""" A directive for including a matplotlib plot in a Sphinx document. By default, in HTML output, `plot` will include a .png file with a link to a high-res .png and .pdf. In LaTeX output, it will include a .pdf. The source code for the plot may be included in one of three ways: 1. **A path to a source file** as the argument to the directive:: .. plot:: path/to/plot.py When a path to a source file is given, the content of the directive may optionally contain a caption for the plot:: .. plot:: path/to/plot.py This is the caption for the plot Additionally, one my specify the name of a function to call (with no arguments) immediately after importing the module:: .. plot:: path/to/plot.py plot_function1 2. Included as **inline content** to the directive:: .. plot:: import matplotlib.pyplot as plt import matplotlib.image as mpimg import numpy as np img = mpimg.imread('_static/stinkbug.png') imgplot = plt.imshow(img) 3. Using **doctest** syntax:: .. plot:: A plotting example: >>> import matplotlib.pyplot as plt >>> plt.plot([1,2,3], [4,5,6]) Options ------- The ``plot`` directive supports the following options: format : {'python', 'doctest'} Specify the format of the input include-source : bool Whether to display the source code. The default can be changed using the `plot_include_source` variable in conf.py encoding : str If this source file is in a non-UTF8 or non-ASCII encoding, the encoding must be specified using the `:encoding:` option. The encoding will not be inferred using the ``-*- coding -*-`` metacomment. context : bool If provided, the code will be run in the context of all previous plot directives for which the `:context:` option was specified. This only applies to inline code plot directives, not those run from files. nofigs : bool If specified, the code block will be run, but no figures will be inserted. This is usually useful with the ``:context:`` option. Additionally, this directive supports all of the options of the `image` directive, except for `target` (since plot will add its own target). These include `alt`, `height`, `width`, `scale`, `align` and `class`. Configuration options --------------------- The plot directive has the following configuration options: plot_include_source Default value for the include-source option plot_pre_code Code that should be executed before each plot. plot_basedir Base directory, to which ``plot::`` file names are relative to. (If None or empty, file names are relative to the directoly where the file containing the directive is.) plot_formats File formats to generate. List of tuples or strings:: [(suffix, dpi), suffix, ...] that determine the file format and the DPI. For entries whose DPI was omitted, sensible defaults are chosen. plot_html_show_formats Whether to show links to the files in HTML. plot_rcparams A dictionary containing any non-standard rcParams that should be applied before each plot. """ import sys, os, glob, shutil, imp, warnings, cStringIO, re, textwrap, \ traceback, exceptions from docutils.parsers.rst import directives from docutils import nodes from docutils.parsers.rst.directives.images import Image align = Image.align import sphinx sphinx_version = sphinx.__version__.split(".") # The split is necessary for sphinx beta versions where the string is # '6b1' sphinx_version = tuple([int(re.split('[a-z]', x)[0]) for x in sphinx_version[:2]]) try: # Sphinx depends on either Jinja or Jinja2 import jinja2 def format_template(template, **kw): return jinja2.Template(template).render(**kw) except ImportError: import jinja def format_template(template, **kw): return jinja.from_string(template, **kw) import matplotlib import matplotlib.cbook as cbook matplotlib.use('Agg') import matplotlib.pyplot as plt from matplotlib import _pylab_helpers __version__ = 2 #------------------------------------------------------------------------------ # Relative pathnames #------------------------------------------------------------------------------ # os.path.relpath is new in Python 2.6 try: from os.path import relpath except ImportError: # Copied from Python 2.7 if 'posix' in sys.builtin_module_names: def relpath(path, start=os.path.curdir): """Return a relative version of a path""" from os.path import sep, curdir, join, abspath, commonprefix, \ pardir if not path: raise ValueError("no path specified") start_list = abspath(start).split(sep) path_list = abspath(path).split(sep) # Work out how much of the filepath is shared by start and path. i = len(commonprefix([start_list, path_list])) rel_list = [pardir] * (len(start_list)-i) + path_list[i:] if not rel_list: return curdir return join(*rel_list) elif 'nt' in sys.builtin_module_names: def relpath(path, start=os.path.curdir): """Return a relative version of a path""" from os.path import sep, curdir, join, abspath, commonprefix, \ pardir, splitunc if not path: raise ValueError("no path specified") start_list = abspath(start).split(sep) path_list = abspath(path).split(sep) if start_list[0].lower() != path_list[0].lower(): unc_path, rest = splitunc(path) unc_start, rest = splitunc(start) if bool(unc_path) ^ bool(unc_start): raise ValueError("Cannot mix UNC and non-UNC paths (%s and %s)" % (path, start)) else: raise ValueError("path is on drive %s, start on drive %s" % (path_list[0], start_list[0])) # Work out how much of the filepath is shared by start and path. for i in range(min(len(start_list), len(path_list))): if start_list[i].lower() != path_list[i].lower(): break else: i += 1 rel_list = [pardir] * (len(start_list)-i) + path_list[i:] if not rel_list: return curdir return join(*rel_list) else: raise RuntimeError("Unsupported platform (no relpath available!)") #------------------------------------------------------------------------------ # Registration hook #------------------------------------------------------------------------------ def plot_directive(name, arguments, options, content, lineno, content_offset, block_text, state, state_machine): return run(arguments, content, options, state_machine, state, lineno) plot_directive.__doc__ = __doc__ def _option_boolean(arg): if not arg or not arg.strip(): # no argument given, assume used as a flag return True elif arg.strip().lower() in ('no', '0', 'false'): return False elif arg.strip().lower() in ('yes', '1', 'true'): return True else: raise ValueError('"%s" unknown boolean' % arg) def _option_format(arg): return directives.choice(arg, ('python', 'doctest')) def _option_align(arg): return directives.choice(arg, ("top", "middle", "bottom", "left", "center", "right")) def mark_plot_labels(app, document): """ To make plots referenceable, we need to move the reference from the "htmlonly" (or "latexonly") node to the actual figure node itself. """ for name, explicit in document.nametypes.iteritems(): if not explicit: continue labelid = document.nameids[name] if labelid is None: continue node = document.ids[labelid] if node.tagname in ('html_only', 'latex_only'): for n in node: if n.tagname == 'figure': sectname = name for c in n: if c.tagname == 'caption': sectname = c.astext() break node['ids'].remove(labelid) node['names'].remove(name) n['ids'].append(labelid) n['names'].append(name) document.settings.env.labels[name] = \ document.settings.env.docname, labelid, sectname break def setup(app): setup.app = app setup.config = app.config setup.confdir = app.confdir options = {'alt': directives.unchanged, 'height': directives.length_or_unitless, 'width': directives.length_or_percentage_or_unitless, 'scale': directives.nonnegative_int, 'align': _option_align, 'class': directives.class_option, 'include-source': _option_boolean, 'format': _option_format, 'context': directives.flag, 'nofigs': directives.flag, 'encoding': directives.encoding } app.add_directive('plot', plot_directive, True, (0, 2, False), **options) app.add_config_value('plot_pre_code', None, True) app.add_config_value('plot_include_source', False, True) app.add_config_value('plot_formats', ['png', 'hires.png', 'pdf'], True) app.add_config_value('plot_basedir', None, True) app.add_config_value('plot_html_show_formats', True, True) app.add_config_value('plot_rcparams', {}, True) app.connect('doctree-read', mark_plot_labels) #------------------------------------------------------------------------------ # Doctest handling #------------------------------------------------------------------------------ def contains_doctest(text): try: # check if it's valid Python as-is compile(text, '', 'exec') return False except SyntaxError: pass r = re.compile(r'^\s*>>>', re.M) m = r.search(text) return bool(m) def unescape_doctest(text): """ Extract code from a piece of text, which contains either Python code or doctests. """ if not contains_doctest(text): return text code = "" for line in text.split("\n"): m = re.match(r'^\s*(>>>|\.\.\.) (.*)$', line) if m: code += m.group(2) + "\n" elif line.strip(): code += "# " + line.strip() + "\n" else: code += "\n" return code def split_code_at_show(text): """ Split code at plt.show() """ parts = [] is_doctest = contains_doctest(text) part = [] for line in text.split("\n"): if (not is_doctest and line.strip() == 'plt.show()') or \ (is_doctest and line.strip() == '>>> plt.show()'): part.append(line) parts.append("\n".join(part)) part = [] else: part.append(line) if "\n".join(part).strip(): parts.append("\n".join(part)) return parts #------------------------------------------------------------------------------ # Template #------------------------------------------------------------------------------ TEMPLATE = """ {{ source_code }} {{ only_html }} {% if source_link or (html_show_formats and not multi_image) %} ( {%- if source_link -%} `Source code <{{ source_link }}>`__ {%- endif -%} {%- if html_show_formats and not multi_image -%} {%- for img in images -%} {%- for fmt in img.formats -%} {%- if source_link or not loop.first -%}, {% endif -%} `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__ {%- endfor -%} {%- endfor -%} {%- endif -%} ) {% endif %} {% for img in images %} .. figure:: {{ build_dir }}/{{ img.basename }}.png {%- for option in options %} {{ option }} {% endfor %} {% if html_show_formats and multi_image -%} ( {%- for fmt in img.formats -%} {%- if not loop.first -%}, {% endif -%} `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__ {%- endfor -%} ) {%- endif -%} {{ caption }} {% endfor %} {{ only_latex }} {% for img in images %} .. image:: {{ build_dir }}/{{ img.basename }}.pdf {% endfor %} """ exception_template = """ .. htmlonly:: [`source code <%(linkdir)s/%(basename)s.py>`__] Exception occurred rendering plot. """ # the context of the plot for all directives specified with the # :context: option plot_context = dict() class ImageFile(object): def __init__(self, basename, dirname): self.basename = basename self.dirname = dirname self.formats = [] def filename(self, format): return os.path.join(self.dirname, "%s.%s" % (self.basename, format)) def filenames(self): return [self.filename(fmt) for fmt in self.formats] 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.path.exists(original) and os.stat(derived).st_mtime < os.stat(original).st_mtime)) class PlotError(RuntimeError): pass def run_code(code, code_path, ns=None, function_name=None): """ Import a Python module from a path, and run the function given by name, if function_name is not None. """ # Change the working directory to the directory of the example, so # it can get at its data files, if any. Add its path to sys.path # so it can import any helper modules sitting beside it. 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) if ns is None: ns = {} if not ns: if setup.config.plot_pre_code is None: exec "import numpy as np\nfrom matplotlib import pyplot as plt\n" in ns else: exec setup.config.plot_pre_code in ns if "__main__" in code: exec "__name__ = '__main__'" in ns exec code in ns if function_name is not None: exec function_name + "()" 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 def clear_state(plot_rcparams): plt.close('all') matplotlib.rc_file_defaults() matplotlib.rcParams.update(plot_rcparams) def render_figures(code, code_path, output_dir, output_base, context, function_name, config): """ Run a pyplot script and save the low and high res PNGs and a PDF in outdir. Save the images under *output_dir* with file names derived from *output_base* """ # -- Parse format list default_dpi = {'png': 80, 'hires.png': 200, 'pdf': 200} formats = [] plot_formats = config.plot_formats if isinstance(plot_formats, (str, unicode)): plot_formats = eval(plot_formats) for fmt in 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 code_pieces = split_code_at_show(code) # Look for single-figure output files first # 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 [(code, [img])] # Then look for multi-figure output files results = [] all_exists = True for i, code_piece in enumerate(code_pieces): images = [] for j in xrange(1000): if len(code_pieces) > 1: img = ImageFile('%s_%02d_%02d' % (output_base, i, j), output_dir) else: img = ImageFile('%s_%02d' % (output_base, j), 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 = (j > 0) break images.append(img) if not all_exists: break results.append((code_piece, images)) if all_exists: return results # We didn't find the files, so build them results = [] if context: ns = plot_context else: ns = {} for i, code_piece in enumerate(code_pieces): if not context: clear_state(config.plot_rcparams) run_code(code_piece, code_path, ns, function_name) images = [] fig_managers = _pylab_helpers.Gcf.get_all_fig_managers() for j, figman in enumerate(fig_managers): if len(fig_managers) == 1 and len(code_pieces) == 1: img = ImageFile(output_base, output_dir) elif len(code_pieces) == 1: img = ImageFile("%s_%02d" % (output_base, j), output_dir) else: img = ImageFile("%s_%02d_%02d" % (output_base, i, j), output_dir) images.append(img) for format, dpi in formats: try: figman.canvas.figure.savefig(img.filename(format), dpi=dpi) except Exception,err: raise PlotError(traceback.format_exc()) img.formats.append(format) results.append((code_piece, images)) if not context: clear_state(config.plot_rcparams) return results def run(arguments, content, options, state_machine, state, lineno): # The user may provide a filename *or* Python code content, but not both if arguments and content: raise RuntimeError("plot:: directive can't have both args and content") document = state_machine.document config = document.settings.env.config nofigs = options.has_key('nofigs') options.setdefault('include-source', config.plot_include_source) context = options.has_key('context') rst_file = document.attributes['source'] rst_dir = os.path.dirname(rst_file) if len(arguments): if not config.plot_basedir: source_file_name = os.path.join(setup.app.builder.srcdir, directives.uri(arguments[0])) else: source_file_name = os.path.join(setup.app.builder.srcdir, config.plot_basedir, directives.uri(arguments[0])) # If there is content, it will be passed as a caption. caption = '\n'.join(content) # If the optional function name is provided, use it if len(arguments) == 2: function_name = arguments[1] else: function_name = None fd = open(source_file_name, 'r') code = fd.read() fd.close() output_base = os.path.basename(source_file_name) else: source_file_name = rst_file code = textwrap.dedent("\n".join(map(str, content))) counter = document.attributes.get('_plot_counter', 0) + 1 document.attributes['_plot_counter'] = counter base, ext = os.path.splitext(os.path.basename(source_file_name)) output_base = '%s-%d.py' % (base, counter) function_name = None caption = '' base, source_ext = os.path.splitext(output_base) if source_ext in ('.py', '.rst', '.txt'): output_base = base else: source_ext = '' # ensure that LaTeX includegraphics doesn't choke in foo.bar.pdf filenames output_base = output_base.replace('.', '-') # is it in doctest format? is_doctest = contains_doctest(code) if options.has_key('format'): if options['format'] == 'python': is_doctest = False else: is_doctest = True # determine output directory name fragment source_rel_name = relpath(source_file_name, setup.app.srcdir) source_rel_dir = os.path.dirname(source_rel_name) while source_rel_dir.startswith(os.path.sep): source_rel_dir = source_rel_dir[1:] # build_dir: where to place output files (temporarily) build_dir = os.path.join(os.path.dirname(setup.app.doctreedir), 'plot_directive', source_rel_dir) # get rid of .. in paths, also changes pathsep # see note in Python docs for warning about symbolic links on Windows. # need to compare source and dest paths at end build_dir = os.path.normpath(build_dir) if not os.path.exists(build_dir): os.makedirs(build_dir) # output_dir: final location in the builder's directory dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir, source_rel_dir)) if not os.path.exists(dest_dir): os.makedirs(dest_dir) # no problem here for me, but just use built-ins # how to link to files from the RST file dest_dir_link = os.path.join(relpath(setup.app.srcdir, rst_dir), source_rel_dir).replace(os.path.sep, '/') build_dir_link = relpath(build_dir, rst_dir).replace(os.path.sep, '/') source_link = dest_dir_link + '/' + output_base + source_ext # make figures try: results = render_figures(code, source_file_name, build_dir, output_base, context, function_name, config) errors = [] except PlotError, err: reporter = state.memo.reporter sm = reporter.system_message( 2, "Exception occurred in plotting %s\n from %s:\n%s" % (output_base, source_file_name, err), line=lineno) results = [(code, [])] errors = [sm] # Properly indent the caption caption = '\n'.join(' ' + line.strip() for line in caption.split('\n')) # generate output restructuredtext total_lines = [] for j, (code_piece, images) in enumerate(results): if options['include-source']: if is_doctest: lines = [''] lines += [row.rstrip() for row in code_piece.split('\n')] else: lines = ['.. code-block:: python', ''] lines += [' %s' % row.rstrip() for row in code_piece.split('\n')] source_code = "\n".join(lines) else: source_code = "" if nofigs: images = [] opts = [':%s: %s' % (key, val) for key, val in options.items() if key in ('alt', 'height', 'width', 'scale', 'align', 'class')] only_html = ".. only:: html" only_latex = ".. only:: latex" if j == 0: src_link = source_link else: src_link = None result = format_template( TEMPLATE, dest_dir=dest_dir_link, build_dir=build_dir_link, source_link=src_link, multi_image=len(images) > 1, only_html=only_html, only_latex=only_latex, options=opts, images=images, source_code=source_code, html_show_formats=config.plot_html_show_formats, caption=caption) total_lines.extend(result.split("\n")) total_lines.extend("\n") if total_lines: state_machine.insert_input(total_lines, source=source_file_name) # copy image files to builder's output directory, if necessary if not os.path.exists(dest_dir): cbook.mkdirs(dest_dir) for code_piece, images in results: for img in images: for fn in img.filenames(): destimg = os.path.join(dest_dir, os.path.basename(fn)) if fn != destimg: shutil.copyfile(fn, destimg) # copy script (if necessary) #if source_file_name == rst_file: target_name = os.path.join(dest_dir, output_base + source_ext) f = open(target_name, 'w') f.write(unescape_doctest(code)) f.close() return errors