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# -*- coding: utf-8 -*-
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"""
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===========
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octavemagic
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===========
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Magics for interacting with Octave via oct2py.
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.. note::
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The ``oct2py`` module needs to be installed separately and
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can be obtained using ``easy_install`` or ``pip``.
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Usage
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=====
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``%octave``
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{OCTAVE_DOC}
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``%octave_push``
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{OCTAVE_PUSH_DOC}
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``%octave_pull``
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{OCTAVE_PULL_DOC}
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"""
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#-----------------------------------------------------------------------------
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# Copyright (C) 2012 The IPython Development Team
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#
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# Distributed under the terms of the BSD License. The full license is in
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# the file COPYING, distributed as part of this software.
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#-----------------------------------------------------------------------------
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import tempfile
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from glob import glob
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from shutil import rmtree
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import numpy as np
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import oct2py
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from xml.dom import minidom
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from IPython.core.displaypub import publish_display_data
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from IPython.core.magic import (Magics, magics_class, line_magic,
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line_cell_magic, needs_local_scope)
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from IPython.testing.skipdoctest import skip_doctest
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from IPython.core.magic_arguments import (
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argument, magic_arguments, parse_argstring
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)
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from IPython.utils.py3compat import unicode_to_str
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class OctaveMagicError(oct2py.Oct2PyError):
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pass
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_mimetypes = {'png' : 'image/png',
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'svg' : 'image/svg+xml',
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'jpg' : 'image/jpeg',
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'jpeg': 'image/jpeg'}
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@magics_class
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class OctaveMagics(Magics):
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"""A set of magics useful for interactive work with Octave via oct2py.
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"""
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def __init__(self, shell):
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"""
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Parameters
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----------
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shell : IPython shell
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"""
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super(OctaveMagics, self).__init__(shell)
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self._oct = oct2py.Oct2Py()
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self._plot_format = 'png'
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# Allow publish_display_data to be overridden for
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# testing purposes.
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self._publish_display_data = publish_display_data
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def _fix_gnuplot_svg_size(self, image, size=None):
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"""
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GnuPlot SVGs do not have height/width attributes. Set
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these to be the same as the viewBox, so that the browser
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scales the image correctly.
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Parameters
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----------
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image : str
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SVG data.
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size : tuple of int
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Image width, height.
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"""
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(svg,) = minidom.parseString(image).getElementsByTagName('svg')
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viewbox = svg.getAttribute('viewBox').split(' ')
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if size is not None:
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width, height = size
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else:
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width, height = viewbox[2:]
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svg.setAttribute('width', '%dpx' % width)
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svg.setAttribute('height', '%dpx' % height)
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return svg.toxml()
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@skip_doctest
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@line_magic
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def octave_push(self, line):
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'''
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Line-level magic that pushes a variable to Octave.
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`line` should be made up of whitespace separated variable names in the
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IPython namespace::
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In [7]: import numpy as np
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In [8]: X = np.arange(5)
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In [9]: X.mean()
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Out[9]: 2.0
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In [10]: %octave_push X
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In [11]: %octave mean(X)
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Out[11]: 2.0
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'''
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inputs = line.split(' ')
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for input in inputs:
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input = unicode_to_str(input)
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self._oct.put(input, self.shell.user_ns[input])
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@skip_doctest
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@line_magic
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def octave_pull(self, line):
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'''
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Line-level magic that pulls a variable from Octave.
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In [18]: _ = %octave x = [1 2; 3 4]; y = 'hello'
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In [19]: %octave_pull x y
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In [20]: x
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Out[20]:
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array([[ 1., 2.],
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[ 3., 4.]])
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In [21]: y
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Out[21]: 'hello'
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'''
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outputs = line.split(' ')
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for output in outputs:
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output = unicode_to_str(output)
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self.shell.push({output: self._oct.get(output)})
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@skip_doctest
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@magic_arguments()
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@argument(
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'-i', '--input', action='append',
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help='Names of input variables to be pushed to Octave. Multiple names '
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'can be passed, separated by commas with no whitespace.'
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)
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@argument(
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'-o', '--output', action='append',
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help='Names of variables to be pulled from Octave after executing cell '
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'body. Multiple names can be passed, separated by commas with no '
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'whitespace.'
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)
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@argument(
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'-s', '--size', action='store',
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help='Pixel size of plots, "width,height". Default is "-s 400,250".'
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)
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@argument(
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'-f', '--format', action='store',
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help='Plot format (png, svg or jpg).'
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)
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@needs_local_scope
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@argument(
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'code',
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nargs='*',
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)
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@line_cell_magic
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def octave(self, line, cell=None, local_ns=None):
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'''
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Execute code in Octave, and pull some of the results back into the
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Python namespace.
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In [9]: %octave X = [1 2; 3 4]; mean(X)
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Out[9]: array([[ 2., 3.]])
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As a cell, this will run a block of Octave code, without returning any
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value::
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In [10]: %%octave
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....: p = [-2, -1, 0, 1, 2]
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....: polyout(p, 'x')
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-2*x^4 - 1*x^3 + 0*x^2 + 1*x^1 + 2
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In the notebook, plots are published as the output of the cell, e.g.
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%octave plot([1 2 3], [4 5 6])
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will create a line plot.
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Objects can be passed back and forth between Octave and IPython via the
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-i and -o flags in line::
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In [14]: Z = np.array([1, 4, 5, 10])
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In [15]: %octave -i Z mean(Z)
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Out[15]: array([ 5.])
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In [16]: %octave -o W W = Z * mean(Z)
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Out[16]: array([ 5., 20., 25., 50.])
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In [17]: W
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Out[17]: array([ 5., 20., 25., 50.])
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The size and format of output plots can be specified::
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In [18]: %%octave -s 600,800 -f svg
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...: plot([1, 2, 3]);
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'''
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args = parse_argstring(self.octave, line)
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# arguments 'code' in line are prepended to the cell lines
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if cell is None:
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code = ''
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return_output = True
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else:
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code = cell
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return_output = False
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code = ' '.join(args.code) + code
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# if there is no local namespace then default to an empty dict
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if local_ns is None:
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local_ns = {}
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if args.input:
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for input in ','.join(args.input).split(','):
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input = unicode_to_str(input)
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try:
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val = local_ns[input]
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except KeyError:
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val = self.shell.user_ns[input]
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self._oct.put(input, val)
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# generate plots in a temporary directory
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plot_dir = tempfile.mkdtemp()
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if args.size is not None:
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size = args.size
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else:
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size = '400,240'
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if args.format is not None:
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plot_format = args.format
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else:
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plot_format = 'png'
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pre_call = '''
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global __ipy_figures = [];
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page_screen_output(0);
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function fig_create(src, event)
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global __ipy_figures;
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__ipy_figures(size(__ipy_figures) + 1) = src;
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set(src, "visible", "off");
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end
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set(0, 'DefaultFigureCreateFcn', @fig_create);
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close all;
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clear ans;
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# ___<end_pre_call>___ #
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'''
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post_call = '''
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# ___<start_post_call>___ #
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# Save output of the last execution
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if exist("ans") == 1
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_ = ans;
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else
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_ = nan;
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end
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for f = __ipy_figures
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outfile = sprintf('%(plot_dir)s/__ipy_oct_fig_%%03d.png', f);
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try
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print(f, outfile, '-d%(plot_format)s', '-tight', '-S%(size)s');
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end
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end
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''' % locals()
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code = ' '.join((pre_call, code, post_call))
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try:
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text_output = self._oct.run(code, verbose=False)
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except (oct2py.Oct2PyError) as exception:
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msg = exception.message
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msg = msg.split('# ___<end_pre_call>___ #')[1]
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msg = msg.split('# ___<start_post_call>___ #')[0]
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raise OctaveMagicError('Octave could not complete execution. '
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'Traceback (currently broken in oct2py): %s'
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% msg)
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key = 'OctaveMagic.Octave'
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display_data = []
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# Publish text output
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if text_output:
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display_data.append((key, {'text/plain': text_output}))
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# Publish images
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images = [open(imgfile, 'rb').read() for imgfile in \
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glob("%s/*" % plot_dir)]
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rmtree(plot_dir)
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plot_mime_type = _mimetypes.get(plot_format, 'image/png')
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width, height = [int(s) for s in size.split(',')]
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for image in images:
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if plot_format == 'svg':
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image = self._fix_gnuplot_svg_size(image, size=(width, height))
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display_data.append((key, {plot_mime_type: image}))
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if args.output:
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for output in ','.join(args.output).split(','):
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output = unicode_to_str(output)
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self.shell.push({output: self._oct.get(output)})
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for source, data in display_data:
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self._publish_display_data(source, data)
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if return_output:
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ans = self._oct.get('_')
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# Unfortunately, Octave doesn't have a "None" object,
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# so we can't return any NaN outputs
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if np.isscalar(ans) and np.isnan(ans):
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ans = None
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return ans
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__doc__ = __doc__.format(
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OCTAVE_DOC = ' '*8 + OctaveMagics.octave.__doc__,
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OCTAVE_PUSH_DOC = ' '*8 + OctaveMagics.octave_push.__doc__,
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OCTAVE_PULL_DOC = ' '*8 + OctaveMagics.octave_pull.__doc__
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)
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def load_ipython_extension(ip):
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"""Load the extension in IPython."""
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ip.register_magics(OctaveMagics)
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