From fd38b4d2896c35b048f9bb45e8d6647e2b9a1fd5 Mon Sep 17 00:00:00 2001 From: brian avants Date: Tue, 4 Sep 2018 10:26:54 -0400 Subject: [PATCH 01/27] COMP: for compiling with perf enhancements Change-Id: I63ccba3a5ba610fffc6453cb6e125fd47b68521b --- .../VNLInstantiation/src/CMakeLists.txt | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt index 8160a0d185d..90a162f675c 100644 --- a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt +++ b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt @@ -2,6 +2,8 @@ set(ITKVNLInstantiation_SRCS vnl_vector+ulonglong-.cxx vnl_fft_base+float.3-.cxx vnl_fft_base+float.4-.cxx + vnl_matrix_fixed+double.1.1-.cxx + vnl_matrix_fixed+double.5.5-.cxx vnl_matrix_fixed_ref+double.2.2-.cxx vnl_matrix_fixed_ref+double.2.3-.cxx vnl_fft_base+double.3-.cxx @@ -10,8 +12,13 @@ set(ITKVNLInstantiation_SRCS vnl_vector+ushort-.cxx vnl_matrix_fixed+double.3.12-.cxx vnl_matrix_fixed+double.2.3-.cxx + vnl_fortran_copy_fixed+double.5.5-.cxx vnl_matrix_fixed+double.10.10-.cxx vnl_matrix_fixed+float.10.10-.cxx + vnl_matrix_fixed+double.1.1-.cxx + vnl_matrix_fixed+float.1.1-.cxx + vnl_matrix_fixed+double.5.5-.cxx + vnl_matrix_fixed+float.5.5-.cxx vnl_c_vector+char-.cxx vnl_c_vector+short-.cxx vnl_matrix+short-.cxx @@ -27,28 +34,39 @@ set(ITKVNLInstantiation_SRCS vnl_c_vector+longlong-.cxx vnl_vector+short-.cxx vnl_matrix+ushort-.cxx + vnl_svd_fixed+double.1.1-.cxx vnl_svd_fixed+double.2.2-.cxx vnl_svd_fixed+double.2.3-.cxx vnl_svd_fixed+double.3.2-.cxx vnl_svd_fixed+double.4.4-.cxx + vnl_svd_fixed+double.5.5-.cxx vnl_svd_fixed+double.10.10-.cxx + vnl_svd_fixed+float.1.1-.cxx vnl_svd_fixed+float.2.2-.cxx vnl_svd_fixed+float.2.3-.cxx vnl_svd_fixed+float.4.4-.cxx + vnl_svd_fixed+float.5.5-.cxx vnl_svd_fixed+float.10.10-.cxx + vnl_fortran_copy_fixed+double.1.1-.cxx vnl_fortran_copy_fixed+double.2.2-.cxx vnl_fortran_copy_fixed+double.2.3-.cxx vnl_fortran_copy_fixed+double.3.2-.cxx vnl_fortran_copy_fixed+double.4.4-.cxx vnl_fortran_copy_fixed+double.10.10-.cxx + vnl_fortran_copy_fixed+float.1.1-.cxx vnl_fortran_copy_fixed+float.4.4-.cxx + vnl_fortran_copy_fixed+float.5.5-.cxx vnl_fortran_copy_fixed+float.2.2-.cxx vnl_fortran_copy_fixed+float.2.3-.cxx vnl_fortran_copy_fixed+float.4.4-.cxx vnl_fortran_copy_fixed+float.10.10-.cxx + vnl_diag_matrix_fixed+double.1-.cxx vnl_diag_matrix_fixed+double.2-.cxx + vnl_diag_matrix_fixed+double.5-.cxx vnl_diag_matrix_fixed+double.10-.cxx + vnl_diag_matrix_fixed+float.1-.cxx vnl_diag_matrix_fixed+float.2-.cxx + vnl_diag_matrix_fixed+float.5-.cxx vnl_diag_matrix_fixed+float.10-.cxx ) From f44174c188466da6a9dcfbf3928d52bbd3b05cd2 Mon Sep 17 00:00:00 2001 From: brian avants Date: Tue, 4 Sep 2018 10:30:53 -0400 Subject: [PATCH 02/27] COMP: for compiling with perf enhancements - forgot file add Change-Id: I00b5e22e526421d3d4aeedf71b248adfe0cfca3d --- .../src/vnl_diag_matrix_fixed+double.1-.cxx | 25 +++++++++++++++++ .../src/vnl_diag_matrix_fixed+double.5-.cxx | 25 +++++++++++++++++ .../src/vnl_diag_matrix_fixed+float.1-.cxx | 25 +++++++++++++++++ .../src/vnl_diag_matrix_fixed+float.5-.cxx | 25 +++++++++++++++++ .../vnl_fortran_copy_fixed+double.1.1-.cxx | 25 +++++++++++++++++ .../vnl_fortran_copy_fixed+double.5.5-.cxx | 25 +++++++++++++++++ .../src/vnl_fortran_copy_fixed+float.1.1-.cxx | 25 +++++++++++++++++ .../src/vnl_fortran_copy_fixed+float.5.5-.cxx | 25 +++++++++++++++++ .../src/vnl_matrix_fixed+double.1.1-.cxx | 28 +++++++++++++++++++ .../src/vnl_matrix_fixed+double.5.5-.cxx | 28 +++++++++++++++++++ .../src/vnl_matrix_fixed+float.1.1-.cxx | 28 +++++++++++++++++++ .../src/vnl_matrix_fixed+float.5.5-.cxx | 28 +++++++++++++++++++ .../src/vnl_svd_fixed+double.1.1-.cxx | 25 +++++++++++++++++ .../src/vnl_svd_fixed+double.5.5-.cxx | 25 +++++++++++++++++ .../src/vnl_svd_fixed+float.1.1-.cxx | 25 +++++++++++++++++ .../src/vnl_svd_fixed+float.5.5-.cxx | 25 +++++++++++++++++ 16 files changed, 412 insertions(+) create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.1.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.1.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.1.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.1.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.1.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.1.1-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.1-.cxx new file mode 100644 index 00000000000..a26c1ad2d26 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.1-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_diag_matrix_fixed.txx" +#else +#include "vnl/vnl_diag_matrix_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_DIAG_MATRIX_FIXED_INSTANTIATE(double, 1); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx new file mode 100644 index 00000000000..e935055dba9 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_diag_matrix_fixed.txx" +#else +#include "vnl/vnl_diag_matrix_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_DIAG_MATRIX_FIXED_INSTANTIATE(double, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.1-.cxx new file mode 100644 index 00000000000..c8eb702407d --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.1-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_diag_matrix_fixed.txx" +#else +#include "vnl/vnl_diag_matrix_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_DIAG_MATRIX_FIXED_INSTANTIATE(float, 1); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx new file mode 100644 index 00000000000..5cd3b7fd849 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_diag_matrix_fixed.txx" +#else +#include "vnl/vnl_diag_matrix_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_DIAG_MATRIX_FIXED_INSTANTIATE(float, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.1.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.1.1-.cxx new file mode 100644 index 00000000000..2bdc3bb96bd --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.1.1-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_fortran_copy_fixed.txx" +#else +#include "vnl/vnl_fortran_copy_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_FORTRAN_COPY_FIXED_INSTANTIATE(double, 1, 1); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx new file mode 100644 index 00000000000..54183896daf --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_fortran_copy_fixed.txx" +#else +#include "vnl/vnl_fortran_copy_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_FORTRAN_COPY_FIXED_INSTANTIATE(double, 5, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.1.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.1.1-.cxx new file mode 100644 index 00000000000..cfc87650149 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.1.1-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_fortran_copy_fixed.txx" +#else +#include "vnl/vnl_fortran_copy_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_FORTRAN_COPY_FIXED_INSTANTIATE(float, 1, 1); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx new file mode 100644 index 00000000000..bd316294452 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_fortran_copy_fixed.txx" +#else +#include "vnl/vnl_fortran_copy_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_FORTRAN_COPY_FIXED_INSTANTIATE(float, 5, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.1.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.1.1-.cxx new file mode 100644 index 00000000000..208312e6fc2 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.1.1-.cxx @@ -0,0 +1,28 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_matrix_fixed.txx" +#include "vnl/vnl_matlab_print.txx" +#else +#include "vnl/vnl_matrix_fixed.hxx" +#include "vnl/vnl_matlab_print.hxx" +#endif +#include "vnl_export_override.h" +VNL_MATRIX_FIXED_INSTANTIATE(double, 1, 1); +template VNL_EXPORT std::ostream &vnl_matlab_print(std::ostream &, vnl_matrix_fixed const&, char const*, vnl_matlab_print_format); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx new file mode 100644 index 00000000000..fdc13668d02 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx @@ -0,0 +1,28 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_matrix_fixed.txx" +#include "vnl/vnl_matlab_print.txx" +#else +#include "vnl/vnl_matrix_fixed.hxx" +#include "vnl/vnl_matlab_print.hxx" +#endif +#include "vnl_export_override.h" +VNL_MATRIX_FIXED_INSTANTIATE(double, 5, 5); +template VNL_EXPORT std::ostream &vnl_matlab_print(std::ostream &, vnl_matrix_fixed const&, char const*, vnl_matlab_print_format); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.1.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.1.1-.cxx new file mode 100644 index 00000000000..b93a71933fb --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.1.1-.cxx @@ -0,0 +1,28 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_matrix_fixed.txx" +#include "vnl/vnl_matlab_print.txx" +#else +#include "vnl/vnl_matrix_fixed.hxx" +#include "vnl/vnl_matlab_print.hxx" +#endif +#include "vnl_export_override.h" +VNL_MATRIX_FIXED_INSTANTIATE(float, 1, 1); +template VNL_EXPORT std::ostream &vnl_matlab_print(std::ostream &, vnl_matrix_fixed const&, char const*, vnl_matlab_print_format); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx new file mode 100644 index 00000000000..f157ef7e001 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx @@ -0,0 +1,28 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_matrix_fixed.txx" +#include "vnl/vnl_matlab_print.txx" +#else +#include "vnl/vnl_matrix_fixed.hxx" +#include "vnl/vnl_matlab_print.hxx" +#endif +#include "vnl_export_override.h" +VNL_MATRIX_FIXED_INSTANTIATE(float, 5, 5); +template VNL_EXPORT std::ostream &vnl_matlab_print(std::ostream &, vnl_matrix_fixed const&, char const*, vnl_matlab_print_format); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.1.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.1.1-.cxx new file mode 100644 index 00000000000..62aacdb9691 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.1.1-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/algo/vnl_svd_fixed.txx" +#else +#include "vnl/algo/vnl_svd_fixed.hxx" +#endif +#include "vnl_algo_export_override.h" +VNL_SVD_FIXED_INSTANTIATE(double, 1, 1); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx new file mode 100644 index 00000000000..dd9736d4c66 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/algo/vnl_svd_fixed.txx" +#else +#include "vnl/algo/vnl_svd_fixed.hxx" +#endif +#include "vnl_algo_export_override.h" +VNL_SVD_FIXED_INSTANTIATE(double, 5, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.1.1-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.1.1-.cxx new file mode 100644 index 00000000000..4b3a6589e73 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.1.1-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/algo/vnl_svd_fixed.txx" +#else +#include "vnl/algo/vnl_svd_fixed.hxx" +#endif +#include "vnl_algo_export_override.h" +VNL_SVD_FIXED_INSTANTIATE(float, 1, 1); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx new file mode 100644 index 00000000000..aa536403b76 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/algo/vnl_svd_fixed.txx" +#else +#include "vnl/algo/vnl_svd_fixed.hxx" +#endif +#include "vnl_algo_export_override.h" +VNL_SVD_FIXED_INSTANTIATE(float, 5, 5); From ccd1d4e870d17d664b5d0161c78a1926c4240423 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Mon, 1 Oct 2018 11:06:52 -0400 Subject: [PATCH 03/27] trying to get a windows build to work --- .../HDF5/src/itkhdf5/src/H5win32defs.h | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) mode change 100644 => 100755 Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h old mode 100644 new mode 100755 index 45222280ba0..62bc99dfae7 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h @@ -47,14 +47,6 @@ typedef __int64 h5_stat_size_t; #define HDmkdir(S,M) _mkdir(S) #define HDnanosleep(N, O) Wnanosleep(N, O) #define HDoff_t __int64 -/* _O_BINARY must be set in Windows to avoid CR-LF <-> LF EOL - * transformations when performing I/O. Note that this will - * produce Unix-style text files, though. - * - * Also note that the variadic macro is using a VC++ extension - * where the comma is dropped if nothing is passed to the ellipsis. - */ -#define HDopen(S,F,...) _open(S, F | _O_BINARY, __VA_ARGS__) #define HDread(F,M,Z) _read(F,M,Z) #define HDrmdir(S) _rmdir(S) #define HDsetvbuf(F,S,M,Z) setvbuf(F,S,M,(Z>1?Z:2)) @@ -68,6 +60,15 @@ typedef __int64 h5_stat_size_t; #ifdef H5_HAVE_VISUAL_STUDIO +/* _O_BINARY must be set in Windows to avoid CR-LF <-> LF EOL + * transformations when performing I/O. Note that this will + * produce Unix-style text files, though. + * + * Also note that the variadic macro is using a VC++ extension + * where the comma is dropped if nothing is passed to the ellipsis. + */ +#define HDopen(S,F,...) _open(S, F | _O_BINARY, __VA_ARGS__) + #if (_MSC_VER < 1800) #ifndef H5_HAVE_STRTOLL #define HDstrtoll(S,R,N) _strtoi64(S,R,N) @@ -150,6 +151,7 @@ extern "C" { #define HDpthread_self_ulong() ((unsigned long)GetCurrentThreadId()) #ifndef H5_HAVE_MINGW +#define HDopen(S,F,M) _open(S, F | _O_BINARY, M) #define HDftruncate(F,L) _chsize_s(F,L) #define HDfseek(F,O,W) _fseeki64(F,O,W) #endif /* H5_HAVE_MINGW */ From 6adf8646103a3b137336f5b98eca97bbe20daf67 Mon Sep 17 00:00:00 2001 From: brian avants Date: Tue, 4 Sep 2018 10:26:54 -0400 Subject: [PATCH 04/27] COMP: for compiling with perf enhancements Change-Id: I63ccba3a5ba610fffc6453cb6e125fd47b68521b --- .../ThirdParty/VNLInstantiation/src/CMakeLists.txt | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt index b4df432eb7a..5a038d20ce5 100644 --- a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt +++ b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt @@ -2,6 +2,8 @@ set(ITKVNLInstantiation_SRCS vnl_vector+ulonglong-.cxx vnl_fft_base+float.3-.cxx vnl_fft_base+float.4-.cxx + vnl_matrix_fixed+double.1.1-.cxx + vnl_matrix_fixed+double.5.5-.cxx vnl_matrix_fixed_ref+double.2.2-.cxx vnl_matrix_fixed_ref+double.2.3-.cxx vnl_fft_base+double.3-.cxx @@ -10,10 +12,13 @@ set(ITKVNLInstantiation_SRCS vnl_vector+ushort-.cxx vnl_matrix_fixed+double.3.12-.cxx vnl_matrix_fixed+double.2.3-.cxx + vnl_fortran_copy_fixed+double.5.5-.cxx vnl_matrix_fixed+double.10.10-.cxx vnl_matrix_fixed+float.10.10-.cxx - vnl_matrix_fixed+float.1.1-.cxx vnl_matrix_fixed+double.1.1-.cxx + vnl_matrix_fixed+float.1.1-.cxx + vnl_matrix_fixed+double.5.5-.cxx + vnl_matrix_fixed+float.5.5-.cxx vnl_c_vector+char-.cxx vnl_c_vector+short-.cxx vnl_matrix+short-.cxx @@ -34,11 +39,13 @@ set(ITKVNLInstantiation_SRCS vnl_svd_fixed+double.2.3-.cxx vnl_svd_fixed+double.3.2-.cxx vnl_svd_fixed+double.4.4-.cxx + vnl_svd_fixed+double.5.5-.cxx vnl_svd_fixed+double.10.10-.cxx vnl_svd_fixed+float.1.1-.cxx vnl_svd_fixed+float.2.2-.cxx vnl_svd_fixed+float.2.3-.cxx vnl_svd_fixed+float.4.4-.cxx + vnl_svd_fixed+float.5.5-.cxx vnl_svd_fixed+float.10.10-.cxx vnl_fortran_copy_fixed+double.1.1-.cxx vnl_fortran_copy_fixed+double.2.2-.cxx @@ -47,6 +54,8 @@ set(ITKVNLInstantiation_SRCS vnl_fortran_copy_fixed+double.4.4-.cxx vnl_fortran_copy_fixed+double.10.10-.cxx vnl_fortran_copy_fixed+float.1.1-.cxx + vnl_fortran_copy_fixed+float.4.4-.cxx + vnl_fortran_copy_fixed+float.5.5-.cxx vnl_fortran_copy_fixed+float.2.2-.cxx vnl_fortran_copy_fixed+float.2.3-.cxx vnl_fortran_copy_fixed+float.3.2-.cxx @@ -54,9 +63,11 @@ set(ITKVNLInstantiation_SRCS vnl_fortran_copy_fixed+float.10.10-.cxx vnl_diag_matrix_fixed+double.1-.cxx vnl_diag_matrix_fixed+double.2-.cxx + vnl_diag_matrix_fixed+double.5-.cxx vnl_diag_matrix_fixed+double.10-.cxx vnl_diag_matrix_fixed+float.1-.cxx vnl_diag_matrix_fixed+float.2-.cxx + vnl_diag_matrix_fixed+float.5-.cxx vnl_diag_matrix_fixed+float.10-.cxx ) From 9b2fff28e3429966e81eda1a453937fb4a1f336f Mon Sep 17 00:00:00 2001 From: brian avants Date: Tue, 4 Sep 2018 10:30:53 -0400 Subject: [PATCH 05/27] COMP: for compiling with perf enhancements - forgot file add Change-Id: I00b5e22e526421d3d4aeedf71b248adfe0cfca3d --- .../src/vnl_diag_matrix_fixed+double.5-.cxx | 25 +++++++++++++++++ .../src/vnl_diag_matrix_fixed+float.5-.cxx | 25 +++++++++++++++++ .../vnl_fortran_copy_fixed+double.5.5-.cxx | 25 +++++++++++++++++ .../src/vnl_fortran_copy_fixed+float.5.5-.cxx | 25 +++++++++++++++++ .../src/vnl_matrix_fixed+double.5.5-.cxx | 28 +++++++++++++++++++ .../src/vnl_matrix_fixed+float.5.5-.cxx | 28 +++++++++++++++++++ .../src/vnl_svd_fixed+double.5.5-.cxx | 25 +++++++++++++++++ .../src/vnl_svd_fixed+float.5.5-.cxx | 25 +++++++++++++++++ 8 files changed, 206 insertions(+) create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx create mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx new file mode 100644 index 00000000000..e935055dba9 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+double.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_diag_matrix_fixed.txx" +#else +#include "vnl/vnl_diag_matrix_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_DIAG_MATRIX_FIXED_INSTANTIATE(double, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx new file mode 100644 index 00000000000..5cd3b7fd849 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_diag_matrix_fixed+float.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_diag_matrix_fixed.txx" +#else +#include "vnl/vnl_diag_matrix_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_DIAG_MATRIX_FIXED_INSTANTIATE(float, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx new file mode 100644 index 00000000000..54183896daf --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+double.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_fortran_copy_fixed.txx" +#else +#include "vnl/vnl_fortran_copy_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_FORTRAN_COPY_FIXED_INSTANTIATE(double, 5, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx new file mode 100644 index 00000000000..bd316294452 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_fortran_copy_fixed+float.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_fortran_copy_fixed.txx" +#else +#include "vnl/vnl_fortran_copy_fixed.hxx" +#endif +#include "vnl_export_override.h" +VNL_FORTRAN_COPY_FIXED_INSTANTIATE(float, 5, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx new file mode 100644 index 00000000000..fdc13668d02 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+double.5.5-.cxx @@ -0,0 +1,28 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_matrix_fixed.txx" +#include "vnl/vnl_matlab_print.txx" +#else +#include "vnl/vnl_matrix_fixed.hxx" +#include "vnl/vnl_matlab_print.hxx" +#endif +#include "vnl_export_override.h" +VNL_MATRIX_FIXED_INSTANTIATE(double, 5, 5); +template VNL_EXPORT std::ostream &vnl_matlab_print(std::ostream &, vnl_matrix_fixed const&, char const*, vnl_matlab_print_format); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx new file mode 100644 index 00000000000..f157ef7e001 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx @@ -0,0 +1,28 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/vnl_matrix_fixed.txx" +#include "vnl/vnl_matlab_print.txx" +#else +#include "vnl/vnl_matrix_fixed.hxx" +#include "vnl/vnl_matlab_print.hxx" +#endif +#include "vnl_export_override.h" +VNL_MATRIX_FIXED_INSTANTIATE(float, 5, 5); +template VNL_EXPORT std::ostream &vnl_matlab_print(std::ostream &, vnl_matrix_fixed const&, char const*, vnl_matlab_print_format); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx new file mode 100644 index 00000000000..dd9736d4c66 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+double.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/algo/vnl_svd_fixed.txx" +#else +#include "vnl/algo/vnl_svd_fixed.hxx" +#endif +#include "vnl_algo_export_override.h" +VNL_SVD_FIXED_INSTANTIATE(double, 5, 5); diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx new file mode 100644 index 00000000000..aa536403b76 --- /dev/null +++ b/Modules/ThirdParty/VNLInstantiation/src/vnl_svd_fixed+float.5.5-.cxx @@ -0,0 +1,25 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#include +#if VXL_VERSION_DATE_FULL < 20160229 +#include "vnl/algo/vnl_svd_fixed.txx" +#else +#include "vnl/algo/vnl_svd_fixed.hxx" +#endif +#include "vnl_algo_export_override.h" +VNL_SVD_FIXED_INSTANTIATE(float, 5, 5); From 2c571cb73fe57eb73f5077af7b4050d69c8ab9f6 Mon Sep 17 00:00:00 2001 From: brian avants Date: Wed, 17 Oct 2018 08:25:59 -0400 Subject: [PATCH 06/27] STYLE: remove annoying warnings Change-Id: I03270c61ffcaaff48aad79f571624193f5aaaf53 --- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c | 6 +- .../ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c | 9 +- .../HDF5/src/itkhdf5/src/H5Fsuper.c | 85 +++++++++---------- 3 files changed, 49 insertions(+), 51 deletions(-) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c index 01fd7db406b..45edb757c2a 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c @@ -505,8 +505,8 @@ H5Fopen(const char *filename, unsigned flags, hid_t fapl_id) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info") /* Open the file */ - if(NULL == (new_file = H5F__open(filename, flags, H5P_FILE_CREATE_DEFAULT, fapl_id))) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, H5I_INVALID_HID, "unable to open file") +// BA if(NULL == (new_file = H5F__open(filename, flags, H5P_FILE_CREATE_DEFAULT, fapl_id))) +// BA HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, H5I_INVALID_HID, "unable to open file") /* Get an atom for the file */ if((ret_value = H5I_register(H5I_FILE, new_file, TRUE)) < 0) @@ -1451,7 +1451,7 @@ H5Fget_mdc_logging_status(hid_t file_id, hbool_t *is_enabled, * Function: H5Fset_libver_bounds * * Purpose: Set to a different low and high bounds while a file is open. - * This public routine is introduced in place of + * This public routine is introduced in place of * H5Fset_latest_format() starting release 1.10.2. * See explanation for H5Fset_latest_format() in H5Fdeprec.c. * diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c index 031f37c5d21..5969e31a376 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c @@ -1396,8 +1396,8 @@ H5F__open(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id) HDassert(filename); /* Open the file */ - if(NULL == (ret_value = H5F_open(filename, flags, fcpl_id, fapl_id))) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file") +// BA if(NULL == (ret_value = H5F_open(filename, flags, fcpl_id, fapl_id))) +// BA HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file") done: FUNC_LEAVE_NOAPI_VOL(ret_value) @@ -1696,8 +1696,8 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id) } /* end if */ else if (1 == shared->nrefs) { /* Read the superblock if it hasn't been read before. */ - if(H5F__super_read(file, a_plist, TRUE) < 0) - HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock") +// BA if(H5F__super_read(file, a_plist, TRUE) < 0) +// BA HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock") /* Create the page buffer before initializing the superblock */ if(page_buf_size) @@ -3684,4 +3684,3 @@ H5F__format_convert(H5F_t *f) done: FUNC_LEAVE_NOAPI_VOL(ret_value) } /* H5F__format_convert() */ - diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c index 9339b3df6ce..85d7dd2e14d 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c @@ -227,10 +227,10 @@ H5F__super_ext_close(H5F_t *f, H5O_loc_t *ext_ptr, hbool_t was_created) /*------------------------------------------------------------------------- * Function: H5F__update_super_ext_driver_msg * - * Purpose: Update the superblock extension file driver info message if + * Purpose: Update the superblock extension file driver info message if * we are using a V 2 superblock. Observe that the function * is a NO-OP if the file driver info message does not exist. - * This is necessary, as the function is called whenever the + * This is necessary, as the function is called whenever the * EOA is updated, and were it to create the file driver info * message, it would find itself in an infinite recursion. * @@ -270,8 +270,8 @@ H5F__update_super_ext_driver_msg(H5F_t *f) /* Check for driver info */ H5_CHECKED_ASSIGN(driver_size, size_t, H5FD_sb_size(f->shared->lf), hsize_t); - /* Nothing to do unless there is both driver info and - * the driver info superblock extension message has + /* Nothing to do unless there is both driver info and + * the driver info superblock extension message has * already been created. */ if(driver_size > 0) { @@ -287,7 +287,7 @@ H5F__update_super_ext_driver_msg(H5F_t *f) /* Write the message to the superblock extension. * - * Note that the superblock extension and the + * Note that the superblock extension and the * file driver info message must already exist. */ drvinfo.len = driver_size; @@ -342,7 +342,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) FUNC_ENTER_PACKAGE_TAG(H5AC__SUPERBLOCK_TAG) /* initialize the drvinfo to NULL -- we will overwrite this if there - * is a driver information block + * is a driver information block */ f->shared->drvinfo = NULL; @@ -407,8 +407,8 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ - if(!H5F_addr_defined(super_addr)) - HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found") +// BA if(!H5F_addr_defined(super_addr)) +// BA HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found") /* Check for userblock present */ if(H5F_addr_gt(super_addr, 0)) { @@ -434,7 +434,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) HGOTO_ERROR(H5E_FILE, H5E_BADTYPE, FAIL, "can't get property list") /* Make certain we can read the fixed-size portion of the superblock */ - if(H5F__set_eoa(f, H5FD_MEM_SUPER, + if(H5F__set_eoa(f, H5FD_MEM_SUPER, (haddr_t)(H5F_SUPERBLOCK_FIXED_SIZE + H5F_SUPERBLOCK_MINIMAL_VARLEN_SIZE)) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "set end of space allocation request failed") @@ -454,12 +454,12 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) if(NULL == (sblock = (H5F_super_t *)H5AC_protect(f, H5AC_SUPERBLOCK, (haddr_t)0, &udata, rw_flags))) HGOTO_ERROR(H5E_FILE, H5E_CANTPROTECT, FAIL, "unable to load superblock") - /* + /* * When opening a file with SWMR-write access, the library will first - * check to ensure that superblock version 3 is used. Otherwise fail + * check to ensure that superblock version 3 is used. Otherwise fail * file open. * - * Then the library will upgrade the file's low_bound depending on + * Then the library will upgrade the file's low_bound depending on * superblock version as follows: * --version 0 or 1: no change to low_bound * --version 2: upgrade low_bound to at least V18 @@ -592,8 +592,8 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) * as the file can appear truncated if only part of it has been * been flushed to disk by the SWMR writer process. */ - /* The EOF check is also skipped when the private property - * H5F_ACS_SKIP_EOF_CHECK_NAME exists in the fapl. + /* The EOF check is also skipped when the private property + * H5F_ACS_SKIP_EOF_CHECK_NAME exists in the fapl. * This property is enabled by the tool h5clear with these * two options: (1) --filesize (2) --increment */ @@ -604,7 +604,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get skip EOF check value") if(H5F_INTENT(f) & H5F_ACC_SWMR_READ) { - /* + /* * When the file is opened for SWMR read access, skip the check if: * --the file is already marked for SWMR writing and * --the file has version 3 superblock for SWMR support @@ -646,10 +646,10 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) drvrinfo_udata.f = f; drvrinfo_udata.driver_addr = sblock->driver_addr; - /* extend EOA so we can read at least the fixed sized - * portion of the driver info block + /* extend EOA so we can read at least the fixed sized + * portion of the driver info block */ - if(H5FD_set_eoa(f->shared->lf, H5FD_MEM_SUPER, sblock->driver_addr + H5F_DRVINFOBLOCK_HDR_SIZE) < 0) /* will extend eoa later if required */ + if(H5FD_set_eoa(f->shared->lf, H5FD_MEM_SUPER, sblock->driver_addr + H5F_DRVINFOBLOCK_HDR_SIZE) < 0) /* will extend eoa later if required */ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "set end of space allocation request failed") /* Look up the driver info block */ @@ -662,7 +662,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) if(((rw_flags & H5AC__READ_ONLY_FLAG) == 0) && H5F_HAS_FEATURE(f, H5FD_FEAT_DIRTY_DRVRINFO_LOAD)) drvinfo_flags |= H5AC__DIRTIED_FLAG; - /* set the pin entry flag so that the driver information block + /* set the pin entry flag so that the driver information block * cache entry will be pinned in the cache. */ drvinfo_flags |= H5AC__PIN_ENTRY_FLAG; @@ -840,7 +840,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) /* As "eoa_pre_fsm_fsalloc" may be undefined for a crashed file * with persistent free space managers, therefore, set - * "first_alloc_dealloc" when the condition + * "first_alloc_dealloc" when the condition * "dropping free-space to the floor is true. * This will ensure that no action is done to settle things on file * close via H5MF_settle_meta_data_fsm() and H5MF_settle_raw_data_fsm(). @@ -854,9 +854,9 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) f->shared->fs_addr[u] = fsinfo.fs_addr[u - 1]; /* If the following two conditions are true: - * (1) file is persisting free-space + * (1) file is persisting free-space * (2) dropping free-space to the floor (null_fsm_addr) - * nullify the addresses of the FSMs + * nullify the addresses of the FSMs */ if(f->shared->fs_persist && null_fsm_addr) for(u = 0; u < NELMTS(fsinfo.fs_addr); u++) @@ -871,7 +871,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) #if 1 /* bug fix test code -- tidy this up if all goes well */ /* JRM */ /* KLUGE ALERT!! * - * H5F__super_ext_write_msg() expects f->shared->sblock to + * H5F__super_ext_write_msg() expects f->shared->sblock to * be set -- verify that it is NULL, and then set it. * Set it back to NULL when we are done. */ @@ -908,12 +908,12 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) /* if the metadata cache image superblock extension message exists, * read its contents and pass the data on to the metadata cache. * Given this data, the cache will load and decode the metadata - * cache image block, decoded it and load its contents into the - * the cache on the test protect call. + * cache image block, decoded it and load its contents into the + * the cache on the test protect call. * - * Further, if the file is opened R/W, the metadata cache will + * Further, if the file is opened R/W, the metadata cache will * delete the metadata cache image superblock extension and free - * the cache image block. Don't do this now as f->shared + * the cache image block. Don't do this now as f->shared * is not fully setup, which complicates matters. */ @@ -964,7 +964,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) #if 1 /* bug fix test code -- tidy this up if all goes well */ /* JRM */ /* KLUGE ALERT!! * - * H5F__super_ext_write_msg() expects f->shared->sblock to + * H5F__super_ext_write_msg() expects f->shared->sblock to * be set -- verify that it is NULL, and then set it. * Set it back to NULL when we are done. */ @@ -1008,10 +1008,10 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) if(sblock && H5AC_unprotect(f, H5AC_SUPERBLOCK, (haddr_t)0, sblock, sblock_flags) < 0) HDONE_ERROR(H5E_FILE, H5E_CANTUNPROTECT, FAIL, "unable to close superblock") - /* If we have failed, make sure no entries are left in the + /* If we have failed, make sure no entries are left in the * metadata cache, so that it can be shut down and discarded. */ - if(ret_value < 0) { + if(ret_value < 0) { /* Unpin and discard drvinfo cache entry */ if(f->shared->drvinfo) { if(H5AC_unpin_entry(f->shared->drvinfo) < 0) @@ -1104,7 +1104,7 @@ H5F__super_init(H5F_t *f) f->shared->fs_page_size == H5F_FILE_SPACE_PAGE_SIZE_DEF)) non_default_fs_settings = TRUE; - /* + /* * When creating a file with write access, the library will: * -- set superblock version to 0, 1 or 2 based on feature enabled * -- no change to low_bound @@ -1113,9 +1113,9 @@ H5F__super_init(H5F_t *f) * -- set superblock version to 3 * -- upgrade low_bound to at least V110 * - * Then the library will finalize superblock version to that allowed by + * Then the library will finalize superblock version to that allowed by * low_bound if that is higher. - * Lastly, the library will check to ensure the superblock version does not + * Lastly, the library will check to ensure the superblock version does not * exceed the version allowed by high_bound. Otherwise fail file open. * * For details, please see RFC:Setting Bounds for Object Creation in HDF5 1.10.0. @@ -1125,12 +1125,12 @@ H5F__super_init(H5F_t *f) * the status_flags field in the superblock. The problem is discussed in * jira issue SWMR-79 and also in the RFC: File Format Changes in HDF5 1.10.0. * The file's low_bound is upgraded for SWMR so that the library will - * use the best format versions available in 1.10. - * Due to the possible upgrade, the fapl returned from H5Fget_access_plist() + * use the best format versions available in 1.10. + * Due to the possible upgrade, the fapl returned from H5Fget_access_plist() * might indicate a low_bound higher than what the user originally set. */ - /* + /* * Creating a file with SWMR-write access will * upgrade superblock version and low_bound */ @@ -1141,10 +1141,10 @@ H5F__super_init(H5F_t *f) /* Bump superblock version to create superblock extension for SOHM info */ } else if(f->shared->sohm_nindexes > 0) super_vers = HDF5_SUPERBLOCK_VERSION_2; - /* + /* * Bump superblock version to create superblock extension for: - * -- non-default file space strategy or - * -- non-default persisting free-space or + * -- non-default file space strategy or + * -- non-default persisting free-space or * -- non-default free-space threshold or * -- non-default page_size */ @@ -1221,7 +1221,7 @@ H5F__super_init(H5F_t *f) /* Compute the size of the driver information block */ H5_CHECKED_ASSIGN(driver_size, size_t, H5FD_sb_size(f->shared->lf), hsize_t); - /* The following code sets driver_size to the valued needed + /* The following code sets driver_size to the valued needed * for the driver info block, and sets the driver info block * address regardless of the version of the superblock. */ @@ -1494,8 +1494,8 @@ H5F_eoa_dirty(H5F_t *f) if(H5F_super_dirty(f) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTMARKDIRTY, FAIL, "unable to mark superblock as dirty") - /* If the driver information block exists, mark it dirty as well - * so that the change in eoa will be reflected there as well if + /* If the driver information block exists, mark it dirty as well + * so that the change in eoa will be reflected there as well if * appropriate. */ if(f->shared->drvinfo) { @@ -1799,4 +1799,3 @@ H5F__super_ext_remove_msg(H5F_t *f, unsigned id) FUNC_LEAVE_NOAPI(ret_value) } /* H5F__super_ext_remove_msg() */ - From e58141e4dff3977f66a0235b142b160ac979f71a Mon Sep 17 00:00:00 2001 From: brian avants Date: Wed, 17 Oct 2018 10:16:04 -0400 Subject: [PATCH 07/27] BUG: undo bad attempt at h5 fix http://review.source.kitware.com/#/c/23783/ is the correct way Change-Id: Ifc2e13c323d128ddc86dd55449f9b782e90b188e --- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c | 4 ++-- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c | 8 ++++---- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c index 45edb757c2a..54e2a889e54 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c @@ -505,8 +505,8 @@ H5Fopen(const char *filename, unsigned flags, hid_t fapl_id) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info") /* Open the file */ -// BA if(NULL == (new_file = H5F__open(filename, flags, H5P_FILE_CREATE_DEFAULT, fapl_id))) -// BA HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, H5I_INVALID_HID, "unable to open file") + if(NULL == (new_file = H5F__open(filename, flags, H5P_FILE_CREATE_DEFAULT, fapl_id))) + HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, H5I_INVALID_HID, "unable to open file") /* Get an atom for the file */ if((ret_value = H5I_register(H5I_FILE, new_file, TRUE)) < 0) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c index 5969e31a376..d7ef8d8d0d8 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c @@ -1396,8 +1396,8 @@ H5F__open(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id) HDassert(filename); /* Open the file */ -// BA if(NULL == (ret_value = H5F_open(filename, flags, fcpl_id, fapl_id))) -// BA HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file") + if(NULL == (ret_value = H5F_open(filename, flags, fcpl_id, fapl_id))) + HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file") done: FUNC_LEAVE_NOAPI_VOL(ret_value) @@ -1696,8 +1696,8 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id) } /* end if */ else if (1 == shared->nrefs) { /* Read the superblock if it hasn't been read before. */ -// BA if(H5F__super_read(file, a_plist, TRUE) < 0) -// BA HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock") + if(H5F__super_read(file, a_plist, TRUE) < 0) + HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock") /* Create the page buffer before initializing the superblock */ if(page_buf_size) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c index 85d7dd2e14d..1ce9aeaae06 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c @@ -407,8 +407,8 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ -// BA if(!H5F_addr_defined(super_addr)) -// BA HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found") + if(!H5F_addr_defined(super_addr)) + HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found") /* Check for userblock present */ if(H5F_addr_gt(super_addr, 0)) { From 1e36cb3dfee329a0a0dc34319a9758ad19485297 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 23 Oct 2018 10:46:23 -0400 Subject: [PATCH 08/27] updated with Modules for VNL --- Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt | 2 -- 1 file changed, 2 deletions(-) diff --git a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt index 81055b88c4c..674426d707d 100644 --- a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt +++ b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt @@ -66,8 +66,6 @@ set(ITKVNLInstantiation_SRCS vnl_fortran_copy_fixed+double.9.9-.cxx vnl_fortran_copy_fixed+double.10.10-.cxx vnl_fortran_copy_fixed+float.1.1-.cxx - vnl_fortran_copy_fixed+float.4.4-.cxx - vnl_fortran_copy_fixed+float.5.5-.cxx vnl_fortran_copy_fixed+float.2.2-.cxx vnl_fortran_copy_fixed+float.2.3-.cxx vnl_fortran_copy_fixed+float.3.2-.cxx From df1172e30c7628f6939532dc0c80c9317bb70fc1 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 1 Nov 2018 14:48:55 -0400 Subject: [PATCH 09/27] got a Cannot find source file: vnl_matrix_fixed+double.1.1-.cxx error --- Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt index 674426d707d..2e1430b9e4e 100644 --- a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt +++ b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt @@ -2,8 +2,8 @@ set(ITKVNLInstantiation_SRCS vnl_fft_base+float.3-.cxx vnl_fft_base+float.4-.cxx - vnl_matrix_fixed+double.1.1-.cxx - vnl_matrix_fixed+double.5.5-.cxx + #vnl_matrix_fixed+double.1.1-.cxx + #vnl_matrix_fixed+double.5.5-.cxx vnl_matrix_fixed_ref+double.2.2-.cxx vnl_matrix_fixed_ref+double.2.3-.cxx vnl_fft_base+double.3-.cxx From 7bf340906af6361e7fff67ac9014bb8e16d099a2 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 1 Nov 2018 14:51:31 -0400 Subject: [PATCH 10/27] updated the cmakelists --- Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt index 2e1430b9e4e..0545f8f4c73 100644 --- a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt +++ b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt @@ -2,8 +2,7 @@ set(ITKVNLInstantiation_SRCS vnl_fft_base+float.3-.cxx vnl_fft_base+float.4-.cxx - #vnl_matrix_fixed+double.1.1-.cxx - #vnl_matrix_fixed+double.5.5-.cxx + vnl_matrix_fixed_ref+double.2.2-.cxx vnl_matrix_fixed_ref+double.2.3-.cxx vnl_fft_base+double.3-.cxx @@ -18,6 +17,7 @@ set(ITKVNLInstantiation_SRCS vnl_matrix_fixed+float.10.10-.cxx # dims 2-4,6 provided by vnl upstream ThirdParty + vnl_matrix_fixed+double.1.1-.cxx vnl_matrix_fixed+double.5.5-.cxx vnl_matrix_fixed+double.7.7-.cxx vnl_matrix_fixed+double.8.8-.cxx From f4727a45c6f170975b7a768e2a1243c720491645 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 1 Nov 2018 15:01:14 -0400 Subject: [PATCH 11/27] removed vnl_matrix_fixed+double.1.1-.cxx" --- Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt index 0545f8f4c73..a013c73186a 100644 --- a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt +++ b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt @@ -17,7 +17,7 @@ set(ITKVNLInstantiation_SRCS vnl_matrix_fixed+float.10.10-.cxx # dims 2-4,6 provided by vnl upstream ThirdParty - vnl_matrix_fixed+double.1.1-.cxx + # vnl_matrix_fixed+double.1.1-.cxx vnl_matrix_fixed+double.5.5-.cxx vnl_matrix_fixed+double.7.7-.cxx vnl_matrix_fixed+double.8.8-.cxx From 186799e02a565e36b4e091202f89927ba42b34e9 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 1 Nov 2018 15:23:56 -0400 Subject: [PATCH 12/27] removed 2.3- - should be good --- Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt index a013c73186a..c19fd98183c 100644 --- a/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt +++ b/Modules/ThirdParty/VNLInstantiation/src/CMakeLists.txt @@ -8,7 +8,7 @@ set(ITKVNLInstantiation_SRCS vnl_fft_base+double.3-.cxx vnl_fft_base+double.4-.cxx vnl_matrix_fixed+double.3.12-.cxx - vnl_matrix_fixed+double.2.3-.cxx + #vnl_matrix_fixed+double.2.3-.cxx # dims 1-6 provided by vnl upstream ThirdParty vnl_matrix_fixed+float.7.7-.cxx From 54f2a08a0ca05cd23e6b5bc7acf60b3cc585199f Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Mon, 5 Nov 2018 13:44:41 -0500 Subject: [PATCH 13/27] removed mod --- .../src/vnl_matrix_fixed+float.5.5-.cxx | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx diff --git a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx b/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx deleted file mode 100644 index f157ef7e001..00000000000 --- a/Modules/ThirdParty/VNLInstantiation/src/vnl_matrix_fixed+float.5.5-.cxx +++ /dev/null @@ -1,28 +0,0 @@ -/*========================================================================= - * - * Copyright Insight Software Consortium - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0.txt - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * - *=========================================================================*/ -#include -#if VXL_VERSION_DATE_FULL < 20160229 -#include "vnl/vnl_matrix_fixed.txx" -#include "vnl/vnl_matlab_print.txx" -#else -#include "vnl/vnl_matrix_fixed.hxx" -#include "vnl/vnl_matlab_print.hxx" -#endif -#include "vnl_export_override.h" -VNL_MATRIX_FIXED_INSTANTIATE(float, 5, 5); -template VNL_EXPORT std::ostream &vnl_matlab_print(std::ostream &, vnl_matrix_fixed const&, char const*, vnl_matlab_print_format); From 6956711741ef8c52ae1c24bc86778e2040fe47af Mon Sep 17 00:00:00 2001 From: adigherman Date: Wed, 16 Jan 2019 16:19:36 -0500 Subject: [PATCH 14/27] adding ## to __VA_ARGS__ --- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h index 45222280ba0..654c558913c 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h @@ -54,7 +54,7 @@ typedef __int64 h5_stat_size_t; * Also note that the variadic macro is using a VC++ extension * where the comma is dropped if nothing is passed to the ellipsis. */ -#define HDopen(S,F,...) _open(S, F | _O_BINARY, __VA_ARGS__) +#define HDopen(S,F,...) _open(S, F | _O_BINARY, ##__VA_ARGS__) #define HDread(F,M,Z) _read(F,M,Z) #define HDrmdir(S) _rmdir(S) #define HDsetvbuf(F,S,M,Z) setvbuf(F,S,M,(Z>1?Z:2)) From 6c4fdf19d0f7efa1ddafd78c3903a4b836f8fc10 Mon Sep 17 00:00:00 2001 From: adigherman Date: Fri, 18 Jan 2019 11:47:49 -0500 Subject: [PATCH 15/27] Removed VCL_COMPILER_DETECTION_HEADER from the vcl_sources set --- Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt index dd83858d156..66f0044f3cb 100644 --- a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt +++ b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt @@ -115,7 +115,7 @@ vxl_configure_file(${CMAKE_CURRENT_LIST_DIR}/vcl_where_root_dir.h.in ${PROJECT_B include_directories(${PROJECT_BINARY_DIR}) set( vcl_sources - vcl_legacy_aliases.h ${VCL_COMPILER_DETECTION_HEADER} + vcl_legacy_aliases.h #${VCL_COMPILER_DETECTION_HEADER} vcl_deprecated.cxx vcl_deprecated.h vcl_cmath.h From a47739c8b02eb8c07708e716f5095b1114cd8159 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Jan 2019 18:58:44 -0500 Subject: [PATCH 16/27] updated the newline bs --- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h | 2 -- 1 file changed, 2 deletions(-) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h index b4eb3beab9e..1305f7db34f 100755 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h @@ -47,7 +47,6 @@ typedef __int64 h5_stat_size_t; #define HDmkdir(S,M) _mkdir(S) #define HDnanosleep(N, O) Wnanosleep(N, O) #define HDoff_t __int64 - /* _O_BINARY must be set in Windows to avoid CR-LF <-> LF EOL * transformations when performing I/O. Note that this will * produce Unix-style text files, though. @@ -55,7 +54,6 @@ typedef __int64 h5_stat_size_t; * Also note that the variadic macro is using a VC++ extension * where the comma is dropped if nothing is passed to the ellipsis. */ - #define HDread(F,M,Z) _read(F,M,Z) #define HDrmdir(S) _rmdir(S) #define HDsetvbuf(F,S,M,Z) setvbuf(F,S,M,(Z>1?Z:2)) From ed152c1aceeed0fd85938c10957b5f19bed5eabd Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Jan 2019 19:00:19 -0500 Subject: [PATCH 17/27] I think the vlc compiler detection should be there --- Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt index 66f0044f3cb..9f90df24d8b 100644 --- a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt +++ b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt @@ -115,7 +115,7 @@ vxl_configure_file(${CMAKE_CURRENT_LIST_DIR}/vcl_where_root_dir.h.in ${PROJECT_B include_directories(${PROJECT_BINARY_DIR}) set( vcl_sources - vcl_legacy_aliases.h #${VCL_COMPILER_DETECTION_HEADER} + vcl_legacy_aliases.h vcl_compiler_detection.h #${VCL_COMPILER_DETECTION_HEADER} vcl_deprecated.cxx vcl_deprecated.h vcl_cmath.h From bfb3df4372e6f48d1cd37bfb406f386b3ccb9bfd Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Tue, 29 Jan 2019 19:03:29 -0500 Subject: [PATCH 18/27] merging with Adis --- Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt index 9f90df24d8b..66f0044f3cb 100644 --- a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt +++ b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt @@ -115,7 +115,7 @@ vxl_configure_file(${CMAKE_CURRENT_LIST_DIR}/vcl_where_root_dir.h.in ${PROJECT_B include_directories(${PROJECT_BINARY_DIR}) set( vcl_sources - vcl_legacy_aliases.h vcl_compiler_detection.h #${VCL_COMPILER_DETECTION_HEADER} + vcl_legacy_aliases.h #${VCL_COMPILER_DETECTION_HEADER} vcl_deprecated.cxx vcl_deprecated.h vcl_cmath.h From 619c3507a490a40f44f44e8659d3ec9355a3d217 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 21 Feb 2019 14:07:12 -0500 Subject: [PATCH 19/27] trying VCL_COMPILER_DETECTION_HEADER to be included --- Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt index 66f0044f3cb..dd83858d156 100644 --- a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt +++ b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt @@ -115,7 +115,7 @@ vxl_configure_file(${CMAKE_CURRENT_LIST_DIR}/vcl_where_root_dir.h.in ${PROJECT_B include_directories(${PROJECT_BINARY_DIR}) set( vcl_sources - vcl_legacy_aliases.h #${VCL_COMPILER_DETECTION_HEADER} + vcl_legacy_aliases.h ${VCL_COMPILER_DETECTION_HEADER} vcl_deprecated.cxx vcl_deprecated.h vcl_cmath.h From 5380a84b7d67501643f98dc435630a1a02601e31 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 27 Feb 2019 12:17:02 -0500 Subject: [PATCH 20/27] updated Cmake for ITK to fit in with other ITK environment variables --- Modules/ThirdParty/Eigen3/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/Eigen3/CMakeLists.txt b/Modules/ThirdParty/Eigen3/CMakeLists.txt index 70f23d99b6f..92214e05479 100644 --- a/Modules/ThirdParty/Eigen3/CMakeLists.txt +++ b/Modules/ThirdParty/Eigen3/CMakeLists.txt @@ -24,7 +24,7 @@ if(ITK_USE_SYSTEM_EIGEN) set(Eigen3_DIR_INSTALL ${Eigen3_DIR}) set(Eigen3_DIR_BUILD ${Eigen3_DIR}) else() - set(Eigen3_DIR_INSTALL "${CMAKE_INSTALL_PREFIX}/${ITK_INSTALL_LIBRARY_DIR}/cmake/ITK-${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}/Modules") + set(Eigen3_DIR_INSTALL "${ITK_MODULES_DIR}") set(Eigen3_DIR_BUILD "${CMAKE_CURRENT_BINARY_DIR}/src/itkeigen") endif() From d9dd9c1e96c3a7cdbb085235428ccd856a9d40d0 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 27 Feb 2019 13:54:15 -0500 Subject: [PATCH 21/27] fixing whitespace crap --- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c | 6 +++--- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c index 54e2a889e54..01fd7db406b 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c @@ -505,8 +505,8 @@ H5Fopen(const char *filename, unsigned flags, hid_t fapl_id) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info") /* Open the file */ - if(NULL == (new_file = H5F__open(filename, flags, H5P_FILE_CREATE_DEFAULT, fapl_id))) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, H5I_INVALID_HID, "unable to open file") + if(NULL == (new_file = H5F__open(filename, flags, H5P_FILE_CREATE_DEFAULT, fapl_id))) + HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, H5I_INVALID_HID, "unable to open file") /* Get an atom for the file */ if((ret_value = H5I_register(H5I_FILE, new_file, TRUE)) < 0) @@ -1451,7 +1451,7 @@ H5Fget_mdc_logging_status(hid_t file_id, hbool_t *is_enabled, * Function: H5Fset_libver_bounds * * Purpose: Set to a different low and high bounds while a file is open. - * This public routine is introduced in place of + * This public routine is introduced in place of * H5Fset_latest_format() starting release 1.10.2. * See explanation for H5Fset_latest_format() in H5Fdeprec.c. * diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c index d7ef8d8d0d8..bde1c5d777d 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c @@ -1396,7 +1396,7 @@ H5F__open(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id) HDassert(filename); /* Open the file */ - if(NULL == (ret_value = H5F_open(filename, flags, fcpl_id, fapl_id))) + if(NULL == (ret_value = H5F_open(filename, flags, fcpl_id, fapl_id))) HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file") done: @@ -1696,8 +1696,8 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id) } /* end if */ else if (1 == shared->nrefs) { /* Read the superblock if it hasn't been read before. */ - if(H5F__super_read(file, a_plist, TRUE) < 0) - HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock") + if(H5F__super_read(file, a_plist, TRUE) < 0) + HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock") /* Create the page buffer before initializing the superblock */ if(page_buf_size) @@ -3683,4 +3683,4 @@ H5F__format_convert(H5F_t *f) done: FUNC_LEAVE_NOAPI_VOL(ret_value) -} /* H5F__format_convert() */ +} /* H5F__format_convert() */ \ No newline at end of file From 25d98ffa3ee0f997a2198e6f0d7dd7f4594524b3 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 27 Feb 2019 13:54:48 -0500 Subject: [PATCH 22/27] fixing whitespace crap --- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c index bde1c5d777d..3e4ee49de85 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c @@ -3683,4 +3683,4 @@ H5F__format_convert(H5F_t *f) done: FUNC_LEAVE_NOAPI_VOL(ret_value) -} /* H5F__format_convert() */ \ No newline at end of file +} /* H5F__format_convert() */ From 8409abbe834096f837f95cb724def9ab11e07979 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 27 Feb 2019 13:57:26 -0500 Subject: [PATCH 23/27] fixing whitespace crap --- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c | 1 + 1 file changed, 1 insertion(+) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c index 3e4ee49de85..031f37c5d21 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c @@ -3684,3 +3684,4 @@ H5F__format_convert(H5F_t *f) done: FUNC_LEAVE_NOAPI_VOL(ret_value) } /* H5F__format_convert() */ + From 2768aefdac65175f968737c964a78881eff2411e Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 27 Feb 2019 13:59:13 -0500 Subject: [PATCH 24/27] fixing whitespace crap --- .../HDF5/src/itkhdf5/src/H5Fsuper.c | 85 ++++++++++--------- 1 file changed, 43 insertions(+), 42 deletions(-) diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c index 1ce9aeaae06..9339b3df6ce 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fsuper.c @@ -227,10 +227,10 @@ H5F__super_ext_close(H5F_t *f, H5O_loc_t *ext_ptr, hbool_t was_created) /*------------------------------------------------------------------------- * Function: H5F__update_super_ext_driver_msg * - * Purpose: Update the superblock extension file driver info message if + * Purpose: Update the superblock extension file driver info message if * we are using a V 2 superblock. Observe that the function * is a NO-OP if the file driver info message does not exist. - * This is necessary, as the function is called whenever the + * This is necessary, as the function is called whenever the * EOA is updated, and were it to create the file driver info * message, it would find itself in an infinite recursion. * @@ -270,8 +270,8 @@ H5F__update_super_ext_driver_msg(H5F_t *f) /* Check for driver info */ H5_CHECKED_ASSIGN(driver_size, size_t, H5FD_sb_size(f->shared->lf), hsize_t); - /* Nothing to do unless there is both driver info and - * the driver info superblock extension message has + /* Nothing to do unless there is both driver info and + * the driver info superblock extension message has * already been created. */ if(driver_size > 0) { @@ -287,7 +287,7 @@ H5F__update_super_ext_driver_msg(H5F_t *f) /* Write the message to the superblock extension. * - * Note that the superblock extension and the + * Note that the superblock extension and the * file driver info message must already exist. */ drvinfo.len = driver_size; @@ -342,7 +342,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) FUNC_ENTER_PACKAGE_TAG(H5AC__SUPERBLOCK_TAG) /* initialize the drvinfo to NULL -- we will overwrite this if there - * is a driver information block + * is a driver information block */ f->shared->drvinfo = NULL; @@ -407,8 +407,8 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ - if(!H5F_addr_defined(super_addr)) - HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found") + if(!H5F_addr_defined(super_addr)) + HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found") /* Check for userblock present */ if(H5F_addr_gt(super_addr, 0)) { @@ -434,7 +434,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) HGOTO_ERROR(H5E_FILE, H5E_BADTYPE, FAIL, "can't get property list") /* Make certain we can read the fixed-size portion of the superblock */ - if(H5F__set_eoa(f, H5FD_MEM_SUPER, + if(H5F__set_eoa(f, H5FD_MEM_SUPER, (haddr_t)(H5F_SUPERBLOCK_FIXED_SIZE + H5F_SUPERBLOCK_MINIMAL_VARLEN_SIZE)) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "set end of space allocation request failed") @@ -454,12 +454,12 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) if(NULL == (sblock = (H5F_super_t *)H5AC_protect(f, H5AC_SUPERBLOCK, (haddr_t)0, &udata, rw_flags))) HGOTO_ERROR(H5E_FILE, H5E_CANTPROTECT, FAIL, "unable to load superblock") - /* + /* * When opening a file with SWMR-write access, the library will first - * check to ensure that superblock version 3 is used. Otherwise fail + * check to ensure that superblock version 3 is used. Otherwise fail * file open. * - * Then the library will upgrade the file's low_bound depending on + * Then the library will upgrade the file's low_bound depending on * superblock version as follows: * --version 0 or 1: no change to low_bound * --version 2: upgrade low_bound to at least V18 @@ -592,8 +592,8 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) * as the file can appear truncated if only part of it has been * been flushed to disk by the SWMR writer process. */ - /* The EOF check is also skipped when the private property - * H5F_ACS_SKIP_EOF_CHECK_NAME exists in the fapl. + /* The EOF check is also skipped when the private property + * H5F_ACS_SKIP_EOF_CHECK_NAME exists in the fapl. * This property is enabled by the tool h5clear with these * two options: (1) --filesize (2) --increment */ @@ -604,7 +604,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get skip EOF check value") if(H5F_INTENT(f) & H5F_ACC_SWMR_READ) { - /* + /* * When the file is opened for SWMR read access, skip the check if: * --the file is already marked for SWMR writing and * --the file has version 3 superblock for SWMR support @@ -646,10 +646,10 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) drvrinfo_udata.f = f; drvrinfo_udata.driver_addr = sblock->driver_addr; - /* extend EOA so we can read at least the fixed sized - * portion of the driver info block + /* extend EOA so we can read at least the fixed sized + * portion of the driver info block */ - if(H5FD_set_eoa(f->shared->lf, H5FD_MEM_SUPER, sblock->driver_addr + H5F_DRVINFOBLOCK_HDR_SIZE) < 0) /* will extend eoa later if required */ + if(H5FD_set_eoa(f->shared->lf, H5FD_MEM_SUPER, sblock->driver_addr + H5F_DRVINFOBLOCK_HDR_SIZE) < 0) /* will extend eoa later if required */ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "set end of space allocation request failed") /* Look up the driver info block */ @@ -662,7 +662,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) if(((rw_flags & H5AC__READ_ONLY_FLAG) == 0) && H5F_HAS_FEATURE(f, H5FD_FEAT_DIRTY_DRVRINFO_LOAD)) drvinfo_flags |= H5AC__DIRTIED_FLAG; - /* set the pin entry flag so that the driver information block + /* set the pin entry flag so that the driver information block * cache entry will be pinned in the cache. */ drvinfo_flags |= H5AC__PIN_ENTRY_FLAG; @@ -840,7 +840,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) /* As "eoa_pre_fsm_fsalloc" may be undefined for a crashed file * with persistent free space managers, therefore, set - * "first_alloc_dealloc" when the condition + * "first_alloc_dealloc" when the condition * "dropping free-space to the floor is true. * This will ensure that no action is done to settle things on file * close via H5MF_settle_meta_data_fsm() and H5MF_settle_raw_data_fsm(). @@ -854,9 +854,9 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) f->shared->fs_addr[u] = fsinfo.fs_addr[u - 1]; /* If the following two conditions are true: - * (1) file is persisting free-space + * (1) file is persisting free-space * (2) dropping free-space to the floor (null_fsm_addr) - * nullify the addresses of the FSMs + * nullify the addresses of the FSMs */ if(f->shared->fs_persist && null_fsm_addr) for(u = 0; u < NELMTS(fsinfo.fs_addr); u++) @@ -871,7 +871,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) #if 1 /* bug fix test code -- tidy this up if all goes well */ /* JRM */ /* KLUGE ALERT!! * - * H5F__super_ext_write_msg() expects f->shared->sblock to + * H5F__super_ext_write_msg() expects f->shared->sblock to * be set -- verify that it is NULL, and then set it. * Set it back to NULL when we are done. */ @@ -908,12 +908,12 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) /* if the metadata cache image superblock extension message exists, * read its contents and pass the data on to the metadata cache. * Given this data, the cache will load and decode the metadata - * cache image block, decoded it and load its contents into the - * the cache on the test protect call. + * cache image block, decoded it and load its contents into the + * the cache on the test protect call. * - * Further, if the file is opened R/W, the metadata cache will + * Further, if the file is opened R/W, the metadata cache will * delete the metadata cache image superblock extension and free - * the cache image block. Don't do this now as f->shared + * the cache image block. Don't do this now as f->shared * is not fully setup, which complicates matters. */ @@ -964,7 +964,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) #if 1 /* bug fix test code -- tidy this up if all goes well */ /* JRM */ /* KLUGE ALERT!! * - * H5F__super_ext_write_msg() expects f->shared->sblock to + * H5F__super_ext_write_msg() expects f->shared->sblock to * be set -- verify that it is NULL, and then set it. * Set it back to NULL when we are done. */ @@ -1008,10 +1008,10 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read) if(sblock && H5AC_unprotect(f, H5AC_SUPERBLOCK, (haddr_t)0, sblock, sblock_flags) < 0) HDONE_ERROR(H5E_FILE, H5E_CANTUNPROTECT, FAIL, "unable to close superblock") - /* If we have failed, make sure no entries are left in the + /* If we have failed, make sure no entries are left in the * metadata cache, so that it can be shut down and discarded. */ - if(ret_value < 0) { + if(ret_value < 0) { /* Unpin and discard drvinfo cache entry */ if(f->shared->drvinfo) { if(H5AC_unpin_entry(f->shared->drvinfo) < 0) @@ -1104,7 +1104,7 @@ H5F__super_init(H5F_t *f) f->shared->fs_page_size == H5F_FILE_SPACE_PAGE_SIZE_DEF)) non_default_fs_settings = TRUE; - /* + /* * When creating a file with write access, the library will: * -- set superblock version to 0, 1 or 2 based on feature enabled * -- no change to low_bound @@ -1113,9 +1113,9 @@ H5F__super_init(H5F_t *f) * -- set superblock version to 3 * -- upgrade low_bound to at least V110 * - * Then the library will finalize superblock version to that allowed by + * Then the library will finalize superblock version to that allowed by * low_bound if that is higher. - * Lastly, the library will check to ensure the superblock version does not + * Lastly, the library will check to ensure the superblock version does not * exceed the version allowed by high_bound. Otherwise fail file open. * * For details, please see RFC:Setting Bounds for Object Creation in HDF5 1.10.0. @@ -1125,12 +1125,12 @@ H5F__super_init(H5F_t *f) * the status_flags field in the superblock. The problem is discussed in * jira issue SWMR-79 and also in the RFC: File Format Changes in HDF5 1.10.0. * The file's low_bound is upgraded for SWMR so that the library will - * use the best format versions available in 1.10. - * Due to the possible upgrade, the fapl returned from H5Fget_access_plist() + * use the best format versions available in 1.10. + * Due to the possible upgrade, the fapl returned from H5Fget_access_plist() * might indicate a low_bound higher than what the user originally set. */ - /* + /* * Creating a file with SWMR-write access will * upgrade superblock version and low_bound */ @@ -1141,10 +1141,10 @@ H5F__super_init(H5F_t *f) /* Bump superblock version to create superblock extension for SOHM info */ } else if(f->shared->sohm_nindexes > 0) super_vers = HDF5_SUPERBLOCK_VERSION_2; - /* + /* * Bump superblock version to create superblock extension for: - * -- non-default file space strategy or - * -- non-default persisting free-space or + * -- non-default file space strategy or + * -- non-default persisting free-space or * -- non-default free-space threshold or * -- non-default page_size */ @@ -1221,7 +1221,7 @@ H5F__super_init(H5F_t *f) /* Compute the size of the driver information block */ H5_CHECKED_ASSIGN(driver_size, size_t, H5FD_sb_size(f->shared->lf), hsize_t); - /* The following code sets driver_size to the valued needed + /* The following code sets driver_size to the valued needed * for the driver info block, and sets the driver info block * address regardless of the version of the superblock. */ @@ -1494,8 +1494,8 @@ H5F_eoa_dirty(H5F_t *f) if(H5F_super_dirty(f) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTMARKDIRTY, FAIL, "unable to mark superblock as dirty") - /* If the driver information block exists, mark it dirty as well - * so that the change in eoa will be reflected there as well if + /* If the driver information block exists, mark it dirty as well + * so that the change in eoa will be reflected there as well if * appropriate. */ if(f->shared->drvinfo) { @@ -1799,3 +1799,4 @@ H5F__super_ext_remove_msg(H5F_t *f, unsigned id) FUNC_LEAVE_NOAPI(ret_value) } /* H5F__super_ext_remove_msg() */ + From 7bed0ded9117c1b6bc92aab1d97d33729be2ad77 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Wed, 27 Feb 2019 16:27:15 -0500 Subject: [PATCH 25/27] fixing vcl again --- Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt index dd83858d156..66f0044f3cb 100644 --- a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt +++ b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt @@ -115,7 +115,7 @@ vxl_configure_file(${CMAKE_CURRENT_LIST_DIR}/vcl_where_root_dir.h.in ${PROJECT_B include_directories(${PROJECT_BINARY_DIR}) set( vcl_sources - vcl_legacy_aliases.h ${VCL_COMPILER_DETECTION_HEADER} + vcl_legacy_aliases.h #${VCL_COMPILER_DETECTION_HEADER} vcl_deprecated.cxx vcl_deprecated.h vcl_cmath.h From e10d3bc6b9b86064ef3b80fac25604476982df25 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 28 Feb 2019 15:48:10 -0500 Subject: [PATCH 26/27] fixing the linking again --- Modules/ThirdParty/Eigen3/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Modules/ThirdParty/Eigen3/CMakeLists.txt b/Modules/ThirdParty/Eigen3/CMakeLists.txt index 92214e05479..adb22b02eaa 100644 --- a/Modules/ThirdParty/Eigen3/CMakeLists.txt +++ b/Modules/ThirdParty/Eigen3/CMakeLists.txt @@ -24,7 +24,7 @@ if(ITK_USE_SYSTEM_EIGEN) set(Eigen3_DIR_INSTALL ${Eigen3_DIR}) set(Eigen3_DIR_BUILD ${Eigen3_DIR}) else() - set(Eigen3_DIR_INSTALL "${ITK_MODULES_DIR}") + set(Eigen3_DIR_INSTALL "\${ITK_MODULES_DIR}") set(Eigen3_DIR_BUILD "${CMAKE_CURRENT_BINARY_DIR}/src/itkeigen") endif() From 5f768c29795b0961f59d8fca786bb91938b988a5 Mon Sep 17 00:00:00 2001 From: muschellij2 Date: Thu, 28 Feb 2019 15:49:08 -0500 Subject: [PATCH 27/27] ENH: Rwindows compatibility --- Modules/ThirdParty/Eigen3/CMakeLists.txt | 2 +- Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h | 11 ++++++++++- Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt | 2 +- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/Modules/ThirdParty/Eigen3/CMakeLists.txt b/Modules/ThirdParty/Eigen3/CMakeLists.txt index 70f23d99b6f..7d11f2d2fac 100644 --- a/Modules/ThirdParty/Eigen3/CMakeLists.txt +++ b/Modules/ThirdParty/Eigen3/CMakeLists.txt @@ -24,7 +24,7 @@ if(ITK_USE_SYSTEM_EIGEN) set(Eigen3_DIR_INSTALL ${Eigen3_DIR}) set(Eigen3_DIR_BUILD ${Eigen3_DIR}) else() - set(Eigen3_DIR_INSTALL "${CMAKE_INSTALL_PREFIX}/${ITK_INSTALL_LIBRARY_DIR}/cmake/ITK-${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}/Modules") + set(Eigen3_DIR_INSTALL "\${ITK_MODULES_DIR}") set(Eigen3_DIR_BUILD "${CMAKE_CURRENT_BINARY_DIR}/src/itkeigen") endif() diff --git a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h index 45222280ba0..1305f7db34f 100644 --- a/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h +++ b/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h @@ -54,7 +54,6 @@ typedef __int64 h5_stat_size_t; * Also note that the variadic macro is using a VC++ extension * where the comma is dropped if nothing is passed to the ellipsis. */ -#define HDopen(S,F,...) _open(S, F | _O_BINARY, __VA_ARGS__) #define HDread(F,M,Z) _read(F,M,Z) #define HDrmdir(S) _rmdir(S) #define HDsetvbuf(F,S,M,Z) setvbuf(F,S,M,(Z>1?Z:2)) @@ -68,6 +67,15 @@ typedef __int64 h5_stat_size_t; #ifdef H5_HAVE_VISUAL_STUDIO +/* _O_BINARY must be set in Windows to avoid CR-LF <-> LF EOL + * transformations when performing I/O. Note that this will + * produce Unix-style text files, though. + * + * Also note that the variadic macro is using a VC++ extension + * where the comma is dropped if nothing is passed to the ellipsis. + */ +#define HDopen(S,F,...) _open(S, F | _O_BINARY, __VA_ARGS__) + #if (_MSC_VER < 1800) #ifndef H5_HAVE_STRTOLL #define HDstrtoll(S,R,N) _strtoi64(S,R,N) @@ -150,6 +158,7 @@ extern "C" { #define HDpthread_self_ulong() ((unsigned long)GetCurrentThreadId()) #ifndef H5_HAVE_MINGW +#define HDopen(S,F,M) _open(S, F | _O_BINARY, M) #define HDftruncate(F,L) _chsize_s(F,L) #define HDfseek(F,O,W) _fseeki64(F,O,W) #endif /* H5_HAVE_MINGW */ diff --git a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt index dd83858d156..66f0044f3cb 100644 --- a/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt +++ b/Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt @@ -115,7 +115,7 @@ vxl_configure_file(${CMAKE_CURRENT_LIST_DIR}/vcl_where_root_dir.h.in ${PROJECT_B include_directories(${PROJECT_BINARY_DIR}) set( vcl_sources - vcl_legacy_aliases.h ${VCL_COMPILER_DETECTION_HEADER} + vcl_legacy_aliases.h #${VCL_COMPILER_DETECTION_HEADER} vcl_deprecated.cxx vcl_deprecated.h vcl_cmath.h