skelet3d 1.5.7

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skelet3d
========

Package is constructed to analyse vessel tree structures. Length, radius and branching angles can be computed.
Skeletonization algorithm is based on [ITKThinningImageFilter3D](http://hdl.handle.net/1926/1292).
There is dynamic linked library installed by cmake. Python and Matlab
scripts call this library.


Prerequisites
=============

* Python (2.7)
* CMake
* ITK
* Numpy
* InsightToolkit

## Ubuntu

Tested on Ubuntu 12.04, 14.04 and 16.04. Check [install notes](install_linux.md) for more information.

Install prerequisites

sudo apt-get install cmake python-numpy libinsighttoolkit3-dev libpng12-dev libgdcm2-dev python-pip

Install python package

pip install skelet3d

To build `.so` libraries you will need download skelet3d sources:

cd build
cmake ..
make
make install

## Windows

Tested on Windows 10 64-bit

* Install numpy. Recommended is installation with [Anaconda](https://www.continuum.io/downloads)
* Download [DLL libraries](http://147.228.240.61/queetech/install/ITK%2bSkelet3D_dll.zip)
into directory in environment PATH (e.g. `c:\Windows\System32` ) or [build it yourself](build_windows.md)
* Install skelet3d

pip install skelet3d



## Matlab

For matlab wrapper run src/compile.m

matlab -nodesktop -nosplash -r "cd src;compile;exit"

Then there is binaryThhinningMex.mexa64 file. It is used by skelet3d.m.

Example
=======

Simple example with donut shape

import skelet3d
import numpy as np

# Create donut shape
data = np.ones([3,7,9])
data [:, 3, 3:6] = 0

skelet = skelet3d.skelet3d(data)

print skelet

Result:

array([[[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0]],

[[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0],
[0, 0, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0]],

[[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0]]], dtype=uint8)


For more examples with skeleton analysis or visualisation see [example directory](https://github.com/mjirik/skelet3d/tree/master/examples)



Troubleshooting
===============

Problems with build
-------------------

In case of any problems You can use binary files and manually copy it into
expected paths. BinaryThinningCxxShared library should be in `/usr/local/lib`
on Linux or somewhere in system `PATH` on windows. Python module `skelet3d.py`
can be used directly.


Cannot find library
-------------------


libBinaryThinningCxxShared.so: cannot open shared object file: No such file or
directory


Probably there is a problem in Ubuntu with `LD_LIBRARY_PATH`. If you do want
to add correct library paths:

echo "include /usr/local/lib" | sudo tee -a /etc/ld.so.conf
sudo ldconfig -v

More information on:

http://bugs.python.org/issue18502

http://ubuntuforums.org/showthread.php?t=1498755


Cannot find library 2
---------------------

`libBinaryThinningCxxShared.so` is expected to be in `/usr/local/lib` and in `~/miniconda2/lib`

OSError
-------

OSError: /home/.../lib-dynload/../../libBinaryThinningCxxShared.so:
undefined symbol: _ZN3itk15ExceptionObject11SetLocationERKSs

WindowsError:[Error193]
-----------------------

You are probably using 32-bit skeleton build with 64-bit python

ld cannot find -lz and -lpng
-----------------------------

Problem is probabli in 32-bit compiling in 64-bit system. You need install fallowing packages.

sudo apt-get install lib32z1-dev libpng12-dev