We provide code, examples, and additional text as supplementary material for our paper.  This file gives a description of the code and examples.


 This code is submitted as supplementary material for a paper by Tabb and Medeiros:

"Fast and robust curve skeletonization for real-world elongated objects," which is currently under review but available at arXiv as arXiv:1702.07619 [cs.CV].



There are no use limitations for the code.  If the results of the code are used as a part of a system described in a publication, we request that the authors cite a published version of the paper, if the work has been published, and the arXiv version(currently on arXiv (arXiv:1702:07619[cs.CV]), if not. 
There are no gaurantees of this code.   It may be used to compare new methods of curve skeletonization, to use the authors' method of curve skeletonization in other systems, or to develop new methods of curve skeletonization.  



There are use limitations for the example data (e.g. three-dimensional models) provided in this record.  The models may be used for evaluation and debugging purposes of the code, and used in published work for evaluations of curve skeletonization algorithms so long as the source paper (currently on arXiv (arXiv:1702:07619[cs.CV]), or a published version, if published) is acknowledged as the source of the model.  It is not necessary to compare using the authors' method in this case.  However, outside of these situations, use of the model in published materials or 3D printed works is not permitted by this public release and authors interested in alternate uses should contact the authors for permission.







 



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Instructions for compilation and linking:
1. This code has been written and tested on Ubuntu 14.04, using Eclipse CDT as the IDE, and is written in C/C++.



2. This code is dependent on the OpenCV-3.* libraries.  These libraries should be in the include path, or specified in your IDE.



3. Compiler flags: we use OpenMP for parallelization and the C++11 standard.  Note that Eclipse's indexer marks some items from C++11 as errors (but still compiles).  
The flags needed using the gnu compiler, openmp, and the C++11 standard are:	
		 -fopenmp  -std=gnu++11
	though depending on the compiler used, you may need different flags: https://www.dartmouth.edu/~rc/classes/intro_openmp/compile_run.html
	


4. 	libraries needed for linking are:
	gomp   [OpenMP]
	opencv_core [OpenCV]
	opencv_legacy
	opencv_highgui
	opencv_imgproc
	opencv_imgcodecs

 

 


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Instructions for use:
We use a file format for representing models that is composed of a text file containing the model points "0.txt" and bounding box in file "BB.txt".  
We include samples of these two types of files in the "examples" folder.  We also have some conversion functions (see 3 in this section).

1. To run the code using the default threshold (1e-12) for rejecting spurious segments, you call with one argument, the name of the directory containing "0.txt" and "BB.txt":
./program_name directory

2. To run the code with different values of the threshold, you call with two argmuents, the directory name followed by the threshold value [0, 1]:
./program_name directory threshold

3. We have chosen the image sequence representation for conversion.  To convert models from any other format, one can use ImageJ/Fiji to load and then save as an image
sequence.  Once a sequence is created, save in a folder titled "rawimages" within the directory.  Then call with three arguments:
./program_name directory threshold 1

We have included in the "examples" folder an image sequence.  The result is saved in a folder called "processedimages", which one can then load with ImageJ/Fiji to visualize in
one's preferred environment.  The result is also saved in the format described below.





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Results format:
The results are written as .ply meshes.  One can view them with free viewer Meshlab.  A sample of results is shown in the examples, "A_Result" directory.



1. The paths_TabbMedeiros.ply file shows the paths computed by the algorithm.



2. The skel_TabbMedeiros.ply shows the 1D skeleton voxels.

3. The initial.ply file shows a mesh of the original object.




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Contact for bug reports or other issues:

Amy Tabb

amy.tabb@ars.usda.gov