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"""A special directive for including a matplotlib plot.
The source code for the plot may be included in one of two 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)
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.
To customize the size of the plot, 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`.
Additionally, if the `:include-source:` option is provided, the
literal source will be displayed inline in the text, (as well as a
link to the source in HTML). If this source file is in a non-UTF8 or
non-ASCII encoding, the encoding must be specified using the
`:encoding:` option.
If the `:context:` option is plotted, 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.
If the ``:nofigs:`` option is specified, the code block will be run,
but no figures will be inserted. This is usually useful with the
``:context:`` option.
The set of file formats to generate can be specified with the
`plot_formats` configuration variable.
Error handling:
Any errors generated during the running of the code are emitted as warnings
using the Python `warnings` module, using a custom category called
`PlotWarning`. To turn the warnings into fatal errors that stop the
documentation build, after adjusting your `sys.path` in your `conf.py` Sphinx
configuration file, use::
import plot_directive
warnings.simplefilter('error', plot_directive.PlotWarning)
"""
import sys, os, shutil, imp, warnings, cStringIO, re
try:
from hashlib import md5
except ImportError:
from md5 import md5
from docutils.parsers.rst import directives
try:
# docutils 0.4
from docutils.parsers.rst.directives.images import align
except ImportError:
# docutils 0.5
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]])
import matplotlib
import matplotlib.cbook as cbook
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.image as image
from matplotlib import _pylab_helpers
from matplotlib.sphinxext import only_directives
class PlotWarning(Warning):
"""Warning category for all warnings generated by this directive.
By printing our warnings with this category, it becomes possible to turn
them into errors by using in your conf.py::
warnings.simplefilter('error', plot_directive.PlotWarning)
This way, you can ensure that your docs only build if all your examples
actually run successfully.
"""
pass
# os.path.relpath is new in Python 2.6
if hasattr(os.path, 'relpath'):
relpath = os.path.relpath
else:
# This code is snagged from Python 2.6
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:]
if rel_list:
return os.path.join(*rel_list)
else:
return ""
template = """
.. htmlonly::
%(links)s
.. figure:: %(prefix)s%(tmpdir)s/%(outname)s.png
%(options)s
%(caption)s
.. latexonly::
.. figure:: %(prefix)s%(tmpdir)s/%(outname)s.pdf
%(options)s
%(caption)s
"""
exception_template = """
.. htmlonly::
[`source code <%(linkdir)s/%(basename)s.py>`__]
Exception occurred rendering plot.
"""
template_content_indent = ' '
# the context of the plot for all directives specified with the
# :context: option
plot_context = dict()
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))
def run_code(plot_path, function_name, plot_code, context=False):
"""
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.
if plot_code is not None:
exec_code = 'import numpy as np; import matplotlib.pyplot as plt\n%s'%plot_code
#print 'CONTEXT', context, plot_context, exec_code
if context:
exec(exec_code, None, plot_context)
else:
exec(exec_code)
else:
pwd = os.getcwd()
path, fname = os.path.split(plot_path)
sys.path.insert(0, os.path.abspath(path))
stdout = sys.stdout
sys.stdout = cStringIO.StringIO()
os.chdir(path)
fd = None
try:
fd = open(fname)
module = imp.load_module(
"__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
finally:
del sys.path[0]
os.chdir(pwd)
sys.stdout = stdout
if fd is not None:
fd.close()
if function_name is not None:
getattr(module, function_name)()
def run_savefig(plot_path, basename, tmpdir, destdir, formats):
"""
Once a plot script has been imported, this function runs savefig
on all of the figures in all of the desired formats.
"""
fig_managers = _pylab_helpers.Gcf.get_all_fig_managers()
for i, figman in enumerate(fig_managers):
for j, (format, dpi) in enumerate(formats):
if len(fig_managers) == 1:
outname = basename
else:
outname = "%s_%02d" % (basename, i)
outname = outname + "." + format
outpath = os.path.join(tmpdir, outname)
try:
figman.canvas.figure.savefig(outpath, dpi=dpi)
except:
s = cbook.exception_to_str("Exception saving plot %s" % plot_path)
warnings.warn(s, PlotWarning)
return 0
if j > 0:
shutil.copyfile(outpath, os.path.join(destdir, outname))
return len(fig_managers)
def clear_state():
plt.close('all')
matplotlib.rc_file_defaults()
def render_figures(plot_path, function_name, plot_code, tmpdir, destdir,
formats, context=False):
"""
Run a pyplot script and save the low and high res PNGs and a PDF
in outdir.
"""
plot_path = str(plot_path) # todo, why is unicode breaking this
basedir, fname = os.path.split(plot_path)
basename, ext = os.path.splitext(fname)
all_exists = True
# Look for single-figure output files first
for format, dpi in formats:
outname = os.path.join(tmpdir, '%s.%s' % (basename, format))
if out_of_date(plot_path, outname):
all_exists = False
break
if not context and all_exists:
return 1
# Then look for multi-figure output files, assuming
# if we have some we have all...
i = 0
while True:
all_exists = True
for format, dpi in formats:
outname = os.path.join(
tmpdir, '%s_%02d.%s' % (basename, i, format))
if out_of_date(plot_path, outname):
all_exists = False
break
if all_exists:
i += 1
else:
break
if not context and i != 0:
return i
# We didn't find the files, so build them
if not context:
clear_state()
try:
run_code(plot_path, function_name, plot_code, context=context)
except:
s = cbook.exception_to_str("Exception running plot %s" % plot_path)
warnings.warn(s, PlotWarning)
return 0
if not all_exists:
num_figs = run_savefig(plot_path, basename, tmpdir, destdir, formats)
if '__plot__' in sys.modules:
del sys.modules['__plot__']
return num_figs
else:
return 1
def _plot_directive(plot_path, basedir, function_name, plot_code, caption,
options, state_machine):
context = options.has_key('context')
if context:
# remove for figure directive
del options['context']
nofigs = options.has_key('nofigs')
if nofigs:
# remove for figure directive
del options['nofigs']
formats = setup.config.plot_formats
if type(formats) == str or type(formats) == unicode:
formats = eval(formats)
fname = os.path.basename(plot_path)
basename, ext = os.path.splitext(fname)
# Get the directory of the rst file, and determine the relative
# path from the resulting html file to the plot_directive links
# (linkdir). This relative path is used for html links *only*,
# and not the embedded image. That is given an absolute path to
# the temporary directory, and then sphinx moves the file to
# build/html/_images for us later.
rstdir, rstfile = os.path.split(state_machine.document.attributes['source'])
outdir = os.path.join('plot_directive', basedir)
reldir = relpath(setup.confdir, rstdir)
linkdir = os.path.join(reldir, outdir)
# tmpdir is where we build all the output files. This way the
# plots won't have to be redone when generating latex after html.
# Prior to Sphinx 0.6, absolute image paths were treated as
# relative to the root of the filesystem. 0.6 and after, they are
# treated as relative to the root of the documentation tree. We
# need to support both methods here.
tmpdir = os.path.join('build', outdir)
tmpdir = os.path.abspath(tmpdir)
if sphinx_version < (0, 6):
prefix = ''
else:
prefix = '/'
if not os.path.exists(tmpdir):
cbook.mkdirs(tmpdir)
# destdir is the directory within the output to store files
# that we'll be linking to -- not the embedded images.
destdir = os.path.abspath(os.path.join(setup.app.builder.outdir, outdir))
if not os.path.exists(destdir):
cbook.mkdirs(destdir)
# Properly indent the caption
caption = '\n'.join(template_content_indent + line.strip()
for line in caption.split('\n'))
# Generate the figures, and return the number of them
num_figs = render_figures(plot_path, function_name, plot_code, tmpdir,
destdir, formats, context=context)
# Now start generating the lines of output
lines = []
if plot_code is None:
shutil.copyfile(plot_path, os.path.join(destdir, fname))
if options.has_key('include-source'):
if plot_code is None:
if sphinx_version > (1,):
include_prefix = '/'
else:
include_prefix = setup.app.builder.srcdir
lines.extend(
['.. include:: %s' % os.path.join(include_prefix, plot_path),
' :literal:'])
if options.has_key('encoding'):
lines.append(' :encoding: %s' % options['encoding'])
del options['encoding']
else:
lines.extend(['::', ''])
lines.extend([' %s' % row.rstrip()
for row in plot_code.split('\n')])
lines.append('')
del options['include-source']
else:
lines = []
if not nofigs:
if num_figs > 0:
options = ['%s:%s: %s' % (template_content_indent, key, val)
for key, val in options.items()]
options = "\n".join(options)
for i in range(num_figs):
if num_figs == 1:
outname = basename
else:
outname = "%s_%02d" % (basename, i)
# Copy the linked-to files to the destination within the build tree,
# and add a link for them
links = []
if plot_code is None:
links.append('`source code <%(linkdir)s/%(basename)s.py>`__')
for format, dpi in formats[1:]:
links.append('`%s <%s/%s.%s>`__' % (format, linkdir, outname, format))
if len(links):
links = '[%s]' % (', '.join(links) % locals())
else:
links = ''
lines.extend((template % locals()).split('\n'))
else:
lines.extend((exception_template % locals()).split('\n'))
if len(lines):
state_machine.insert_input(
lines, state_machine.input_lines.source(0))
return []
def plot_directive(name, arguments, options, content, lineno,
content_offset, block_text, state, state_machine):
"""
Handle the arguments to the plot directive. The real work happens
in _plot_directive.
"""
# The user may provide a filename *or* Python code content, but not both
if len(arguments):
plot_path = directives.uri(arguments[0])
basedir = relpath(os.path.dirname(plot_path), setup.app.builder.srcdir)
# If there is content, it will be passed as a caption.
# Indent to match expansion below. XXX - The number of spaces matches
# that of the 'options' expansion further down. This should be moved
# to common code to prevent them from diverging accidentally.
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
return _plot_directive(plot_path, basedir, function_name, None, caption,
options, state_machine)
else:
plot_code = '\n'.join(content)
# Since we don't have a filename, use a hash based on the content
plot_path = md5(plot_code).hexdigest()[-10:]
return _plot_directive(plot_path, 'inline', None, plot_code, '', options,
state_machine)
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': align,
'class': directives.class_option,
'include-source': directives.flag,
'context': directives.flag,
'nofigs': directives.flag,
'encoding': directives.encoding }
app.add_directive('plot', plot_directive, True, (0, 2, 0), **options)
app.add_config_value(
'plot_formats',
[('png', 80), ('hires.png', 200), ('pdf', 50)],
True)
app.connect('doctree-read', mark_plot_labels)