ENH: Add graph kernel support

Change-Id: I884f934f7ba2098c10b5dac551dc0e81a29d2777
Add: tubeGraphKernel - Graph kernel driver (depends on BOOST 1.51)
Add: Shortest path kernel
Add: First draft for 'Experiments' directory
Add: VascularAtlasFormation experiment + Driver Script
ENH: Added Matt's review comments and WIP on TubeImageQuantiles

ENH: TubeGraphKernel modified with Matt's comments
ENH: AtlasGenerationDriver not dependent on env. variable anymore
ENH: Conditional compilation for Boost related code (TubeTK_USE_Boost)
WIP: TubeImageQuantiles to compute user-specified quantiles

Change-Id: If1932a1294575b501389cc770e52273dadb24330
ENH: Added CLI arguments to specify kernel type to VascularAtlasGeneration

Change-Id: Ie7a593c507e5568b2ce350385dc6878b181a3b44
ENH: Enhancements of Experiments driver and automatic Midas data download

Change-Id: Ie6b8690cfb8a2f665bd295f3dcbd699ae728f362
Enh: Renamed AtlasGenerationDriver.py to ExperimentsDriver.py
Enh: Adapted README file to reflect changes
Enh: Removed 'dir' variables in ExperimentsDriver.py
Enh: Better readability of example config files
Add: Download.py to automatically download data from MIDAS
Add: Pydas-Config.json.example (MIDAS credentials config)
BUG: Bug fix in experiments driver and removal of 'using XXX' directive

Change-Id: Id6c1e1a7284017bf03d54b38712609cf1b960508
BUG: Fixed bug accidentially introduced in TubeDensityProbability

Change-Id: I9ef28204ebf2ab12edcadc7ad7351f2657e91b90
ENH: Added default node labeling support and experiment enhancements

Change-Id: I456e7234f2721906c1d398ee2bde3befccc55eb3
ADD: Support to choose default node labeling (degree, ID)
ADD: Support to choose phantom type in experiments driver
ADD: Graph kernel evaluation, based on full kernel matrix
ADD: Computation of kernel between graph and group-wise summary graphs
ENH: Random seed (e.g., for CVT init.) is passed via ExperimentsDriver.py
ENH: Skip zero-weight edges in WLSubtreeKernel
DOC: Updated documentation in experiments driver scripts
STYLE: Variable renaming for consistency and simple fixes in graph kernels

Change-Id: I6578df4f1a04943c00e8afb0414e4805a7f76625
Add: Support for absolute AND relative path for loading graphs
Enh: Variable naming for user-given CLI parameters
Enh: Support to omit labeled regions in TransferLabelsToRegions
Enh: Reflect renaming changes in Experiments JSON files
ENH: Added support for global label file when loading graphs

Change-Id: I6c62aa5e06ce16631f89a2fb1f78593aed7f6a7e
ENH: Support for a global label file

Change-Id: I6b0821e0ece99202195c1918188a77a77cf8773c
ENH: Refinement of VascularAtlasGeneration

ENH: CLI documentation in TransferLabelsToRegions.
ENH: Adjusted ExperimentsDriver CLI arguments to reflect args of
     the binaries they are passed to.
ADD: Support in ExperimentsDriver to compute global label maps using
     TransferLabelsToRegions.
Change-Id: I76a02c1484a9be71c95bb999d5add61d346927d7
ENH: Added support to write SVM info files (with #SVs, predictions, etc.)

Change-Id: I68c0c88fd35cea61eccde0ef8ae16334f92e24a7
STYLE: Remove tabs and spaces at EOL

Change-Id: Id3fab69a2049b0e3894089b60220ac0208e6e507
STYLE: Add README markdown files for each folder

Documentation will gradually be added to the markdown files, but for now they
contain a title and a generic footer. Also created a Base/Common folder, into
which some of the files from Utilities will be added, per discussion in meeting.

ENH: Update Cppcheck suppressions
ENH: Suppress CTK manually-specified variables CMake warning

Change-Id: I43196f8ff70666a1f315be2b90bce42441db8032
BUG: Fix inconsistent capitalization of -build/-Build directories

Change-Id: Ia64ab834c7a7b58bf00c68698e3e6f2ff208bb88
ENH: Add README, LICENSE, and .gitignore files