matlab.py

# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Interfaces to run MATLAB scripts."""
import os

from .. import config
from .base import (
    CommandLineInputSpec,
    InputMultiPath,
    isdefined,
    CommandLine,
    traits,
    File,
    Directory,
)


def get_matlab_command():
    """Determine whether Matlab is installed and can be executed."""
    if "NIPYPE_NO_MATLAB" not in os.environ:
        from nipype.utils.filemanip import which

        return which(os.getenv("MATLABCMD", "matlab"))


no_matlab = get_matlab_command() is None


class MatlabInputSpec(CommandLineInputSpec):
    """Basic expected inputs to Matlab interface"""

    script = traits.Str(
        argstr='-r "%s;exit"', desc="m-code to run", mandatory=True, position=-1
    )
    uses_mcr = traits.Bool(
        desc="use MCR interface",
        xor=["nodesktop", "nosplash", "single_comp_thread"],
        nohash=True,
    )
    nodesktop = traits.Bool(
        True,
        argstr="-nodesktop",
        usedefault=True,
        desc="Switch off desktop mode on unix platforms",
        nohash=True,
    )
    nosplash = traits.Bool(
        True,
        argstr="-nosplash",
        usedefault=True,
        desc="Switch of splash screen",
        nohash=True,
    )
    logfile = File(argstr="-logfile %s", desc="Save matlab output to log")
    single_comp_thread = traits.Bool(
        argstr="-singleCompThread", desc="force single threaded operation", nohash=True
    )
    # non-commandline options
    mfile = traits.Bool(True, desc="Run m-code using m-file", usedefault=True)
    script_file = File(
        "pyscript.m", usedefault=True, desc="Name of file to write m-code to"
    )
    paths = InputMultiPath(Directory(), desc="Paths to add to matlabpath")
    prescript = traits.List(
        ["ver,", "try,"], usedefault=True, desc="prescript to be added before code"
    )
    postscript = traits.List(
        [
            "\n,catch ME,",
            "fprintf(2,'MATLAB code threw an exception:\\n');",
            "fprintf(2,'%s\\n',ME.message);",
            "if length(ME.stack) ~= 0, fprintf(2,'File:%s\\nName:%s\\nLine:%d\\n',ME.stack.file,ME.stack.name,ME.stack.line);, end;",
            "end;",
        ],
        desc="script added after code",
        usedefault=True,
    )


class MatlabCommand(CommandLine):
    """Interface that runs matlab code

    >>> import nipype.interfaces.matlab as matlab
    >>> mlab = matlab.MatlabCommand(mfile=False)  # don't write script file
    >>> mlab.inputs.script = "which('who')"
    >>> out = mlab.run()  # doctest: +SKIP
    """

    _cmd = "matlab"
    _default_matlab_cmd = None
    _default_mfile = None
    _default_paths = None
    input_spec = MatlabInputSpec

    def __init__(self, matlab_cmd=None, **inputs):
        """initializes interface to matlab
        (default 'matlab -nodesktop -nosplash')
        """
        super(MatlabCommand, self).__init__(**inputs)
        if matlab_cmd and isdefined(matlab_cmd):
            self._cmd = matlab_cmd
        elif self._default_matlab_cmd:
            self._cmd = self._default_matlab_cmd

        if self._default_mfile and not isdefined(self.inputs.mfile):
            self.inputs.mfile = self._default_mfile

        if self._default_paths and not isdefined(self.inputs.paths):
            self.inputs.paths = self._default_paths

        if not isdefined(self.inputs.single_comp_thread) and not isdefined(
            self.inputs.uses_mcr
        ):
            if config.getboolean("execution", "single_thread_matlab"):
                self.inputs.single_comp_thread = True
        # For matlab commands force all output to be returned since matlab
        # does not have a clean way of notifying an error
        self.terminal_output = "allatonce"

    @classmethod
    def set_default_matlab_cmd(cls, matlab_cmd):
        """Set the default MATLAB command line for MATLAB classes.

        This method is used to set values for all MATLAB
        subclasses.  However, setting this will not update the output
        type for any existing instances.  For these, assign the
        <instance>.inputs.matlab_cmd.
        """
        cls._default_matlab_cmd = matlab_cmd

    @classmethod
    def set_default_mfile(cls, mfile):
        """Set the default MATLAB script file format for MATLAB classes.

        This method is used to set values for all MATLAB
        subclasses.  However, setting this will not update the output
        type for any existing instances.  For these, assign the
        <instance>.inputs.mfile.
        """
        cls._default_mfile = mfile

    @classmethod
    def set_default_paths(cls, paths):
        """Set the default MATLAB paths for MATLAB classes.

        This method is used to set values for all MATLAB
        subclasses.  However, setting this will not update the output
        type for any existing instances.  For these, assign the
        <instance>.inputs.paths.
        """
        cls._default_paths = paths

    def _run_interface(self, runtime):
        self.terminal_output = "allatonce"
        runtime = super(MatlabCommand, self)._run_interface(runtime)
        try:
            # Matlab can leave the terminal in a barbbled state
            os.system("stty sane")
        except:
            # We might be on a system where stty doesn't exist
            pass
        if "MATLAB code threw an exception" in runtime.stderr:
            self.raise_exception(runtime)
        return runtime

    def _format_arg(self, name, trait_spec, value):
        if name in ["script"]:
            argstr = trait_spec.argstr
            if self.inputs.uses_mcr:
                argstr = "%s"
            return self._gen_matlab_command(argstr, value)
        return super(MatlabCommand, self)._format_arg(name, trait_spec, value)

    def _gen_matlab_command(self, argstr, script_lines):
        """Generates commands and, if mfile specified, writes it to disk."""
        cwd = os.getcwd()
        mfile = self.inputs.mfile or self.inputs.uses_mcr
        paths = []
        if isdefined(self.inputs.paths):
            paths = self.inputs.paths
        # prescript
        prescript = self.inputs.prescript
        postscript = self.inputs.postscript

        # prescript takes different default value depending on the mfile argument
        if mfile:
            prescript.insert(
                0, "fprintf(1,'Executing %s at %s:\\n',mfilename(),datestr(now));"
            )
        else:
            prescript.insert(0, "fprintf(1,'Executing code at %s:\\n',datestr(now));")
        for path in paths:
            # addpath() is not available after compilation
            # https://www.mathworks.com/help/compiler/ismcc.html
            # https://www.mathworks.com/help/compiler/isdeployed.html
            prescript.append("if ~(ismcc || isdeployed), addpath('%s'); end;\n" % path)

        if not mfile:
            # clean up the code of comments and replace newlines with commas
            script_lines = ",".join(
                [
                    line
                    for line in script_lines.split("\n")
                    if not line.strip().startswith("%")
                ]
            )

        script_lines = "\n".join(prescript) + script_lines + "\n".join(postscript)
        if mfile:
            with open(os.path.join(cwd, self.inputs.script_file), "wt") as mfile:
                mfile.write(script_lines)
            if self.inputs.uses_mcr:
                script = "%s" % (os.path.join(cwd, self.inputs.script_file))
            else:
                script = "addpath('%s');%s" % (
                    cwd,
                    self.inputs.script_file.split(".")[0],
                )
        else:
            script = "".join(script_lines.split("\n"))
        return argstr % script