30 | wsipre 0.1.2 documentation 31 |
45 |
82 |
93 |
100 |
101 |
102 |
103 |
--------------------------------------------------------------------------------
/docs/_build/html/py-modindex.html:
--------------------------------------------------------------------------------
1 |
2 |
4 |
5 |
6 |
7 |
8 |
9 |
46 |
76 |
80 |
81 |
47 |
75 |
48 |
49 |
74 | Search
50 |
51 |
52 |
57 | 53 | Please activate JavaScript to enable the search 54 | functionality. 55 |
56 |58 | From here you can search these documents. Enter your search 59 | words into the box below and click "search". Note that the search 60 | function will automatically search for all of the words. Pages 61 | containing fewer words won't appear in the result list. 62 |
63 | 68 | 69 |
70 |
71 |
72 |
73 | 28 | wsipre 0.1.2 documentation 29 |
43 |
74 |
85 |
86 |
87 |
98 |
105 |
106 |
107 |
108 |
--------------------------------------------------------------------------------
/docs/_build/html/beyondwsipre.html:
--------------------------------------------------------------------------------
1 |
2 |
4 |
5 |
6 |
7 |
8 |
9 | 23 | wsipre 0.1.2 documentation 24 |
46 |
79 |
98 |
105 |
106 |
107 |
108 |
--------------------------------------------------------------------------------
/docs/_build/html/_static/pygments.css:
--------------------------------------------------------------------------------
1 | .highlight .hll { background-color: #ffffcc }
2 | .highlight { background: #eeffcc; }
3 | .highlight .c { color: #408090; font-style: italic } /* Comment */
4 | .highlight .err { border: 1px solid #FF0000 } /* Error */
5 | .highlight .k { color: #007020; font-weight: bold } /* Keyword */
6 | .highlight .o { color: #666666 } /* Operator */
7 | .highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */
8 | .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
9 | .highlight .cp { color: #007020 } /* Comment.Preproc */
10 | .highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
11 | .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
12 | .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
13 | .highlight .gd { color: #A00000 } /* Generic.Deleted */
14 | .highlight .ge { font-style: italic } /* Generic.Emph */
15 | .highlight .gr { color: #FF0000 } /* Generic.Error */
16 | .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
17 | .highlight .gi { color: #00A000 } /* Generic.Inserted */
18 | .highlight .go { color: #333333 } /* Generic.Output */
19 | .highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
20 | .highlight .gs { font-weight: bold } /* Generic.Strong */
21 | .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
22 | .highlight .gt { color: #0044DD } /* Generic.Traceback */
23 | .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
24 | .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
25 | .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
26 | .highlight .kp { color: #007020 } /* Keyword.Pseudo */
27 | .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
28 | .highlight .kt { color: #902000 } /* Keyword.Type */
29 | .highlight .m { color: #208050 } /* Literal.Number */
30 | .highlight .s { color: #4070a0 } /* Literal.String */
31 | .highlight .na { color: #4070a0 } /* Name.Attribute */
32 | .highlight .nb { color: #007020 } /* Name.Builtin */
33 | .highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
34 | .highlight .no { color: #60add5 } /* Name.Constant */
35 | .highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
36 | .highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
37 | .highlight .ne { color: #007020 } /* Name.Exception */
38 | .highlight .nf { color: #06287e } /* Name.Function */
39 | .highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
40 | .highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
41 | .highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
42 | .highlight .nv { color: #bb60d5 } /* Name.Variable */
43 | .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
44 | .highlight .w { color: #bbbbbb } /* Text.Whitespace */
45 | .highlight .mb { color: #208050 } /* Literal.Number.Bin */
46 | .highlight .mf { color: #208050 } /* Literal.Number.Float */
47 | .highlight .mh { color: #208050 } /* Literal.Number.Hex */
48 | .highlight .mi { color: #208050 } /* Literal.Number.Integer */
49 | .highlight .mo { color: #208050 } /* Literal.Number.Oct */
50 | .highlight .sa { color: #4070a0 } /* Literal.String.Affix */
51 | .highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
52 | .highlight .sc { color: #4070a0 } /* Literal.String.Char */
53 | .highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */
54 | .highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
55 | .highlight .s2 { color: #4070a0 } /* Literal.String.Double */
56 | .highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
57 | .highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
58 | .highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
59 | .highlight .sx { color: #c65d09 } /* Literal.String.Other */
60 | .highlight .sr { color: #235388 } /* Literal.String.Regex */
61 | .highlight .s1 { color: #4070a0 } /* Literal.String.Single */
62 | .highlight .ss { color: #517918 } /* Literal.String.Symbol */
63 | .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
64 | .highlight .fm { color: #06287e } /* Name.Function.Magic */
65 | .highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
66 | .highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
67 | .highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
68 | .highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
69 | .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
--------------------------------------------------------------------------------
/docs/_build/html/wsiprein5minutes.html:
--------------------------------------------------------------------------------
1 |
2 |
4 |
5 |
6 |
7 |
8 |
9 |
47 |
60 |
77 |
78 |
48 |
59 |
49 |
50 |
58 | Coming soon…
51 |
52 |
55 |
56 |
57 | Beyond wsipre¶
53 |Ways to use and extend wsipre’s output.
54 |23 | wsipre 0.0.1 documentation 24 |
46 |
84 |
103 |
110 |
111 |
112 |
113 |
--------------------------------------------------------------------------------
/docs/conf.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python3
2 | # -*- coding: utf-8 -*-
3 | #
4 | # wsipre documentation build configuration file, created by
5 | # sphinx-quickstart on Thu Dec 6 08:07:27 2018.
6 | #
7 | # This file is execfile()d with the current directory set to its
8 | # containing dir.
9 | #
10 | # Note that not all possible configuration values are present in this
11 | # autogenerated file.
12 | #
13 | # All configuration values have a default; values that are commented out
14 | # serve to show the default.
15 |
16 | # If extensions (or modules to document with autodoc) are in another directory,
17 | # add these directories to sys.path here. If the directory is relative to the
18 | # documentation root, use os.path.abspath to make it absolute, like shown here.
19 | #
20 | import os
21 | import sys
22 | sys.path.insert(0, os.path.abspath('../wsipre'))
23 |
24 | # -- General configuration ------------------------------------------------
25 |
26 | # If your documentation needs a minimal Sphinx version, state it here.
27 | #
28 | # needs_sphinx = '1.0'
29 |
30 | # Add any Sphinx extension module names here, as strings. They can be
31 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
32 | # ones.
33 | extensions = [
34 | 'sphinx.ext.autodoc',
35 | 'numpydoc',
36 | 'sphinx.ext.doctest',
37 | 'sphinx.ext.todo',
38 | 'sphinx.ext.coverage',
39 | 'sphinx.ext.mathjax',
40 | 'sphinx.ext.viewcode',
41 | 'sphinx.ext.githubpages'
42 | ]
43 |
44 | # Add any paths that contain templates here, relative to this directory.
45 | templates_path = ['_templates']
46 |
47 | # The suffix(es) of source filenames.
48 | # You can specify multiple suffix as a list of string:
49 | #
50 | # source_suffix = ['.rst', '.md']
51 | source_suffix = '.rst'
52 |
53 | # The master toctree document.
54 | master_doc = 'index'
55 |
56 | # General information about the project.
57 | project = 'wsipre'
58 | copyright = '2019, Luis A. Vale Silva'
59 | author = 'Luis A. Vale Silva'
60 |
61 | # The version info for the project you're documenting, acts as replacement for
62 | # |version| and |release|, also used in various other places throughout the
63 | # built documents.
64 | #
65 | # The short X.Y version.
66 | version = '0.1'
67 | # The full version, including alpha/beta/rc tags.
68 | release = '0.1.2'
69 |
70 | # The language for content autogenerated by Sphinx. Refer to documentation
71 | # for a list of supported languages.
72 | #
73 | # This is also used if you do content translation via gettext catalogs.
74 | # Usually you set "language" from the command line for these cases.
75 | language = None
76 |
77 | # List of patterns, relative to source directory, that match files and
78 | # directories to ignore when looking for source files.
79 | # This patterns also effect to html_static_path and html_extra_path
80 | exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
81 |
82 | # The name of the Pygments (syntax highlighting) style to use.
83 | pygments_style = 'sphinx'
84 |
85 | # If true, `todo` and `todoList` produce output, else they produce nothing.
86 | todo_include_todos = True
87 |
88 |
89 | # -- Options for HTML output ----------------------------------------------
90 |
91 | # The theme to use for HTML and HTML Help pages. See the documentation for
92 | # a list of builtin themes.
93 | #
94 | #html_theme = 'alabaster'
95 | from better import better_theme_path
96 | html_theme_path = [better_theme_path]
97 | html_theme = 'better'
98 |
99 | html_short_title = "Home"
100 |
101 | # Theme options are theme-specific and customize the look and feel of a theme
102 | # further. For a list of options available for each theme, see the
103 | # documentation.
104 | #
105 | # html_theme_options = {}
106 |
107 | # Add any paths that contain custom static files (such as style sheets) here,
108 | # relative to this directory. They are copied after the builtin static files,
109 | # so a file named "default.css" will overwrite the builtin "default.css".
110 | html_static_path = ['_static']
111 |
112 | # Custom sidebar templates, must be a dictionary that maps document names
113 | # to template names.
114 | #
115 | # This is required for the alabaster theme
116 | # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
117 | html_sidebars = {
118 | '**': [
119 | 'relations.html', # needs 'show_related': True theme option to display
120 | 'searchbox.html',
121 | ]
122 | }
123 |
124 |
125 | # -- Options for HTMLHelp output ------------------------------------------
126 |
127 | # Output file base name for HTML help builder.
128 | htmlhelp_basename = 'wsipredoc'
129 |
130 |
131 | # -- Options for LaTeX output ---------------------------------------------
132 |
133 | latex_elements = {
134 | # The paper size ('letterpaper' or 'a4paper').
135 | #
136 | # 'papersize': 'letterpaper',
137 |
138 | # The font size ('10pt', '11pt' or '12pt').
139 | #
140 | # 'pointsize': '10pt',
141 |
142 | # Additional stuff for the LaTeX preamble.
143 | #
144 | # 'preamble': '',
145 |
146 | # Latex figure (float) alignment
147 | #
148 | # 'figure_align': 'htbp',
149 | }
150 |
151 | # Grouping the document tree into LaTeX files. List of tuples
152 | # (source start file, target name, title,
153 | # author, documentclass [howto, manual, or own class]).
154 | latex_documents = [
155 | (master_doc, 'wsipre.tex', 'wsipre Documentation',
156 | 'Luis A. Vale Silva', 'manual'),
157 | ]
158 |
159 |
160 | # -- Options for manual page output ---------------------------------------
161 |
162 | # One entry per manual page. List of tuples
163 | # (source start file, name, description, authors, manual section).
164 | man_pages = [
165 | (master_doc, 'wsipre', 'wsipre Documentation',
166 | [author], 1)
167 | ]
168 |
169 |
170 | # -- Options for Texinfo output -------------------------------------------
171 |
172 | # Grouping the document tree into Texinfo files. List of tuples
173 | # (source start file, target name, title, author,
174 | # dir menu entry, description, category)
175 | texinfo_documents = [
176 | (master_doc, 'wsipre', 'wsipre Documentation',
177 | author, 'wsipre', 'One line description of project.',
178 | 'Miscellaneous'),
179 | ]
180 |
181 |
182 |
183 |
--------------------------------------------------------------------------------
/docs/_build/html/_static/better.css:
--------------------------------------------------------------------------------
1 | @import url("better_basic.css");
2 |
3 |
4 |
5 |
6 | /* main styles */
7 |
8 | body {
9 | font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
10 | font-size: 100%;
11 | color: #000000;
12 | margin: 0;
13 | padding: 0;
14 | line-height: 135%;
15 | }
16 |
17 | a {
18 | color: #008;
19 | text-decoration: none;
20 | }
21 |
22 | a:visited {
23 | color: #208;
24 | text-decoration: none;
25 | }
26 |
27 | a:hover {
28 | text-decoration: underline;
29 | }
30 |
31 | a.toc-backref {
32 | color: #000000;
33 | }
34 |
35 | p {
36 | margin: 1rem 0;
37 | }
38 |
39 | h1, h2, h3, h4, h5, h6 {
40 | margin-top: 1em;
41 | margin-bottom: 0.5em;
42 | color: #000000;
43 | line-height: 135%;
44 | }
45 |
46 | .body .section:first-child > :first-child,
47 | .sphinxsidebarwrapper > :first-child,
48 | .sphinxsidebar .search:first-child
49 | {
50 | margin-top: 1rem;
51 | }
52 |
53 | h1 { font-size: 1.5rem; font-weight: bold; }
54 | h2 { font-size: 1.5rem; font-weight: normal; }
55 | h3 { font-size: 1.25rem; font-weight: bold; }
56 | h4 { font-size: 1.25rem; font-weight: normal; }
57 | h5 { font-size: 1rem; font-weight: bold; }
58 | h6 { font-size: 1rem; font-weight: normal; }
59 |
60 | /* page-level layout of containers */
61 |
62 | header#pageheader, footer#pagefooter, .related, .document {
63 | width: 100%;
64 | max-width: 60rem;
65 | margin: auto;
66 | }
67 |
68 | .documentwrapper {
69 | float: left;
70 | width: 100%;
71 | }
72 |
73 | .bodywrapper {
74 | margin: 0 0 0 15rem;
75 | }
76 |
77 | footer#pagefooter, footer#pagefooter a {
78 | color: #000000;
79 | }
80 |
81 |
82 | footer#pagefooter {
83 | padding-top: 2rem;
84 | padding-bottom: 2rem;
85 | text-align: center;
86 | }
87 |
88 | footer#pagefooter a {
89 | text-decoration: underline;
90 | }
91 |
92 | /* header styles */
93 |
94 | body > header h1 a, body > header h1 a:visited {
95 | color: #000000;
96 | }
97 |
98 | a.headerlink {
99 | font-size: 0.8em;
100 | padding: 0 4px 0 4px;
101 | text-decoration: none;
102 | }
103 |
104 | /* code styles */
105 |
106 | pre, tt {
107 | background-color: #eee;
108 | color: #333;
109 | }
110 |
111 | pre {
112 | font-family: Monaco, Consolas, "Lucida Console", monospace;
113 | margin: 1rem -5px;
114 | padding: 5px;
115 | border-left: none;
116 | border-right: none;
117 | font-size: 0.8rem;
118 | line-height: 1rem;
119 | }
120 |
121 | tt {
122 | padding: 0 1px 0 1px;
123 | font-family: Consolas, Monaco, monospace;
124 | }
125 |
126 | /* API doc styles */
127 |
128 | dl.function,
129 | dl.class,
130 | dl.method,
131 | dl.attribute,
132 | dl.data,
133 | dl.classmethod {
134 | margin-bottom: 2rem;
135 | }
136 |
137 | /* relbar */
138 |
139 | .related {
140 | line-height: 30px;
141 | width: 100%;
142 | font-size: 0.9rem;
143 | }
144 |
145 | .related.top {
146 | border-bottom: 1px solid #aaa;
147 | }
148 |
149 | .related.bottom {
150 | border-top: 1px solid #aaa;
151 | }
152 |
153 | .related ul {
154 | padding: 0;
155 | margin: 0;
156 | list-style: none;
157 | }
158 |
159 | .related li {
160 | display: inline;
161 | }
162 |
163 | nav#rellinks {
164 | float: right;
165 | }
166 |
167 | nav#rellinks li+li:before {
168 | content: "|";
169 | }
170 |
171 | nav#breadcrumbs li+li:before {
172 | content: "\00BB";
173 | }
174 |
175 | /* sidebar */
176 |
177 | .sphinxsidebarwrapper {
178 | padding: 0 1rem 0 0;
179 | }
180 |
181 | .sphinxsidebar {
182 | width: 15rem;
183 | margin-left: -100%;
184 | font-size: 0.9rem;
185 | float: left;
186 | }
187 |
188 | .sphinxsidebar h3 a {
189 | color: #000000;
190 | }
191 |
192 | .sphinxsidebar p.topless {
193 | margin: 5px 10px 10px 10px;
194 | }
195 |
196 | .sphinxsidebar ul {
197 | margin: 0;
198 | padding: 0;
199 | margin-bottom: 1rem;
200 | list-style: none;
201 | }
202 |
203 | .sphinxsidebar ul ul,
204 | .sphinxsidebar ul.want-points {
205 | margin-left: 20px;
206 | list-style: square;
207 | }
208 |
209 | .sphinxsidebar ul ul {
210 | margin-top: 0;
211 | margin-bottom: 0;
212 | }
213 |
214 | .sphinxsidebar input {
215 | box-sizing: border-box;
216 | -moz-box-sizing: border-box;
217 | -webkit-box-sizing: border-box;
218 | height: 1.5rem;
219 | font-size: 0.9rem;
220 | margin: 0;
221 |
222 | background-color: white;
223 | border: 1px solid #ccc;
224 | color: #555;
225 | }
226 |
227 | .sphinxsidebar .search {
228 | margin-top: 2rem;
229 | }
230 |
231 | .sphinxsidebar .search input[type=text] {
232 | width: 90%;
233 | display: inline-block;
234 | }
235 |
236 | .sphinxsidebar .search input[type=submit] {
237 | width: 4rem;
238 | display: inline-block;
239 | }
240 |
241 | /* paragraph-level markup */
242 |
243 | .admonition p.admonition-title + p {
244 | display: inline;
245 | }
246 |
247 | .admonition p {
248 | margin-bottom: 5px;
249 | }
250 |
251 | .admonition pre {
252 | margin-bottom: 5px;
253 | }
254 |
255 | .admonition ul, .admonition ol {
256 | margin-bottom: 5px;
257 | }
258 |
259 | p.admonition-title {
260 | display: inline;
261 | margin-right: 0;
262 | }
263 |
264 | p.admonition-title:after {
265 | content: ":";
266 | }
267 |
268 | .note {
269 | background-color: #eee;
270 | border: 1px solid #ccc;
271 | }
272 |
273 | .seealso {
274 | background-color: #ffc;
275 | border: 1px solid #ff6;
276 | }
277 |
278 | .topic {
279 | background-color: #eee;
280 | }
281 |
282 | .warning {
283 | background-color: #ffe4e4;
284 | border: 1px solid #f66;
285 | }
286 |
287 | .warning tt {
288 | background: #efc2c2;
289 | }
290 |
291 | .note tt {
292 | background: #d6d6d6;
293 | }
294 |
295 | .viewcode-block:target {
296 | background-color: #f4debf;
297 | border-top: 1px solid #ac9;
298 | border-bottom: 1px solid #ac9;
299 | }
300 |
301 | /* responsive styles */
302 |
303 | @media (max-width: 820px) {
304 | /* kill the sidebar */
305 | .bodywrapper { margin: 0; }
306 | .sphinxsidebar {
307 | display: none;
308 | }
309 | header#pageheader, footer#pagefooter, .related, .document {
310 | margin: 0 1rem;
311 | width: calc(100% - 2rem);
312 | width: -webkit-calc(100% - 2rem);
313 | }
314 | }
--------------------------------------------------------------------------------
/docs/_build/html/searchindex.js:
--------------------------------------------------------------------------------
1 | Search.setIndex({docnames:["beyondwsipre","index","quick_intro","show","slide"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.todo":1,"sphinx.ext.viewcode":1,sphinx:55},filenames:["beyondwsipre.rst","index.rst","quick_intro.rst","show.rst","slide.rst"],objects:{"":{show:[3,0,0,"-"],slide:[4,0,0,"-"]},"show.Figure":{show_annotation:[3,2,1,""],show_image:[3,2,1,""],show_image_with_annotation:[3,2,1,""],show_label_colors:[3,2,1,""]},"slide.Slide":{associated_images:[4,3,1,""],close:[4,2,1,""],detect_format:[4,4,1,""],dimensions:[4,3,1,""],get_best_level_for_downsample:[4,2,1,""],get_thumbnail:[4,2,1,""],get_thumbnail_with_annotation:[4,2,1,""],get_tissue_mask:[4,2,1,""],level_count:[4,3,1,""],level_dimensions:[4,3,1,""],level_downsamples:[4,3,1,""],properties:[4,3,1,""],read_random_patch:[4,2,1,""],read_random_tissue_patch:[4,2,1,""],read_region:[4,2,1,""],read_region_with_annotation:[4,2,1,""]},show:{Figure:[3,1,1,""]},slide:{Slide:[4,1,1,""]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","classmethod","Python class method"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:attribute","4":"py:classmethod"},terms:{"class":[2,3,4],"final":[],"float":4,"function":[1,4],"import":[1,2,3,4],"int":[2,3,4],"new":[],"return":[3,4],"true":[2,3],Added:4,The:[1,2,3,4],Then:[],__library_version__:1,__wsipre__:[],_openslid:[],about:4,access:4,accord:4,add:[],aditya:4,aim_for_tumor:[],algorithm:4,all:[],allow:[1,4],also:1,andrew:4,annot:[1,2,3,4],annotatedopenslid:4,annotation_filenam:[2,4],anoth:[],api:1,applic:[],area:[2,4],argument:4,arrai:[3,4],arxiv:4,asap:[2,4],associ:4,associated_imag:4,attribut:[3,4],automat:[2,4],avail:4,avoid:[1,4],avoid_label:[2,4],bar:3,base:4,basic:2,beck:4,been:1,best:4,between:[2,3,4],beyond:1,binari:4,black:2,bool:3,breast:4,briefli:4,build:[],camelyon:2,can:1,cancer:4,censor_mixed_class:[],central:4,challeng:[2,4],channel:4,check:[1,2],classmethod:4,close:4,closest:4,code:1,color:[2,3,4],color_map:[2,3],com:[],combin:3,come:0,compress:4,comput:4,conserv:1,consist:4,contain:4,content:4,convert:4,coordin:4,corner:[],correspond:[3,4],cover:[],crash:1,crop:4,current:1,cybern:4,data:4,data_sourc:[],dataset:4,dayong:4,deep:[1,4],defin:4,demo:1,describ:4,desir:4,detail:1,detect:4,detect_format:4,detector:4,determin:4,develop:1,dict:[3,4],differ:[],dimens:4,displai:[1,3,4],distribut:1,doc:2,document:[],doubl:2,down:4,downsampl:[1,4],downsampled_slid:[2,4],downsampling_factor:[2,4],draw:4,drive:[],dwnspl_factor:4,each:[3,4],earlier:1,easi:[],easili:[],edg:4,equal:[],exampl:[3,4],excel:1,exhaust:1,extend:[0,1],factor:4,fals:2,fig:[2,3],figur:[1,2],file:[1,4],filenam:[2,4],fill:4,first:2,fit:4,follow:[1,2,4],font:3,font_color:3,font_siz:3,form:2,format:[1,4],found:4,frame:4,from:[1,2,3,4],from_annot:[],full:4,gargeya:4,gener:[1,2,4],get:4,get_annotated_thumbnail:[],get_best_level_for_downsampl:4,get_thumbnail:4,get_thumbnail_with_annot:[2,4],get_tissue_mask:[2,4],github:1,give:4,given:4,grai:4,handl:1,has:[1,2],have:1,heavili:[],height:[3,4],here:2,histogram:4,histolog:4,hole:[1,4],host:1,hsv:4,http:[],humayun:4,identifi:4,ieee:4,illustr:[2,3],imag:[1,2,3,4],imshow:2,index:[1,2],input:3,inspir:4,instal:[],instanc:4,integ:4,interest:4,interfac:[1,4],interpret:1,intro:2,introduct:1,ipynb:[],irshad:4,iter:4,its:[2,4],jupyt:1,kei:[],khosla:4,known:1,label:[2,3,4],label_map:4,lack:1,latest:[],learn:[1,4],left:4,len:4,lesion:[],level:[1,2,4],level_count:4,level_dimens:4,level_downsampl:4,librari:1,lide:1,line:[2,4],line_thick:[2,4],linux:1,list:[1,3,4],load:[2,3],loc:2,locat:[2,4],luisvalesilva:[],machin:1,made:[],mage:1,mai:[],main:2,mainli:[],make:[1,4],man:4,manag:1,map:[2,3,4],mask:[2,3,4],mask_class_remap:[],mask_region:2,matplotlib:[2,3],maximum:4,memori:4,metadata:4,metastat:4,method:[3,4],min_area:[],min_class_area:[],min_class_area_ratio:[2,4],minimum:4,minut:[],mit:1,modul:[1,2],monospac:[],more:[],must:4,name:4,namesak:4,nobuyuki:4,non:1,none:4,note:[],notebook:1,number:4,numpi:[1,3,4],object:[1,4],one:4,onli:2,open:[3,4],opencv:1,openslid:[1,4],optim:4,option:4,org:[],origin:[],other:1,otsu:4,out:[],outdat:1,output:0,overlai:3,overlap:1,packag:2,page:1,palett:[],param:[],paramet:[3,4],part:[],particularli:1,patch:[2,4],path:4,patient_012_node_0:2,perform:1,pil:[3,4],pip:1,pixel:[3,4],pleas:1,plot:[2,3],plt:2,plu:4,polygon:4,polygon_typ:[2,4],pre:1,premultipli:4,prepar:1,preprocess:[],prob:[],probabl:[],problem:1,process:[1,2],project:1,properti:4,provid:[1,4],pypi:1,pyplot:2,python:1,quick:1,random:[2,4],ratio:4,rb7b6abb48578:[],read:[1,2,3],read_annotated_region:[],read_random_patch:[2,4],read_random_region:[],read_random_tissue_patch:[2,4],read_region:4,read_region_with_annot:[2,4],recent:1,recogn:4,rectangl:3,red:2,refer:4,region:[1,2,3,4],rel:4,releas:4,reli:[],remap:[],remap_annotation_label:[],remov:4,reproduc:[],requir:[1,4],return_patch_class:[],rgb:[3,4],rgba:4,rishab:4,roi:4,run:[1,4],sampl:2,satur:4,scale:4,search:1,see:[1,2],segment:4,select:4,should:1,show:[2,3],show_annot:3,show_imag:3,show_image_with_annot:[2,3],show_label_color:[2,3],side:3,sinc:4,singl:[],size:[2,3,4],slide:[1,2],slide_region:[2,4],small:[1,4],smaller:[2,4],some:1,soon:0,sourc:[1,3,4],space:4,specif:[],specifi:4,split:[2,3],squar:[],start:4,step:4,str:4,string:4,structur:[],support:1,sure:1,syst:4,target:4,target_class:[2,4],task:1,term:1,test:1,text:[],thi:[1,4],thick:4,threshold:4,thu:[],thumbnail:[2,3,4],tif:[2,4],tile:1,time:[],tissu:[2,4],tissue_label_map:4,tissue_mask:[2,4],tissue_patch:2,titl:[],todo:[],togeth:4,top:4,total:4,tran:4,transfer:4,triplet:3,tumor:2,tumor_001:4,tupl:4,two:2,type:4,typic:4,tytient_012_node_0:[],under:1,underli:1,underlin:[],unlik:4,updat:[],upon:1,usag:2,use:0,used:[1,2,3,4],using:[2,4],valu:[3,4],vendor:4,version:1,via:4,view:1,virtual:1,visual:[2,3,4],wai:0,wang:4,want:[],when:4,whether:3,which:1,white:[],whole:[1,4],wholeslideimagesampl:1,wide:[],width:[3,4],wise:3,within:4,without:4,work:1,wrapper:1,write:[],wrong:1,wshole:[],wsi:[1,2,3,4],wsipr:[2,3,4],xml:[2,4],xml_style:[2,4],yellow:2,you:1,zoom:2},titles:["Beyond wsipre","wsipre","Quick introduction","Figure","Slide"],titleterms:{api:[],beyond:0,depend:1,document:[],figur:3,guid:1,indic:1,instal:1,intro:[],introduct:2,licens:1,main:1,minut:[],more:[],packag:1,quick:2,refer:1,slide:4,tabl:1,titl:[],user:1,welcom:[],wsipr:[0,1]}})
--------------------------------------------------------------------------------
/wsipre/show.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
3 | """
4 | Show images, such as thumbnails or regions extracted from whole-slide images
5 | (WSI; also known as virtual slides).
6 |
7 | """
8 |
9 | import numpy as np
10 | from matplotlib import pyplot as plt
11 | import matplotlib.patches as mpatch
12 |
13 |
14 | class Figure(object):
15 | """An open *annotated* WSI.
16 |
17 | Parameters
18 | ----------
19 | image: PIL Image
20 | Image to display; a thumbnail or region read from WSI.
21 | annotation: Numpy 2D array
22 | Annotation labels for each pixel in the input ``image``.
23 | color_map: dict {label int: RGB color list}
24 | Mapping of RGB color values to class labels. Colors are triplet lists
25 | of the R, G, and B values.
26 |
27 | Attributes
28 | ----------
29 | image: PIL Image
30 | The input ``image``.
31 | annotation: Numpy 2D array
32 | The input ``annotation``.
33 | color_map: dict {label: color}
34 | Mapping between each label and the color for visualization.
35 |
36 | Examples
37 | --------
38 | >>> from wsipre import show
39 | >>> colors = {0: (0, 0, 0), 2: (1, 0, 0)}
40 | >>> fig = show.Figure(image=image, annotation=mask, color_map=colors)
41 | >>> fig.color_map
42 | {0: (0, 0, 0), 2: (1, 0, 0)}
43 |
44 | >>> fig.show_label_colors(height=5)
45 |
46 | >>> fig.show_image_with_annotation()
47 |
48 | """
49 |
50 | def __init__(self, image, annotation, color_map={0: (0., 0., 0.),
51 | 1: (0., .8, 1.),
52 | 2: (1., .8, 0.),
53 | 3: (1., .4, 0.)}):
54 | self.image = image
55 | self.annotation = annotation.astype(np.float32) # In case it's boolean
56 | self.color_map = color_map
57 |
58 | # RGBA values should be within 0-1 range
59 | if all([0 <= channel <= 255 for color in self.color_map.values()
60 | for channel in color]):
61 | if any([channel > 1 for color in self.color_map.values()
62 | for channel in color]):
63 | self.color_map = {key: [channel / 255.0 for channel in color]
64 | for (key, color) in self.color_map.items()}
65 | else:
66 | raise ValueError(
67 | 'Please make sure color triplets values in "color_map" are ' +
68 | 'either between 0-1 or 0-255 range.')
69 |
70 | # Are there enough colors?
71 | labels = np.unique(self.annotation)
72 | labels_not_in_map = [label not in color_map.keys() for label in labels]
73 | if any(labels_not_in_map):
74 | raise ValueError(
75 | 'No color provided in "color_map" for label(s) ' +
76 | f' {list(labels[labels_not_in_map])}.')
77 |
78 | def show_label_colors(self, width=20, height=6, font_color='w',
79 | font_size=14):
80 | """Display a color bar with the colors and overlayed labels.
81 |
82 | Parameters
83 | ----------
84 | width: int
85 | Width of each class rectangle in plot.
86 | height: int
87 | Height of each class rectangle in plot.
88 | font_size: int
89 | Size of the font used to display class labels.
90 |
91 | Returns
92 | -------
93 | Matplotlib image illustrating mapping between class label and color.
94 |
95 | """
96 | rectangles = [mpatch.Rectangle((0 + width * i, 0), width, height,
97 | color=list(self.color_map.values())[i])
98 | for i in range(len(self.color_map.keys()))]
99 | rectangles = {list(self.color_map.keys())[i]: rect
100 | for i, rect in enumerate(rectangles)}
101 |
102 | fig, ax = plt.subplots()
103 |
104 | for r in rectangles:
105 | ax.add_artist(rectangles[r])
106 | rx, ry = rectangles[r].get_xy()
107 | cx = rx + rectangles[r].get_width() / 2.0
108 | cy = ry + rectangles[r].get_height() / 2.0
109 |
110 | ax.annotate(r, (cx, cy), color=font_color, weight='bold',
111 | fontsize=font_size, ha='center', va='center')
112 |
113 | ax.set_xlim((0, width * len(rectangles)))
114 | ax.set_ylim((0, height))
115 | ax.set_aspect('equal')
116 | ax.axis('off')
117 | plt.show()
118 |
119 | def show_image(self):
120 | """Show loaded image.
121 |
122 | Display the loaded WSI thumbnail or region.
123 |
124 | Returns
125 | -------
126 | Matplotlib image.
127 |
128 | """
129 | plt.imshow(self.image)
130 | plt.show()
131 |
132 | def _paint_annotation_mask(self):
133 | """Convert 2D mask to 3D format (RGB image)."""
134 | red = self.annotation.copy()
135 | green = self.annotation.copy()
136 | blue = self.annotation.copy()
137 |
138 | for label, color in self.color_map.items():
139 | idx = self.annotation == label
140 | red[idx], green[idx], blue[idx] = color
141 |
142 | rgb = np.stack([red, green, blue], axis=2)
143 |
144 | return rgb
145 |
146 | def show_annotation(self):
147 | """Show loaded image annotation.
148 |
149 | Display the loaded WSI thumbnail or region annotation, corresponding to
150 | a mask of pixel-wise labels.
151 |
152 | Returns
153 | -------
154 | Matplotlib image.
155 |
156 | """
157 | rgb_mask = self._paint_annotation_mask()
158 | plt.imshow(rgb_mask)
159 | plt.show()
160 |
161 | def show_image_with_annotation(self, split=True):
162 | """Show loaded image and annotation.
163 |
164 | Parameters
165 | ----------
166 | split: bool
167 | Whether to display the split image and annotation side-by-side or a
168 | combined visualization of the annotation on the image.
169 |
170 | Returns
171 | -------
172 | Matplotlib image.
173 |
174 | """
175 | if split:
176 | rgb_mask = self._paint_annotation_mask()
177 |
178 | f, (ax1, ax2) = plt.subplots(1, 2, sharey=True)
179 | ax1.imshow(np.array(self.image))
180 | ax2.imshow(rgb_mask)
181 | plt.show()
182 | else:
183 | image = np.array(self.image)[:, :, :3]
184 | if np.max(image) > 1:
185 | image = image / 255.
186 |
187 | for label, color in self.color_map.items():
188 | if label == 0:
189 | continue
190 | idx = self.annotation == label
191 | image[idx] = color
192 |
193 | plt.imshow(image)
194 | plt.show()
195 |
--------------------------------------------------------------------------------
/docs/_build/html/genindex.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
5 |
6 |
7 |
8 |
9 |
10 |
47 |
65 |
82 |
83 |
48 |
64 |
49 |
50 |
63 |
51 |
60 |
61 |
62 | wsipre in 5 minutes¶
52 |wsipre (Whole-Slide Image PREprocessing) 53 | is a wrapper of the excellent OpenSlide Python package, which 54 | allows reading whole-slide images (WSI), also known as virtual slides. 55 | wsipre conserves OpenSlide Python’s API and extends it to handle WSI 56 | annotations and to perform some slide processing tasks. The driving objective 57 | is the preprocessing of WSIs, with or without annotations, for Machine Learning 58 | (ML), particularly Deep Learning (DL), applications.
59 |22 | wsipre 0.1.2 documentation 23 |
37 |
186 |
197 |
204 |
205 |
206 |
207 |
--------------------------------------------------------------------------------
/docs/_build/html/index.html:
--------------------------------------------------------------------------------
1 |
2 |
4 |
5 |
6 |
7 |
8 |
9 |
38 |
173 |
184 |
185 |
39 |
172 |
40 |
41 |
42 |
63 |
64 |
71 |
72 |
83 |
84 |
91 |
92 |
107 |
108 |
121 |
122 |
129 |
130 |
145 |
146 |
167 |
168 |
169 |
170 |
171 | Index
43 | 44 | 56 |A
57 |
|
62 |
C
65 |
|
70 |
D
73 |
|
78 |
|
82 |
F
85 |
|
90 |
G
93 |
|
100 |
|
106 |
L
109 |
|
114 |
|
120 |
P
123 |
|
128 |
R
131 |
|
138 |
|
144 |
S
147 |
|
156 |
|
166 |
22 | wsipre 0.1.2 documentation 23 |
41 |
155 |
170 |
177 |
178 |
179 |
180 |
--------------------------------------------------------------------------------
/docs/_build/html/_static/better_basic.css:
--------------------------------------------------------------------------------
1 | /* basic.css_t from Sphinx project modified for sphinx-better-theme */
2 |
3 | /* -- main layout ----------------------------------------------------------- */
4 |
5 | div.clearer {
6 | clear: both;
7 | }
8 |
9 | /* -- search page ----------------------------------------------------------- */
10 |
11 | ul.search {
12 | margin: 10px 0 0 20px;
13 | padding: 0;
14 | }
15 |
16 | ul.search li {
17 | padding: 5px 0 5px 20px;
18 | background-image: url(file.png);
19 | background-repeat: no-repeat;
20 | background-position: 0 7px;
21 | }
22 |
23 | ul.search li a {
24 | font-weight: bold;
25 | }
26 |
27 | ul.search li div.context {
28 | color: #888;
29 | margin: 2px 0 0 30px;
30 | text-align: left;
31 | }
32 |
33 | ul.keywordmatches li.goodmatch a {
34 | font-weight: bold;
35 | }
36 |
37 | /* -- index page ------------------------------------------------------------ */
38 |
39 | table.contentstable {
40 | width: 90%;
41 | }
42 |
43 | table.contentstable p.biglink {
44 | line-height: 150%;
45 | }
46 |
47 | a.biglink {
48 | font-size: 1.3em;
49 | }
50 |
51 | span.linkdescr {
52 | font-style: italic;
53 | padding-top: 5px;
54 | font-size: 90%;
55 | }
56 |
57 | /* -- general index --------------------------------------------------------- */
58 |
59 | table.indextable {
60 | width: 100%;
61 | }
62 |
63 | table.indextable td {
64 | text-align: left;
65 | vertical-align: top;
66 | }
67 |
68 | table.indextable dl, table.indextable dd {
69 | margin-top: 0;
70 | margin-bottom: 0;
71 | }
72 |
73 | table.indextable tr.pcap {
74 | height: 10px;
75 | }
76 |
77 | table.indextable tr.cap {
78 | margin-top: 10px;
79 | background-color: #f2f2f2;
80 | }
81 |
82 | img.toggler {
83 | margin-right: 3px;
84 | margin-top: 3px;
85 | cursor: pointer;
86 | }
87 |
88 | div.modindex-jumpbox {
89 | border-top: 1px solid #ddd;
90 | border-bottom: 1px solid #ddd;
91 | margin: 1em 0 1em 0;
92 | padding: 0.4em;
93 | }
94 |
95 | div.genindex-jumpbox {
96 | border-top: 1px solid #ddd;
97 | border-bottom: 1px solid #ddd;
98 | margin: 1em 0 1em 0;
99 | padding: 0.4em;
100 | }
101 |
102 | /* -- general body styles --------------------------------------------------- */
103 |
104 | a.headerlink {
105 | visibility: hidden;
106 | }
107 |
108 | h1:hover > a.headerlink,
109 | h2:hover > a.headerlink,
110 | h3:hover > a.headerlink,
111 | h4:hover > a.headerlink,
112 | h5:hover > a.headerlink,
113 | h6:hover > a.headerlink,
114 | dt:hover > a.headerlink {
115 | visibility: visible;
116 | }
117 |
118 | div.body p.caption {
119 | text-align: inherit;
120 | }
121 |
122 | div.body td {
123 | text-align: left;
124 | }
125 |
126 | .field-list ul {
127 | padding-left: 1em;
128 | }
129 |
130 | .first {
131 | margin-top: 0 !important;
132 | }
133 |
134 | p.rubric {
135 | margin-top: 30px;
136 | font-weight: bold;
137 | }
138 |
139 | img.align-left, .figure.align-left, object.align-left {
140 | clear: left;
141 | float: left;
142 | margin-right: 1em;
143 | }
144 |
145 | img.align-right, .figure.align-right, object.align-right {
146 | clear: right;
147 | float: right;
148 | margin-left: 1em;
149 | }
150 |
151 | img.align-center, .figure.align-center, object.align-center {
152 | display: block;
153 | margin-left: auto;
154 | margin-right: auto;
155 | }
156 |
157 | .align-left {
158 | text-align: left;
159 | }
160 |
161 | .align-center {
162 | text-align: center;
163 | }
164 |
165 | .align-right {
166 | text-align: right;
167 | }
168 |
169 | /* -- sidebars -------------------------------------------------------------- */
170 |
171 | div.sidebar {
172 | margin: 0 0 0.5em 1em;
173 | border: 1px solid #ddb;
174 | padding: 7px 7px 0 7px;
175 | background-color: #ffe;
176 | width: 40%;
177 | float: right;
178 | }
179 |
180 | p.sidebar-title {
181 | font-weight: bold;
182 | }
183 |
184 | /* -- topics ---------------------------------------------------------------- */
185 |
186 | div.topic {
187 | border: 1px solid #ccc;
188 | padding: 7px 7px 0 7px;
189 | margin: 10px 0 10px 0;
190 | }
191 |
192 | p.topic-title {
193 | font-size: 1.1em;
194 | font-weight: bold;
195 | margin-top: 10px;
196 | }
197 |
198 | /* -- admonitions ----------------------------------------------------------- */
199 |
200 | div.admonition {
201 | margin-top: 10px;
202 | margin-bottom: 10px;
203 | padding: 7px;
204 | }
205 |
206 | div.admonition dt {
207 | font-weight: bold;
208 | }
209 |
210 | div.admonition dl {
211 | margin-bottom: 0;
212 | }
213 |
214 | p.admonition-title {
215 | margin: 0px 10px 5px 0px;
216 | font-weight: bold;
217 | }
218 |
219 | div.body p.centered {
220 | text-align: center;
221 | margin-top: 25px;
222 | }
223 |
224 | /* -- tables ---------------------------------------------------------------- */
225 |
226 | table.docutils {
227 | border: 0;
228 | border-collapse: collapse;
229 | }
230 |
231 | table.docutils td, table.docutils th {
232 | padding: 1px 8px 1px 5px;
233 | border-top: 0;
234 | border-left: 0;
235 | border-right: 0;
236 | border-bottom: 1px solid #aaa;
237 | }
238 |
239 | table.field-list td, table.field-list th {
240 | border: 0 !important;
241 | }
242 |
243 | table.footnote td, table.footnote th {
244 | border: 0 !important;
245 | }
246 |
247 | th {
248 | text-align: left;
249 | padding-right: 5px;
250 | }
251 |
252 | table.citation {
253 | border-left: solid 1px gray;
254 | margin-left: 1px;
255 | }
256 |
257 | table.citation td {
258 | border-bottom: none;
259 | }
260 |
261 | /* -- other body styles ----------------------------------------------------- */
262 |
263 | ol.arabic {
264 | list-style: decimal;
265 | }
266 |
267 | ol.loweralpha {
268 | list-style: lower-alpha;
269 | }
270 |
271 | ol.upperalpha {
272 | list-style: upper-alpha;
273 | }
274 |
275 | ol.lowerroman {
276 | list-style: lower-roman;
277 | }
278 |
279 | ol.upperroman {
280 | list-style: upper-roman;
281 | }
282 |
283 | dl {
284 | margin-bottom: 15px;
285 | }
286 |
287 | dd p {
288 | margin-top: 0px;
289 | }
290 |
291 | dd ul, dd table {
292 | margin-bottom: 10px;
293 | }
294 |
295 | dd {
296 | margin-top: 3px;
297 | margin-bottom: 10px;
298 | margin-left: 30px;
299 | }
300 |
301 | dt:target, .highlighted {
302 | background-color: #fbe54e;
303 | }
304 |
305 | dl.glossary dt {
306 | font-weight: bold;
307 | font-size: 1.1em;
308 | }
309 |
310 | .field-list ul {
311 | margin: 0;
312 | padding-left: 1em;
313 | }
314 |
315 | .field-list p {
316 | margin: 0;
317 | }
318 |
319 | .refcount {
320 | color: #060;
321 | }
322 |
323 | .optional {
324 | font-size: 1.3em;
325 | }
326 |
327 | .versionmodified {
328 | font-style: italic;
329 | }
330 |
331 | .system-message {
332 | background-color: #fda;
333 | padding: 5px;
334 | border: 3px solid red;
335 | }
336 |
337 | .footnote:target {
338 | background-color: #ffa;
339 | }
340 |
341 | .line-block {
342 | display: block;
343 | margin-top: 1em;
344 | margin-bottom: 1em;
345 | }
346 |
347 | .line-block .line-block {
348 | margin-top: 0;
349 | margin-bottom: 0;
350 | margin-left: 1.5em;
351 | }
352 |
353 | .guilabel, .menuselection {
354 | font-family: sans-serif;
355 | }
356 |
357 | .accelerator {
358 | text-decoration: underline;
359 | }
360 |
361 | .classifier {
362 | font-style: oblique;
363 | }
364 |
365 | abbr, acronym {
366 | border-bottom: dotted 1px;
367 | cursor: help;
368 | }
369 |
370 | /* -- code displays --------------------------------------------------------- */
371 |
372 | pre {
373 | overflow: auto;
374 | overflow-y: hidden; /* fixes display issues on Chrome browsers */
375 | }
376 |
377 | td.linenos pre {
378 | padding: 5px 0px;
379 | border: 0;
380 | background-color: transparent;
381 | color: #aaa;
382 | }
383 |
384 | table.highlighttable {
385 | margin-left: 0.5em;
386 | }
387 |
388 | table.highlighttable td {
389 | padding: 0 0.5em 0 0.5em;
390 | }
391 |
392 | tt.descname {
393 | background-color: transparent;
394 | font-weight: bold;
395 | font-size: 1.2em;
396 | }
397 |
398 | tt.descclassname {
399 | background-color: transparent;
400 | }
401 |
402 | tt.xref, a tt {
403 | background-color: transparent;
404 | font-weight: bold;
405 | }
406 |
407 | h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
408 | background-color: transparent;
409 | }
410 |
411 | .viewcode-link {
412 | float: right;
413 | }
414 |
415 | .viewcode-back {
416 | float: right;
417 | font-family: sans-serif;
418 | }
419 |
420 | div.viewcode-block:target {
421 | margin: -1px -10px;
422 | padding: 0 10px;
423 | }
424 |
425 | /* -- math display ---------------------------------------------------------- */
426 |
427 | img.math {
428 | vertical-align: middle;
429 | }
430 |
431 | div.body div.math p {
432 | text-align: center;
433 | }
434 |
435 | span.eqno {
436 | float: right;
437 | }
438 |
439 | /* -- printout stylesheet --------------------------------------------------- */
440 |
441 | @media print {
442 | div.document,
443 | div.documentwrapper,
444 | div.bodywrapper {
445 | margin: 0 !important;
446 | width: 100%;
447 | }
448 |
449 | div.sphinxsidebar,
450 | div.related,
451 | div.footer,
452 | #top-link {
453 | display: none;
454 | }
455 | }
--------------------------------------------------------------------------------
/docs/_build/html/_static/doctools.js:
--------------------------------------------------------------------------------
1 | /*
2 | * doctools.js
3 | * ~~~~~~~~~~~
4 | *
5 | * Sphinx JavaScript utilities for all documentation.
6 | *
7 | * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
8 | * :license: BSD, see LICENSE for details.
9 | *
10 | */
11 |
12 | /**
13 | * select a different prefix for underscore
14 | */
15 | $u = _.noConflict();
16 |
17 | /**
18 | * make the code below compatible with browsers without
19 | * an installed firebug like debugger
20 | if (!window.console || !console.firebug) {
21 | var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
22 | "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
23 | "profile", "profileEnd"];
24 | window.console = {};
25 | for (var i = 0; i < names.length; ++i)
26 | window.console[names[i]] = function() {};
27 | }
28 | */
29 |
30 | /**
31 | * small helper function to urldecode strings
32 | */
33 | jQuery.urldecode = function(x) {
34 | return decodeURIComponent(x).replace(/\+/g, ' ');
35 | };
36 |
37 | /**
38 | * small helper function to urlencode strings
39 | */
40 | jQuery.urlencode = encodeURIComponent;
41 |
42 | /**
43 | * This function returns the parsed url parameters of the
44 | * current request. Multiple values per key are supported,
45 | * it will always return arrays of strings for the value parts.
46 | */
47 | jQuery.getQueryParameters = function(s) {
48 | if (typeof s === 'undefined')
49 | s = document.location.search;
50 | var parts = s.substr(s.indexOf('?') + 1).split('&');
51 | var result = {};
52 | for (var i = 0; i < parts.length; i++) {
53 | var tmp = parts[i].split('=', 2);
54 | var key = jQuery.urldecode(tmp[0]);
55 | var value = jQuery.urldecode(tmp[1]);
56 | if (key in result)
57 | result[key].push(value);
58 | else
59 | result[key] = [value];
60 | }
61 | return result;
62 | };
63 |
64 | /**
65 | * highlight a given string on a jquery object by wrapping it in
66 | * span elements with the given class name.
67 | */
68 | jQuery.fn.highlightText = function(text, className) {
69 | function highlight(node, addItems) {
70 | if (node.nodeType === 3) {
71 | var val = node.nodeValue;
72 | var pos = val.toLowerCase().indexOf(text);
73 | if (pos >= 0 &&
74 | !jQuery(node.parentNode).hasClass(className) &&
75 | !jQuery(node.parentNode).hasClass("nohighlight")) {
76 | var span;
77 | var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
78 | if (isInSVG) {
79 | span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
80 | } else {
81 | span = document.createElement("span");
82 | span.className = className;
83 | }
84 | span.appendChild(document.createTextNode(val.substr(pos, text.length)));
85 | node.parentNode.insertBefore(span, node.parentNode.insertBefore(
86 | document.createTextNode(val.substr(pos + text.length)),
87 | node.nextSibling));
88 | node.nodeValue = val.substr(0, pos);
89 | if (isInSVG) {
90 | var bbox = span.getBBox();
91 | var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
92 | rect.x.baseVal.value = bbox.x;
93 | rect.y.baseVal.value = bbox.y;
94 | rect.width.baseVal.value = bbox.width;
95 | rect.height.baseVal.value = bbox.height;
96 | rect.setAttribute('class', className);
97 | var parentOfText = node.parentNode.parentNode;
98 | addItems.push({
99 | "parent": node.parentNode,
100 | "target": rect});
101 | }
102 | }
103 | }
104 | else if (!jQuery(node).is("button, select, textarea")) {
105 | jQuery.each(node.childNodes, function() {
106 | highlight(this, addItems);
107 | });
108 | }
109 | }
110 | var addItems = [];
111 | var result = this.each(function() {
112 | highlight(this, addItems);
113 | });
114 | for (var i = 0; i < addItems.length; ++i) {
115 | jQuery(addItems[i].parent).before(addItems[i].target);
116 | }
117 | return result;
118 | };
119 |
120 | /*
121 | * backward compatibility for jQuery.browser
122 | * This will be supported until firefox bug is fixed.
123 | */
124 | if (!jQuery.browser) {
125 | jQuery.uaMatch = function(ua) {
126 | ua = ua.toLowerCase();
127 |
128 | var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
129 | /(webkit)[ \/]([\w.]+)/.exec(ua) ||
130 | /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
131 | /(msie) ([\w.]+)/.exec(ua) ||
132 | ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
133 | [];
134 |
135 | return {
136 | browser: match[ 1 ] || "",
137 | version: match[ 2 ] || "0"
138 | };
139 | };
140 | jQuery.browser = {};
141 | jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
142 | }
143 |
144 | /**
145 | * Small JavaScript module for the documentation.
146 | */
147 | var Documentation = {
148 |
149 | init : function() {
150 | this.fixFirefoxAnchorBug();
151 | this.highlightSearchWords();
152 | this.initIndexTable();
153 | if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
154 | this.initOnKeyListeners();
155 | }
156 | },
157 |
158 | /**
159 | * i18n support
160 | */
161 | TRANSLATIONS : {},
162 | PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
163 | LOCALE : 'unknown',
164 |
165 | // gettext and ngettext don't access this so that the functions
166 | // can safely bound to a different name (_ = Documentation.gettext)
167 | gettext : function(string) {
168 | var translated = Documentation.TRANSLATIONS[string];
169 | if (typeof translated === 'undefined')
170 | return string;
171 | return (typeof translated === 'string') ? translated : translated[0];
172 | },
173 |
174 | ngettext : function(singular, plural, n) {
175 | var translated = Documentation.TRANSLATIONS[singular];
176 | if (typeof translated === 'undefined')
177 | return (n == 1) ? singular : plural;
178 | return translated[Documentation.PLURALEXPR(n)];
179 | },
180 |
181 | addTranslations : function(catalog) {
182 | for (var key in catalog.messages)
183 | this.TRANSLATIONS[key] = catalog.messages[key];
184 | this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
185 | this.LOCALE = catalog.locale;
186 | },
187 |
188 | /**
189 | * add context elements like header anchor links
190 | */
191 | addContextElements : function() {
192 | $('div[id] > :header:first').each(function() {
193 | $('\u00B6').
194 | attr('href', '#' + this.id).
195 | attr('title', _('Permalink to this headline')).
196 | appendTo(this);
197 | });
198 | $('dt[id]').each(function() {
199 | $('\u00B6').
200 | attr('href', '#' + this.id).
201 | attr('title', _('Permalink to this definition')).
202 | appendTo(this);
203 | });
204 | },
205 |
206 | /**
207 | * workaround a firefox stupidity
208 | * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
209 | */
210 | fixFirefoxAnchorBug : function() {
211 | if (document.location.hash && $.browser.mozilla)
212 | window.setTimeout(function() {
213 | document.location.href += '';
214 | }, 10);
215 | },
216 |
217 | /**
218 | * highlight the search words provided in the url in the text
219 | */
220 | highlightSearchWords : function() {
221 | var params = $.getQueryParameters();
222 | var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
223 | if (terms.length) {
224 | var body = $('div.body');
225 | if (!body.length) {
226 | body = $('body');
227 | }
228 | window.setTimeout(function() {
229 | $.each(terms, function() {
230 | body.highlightText(this.toLowerCase(), 'highlighted');
231 | });
232 | }, 10);
233 | $('
42 |
139 |
153 |
154 |
43 |
138 |
44 |
45 |
137 |
46 |
61 | wsipre¶
47 |wsipre (Whole-Slide Image PREprocessing) is a small 48 | Python package to handle whole-slide images (WSI; also known as 49 | virtual slides) with region-level annotations.
50 |wsipre is a wrapper of the OpenSlide Python package, an interface to the 51 | excellent OpenSlide C library which allows reading WSIs. wsipre 52 | conserves OpenSlide Python’s API and extends it to handle WSI annotations and 53 | to perform processing tasks. The underlying objective is the preparation of 54 | WSIs for Machine Learning (particularly Deep Learning).
55 |Other Python projects providing overlapping functionality (non-exhaustive list):
56 |-
57 |
- py-wsi 58 |
- WholeSlideImageSampler 59 |
62 |
71 | User guide¶
63 |
64 |
70 | -
65 |
- Quick introduction 66 |
- Jupyter notebook demo 67 |
- Beyond wsipre 68 |
72 |
112 | Installation¶
73 |
74 |
103 |
111 | Main dependencies¶
75 |wsipre was developed in Python version 3.7.1. It has not been tested with 76 | earlier versions, but it should generally work with Python version 3.*. 77 | The main requirements are the following packages (the versions used for 78 | development are listed):
79 |80 |87 |81 |
86 |- OpenSlide C library (v3.4.1)
82 |- OpenSlide Python (v1.1.1)
83 |- Numpy (v1.15.4)
84 |- OpenCV-Python (v3.4.4.19)
85 |
88 |
100 |
101 |
102 | Note
89 |Some linux package managers currently distribute an outdated version 90 | of the OpenSlide C library: version 3.4.0. This version lacks support for 91 | some recent WSI formats, displaying wrong tiled downsampled views of the 92 | slides and crashing upon reading some regions. To avoid these problems 93 | please make sure you have OpenSlide version 3.4.1.
94 |You can check the installed version by running the following code in a 95 | Python interpreter:
96 |>>> import openslide
97 | >>> openslide.__library_version__
98 | '3.4.1'
99 |
113 |
117 |
126 | License¶
114 |This project is licensed under the terms of the MIT license. See LICENSE 115 | file for details.
116 |
127 |
134 |
135 |
136 | Indices and tables¶
128 |-
129 |
- Index 130 |
- Module Index 131 |
- Search Page 132 |
' + _('Hide Search Matches') + '
') 235 | .appendTo($('#searchbox')); 236 | } 237 | }, 238 | 239 | /** 240 | * init the domain index toggle buttons 241 | */ 242 | initIndexTable : function() { 243 | var togglers = $('img.toggler').click(function() { 244 | var src = $(this).attr('src'); 245 | var idnum = $(this).attr('id').substr(7); 246 | $('tr.cg-' + idnum).toggle(); 247 | if (src.substr(-9) === 'minus.png') 248 | $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); 249 | else 250 | $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); 251 | }).css('display', ''); 252 | if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { 253 | togglers.click(); 254 | } 255 | }, 256 | 257 | /** 258 | * helper function to hide the search marks again 259 | */ 260 | hideSearchWords : function() { 261 | $('#searchbox .highlight-link').fadeOut(300); 262 | $('span.highlighted').removeClass('highlighted'); 263 | }, 264 | 265 | /** 266 | * make the url absolute 267 | */ 268 | makeURL : function(relativeURL) { 269 | return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; 270 | }, 271 | 272 | /** 273 | * get the current relative url 274 | */ 275 | getCurrentURL : function() { 276 | var path = document.location.pathname; 277 | var parts = path.split(/\//); 278 | $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { 279 | if (this === '..') 280 | parts.pop(); 281 | }); 282 | var url = parts.join('/'); 283 | return path.substring(url.lastIndexOf('/') + 1, path.length - 1); 284 | }, 285 | 286 | initOnKeyListeners: function() { 287 | $(document).keyup(function(event) { 288 | var activeElementType = document.activeElement.tagName; 289 | // don't navigate when in search box or textarea 290 | if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') { 291 | switch (event.keyCode) { 292 | case 37: // left 293 | var prevHref = $('link[rel="prev"]').prop('href'); 294 | if (prevHref) { 295 | window.location.href = prevHref; 296 | return false; 297 | } 298 | case 39: // right 299 | var nextHref = $('link[rel="next"]').prop('href'); 300 | if (nextHref) { 301 | window.location.href = nextHref; 302 | return false; 303 | } 304 | } 305 | } 306 | }); 307 | } 308 | }; 309 | 310 | // quick alias for translations 311 | _ = Documentation.gettext; 312 | 313 | $(document).ready(function() { 314 | Documentation.init(); 315 | }); 316 | -------------------------------------------------------------------------------- /docs/_build/html/_static/underscore.js: -------------------------------------------------------------------------------- 1 | // Underscore.js 1.3.1 2 | // (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. 3 | // Underscore is freely distributable under the MIT license. 4 | // Portions of Underscore are inspired or borrowed from Prototype, 5 | // Oliver Steele's Functional, and John Resig's Micro-Templating. 6 | // For all details and documentation: 7 | // http://documentcloud.github.com/underscore 8 | (function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source== 9 | c.source&&a.global==c.global&&a.multiline==c.multiline&&a.ignoreCase==c.ignoreCase}if(typeof a!="object"||typeof c!="object")return false;for(var f=d.length;f--;)if(d[f]==a)return true;d.push(a);var f=0,g=true;if(e=="[object Array]"){if(f=a.length,g=f==c.length)for(;f--;)if(!(g=f in a==f in c&&q(a[f],c[f],d)))break}else{if("constructor"in a!="constructor"in c||a.constructor!=c.constructor)return false;for(var h in a)if(b.has(a,h)&&(f++,!(g=b.has(c,h)&&q(a[h],c[h],d))))break;if(g){for(h in c)if(b.has(c, 10 | h)&&!f--)break;g=!f}}d.pop();return g}var r=this,G=r._,n={},k=Array.prototype,o=Object.prototype,i=k.slice,H=k.unshift,l=o.toString,I=o.hasOwnProperty,w=k.forEach,x=k.map,y=k.reduce,z=k.reduceRight,A=k.filter,B=k.every,C=k.some,p=k.indexOf,D=k.lastIndexOf,o=Array.isArray,J=Object.keys,s=Function.prototype.bind,b=function(a){return new m(a)};if(typeof exports!=="undefined"){if(typeof module!=="undefined"&&module.exports)exports=module.exports=b;exports._=b}else r._=b;b.VERSION="1.3.1";var j=b.each= 11 | b.forEach=function(a,c,d){if(a!=null)if(w&&a.forEach===w)a.forEach(c,d);else if(a.length===+a.length)for(var e=0,f=a.length;e21 | wsipre 0.1.2 documentation 22 |
36 |
237 |
248 |
255 |
256 |
257 |
258 |
--------------------------------------------------------------------------------
/docs/_build/html/_static/basic.css:
--------------------------------------------------------------------------------
1 | /*
2 | * basic.css
3 | * ~~~~~~~~~
4 | *
5 | * Sphinx stylesheet -- basic theme.
6 | *
7 | * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
8 | * :license: BSD, see LICENSE for details.
9 | *
10 | */
11 |
12 | /* -- main layout ----------------------------------------------------------- */
13 |
14 | div.clearer {
15 | clear: both;
16 | }
17 |
18 | /* -- relbar ---------------------------------------------------------------- */
19 |
20 | div.related {
21 | width: 100%;
22 | font-size: 90%;
23 | }
24 |
25 | div.related h3 {
26 | display: none;
27 | }
28 |
29 | div.related ul {
30 | margin: 0;
31 | padding: 0 0 0 10px;
32 | list-style: none;
33 | }
34 |
35 | div.related li {
36 | display: inline;
37 | }
38 |
39 | div.related li.right {
40 | float: right;
41 | margin-right: 5px;
42 | }
43 |
44 | /* -- sidebar --------------------------------------------------------------- */
45 |
46 | div.sphinxsidebarwrapper {
47 | padding: 10px 5px 0 10px;
48 | }
49 |
50 | div.sphinxsidebar {
51 | float: left;
52 | width: 15rem;
53 | margin-left: -100%;
54 | font-size: 90%;
55 | word-wrap: break-word;
56 | overflow-wrap : break-word;
57 | }
58 |
59 | div.sphinxsidebar ul {
60 | list-style: none;
61 | }
62 |
63 | div.sphinxsidebar ul ul,
64 | div.sphinxsidebar ul.want-points {
65 | margin-left: 20px;
66 | list-style: square;
67 | }
68 |
69 | div.sphinxsidebar ul ul {
70 | margin-top: 0;
71 | margin-bottom: 0;
72 | }
73 |
74 | div.sphinxsidebar form {
75 | margin-top: 10px;
76 | }
77 |
78 | div.sphinxsidebar input {
79 | border: 1px solid #98dbcc;
80 | font-family: sans-serif;
81 | font-size: 1em;
82 | }
83 |
84 | div.sphinxsidebar #searchbox form.search {
85 | overflow: hidden;
86 | }
87 |
88 | div.sphinxsidebar #searchbox input[type="text"] {
89 | float: left;
90 | width: 80%;
91 | padding: 0.25em;
92 | box-sizing: border-box;
93 | }
94 |
95 | div.sphinxsidebar #searchbox input[type="submit"] {
96 | float: left;
97 | width: 20%;
98 | border-left: none;
99 | padding: 0.25em;
100 | box-sizing: border-box;
101 | }
102 |
103 |
104 | img {
105 | border: 0;
106 | max-width: 100%;
107 | }
108 |
109 | /* -- search page ----------------------------------------------------------- */
110 |
111 | ul.search {
112 | margin: 10px 0 0 20px;
113 | padding: 0;
114 | }
115 |
116 | ul.search li {
117 | padding: 5px 0 5px 20px;
118 | background-image: url(file.png);
119 | background-repeat: no-repeat;
120 | background-position: 0 7px;
121 | }
122 |
123 | ul.search li a {
124 | font-weight: bold;
125 | }
126 |
127 | ul.search li div.context {
128 | color: #888;
129 | margin: 2px 0 0 30px;
130 | text-align: left;
131 | }
132 |
133 | ul.keywordmatches li.goodmatch a {
134 | font-weight: bold;
135 | }
136 |
137 | /* -- index page ------------------------------------------------------------ */
138 |
139 | table.contentstable {
140 | width: 90%;
141 | margin-left: auto;
142 | margin-right: auto;
143 | }
144 |
145 | table.contentstable p.biglink {
146 | line-height: 150%;
147 | }
148 |
149 | a.biglink {
150 | font-size: 1.3em;
151 | }
152 |
153 | span.linkdescr {
154 | font-style: italic;
155 | padding-top: 5px;
156 | font-size: 90%;
157 | }
158 |
159 | /* -- general index --------------------------------------------------------- */
160 |
161 | table.indextable {
162 | width: 100%;
163 | }
164 |
165 | table.indextable td {
166 | text-align: left;
167 | vertical-align: top;
168 | }
169 |
170 | table.indextable ul {
171 | margin-top: 0;
172 | margin-bottom: 0;
173 | list-style-type: none;
174 | }
175 |
176 | table.indextable > tbody > tr > td > ul {
177 | padding-left: 0em;
178 | }
179 |
180 | table.indextable tr.pcap {
181 | height: 10px;
182 | }
183 |
184 | table.indextable tr.cap {
185 | margin-top: 10px;
186 | background-color: #f2f2f2;
187 | }
188 |
189 | img.toggler {
190 | margin-right: 3px;
191 | margin-top: 3px;
192 | cursor: pointer;
193 | }
194 |
195 | div.modindex-jumpbox {
196 | border-top: 1px solid #ddd;
197 | border-bottom: 1px solid #ddd;
198 | margin: 1em 0 1em 0;
199 | padding: 0.4em;
200 | }
201 |
202 | div.genindex-jumpbox {
203 | border-top: 1px solid #ddd;
204 | border-bottom: 1px solid #ddd;
205 | margin: 1em 0 1em 0;
206 | padding: 0.4em;
207 | }
208 |
209 | /* -- domain module index --------------------------------------------------- */
210 |
211 | table.modindextable td {
212 | padding: 2px;
213 | border-collapse: collapse;
214 | }
215 |
216 | /* -- general body styles --------------------------------------------------- */
217 |
218 | div.body {
219 | min-width: 450px;
220 | max-width: 800px;
221 | }
222 |
223 | div.body p, div.body dd, div.body li, div.body blockquote {
224 | -moz-hyphens: auto;
225 | -ms-hyphens: auto;
226 | -webkit-hyphens: auto;
227 | hyphens: auto;
228 | }
229 |
230 | a.headerlink {
231 | visibility: hidden;
232 | }
233 |
234 | h1:hover > a.headerlink,
235 | h2:hover > a.headerlink,
236 | h3:hover > a.headerlink,
237 | h4:hover > a.headerlink,
238 | h5:hover > a.headerlink,
239 | h6:hover > a.headerlink,
240 | dt:hover > a.headerlink,
241 | caption:hover > a.headerlink,
242 | p.caption:hover > a.headerlink,
243 | div.code-block-caption:hover > a.headerlink {
244 | visibility: visible;
245 | }
246 |
247 | div.body p.caption {
248 | text-align: inherit;
249 | }
250 |
251 | div.body td {
252 | text-align: left;
253 | }
254 |
255 | .first {
256 | margin-top: 0 !important;
257 | }
258 |
259 | p.rubric {
260 | margin-top: 30px;
261 | font-weight: bold;
262 | }
263 |
264 | img.align-left, .figure.align-left, object.align-left {
265 | clear: left;
266 | float: left;
267 | margin-right: 1em;
268 | }
269 |
270 | img.align-right, .figure.align-right, object.align-right {
271 | clear: right;
272 | float: right;
273 | margin-left: 1em;
274 | }
275 |
276 | img.align-center, .figure.align-center, object.align-center {
277 | display: block;
278 | margin-left: auto;
279 | margin-right: auto;
280 | }
281 |
282 | .align-left {
283 | text-align: left;
284 | }
285 |
286 | .align-center {
287 | text-align: center;
288 | }
289 |
290 | .align-right {
291 | text-align: right;
292 | }
293 |
294 | /* -- sidebars -------------------------------------------------------------- */
295 |
296 | div.sidebar {
297 | margin: 0 0 0.5em 1em;
298 | border: 1px solid #ddb;
299 | padding: 7px 7px 0 7px;
300 | background-color: #ffe;
301 | width: 40%;
302 | float: right;
303 | }
304 |
305 | p.sidebar-title {
306 | font-weight: bold;
307 | }
308 |
309 | /* -- topics ---------------------------------------------------------------- */
310 |
311 | div.topic {
312 | border: 1px solid #ccc;
313 | padding: 7px 7px 0 7px;
314 | margin: 10px 0 10px 0;
315 | }
316 |
317 | p.topic-title {
318 | font-size: 1.1em;
319 | font-weight: bold;
320 | margin-top: 10px;
321 | }
322 |
323 | /* -- admonitions ----------------------------------------------------------- */
324 |
325 | div.admonition {
326 | margin-top: 10px;
327 | margin-bottom: 10px;
328 | padding: 7px;
329 | }
330 |
331 | div.admonition dt {
332 | font-weight: bold;
333 | }
334 |
335 | div.admonition dl {
336 | margin-bottom: 0;
337 | }
338 |
339 | p.admonition-title {
340 | margin: 0px 10px 5px 0px;
341 | font-weight: bold;
342 | }
343 |
344 | div.body p.centered {
345 | text-align: center;
346 | margin-top: 25px;
347 | }
348 |
349 | /* -- tables ---------------------------------------------------------------- */
350 |
351 | table.docutils {
352 | border: 0;
353 | border-collapse: collapse;
354 | }
355 |
356 | table.align-center {
357 | margin-left: auto;
358 | margin-right: auto;
359 | }
360 |
361 | table caption span.caption-number {
362 | font-style: italic;
363 | }
364 |
365 | table caption span.caption-text {
366 | }
367 |
368 | table.docutils td, table.docutils th {
369 | padding: 1px 8px 1px 5px;
370 | border-top: 0;
371 | border-left: 0;
372 | border-right: 0;
373 | border-bottom: 1px solid #aaa;
374 | }
375 |
376 | table.footnote td, table.footnote th {
377 | border: 0 !important;
378 | }
379 |
380 | th {
381 | text-align: left;
382 | padding-right: 5px;
383 | }
384 |
385 | table.citation {
386 | border-left: solid 1px gray;
387 | margin-left: 1px;
388 | }
389 |
390 | table.citation td {
391 | border-bottom: none;
392 | }
393 |
394 | /* -- figures --------------------------------------------------------------- */
395 |
396 | div.figure {
397 | margin: 0.5em;
398 | padding: 0.5em;
399 | }
400 |
401 | div.figure p.caption {
402 | padding: 0.3em;
403 | }
404 |
405 | div.figure p.caption span.caption-number {
406 | font-style: italic;
407 | }
408 |
409 | div.figure p.caption span.caption-text {
410 | }
411 |
412 | /* -- field list styles ----------------------------------------------------- */
413 |
414 | table.field-list td, table.field-list th {
415 | border: 0 !important;
416 | }
417 |
418 | .field-list ul {
419 | margin: 0;
420 | padding-left: 1em;
421 | }
422 |
423 | .field-list p {
424 | margin: 0;
425 | }
426 |
427 | .field-name {
428 | -moz-hyphens: manual;
429 | -ms-hyphens: manual;
430 | -webkit-hyphens: manual;
431 | hyphens: manual;
432 | }
433 |
434 | /* -- hlist styles ---------------------------------------------------------- */
435 |
436 | table.hlist td {
437 | vertical-align: top;
438 | }
439 |
440 |
441 | /* -- other body styles ----------------------------------------------------- */
442 |
443 | ol.arabic {
444 | list-style: decimal;
445 | }
446 |
447 | ol.loweralpha {
448 | list-style: lower-alpha;
449 | }
450 |
451 | ol.upperalpha {
452 | list-style: upper-alpha;
453 | }
454 |
455 | ol.lowerroman {
456 | list-style: lower-roman;
457 | }
458 |
459 | ol.upperroman {
460 | list-style: upper-roman;
461 | }
462 |
463 | dl {
464 | margin-bottom: 15px;
465 | }
466 |
467 | dd p {
468 | margin-top: 0px;
469 | }
470 |
471 | dd ul, dd table {
472 | margin-bottom: 10px;
473 | }
474 |
475 | dd {
476 | margin-top: 3px;
477 | margin-bottom: 10px;
478 | margin-left: 30px;
479 | }
480 |
481 | dt:target, span.highlighted {
482 | background-color: #fbe54e;
483 | }
484 |
485 | rect.highlighted {
486 | fill: #fbe54e;
487 | }
488 |
489 | dl.glossary dt {
490 | font-weight: bold;
491 | font-size: 1.1em;
492 | }
493 |
494 | .optional {
495 | font-size: 1.3em;
496 | }
497 |
498 | .sig-paren {
499 | font-size: larger;
500 | }
501 |
502 | .versionmodified {
503 | font-style: italic;
504 | }
505 |
506 | .system-message {
507 | background-color: #fda;
508 | padding: 5px;
509 | border: 3px solid red;
510 | }
511 |
512 | .footnote:target {
513 | background-color: #ffa;
514 | }
515 |
516 | .line-block {
517 | display: block;
518 | margin-top: 1em;
519 | margin-bottom: 1em;
520 | }
521 |
522 | .line-block .line-block {
523 | margin-top: 0;
524 | margin-bottom: 0;
525 | margin-left: 1.5em;
526 | }
527 |
528 | .guilabel, .menuselection {
529 | font-family: sans-serif;
530 | }
531 |
532 | .accelerator {
533 | text-decoration: underline;
534 | }
535 |
536 | .classifier {
537 | font-style: oblique;
538 | }
539 |
540 | abbr, acronym {
541 | border-bottom: dotted 1px;
542 | cursor: help;
543 | }
544 |
545 | /* -- code displays --------------------------------------------------------- */
546 |
547 | pre {
548 | overflow: auto;
549 | overflow-y: hidden; /* fixes display issues on Chrome browsers */
550 | }
551 |
552 | span.pre {
553 | -moz-hyphens: none;
554 | -ms-hyphens: none;
555 | -webkit-hyphens: none;
556 | hyphens: none;
557 | }
558 |
559 | td.linenos pre {
560 | padding: 5px 0px;
561 | border: 0;
562 | background-color: transparent;
563 | color: #aaa;
564 | }
565 |
566 | table.highlighttable {
567 | margin-left: 0.5em;
568 | }
569 |
570 | table.highlighttable td {
571 | padding: 0 0.5em 0 0.5em;
572 | }
573 |
574 | div.code-block-caption {
575 | padding: 2px 5px;
576 | font-size: small;
577 | }
578 |
579 | div.code-block-caption code {
580 | background-color: transparent;
581 | }
582 |
583 | div.code-block-caption + div > div.highlight > pre {
584 | margin-top: 0;
585 | }
586 |
587 | div.code-block-caption span.caption-number {
588 | padding: 0.1em 0.3em;
589 | font-style: italic;
590 | }
591 |
592 | div.code-block-caption span.caption-text {
593 | }
594 |
595 | div.literal-block-wrapper {
596 | padding: 1em 1em 0;
597 | }
598 |
599 | div.literal-block-wrapper div.highlight {
600 | margin: 0;
601 | }
602 |
603 | code.descname {
604 | background-color: transparent;
605 | font-weight: bold;
606 | font-size: 1.2em;
607 | }
608 |
609 | code.descclassname {
610 | background-color: transparent;
611 | }
612 |
613 | code.xref, a code {
614 | background-color: transparent;
615 | font-weight: bold;
616 | }
617 |
618 | h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
619 | background-color: transparent;
620 | }
621 |
622 | .viewcode-link {
623 | float: right;
624 | }
625 |
626 | .viewcode-back {
627 | float: right;
628 | font-family: sans-serif;
629 | }
630 |
631 | div.viewcode-block:target {
632 | margin: -1px -10px;
633 | padding: 0 10px;
634 | }
635 |
636 | /* -- math display ---------------------------------------------------------- */
637 |
638 | img.math {
639 | vertical-align: middle;
640 | }
641 |
642 | div.body div.math p {
643 | text-align: center;
644 | }
645 |
646 | span.eqno {
647 | float: right;
648 | }
649 |
650 | span.eqno a.headerlink {
651 | position: relative;
652 | left: 0px;
653 | z-index: 1;
654 | }
655 |
656 | div.math:hover a.headerlink {
657 | visibility: visible;
658 | }
659 |
660 | /* -- printout stylesheet --------------------------------------------------- */
661 |
662 | @media print {
663 | div.document,
664 | div.documentwrapper,
665 | div.bodywrapper {
666 | margin: 0 !important;
667 | width: 100%;
668 | }
669 |
670 | div.sphinxsidebar,
671 | div.related,
672 | div.footer,
673 | #top-link {
674 | display: none;
675 | }
676 | }
--------------------------------------------------------------------------------
/docs/_build/html/_static/alabaster.css:
--------------------------------------------------------------------------------
1 | @import url("basic.css");
2 |
3 | /* -- page layout ----------------------------------------------------------- */
4 |
5 | body {
6 | font-family: Georgia, serif;
7 | font-size: 17px;
8 | background-color: #fff;
9 | color: #000;
10 | margin: 0;
11 | padding: 0;
12 | }
13 |
14 |
15 | div.document {
16 | width: 940px;
17 | margin: 30px auto 0 auto;
18 | }
19 |
20 | div.documentwrapper {
21 | float: left;
22 | width: 100%;
23 | }
24 |
25 | div.bodywrapper {
26 | margin: 0 0 0 220px;
27 | }
28 |
29 | div.sphinxsidebar {
30 | width: 220px;
31 | font-size: 14px;
32 | line-height: 1.5;
33 | }
34 |
35 | hr {
36 | border: 1px solid #B1B4B6;
37 | }
38 |
39 | div.body {
40 | background-color: #fff;
41 | color: #3E4349;
42 | padding: 0 30px 0 30px;
43 | }
44 |
45 | div.body > .section {
46 | text-align: left;
47 | }
48 |
49 | div.footer {
50 | width: 940px;
51 | margin: 20px auto 30px auto;
52 | font-size: 14px;
53 | color: #888;
54 | text-align: right;
55 | }
56 |
57 | div.footer a {
58 | color: #888;
59 | }
60 |
61 | p.caption {
62 | font-family: inherit;
63 | font-size: inherit;
64 | }
65 |
66 |
67 | div.relations {
68 | display: none;
69 | }
70 |
71 |
72 | div.sphinxsidebar a {
73 | color: #444;
74 | text-decoration: none;
75 | border-bottom: 1px dotted #999;
76 | }
77 |
78 | div.sphinxsidebar a:hover {
79 | border-bottom: 1px solid #999;
80 | }
81 |
82 | div.sphinxsidebarwrapper {
83 | padding: 18px 10px;
84 | }
85 |
86 | div.sphinxsidebarwrapper p.logo {
87 | padding: 0;
88 | margin: -10px 0 0 0px;
89 | text-align: center;
90 | }
91 |
92 | div.sphinxsidebarwrapper h1.logo {
93 | margin-top: -10px;
94 | text-align: center;
95 | margin-bottom: 5px;
96 | text-align: left;
97 | }
98 |
99 | div.sphinxsidebarwrapper h1.logo-name {
100 | margin-top: 0px;
101 | }
102 |
103 | div.sphinxsidebarwrapper p.blurb {
104 | margin-top: 0;
105 | font-style: normal;
106 | }
107 |
108 | div.sphinxsidebar h3,
109 | div.sphinxsidebar h4 {
110 | font-family: Georgia, serif;
111 | color: #444;
112 | font-size: 24px;
113 | font-weight: normal;
114 | margin: 0 0 5px 0;
115 | padding: 0;
116 | }
117 |
118 | div.sphinxsidebar h4 {
119 | font-size: 20px;
120 | }
121 |
122 | div.sphinxsidebar h3 a {
123 | color: #444;
124 | }
125 |
126 | div.sphinxsidebar p.logo a,
127 | div.sphinxsidebar h3 a,
128 | div.sphinxsidebar p.logo a:hover,
129 | div.sphinxsidebar h3 a:hover {
130 | border: none;
131 | }
132 |
133 | div.sphinxsidebar p {
134 | color: #555;
135 | margin: 10px 0;
136 | }
137 |
138 | div.sphinxsidebar ul {
139 | margin: 10px 0;
140 | padding: 0;
141 | color: #000;
142 | }
143 |
144 | div.sphinxsidebar ul li.toctree-l1 > a {
145 | font-size: 120%;
146 | }
147 |
148 | div.sphinxsidebar ul li.toctree-l2 > a {
149 | font-size: 110%;
150 | }
151 |
152 | div.sphinxsidebar input {
153 | border: 1px solid #CCC;
154 | font-family: Georgia, serif;
155 | font-size: 1em;
156 | }
157 |
158 | div.sphinxsidebar hr {
159 | border: none;
160 | height: 1px;
161 | color: #AAA;
162 | background: #AAA;
163 |
164 | text-align: left;
165 | margin-left: 0;
166 | width: 50%;
167 | }
168 |
169 | div.sphinxsidebar .badge {
170 | border-bottom: none;
171 | }
172 |
173 | div.sphinxsidebar .badge:hover {
174 | border-bottom: none;
175 | }
176 |
177 | /* To address an issue with donation coming after search */
178 | div.sphinxsidebar h3.donation {
179 | margin-top: 10px;
180 | }
181 |
182 | /* -- body styles ----------------------------------------------------------- */
183 |
184 | a {
185 | color: #004B6B;
186 | text-decoration: underline;
187 | }
188 |
189 | a:hover {
190 | color: #6D4100;
191 | text-decoration: underline;
192 | }
193 |
194 | div.body h1,
195 | div.body h2,
196 | div.body h3,
197 | div.body h4,
198 | div.body h5,
199 | div.body h6 {
200 | font-family: Georgia, serif;
201 | font-weight: normal;
202 | margin: 30px 0px 10px 0px;
203 | padding: 0;
204 | }
205 |
206 | div.body h1 { margin-top: 0; padding-top: 0; font-size: 240%; }
207 | div.body h2 { font-size: 180%; }
208 | div.body h3 { font-size: 150%; }
209 | div.body h4 { font-size: 130%; }
210 | div.body h5 { font-size: 100%; }
211 | div.body h6 { font-size: 100%; }
212 |
213 | a.headerlink {
214 | color: #DDD;
215 | padding: 0 4px;
216 | text-decoration: none;
217 | }
218 |
219 | a.headerlink:hover {
220 | color: #444;
221 | background: #EAEAEA;
222 | }
223 |
224 | div.body p, div.body dd, div.body li {
225 | line-height: 1.4em;
226 | }
227 |
228 | div.admonition {
229 | margin: 20px 0px;
230 | padding: 10px 30px;
231 | background-color: #EEE;
232 | border: 1px solid #CCC;
233 | }
234 |
235 | div.admonition tt.xref, div.admonition code.xref, div.admonition a tt {
236 | background-color: #FBFBFB;
237 | border-bottom: 1px solid #fafafa;
238 | }
239 |
240 | div.admonition p.admonition-title {
241 | font-family: Georgia, serif;
242 | font-weight: normal;
243 | font-size: 24px;
244 | margin: 0 0 10px 0;
245 | padding: 0;
246 | line-height: 1;
247 | }
248 |
249 | div.admonition p.last {
250 | margin-bottom: 0;
251 | }
252 |
253 | div.highlight {
254 | background-color: #fff;
255 | }
256 |
257 | dt:target, .highlight {
258 | background: #FAF3E8;
259 | }
260 |
261 | div.warning {
262 | background-color: #FCC;
263 | border: 1px solid #FAA;
264 | }
265 |
266 | div.danger {
267 | background-color: #FCC;
268 | border: 1px solid #FAA;
269 | -moz-box-shadow: 2px 2px 4px #D52C2C;
270 | -webkit-box-shadow: 2px 2px 4px #D52C2C;
271 | box-shadow: 2px 2px 4px #D52C2C;
272 | }
273 |
274 | div.error {
275 | background-color: #FCC;
276 | border: 1px solid #FAA;
277 | -moz-box-shadow: 2px 2px 4px #D52C2C;
278 | -webkit-box-shadow: 2px 2px 4px #D52C2C;
279 | box-shadow: 2px 2px 4px #D52C2C;
280 | }
281 |
282 | div.caution {
283 | background-color: #FCC;
284 | border: 1px solid #FAA;
285 | }
286 |
287 | div.attention {
288 | background-color: #FCC;
289 | border: 1px solid #FAA;
290 | }
291 |
292 | div.important {
293 | background-color: #EEE;
294 | border: 1px solid #CCC;
295 | }
296 |
297 | div.note {
298 | background-color: #EEE;
299 | border: 1px solid #CCC;
300 | }
301 |
302 | div.tip {
303 | background-color: #EEE;
304 | border: 1px solid #CCC;
305 | }
306 |
307 | div.hint {
308 | background-color: #EEE;
309 | border: 1px solid #CCC;
310 | }
311 |
312 | div.seealso {
313 | background-color: #EEE;
314 | border: 1px solid #CCC;
315 | }
316 |
317 | div.topic {
318 | background-color: #EEE;
319 | }
320 |
321 | p.admonition-title {
322 | display: inline;
323 | }
324 |
325 | p.admonition-title:after {
326 | content: ":";
327 | }
328 |
329 | pre, tt, code {
330 | font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
331 | font-size: 0.9em;
332 | }
333 |
334 | .hll {
335 | background-color: #FFC;
336 | margin: 0 -12px;
337 | padding: 0 12px;
338 | display: block;
339 | }
340 |
341 | img.screenshot {
342 | }
343 |
344 | tt.descname, tt.descclassname, code.descname, code.descclassname {
345 | font-size: 0.95em;
346 | }
347 |
348 | tt.descname, code.descname {
349 | padding-right: 0.08em;
350 | }
351 |
352 | img.screenshot {
353 | -moz-box-shadow: 2px 2px 4px #EEE;
354 | -webkit-box-shadow: 2px 2px 4px #EEE;
355 | box-shadow: 2px 2px 4px #EEE;
356 | }
357 |
358 | table.docutils {
359 | border: 1px solid #888;
360 | -moz-box-shadow: 2px 2px 4px #EEE;
361 | -webkit-box-shadow: 2px 2px 4px #EEE;
362 | box-shadow: 2px 2px 4px #EEE;
363 | }
364 |
365 | table.docutils td, table.docutils th {
366 | border: 1px solid #888;
367 | padding: 0.25em 0.7em;
368 | }
369 |
370 | table.field-list, table.footnote {
371 | border: none;
372 | -moz-box-shadow: none;
373 | -webkit-box-shadow: none;
374 | box-shadow: none;
375 | }
376 |
377 | table.footnote {
378 | margin: 15px 0;
379 | width: 100%;
380 | border: 1px solid #EEE;
381 | background: #FDFDFD;
382 | font-size: 0.9em;
383 | }
384 |
385 | table.footnote + table.footnote {
386 | margin-top: -15px;
387 | border-top: none;
388 | }
389 |
390 | table.field-list th {
391 | padding: 0 0.8em 0 0;
392 | }
393 |
394 | table.field-list td {
395 | padding: 0;
396 | }
397 |
398 | table.field-list p {
399 | margin-bottom: 0.8em;
400 | }
401 |
402 | /* Cloned from
403 | * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68
404 | */
405 | .field-name {
406 | -moz-hyphens: manual;
407 | -ms-hyphens: manual;
408 | -webkit-hyphens: manual;
409 | hyphens: manual;
410 | }
411 |
412 | table.footnote td.label {
413 | width: .1px;
414 | padding: 0.3em 0 0.3em 0.5em;
415 | }
416 |
417 | table.footnote td {
418 | padding: 0.3em 0.5em;
419 | }
420 |
421 | dl {
422 | margin: 0;
423 | padding: 0;
424 | }
425 |
426 | dl dd {
427 | margin-left: 30px;
428 | }
429 |
430 | blockquote {
431 | margin: 0 0 0 30px;
432 | padding: 0;
433 | }
434 |
435 | ul, ol {
436 | /* Matches the 30px from the narrow-screen "li > ul" selector below */
437 | margin: 10px 0 10px 30px;
438 | padding: 0;
439 | }
440 |
441 | pre {
442 | background: #EEE;
443 | padding: 7px 30px;
444 | margin: 15px 0px;
445 | line-height: 1.3em;
446 | }
447 |
448 | div.viewcode-block:target {
449 | background: #ffd;
450 | }
451 |
452 | dl pre, blockquote pre, li pre {
453 | margin-left: 0;
454 | padding-left: 30px;
455 | }
456 |
457 | tt, code {
458 | background-color: #ecf0f3;
459 | color: #222;
460 | /* padding: 1px 2px; */
461 | }
462 |
463 | tt.xref, code.xref, a tt {
464 | background-color: #FBFBFB;
465 | border-bottom: 1px solid #fff;
466 | }
467 |
468 | a.reference {
469 | text-decoration: none;
470 | border-bottom: 1px dotted #004B6B;
471 | }
472 |
473 | /* Don't put an underline on images */
474 | a.image-reference, a.image-reference:hover {
475 | border-bottom: none;
476 | }
477 |
478 | a.reference:hover {
479 | border-bottom: 1px solid #6D4100;
480 | }
481 |
482 | a.footnote-reference {
483 | text-decoration: none;
484 | font-size: 0.7em;
485 | vertical-align: top;
486 | border-bottom: 1px dotted #004B6B;
487 | }
488 |
489 | a.footnote-reference:hover {
490 | border-bottom: 1px solid #6D4100;
491 | }
492 |
493 | a:hover tt, a:hover code {
494 | background: #EEE;
495 | }
496 |
497 |
498 | @media screen and (max-width: 870px) {
499 |
500 | div.sphinxsidebar {
501 | display: none;
502 | }
503 |
504 | div.document {
505 | width: 100%;
506 |
507 | }
508 |
509 | div.documentwrapper {
510 | margin-left: 0;
511 | margin-top: 0;
512 | margin-right: 0;
513 | margin-bottom: 0;
514 | }
515 |
516 | div.bodywrapper {
517 | margin-top: 0;
518 | margin-right: 0;
519 | margin-bottom: 0;
520 | margin-left: 0;
521 | }
522 |
523 | ul {
524 | margin-left: 0;
525 | }
526 |
527 | li > ul {
528 | /* Matches the 30px from the "ul, ol" selector above */
529 | margin-left: 30px;
530 | }
531 |
532 | .document {
533 | width: auto;
534 | }
535 |
536 | .footer {
537 | width: auto;
538 | }
539 |
540 | .bodywrapper {
541 | margin: 0;
542 | }
543 |
544 | .footer {
545 | width: auto;
546 | }
547 |
548 | .github {
549 | display: none;
550 | }
551 |
552 |
553 |
554 | }
555 |
556 |
557 |
558 | @media screen and (max-width: 875px) {
559 |
560 | body {
561 | margin: 0;
562 | padding: 20px 30px;
563 | }
564 |
565 | div.documentwrapper {
566 | float: none;
567 | background: #fff;
568 | }
569 |
570 | div.sphinxsidebar {
571 | display: block;
572 | float: none;
573 | width: 102.5%;
574 | margin: 50px -30px -20px -30px;
575 | padding: 10px 20px;
576 | background: #333;
577 | color: #FFF;
578 | }
579 |
580 | div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p,
581 | div.sphinxsidebar h3 a {
582 | color: #fff;
583 | }
584 |
585 | div.sphinxsidebar a {
586 | color: #AAA;
587 | }
588 |
589 | div.sphinxsidebar p.logo {
590 | display: none;
591 | }
592 |
593 | div.document {
594 | width: 100%;
595 | margin: 0;
596 | }
597 |
598 | div.footer {
599 | display: none;
600 | }
601 |
602 | div.bodywrapper {
603 | margin: 0;
604 | }
605 |
606 | div.body {
607 | min-height: 0;
608 | padding: 0;
609 | }
610 |
611 | .rtd_doc_footer {
612 | display: none;
613 | }
614 |
615 | .document {
616 | width: auto;
617 | }
618 |
619 | .footer {
620 | width: auto;
621 | }
622 |
623 | .footer {
624 | width: auto;
625 | }
626 |
627 | .github {
628 | display: none;
629 | }
630 | }
631 |
632 |
633 | /* misc. */
634 |
635 | .revsys-inline {
636 | display: none!important;
637 | }
638 |
639 | /* Make nested-list/multi-paragraph items look better in Releases changelog
640 | * pages. Without this, docutils' magical list fuckery causes inconsistent
641 | * formatting between different release sub-lists.
642 | */
643 | div#changelog > div.section > ul > li > p:only-child {
644 | margin-bottom: 0;
645 | }
646 |
647 | /* Hide fugly table cell borders in ..bibliography:: directive output */
648 | table.docutils.citation, table.docutils.citation td, table.docutils.citation th {
649 | border: none;
650 | /* Below needed in some edge cases; if not applied, bottom shadows appear */
651 | -moz-box-shadow: none;
652 | -webkit-box-shadow: none;
653 | box-shadow: none;
654 | }
655 |
656 |
657 | /* relbar */
658 |
659 | .related {
660 | line-height: 30px;
661 | width: 100%;
662 | font-size: 0.9rem;
663 | }
664 |
665 | .related.top {
666 | border-bottom: 1px solid #EEE;
667 | margin-bottom: 20px;
668 | }
669 |
670 | .related.bottom {
671 | border-top: 1px solid #EEE;
672 | }
673 |
674 | .related ul {
675 | padding: 0;
676 | margin: 0;
677 | list-style: none;
678 | }
679 |
680 | .related li {
681 | display: inline;
682 | }
683 |
684 | nav#rellinks {
685 | float: right;
686 | }
687 |
688 | nav#rellinks li+li:before {
689 | content: "|";
690 | }
691 |
692 | nav#breadcrumbs li+li:before {
693 | content: "\00BB";
694 | }
695 |
696 | /* Hide certain items when printing */
697 | @media print {
698 | div.related {
699 | display: none;
700 | }
701 | }
--------------------------------------------------------------------------------
/docs/_build/html/_static/searchtools.js:
--------------------------------------------------------------------------------
1 | /*
2 | * searchtools.js
3 | * ~~~~~~~~~~~~~~~~
4 | *
5 | * Sphinx JavaScript utilities for the full-text search.
6 | *
7 | * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
8 | * :license: BSD, see LICENSE for details.
9 | *
10 | */
11 |
12 | if (!Scorer) {
13 | /**
14 | * Simple result scoring code.
15 | */
16 | var Scorer = {
17 | // Implement the following function to further tweak the score for each result
18 | // The function takes a result array [filename, title, anchor, descr, score]
19 | // and returns the new score.
20 | /*
21 | score: function(result) {
22 | return result[4];
23 | },
24 | */
25 |
26 | // query matches the full name of an object
27 | objNameMatch: 11,
28 | // or matches in the last dotted part of the object name
29 | objPartialMatch: 6,
30 | // Additive scores depending on the priority of the object
31 | objPrio: {0: 15, // used to be importantResults
32 | 1: 5, // used to be objectResults
33 | 2: -5}, // used to be unimportantResults
34 | // Used when the priority is not in the mapping.
35 | objPrioDefault: 0,
36 |
37 | // query found in title
38 | title: 15,
39 | // query found in terms
40 | term: 5
41 | };
42 | }
43 |
44 | if (!splitQuery) {
45 | function splitQuery(query) {
46 | return query.split(/\s+/);
47 | }
48 | }
49 |
50 | /**
51 | * Search Module
52 | */
53 | var Search = {
54 |
55 | _index : null,
56 | _queued_query : null,
57 | _pulse_status : -1,
58 |
59 | init : function() {
60 | var params = $.getQueryParameters();
61 | if (params.q) {
62 | var query = params.q[0];
63 | $('input[name="q"]')[0].value = query;
64 | this.performSearch(query);
65 | }
66 | },
67 |
68 | loadIndex : function(url) {
69 | $.ajax({type: "GET", url: url, data: null,
70 | dataType: "script", cache: true,
71 | complete: function(jqxhr, textstatus) {
72 | if (textstatus != "success") {
73 | document.getElementById("searchindexloader").src = url;
74 | }
75 | }});
76 | },
77 |
78 | setIndex : function(index) {
79 | var q;
80 | this._index = index;
81 | if ((q = this._queued_query) !== null) {
82 | this._queued_query = null;
83 | Search.query(q);
84 | }
85 | },
86 |
87 | hasIndex : function() {
88 | return this._index !== null;
89 | },
90 |
91 | deferQuery : function(query) {
92 | this._queued_query = query;
93 | },
94 |
95 | stopPulse : function() {
96 | this._pulse_status = 0;
97 | },
98 |
99 | startPulse : function() {
100 | if (this._pulse_status >= 0)
101 | return;
102 | function pulse() {
103 | var i;
104 | Search._pulse_status = (Search._pulse_status + 1) % 4;
105 | var dotString = '';
106 | for (i = 0; i < Search._pulse_status; i++)
107 | dotString += '.';
108 | Search.dots.text(dotString);
109 | if (Search._pulse_status > -1)
110 | window.setTimeout(pulse, 500);
111 | }
112 | pulse();
113 | },
114 |
115 | /**
116 | * perform a search for something (or wait until index is loaded)
117 | */
118 | performSearch : function(query) {
119 | // create the required interface elements
120 | this.out = $('#search-results');
121 | this.title = $('
37 |
224 |
235 |
236 |
38 |
223 |
39 |
40 |
222 |
41 |
219 |
220 |
221 | Figure¶
42 |-
43 |
-
44 | class
show.Figure(image, annotation, color_map={0: (0.0, 0.0, 0.0), 1: (0.0, 0.8, 1.0), 2: (1.0, 0.8, 0.0), 3: (1.0, 0.4, 0.0)})[source]¶
45 | An open annotated WSI.
46 |47 |
66 |48 | 49 | 50 | Parameters: -
51 |
- image: PIL Image 52 |
Image to display; a thumbnail or region read from WSI.
53 |
54 | - annotation: Numpy 2D array 55 |
Annotation labels for each pixel in the input
56 |image.
57 | - color_map: dict {label int: RGB color list} 58 |
Mapping of RGB color values to class labels. Colors are triplet lists 59 | of the R, G, and B values.
60 |
61 |
Examples
67 |74 |73 |>>> from wsipre import show 68 | >>> colors = {0: (0, 0, 0), 2: (1, 0, 0)} 69 | >>> fig = show.Figure(image=image, annotation=mask, color_map=colors) 70 | >>> fig.color_map 71 | {0: (0, 0, 0), 2: (1, 0, 0)} 72 |
77 |76 |>>> fig.show_label_colors(height=5) 75 |
80 |79 |>>> fig.show_image_with_annotation() 78 |
81 |
99 |82 | 83 | 84 | Attributes: -
85 |
- image: PIL Image 86 |
The input
87 |image.
88 | - annotation: Numpy 2D array 89 |
The input
90 |annotation.
91 | - color_map: dict {label: color} 92 |
Mapping between each label and the color for visualization.
93 |
94 |
Methods
100 |101 |
120 |102 | 105 | 106 |103 | 104 | show_annotation()Show loaded image annotation. 108 |show_image()Show loaded image. 111 |show_image_with_annotation([split])Show loaded image and annotation. 114 |show_label_colors([width, height, …])Display a color bar with the colors and overlayed labels. 117 |-
121 |
-
122 |
show_annotation()[source]¶
123 | Show loaded image annotation.
124 |Display the loaded WSI thumbnail or region annotation, corresponding to 125 | a mask of pixel-wise labels.
126 |127 |
138 |128 | 129 | 130 | Returns: -
131 |
- Matplotlib image. 132 | 133 |
-
141 |
-
142 |
show_image()[source]¶
143 | Show loaded image.
144 |Display the loaded WSI thumbnail or region.
145 |146 |
157 |147 | 148 | 149 | Returns: -
150 |
- Matplotlib image. 151 | 152 |
-
160 |
-
161 |
show_image_with_annotation(split=True)[source]¶
162 | Show loaded image and annotation.
163 |164 |
183 |165 | 166 | 167 | Parameters: -
168 |
- split: bool 169 |
Whether to display the split image and annotation side-by-side or a 170 | combined visualization of the annotation on the image.
171 |
172 |
Returns: -
176 |
- Matplotlib image. 177 | 178 |
-
186 |
-
187 |
show_label_colors(width=20, height=6, font_color='w', font_size=14)[source]¶
188 | Display a color bar with the colors and overlayed labels.
189 |190 |
214 |191 | 192 | 193 | Parameters: -
194 |
- width: int 195 |
Width of each class rectangle in plot.
196 |
197 | - height: int 198 |
Height of each class rectangle in plot.
199 |
200 | - font_size: int 201 |
Size of the font used to display class labels.
202 |
203 |
Returns: -
207 |
- Matplotlib image illustrating mapping between class label and color. 208 | 209 |
' + _('Searching') + '
').appendTo(this.out); 122 | this.dots = $('').appendTo(this.title); 123 | this.status = $('').appendTo(this.out); 124 | this.output = $('23 | wsipre 0.1.2 documentation 24 |
46 |
158 |
177 |
184 |
185 |
186 |
187 |
--------------------------------------------------------------------------------
47 |
139 |
156 |
157 |
48 |
138 |
49 |
50 |
137 |
51 |
64 |
65 |
70 |
71 |
83 |
84 | 
85 |
96 |
97 | 
98 |
107 |
108 | 
109 |
115 |
116 | 
117 |
126 |
127 | 
128 |
131 |
132 | 
133 |
134 |
135 |
136 | Quick introduction¶
52 |wsipre has two main modules (see Module Index for docs):
53 |54 |59 |55 |
58 |- 56 |
slide: load and process WSIs- 57 |
show: visualize images generated usingslide
The following quick intro illustrates basic usage of these modules. First, load 60 | packages (Matplotlib is only used here to plot images with no annotation).
61 |>>> from matplotlib import pyplot as plt
62 | >>> from wsipre import slide, show
63 | Load WSI form the CAMELYON challenge with its region-level tumor annotation.
66 |>>> wsi = slide.Slide(filename='patient_012_node_0.tif',
67 | ... annotation_filename='patient_012_node_0.xml',
68 | ... xml_style='asap')
69 | Generate and show a thumbnail.
72 |>>> thumbnail, mask, downsampling_factor = wsi.get_thumbnail_with_annotation(
73 | ... size=(3000, 3000), polygon_type='line', line_thickness=8)
74 |
75 | >>> black = (0, 0, 0)
76 | >>> red = (1, 0, 0)
77 | >>> yellow = (1, 1, 0)
78 | >>> colors = {0: black, 1: black, 2: red}
79 |
80 | >>> fig = show.Figure(image=thumbnail, annotation=mask, color_map=colors)
81 | >>> fig.show_image_with_annotation(split=False)
82 |
85 | Zoom in and read a smaller region from the WSI.
86 |>>> loc = (int(150*downsampling_factor), int(1450*downsampling_factor))
87 |
88 | >>> slide_region, mask_region = wsi.read_region_with_annotation(
89 | ... location=loc, level=2, size=(1000, 1000), polygon_type='line',
90 | ... line_thickness=20)
91 |
92 | >>> fig = show.Figure(
93 | ... image=slide_region, annotation=mask_region, color_map=colors)
94 | >>> fig.show_image_with_annotation(split=False)
95 |
98 | Locate tissue regions in the WSI automatically.
99 |>>> wsi.get_tissue_mask(polygon_type='line', line_thickness=15)
100 | Slide('patient_012_node_0.tif')
101 |
102 | >>> fig = show.Figure(image=wsi.downsampled_slide,
103 | ... annotation=wsi.tissue_mask,
104 | ... color_map={0: black, 1: yellow})
105 | >>> fig.show_image_with_annotation(split=False)
106 |
109 | Sample a random patch from tissue regions.
110 |>>> tissue_patch = wsi.read_random_tissue_patch(level=2, size=(224, 224),
111 | ... avoid_labels=[2])
112 | >>> plt.imshow(tissue_patch)
113 | >>> plt.show()
114 |
117 | Sample a random patch from regions annotated as tumor (label 2).
118 |>>> slide_region, mask_region = wsi.read_random_patch(
119 | ... level=2, size=(299, 299), target_class=2,
120 | ... min_class_area_ratio=0.75, polygon_type='area')
121 |
122 | >>> fig = show.Figure(slide_region, mask_region, {0: black, 2:red})
123 |
124 | >>> fig.show_image_with_annotation(split=True)
125 |
128 | Double check the mapping between class label and color.
129 |>>> fig.show_label_colors()
130 |
133 |