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So I am in a bit of a pickle. I am trying to write plotting and fitting extensions to a Fortran77 (why this program was rewritten in F77 is a mystery too me, btw) code that requires command line input, i.e. it prompts the user for input. Currently the program uses GNUplot to plot, but the GNUplot fitting routine is less than ideal in my eyes, and calling GNUplot from Fortran is a pain in the ass to say the least.

I have mostly been working with Numpy, Scipy and Matplotlib to satisfy my fitting and plotting needs. I was wondering if there is a way to call the F77 program in Python and then have it run like I would any other F77 program until the portion where I need it to fit and spit out some nice plots (none of this GNUplot stuff).

I know about F2PY, but I have heard mixed things about it. I have also contemplated using pyexpect and go from there, but I have have bad experience with the way it handles changing expected prompts on the screen (or I am just using it incorrectly).

Thanks for any info on this.

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  • So the Fortran program is an interactive program that prompts the user for input? Could you rewrite it to accept command line parameters or other scriptable input instead? Commented Mar 28, 2011 at 22:56
  • Yes, it basically asks you what data channel you want to analyze and whether or not you want set the limits or it uses a default set. I know that I can automate parts of fairly easily by just running a shell script over it, but the problem being is that we go back and forth between different channels and might want to tweak some of the parameters without running the whole thing again. And the reason for the current format is in the comment below @greg Commented Mar 28, 2011 at 23:06
  • If you intending to get the output from FORTAN via stdout or an output file (which can be quite fast with a ramdisk), you can use subprocess. But I think you are hoping to get access to the running FORTRAN program memory as a numpy array? Commented Mar 28, 2011 at 23:15
  • What I was thinking about doing was writing a wrapper that lets the F77 code do its things until it is done and then the python takes over and extracts all the necessary data from FITS output file that the F77 program generates. @Paul Commented Mar 28, 2011 at 23:20

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Can't you just dump the data generated by the Fortran program to a file and then read it from python ?

Numpy can read a binary file and treat it as a array. Going from here to matplotlib then should be a breeeze.

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7 Comments

Everything is actually stored in FITS files, which are a breeze to work with python with pyfits and a pain in F77. The problem is that my boss wants everything to be in one package instead having 20 different programs in 2 languages (that is how the old version of the code was set up). He believes that makes it more "easily maintainable." @fabrizioM
@madtowneast: "one package instead having 20 different programs in 2 languages"? Does that mean you're rewriting the Fortran? If so, then change the question. If you're not rewriting the fortran, then what's wrong with this answer? You'll still have two languages, why not run one from the other?
@S.Lott: I haven't written in F77 at all, I come from the C++, python world. We have only had problems with using two languages, esp. considering that one of them is proprietary (IDL), and the interplay between the two is less than ideal. The fortran code has been rewritten by someone else from DEC fortran to F77, but I get the honor of debugging and adding on the pieces he left out. And again my boss wants fortran and nothing else. I am not saying the answer is wrong, personally I would do what @fabrizioM is saying, but I want to offer my boss a compromise, F77 here python there.
@madtowneast: If the code all F77, why is the question tagged Python?
@S.Lott: The title states that I want to run F77 code within Python... The fitting part is not yet written and I wanted to write it in Python, but rather than tagging something on/run a separate program, I want to wrap python around the F77. The problem being the F77 requires user input by graphical selection and command line. So is the Python tag still wrong?
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It sounds like all you want to do is run the F77 program and then parse the output files, all from python (correct me if I'm wrong). The simplest thing to do, assuming that the fortran program runs to completion is to just set up python to take the inputs from the user or a config file (see http://docs.python.org/library/configparser.html), then feed those inputs into the python process module:

http://docs.python.org/library/subprocess.html

have it run the F77 executable, and then collect the outputs and analyze/plot them. All the python script would have to do is prepare the inputs to the fortran and then grab the results from some specified place later.

Check out this good tutorial from Doug Hellmann on subprocess:

http://www.doughellmann.com/PyMOTW/subprocess/

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The problem with passing the config file to F77 is that basically the user gets prompted with selection of channels at the beginning and as the processing continues has to select a number of parameters from GNUPlot graphs. I have looked at subprocessor before, but was not sure if it is able to do what I need it to do, esp. with the whole plotting part in GNUPlot.
@madtowneast: this is what the STDIN and STDOUT pipes do. doughellmann.com/PyMOTW/subprocess/#working-with-pipes-directly You'll either have to pass the FORTRAN pipes to the Python user or let python guess the options.
@madtowneast: Are the parameters keyed in, or graphically selected on the GNUplot?
@Paul: Graphically selected. I am trying to get it work atm, at least the channel selection part, but getting the error that the output file of the fortran code does not exist... weird.

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