mirror of
https://github.com/wassname/scikit-image.git
synced 2026-07-19 11:27:45 +08:00
Merge Emmanuelle's work on documentation examples / build.
This commit is contained in:
Stefan van der Walt
+5
-1
@@ -44,7 +44,8 @@
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Incorporating CellProfiler's Sobel edge detector, build and bug fixes.
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- Emmanuelle Guillart
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Total variation noise filtering
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Total variation noise filtering, integration of CellProfiler's
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mathematical morphology tools.
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- Maël Primet
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Total variation noise filtering
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@@ -60,3 +61,6 @@
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- Kyle Mandli
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CSV to ReST code for feature comparison table.
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- The Scikit Learn team
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From whom we borrowed the example generation tools.
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@@ -0,0 +1,6 @@
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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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@@ -0,0 +1,52 @@
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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
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using the total variation denoising filter. The result of this filter
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is an image that has a minimal total variation norm, while being as
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close to the initial image as possible. The total variation is the L1
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norm of the gradient of the image, and minimizing the total variation
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typically produces "posterized" images with flat domains separated by
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sharp edges.
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It is possible to change the degree of posterization by controlling
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the 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 matplotlib.pyplot as plt
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from scikits.image import data
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from scikits.image.filter import tv_denoise
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l = data.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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plt.show()
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@@ -66,3 +66,46 @@ products or services of Licensee, or any third party.
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8. By copying, installing or otherwise using matplotlib 0.98.3,
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Licensee agrees to be bound by the terms and conditions of this
|
||||
License Agreement.
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The file
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- gen_rst.py
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was taken from the scikit-learn (http://scikit-learn.sourceforge.net), which
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has the following license:
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New BSD License
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||||
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Copyright (c) 2007 - 2011 The scikit-learn developers.
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All rights reserved.
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||||
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||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions are met:
|
||||
|
||||
a. Redistributions of source code must retain the above copyright notice,
|
||||
this list of conditions and the following disclaimer.
|
||||
b. Redistributions in binary form must reproduce the above copyright
|
||||
notice, this list of conditions and the following disclaimer in the
|
||||
documentation and/or other materials provided with the distribution.
|
||||
c. Neither the name of the Scikit-learn Developers nor the names of
|
||||
its contributors may be used to endorse or promote products
|
||||
derived from this software without specific prior written
|
||||
permission.
|
||||
|
||||
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||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||
ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
|
||||
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
||||
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
|
||||
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
|
||||
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
|
||||
DAMAGE.
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|
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@@ -0,0 +1,305 @@
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"""
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Example generation for the scikit image.
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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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This code was taken from the scikit-learn.
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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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|
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|
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%s
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|
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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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|
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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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|
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<div style="clear: both"></div>
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""") # clear at the end of the section
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|
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|
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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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|
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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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|
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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
|
||||
# starts with plot and if it is more recent than an
|
||||
# existing image.
|
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first_image_file = image_path % 1
|
||||
|
||||
if (not os.path.exists(first_image_file) or
|
||||
os.stat(first_image_file).st_mtime <=
|
||||
os.stat(src_file).st_mtime):
|
||||
# We need to execute the code
|
||||
print 'plotting %s' % fname
|
||||
import matplotlib.pyplot as plt
|
||||
plt.close('all')
|
||||
cwd = os.getcwd()
|
||||
try:
|
||||
# First CD in the original example dir, so that any file created
|
||||
# by the example get created in this directory
|
||||
os.chdir(os.path.dirname(src_file))
|
||||
execfile(os.path.basename(src_file), {'pl' : plt})
|
||||
os.chdir(cwd)
|
||||
|
||||
# In order to save every figure we have two solutions :
|
||||
# * iterate from 1 to infinity and call plt.fignum_exists(n)
|
||||
# (this requires the figures to be numbered
|
||||
# incrementally: 1, 2, 3 and not 1, 2, 5)
|
||||
# * iterate over [fig_mngr.num for fig_mngr in
|
||||
# matplotlib._pylab_helpers.Gcf.get_all_fig_managers()]
|
||||
for fig_num in (fig_mngr.num for fig_mngr in
|
||||
matplotlib._pylab_helpers.Gcf.get_all_fig_managers()):
|
||||
# Set the fig_num figure as the current figure as we can't
|
||||
# save a figure that's not the current figure.
|
||||
plt.figure(fig_num)
|
||||
plt.savefig(image_path % fig_num)
|
||||
figure_list.append(image_fname % fig_num)
|
||||
except:
|
||||
print 80*'_'
|
||||
print '%s is not compiling:' % fname
|
||||
traceback.print_exc()
|
||||
print 80*'_'
|
||||
finally:
|
||||
os.chdir(cwd)
|
||||
else:
|
||||
figure_list = [f[len(image_dir):]
|
||||
for f in glob.glob(image_path % '[1-9]')]
|
||||
#for f in glob.glob(image_path % '*')]
|
||||
|
||||
# generate thumb file
|
||||
this_template = plot_rst_template
|
||||
from matplotlib import image
|
||||
if os.path.exists(first_image_file):
|
||||
image.thumbnail(first_image_file, thumb_file, 0.2)
|
||||
|
||||
if not os.path.exists(thumb_file):
|
||||
# create something not to replace the thumbnail
|
||||
shutil.copy('images/blank_image.png', thumb_file)
|
||||
|
||||
docstring, short_desc, end_row = extract_docstring(example_file)
|
||||
|
||||
# Depending on whether we have one or more figures, we're using a
|
||||
# horizontal list or a single rst call to 'image'.
|
||||
if len(figure_list) == 1:
|
||||
figure_name = figure_list[0]
|
||||
image_list = SINGLE_IMAGE % figure_name.lstrip('/')
|
||||
else:
|
||||
image_list = HLIST_HEADER
|
||||
for figure_name in figure_list:
|
||||
image_list += HLIST_IMAGE_TEMPLATE % figure_name.lstrip('/')
|
||||
|
||||
f = open(os.path.join(target_dir, fname[:-2] + 'txt'),'w')
|
||||
f.write(this_template % locals())
|
||||
f.flush()
|
||||
|
||||
|
||||
def setup(app):
|
||||
app.connect('builder-inited', generate_example_rst)
|
||||
app.add_config_value('plot_gallery', True, 'html')
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 1.5 KiB |
+7
-1
@@ -23,11 +23,17 @@ sys.path.append(os.path.join(curpath, '..', 'ext'))
|
||||
|
||||
# -- General configuration -----------------------------------------------------
|
||||
|
||||
try:
|
||||
import gen_rst
|
||||
except:
|
||||
pass
|
||||
|
||||
|
||||
# Add any Sphinx extension module names here, as strings. They can be extensions
|
||||
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
|
||||
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.pngmath', 'numpydoc',
|
||||
'sphinx.ext.autosummary', 'sphinx.ext.inheritance_diagram',
|
||||
'plot_directive']
|
||||
'plot_directive', 'gen_rst']
|
||||
|
||||
# Add any paths that contain templates here, relative to this directory.
|
||||
templates_path = ['_templates']
|
||||
|
||||
Regular → Executable
+5
-5
@@ -40,16 +40,16 @@ def calculate_coverage(reader):
|
||||
total_items += 1
|
||||
if ":done:" in row[2] or ":done:" in row[3]:
|
||||
done_items += 1
|
||||
elif ":partial:" in row[2] or ":partial:" in row[3]:
|
||||
if ":partial:" in row[2] or ":partial:" in row[3]:
|
||||
partial_items += 1
|
||||
elif ":na:" in row[2] or ":na:" in row[3]:
|
||||
if ":na:" in row[2] or ":na:" in row[3]:
|
||||
na_items += 1
|
||||
|
||||
counts = (done_items,
|
||||
partial_items,
|
||||
total_items - (partial_items + done_items + na_items),
|
||||
na_items)
|
||||
|
||||
|
||||
return list(i / total_items for i in counts)
|
||||
|
||||
def read_table_titles(reader):
|
||||
@@ -235,7 +235,7 @@ Coverage Bar
|
||||
|
||||
for item, style in enumerate(('done-bar', 'partial-bar',
|
||||
'missing-bar', 'na-bar')):
|
||||
stream.write('<td width="%s" class="%s">XX</td>' % \
|
||||
stream.write('<td width="%s%%" class="%s"> </td>' % \
|
||||
(item_counts[item] * 100, style))
|
||||
|
||||
stream.write("</tr></table>\n\n")
|
||||
@@ -269,6 +269,6 @@ if __name__ == "__main__":
|
||||
generate_page(csv_path,output)
|
||||
output.close()
|
||||
|
||||
print "Generated %s from %s." % (output_path,csv_path)
|
||||
print("Generated %s from %s." % (output_path,csv_path))
|
||||
|
||||
|
||||
|
||||
@@ -39,6 +39,11 @@ Sections
|
||||
Conditions on the use and redistribution of this package.
|
||||
|
||||
|
||||
|
||||
`Examples <auto_examples/index.html>`_
|
||||
|
||||
Introductory examples
|
||||
|
||||
Indices and Tables
|
||||
==================
|
||||
|
||||
|
||||
@@ -0,0 +1,4 @@
|
||||
import scipy.misc as _m
|
||||
|
||||
lena = _m.lena
|
||||
|
||||
@@ -11,6 +11,7 @@ def configuration(parent_package='', top_path=None):
|
||||
config.add_subpackage('morphology')
|
||||
config.add_subpackage('filter')
|
||||
config.add_subpackage('transform')
|
||||
config.add_subpackage('data')
|
||||
|
||||
def add_test_directories(arg, dirname, fnames):
|
||||
if dirname.split(os.path.sep)[-1] == 'tests':
|
||||
|
||||
Reference in New Issue
Block a user