"""Core oct2py functionality."""
# Copyright (c) oct2py developers.
# Distributed under the terms of the MIT License.
import atexit
import logging
import os
import os.path as osp
import shutil
import tempfile
import warnings
import numpy as np
from metakernel.pexpect import EOF, TIMEOUT # type:ignore[import-untyped]
from octave_kernel.kernel import STDIN_PROMPT, OctaveEngine # type:ignore[import-untyped]
from .dynamic import (
OctavePtr,
_make_function_ptr_instance,
_make_user_class,
_make_variable_ptr_instance,
)
from .io import Cell, StructArray, read_file, write_file
from .utils import Oct2PyError, get_log
HERE = osp.realpath(osp.dirname(__file__))
[docs]
class Oct2Py:
"""Manages an Octave session.
Uses MAT files to pass data between Octave and Numpy.
The function must either exist as an m-file in this directory or
on Octave's path.
The first command will take about 0.5s for Octave to load up.
The subsequent commands will be much faster.
You may provide a logger object for logging events, or the oct2py.get_log()
default will be used. When calling commands, logger.info() will be used
to stream output, unless a `stream_handler` is provided.
Parameters
----------
logger : logging object, optional
Optional logger to use for Oct2Py session
timeout : float, optional
Timeout in seconds for commands
oned_as : {'row', 'column'}, optional
If 'column', write 1-D numpy arrays as column vectors.
If 'row', write 1-D numpy arrays as row vectors.}
temp_dir : str, optional
If specified, the session's MAT files will be created in the
directory, otherwise a default directory is used. This can be
a shared memory (tmpfs) path.
convert_to_float : bool, optional
If true, convert integer types to float when passing to Octave.
backend: string, optional
The graphics_toolkit to use for plotting.
"""
def __init__( # noqa
self,
logger=None,
timeout=None,
oned_as="row",
temp_dir=None,
convert_to_float=True,
backend=None,
):
"""Start Octave and set up the session."""
self._oned_as = oned_as
self._engine = None
self._logger = None
self.logger = logger
self.timeout = timeout
self.backend = backend or "default"
if temp_dir is None:
temp_dir_obj = tempfile.mkdtemp()
self.temp_dir = temp_dir_obj
atexit.register(shutil.rmtree, self.temp_dir)
else:
self.temp_dir = temp_dir
self.convert_to_float = convert_to_float
self._user_classes = {}
self._function_ptrs = {}
self.restart()
@property
def logger(self):
"""The logging instance used by the session."""
return self._logger
@logger.setter
def logger(self, value):
self._logger = value or get_log()
if self._engine:
self._engine.logger = self._logger
def __enter__(self):
"""Return octave object, restart session if necessary"""
if not self._engine:
self.restart()
return self
def __exit__(self, type_, value, traceback):
"""Close session"""
self.exit()
def __del__(self):
"""Delete session"""
self.exit()
[docs]
def exit(self):
"""Quits this octave session and cleans up."""
if self._engine:
self._engine.repl.terminate()
self._engine = None
[docs]
def push(self, name, var, timeout=None, verbose=True):
"""
Put a variable or variables into the Octave session.
Parameters
----------
name : str or list
Name of the variable(s).
var : object or list
The value(s) to pass.
timeout : float
Time to wait for response from Octave (per line).
**kwargs: Deprecated kwargs, ignored.
Examples
--------
>>> from oct2py import octave
>>> y = [1, 2]
>>> octave.push('y', y)
>>> octave.pull('y')
array([[1., 2.]])
>>> octave.push(['x', 'y'], ['spam', [1, 2, 3, 4]])
>>> octave.pull(['x', 'y']) # doctest: +SKIP
[u'spam', array([[1, 2, 3, 4]])]
Notes
-----
Integer type arguments will be converted to floating point
unless `convert_to_float=False`.
"""
if isinstance(name, str):
name = [name]
var = [var]
for n, v in zip(name, var):
self.feval("assignin", "base", n, v, nout=0, timeout=timeout, verbose=verbose)
[docs]
def pull(self, var, timeout=None, verbose=True):
"""
Retrieve a value or values from the Octave session.
Parameters
----------
var : str or list
Name of the variable(s) to retrieve.
timeout : float, optional.
Time to wait for response from Octave (per line).
**kwargs: Deprecated kwargs, ignored.
Returns
-------
out : object
Object returned by Octave.
Raises
------
Oct2PyError
If the variable does not exist in the Octave session.
Examples
--------
>>> from oct2py import octave
>>> y = [1, 2]
>>> octave.push('y', y)
>>> octave.pull('y')
array([[1., 2.]])
>>> octave.push(['x', 'y'], ['spam', [1, 2, 3, 4]])
>>> octave.pull(['x', 'y']) # doctest: +SKIP
[u'spam', array([[1, 2, 3, 4]])]
"""
if isinstance(var, str):
var = [var]
outputs = []
for name in var:
exist = self._exist(name)
if exist == 1:
outputs.append(self.feval("evalin", "base", name, timeout=timeout, verbose=verbose))
else:
outputs.append(self.get_pointer(name, timeout=timeout))
if len(outputs) == 1:
return outputs[0]
return outputs
[docs]
def get_pointer(self, name, timeout=None):
"""Get a pointer to a named object in the Octave workspace.
Parameters
----------
name: str
The name of the object in the Octave workspace.
timeout: float, optional.
Time to wait for response from Octave (per line).
Examples
--------
>>> from oct2py import octave
>>> octave.eval('foo = [1, 2];')
>>> ptr = octave.get_pointer('foo')
>>> ptr.value
array([[1., 2.]])
>>> ptr.address
'foo'
>>> # Can be passed as an argument
>>> octave.disp(ptr) # doctest: +SKIP
1 2
>>> from oct2py import octave
>>> sin = octave.get_pointer('sin') # equivalent to `octave.sin`
>>> sin.address
'@sin'
>>> x = octave.quad(sin, 0, octave.pi())
>>> x
2.0
Notes
-----
Pointers can be passed to `feval` or dynamic functions as function
arguments. A pointer passed as a nested value will be passed by value
instead.
Raises
------
Oct2PyError
If the variable does not exist in the Octave session or is of
unknown type.
Returns
-------
A variable, object, user class, or function pointer as appropriate.
"""
exist = self._exist(name)
isobject = self._isobject(name, exist)
if exist == 0:
raise Oct2PyError('"%s" is undefined' % name)
elif exist == 1:
return _make_variable_ptr_instance(self, name)
elif isobject:
return self._get_user_class(name)
elif exist in [2, 3, 5]:
return self._get_function_ptr(name)
raise Oct2PyError('Unknown type for object "%s"' % name)
[docs]
def feval(self, func_path, *func_args, **kwargs):
"""Run a function in Octave and return the result.
Parameters
----------
func_path: str
Name of function to run or a path to an m-file.
func_args: object, optional
Args to send to the function.
nout: int or str, optional.
The desired number of returned values, defaults to 1. If nout
value is 'max_nout', _get_max_nout() will be used.
store_as: str, optional
If given, saves the result to the given Octave variable name
instead of returning it.
verbose : bool, optional
Log Octave output at INFO level. If False, log at DEBUG level.
stream_handler: callable, optional
A function that is called for each line of output from the
evaluation.
timeout: float, optional
The timeout in seconds for the call.
plot_dir: str, optional
If specified, save the session's plot figures to the plot
directory instead of displaying the plot window.
plot_backend: str, optional
The plotting back end to use.
plot_name : str, optional
Saved plots will start with `plot_name` and
end with "_%%.xxx' where %% is the plot number and
xxx is the `plot_format`.
plot_format: str, optional
The format in which to save the plot.
plot_width: int, optional
The plot with in pixels.
plot_height: int, optional
The plot height in pixels.
Notes
-----
The function arguments passed follow Octave calling convention, not
Python. That is, all values must be passed as a comma separated list,
not using `x=foo` assignment.
Examples
--------
>>> from oct2py import octave
>>> cell = octave.feval('cell', 10, 10, 10)
>>> cell.shape
(10, 10, 10)
>>> from oct2py import octave
>>> x = octave.feval('linspace', 0, octave.pi() / 2)
>>> x.shape
(1, 100)
>>> from oct2py import octave
>>> x = octave.feval('svd', octave.hilb(3))
>>> x
array([[1.40831893],
[0.12232707],
[0.00268734]])
>>> # specify three return values
>>> (u, v, d) = octave.feval('svd', octave.hilb(3), nout=3)
>>> u.shape
(3, 3)
Returns
-------
The Python value(s) returned by the Octave function call.
"""
if not self._engine:
msg = "Session is not open"
raise Oct2PyError(msg)
# nout handler
nout = kwargs.get("nout", None)
if nout is None:
nout = 1
elif nout == "max_nout":
nout = self._get_max_nout(func_path)
plot_dir = kwargs.get("plot_dir")
# Choose appropriate plot backend.
default_backend = "inline" if plot_dir else self.backend
backend = kwargs.get("plot_backend", default_backend)
settings = dict(
backend=backend,
format=kwargs.get("plot_format"),
name=kwargs.get("plot_name"),
width=kwargs.get("plot_width"),
height=kwargs.get("plot_height"),
resolution=kwargs.get("plot_res"),
)
self._engine.plot_settings = settings
dname = osp.dirname(func_path)
fname = osp.basename(func_path)
func_name, ext = osp.splitext(fname)
if ext and ext != ".m":
msg = "Need to give path to .m file"
raise TypeError(msg)
if func_name == "clear":
msg = 'Cannot use `clear` command directly, use eval("clear(var1, var2)")'
raise Oct2PyError(msg)
stream_handler = kwargs.get("stream_handler")
verbose = kwargs.get("verbose", True)
store_as = kwargs.get("store_as", "")
timeout = kwargs.get("timeout", self.timeout)
if not stream_handler:
stream_handler = self.logger.info if verbose else self.logger.debug
return self._feval(
func_name,
func_args,
dname=dname,
nout=nout,
timeout=timeout,
stream_handler=stream_handler,
store_as=store_as,
plot_dir=plot_dir,
)
[docs]
def eval( # noqa
self,
cmds,
verbose=True,
timeout=None,
stream_handler=None,
temp_dir=None,
plot_dir=None,
plot_name="plot",
plot_format="svg",
plot_backend=None,
plot_width=None,
plot_height=None,
plot_res=None,
nout=0,
**kwargs,
):
"""
Evaluate an Octave command or commands.
Parameters
----------
cmds : str or list
Commands(s) to pass to Octave.
verbose : bool, optional
Log Octave output at INFO level. If False, log at DEBUG level.
stream_handler: callable, optional
A function that is called for each line of output from the
evaluation.
timeout : float, optional
Time to wait for response from Octave (per line). If not given,
the instance `timeout` is used.
nout : int or str, optional.
The desired number of returned values, defaults to 0. If nout
is 0, the `ans` will be returned as the return value. If nout
value is 'max_nout', _get_max_nout() will be used.
temp_dir: str, optional
If specified, the session's MAT files will be created in the
directory, otherwise a the instance `temp_dir` is used.
a shared memory (tmpfs) path.
plot_dir: str, optional
If specified, save the session's plot figures to the plot
directory instead of displaying the plot window.
plot_name : str, optional
Saved plots will start with `plot_name` and
end with "_%%.xxx' where %% is the plot number and
xxx is the `plot_format`.
plot_format: str, optional
The format in which to save the plot (PNG by default).
plot_width: int, optional
The plot with in pixels.
plot_height: int, optional
The plot height in pixels.
plot_backend: str, optional
The plot backend to use.
plot_res: int, optional
The plot resolution in pixels per inch.
**kwargs Deprecated kwargs.
Examples
--------
>>> from oct2py import octave
>>> octave.eval('disp("hello")') # doctest: +SKIP
hello
>>> x = octave.eval('round(quad(@sin, 0, pi/2));')
>>> x
1.0
>>> a = octave.eval('disp("hello");1;') # doctest: +SKIP
hello
>>> a = octave.eval('disp("hello");1;', verbose=False)
>>> a
1.0
>>> from oct2py import octave
>>> lines = []
>>> octave.eval('for i = 1:3; disp(i);end', \
stream_handler=lines.append)
>>> lines # doctest: +SKIP
[' 1', ' 2', ' 3']
Returns
-------
out : object
Octave "ans" variable, or None.
Notes
-----
The deprecated `log` kwarg will temporarily set the `logger` level to
`WARN`. Using the `logger` settings directly is preferred.
The deprecated `return_both` kwarg will still work, but the preferred
method is to use the `stream_handler`. If `stream_handler` is given,
the `return_both` kwarg will be honored but will give an empty string
as the response.
Raises
------
Oct2PyError
If the command(s) fail.
"""
if isinstance(cmds, str):
cmds = [cmds]
prev_temp_dir = self.temp_dir
self.temp_dir = temp_dir or self.temp_dir
prev_log_level = self.logger.level
if kwargs.get("log") is False:
self.logger.setLevel(logging.WARN)
for name in ["log", "return_both"]:
if name not in kwargs:
continue
msg = "Using deprecated `%s` kwarg, see docs on `Oct2Py.eval()`"
warnings.warn(msg % name, stacklevel=2)
return_both = kwargs.pop("return_both", False)
lines: list[str] = []
if return_both and not stream_handler:
stream_handler = lines.append
ans = None
for cmd in cmds:
resp = self.feval(
"evalin",
"base",
cmd,
nout=nout,
timeout=timeout,
stream_handler=stream_handler,
verbose=verbose,
plot_dir=plot_dir,
plot_name=plot_name,
plot_format=plot_format,
plot_backend=plot_backend,
plot_width=plot_width,
plot_height=plot_height,
plot_res=plot_res,
)
if resp is not None:
ans = resp
self.temp_dir = prev_temp_dir
self.logger.setLevel(prev_log_level)
if return_both:
return "\n".join(lines), ans
return ans
[docs]
def restart(self):
"""Restart an Octave session in a clean state"""
if self._engine:
self._engine.repl.terminate()
if "OCTAVE_EXECUTABLE" not in os.environ and "OCTAVE" in os.environ:
os.environ["OCTAVE_EXECUTABLE"] = os.environ["OCTAVE"]
try:
self._engine = OctaveEngine(stdin_handler=self._handle_stdin, logger=self.logger)
except Exception as e:
raise Oct2PyError(str(e)) from None
# Add local Octave scripts.
self._engine.eval('addpath("%s");' % HERE.replace(osp.sep, "/"))
def _feval( # noqa
self,
func_name,
func_args=(),
dname="",
nout=0,
timeout=None,
stream_handler=None,
store_as="",
plot_dir=None,
):
"""Run the given function with the given args."""
engine = self._engine
if engine is None:
msg = "Session is closed"
raise Oct2PyError(msg)
# Set up our mat file paths.
out_file = osp.join(self.temp_dir, "writer.mat")
out_file = out_file.replace(osp.sep, "/")
in_file = osp.join(self.temp_dir, "reader.mat")
in_file = in_file.replace(osp.sep, "/")
func_args = list(func_args)
ref_indices = []
for i, value in enumerate(func_args):
if isinstance(value, OctavePtr):
ref_indices.append(i + 1)
func_args[i] = value.address
ref_arr = np.array(ref_indices)
# Save the request data to the output file.
req = dict(
func_name=func_name,
func_args=tuple(func_args),
dname=dname or "",
nout=nout,
store_as=store_as or "",
ref_indices=ref_arr,
)
write_file(req, out_file, oned_as=self._oned_as, convert_to_float=self.convert_to_float)
# Set up the engine and evaluate the `_pyeval()` function.
engine.line_handler = stream_handler or self.logger.info
if timeout is None:
timeout = self.timeout
try:
engine.eval(f'_pyeval("{out_file}", "{in_file}");', timeout=timeout)
except KeyboardInterrupt:
stream_handler(engine.repl.interrupt())
raise
except TIMEOUT:
stream_handler(engine.repl.interrupt())
msg = "Timed out, interrupting"
raise Oct2PyError(msg) from None
except EOF:
if not self._engine:
return
stream_handler(engine.repl.child.before)
self.restart()
msg = "Session died, restarting"
raise Oct2PyError(msg) from None
# Read in the output.
resp = read_file(in_file, self)
if resp["err"]:
msg = self._parse_error(resp["err"])
raise Oct2PyError(msg)
result = resp["result"].ravel().tolist()
if isinstance(result, list) and len(result) == 1:
result = result[0]
# Check for sentinel value.
if (
isinstance(result, Cell)
and result.size == 1
and isinstance(result[0], str)
and result[0] == "__no_value__"
):
result = None
if plot_dir:
engine.make_figures(plot_dir)
return result
def _parse_error(self, err):
"""Create a traceback for an Octave evaluation error."""
self.logger.debug(err)
stack = err.get("stack", [])
if not err["message"].startswith("parse error:"):
err["message"] = "error: " + err["message"]
errmsg = "Octave evaluation error:\n%s" % err["message"]
if not isinstance(stack, StructArray):
return errmsg
errmsg += "\nerror: called from:"
for item in stack[:-1]:
errmsg += "\n %(name)s at line %(line)d" % item
try: # noqa
errmsg += ", column %(column)d" % item
except Exception: # noqa
pass
return errmsg
def _handle_stdin(self, line):
"""Handle a stdin request from the session."""
return input(line.replace(STDIN_PROMPT, ""))
def _print_doc(self, name):
"""
Print the documentation of an Octave procedure or object.
Parameters
----------
name : str
Function name to search for.
Returns
-------
out : None
"""
print(self._get_doc(name)) # noqa
def _get_doc(self, name):
"""
Get the documentation of an Octave procedure or object.
Parameters
----------
name : str
Function name to search for.
Returns
-------
out : str
Documentation string.
Raises
------
Oct2PyError
If the procedure or object function has a syntax error.
"""
doc = "No documentation for %s" % name
engine = self._engine
if not engine:
msg = "Session is not open"
raise Oct2PyError(msg)
doc = engine.eval('help("%s")' % name, silent=True)
if "syntax error:" in doc.lower():
raise Oct2PyError(doc)
if "error:" in doc.lower():
doc = engine.eval('type("%s")' % name, silent=True)
doc = "\n".join(doc.splitlines()[:3])
default = self.feval.__doc__
default = (
" " + default[default.find("func_args:") :] # type:ignore[index,union-attr]
)
default = "\n".join([line[8:] for line in default.splitlines()])
doc = "\n".join(doc.splitlines())
doc = "\n" + doc + "\n\nParameters\n----------\n" + default
doc += "\n**kwargs - Deprecated keyword arguments\n\n"
doc += "Notes\n-----\n"
doc += "Keyword arguments to dynamic functions are deprecated.\n"
doc += "The `plot_*` kwargs will be ignored, but the rest will\n"
doc += "used as key - value pairs as in version 3.x.\n"
doc += "Use `set_plot_settings()` for plot settings, and use\n"
doc += "`func_args` directly for key - value pairs."
return doc
def _exist(self, name):
"""Test whether a name exists and return the name code.
Raises an error when the name does not exist.
"""
cmd = 'exist("%s")' % name
if not self._engine:
msg = "Session is not open"
raise Oct2PyError(msg)
resp = self._engine.eval(cmd, silent=True).strip()
exist = int(resp.split()[-1])
if exist == 0:
cmd = "class(%s)" % name
resp = self._engine.eval(cmd, silent=True).strip()
if "error:" in resp:
msg = 'Value "%s" does not exist in Octave workspace'
raise Oct2PyError(msg % name)
else:
exist = 2
return exist
def _isobject(self, name, exist):
"""Test whether the name is an object."""
if exist in [2, 5]:
return False
cmd = "isobject(%s)" % name
if not self._engine:
msg = "Session is not open"
raise Oct2PyError(msg)
resp = self._engine.eval(cmd, silent=True).strip()
return resp == "ans = 1"
def _get_function_ptr(self, name):
"""Get or create a function pointer of the given name."""
func = _make_function_ptr_instance
self._function_ptrs.setdefault(name, func(self, name))
return self._function_ptrs[name]
def _get_user_class(self, name):
"""Get or create a user class of the given type."""
self._user_classes.setdefault(name, _make_user_class(self, name))
return self._user_classes[name]
def __getattr__(self, attr):
"""Automatically creates a wrapper to an Octave function or object.
Adapted from the mlabwrap project.
"""
# needed for help(Oct2Py())
if attr.startswith("__"):
return super().__getattr__(attr) # type:ignore[misc]
# close_ -> close
name = attr[:-1] if attr[-1] == "_" else attr
if self._engine is None:
msg = "Session is closed"
raise Oct2PyError(msg)
# Make sure the name exists.
exist = self._exist(name)
if exist not in [2, 3, 5, 103]:
msg = 'Name "%s" is not a valid callable, use `pull` for variables'
raise Oct2PyError(msg % name)
if name == "clear":
msg = 'Cannot use `clear` command directly, use `eval("clear(var1, var2)")`'
raise Oct2PyError(msg)
# Check for user defined class.
if self._isobject(name, exist):
obj = self._get_user_class(name)
else:
obj = self._get_function_ptr(name)
# !!! attr, *not* name, because we might have python keyword name!
setattr(self, attr, obj)
return obj
def _get_max_nout(self, func_path):
"""Get or count maximum nout of .m function."""
if not osp.isabs(func_path):
func_path = self.which(func_path)
nout = 0 # default nout of eval
status = "NOT FUNCTION"
if func_path.endswith(".m"): # only if `func_path` is .m file
with open(func_path, encoding="utf8") as fid:
for line in fid:
if line[0] != "f": # noqa # not function
if status == "NOT FUNCTION":
continue
line = line.translate( # noqa
str.maketrans("", "", "[]()")
).split() # type:ignore[assignment]
try: # noqa
line.remove("function") # type:ignore[attr-defined]
except Exception: # noqa
pass
for char in line:
if char == "...":
status = "FUNCTION"
continue
if char != "=":
nout += 1
else:
return nout
return nout