mirror of
https://github.com/wassname/scikit-image.git
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Example generation from scripts, taken from scikit learn
(ext/gen_rst.py)
This commit is contained in:
Emmanuelle Gouillart
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General examples
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-------------------
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General-purpose and introductory examples for the scikit.
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"""
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====================================================
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Denoising the picture of Lena using total variation
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====================================================
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In this example, we denoise a noisy version of the picture of Lena using the
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total variation denoising filter. The result of this filter is an image that
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has a minimal total variation norm, while being as close to the initial image
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as possible. The total variation is the L1 norm of the gradient of the image,
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and minimizing the total variation typically produces "posterized" images with
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flat domains separated by sharp edges.
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It is possible to change the degree of posterization by controlling the
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tradeoff between denoising and faithfulness to the original image.
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"""
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import numpy as np
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import scipy
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from scipy import ndimage
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import matplotlib.pyplot as plt
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from scikits.image.filter import tv_denoise
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l = scipy.lena()
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l = l[230:290, 220:320]
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noisy = l + 0.4*l.std()*np.random.random(l.shape)
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tv_denoised = tv_denoise(noisy, weight=10)
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plt.figure(figsize=(12,2.8))
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plt.subplot(131)
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plt.imshow(noisy, cmap=plt.cm.gray, vmin=40, vmax=220)
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plt.axis('off')
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plt.title('noisy', fontsize=20)
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plt.subplot(132)
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plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
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plt.axis('off')
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plt.title('TV denoising', fontsize=20)
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tv_denoised = tv_denoise(noisy, weight=50)
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plt.subplot(133)
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plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
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plt.axis('off')
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plt.title('(more) TV denoising', fontsize=20)
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plt.subplots_adjust(wspace=0.02, hspace=0.02, top=0.9, bottom=0, left=0,
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right=1)
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@@ -0,0 +1,303 @@
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"""
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Example generation for the scikit learn
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Generate the rst files for the examples by iterating over the python
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example files.
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Files that generate images should start with 'plot'
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"""
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import os
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import shutil
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import traceback
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import glob
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import matplotlib
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matplotlib.use('Agg')
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import token, tokenize
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rst_template = """
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.. _example_%(short_fname)s:
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%(docstring)s
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**Python source code:** :download:`%(fname)s <%(fname)s>`
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.. literalinclude:: %(fname)s
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:lines: %(end_row)s-
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"""
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plot_rst_template = """
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.. _example_%(short_fname)s:
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%(docstring)s
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%(image_list)s
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**Python source code:** :download:`%(fname)s <%(fname)s>`
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.. literalinclude:: %(fname)s
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:lines: %(end_row)s-
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"""
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# The following strings are used when we have several pictures: we use
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# an html div tag that our CSS uses to turn the lists into horizontal
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# lists.
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HLIST_HEADER = """
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.. rst-class:: horizontal
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"""
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HLIST_IMAGE_TEMPLATE = """
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*
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.. image:: images/%s
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:scale: 50
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"""
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SINGLE_IMAGE = """
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.. image:: images/%s
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:align: center
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"""
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def extract_docstring(filename):
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""" Extract a module-level docstring, if any
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"""
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lines = file(filename).readlines()
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start_row = 0
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if lines[0].startswith('#!'):
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lines.pop(0)
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start_row = 1
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docstring = ''
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first_par = ''
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tokens = tokenize.generate_tokens(lines.__iter__().next)
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for tok_type, tok_content, _, (erow, _), _ in tokens:
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tok_type = token.tok_name[tok_type]
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if tok_type in ('NEWLINE', 'COMMENT', 'NL', 'INDENT', 'DEDENT'):
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continue
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elif tok_type == 'STRING':
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docstring = eval(tok_content)
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# If the docstring is formatted with several paragraphs, extract
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# the first one:
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paragraphs = '\n'.join(line.rstrip()
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for line in docstring.split('\n')).split('\n\n')
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if len(paragraphs) > 0:
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first_par = paragraphs[0]
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break
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return docstring, first_par, erow+1+start_row
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def generate_example_rst(app):
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""" Generate the list of examples, as well as the contents of
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examples.
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"""
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root_dir = os.path.join(app.builder.srcdir, 'auto_examples')
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example_dir = os.path.abspath(app.builder.srcdir + '/../' + 'examples')
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try:
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plot_gallery = eval(app.builder.config.plot_gallery)
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except TypeError:
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plot_gallery = bool(app.builder.config.plot_gallery)
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if not os.path.exists(example_dir):
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os.makedirs(example_dir)
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if not os.path.exists(root_dir):
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os.makedirs(root_dir)
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# we create an index.rst with all examples
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fhindex = file(os.path.join(root_dir, 'index.txt'), 'w')
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fhindex.write("""\
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.. raw:: html
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<style type="text/css">
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.figure {
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float: left;
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margin: 10px;
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width: auto;
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height: 200px;
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width: 180px;
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}
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.figure img {
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display: inline;
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}
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.figure .caption {
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width: 170px;
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text-align: center !important;
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}
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</style>
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Examples
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========
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.. _examples-index:
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""")
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# Here we don't use an os.walk, but we recurse only twice: flat is
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# better than nested.
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generate_dir_rst('.', fhindex, example_dir, root_dir, plot_gallery)
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for dir in sorted(os.listdir(example_dir)):
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if os.path.isdir(os.path.join(example_dir, dir)):
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generate_dir_rst(dir, fhindex, example_dir, root_dir, plot_gallery)
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fhindex.flush()
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def generate_dir_rst(dir, fhindex, example_dir, root_dir, plot_gallery):
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""" Generate the rst file for an example directory.
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"""
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if not dir == '.':
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target_dir = os.path.join(root_dir, dir)
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src_dir = os.path.join(example_dir, dir)
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else:
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target_dir = root_dir
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src_dir = example_dir
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if not os.path.exists(os.path.join(src_dir, 'README.txt')):
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print 80*'_'
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print ('Example directory %s does not have a README.txt file'
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% src_dir)
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print 'Skipping this directory'
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print 80*'_'
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return
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fhindex.write("""
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%s
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""" % file(os.path.join(src_dir, 'README.txt')).read())
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if not os.path.exists(target_dir):
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os.makedirs(target_dir)
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def sort_key(a):
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# put last elements without a plot
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if not a.startswith('plot') and a.endswith('.py'):
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return 'zz' + a
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return a
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for fname in sorted(os.listdir(src_dir), key=sort_key):
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if fname.endswith('py'):
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generate_file_rst(fname, target_dir, src_dir, plot_gallery)
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thumb = os.path.join(dir, 'images', 'thumb', fname[:-3] + '.png')
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link_name = os.path.join(dir, fname).replace(os.path.sep, '_')
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fhindex.write('.. figure:: %s\n' % thumb)
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if link_name.startswith('._'):
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link_name = link_name[2:]
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if dir != '.':
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fhindex.write(' :target: ./%s/%s.html\n\n' % (dir, fname[:-3]))
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else:
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fhindex.write(' :target: ./%s.html\n\n' % link_name[:-3])
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fhindex.write(' :ref:`example_%s`\n\n' % link_name)
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fhindex.write("""
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.. raw:: html
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<div style="clear: both"></div>
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""") # clear at the end of the section
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def generate_file_rst(fname, target_dir, src_dir, plot_gallery):
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""" Generate the rst file for a given example.
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"""
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base_image_name = os.path.splitext(fname)[0]
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image_fname = '%s_%%s.png' % base_image_name
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this_template = rst_template
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last_dir = os.path.split(src_dir)[-1]
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# to avoid leading . in file names, and wrong names in links
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if last_dir == '.' or last_dir == 'examples':
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last_dir = ''
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else:
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last_dir += '_'
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short_fname = last_dir + fname
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src_file = os.path.join(src_dir, fname)
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example_file = os.path.join(target_dir, fname)
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shutil.copyfile(src_file, example_file)
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# The following is a list containing all the figure names
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figure_list = []
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image_dir = os.path.join(target_dir, 'images')
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thumb_dir = os.path.join(image_dir, 'thumb')
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if not os.path.exists(image_dir):
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os.makedirs(image_dir)
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if not os.path.exists(thumb_dir):
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os.makedirs(thumb_dir)
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image_path = os.path.join(image_dir, image_fname)
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thumb_file = os.path.join(thumb_dir, fname[:-3] + '.png')
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if plot_gallery and fname.startswith('plot'):
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# generate the plot as png image if file name
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# starts with plot and if it is more recent than an
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# existing image.
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first_image_file = image_path % 1
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if (not os.path.exists(first_image_file) or
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os.stat(first_image_file).st_mtime <=
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os.stat(src_file).st_mtime):
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# We need to execute the code
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print 'plotting %s' % fname
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import matplotlib.pyplot as plt
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plt.close('all')
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cwd = os.getcwd()
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try:
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# First CD in the original example dir, so that any file created
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# by the example get created in this directory
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os.chdir(os.path.dirname(src_file))
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execfile(os.path.basename(src_file), {'pl' : plt})
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os.chdir(cwd)
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# In order to save every figure we have two solutions :
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# * iterate from 1 to infinity and call plt.fignum_exists(n)
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# (this requires the figures to be numbered
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# incrementally: 1, 2, 3 and not 1, 2, 5)
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# * iterate over [fig_mngr.num for fig_mngr in
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# matplotlib._pylab_helpers.Gcf.get_all_fig_managers()]
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for fig_num in (fig_mngr.num for fig_mngr in
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matplotlib._pylab_helpers.Gcf.get_all_fig_managers()):
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# Set the fig_num figure as the current figure as we can't
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# save a figure that's not the current figure.
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plt.figure(fig_num)
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plt.savefig(image_path % fig_num)
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figure_list.append(image_fname % fig_num)
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except:
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print 80*'_'
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print '%s is not compiling:' % fname
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traceback.print_exc()
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print 80*'_'
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finally:
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os.chdir(cwd)
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else:
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figure_list = [f[len(image_dir):]
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for f in glob.glob(image_path % '[1-9]')]
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#for f in glob.glob(image_path % '*')]
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# generate thumb file
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this_template = plot_rst_template
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from matplotlib import image
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if os.path.exists(first_image_file):
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image.thumbnail(first_image_file, thumb_file, 0.2)
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if not os.path.exists(thumb_file):
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# create something not to replace the thumbnail
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shutil.copy('images/blank_image.png', thumb_file)
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docstring, short_desc, end_row = extract_docstring(example_file)
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# Depending on whether we have one or more figures, we're using a
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# horizontal list or a single rst call to 'image'.
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if len(figure_list) == 1:
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figure_name = figure_list[0]
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image_list = SINGLE_IMAGE % figure_name.lstrip('/')
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else:
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image_list = HLIST_HEADER
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for figure_name in figure_list:
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image_list += HLIST_IMAGE_TEMPLATE % figure_name.lstrip('/')
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f = open(os.path.join(target_dir, fname[:-2] + 'txt'),'w')
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f.write(this_template % locals())
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f.flush()
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def setup(app):
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app.connect('builder-inited', generate_example_rst)
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app.add_config_value('plot_gallery', True, 'html')
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+7
-1
@@ -23,11 +23,17 @@ sys.path.append(os.path.join(curpath, '..', 'ext'))
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# -- General configuration -----------------------------------------------------
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try:
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import gen_rst
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except:
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pass
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# Add any Sphinx extension module names here, as strings. They can be extensions
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# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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extensions = ['sphinx.ext.autodoc', 'sphinx.ext.pngmath', 'numpydoc',
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'sphinx.ext.autosummary', 'sphinx.ext.inheritance_diagram',
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'plot_directive']
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'plot_directive', 'gen_rst']
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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@@ -39,6 +39,11 @@ Sections
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Conditions on the use and redistribution of this package.
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`Examples <auto_examples/index.html>`_
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Introductory examples
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Indices and Tables
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==================
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@@ -0,0 +1,51 @@
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"""
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====================================================
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Denoising the picture of Lena using total variation
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====================================================
|
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|
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In this example, we denoise a noisy version of the picture of Lena using the
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total variation denoising filter. The result of this filter is an image that
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has a minimal total variation norm, while being as close to the initial image
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as possible. The total variation is the L1 norm of the gradient of the image,
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and minimizing the total variation typically produces "posterized" images with
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flat domains separated by sharp edges.
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It is possible to change the degree of posterization by controlling the
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tradeoff between denoising and faithfulness to the original image.
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"""
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import numpy as np
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import scipy
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from scipy import ndimage
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import matplotlib.pyplot as plt
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from scikits.image.filter import tv_denoise
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l = scipy.lena()
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l = l[230:290, 220:320]
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noisy = l + 0.4*l.std()*np.random.random(l.shape)
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tv_denoised = tv_denoise(noisy, weight=10)
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plt.figure(figsize=(12,2.8))
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plt.subplot(131)
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plt.imshow(noisy, cmap=plt.cm.gray, vmin=40, vmax=220)
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plt.axis('off')
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plt.title('noisy', fontsize=20)
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plt.subplot(132)
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plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
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plt.axis('off')
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plt.title('TV denoising', fontsize=20)
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tv_denoised = tv_denoise(noisy, weight=50)
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plt.subplot(133)
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plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
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plt.axis('off')
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plt.title('(more) TV denoising', fontsize=20)
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plt.subplots_adjust(wspace=0.02, hspace=0.02, top=0.9, bottom=0, left=0,
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right=1)
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