Most-Likely Point Paradigm

This repository provides data and source code for algorithms developed within the Most-Likely Point and Deformable Most-Likely Point paradigms described in the following papers:

IMLP: Seth D. Billings, Emad M. Boctor, and Russell H. Taylor, "Iterative Most-Likely Point Registration (IMLP): A Robust Algorithm for Computing Optimal Shape Alignment", PLOS One 10 (3): e0117688 (2015)

IMLOP: Seth D. Billings, Russell H. Taylor, "Iterative most likely oriented point registration", Medical Image Computing and Computer-Assisted Intervention, Lecture Notes in Computer Science 8673: 178--185 (2014)

G-IMLOP: Seth D. Billings, Russell H. Taylor, "Generalized iterative most likely oriented-point (G-IMLOP) registration", International Journal of Computer Assisted Radiology and Surgery 10 (8): 1213--1226 (2015)

P-IMLOP: Seth D. Billings, Hyun J. Kang, Alexis Cheng, Emad M. Boctor, Peter Kazanzides, Russell H. Taylor, "Minimally invasive registration for computer-assisted orthopedic surgery: combining tracked ultrasound and bone surface points via the P-IMLOP algorithm", International Journal of Computer Assisted Radiology and Surgery 10 (6): 761--771 (2015)

D-IMLP: Ayushi Sinha, Seth D. Billings, Austin Reiter, Masaru Ishii, Gregory D. Hager, Russell H. Taylor, "The deformable most likely point paradigm", TBP

D-IMLOP: Ayushi Sinha, Seth D. Billings, Austin Reiter, Masaru Ishii, Gregory D. Hager, Russell H. Taylor, "The deformable most likely point paradigm", TBP

GD-IMLOP: Ayushi Sinha, Xington Liu, Austin Reiter, Masaru Ishii, Gregory D. Hager, Russell H. Taylor, "Endoscopic navigation in the absence of CT imaging", Medical Image Computing and Computer-Assisted Intervention, Lecture Notes in Computer Science (2018)

NOTE: This repository also contains an implementation of ICP, directional ICP and robust ICP. Other algorithms evaluated in these papers, for which source code is not included in this repository, include:

GICP

downloaded from http://www.robots.ox.ac.uk/~avsegal/generalized_icp.html

see IMLP paper for minor modifications required for termination condition and to set covariance matrices
CPD

downloaded from https://sites.google.com/site/myronenko/research/cpd

see IMLP paper for minor modifications required for termination condition

NOTE: To run experiments described in the IMLP paper, go to https://github.com/sbillin/IMLP. Compile the source code following instructions there (or here) and run the experiments in the PLOSONE folder.

Required Software Dependencies

CMake (http://www.cmake.org)
Visual Studio for Windows (http://www.visualstudio.com/downloads/download-visual-studio-vs)

application was developed in Visual Studio 2013
CISST Libraries (https://github.com/jhu-cisst/cisst/)

must compile this from source (instructions below)
WildMagic5 Libraries (http://www.geometrictools.com/Downloads/Downloads.html)

requires: Wm5Core.lib, Wm5Mathematics.lib

must compile these from source (instructions below)

included in dependencies folder
DLib (http://dlib.net/)

for iterative solutions to our minimization problems

included in dependencies folder
Numerical Recipes (http://numerical.recipes/)

needed only for G-IMLOP and GD-IMLOP algorithm; other algorithms don't use it and the code can be built without it
RPly Library

for reading/writing PLY files

included in dependencies folder
PLY_IO Library (if using Matlab)

for reading/writing PLY files in Matlab

included in dependencies/Matlab Dependencies folder

NOTE: Visual Studio 12 2013 Win64 was used successfully when creating this README. Visual Stuido 14 2015 Win64 did not work due to errors such as cisstNetlib_f2c.lib(endfile.obj) : error LNK2001: unresolved external symbol __imp_sprintf. This issue has not been solved and it is recommended to build the cisstICP application using Visual Studio 2013.

Instructions for Compiling Dependencies

CISST Libraries:

https://github.com/jhu-cisst/cisst/

Clone cisst repository from github

git clone https://github.com/jhu-cisst/cisst/

only jhu-cisst/cisst required (not cisst-saw, etc.)
Create a build directory cisst_build alongside (not inside) the cisst directory that was cloned from git
Create Visual Studio solution for CISST Libraries using CMake

run CMake on cisst source directory with build directory set to cisst_build
```
-- check boxes for libraries: CISST_cisstCommon, CISST_cisstVector, CISST_cisstNumerical, CISST_cisstOSAbstraction

-- uncheck boxes for cisstMultitask, cisstMutliTask_, cisstParameterTypes, cisstRobot_ 

-- check box for CISST_HAS_CISSTNETLIB 
```
configure with Visual Studio 12 2013 Win64 as the compiler -- check box: CISSTNETLIB_DOWNLOAD_NOW

configure and generate project

open the cisst_build/cisst.sln file and build in Visual Studio with build mode set to Release and x64

WildMagic5 Libraries:

http://www.geometrictools.com/Downloads/Downloads.html These libraries are used solely for the closed-form implementation of computing the decomposition of a 3x3 covariance matrix. The libraries are no longer available online from their author, but they are included in the dependencies folder of the cisstICP repo.

Build WildMagic5

extract source from the WildMagic5p13.zip file located in the dependencies folder

open the GeometricTools\WildMagic5\WildMagic5Wgl_VC120.sln file in Visual Studio and set build configurations to Release and x64

compile Wm5Core.lib and Wm5Mathematics.lib by right clicking LibCore_VC120 and LibMathematics_VC120 and selecting build
See website of WildMagic5 for more instructions on this

Dlib Libraries:

Extract source from the dlib-a8.6.7z file located in the dependencies folder

Numerical Recipes:

License to use the source code for this must be bought (usually available on amazon along with the book)
Contact sinha(at)jhu(dot)edu for modifications in numerical recipes code once license is obtained

RPly Libraries:

Extract source from the rply-1.1.4.zip file located in the dependencies folder

PLY_IO Libraries:

If using Matlab

Extract source from the PLY_IO file located in the dependencies/Matlab Dependencies folder

Instructions for Compiling Source Code

These instructions are based on the Windows platform with VisualStudio 2013. The output is a static library (cisstICP.lib).

Compile cisstICP Library:

Clone cisstICP repository from github

git clone https://github.com/AyushiSinha/cisstICP
Create a build directory cisstICP_build within the cisstICP directory that was cloned from git
run CMake on source directory cisstICP

specify paths to cisstICP source code and build directories (cisstICP and cisstICP_build) and configure

set cisst_DIR to location of CISST Library build cisst/cisst_build and configure again. If the compiled CISST libraries were found correctly by CMake, then CISST_USE_FILE should now automatically contain a path to the file Usecisst.cmake

specify path to WildMagic5 base directory by setting WM5_BASE_DIR to cisstICP/dependencies/WildMagic5p13/GeometricTools/WildMagic5 (other WildMagic5 fields should auto-detect)

set DLIB_INCLUDE to the path to the extracted dlib folder

set RPLY_DIR to the path to cisstICP/dependencies/rply-1.1.4

optionally, check USE_EXTRA_ALGORITHMS to include IMLP_CP (closest point), IMLP_MD (mahalanobis distance) and RobustICP in the build

configure and generate project
Build cisstICP library in Visual Studio

open cisstICP_build/cisstICP.sln

build with build mode set to Release and x64

Compile cisstICP_App:

Create a build directory cisstICP_App_build within the cisstICP_App directory

specify paths to cisstICP source code and build directories (cisstICP_App and cisstICP_App_build)
run CMake on source directory cisstICP_App and configure

set cisst_DIR to the path to the cisst/cisst_build folder and configure again. If the compiled CISST libraries were found correctly by CMake, then CISST_USE_FILE should now automatically contain a path to the file Usecisst.cmake

set DLIB_INCLUDE to the path to the extracted dlib folder.

set WM5_BASE_DIR to the path to cisstICP/dependencies/WildMagic5p13/GeometricTools/WildMagic5

set MATLAB_ENGINE_INCLUDE_DIR and MATLAB_ENGINE_LIB_DIR to your system paths for Matlab, such as C:/Program Files/MATLAB/R2015a/extern/include and C:/Program Files/MATLAB/R2015a/extern/lib/win64/microsoft (these paths will change depending on the Matlab version).

set cisstICP_LIB to the path to /cisstICP/cisstICP_build/Release/cisstICP.lib

set cisstICP_LIB_INCLUDE to the path to cisstICP/cisstICP

configure again and Generate
Build cisstICP_App library in Visual Studio

open the cisstICP_App_build/cisstICP_App.sln file in Visual Studio, set the build options to 'Release' and 'x64', and build the solution.

Compile matlabICP Library:

This library provides a Matlab interface to the C++ code of the cisstICP Library. This library is not maintained by me.

Create a matlabICP_build folder alongside the matlabICP folder in the cloned repo

set CMake's source and build locations to these folders (matlabICP and matlabICP_build)
run CMake on source directory matlabICP and configure

set cisst_DIR to the path to the cisst/cisst_build folder and configure again. If the compiled CISST libraries were found correctly by CMake, then CISST_USE_FILE should now automatically contain a path to the file Usecisst.cmake.

set DLIB_INCLUDE to the path to the extracted dlib folder.

set WM5_BASE_DIR to the path to cisstICP/dependencies/WildMagic5p13/GeometricTools/WildMagic5

set MATLAB_ENGINE_INCLUDE_DIR and MATLAB_ENGINE_LIB_DIR to your system paths for Matlab, such as C:/Program Files/MATLAB/R2015a/extern/include and C:/Program Files/MATLAB/R2015a/extern/lib/win64/microsoft (these paths will change depending on the Matlab version).

set cisstICP_LIB to the path to /cisstICP/cisstICP_build/Release/cisstICP.lib

set cisstICP_LIB_INCLUDE to the path to cisstICP/cisstICP

configure again and Generate
Build matlabICP library in Visual Studio

open the matlabICP_build/matlabICP.sln file in Visual Studio, set the build options to 'Release' and 'x64', and build the solution.
Add to Matlab

extract the /cisstICP/dependencies/MatlabDependencies/mtimesx.zip and add it to your Matlab path.

add /cisstICP/dependencies/MatlabDependencies/PLY_IO to your Matlab path. Note that the PLY_IO library code included here containes a bug fix for ply_read.m, changing line 571 from

        if ( ( nargin > 1 & strcmpi(Str,'Tri') ) || nargout > 2 )

to

        if ( ( nargin > 1 && strcmpi(Str,'Tri') ) || nargout > 2 )

NOTE: If you do not have the Numerical Recipes code, then the Matlab interface for GIMLOP will fail to compile (since GIMLOP will not have been compiled in the C++ library), giving an error. This is not a problem, as the Matlab interfaces for the other algorithms won't be affected and can still be used.

Test Run

cd to cisstICP_App/cisstICP_App_build/Release/ and run ICP_App via command line

this should run the executable with default settings
Test whether everything is running correctly

run the following commands:

    ICP_App --alg IMLP --out testingforrelease
    ICP_App --alg DIMLP --out testingforrelease
    ICP_App --alg IMLOP --out testingforrelease
    ICP_App --alg DIMLOP --out testingforrelease
    ICP_App --alg GIMLOP --out testingforrelease
    ICP_App --alg GDIMLOP --out testingforrelease
    ICP_App --alg PIMLOP --out testingforrelease

cd into cisstICP_App/tests and run compare_outputs_script.m in Matlab. If all algorithms pass, then everything is running correctly. This is a good test to run when developing to make sure changes to the code have not broken anything
Test if the matlabICP libraries are working (if using Matlab)

cd to matlabICP/TestApps/ and run App_Test_IMLOP.m in Matlab (not maintained)

Name		Name	Last commit message	Last commit date
Latest commit History 108 Commits
cisstICP		cisstICP
cisstICP_App		cisstICP_App
dependencies		dependencies
matlabICP		matlabICP
test_data		test_data
.gitignore		.gitignore
LICENSE.txt		LICENSE.txt
README.md		README.md

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Most-Likely Point Paradigm

Required Software Dependencies

Instructions for Compiling Dependencies

CISST Libraries:

WildMagic5 Libraries:

Dlib Libraries:

Numerical Recipes:

RPly Libraries:

PLY_IO Libraries:

Instructions for Compiling Source Code

Compile cisstICP Library:

Compile cisstICP_App:

Compile matlabICP Library:

Test Run

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Most-Likely Point Paradigm

Required Software Dependencies

Instructions for Compiling Dependencies

CISST Libraries:

WildMagic5 Libraries:

Dlib Libraries:

Numerical Recipes:

RPly Libraries:

PLY_IO Libraries:

Instructions for Compiling Source Code

Compile cisstICP Library:

Compile cisstICP_App:

Compile matlabICP Library:

Test Run

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