i.e. .2. Also note that this will match numbers that match the pattern in any file that you feed it, so it is generalized. For how to match floating point numbers, see this site (I changed it a bit though to add the e portion for scientific notation).
I was able to test the regexp and str2double operations on a remote machine, and it looks like building your data array directly works. I was unable to test the file I/O portion, so there may be some bugs there still.
Python Option (my favorite)
I suggest using regular expressions in Python for this sort of thing. I had to do something similar with a CMM once and it was easy to do in Python with something like:
import re
# Make pattern to match scientific notation numbers
pattern = re.compile(r"[+-]?\d+\.?\d*e?[+-]?\d*")
with open("your_input_file.txt", "r") as in_file:
with open("your_output_file.txt", "w") as out_file:
for line in in_file:
match = pattern.findall(line) # find all matches in the line
out_file.write("\t".join(match) + "\n") # write the results to a line in your output
For a good introduction to regex in Python, see Dive Into Python 3, which I recommend just about everybody reads. I tested this on your example file and it gives me:
1 1.3 -2.1 0 1.3e+0 -2.1e+0 1.4e-3 2.0e-3 -0.6 0.4
2 1.4 -2.1 0 1.4e+0 -2.1e+0 2.8e-3 1.5e-3 -0.6 0.4
3 -1.9 1.9 0 -1.9e+0 1.9e+0 -8.9e-2 1.4e-1 0.7 -0.2
in your_output_file.txt, so I think it works! The last step then is to just dlmread('your_output_file.txt', 'delimeter', '\t') in MATLAB and you should be good to go.
If you want to get fancy, you could upgrade your Python script so that it can be called from the command line with your input and output files as arguments (look into the sys.argv method), but this gets a bit more complicated and it is easy enough to just open the script and change the filename manually. Unless you need to do this all the time on differently-named files, in which case arguments are a good route. There is a good example of this here.