Fix vtkDICOMReader tilted-gantry PatientMatrix for BottomUp.
This is required in order for vtkDICOMCTRectifer to work when
the reader uses "BottomUp" row order (which is the default).

This fixes a potential infinite loop while parsing files that
end in garbage, and updates the DICOM dictionary to 2020e.

JackGuyver authored 3 years ago and David Gobbi committed 3 years ago

Based on the discussion within the merge request !7880 the possibility
to convert a numpy array containing single characters of any type has
been removed without replacement, since these arrays have no appropriate
counterpart in VTK.
For more information see:
!7880

JackGuyver authored 3 years ago and David Gobbi committed 3 years ago

Numpy VTK array conversion contains the the type numpy.character, which
is deprecated since NumPy version 1.19
See: https://numpy.org/doc/stable/reference/arrays.dtypes.html
section Generic types.

Ben Boeckel authored 3 years ago and Kitware Robot committed 3 years ago

06fb754e Merge topic 'ci-properly-tagged-wheels' into backport-missed-mrs-9.0.2
a19895c2 Merge topic 'minimize-wheel-size' into backport-missed-mrs-9.0.2
6ccb2b79 gitlab-ci: use the audited wheels on Linux
ae5bcb1a Merge topic 'ci-macos-arm64-wheel' into backport-missed-mrs-9.0.2
710b8895 wheel: reduce the size of Linux and macOS wheels
6efec1cd gitlab-ci: enable macOS arm64 wheels again

Acked-by: Kitware Robot <kwrobot@kitware.com>
Merge-request: !8070

Merge-request: !8065

Merge-request: !8062

(cherry picked from commit fc8cd99c)

Merge-request: !8050

Wheels make copies of files instead of storing symlinks. Drop the
information in wheels to save space since they're not really reusable as
SDKs anyways.

(cherry picked from commit dfe5b509)

The _PYTHON_HOST_PLATFORM variable should avoid universal2 assumptions.

(cherry picked from commit 2f22c897)

Ben Boeckel authored 3 years ago and Kitware Robot committed 3 years ago

36dc6577 ci: force Python3 for wheels in CI
c002bd30 gitlab-ci: backport wheel build jobs from master
aff6b008 wheel: add the required rpath entry for wheels
2412480a vtkWheelPreparation: silence legacy messages
2c610e45 vtkWheelPreparation: fix library destinations for wheels
974b207b setup.py: fix canonical issue URL
4806f36f setup.py: fix macOS library inclusion
610224b5 setup.py: add `vtkmodules.web` if the web feature is available
...

Acked-by: Kitware Robot <kwrobot@kitware.com>
Merge-request: !8045

Everything not related to wheels has been stripped out.

The wheel infrastructure assumes this is the case.

Chuck Atkins authored 3 years ago and Kitware Robot committed 3 years ago

f727b8e7 vtkmpi: Expand no-cpp defines to cover SGI MPT

Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Ben Boeckel <ben.boeckel@kitware.com>
Merge-request: !7891

Ben Boeckel authored 4 years ago and Kitware Robot committed 4 years ago

61e81bb2 Merge branch 'upstream-hdf5' into HEAD
6deba064 hdf5 2021-02-24 (3f65de94)
f1de83f6 Bumped hdf5 to for/vtk-20210227-1.10.6 tag

Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Ben Boeckel <ben.boeckel@kitware.com>
Merge-request: !7698

# By HDF Upstream
* upstream-hdf5:
  hdf5 2021-02-24 (3f65de94)

Kitware Robot authored 4 years ago and Ben Boeckel committed 4 years ago

Code extracted from:

    https://gitlab.kitware.com/third-party/hdf5.git

at commit 3f65de9445b8712ed5b0440d652414a61bf0bb56 (for/vtk-20210227-1.10.6).

Sean McBride authored 4 years ago and Kitware Robot committed 4 years ago

86b1c9de Fixed cmake 3.20rc3 CMP0115 warning

Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Ben Boeckel <ben.boeckel@kitware.com>
Merge-request: !7729

Just fully specify a filename, with extension.

Increased from for/vtk-20200818-1.10.6 tag.

Notably this will allow building as Universal Binary on macOS.

Sean McBride authored 4 years ago and Kitware Robot committed 4 years ago

8c9edd68 vtkPSystemTools: Fix GetCurrentWorkingDirectory for KWSys change

Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Ben Boeckel <ben.boeckel@kitware.com>
Merge-request: !7710

KWSys no longer offers the `collapse` argument. Just removed it.

This is backported from 9518a984 from master.

Cory Quammen authored 4 years ago and Kitware Robot committed 4 years ago

d747f524 For unstructured grids, enable point merging when requested

Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Mathieu Westphal <mathieu.westphal@kitware.com>
Merge-request: !7660

For vtkCutter, point merging is not an explicit option. It is enabled
by setting a vtkPointLocator that merges points. However, if a
vtkNonMergingPointLocator is set as the point locator, then points
will not be merged. Pass along the inferred merging option to
vtk3DLinearGridPlaneCutter when execution is deferred to it.

(cherry picked from commit cbdb93fc)

Brad King authored 4 years ago and Kitware Robot committed 4 years ago

390edb98 Merge branch 'upstream-KWSys' into update-kwsys-2021-02-10
89276e0a KWSys 2021-02-10 (dda7a943)

Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Ben Boeckel <ben.boeckel@kitware.com>
Merge-request: !7615

# By KWSys Upstream
* upstream-KWSys:
  KWSys 2021-02-10 (dda7a943)

Kitware Robot authored 4 years ago and Sean McBride committed 4 years ago

Code extracted from:

    https://gitlab.kitware.com/utils/kwsys.git

at commit dda7a943856ad22e374a9b0434727285461770a6 (master).

Upstream Shortlog
-----------------

Ben Boeckel (10):
      ccab3808 clang-tidy: address readability-isolate-declaration lints
      87b57076 clang-tidy: address readability-braces-around-statements lints
      13b45a41 clang-tidy: address readability-else-after-return lints
      ebb48d58 clang-tidy: address google-readability-casting lint
      09942f51 testSystemTools: add tests for SplitString
      986519af SystemTools: handle splitting a string starting with the separator
      83b20b65 clang-tidy: address `readability-braces-around-statements` lint
      535633fa clang-tidy: address `readability-isolate-declaration` lint
      de210648 clang-tidy: address `readability-else-after-return` lint
      39fd4817 testProcess: fix another clang-tidy warning

Brad King (16):
      313b2f7a SystemTools: Make SystemToolsStatic singleton private to implementation file
      019afb6e SystemTools: Drop GetCurrentWorkingDirectory 'collapse' argument
      c35a377f SystemTools: Refactor CollapseFullPath to call getcwd only when needed
      e3989b18 SystemTools: Restore GetCurrentWorkingDirectory slash conversion on Windows
      41700ca4 SystemTools: Fix FileIsExecutable on Windows
      b8177b56 testProcess: Disable unreliable test case 7
      e093a985 Glob: Append warning message only if destination is non-null
      25775078 Glob: Do not warn if top-level directory does not exist
      ce4941c9 IOStream: Drop this component of KWSys
      49d04c2c hashtable: Drop this component of KWSys
      a0bd892c SystemInformation: Use 'long long' unconditionally
      441dd494 Drop unused checks for 'long long' and '__int64'
      2b749749 Drop unused C type macros check
      74daf33b Drop unused Borland and OpenWatcom preprocessor conditions
      c4e8126a Drop unused CXX cstdio check
      6e51fe76 FStream: Add std::fstream wrapper for in/out file streams

Deniz Bahadir (1):
      8bc06cf8 Regex: Double the maximal allowed size for a regex (to 2^{16}-1)

Dmitry Kalinkin (3):
      9a3f9799 Directory: implement error reporting
      f33ef4e3 Glob: issue warnings on Directory errors
      97f880e6 Directory: add extra tests involving errorMessage

Dylan Fan (1):
      e6cc4679 SystemInformation: Add Zhaoxin x86 processor

Hernan Martinez (1):
      00629420 SystemInformation: Add support for Windows on ARM64

Jack Guo (1):
      22216d56 SystemTools: Fix Touch() on broken symlink when create==false

Lemures Lemniscati (3):
      be39cd88 Glob: Use case-sensitive globbing on Cygwin
      63dbb0ca SystemInformation: Improve CPU info lookup on Cygwin
      4ef36a00 SystemTools: Remove Cygwin-specific file lookup optimization

Martin Storsjö (1):
      fca5ad3a Process: Fix execute error handling re working dir on windows

Robert Maynard (2):
      4b537c59 Tests: Handle that root users on linux can always write to files
      29096513 Process: Prefer normative terms to express subprocess failures

Rolf Eike Beer (1):
      c55e5dc3 CTestConfig: allow nightly build submission using https

Sean McBride (7):
      c58d4b47 SystemTools: On Windows, strip 'e' from Fopen mode
      cb541c31 Auto-fixed various clang-tidy warnings
      2c179921 Applied clang-tidy modernize-deprecated-headers
      775296c8 Applied clang-tidy bugprone-suspicious-string-compare fixes
      a19f0ac6 Fixed clang -Wstrict-prototypes warning
      eb6820b6 Glob: Explicitly delete copy construction and assignment
      45e42f63 SystemInformation: Improve ParseSysCtl error checking

Vladimir Menshakov (1):
      66724af8 SystemTools: Teach FindProgram to find non-readable programs