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First batch of updates for Mediawiki-sphinx conversions #108

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mseng10 and others added 7 commits June 5, 2019 15:19
When building ITKEx, ensure that the appropriate level of
compiler standard is used.
  - Add ComputeMatrix
  - Add GaussianBlurImageFunction
  - Add GaussianBlurImageFunctionFilter
  - Add IterateOverARegionWithAShapedNeighborhoodIteratorManual from wiki examples.
  - Add MedianImageFunction
  - Add MultiplyKernalWithAnImageAtLocation
  - Add WriteAPointSet
  - Adding DistanceBetweenIndices and DistanceBetweenPoints from wiki examples.
  - Adding UpsampleAnImage from wiki examples.
  - Adding VectorDotProduct from wiki examples.
  - Adding WritePointSet from wiki examples.
  - Created ConvertImageToAnotherType sphinx example from wiki
  - Created MultiplyKernelWithAnImageAtLocation sphinx example from wiki
  - Finished Add IterateOverARegionWithAShapedNeighborhoodIteratorManual from wiki examples.
  - Finished Adding UpsampleAnImage from wiki examples.
  - Fixed mistake, wrong example creation
  - Moved wiki AddConstantToEveryPixel to sphinx
  - Moved wiki AddTwoImages to sphinx
  - Moved wiki AmoebaOptimization to sphinx
  - Moved wiki ApproxDistanceMapOfBinary to sphinx
  - Moved wiki BresenhamLine to sphinx
  - Moved wiki ColorBoundariesOfRegions to sphinx
  - Moved wiki ColorLabeledRegions to sphinx
  - Moved wiki ComputeMedianOfImageAtPixel to sphinx
  - Moved wiki ConvertArrayToImage to sphinx
  - Moved wiki ConvertImageWithLabelsToShapeLabelMap to sphinx
  - Moved wiki ConvertLabelMapToImage to sphinx
  - Moved wiki DerivativeImage to sphinx
  - Moved wiki FindZeroCrossings to sphinx
  - Moved wiki GaussianBlurImageFunction to sphinx
  - Moved wiki GeometricPropertiesOfRegion to sphinx
  - Moved wiki KeepBinaryRegionsThatMeetSpecific to sphinx
  - Moved wiki KeepRegionsAboveLevel to sphinx
  - Moved wiki KeepRegionsThatMeetSpecific to sphinx
  - Moved wiki LabelBinaryRegionsAndGetProperties to sphinx
  - Moved wiki LabelBinaryRegionsInImage to sphinx
  - Moved wiki LevenbergMarquardtOptimization to sphinx
  - Moved wiki Matrix to sphinx
  - Moved wiki MatrixInverse to sphinx
  - Moved wiki MaurerDistanceMapOfBinary to sphinx
  - Moved wiki MergeLabelMaps to sphinx
  - Moved wiki MultiresolutionPyramidFromImage to sphinx
  - Moved wiki NormalizedCorrelation to sphinx
  - Moved wiki NormalizedCorrelationOfMaskedImage to sphinx
  - Moved wiki NormalizedCorrelationUsingFFT to sphinx
  - Moved wiki NormalizedCorrelationUsingFFTWithMaskImages to sphinx
  - Moved wiki OverlayLabelMapOnImage to sphinx
  - Moved wiki Pi to sphinx
  - Moved wiki PixelDivisionOfTwoImages to sphinx
  - Moved wiki ReadTransformFromFile to sphinx
  - Moved wiki RegionalMaximal to sphinx
  - Moved wiki RegionalMinimal to sphinx
  - Moved wiki RegisterTransformWithTransformFactory to sphinx
  - Moved wiki RemoveLabelsFromLabelMap to sphinx
  - Moved wiki ResampleDICOMSeries to sphinx
  - Moved wiki ResampleRGBImage to sphinx
  - Moved wiki ResampleSegmentedImage to sphinx
  - Moved wiki ScaleAnImage and RequestedRegion to sphinx
  - Moved wiki ScalePixelSumToConstant to sphinx
  - Moved wiki ShapeAttributesForBinaryImage to sphinx
  - Moved wiki SharpenImage to sphinx
  - Moved wiki SignedDistanceMapOfBinary to sphinx
  - Moved wiki StatisticalPropertiesOfRegions to sphinx
  - Moved wiki ThinImage to sphinx
  - Moved wiki Transparency to sphinx
  - Moved wiki VariableLengthVector to sphinx
  - Moved wiki WriteTransformToFile to sphinx
@hjmjohnson hjmjohnson requested review from thewtex and dzenanz and removed request for thewtex June 5, 2019 20:38
@hjmjohnson hjmjohnson self-assigned this Jun 5, 2019
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The build errors look like to be due to urllib3 package getting updated:

[15/32] Performing install step for 'ITKPython'
FAILED: ITKPython-prefix/src/ITKPython-stamp/ITKPython-install 
cd /home/vsts/work/1/ITKEx-bld/ITKPython-prefix/src/ITKPython-build && /home/vsts/work/1/ITKEx-bld/itkpython/bin/python -m pip install --pre itk sphinx && /usr/local/bin/cmake -E touch /home/vsts/work/1/ITKEx-bld/ITKPython-prefix/src/ITKPython-stamp/ITKPython-install
Collecting itk
  Downloading https://files.pythonhosted.org/packages/e0/a0/2fb5c9d964d77361dbdd3c3022928d83d2f0cf4655c36eb888655dcba917/itk-5.0.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting sphinx
  Downloading https://files.pythonhosted.org/packages/e1/81/1dd79c5cd4320f2e904d7fbed7990d07c3b4e7a21efd2071be88dd5806f1/Sphinx-2.1.0-py2.py3-none-any.whl (3.2MB)
Collecting itk-registration==5.0.0 (from itk)
  Downloading https://files.pythonhosted.org/packages/44/50/fab9b0b28c90c3679779bd2b65a1a2d86123af364058f5d2013f3fa483ae/itk_registration-5.0.0-cp35-cp35m-manylinux1_x86_64.whl (11.1MB)
Collecting itk-core==5.0.0 (from itk)
Exception:
Traceback (most recent call last):
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/urllib3-1.13.1-py2.py3-none-any.whl/urllib3/connectionpool.py", line 377, in _make_request
    httplib_response = conn.getresponse(buffering=True)
TypeError: getresponse() got an unexpected keyword argument 'buffering'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/urllib3-1.13.1-py2.py3-none-any.whl/urllib3/connectionpool.py", line 379, in _make_request
    httplib_response = conn.getresponse()
  File "/usr/lib/python3.5/http/client.py", line 1197, in getresponse
    response.begin()
  File "/usr/lib/python3.5/http/client.py", line 297, in begin
    version, status, reason = self._read_status()
  File "/usr/lib/python3.5/http/client.py", line 258, in _read_status
    line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
  File "/usr/lib/python3.5/socket.py", line 575, in readinto
    return self._sock.recv_into(b)
  File "/usr/lib/python3.5/ssl.py", line 929, in recv_into
    return self.read(nbytes, buffer)
  File "/usr/lib/python3.5/ssl.py", line 791, in read
    return self._sslobj.read(len, buffer)
  File "/usr/lib/python3.5/ssl.py", line 575, in read
    v = self._sslobj.read(len, buffer)
socket.timeout: The read operation timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/urllib3-1.13.1-py2.py3-none-any.whl/urllib3/connectionpool.py", line 560, in urlopen
    body=body, headers=headers)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/urllib3-1.13.1-py2.py3-none-any.whl/urllib3/connectionpool.py", line 381, in _make_request
    self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/urllib3-1.13.1-py2.py3-none-any.whl/urllib3/connectionpool.py", line 309, in _raise_timeout
    raise ReadTimeoutError(self, url, "Read timed out. (read timeout=%s)" % timeout_value)
requests.packages.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/basecommand.py", line 209, in main
    status = self.run(options, args)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/commands/install.py", line 328, in run
    wb.build(autobuilding=True)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/wheel.py", line 748, in build
    self.requirement_set.prepare_files(self.finder)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/req/req_set.py", line 360, in prepare_files
    ignore_dependencies=self.ignore_dependencies))
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/req/req_set.py", line 577, in _prepare_file
    session=self.session, hashes=hashes)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/download.py", line 810, in unpack_url
    hashes=hashes
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/download.py", line 649, in unpack_http_url
    hashes)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/download.py", line 842, in _download_http_url
    stream=True,
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/requests-2.9.1-py2.py3-none-any.whl/requests/sessions.py", line 480, in get
    return self.request('GET', url, **kwargs)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/lib/python3.5/site-packages/pip/download.py", line 378, in request
    return super(PipSession, self).request(method, url, *args, **kwargs)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/requests-2.9.1-py2.py3-none-any.whl/requests/sessions.py", line 468, in request
    resp = self.send(prep, **send_kwargs)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/requests-2.9.1-py2.py3-none-any.whl/requests/sessions.py", line 576, in send
    r = adapter.send(request, **kwargs)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/CacheControl-0.11.5-py2.py3-none-any.whl/cachecontrol/adapter.py", line 46, in send
    resp = super(CacheControlAdapter, self).send(request, **kw)
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/requests-2.9.1-py2.py3-none-any.whl/requests/adapters.py", line 376, in send
    timeout=timeout
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/urllib3-1.13.1-py2.py3-none-any.whl/urllib3/connectionpool.py", line 610, in urlopen
    _stacktrace=sys.exc_info()[2])
  File "/home/vsts/work/1/ITKEx-bld/itkpython/share/python-wheels/urllib3-1.13.1-py2.py3-none-any.whl/urllib3/util/retry.py", line 228, in increment
    total -= 1
TypeError: unsupported operand type(s) for -=: 'Retry' and 'int'

@hjmjohnson
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Superceeded by #109

@hjmjohnson hjmjohnson closed this Jun 10, 2019
@hjmjohnson hjmjohnson deleted the mediawiki-sphinx-part1 branch June 10, 2019 01:17
jhlegarreta added a commit to jhlegarreta/ITKSoftwareGuide that referenced this pull request May 12, 2020
Miscellaneus fixes in the `Introduction` and `Installation` chapters:
- Fix the development environment names.
- Remove compiler support dates prior to 2016 from the compiler support
  table.
- Remove the deprecated reference to the Wiki Examples: examples are
  entirely hosted in https://itk.org/ITKExamples/ since a series of PRs
  including
  InsightSoftwareConsortium/ITKSphinxExamples#108 and
  InsightSoftwareConsortium/ITKSphinxExamples#109.
- Fix the `Utilities` and `Wrapping` parent folders.
- Tke advantage of the commit to order alphabetically the ITK's main
  folders.

Take advantage of the commit for other minor style changes (e.g. period at
the end of sentences, proper LaTex quote syntax, etc.).

Take advantage of the commit to limit the line length to 79 characters in
the ITK's folder structure bullet points.
jhlegarreta added a commit to jhlegarreta/ITKSoftwareGuide that referenced this pull request May 12, 2020
Miscellaneus fixes in the `Introduction` and `Installation` chapters:
- Fix the development environment names.
- Remove compiler support dates prior to 2016 from the compiler support
  table.
- Remove the deprecated reference to the Wiki Examples: examples are
  entirely hosted in https://itk.org/ITKExamples/ since a series of PRs
  including
  InsightSoftwareConsortium/ITKSphinxExamples#108 and
  InsightSoftwareConsortium/ITKSphinxExamples#109.
- Fix the `Utilities` and `Wrapping` parent folders.
- Tke advantage of the commit to order alphabetically the ITK's main
  folders.

Take advantage of the commit for other minor style changes (e.g. period at
the end of sentences, proper LaTex quote syntax, etc.).

Take advantage of the commit to limit the line length to 79 characters in
the ITK's folder structure bullet points.
jhlegarreta added a commit to jhlegarreta/ITKSoftwareGuide that referenced this pull request May 12, 2020
Miscellaneus fixes in the `Introduction` and `Installation` chapters:
- Fix the development environment names.
- Remove compiler support dates prior to 2016 from the compiler support
  table.
- Remove the deprecated reference to the Wiki Examples: examples are
  entirely hosted in https://itk.org/ITKExamples/ since a series of PRs
  including
  InsightSoftwareConsortium/ITKSphinxExamples#108 and
  InsightSoftwareConsortium/ITKSphinxExamples#109.
- Fix the `Utilities` and `Wrapping` parent folders.
- Mention the raw binary files and the SHA512 hash files in the `Testing`
  folder paragraph.
- Tke advantage of the commit to order alphabetically the ITK's main
  folders.

Take advantage of the commit for other minor style changes (e.g. period at
the end of sentences, proper LaTex quote syntax, etc.).

Take advantage of the commit to limit the line length to 79 characters in
the ITK's folder structure bullet points.
jhlegarreta added a commit to jhlegarreta/ITKSoftwareGuide that referenced this pull request May 13, 2020
Miscellaneus fixes in the `Introduction` and `Installation` chapters:
- Fix the development environment names.
- Remove compiler support dates prior to 2016 from the compiler support
  table.
- Remove the deprecated reference to the Wiki Examples: examples are
  entirely hosted in https://itk.org/ITKExamples/ since a series of PRs
  including
  InsightSoftwareConsortium/ITKSphinxExamples#108 and
  InsightSoftwareConsortium/ITKSphinxExamples#109.
- Fix the `Utilities` and `Wrapping` parent folders.
- Mention the raw binary files and the SHA512 hash files in the `Testing`
  folder paragraph.
- Take advantage of the commit to order alphabetically the ITK's main
  folders.

Take advantage of the commit for other minor style changes (e.g. period at
the end of sentences, proper LaTex quote syntax, etc.).

Take advantage of the commit to limit the line length to 79 characters in
the ITK's folder structure bullet points.
thewtex pushed a commit to jhlegarreta/ITKSoftwareGuide that referenced this pull request May 14, 2020
Miscellaneus fixes in the `Introduction` and `Installation` chapters:
- Fix the development environment names.
- Remove compiler support dates prior to 2016 from the compiler support
  table.
- Remove the deprecated reference to the Wiki Examples: examples are
  entirely hosted in https://itk.org/ITKExamples/ since a series of PRs
  including
  InsightSoftwareConsortium/ITKSphinxExamples#108 and
  InsightSoftwareConsortium/ITKSphinxExamples#109.
- Fix the `Utilities` and `Wrapping` parent folders.
- Mention the raw binary files and the SHA512 hash files in the `Testing`
  folder paragraph.
- Take advantage of the commit to order alphabetically the ITK's main
  folders.

Take advantage of the commit for other minor style changes (e.g. period at
the end of sentences, proper LaTex quote syntax, etc.).

Take advantage of the commit to limit the line length to 79 characters in
the ITK's folder structure bullet points.
jhlegarreta added a commit to jhlegarreta/ITKSoftwareGuide that referenced this pull request May 14, 2020
Miscellaneus fixes in the `Introduction` and `Installation` chapters:
- Fix the development environment names.
- Rework the compiler list: update to currently supported versions.
- Remove the compiler support/deprecation cycle table due to difficulties
  in keeping it up to date.
- Remove the deprecated reference to the Wiki Examples: examples are
  entirely hosted in https://itk.org/ITKExamples/ since a series of PRs
  including
  InsightSoftwareConsortium/ITKSphinxExamples#108 and
  InsightSoftwareConsortium/ITKSphinxExamples#109.
- Update the `vxl` link.
- Fix the `Utilities` and `Wrapping` parent folders.
- Mention the raw binary files and the SHA512 hash files in the `Testing`
  folder paragraph.
- Take advantage of the commit to order alphabetically the ITK's main
  folders.

Take advantage of the commit for other minor style changes (e.g. period at
the end of sentences, proper LaTex quote syntax, etc.).

Take advantage of the commit to limit the line length to 79 characters in
the ITK's folder structure bullet points.
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3 participants