564 lines
17 KiB
Python
564 lines
17 KiB
Python
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"""
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A special directive for generating a matplotlib plot.
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.. warning::
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This is a hacked version of plot_directive.py from Matplotlib.
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It's very much subject to change!
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Usage
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-----
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Can be used like this::
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.. plot:: examples/example.py
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.. plot::
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import matplotlib.pyplot as plt
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plt.plot([1,2,3], [4,5,6])
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.. plot::
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A plotting example:
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>>> import matplotlib.pyplot as plt
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>>> plt.plot([1,2,3], [4,5,6])
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The content is interpreted as doctest formatted if it has a line starting
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with ``>>>``.
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The ``plot`` directive supports the options
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format : {'python', 'doctest'}
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Specify the format of the input
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include-source : bool
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Whether to display the source code. Default can be changed in conf.py
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and the ``image`` directive options ``alt``, ``height``, ``width``,
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``scale``, ``align``, ``class``.
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Configuration options
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---------------------
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The plot directive has the following configuration options:
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plot_include_source
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Default value for the include-source option
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plot_pre_code
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Code that should be executed before each plot.
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plot_basedir
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Base directory, to which plot:: file names are relative to.
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(If None or empty, file names are relative to the directoly where
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the file containing the directive is.)
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plot_formats
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File formats to generate. List of tuples or strings::
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[(suffix, dpi), suffix, ...]
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that determine the file format and the DPI. For entries whose
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DPI was omitted, sensible defaults are chosen.
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TODO
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----
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* Refactor Latex output; now it's plain images, but it would be nice
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to make them appear side-by-side, or in floats.
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"""
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import sys, os, glob, shutil, imp, warnings, cStringIO, re, textwrap, traceback
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import sphinx
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import warnings
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warnings.warn("A plot_directive module is also available under "
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"matplotlib.sphinxext; expect this numpydoc.plot_directive "
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"module to be deprecated after relevant features have been "
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"integrated there.",
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FutureWarning, stacklevel=2)
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#------------------------------------------------------------------------------
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# Registration hook
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#------------------------------------------------------------------------------
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def setup(app):
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setup.app = app
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setup.config = app.config
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setup.confdir = app.confdir
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app.add_config_value('plot_pre_code', '', True)
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app.add_config_value('plot_include_source', False, True)
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app.add_config_value('plot_formats', ['png', 'hires.png', 'pdf'], True)
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app.add_config_value('plot_basedir', None, True)
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app.add_directive('plot', plot_directive, True, (0, 1, False),
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**plot_directive_options)
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#------------------------------------------------------------------------------
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# plot:: directive
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#------------------------------------------------------------------------------
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from docutils.parsers.rst import directives
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from docutils import nodes
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def plot_directive(name, arguments, options, content, lineno,
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content_offset, block_text, state, state_machine):
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return run(arguments, content, options, state_machine, state, lineno)
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plot_directive.__doc__ = __doc__
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def _option_boolean(arg):
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if not arg or not arg.strip():
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# no argument given, assume used as a flag
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return True
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elif arg.strip().lower() in ('no', '0', 'false'):
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return False
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elif arg.strip().lower() in ('yes', '1', 'true'):
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return True
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else:
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raise ValueError('"%s" unknown boolean' % arg)
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def _option_format(arg):
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return directives.choice(arg, ('python', 'lisp'))
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def _option_align(arg):
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return directives.choice(arg, ("top", "middle", "bottom", "left", "center",
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"right"))
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plot_directive_options = {'alt': directives.unchanged,
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'height': directives.length_or_unitless,
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'width': directives.length_or_percentage_or_unitless,
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'scale': directives.nonnegative_int,
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'align': _option_align,
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'class': directives.class_option,
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'include-source': _option_boolean,
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'format': _option_format,
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}
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#------------------------------------------------------------------------------
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# Generating output
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#------------------------------------------------------------------------------
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from docutils import nodes, utils
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try:
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# Sphinx depends on either Jinja or Jinja2
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import jinja2
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def format_template(template, **kw):
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return jinja2.Template(template).render(**kw)
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except ImportError:
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import jinja
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def format_template(template, **kw):
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return jinja.from_string(template, **kw)
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TEMPLATE = """
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{{ source_code }}
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{{ only_html }}
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{% if source_code %}
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(`Source code <{{ source_link }}>`__)
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.. admonition:: Output
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:class: plot-output
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{% endif %}
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{% for img in images %}
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.. figure:: {{ build_dir }}/{{ img.basename }}.png
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{%- for option in options %}
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{{ option }}
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{% endfor %}
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(
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{%- if not source_code -%}
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`Source code <{{source_link}}>`__
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{%- for fmt in img.formats -%}
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, `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
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{%- endfor -%}
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{%- else -%}
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{%- for fmt in img.formats -%}
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{%- if not loop.first -%}, {% endif -%}
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`{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
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{%- endfor -%}
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{%- endif -%}
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)
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{% endfor %}
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{{ only_latex }}
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{% for img in images %}
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.. image:: {{ build_dir }}/{{ img.basename }}.pdf
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{% endfor %}
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"""
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class ImageFile(object):
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def __init__(self, basename, dirname):
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self.basename = basename
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self.dirname = dirname
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self.formats = []
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def filename(self, format):
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return os.path.join(self.dirname, "%s.%s" % (self.basename, format))
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def filenames(self):
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return [self.filename(fmt) for fmt in self.formats]
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def run(arguments, content, options, state_machine, state, lineno):
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if arguments and content:
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raise RuntimeError("plot:: directive can't have both args and content")
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document = state_machine.document
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config = document.settings.env.config
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options.setdefault('include-source', config.plot_include_source)
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# determine input
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rst_file = document.attributes['source']
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rst_dir = os.path.dirname(rst_file)
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if arguments:
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if not config.plot_basedir:
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source_file_name = os.path.join(rst_dir,
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directives.uri(arguments[0]))
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else:
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source_file_name = os.path.join(setup.confdir, config.plot_basedir,
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directives.uri(arguments[0]))
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code = open(source_file_name, 'r').read()
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output_base = os.path.basename(source_file_name)
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else:
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source_file_name = rst_file
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code = textwrap.dedent("\n".join(map(str, content)))
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counter = document.attributes.get('_plot_counter', 0) + 1
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document.attributes['_plot_counter'] = counter
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base, ext = os.path.splitext(os.path.basename(source_file_name))
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output_base = '%s-%d.py' % (base, counter)
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base, source_ext = os.path.splitext(output_base)
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if source_ext in ('.py', '.rst', '.txt'):
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output_base = base
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else:
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source_ext = ''
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# ensure that LaTeX includegraphics doesn't choke in foo.bar.pdf filenames
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output_base = output_base.replace('.', '-')
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# is it in doctest format?
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is_doctest = contains_doctest(code)
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if options.has_key('format'):
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if options['format'] == 'python':
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is_doctest = False
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else:
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is_doctest = True
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# determine output directory name fragment
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source_rel_name = relpath(source_file_name, setup.confdir)
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source_rel_dir = os.path.dirname(source_rel_name)
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while source_rel_dir.startswith(os.path.sep):
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source_rel_dir = source_rel_dir[1:]
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# build_dir: where to place output files (temporarily)
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build_dir = os.path.join(os.path.dirname(setup.app.doctreedir),
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'plot_directive',
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source_rel_dir)
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if not os.path.exists(build_dir):
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os.makedirs(build_dir)
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# output_dir: final location in the builder's directory
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dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir,
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source_rel_dir))
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# how to link to files from the RST file
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dest_dir_link = os.path.join(relpath(setup.confdir, rst_dir),
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source_rel_dir).replace(os.path.sep, '/')
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build_dir_link = relpath(build_dir, rst_dir).replace(os.path.sep, '/')
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source_link = dest_dir_link + '/' + output_base + source_ext
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# make figures
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try:
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images = makefig(code, source_file_name, build_dir, output_base,
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config)
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except PlotError, err:
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reporter = state.memo.reporter
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sm = reporter.system_message(
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3, "Exception occurred in plotting %s: %s" % (output_base, err),
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line=lineno)
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return [sm]
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# generate output restructuredtext
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if options['include-source']:
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if is_doctest:
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lines = ['']
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lines += [row.rstrip() for row in code.split('\n')]
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else:
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lines = ['.. code-block:: python', '']
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lines += [' %s' % row.rstrip() for row in code.split('\n')]
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source_code = "\n".join(lines)
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else:
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source_code = ""
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opts = [':%s: %s' % (key, val) for key, val in options.items()
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if key in ('alt', 'height', 'width', 'scale', 'align', 'class')]
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if sphinx.__version__ >= "0.6":
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only_html = ".. only:: html"
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only_latex = ".. only:: latex"
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else:
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only_html = ".. htmlonly::"
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only_latex = ".. latexonly::"
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result = format_template(
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TEMPLATE,
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dest_dir=dest_dir_link,
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build_dir=build_dir_link,
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source_link=source_link,
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only_html=only_html,
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only_latex=only_latex,
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options=opts,
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images=images,
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source_code=source_code)
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lines = result.split("\n")
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if len(lines):
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state_machine.insert_input(
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lines, state_machine.input_lines.source(0))
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# copy image files to builder's output directory
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if not os.path.exists(dest_dir):
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os.makedirs(dest_dir)
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for img in images:
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for fn in img.filenames():
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shutil.copyfile(fn, os.path.join(dest_dir, os.path.basename(fn)))
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# copy script (if necessary)
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if source_file_name == rst_file:
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target_name = os.path.join(dest_dir, output_base + source_ext)
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f = open(target_name, 'w')
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f.write(unescape_doctest(code))
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f.close()
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return []
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#------------------------------------------------------------------------------
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# Run code and capture figures
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#------------------------------------------------------------------------------
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import matplotlib
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matplotlib.use('Agg')
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import matplotlib.pyplot as plt
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import matplotlib.image as image
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from matplotlib import _pylab_helpers
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import exceptions
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def contains_doctest(text):
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try:
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# check if it's valid Python as-is
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compile(text, '<string>', 'exec')
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return False
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except SyntaxError:
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pass
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r = re.compile(r'^\s*>>>', re.M)
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m = r.search(text)
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return bool(m)
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def unescape_doctest(text):
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"""
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Extract code from a piece of text, which contains either Python code
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or doctests.
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"""
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if not contains_doctest(text):
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return text
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code = ""
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for line in text.split("\n"):
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m = re.match(r'^\s*(>>>|\.\.\.) (.*)$', line)
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if m:
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code += m.group(2) + "\n"
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elif line.strip():
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code += "# " + line.strip() + "\n"
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else:
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code += "\n"
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return code
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|
|
||
|
|
class PlotError(RuntimeError):
|
||
|
|
pass
|
||
|
|
|
||
|
|
def run_code(code, code_path):
|
||
|
|
# Change the working directory to the directory of the example, so
|
||
|
|
# it can get at its data files, if any.
|
||
|
|
pwd = os.getcwd()
|
||
|
|
old_sys_path = list(sys.path)
|
||
|
|
if code_path is not None:
|
||
|
|
dirname = os.path.abspath(os.path.dirname(code_path))
|
||
|
|
os.chdir(dirname)
|
||
|
|
sys.path.insert(0, dirname)
|
||
|
|
|
||
|
|
# Redirect stdout
|
||
|
|
stdout = sys.stdout
|
||
|
|
sys.stdout = cStringIO.StringIO()
|
||
|
|
|
||
|
|
# Reset sys.argv
|
||
|
|
old_sys_argv = sys.argv
|
||
|
|
sys.argv = [code_path]
|
||
|
|
|
||
|
|
try:
|
||
|
|
try:
|
||
|
|
code = unescape_doctest(code)
|
||
|
|
ns = {}
|
||
|
|
exec setup.config.plot_pre_code in ns
|
||
|
|
exec code in ns
|
||
|
|
except (Exception, SystemExit), err:
|
||
|
|
raise PlotError(traceback.format_exc())
|
||
|
|
finally:
|
||
|
|
os.chdir(pwd)
|
||
|
|
sys.argv = old_sys_argv
|
||
|
|
sys.path[:] = old_sys_path
|
||
|
|
sys.stdout = stdout
|
||
|
|
return ns
|
||
|
|
|
||
|
|
|
||
|
|
#------------------------------------------------------------------------------
|
||
|
|
# Generating figures
|
||
|
|
#------------------------------------------------------------------------------
|
||
|
|
|
||
|
|
def out_of_date(original, derived):
|
||
|
|
"""
|
||
|
|
Returns True if derivative is out-of-date wrt original,
|
||
|
|
both of which are full file paths.
|
||
|
|
"""
|
||
|
|
return (not os.path.exists(derived)
|
||
|
|
or os.stat(derived).st_mtime < os.stat(original).st_mtime)
|
||
|
|
|
||
|
|
|
||
|
|
def makefig(code, code_path, output_dir, output_base, config):
|
||
|
|
"""
|
||
|
|
Run a pyplot script *code* and save the images under *output_dir*
|
||
|
|
with file names derived from *output_base*
|
||
|
|
|
||
|
|
"""
|
||
|
|
|
||
|
|
# -- Parse format list
|
||
|
|
default_dpi = {'png': 80, 'hires.png': 200, 'pdf': 50}
|
||
|
|
formats = []
|
||
|
|
for fmt in config.plot_formats:
|
||
|
|
if isinstance(fmt, str):
|
||
|
|
formats.append((fmt, default_dpi.get(fmt, 80)))
|
||
|
|
elif type(fmt) in (tuple, list) and len(fmt)==2:
|
||
|
|
formats.append((str(fmt[0]), int(fmt[1])))
|
||
|
|
else:
|
||
|
|
raise PlotError('invalid image format "%r" in plot_formats' % fmt)
|
||
|
|
|
||
|
|
# -- Try to determine if all images already exist
|
||
|
|
|
||
|
|
# Look for single-figure output files first
|
||
|
|
all_exists = True
|
||
|
|
img = ImageFile(output_base, output_dir)
|
||
|
|
for format, dpi in formats:
|
||
|
|
if out_of_date(code_path, img.filename(format)):
|
||
|
|
all_exists = False
|
||
|
|
break
|
||
|
|
img.formats.append(format)
|
||
|
|
|
||
|
|
if all_exists:
|
||
|
|
return [img]
|
||
|
|
|
||
|
|
# Then look for multi-figure output files
|
||
|
|
images = []
|
||
|
|
all_exists = True
|
||
|
|
for i in xrange(1000):
|
||
|
|
img = ImageFile('%s_%02d' % (output_base, i), output_dir)
|
||
|
|
for format, dpi in formats:
|
||
|
|
if out_of_date(code_path, img.filename(format)):
|
||
|
|
all_exists = False
|
||
|
|
break
|
||
|
|
img.formats.append(format)
|
||
|
|
|
||
|
|
# assume that if we have one, we have them all
|
||
|
|
if not all_exists:
|
||
|
|
all_exists = (i > 0)
|
||
|
|
break
|
||
|
|
images.append(img)
|
||
|
|
|
||
|
|
if all_exists:
|
||
|
|
return images
|
||
|
|
|
||
|
|
# -- We didn't find the files, so build them
|
||
|
|
|
||
|
|
# Clear between runs
|
||
|
|
plt.close('all')
|
||
|
|
|
||
|
|
# Run code
|
||
|
|
run_code(code, code_path)
|
||
|
|
|
||
|
|
# Collect images
|
||
|
|
images = []
|
||
|
|
|
||
|
|
fig_managers = _pylab_helpers.Gcf.get_all_fig_managers()
|
||
|
|
for i, figman in enumerate(fig_managers):
|
||
|
|
if len(fig_managers) == 1:
|
||
|
|
img = ImageFile(output_base, output_dir)
|
||
|
|
else:
|
||
|
|
img = ImageFile("%s_%02d" % (output_base, i), output_dir)
|
||
|
|
images.append(img)
|
||
|
|
for format, dpi in formats:
|
||
|
|
try:
|
||
|
|
figman.canvas.figure.savefig(img.filename(format), dpi=dpi)
|
||
|
|
except exceptions.BaseException, err:
|
||
|
|
raise PlotError(traceback.format_exc())
|
||
|
|
img.formats.append(format)
|
||
|
|
|
||
|
|
return images
|
||
|
|
|
||
|
|
|
||
|
|
#------------------------------------------------------------------------------
|
||
|
|
# Relative pathnames
|
||
|
|
#------------------------------------------------------------------------------
|
||
|
|
|
||
|
|
try:
|
||
|
|
from os.path import relpath
|
||
|
|
except ImportError:
|
||
|
|
def relpath(target, base=os.curdir):
|
||
|
|
"""
|
||
|
|
Return a relative path to the target from either the current
|
||
|
|
dir or an optional base dir. Base can be a directory
|
||
|
|
specified either as absolute or relative to current dir.
|
||
|
|
"""
|
||
|
|
|
||
|
|
if not os.path.exists(target):
|
||
|
|
raise OSError, 'Target does not exist: '+target
|
||
|
|
|
||
|
|
if not os.path.isdir(base):
|
||
|
|
raise OSError, 'Base is not a directory or does not exist: '+base
|
||
|
|
|
||
|
|
base_list = (os.path.abspath(base)).split(os.sep)
|
||
|
|
target_list = (os.path.abspath(target)).split(os.sep)
|
||
|
|
|
||
|
|
# On the windows platform the target may be on a completely
|
||
|
|
# different drive from the base.
|
||
|
|
if os.name in ['nt','dos','os2'] and base_list[0] <> target_list[0]:
|
||
|
|
raise OSError, 'Target is on a different drive to base. Target: '+target_list[0].upper()+', base: '+base_list[0].upper()
|
||
|
|
|
||
|
|
# Starting from the filepath root, work out how much of the
|
||
|
|
# filepath is shared by base and target.
|
||
|
|
for i in range(min(len(base_list), len(target_list))):
|
||
|
|
if base_list[i] <> target_list[i]: break
|
||
|
|
else:
|
||
|
|
# If we broke out of the loop, i is pointing to the first
|
||
|
|
# differing path elements. If we didn't break out of the
|
||
|
|
# loop, i is pointing to identical path elements.
|
||
|
|
# Increment i so that in all cases it points to the first
|
||
|
|
# differing path elements.
|
||
|
|
i+=1
|
||
|
|
|
||
|
|
rel_list = [os.pardir] * (len(base_list)-i) + target_list[i:]
|
||
|
|
return os.path.join(*rel_list)
|