I want to capture the output of the following ipython command into a file:
commands and outputs areas follows:
`decoder.get_hyp()`
WARNING: "ngram_search.c", line 1000: </s> not found in last frame, using ++NOISE++ instead
INFO: ngram_search.c(1046): lattice start node <s>.0 end node ++NOISE++.171
INFO: ps_lattice.c(1225): Normalizer P(O) = alpha(++NOISE++:171:185) = -2003082
INFO: ps_lattice.c(1263): Joint P(O,S) = -2036704 P(S|O) = -33622
Out[7]: ('WELCOME TO MY TALK', '000000000', -36704586)
I want to capture only the part "wellcome to my talk" into my file.
Use the IPython magic function store
%store foo >a.txt # Store (overwrite) value of foo to file a.txt
%store foo >>a.txt # Append value of foo to file a.txt
Just do as follow:
%save file_name.py _oh[7]
PS: Some additional useful command:
%save file_name.py _
'_' refers to the previous output.
Or you can:
%save file_name.py _oh[i]
'i' refers to the output history number, you can see output first via:
_oh
The %%capture cell magic saves the stdout/stderr output of running a command, if that's what you need. Here's the usage syntax:
%%capture [--no-stderr] [--no-stdout] [--no-display] [output]
And, here's a usage example:
In [1]: %%capture my_print_output
...: print('test')
...:
In [2]: my_print_output
Out[2]: <IPython.utils.capture.CapturedIO at 0x7f2efa2c12d0>
In [3]: test_output.show()
test
The output object is an instance of IPython.utils.capture.CapturedIO, which has a neat interface for accessing stdout/stderr or combined output.
IPython captures the value (output) of the last command in the variable _ (underscore).
%edit some_variable
will open the value of a variable in your editor.
So, "%edit _", should enable you to edit and save the value of the last command.
See the History section of the IPython docs
And to learn about the possible arguments to the %edit magic function, type the following at the ipython prompt:
%edit?
Related
I need perform 50 Abaqus simulations, each simulation analyses a certain material property and each differs by changing one parameter. So the idea is to write a Matlab script that:
opens the .inp file
edits the material parameter of interest
prints it into a new file which will be the new .inp file
runs it to perform the simulation
This is what I accomplished so far in a very simplified version:
f= fopen('PRD8_30s.inp');
c = textscan(f,'%s %s %s %s %s ','delimiter',',');
fclose(f) ;
S = [c{1}];
A = {'5e-08'} ;
S(12496) = A ;
fid = fopen('file.inp','w') ;
fprintf(fid,'%s \n',S{:} );
fclose(fid) ;
PRD_8_30s.inp
I manually found out the position of the parameter of interest (A at 12496 hence below the line *Viscoelastic). The code actually changes the parameter I need but there are major problems: it prints a new file with additional lines with respect to the original .inp (12552 vs 8737) and it doesn't print the entire .inp but only the first column.
How can I edit the .inp changing the parameter and obtaining a new .inp with the edited parameter that can be used to run the new simulation?
Thank you in advance for your help!
If your input file is not multiple Gb in size, The following might help.
create a template input and mark the parameter you want to change as, for example para_xxxx
Use the following script:
text=fileread('template.inp');
newtext=replace(text,'para_xxxx',newParameter);
fid=fopen('newcase.inp','w');
fprintf(fid,newtext);
fclose(fid);
The file name 'newcase.inp' should be updated each time in the loop.
The documentation for the %store magic states that you can store your variables to a file.
http://ipython.org/ipython-doc/rel-0.12/config/extensions/storemagic.html
ie: %store foo >a.txt - Store value of foo to new file a.txt
%store foo >>a.txt - Append value of foo to file a.txt
I have been able to successfully write the variables to a file, which is readable in plain text. (although it appears that it leaves out some data, since there are ellipse).
How do i restore these variables? The typical command is %store -r, but %store doesn't show any variables.
I can't find in the documentation how to "load" from file after using %store. I guess the %store -r var_name is only meant when you saved on the "default" storage used by %store.
https://ipython.readthedocs.io/en/stable/config/extensions/storemagic.html
But here are 2 ways. I'd love to see a better one.
Saving
Loading with %load
%load file_to_load
Load "manually" (just one way)
x=!cat out_file.txt
x
y=eval(''.join(x)) # Always be careful when using 'eval'
y
This is probably too easy, but I cannot google the answer for this: how can I get command line arguments in matlab script.
I run matlab as matlab -nodisplay -r "run('script.m')" and I want to return all arguments as a list. Something similar to python sys.argv. How can I do this?
I'm using Linux Mint and MATLAB 2015a.
I came up with a simple function that works on both Windows and Linux (Ubuntu):
function args = GetCommandLineArgs()
if isunix
fid = fopen(['/proc/' num2str(feature('getpid')) '/cmdline'], 'r');
args = textscan(fid, '%s', 'Delimiter', char(0));
fclose(fid);
else
kernel32WasAlreadyLoaded = libisloaded('kernel32');
if ~kernel32WasAlreadyLoaded
temporaryHeaderName = [gettempfolder '\GetCommandLineA.h'];
dlmwrite(temporaryHeaderName, 'char* __stdcall GetCommandLineA(void);', '');
loadlibrary('kernel32', temporaryHeaderName);
delete(temporaryHeaderName);
end
args = textscan(calllib('kernel32', 'GetCommandLineA'), '%q');
if ~kernel32WasAlreadyLoaded
unloadlibrary kernel32;
end
end
args = args{1};
On your sample call, it would return this:
>> GetCommandLineArgs
args =
'/[path-to-matlab-home-folder]/'
'-nodisplay'
'-r'
'run('script.m')'
It returns a cell array of strings, where the first string is the path to MATLAB home folder (on Linux) or the full path to MATLAB executable (on Windows) and the others are the program arguments (if any).
How it works:
On Linux: the function gets the current Matlab process ID using the feature function (be aware it's an undocumented feature). And reads the /proc/[PID]/cmdline file, which on Linux gives the command line arguments of any process. The values are separated by the null character \0, hence the textscan with delimiter = char(0).
On Windows: the function calls GetCommandLineA, which returns the command line arguments on a string. Then it uses textscan to split the arguments on individual strings. The GetCommandLineA function is called using MATLAB's calllib. It requires a header file. Since we only want to use one function, it creates the header file on the fly on the temporary folder and deletes it after it's no longer needed. Also the function takes care not to unload the library in case it was already loaded (for example, if the calling script already loads it for some other purpose).
I am not aware of a direction solution (like an inbuilt function).
However, you can use one of the following workarounds:
1. method
This only works in Linux:
Create a file pid_wrapper.m with the following contents:
function [] = pid_wrapper( parent_pid )
[~, matlab_pid] = system(['pgrep -P' num2str(parent_pid)]);
matlab_pid = strtrim(matlab_pid);
[~, matlab_args] = system(['ps -h -ocommand ' num2str(matlab_pid)]);
matlab_args = strsplit(strtrim(matlab_args));
disp(matlab_args);
% call your script with the extracted arguments in matlab_args
% ...
end
Invoke MATLAB like this:
matlab -nodisplay -r "pid_wrapper($$)"
This will pass the process id of MATLAB's parent process (i.e. the shell which launches MATLAB) to wrapper. This can then be used to find out the child MATLAB process and its command line arguments which you then can access in matlab_args.
2. method
This method is OS independent and does not really find out the command line arguments, but since your goal is to pass additional parameters to a script, it might work for you.
Create a file vararg_wrapper.m with the following contents:
function [] = wrapper( varargin )
% all parameters can be accessed in varargin
for i=1:nargin
disp(varargin{i});
end
% call your script with the supplied parameters
% ...
end
Invoke MATLAB like this:
matlab -nodisplay -r "vararg_wrapper('first_param', 'second_param')"
This will pass {'first_param', 'second_param'} to vararg_wrapper which you can then forward to your script.
I am trying to implement shell commands in knitr and display the output in the knitted pdf document as shown here:
```{r shell commands, engine="sh"}
wc -wlmc en_US.blogs.txt
```
I am not sure whether this is even being evaluated, as there is no output.
just realized that I can call this with system(), which will print to device! Therefore,
system("wc -l en_US.blogs.txt")
will print to the display.
Use intern=TRUE to return result of system() as character vector, then cat with past and collapse. Example.
x <- system("tree", intern=TRUE)
cat(paste(x, collapse="\n"))
places tree of working directory in output document using knitr.
I have a file full of ascii data. How would I append a string to the first line of the file? I cannot find that sort of functionality using fopen (it seems to only append at the end and nothing else.)
The following is a pure MATLAB solution:
% write first line
dlmwrite('output.txt', 'string 1st line', 'delimiter', '')
% append rest of file
dlmwrite('output.txt', fileread('input.txt'), '-append', 'delimiter', '')
% overwrite on original file
movefile('output.txt', 'input.txt')
Option 1:
I would suggest calling some system commands from within MATLAB. One possibility on Windows is to write your new line of text to its own file and then use the DOS for command to concatenate the two files. Here's what the call would look like in MATLAB:
!for %f in ("file1.txt", "file2.txt") do type "%f" >> "new.txt"
I used the ! (bang) operator to invoke the command from within MATLAB. The command above sequentially pipes the contents of "file1.txt" and "file2.txt" to the file "new.txt". Keep in mind that you will probably have to end the first file with a new line character to get things to append correctly.
Another alternative to the above command would be:
!for %f in ("file2.txt") do type "%f" >> "file1.txt"
which appends the contents of "file2.txt" to "file1.txt", resulting in "file1.txt" containing the concatenated text instead of creating a new file.
If you have your file names in strings, you can create the command as a string and use the SYSTEM command instead of the ! operator. For example:
a = 'file1.txt';
b = 'file2.txt';
system(['for %f in ("' b '") do type "%f" >> "' a '"']);
Option 2:
One MATLAB only solution, in addition to Amro's, is:
dlmwrite('file.txt',['first line' 13 10 fileread('file.txt')],'delimiter','');
This uses FILEREAD to read the text file contents into a string, concatenates the new line you want to add (along with the ASCII codes for a carriage return and a line feed/new line), then overwrites the original file using DLMWRITE.
I get the feeling Option #1 might perform faster than this pure MATLAB solution for huge text files, but I don't know that for sure. ;)
How about using the frewind(fid) function to take the pointer to the beginning of the file?
I had a similar requirement and tried frewind() followed by the necessary fprintf() statement.
But, warning: It will overwrite on whichever is the 1st line. Since in my case, I was the one writing the file, I put a dummy data at the starting of the file and then at the end, let that be overwritten after the operations specified above.
BTW, even I am facing one problem with this solution, that, depending on the length(/size) of the dummy data and actual data, the program either leaves part of the dummy data on the same line, or bring my new data to the 2nd line..
Any tip in this regards is highly appreciated.