ITK 5.2 migration #382

dzenanz · 2020-11-02T19:14:19Z

A cleaned-up version of #378. Closes #378.

Missing typename directives in declarations. Confusion between long and long long Use of itkMutexLock instead of std::mutex. Failure to include <itkMacro.h>. Use of ComposeRGBImageFilter instead of ComposeImageFilter. Use of NULL instead of nullptr. Use of vcl_sqrt instead of std::sqrt, etc. itk::MultiThreader --> itk::MultiThreaderBase. Removal of inappropriate Seg3D:: explicit qualification.

M:\Dev\Seg3D\src\Application\LayerIO\Matlab73LayerImporter.cc(32,10): fatal error C1083: Cannot open include file: 'itkhdf5/H5LTpublic.h': No such file or directory H5 HL library is disabled in ITK's internal configuration: https://github.com/InsightSoftwareConsortium/ITK/blob/v5.1.1/Modules/ThirdParty/HDF5/src/CMakeLists.txt#L12

registration->StartRegistration() ==> registration->Update() GetJacobian(...) ==> ComputeJacobianWithRespectToPosition(...)

so we don't need to have it as a dependency.

src/Application/Project/Project.cc

src/Application/ProjectManager/ProjectManager.cc

src/ThirdParty/tinyxml/tinyxml.h

src/ThirdParty/tinyxml/tinyxmlparser.cpp

nullptr to NULL

tarkpate · 2020-11-04T00:07:01Z

Built on Arch Linux w/ Qt 5.15.1

This is the error I get building with default settings.

In file included from /home/tpat/repos/seg3d/src/Application/LayerIO/Matlab73LayerImporter.cc:31:
/home/tpat/repos/seg3d/bin/Externals/Install/ITK_external/include/ITK-5.1/itk_H5Cpp.h:27:11: fatal error: itkhdf5/cpp/H5Cpp.h: No such file or directory
   27 | # include "itkhdf5/cpp/H5Cpp.h"

This is what I get if I try setting ITK_USE_SYSTEM_HDF5=ON in cmake.

/home/tpat/repos/seg3d/src/Application/LayerIO/Matlab73LayerImporter.cc: In member function 'bool Seg3D::Matlab73LayerImporterPrivate::scan_mat_struct(hid_t, H5::Group&, std::string&)':
/home/tpat/repos/seg3d/src/Application/LayerIO/Matlab73LayerImporter.cc:519:40: error: too few arguments to function 'herr_t H5Oget_info3(hid_t, H5O_info2_t*, unsigned int)'
  519 |       if (H5Oget_info(obj_id, &obj_info) < 0)

dzenanz · 2020-11-04T16:15:40Z

src/Application/DatabaseManager/DatabaseManager.cc

    // Copy the database content from the source
    sqlite3_backup* db_backup_obj = sqlite3_backup_init( this->private_->database_,
      "main", src.private_->database_, "main" );
-    if ( db_backup_obj == nullptr )


I think that DatabaseManager is pure C++ file, so leaving nullptr in here is fine. I will edit this commit.

Anything that has to do with SQL requires NULL and not nullptr. They need to stay NULL or there will be SQL errors. When I was investigate the errors, I found them in DatabaseManager and Project.

I just tried building and running. There are no SQL errors now like there were before.

nullptr to NULL

dzenanz · 2020-11-04T16:37:35Z

@RubioJr9 switch from ITK 5.1 to master (provisionally 5.2) breaks the incremental build. You could try cleaning up only ITK-related part of superbuild, but the best way is to make a clean build of Seg3D (configure + build in a new binary directory).

dzenanz · 2020-11-04T16:40:05Z

I think this is ready. Should I beautify history by squashing and possibly reordering commits?

dzenanz · 2020-11-04T18:23:51Z

I created beautified commit history in #384. It is up to you whether to merge this (#382) or #384.

allywarner · 2020-11-04T20:30:11Z

@dzenanz thank you!

tarkpate · 2020-11-04T23:34:56Z

I wiped my bin folder and that got rid of the issue I was having. However, I'm getting this error now:

/home/tpat/repos/seg3d/src/Core/ITKCommon/Optimizers/itkImageMosaicVarianceMetric.txx:435:59: 
    error: cannot bind non-const lvalue reference of type 'itk::Transform<double, 2, 2>::JacobianPositionType&' {aka 'vnl_matrix_fixed<double, 2, 2>&'} 
    to an rvalue of type 'itk::Transform<double, 2, 2>::JacobianPositionType' {aka 'vnl_matrix_fixed<double, 2, 2>'}
  435 |       t->ComputeJacobianWithRespectToPosition(point, data.J_);

dzenanz · 2020-11-04T23:57:08Z

@RubioJr9 which compiler/OS and their versions are you using?

tarkpate · 2020-11-05T00:46:23Z

OS: Arch Linux(rolling release so no versioning)
Compiler: gcc 10.2.0

… pr/382

dzenanz · 2020-11-05T22:15:31Z

@RubioJr9 By reading this SO question, it seems that data.J_ is not the same type which ComputeJacobianWithRespectToPosition expects, so implicit conversion is creating a temporary. I looked at the code and couldn't quite figure out why. Can you copy-paste the full error message with context (instantiation types etc)?

tarkpate · 2020-11-06T02:06:49Z

I posted the log in the new PR. Let me know if you need more info.

dzenanz and others added 16 commits September 29, 2020 10:50

First step in completing migration from ITKv3 to ITKv4

3a80dab

Disable ITKV3_COMPATIBILITY

e51885c

Finish migration to ITKv4

172d606

Prepare for migration to ITKv5

61dc389

Update ITK version to 5.1.0

092f263

7 errors left

b6b6599

Use main ITK repository directly

efbe607

Avoid use of legacy code

feb5255

Exposing H5HL in ITK seems to work (it is on by default)

5e8c755

ENH: Migration to ITK 5.1.0

386b258

registration->StartRegistration() ==> registration->Update() GetJacobian(...) ==> ComputeJacobianWithRespectToPosition(...)

Copy implementations of 4 functions from H5LTpublic.h

c396034

so we don't need to have it as a dependency.

Using ITK master

6c6404b

Disabling ITKV4 compatibility

0217159

Remove ITK legacy code

840b28c

dzenanz mentioned this pull request Nov 2, 2020

ITK 5.2 upgrade #378

Closed

allywarner requested review from jessdtate and dcwhite November 3, 2020 21:10

dcwhite requested changes Nov 3, 2020

View reviewed changes

allywarner added 4 commits November 3, 2020 14:48

SQL errors

8a07fa2

Update extraxt filter

e173aca

SQL errors

2430c96

Tinyxml updates

9797810

nullptr to NULL

allywarner requested a review from dcwhite November 3, 2020 21:56

allywarner assigned allywarner and dzenanz Nov 3, 2020

allywarner requested a review from tarkpate November 3, 2020 22:03

allywarner unassigned dzenanz and allywarner Nov 3, 2020

allywarner assigned allywarner and dzenanz Nov 3, 2020

dzenanz commented Nov 4, 2020

View reviewed changes

allywarner and others added 5 commits November 4, 2020 11:17

SQL errors

92bf2b5

Update extraxt filter

f84f590

SQL errors

67e114f

Tinyxml updates

c4e85e4

nullptr to NULL

Removing fiddling with HDF5 library which is no longer needed

cb172d7

dzenanz force-pushed the itk5migration branch from 9797810 to cb172d7 Compare November 4, 2020 16:36

dzenanz mentioned this pull request Nov 4, 2020

ITK5 migration #384

Merged

Merge branch 'itk5migration' of https://github.com/dzenanz/Seg3D into…

ce479c2

… pr/382

allywarner closed this Nov 10, 2020

allywarner added this to the 2.5.1 milestone Nov 10, 2020

ITK 5.2 migration #382

ITK 5.2 migration #382

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