INSTALL

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INSTALLATION
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1) Unzip the code into any directory

2) In Matlab set the bash variable OCT_CODE_DIR to the directory from step 1) via 

setenv('OCT_CODE_DIR',xxx);

where xxx is a string pointing to that directory

3) call function compileMex to compile all C-Functions


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EXAMPLES
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The package provides two models (datafiles/modelFiles) for circular scans and 3-D volumes, that where trained using our labeled ground truth. 
Unfortunately we are not allow to publish any of these scans. For 2-D we have one demoscan provided, for 3-D we have demo scripts that use an external dataset.

2-D
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1) run useExampleScan2D.m to obtain a segmentation for the circular scan that is included in the package
2) run octGUI: Load the matfile circularScan.mat (datafiles/exampleScans) and the model file (datafiles/modelFiles) and run the model by clicking on 'Segment'


3-D
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1) Download the dataset of Srinivasan et al. from http://people.duke.edu/~sf59/Srinivasan_BOE_2014_dataset.htm 
2) Run the script predSrinivasan.m for a demonstration how to segment volumes (uses the model provided in the package)
3) Run the script trainSrinivasan.m for a demonstration how to train a model for volumes using as ground truth the predictions from 2)