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Merge changes from 2017 made during finalisation of PhD thesis #652

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merged 294 commits into from Apr 8, 2018

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schuhschuh commented Apr 8, 2018

This merges all changes of my personal develop branch into the master of the official repository. It's the first step in preparing a new MIRTK release version, which corresponds to the software used for the experiments in my submitted PhD thesis.

The next step will be to update the online documentation, especially installation instructions.

The following contains too many changes to summarise them all, but the most important are:

  • Update CMake configuration files to consider VTK 8 when looking for a VTK installation.

  • Add Linear Energy constraint to image registration.

  • Add "NegDetJac" penalty for SVFFD model.

  • Remove obsolete "MinDetJac" penalty.

  • Registration contraints "with respect to world" options.

  • Various FFD gradient approximations, including via convolution with B-spline and directly manipulated FFD (DMFFD) approach.

  • Linear extension of Jacobian-based penalties below an epsilon threshold.

  • SVFFD option: "Use dense BCH lattice"

  • Add HistogramMatching filter and corresponding match-histogram command.

  • Extend convert-dof to convert from Elastix, LCC LogDemons (ITK), and DRAMMS to MIRTK format.

  • Add further flip-image and reflect-image options.

  • Enable saving 2D images to PNG files.

  • Groupwise spatio-temporal atlas construction and evaluation commands.

  • Attention: Scale of similarity gradient changed!

    • This means users have to adjust their weights in order to replicate previous results...

Closes #648.

schuhschuh added some commits Jul 12, 2017

enh: Jacobian based penalty gradient computation [Transformation]
- Add pure virtual Penalty and DerivativeWrtJacobianDet to base class.
- Move code to evaluate penalty and compute gradient to base class.
- TopologyPreservation gradient computation using base class.
- Remove obsolete MinJacobianConstraint, use TopologyPreservation instead.
enh: Jacobian based penalty gradient computation [Transformation]
- Add pure virtual Penalty and DerivativeWrtJacobianDet to base class.
- Move code to evaluate penalty and compute gradient to base class.
- TopologyPreservation gradient computation using base class.
- Remove obsolete MinJacobianConstraint, use TopologyPreservation instead.

@schuhschuh schuhschuh added this to the v1.2.0 milestone Apr 8, 2018

@schuhschuh schuhschuh self-assigned this Apr 8, 2018

schuhschuh added some commits Apr 8, 2018

fix: Remove set -e from install_depends.sh script
This may be the cause for Homebrew error “shell_session_update: command not found” which according to others can be safely ignored.
Revert "fix: Clang warning of missign definitions of static LookupTab…
…le members of BSpline template [Numerics]"

This reverts commit 07d5589.

# Conflicts:
#	Modules/Numerics/include/mirtk/BSpline.h
Revert "fix: Build with MSVC, Clang warning regarding Sinc::LookupTab…
…le [Numerics]"

This reverts commit 4e23f76.

# Conflicts:
#	Modules/Numerics/include/mirtk/BSpline.h

@schuhschuh schuhschuh merged commit a17af82 into BioMedIA:master Apr 8, 2018

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@schuhschuh schuhschuh deleted the schuhschuh:develop branch Apr 8, 2018

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