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  1. .gitattributes +1 -0
  2. my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/Markdown-3.3.7.dist-info/INSTALLER +1 -0
  3. my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/Markdown-3.3.7.dist-info/LICENSE.md +29 -0
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.gitattributes CHANGED
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my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/Markdown-3.3.7.dist-info/INSTALLER ADDED
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my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/Markdown-3.3.7.dist-info/LICENSE.md ADDED
@@ -0,0 +1,29 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Copyright 2007, 2008 The Python Markdown Project (v. 1.7 and later)
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+ Copyright 2004, 2005, 2006 Yuri Takhteyev (v. 0.2-1.6b)
3
+ Copyright 2004 Manfred Stienstra (the original version)
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+
5
+ All rights reserved.
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+
7
+ Redistribution and use in source and binary forms, with or without
8
+ modification, are permitted provided that the following conditions are met:
9
+
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+ * Redistributions of source code must retain the above copyright
11
+ notice, this list of conditions and the following disclaimer.
12
+ * Redistributions in binary form must reproduce the above copyright
13
+ notice, this list of conditions and the following disclaimer in the
14
+ documentation and/or other materials provided with the distribution.
15
+ * Neither the name of the Python Markdown Project nor the
16
+ names of its contributors may be used to endorse or promote products
17
+ derived from this software without specific prior written permission.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE PYTHON MARKDOWN PROJECT ''AS IS'' AND ANY
20
+ EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22
+ DISCLAIMED. IN NO EVENT SHALL ANY CONTRIBUTORS TO THE PYTHON MARKDOWN PROJECT
23
+ BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
24
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
25
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
26
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
27
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
28
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
29
+ POSSIBILITY OF SUCH DAMAGE.
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+ Metadata-Version: 2.1
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+ Name: Markdown
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+ Version: 3.3.7
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+ Summary: Python implementation of Markdown.
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+ Home-page: https://Python-Markdown.github.io/
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+ Author: Manfred Stienstra, Yuri takhteyev and Waylan limberg
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+ Author-email: python.markdown@gmail.com
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+ Maintainer: Waylan Limberg
9
+ Maintainer-email: python.markdown@gmail.com
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+ License: BSD License
11
+ Project-URL: Documentation, https://Python-Markdown.github.io/
12
+ Project-URL: GitHub Project, https://github.com/Python-Markdown/markdown
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+ Project-URL: Issue Tracker, https://github.com/Python-Markdown/markdown/issues
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+ Platform: UNKNOWN
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+ Classifier: Development Status :: 5 - Production/Stable
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+ Classifier: License :: OSI Approved :: BSD License
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Programming Language :: Python
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.6
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+ Classifier: Programming Language :: Python :: 3.7
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+ Classifier: Programming Language :: Python :: 3.8
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+ Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3 :: Only
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+ Classifier: Programming Language :: Python :: Implementation :: CPython
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+ Classifier: Programming Language :: Python :: Implementation :: PyPy
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+ Classifier: Topic :: Communications :: Email :: Filters
29
+ Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content :: CGI Tools/Libraries
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+ Classifier: Topic :: Internet :: WWW/HTTP :: Site Management
31
+ Classifier: Topic :: Software Development :: Documentation
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+ Classifier: Topic :: Software Development :: Libraries :: Python Modules
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+ Classifier: Topic :: Text Processing :: Filters
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+ Classifier: Topic :: Text Processing :: Markup :: HTML
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+ Classifier: Topic :: Text Processing :: Markup :: Markdown
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+ Requires-Python: >=3.6
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE.md
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+ Requires-Dist: importlib-metadata (>=4.4) ; python_version < "3.10"
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+ Provides-Extra: testing
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+ Requires-Dist: coverage ; extra == 'testing'
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+ Requires-Dist: pyyaml ; extra == 'testing'
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+
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+ [Python-Markdown][]
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+ ===================
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+
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+ [![Build Status][build-button]][build]
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+ [![Coverage Status][codecov-button]][codecov]
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+ [![Latest Version][mdversion-button]][md-pypi]
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+ [![Python Versions][pyversion-button]][md-pypi]
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+ [![BSD License][bsdlicense-button]][bsdlicense]
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+ [![Code of Conduct][codeofconduct-button]][Code of Conduct]
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+
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+ [build-button]: https://github.com/Python-Markdown/markdown/workflows/CI/badge.svg?event=push
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+ [build]: https://github.com/Python-Markdown/markdown/actions?query=workflow%3ACI+event%3Apush
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+ [codecov-button]: https://codecov.io/gh/Python-Markdown/markdown/branch/master/graph/badge.svg
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+ [codecov]: https://codecov.io/gh/Python-Markdown/markdown
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+ [mdversion-button]: https://img.shields.io/pypi/v/Markdown.svg
59
+ [md-pypi]: https://pypi.org/project/Markdown/
60
+ [pyversion-button]: https://img.shields.io/pypi/pyversions/Markdown.svg
61
+ [bsdlicense-button]: https://img.shields.io/badge/license-BSD-yellow.svg
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+ [bsdlicense]: https://opensource.org/licenses/BSD-3-Clause
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+ [codeofconduct-button]: https://img.shields.io/badge/code%20of%20conduct-contributor%20covenant-green.svg?style=flat-square
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+ [Code of Conduct]: https://github.com/Python-Markdown/markdown/blob/master/CODE_OF_CONDUCT.md
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+
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+ This is a Python implementation of John Gruber's [Markdown][].
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+ It is almost completely compliant with the reference implementation,
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+ though there are a few known issues. See [Features][] for information
69
+ on what exactly is supported and what is not. Additional features are
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+ supported by the [Available Extensions][].
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+
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+ [Python-Markdown]: https://Python-Markdown.github.io/
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+ [Markdown]: https://daringfireball.net/projects/markdown/
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+ [Features]: https://Python-Markdown.github.io#Features
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+ [Available Extensions]: https://Python-Markdown.github.io/extensions
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+
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+ Documentation
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+ -------------
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+
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+ ```bash
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+ pip install markdown
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+ ```
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+ ```python
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+ import markdown
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+ html = markdown.markdown(your_text_string)
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+ ```
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+
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+ For more advanced [installation] and [usage] documentation, see the `docs/` directory
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+ of the distribution or the project website at <https://Python-Markdown.github.io/>.
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+
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+ [installation]: https://python-markdown.github.io/install/
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+ [usage]: https://python-markdown.github.io/reference/
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+
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+ See the change log at <https://Python-Markdown.github.io/change_log>.
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+
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+ Support
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+ -------
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+
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+ You may report bugs, ask for help, and discuss various other issues on the [bug tracker][].
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+
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+ [bug tracker]: https://github.com/Python-Markdown/markdown/issues
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+
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+ Code of Conduct
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+ ---------------
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+
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+ Everyone interacting in the Python-Markdown project's codebases, issue trackers,
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+ and mailing lists is expected to follow the [Code of Conduct].
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+
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+
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+ Nico Kemnitz <nkemnitz@princeton.edu>
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+ William Silversmith <william.silversmith@gmail.com>
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my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/connected_components_3d-3.23.0.dist-info/COPYING.LESSER ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ GNU LESSER GENERAL PUBLIC LICENSE
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my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/connected_components_3d-3.23.0.dist-info/INSTALLER ADDED
@@ -0,0 +1 @@
 
 
1
+ pip
my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/connected_components_3d-3.23.0.dist-info/METADATA ADDED
@@ -0,0 +1,513 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Metadata-Version: 2.1
2
+ Name: connected-components-3d
3
+ Version: 3.23.0
4
+ Summary: Connected components on discrete and continuous multilabel 3D and 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6).
5
+ Home-page: https://github.com/seung-lab/connected-components-3d/
6
+ Author: William Silversmith
7
+ Author-email: ws9@princeton.edu
8
+ License: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
9
+ Keywords: connected-components CCL volumetric-data numpy connectomics image-processing biomedical-image-processing decision-tree union-find sauf 2d 3d
10
+ Classifier: Intended Audience :: Developers
11
+ Classifier: Development Status :: 5 - Production/Stable
12
+ Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
13
+ Classifier: Programming Language :: Python
14
+ Classifier: Programming Language :: Python :: 3
15
+ Classifier: Programming Language :: Python :: 3.8
16
+ Classifier: Programming Language :: Python :: 3.9
17
+ Classifier: Programming Language :: Python :: 3.10
18
+ Classifier: Programming Language :: Python :: 3.11
19
+ Classifier: Programming Language :: Python :: 3.12
20
+ Classifier: Programming Language :: Python :: 3.13
21
+ Classifier: Topic :: Scientific/Engineering
22
+ Classifier: Intended Audience :: Science/Research
23
+ Classifier: Operating System :: POSIX
24
+ Classifier: Operating System :: MacOS
25
+ Classifier: Operating System :: Microsoft :: Windows :: Windows 10
26
+ Requires-Python: >=3.8,<4.0
27
+ Description-Content-Type: text/markdown
28
+ License-File: COPYING
29
+ License-File: COPYING.LESSER
30
+ License-File: AUTHORS
31
+ Requires-Dist: numpy
32
+
33
+ [![PyPI version](https://badge.fury.io/py/connected-components-3d.svg)](https://badge.fury.io/py/connected-components-3d) [![DOI](https://zenodo.org/badge/146368855.svg)](https://zenodo.org/badge/latestdoi/146368855)
34
+
35
+ cc3d: Connected Components on Multilabel 3D Images
36
+ =======================
37
+
38
+ <p style="font-style: italics;" align="center">
39
+ <img height=348 src="https://raw.githubusercontent.com/seung-lab/connected-components-3d/master/ccl_figure.png" alt="Binary and multilabel connected components. (a) A binary image (foreground white, background black) (b) 4-connected CCL of binary image (c) 8-connected CCL of binary image (d) A multilabel image (e) 4-connected CCL of multilabel image (f) 8-connected CCL of multilabel image" /><br>
40
+ <b>Fig. 1. Binary and Multilabel Connected Components Labeling (CCL)</b> 2D images are shown for simplicity. Black is the background color (zero). (a) A binary image (foreground white, background black) (b) 4-connected CCL of binary image (c) 8-connected CCL of binary image (d) A multilabel image (e) 4-connected CCL of multilabel image (f) 8-connected CCL of multilabel image.
41
+ </p>
42
+
43
+ <p style="font-style: italics;" align="center">
44
+ <img height=348 src="https://raw.githubusercontent.com/seung-lab/connected-components-3d/master/continuous_ccl_figure.png" alt="Continuous value connected components (top) A three tone grayscale image with signed additive low magnitude noise (bottom) Extracted components using continuous value CCL with a delta value greater than the noise magnitude but smaller than the difference between tones" /><br>
45
+ <b>Fig. 2. Continuous Value Connected Components Labeling (CCL)</b> (top) A three tone grayscale image with signed additive low magnitude noise (bottom) Extracted components using continuous value CCL with a delta value greater than the noise magnitude but smaller than the difference between tones
46
+ </p>
47
+
48
+ cc3d is an implementation of connected components in three dimensions using a 26, 18, or 6-connected neighborhood in 3D or 4 and 8-connected in 2D. This package uses a 3D variant of the two pass method by Rosenfeld and Pflatz augmented with Union-Find and a decision tree based on the 2D 8-connected work of Wu, Otoo, and Suzuki. This implementation is compatible with images containing many different labels, not just binary images. It also supports continuously valued images such as grayscale microscope images with an algorithm that joins together nearby values.
49
+
50
+ I wrote this package because I was working on densely labeled 3D biomedical images of brain tissue (e.g. 512x512x512 voxels). Other off the shelf implementations I reviewed were limited to binary images. This rendered these other packages too slow for my use case as it required masking each label and running the connected components algorithm once each time. For reference, there are often between hundreds to thousands of labels in a given volume. The benefit of this package is that it labels all connected components in one shot, improving performance by one or more orders of magnitude.
51
+
52
+ In general, binary images are much more common (usually resulting from image thresholding), but multi-label images crop up in instance segmentation and semantic labeling as a classifier may label touching clusters of adjacent pixels differently. If a gap between different labels is guaranteed, then the problem degenerates into the binary version.
53
+
54
+ Check out [benchmarks](https://github.com/seung-lab/connected-components-3d/tree/master/benchmarks) to see a comparison with SciPy on a few different tasks.
55
+
56
+ ## Python `pip` Installaction
57
+
58
+ If compatible binaries are available for your platform, installation is particularly simple.
59
+
60
+ ```bash
61
+ pip install connected-components-3d
62
+ ```
63
+
64
+ If compatible binaries are not available, you can install from source as follows.
65
+
66
+ *Requires a C++ compiler.*
67
+
68
+ ```bash
69
+ pip install numpy
70
+ pip install connected-components-3d --no-binary :all:
71
+ ```
72
+
73
+ Occasionally, you may appear to successfully install cc3d, but on import you'll see an error that includes: `numpy.ufunc size changed, may indicate binary incompatibility`. You can either try upgrading numpy or compiling cc3d from source in this case.
74
+
75
+ ## Python Manual Installation
76
+
77
+ *Requires a C++ compiler.*
78
+
79
+ ```bash
80
+ pip install -r requirements.txt
81
+ python setup.py develop
82
+ ```
83
+
84
+ ## Python Use
85
+
86
+ The following functions are available with examples below:
87
+ - Connected Component Labeling (CCL)
88
+ - Calculating centroids, bounding boxes, and voxel counts
89
+ - Removal of small objects ("dust") (or large objects)
90
+ - Extraction of k largest objects
91
+ - Fast extraction of all objects one-by-one
92
+ - Calculation of contact surface area and contact network
93
+ - Extraction and coloring of a per voxel connectivity graph
94
+
95
+ ```python
96
+ import cc3d
97
+ import numpy as np
98
+
99
+ labels_in = np.ones((512, 512, 512), dtype=np.int32)
100
+ labels_out = cc3d.connected_components(labels_in) # 26-connected
101
+
102
+ connectivity = 6 # only 4,8 (2D) and 26, 18, and 6 (3D) are allowed
103
+ labels_out = cc3d.connected_components(labels_in, connectivity=connectivity)
104
+
105
+ # By default, cc3d works on multivalued labelings, but sometimes you want
106
+ # to treat a grayscale image as a binary image directly. It is also possible
107
+ # to process binary images more effectively. Binary image specific optimizations
108
+ # are not implemented yet though, but may be in the future.
109
+ labels_out = cc3d.connected_components(labels_in, binary_image=True)
110
+ # same as above, but less efficient
111
+ labels_out = cc3d.connected_components(labels_in > 0)
112
+
113
+ # If you need the borders to wrap around (e.g. for simulations, world maps)
114
+ # specify periodic_boundary=True, currently only supported for
115
+ # 4 and 8 (2d) and 6 (3d) connectivities.
116
+ labels_out = cc3d.connected_components(
117
+ labels_in, connectivity=connectivity, periodic_boundary=True
118
+ )
119
+
120
+ # If you need a particular dtype you can specify np.uint16, np.uint32, or np.uint64
121
+ # You can go bigger, not smaller, than the default which is selected
122
+ # to be the smallest that can be safely used. This can save you the copy
123
+ # operation needed by labels_out.astype(...).
124
+ labels_out = cc3d.connected_components(labels_in, out_dtype=np.uint64)
125
+
126
+ # If you're working with continuously valued images like microscopy
127
+ # images you can use cc3d to perform a very rough segmentation.
128
+ # If delta = 0, standard high speed processing. If delta > 0, then
129
+ # neighbor voxel values <= delta are considered the same component.
130
+ # The algorithm can be 2-10x slower though. Zero is considered
131
+ # background and will not join to any other voxel.
132
+ labels_out = cc3d.connected_components(labels_in, delta=10)
133
+
134
+ # If you're working with an image that's larger than memory you can
135
+ # use mmapped files. The input and output files can be used independently.
136
+ # In this case an array labels.bin that is 5000x5000x2000 voxels and uint32_t
137
+ # in Fortran order is computed and the results are written to out.bin in Fortran
138
+ # order. You can find the properties of the file (shape, dtype, order) by inspecting
139
+ # labels_out.
140
+ labels_in = np.memmap("labels.bin", order="F", dtype=np.uint32, shape=(5000, 5000, 2000))
141
+ labels_out = cc3d.connected_components(labels_in, out_file="out.bin")
142
+
143
+ # Here's another strategy that you can use for huge files that won't even
144
+ # take up any disk space. Provide any iterator to this function that produces
145
+ # thick z sections of the input array that are in sequential order.
146
+ # The output is a highly compressed CrackleArray that is still random access.
147
+ # See: https://github.com/seung-lab/crackle
148
+ # You need to pip install connected-components-3d[stack] to get the extra modules.
149
+ def sections(labels_in):
150
+ """
151
+ A generator that produces thick Z slices
152
+ of an image
153
+ """
154
+ for z in range(0, labels_in.shape[2], 100):
155
+ yield labels_in[:,:,z:z+100]
156
+
157
+ # You can access compressed_labels_out using array notation
158
+ compressed_labels_out = cc3d.connected_components_stack(sections(labels))
159
+ # convert to numpy array, probably a big mistake since
160
+ # you probably expected it was going to blow up RAM
161
+ cc_labels = compressed_labels_out.numpy()
162
+ # if you don't like hanging onto this exotic format, you
163
+ # can write it as a numpy array to disk in a memory efficient way.
164
+ compressed_labels_out.save("example.npy.gz")
165
+ # or hang onto it
166
+ compressed_labels_out.save("example.ckl")
167
+
168
+
169
+ # You can extract the number of labels (which is also the maximum
170
+ # label value) like so:
171
+ labels_out, N = cc3d.connected_components(labels_in, return_N=True) # free
172
+ # -- OR --
173
+ labels_out = cc3d.connected_components(labels_in)
174
+ N = np.max(labels_out) # costs a full read
175
+
176
+ # You can extract individual components using numpy operators
177
+ # This approach is slow, but makes a mutable copy.
178
+ for segid in range(1, N+1):
179
+ extracted_image = labels_out * (labels_out == segid)
180
+ process(extracted_image) # stand in for whatever you'd like to do
181
+
182
+ # If a read-only image is ok, this approach is MUCH faster
183
+ # if the image has many contiguous regions. A random image
184
+ # can be slower. binary=True yields binary images instead
185
+ # of numbered images.
186
+ for label, image in cc3d.each(labels_out, binary=False, in_place=True):
187
+ process(image) # stand in for whatever you'd like to do
188
+
189
+ # Image statistics like voxel counts, bounding boxes, and centroids.
190
+ stats = cc3d.statistics(labels_out)
191
+
192
+ # Remove dust from the input image. Removes objects with
193
+ # fewer than `threshold` voxels.
194
+ labels_out = cc3d.dust(
195
+ labels_in, threshold=100,
196
+ connectivity=26, in_place=False
197
+ )
198
+ # Removes objects with >= `threshold` voxels.
199
+ labels_out = cc3d.dust(labels_in, threshold=100, invert=True)
200
+ # Removes objects with < `threshold[0]` voxels and >= threshold[1]
201
+ labels_out = cc3d.dust(labels_in, threshold=[50,100])
202
+ # Removes objects with >= `threshold[0]` voxels and < threshold[1]
203
+ labels_out = cc3d.dust(labels_in, threshold=[50,100], invert=True)
204
+
205
+ # Get a labeling of the k largest objects in the image.
206
+ # The output will be relabeled from 1 to N.
207
+ labels_out, N = cc3d.largest_k(
208
+ labels_in, k=10,
209
+ connectivity=26, delta=0,
210
+ return_N=True,
211
+ )
212
+ labels_in *= (labels_out > 0) # to get original labels
213
+
214
+ # Compute the contact surface area between all labels.
215
+ # Only face contacts are counted as edges and corners
216
+ # have zero area. To get a simple count of all contacting
217
+ # voxels, set `surface_area=False`.
218
+ # { (1,2): 16 } aka { (label_1, label_2): contact surface area }
219
+ surface_per_contact = cc3d.contacts(
220
+ labels_out, connectivity=connectivity,
221
+ surface_area=True, anisotropy=(4,4,40)
222
+ )
223
+ # same as set(surface_per_contact.keys())
224
+ edges = cc3d.region_graph(labels_out, connectivity=connectivity)
225
+
226
+ # You can also generate a voxel connectivty graph that encodes
227
+ # which directions are passable from a given voxel as a bitfield.
228
+ # This could also be seen as a method of eroding voxels fractionally
229
+ # based on their label adjacencies.
230
+ # See help(cc3d.voxel_connectivity_graph) for details.
231
+ graph = cc3d.voxel_connectivity_graph(labels, connectivity=connectivity)
232
+
233
+ # ...and turn it back into labeled values (probably
234
+ # not exactly the same ones). Note: this function currently
235
+ # assumes an undirected graph, so single voxel alterations are
236
+ # likely to go awry.
237
+ new_labels = cc3d.color_connectivity_graph(graph, connectivity=connectivity)
238
+ ```
239
+
240
+ *Note: C and Fortran order arrays will be processed in row major and column major order respectively, so the numbering of labels will be "transposed". The scare quotes are there because the dimensions of the array will not change.*
241
+
242
+ ## C++ Use
243
+
244
+ ```cpp
245
+ #include "cc3d.hpp"
246
+
247
+ // 3d array represented as 1d array
248
+ int* labels = new int[512*512*512]();
249
+
250
+ uint32_t* cc_labels = cc3d::connected_components3d<int>(
251
+ labels, /*sx=*/512, /*sy=*/512, /*sz=*/512
252
+ );
253
+
254
+ // The default template parameter for output type is uint32_t
255
+ uint64_t* cc_labels = cc3d::connected_components3d<int, uint64_t>(
256
+ labels, /*sx=*/512, /*sy=*/512, /*sz=*/512
257
+ );
258
+
259
+ uint16_t* cc_labels = cc3d::connected_components3d<int, uint16_t>(
260
+ labels, /*sx=*/512, /*sy=*/512, /*sz=*/512,
261
+ /*connectivity=*/18 // default is 26 connected
262
+ );
263
+
264
+ size_t N = 0;
265
+ uint16_t* cc_labels = cc3d::connected_components3d<int, uint16_t>(
266
+ labels, /*sx=*/512, /*sy=*/512, /*sz=*/512,
267
+ /*connectivity=*/26, /*N=*/N // writes number of labels to N
268
+ );
269
+
270
+ #include "cc3d_continuous.hpp"
271
+
272
+ // For handling grayscale images. Note that the difference
273
+ // is the addition of the "delta" argument.
274
+ uint16_t* cc_labels = cc3d::connected_components3d<int, uint16_t>(
275
+ labels, /*sx=*/512, /*sy=*/512, /*sz=*/512,
276
+ /*delta=*/10, /*connectivity=*/6 // default is 26 connected
277
+ );
278
+
279
+ #include "cc3d_graphs.hpp"
280
+
281
+ // edges is [ e11, e12, e21, e22, ... ]
282
+ std::vector<uint64_t> edges = cc3d::extract_region_graph<uint64_t>(
283
+ labels, /*sx=*/512, /*sy=*/512, /*sz=*/512,
284
+ /*connectivity=*/18 // default is 26 connected
285
+ );
286
+
287
+ // graph is a series of bitfields that describe inter-voxel
288
+ // connectivity based on adjacent labels. See "cc3d_graphs.hpp"
289
+ // for details on the bitfield.
290
+ uint32_t* graph = extract_voxel_connectivity_graph<T>(
291
+ labels, /*sx=*/512, /*sy=*/512, /*sz=*/512,
292
+ /*connectivity=*/6 // default is 26 connected
293
+ );
294
+
295
+ ```
296
+
297
+ ## 26-Connected CCL Algorithm
298
+
299
+ The algorithm contained in this package is an elaboration into 3D images of the 2D image connected components algorithm described by Rosenfeld and Pflatz (RP) in 1968 [1] (which is well illustrated by [this youtube video](https://www.youtube.com/watch?v=ticZclUYy88)) using an equivalency list implemented as Tarjan's Union-Find disjoint set with path compression and balancing [2] and augmented with a decision tree based on work by Wu, Otoo, and Suzuki (WOS), an approach commonly known as Scan plus Array-based Union-Find (SAUF). [3] The description below describes the 26-connected algorithm, but once you understand it, deriving 18 and 6 are simple. However, we recently made some changes that warrant further discursion on 6-connected.
300
+
301
+ ### First Principles in 2D
302
+
303
+ In RP's 4-connected two-pass method for binary 2D images, the algorithm raster scans and every time it first encounters a foreground pixel (the pixels to its top and left are background), it marks it with a new label. If there is a preexisting label in its neighborhood, it uses that label instead. Whenever two labels are adjacent, it records they are equivalent so that they can be relabeled consistently in the second pass. This equivalency table can be constructed in several ways, but some popular approaches are Union-Find with path compression with balancing by rank and Selkow's algorithm (which can avoid pipeline stalls). [4] However, Selkow's algorithm is designed for two trees of depth two, appropriate for binary images. We would like to process multiple labels at the same time, making Union-Find preferable.
304
+
305
+ In the second pass, the pixels are relabeled using the equivalency table. Union-Find establishes one label as the root label of a tree, and the root is considered the representative label. Each pixel is then labeled with the representative label. Union-Find is therefore appropriate for representing disjoint sets. Path compression with balancing radically reduces the height of the tree, which accelerates the second pass.
306
+
307
+ WOS approached the problem of accelerating 8-connected 2D connected components on binary images. 8-connected labeling is achieved by extending RP's forward pass mask to the top left and top right corner pixels. In Union-Find based connected components algorithms, the unify step in the first pass is the most expensive step. WOS showed how to optimize away a large fraction of these calls using a decision tree that takes advantage of local topology. For example, since the top-center neighbor of the current pixel is also adjacent to the other mask elements, all of which have already been processed by virtue of the raster scan direction, if it is present it is sufficient to copy its value and move on. If it is absent, pick one of the remaining foreground pixels, copy their value, and use unify for the mask element on the right as it is now known to be non-neighboring with the left hand side. WOS's algorithm continues in this fashion until a match is found or all mask elements are processed at which point a new label is created.
308
+
309
+ For several years, this algorithm was the world's fastest, though it has been superceded by a newer work that exchanges the static decision tree for a dynamic one or precalculated generated one amongst other improvements. However, WOS's work is significant for both its simplicity and speed and thus serves as the inspiration for this library. For 2D 8-connected images, we provide a specialization using Wu et al's original decision tree for a slight performance boost.
310
+
311
+ We're interested in exploring the block based approaches of Grana, Borghesani, and Cucchiara ([5],[7]), however their approach appears to critically rely on binary images. We'll continue to think about ways to incorporate it. We also considered the approach of He et al [8] which is also supposed to modestly faster than than WOS. However, it substitutes the Union-Find data structure (one array) with three arrays, which imposes a memory requirement that is at odds with our goal of processing large images.
312
+
313
+ ### Extending to 3D
314
+
315
+ The approach presented below is very similar to that of Sutheebanjard [6]. To move to a 3D 26-connected neighborhood, the mask must be extended into three dimensions in order to connect neighboring planes. Observe that the 8-connected mask covers the trailing half of the neighborhood (the part that will have been already processed) such that the current pixel can rely on those labels. Thus the mask for the 26-connected neighborhood covers only two out of three potential planes: the entire lower plane (nine voxels), and a mask identical to WOS's (four voxels) on the current plane. While some further optimizations are possible, to begin, the problem can be conceptually decomposed into two parts: establishing a 9-connected link to the bottom plane and then an 8-connected link to the current plane. This works because the current pixel functions as a hub that transmits the connection information from the 9-connected step to the 8-connected step.
316
+
317
+ Fig. 1: Mask for an 8-connected plane. If J,K,L, and M are all eliminated, only N remains and a new label is assigned.
318
+
319
+ | j | k | l |
320
+ |---|---|---|
321
+ | m | n | . |
322
+ | . | . | . |
323
+
324
+ The very first Z plane (Z=0) the algorithm runs against is special: the edge effect omits the bottom plane of the mask. Therefore, as the remaining mask is only comprosed of the 8-connected 2D mask, after this pass, the bottom of the image is 8-connected. At Z=1, the 9-connected part of the mask kicks in, forming connections to Z=0, making the current plane now (8 + 9) 17-connected. At Z=2, the 9-connected bottom mask now forms connections from Z=1 to Z=2 on the top, making Z=1 (17 + 9) 26-connected. By induction, when this process proceeds to completion it results in a 26-connected labeling of the volume.
325
+
326
+ Following inspiration from WOS, we construct a decision tree on the densely labeled bottom plane that minimizes the number of unifications we need to perform.
327
+
328
+ Fig 2. The mask for the lower plane in 3D.
329
+
330
+ | a | b | c |
331
+ |---|---|---|
332
+ | d | e | f |
333
+ | g | h | i |
334
+
335
+ As `e` is connected to all other voxels, if present, it can simply be copied. If `e` is absent, `b` and `h` fully cover the mask. If `b` is absent, `h`, `a`, `c` comprise a covering. If `h` is absent, `b`, `g`, `i` are one. Below is a list of coverings such that each proceeding entry in the list assumes the first letters in the entries above are background.
336
+
337
+ 1. `e`
338
+ 2. `k`, (`h` | `g`, `i`)
339
+ 3. `b`, (`h` | `g`, `i`)
340
+ 4. `h`, `a`, `c`
341
+ 5. `m`, (`f` | `c`, `i`)
342
+ 6. `d`, (`f` | `c`, `i`)
343
+ 7. `f`, `g`, `a`
344
+ 8. `a`, `c`, `g`, `i`
345
+ 9. `c`, `g`, `i`
346
+ 10. `g`, `i`
347
+ 11. `i`
348
+
349
+ The decision tree is then constructed such that each of these coverings will be evaluated using the fewest unifications possible. It's possible to further optimize this by noting that `e` and `b` are both fully connected to the upper 2D mask. Therefore, if either of them are present, we can skip the 8-connected unification step. It's also possible to try the DF covering first if B is background, which would save one unification versus HAC given even statistics, but it seems to be slightly slower on the dataset I attempted. To move from binary data to multilabel data, I simply replaced tests for foreground and background with tests for matching labels.
350
+
351
+ In order to make a reasonably fast implementation, I implemented union-find with path compression. I conservatively used an IDs array qual to the size of the image for the union-find data structure instead of a sparse map. The union-find data structure plus the output labels means the memory consumption will be input + output + rank + equivalences. If your input labels are 32-bit, the memory usage will be 4x the input size. This becomes more problematic when 64-bit labels are used, but if you know something about your data, you can decrease the size of the union-find data structure. I previously used union-by-size but for some reason it merely reduced performance and increased memory usage so it was removed.
352
+
353
+ For more information on the history of connected components algorithms, and an even faster approach for 2D 8-connected components, consult Grana et al's paper on Block Based Decision Trees. [5,7]
354
+
355
+ ## Phantom Labels
356
+
357
+ In the course of thinking of improvements to several algorithms, we developed a technique we term "Phantom Labeling" for improving the SAUF method directly.
358
+
359
+ ```
360
+ Definition: Phantom Labels are elements of a CCL mask that
361
+ transmit connectivity information between other elements of the
362
+ mask but cannot directly pass their value to the current pixel
363
+ during the first pass of a SAUF derived algorithm.
364
+ ```
365
+
366
+ Reproducing Fig. 1 again, but with new letters for the more limited problem, the standard SAUF mask appears like so:
367
+
368
+ Fig. 3: Mask for an 8-connected plane.
369
+
370
+ | a | b | c |
371
+ |---|---|---|
372
+ | d | x | . |
373
+ | . | . | . |
374
+
375
+ This results in a decision tree like so assuming x is a foreground pixel.
376
+
377
+ ```
378
+ if b:
379
+ x := b
380
+ elif a:
381
+ x := a
382
+ if c:
383
+ unify(a,c)
384
+ elif d:
385
+ x := d
386
+ if c:
387
+ unify(c,d)
388
+ elif c:
389
+ x := c
390
+ else:
391
+ x := new label
392
+ ```
393
+
394
+ There is an opportunity here for eliminating up to half of the unify calls, one of the more expensive operations in modern CCL by slightly modifying the mask:
395
+
396
+ Fig. 4: 8-connected mask modified to include phantom label P.
397
+
398
+ | . | P | . |
399
+ |---|---|---|
400
+ | a | b | c |
401
+ | d | x | . |
402
+ | . | . | . |
403
+
404
+ This results in a modified decision tree.
405
+
406
+ ```
407
+ if b:
408
+ x := b
409
+ elif a:
410
+ x := a
411
+ if c and not P: <--- change here
412
+ unify(a,c)
413
+ elif d:
414
+ x := d
415
+ if c:
416
+ unify(c,d)
417
+ elif c:
418
+ x := c
419
+ else:
420
+ x := new label
421
+ ```
422
+
423
+ The novelty of this technique is unclear, but it is very simple to apply and results in substantial speed ups for the 4 and 6 connected problems, a minor improvement for 8-connected, and is readily compatible with the multi-label approach unlike block based approaches.
424
+
425
+ ## 4 and 6-Connected CCL Algorithm
426
+
427
+ Here is where the phantom label technique shines. It's a bit harder to find 4 and 6 connected algorithms in the literature, I assume because many of the techniques invented for the 8-way problem, such as the Union-Find data structure for the equivalency table and run-based approaches, are applicable to the simpler problem. However, the SAUF decision tree approach was lacking as every pixel required a unify call in the 4-way problem and two in the 6-way problem.
428
+
429
+ Fig. 5: 4-connected mask modified to include phantom label P.
430
+
431
+ | P | b | . |
432
+ |---|---|---|
433
+ | a | x | . |
434
+
435
+ ```
436
+ if a:
437
+ x := a
438
+ if b and not P:
439
+ unify(a,b)
440
+ elif b:
441
+ x := b
442
+ else:
443
+ x := new label
444
+ ```
445
+
446
+ This gives a decent improvement on the order of 10-20%. If you're lucky, you might not incur even a single label merge operation. In the 6-way problem, there are three phantom labels that can be exploited and the improvement is closer to 50% on our data, a fairly substantial amount. Again, with luck you might avoid any unify operations at all.
447
+
448
+ Fig. 6: Mask for the 6-way problem with phantom labels P, Q, and R added.
449
+
450
+ | P | b |
451
+ |---|---|
452
+ | a | x |
453
+
454
+ | . | Q |
455
+ |---|---|
456
+ | R | c |
457
+
458
+ You can even use multiple routes to propagate information if a label is missing. For example, if path (a,P,b) is unavailable due to a missing P, you could potentially transmit information using path (a,R,c,Q,b).
459
+
460
+ ## Four Pass Algorithm
461
+
462
+ We introduce two additional passes over the image label prior to running the two-pass SAUF algorithm. These additional passes are used to collect statistcs for optimizing the SAUF passes.
463
+
464
+ ### Estimating Provisional Labels
465
+
466
+ The first additional pass is used to over-estimate the number of provisional labels generated by the first SAUF pass. A better estimation allows a smaller allocation for the Union-Find datastructure. For some operating systems, the reduced size of the allocation and improved caching recovers more time than is spent collecting statistics.
467
+
468
+ This can be computed by counting the number of transitions between labels along each row of the image. This scan is easily written such that the instructions can be vectorized to minimize the cost of the scan. The number of transitions is guaranteed to be larger than or equal to the number of provisional labels as all provisional labels are generated in this fashion and then reduced by stealing a label from a neighboring voxel.
469
+
470
+ A hierarchy of estimators can be written as:
471
+
472
+ ```
473
+ 0 <= provisional labels <= X transitions <= static estimate <= voxels
474
+ ```
475
+
476
+ Binary images can also be estimated statically as `voxels / 2` for 4 and 6-way, `voxels / 4` for 8 and 18 way, and `voxels / 8` for 26 connected. For multi-label images, the best static estimate is `voxels` as no assumptions can be made about how labels connect to each other (in the worst case all eight voxels in a cube have different labels).
477
+
478
+ It is also possible to check XY and XYZ transitions to get a tighter bound, but in experiments, the amount of time spent checking those directions exceeded the benefit obtained by checking the X pass. Often the X pass alone results in factors as high as `voxels / 100`.
479
+
480
+ Estimation of the number of labels also allows aborting processing before the first SAUF pass in the case of an all background cube.
481
+
482
+ ### Estimating Foreground Location
483
+
484
+ The second additional pass is estimating the location of the foreground. In the literature, this strategy is sometimes referred to as a "one-and-a-half pass" where the foreground location is computed during the first SAUF pass and then used to skip processing of background voxels during the relabeling pass.
485
+
486
+ Here we perform this check up front so that it can be performed minimally. Instead of integrating the calculation into the first pass which could force some computation on every voxel, we scan each row from the left to find the first foreground voxel and then scan from the right to the find the foreground voxel at the end. The results are tabulated in a uint32 table of starts and ends to each row of size `2 * sy * sz`. This ensures that the volume is scanned at most once, and most likely much less if the shapes fill the space reasonably well. Then, both passes of the SAUF method scan only the part of each row indicated by this table.
487
+
488
+ Certain shapes and distributions defeat the efficiency of scanning only the starts and ends of the row (such as random images or an image with foreground on the start and end of each row and nowhere else). However, for a great many shapes, this provides substantial efficiencies and minimal downside for a dense multi-label image as only two YZ slices of the images are scanned before the table is completed.
489
+
490
+ ### Early Abortion Points
491
+
492
+ There are three locations in the algorithm at which further processing can be aborted early without changing the result.
493
+
494
+ 1. After estimating provisional labels if zero transitions are detected (an all zeros volume). A black image is returned.
495
+ 2. After the first SAUF pass if the number of provisional labels is zero or one. In this case, the provisional labels are guaranteed to be identical to final labels.
496
+ 3. After assigning final labels to each provisional label in a translation array. If the number of final labels equals the number of provisional labels, the provisional labels were accurately assigned and the relabeling scan can be skipped.
497
+
498
+ ## Papers Using cc3d
499
+
500
+ A number of papers are using cc3d now. Many of them seem to be deep learning applications as instance segmentation is liable to generate touching non-binary labels. Some are in geoscience, neuroscience, and medical fields. If cc3d is helpful to you, please feel free to [email us](https://github.com/william-silversmith/) and let us know. We might be able to offer some tips if its performance critical (though we can't guarantee timeliness of response). There are so many variations of the CCL problem, you might be surprised at what you can do.
501
+
502
+ https://scholar.google.com/scholar?as_ylo=2019&q=connected-components-3d&hl=en&as_sdt=0,31
503
+
504
+ ## References
505
+
506
+ 1. A. Rosenfeld and J. Pfaltz. "Sequential Operations in Digital Picture Processing". Journal of the ACM. Vol. 13, Issue 4, Oct. 1966, Pg. 471-494. doi: 10.1145/321356.321357 ([link](https://dl.acm.org/citation.cfm?id=321357))
507
+ 2. R. E. Tarjan. "Efficiency of a good but not linear set union algorithm". Journal of the ACM, 22:215-225, 1975. ([link](https://dl.acm.org/citation.cfm?id=321884))
508
+ 3. K. Wu, E. Otoo, K. Suzuki. "Two Strategies to Speed up Connected Component Labeling Algorithms". Lawrence Berkeley National Laboratory. LBNL-29102, 2005. ([link](https://www.osti.gov/servlets/purl/929013))
509
+ 4. S. Selkow. "The Tree-to-Tree Editing Problem". Information Processing Letters. Vol. 6, No. 6. June 1977. doi: 10.1016/0020-0190(77)90064-3 ([link](http://www.grantjenks.com/wiki/_media/ideas:tree-to-tree_editing_problem.pdf))
510
+ 5. C. Grana, D. Borghesani, R. Cucchiara. "Optimized Block-based Connected Components Labeling with Decision Trees". IEEE Transactions on Image Processing. Vol. 19, Iss. 6. June 2010. doi: 10.1109/TIP.2010.2044963 ([link](http://imagelab.ing.unimore.it/imagelab/pubblicazioni/2009TIPlabeling.pdf))
511
+ 6. P. Sutheebanjard. "Decision Tree for 3-D Connected Components Labeling". Proc. 2012 International Symposium on Information Technology in Medicine and Education. doi: 10.1109/ITiME.2012.6291402 ([link](https://ieeexplore.ieee.org/abstract/document/6291402/authors#authors))
512
+ 7. C. Grana, D. Borghesani, R. Cucchiara. "Fast Block Based Connected Components Labeling". Proc. 16th IEEE Intl. Conf. on Image Processing. 2009. doi: 10.1109/ICIP.2009.5413731 ([link](https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=5413731&casa_token=grvS_69THEYAAAAA:DKpVSoo6nUnI6liLel54kiGdK_ee1qMyPaFYXe_9OGKX0iBDtf9p6ks6mf9twZdK0YPM_SQb&tag=1))
513
+ 8. L. He, Y. Chao and K. Suzuki, "A Linear-Time Two-Scan Labeling Algorithm", IEEE International Conference on Image Processing, vol. 5, pp. 241-244, 2007.
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+ Copyright (c) 2004 Infrae. All rights reserved.
2
+
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+ Redistribution and use in source and binary forms, with or without
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+ modification, are permitted provided that the following conditions are
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+ met:
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+
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+ 1. Redistributions of source code must retain the above copyright
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+ notice, this list of conditions and the following disclaimer.
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+
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+ 2. Redistributions in binary form must reproduce the above copyright
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+ notice, this list of conditions and the following disclaimer in
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+ the documentation and/or other materials provided with the
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+ distribution.
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+
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+ 3. Neither the name of Infrae nor the names of its contributors may
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+ be used to endorse or promote products derived from this software
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+ without specific prior written permission.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL INFRAE OR
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+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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2
+ doc/licenses/BSD.txt), with the following exceptions:
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+
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+ Some code, such a selftest.py, selftest2.py and
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10
+
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12
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15
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+
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+ The isoschematron implementation uses several XSL and RelaxNG resources:
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+ * The (XML syntax) RelaxNG schema for schematron, copyright International
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+ Organization for Standardization (see
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+ src/lxml/isoschematron/resources/rng/iso-schematron.rng for the license
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+ text)
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+ Requires-Dist: BeautifulSoup4 ; extra == 'htmlsoup'
40
+ Provides-Extra: source
41
+ Requires-Dist: Cython (>=0.29.7) ; extra == 'source'
42
+
43
+ lxml is a Pythonic, mature binding for the libxml2 and libxslt libraries. It
44
+ provides safe and convenient access to these libraries using the ElementTree
45
+ API.
46
+
47
+ It extends the ElementTree API significantly to offer support for XPath,
48
+ RelaxNG, XML Schema, XSLT, C14N and much more.
49
+
50
+ To contact the project, go to the `project home page
51
+ <https://lxml.de/>`_ or see our bug tracker at
52
+ https://launchpad.net/lxml
53
+
54
+ In case you want to use the current in-development version of lxml,
55
+ you can get it from the github repository at
56
+ https://github.com/lxml/lxml . Note that this requires Cython to
57
+ build the sources, see the build instructions on the project home
58
+ page. To the same end, running ``easy_install lxml==dev`` will
59
+ install lxml from
60
+ https://github.com/lxml/lxml/tarball/master#egg=lxml-dev if you have
61
+ an appropriate version of Cython installed.
62
+
63
+
64
+ After an official release of a new stable series, bug fixes may become
65
+ available at
66
+ https://github.com/lxml/lxml/tree/lxml-4.9 .
67
+ Running ``easy_install lxml==4.9bugfix`` will install
68
+ the unreleased branch state from
69
+ https://github.com/lxml/lxml/tarball/lxml-4.9#egg=lxml-4.9bugfix
70
+ as soon as a maintenance branch has been established. Note that this
71
+ requires Cython to be installed at an appropriate version for the build.
72
+
73
+ 4.9.1 (2022-07-01)
74
+ ==================
75
+
76
+ Bugs fixed
77
+ ----------
78
+
79
+ * A crash was resolved when using ``iterwalk()`` (or ``canonicalize()``)
80
+ after parsing certain incorrect input. Note that ``iterwalk()`` can crash
81
+ on *valid* input parsed with the same parser *after* failing to parse the
82
+ incorrect input.
83
+
84
+
my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/lxml-4.9.1.dist-info/RECORD ADDED
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+
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+ Copyright (c) 2019 The OAuthlib Community
2
+ All rights reserved.
3
+
4
+ Redistribution and use in source and binary forms, with or without
5
+ modification, are permitted provided that the following conditions are met:
6
+
7
+ 1. Redistributions of source code must retain the above copyright notice,
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+ this list of conditions and the following disclaimer.
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+
10
+ 2. Redistributions in binary form must reproduce the above copyright
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+ notice, this list of conditions and the following disclaimer in the
12
+ documentation and/or other materials provided with the distribution.
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+
14
+ 3. Neither the name of this project nor the names of its contributors may
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+ be used to endorse or promote products derived from this software without
16
+ specific prior written permission.
17
+
18
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
22
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
23
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
24
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
25
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
26
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
27
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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+ Metadata-Version: 2.1
2
+ Name: omegaconf
3
+ Version: 2.2.3
4
+ Summary: A flexible configuration library
5
+ Home-page: https://github.com/omry/omegaconf
6
+ Author: Omry Yadan
7
+ Author-email: omry@yadan.net
8
+ Keywords: yaml configuration config
9
+ Classifier: Programming Language :: Python :: 3.6
10
+ Classifier: Programming Language :: Python :: 3.7
11
+ Classifier: Programming Language :: Python :: 3.8
12
+ Classifier: Programming Language :: Python :: 3.9
13
+ Classifier: Programming Language :: Python :: 3.10
14
+ Classifier: License :: OSI Approved :: BSD License
15
+ Classifier: Operating System :: OS Independent
16
+ Requires-Python: >=3.6
17
+ Description-Content-Type: text/markdown
18
+ License-File: LICENSE
19
+ Requires-Dist: antlr4-python3-runtime (==4.9.*)
20
+ Requires-Dist: PyYAML (>=5.1.0)
21
+ Requires-Dist: dataclasses ; python_version == "3.6"
22
+
23
+ # OmegaConf
24
+ | | Description |
25
+ | --- | --- |
26
+ | Project | [![PyPI version](https://badge.fury.io/py/omegaconf.svg)](https://badge.fury.io/py/omegaconf)[![Downloads](https://pepy.tech/badge/omegaconf/month)](https://pepy.tech/project/omegaconf?versions=1.4.*&versions=2.0.*&versions=2.1.*)![PyPI - Python Version](https://img.shields.io/pypi/pyversions/omegaconf.svg) |
27
+ | Code quality| [![CircleCI](https://img.shields.io/circleci/build/github/omry/omegaconf?logo=s&token=5de2f8dc2a0dd78438520575431aa533150806e3)](https://circleci.com/gh/omry/omegaconf)[![Coverage Status](https://coveralls.io/repos/github/omry/omegaconf/badge.svg)](https://coveralls.io/github/omry/omegaconf)[![Total alerts](https://img.shields.io/lgtm/alerts/g/omry/omegaconf.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/omry/omegaconf/alerts/)[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/omry/omegaconf.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/omry/omegaconf/context:python)|
28
+ | Docs and support |[![Documentation Status](https://readthedocs.org/projects/omegaconf/badge/?version=2.0_branch)](https://omegaconf.readthedocs.io/en/2.1_branch/)[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/omry/omegaconf/master?filepath=docs%2Fnotebook%2FTutorial.ipynb)[![](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://hydra-framework.zulipchat.com)|
29
+
30
+
31
+ OmegaConf is a hierarchical configuration system, with support for merging configurations from multiple sources (YAML config files, dataclasses/objects and CLI arguments)
32
+ providing a consistent API regardless of how the configuration was created.
33
+
34
+ ## Releases
35
+
36
+ ### Stable (2.2)
37
+ OmegaConf 2.2 is the current stable version.
38
+ * [What's new](https://github.com/omry/omegaconf/releases/tag/v2.2.1)
39
+ * [Source code](https://github.com/omry/omegaconf/tree/2.2_branch)
40
+
41
+ Install with `pip install --upgrade omegaconf`
42
+
43
+ ### Previous release (2.1)
44
+ OmegaConf 2.1 is the current stable version.
45
+ * [What's new](https://github.com/omry/omegaconf/releases/tag/v2.1.1)
46
+ * [Documentation](https://omegaconf.readthedocs.io/en/2.1_branch/)
47
+ * [Slides](https://docs.google.com/presentation/d/e/2PACX-1vT_UIV7hCnquIbLUm4NnkUpXvPEh33IKiUEvPRF850WKA8opOlZOszjKdZ3tPmf8u7hGNP6HpqS-NT5/pub?start=false&loop=false&delayms=3000)
48
+ * [Source code](https://github.com/omry/omegaconf/tree/2.1_branch)
49
+
50
+ Install with `pip install omegaconf==2.1`
51
+
52
+ ### Previous release (2.0)
53
+
54
+ * [What's new](https://github.com/omry/omegaconf/releases/tag/v2.0.0)
55
+ * [Documentation](https://omegaconf.readthedocs.io/en/2.0_branch/)
56
+ * [Slides](https://docs.google.com/presentation/d/e/2PACX-1vT_UIV7hCnquIbLUm4NnkUpXvPEh33IKiUEvPRF850WKA8opOlZOszjKdZ3tPmf8u7hGNP6HpqS-NT5/pub?start=false&loop=false&delayms=3000)
57
+ * [Source code](https://github.com/omry/omegaconf/tree/2.0_branch)
58
+
59
+ Install with `pip install omegaconf==2.0.6`
60
+
61
+ ## Live tutorial
62
+ Run the live tutorial: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/omry/omegaconf/master?filepath=docs%2Fnotebook%2FTutorial.ipynb)
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@@ -0,0 +1,2 @@
 
 
 
1
+ omegaconf
2
+ pydevd_plugins
my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/pip/__init__.py ADDED
@@ -0,0 +1,13 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ from typing import List, Optional
2
+
3
+ __version__ = "24.0"
4
+
5
+
6
+ def main(args: Optional[List[str]] = None) -> int:
7
+ """This is an internal API only meant for use by pip's own console scripts.
8
+
9
+ For additional details, see https://github.com/pypa/pip/issues/7498.
10
+ """
11
+ from pip._internal.utils.entrypoints import _wrapper
12
+
13
+ return _wrapper(args)
my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/pip/__pip-runner__.py ADDED
@@ -0,0 +1,50 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Execute exactly this copy of pip, within a different environment.
2
+
3
+ This file is named as it is, to ensure that this module can't be imported via
4
+ an import statement.
5
+ """
6
+
7
+ # /!\ This version compatibility check section must be Python 2 compatible. /!\
8
+
9
+ import sys
10
+
11
+ # Copied from setup.py
12
+ PYTHON_REQUIRES = (3, 7)
13
+
14
+
15
+ def version_str(version): # type: ignore
16
+ return ".".join(str(v) for v in version)
17
+
18
+
19
+ if sys.version_info[:2] < PYTHON_REQUIRES:
20
+ raise SystemExit(
21
+ "This version of pip does not support python {} (requires >={}).".format(
22
+ version_str(sys.version_info[:2]), version_str(PYTHON_REQUIRES)
23
+ )
24
+ )
25
+
26
+ # From here on, we can use Python 3 features, but the syntax must remain
27
+ # Python 2 compatible.
28
+
29
+ import runpy # noqa: E402
30
+ from importlib.machinery import PathFinder # noqa: E402
31
+ from os.path import dirname # noqa: E402
32
+
33
+ PIP_SOURCES_ROOT = dirname(dirname(__file__))
34
+
35
+
36
+ class PipImportRedirectingFinder:
37
+ @classmethod
38
+ def find_spec(self, fullname, path=None, target=None): # type: ignore
39
+ if fullname != "pip":
40
+ return None
41
+
42
+ spec = PathFinder.find_spec(fullname, [PIP_SOURCES_ROOT], target)
43
+ assert spec, (PIP_SOURCES_ROOT, fullname)
44
+ return spec
45
+
46
+
47
+ sys.meta_path.insert(0, PipImportRedirectingFinder())
48
+
49
+ assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module"
50
+ runpy.run_module("pip", run_name="__main__", alter_sys=True)
my_container_sandbox/workspace/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py ADDED
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