Detecting phyllotactic mode and simulations

There are two project folders. PARASTICHIES should be executed first, followed by SIMULATIONS.The PARASTICHIES code takes top-down photos of Mammillaria and converts them into polar images. The polar images are converted into frequency vectors by: performing row-wise FFT, applying a sliding window for smoothing, summing across columns, remove frequencies <5, use log function detrending artifacts, and z-score normalization of frequency vectors up to 55. Metadata that identifies high quality tracings of parastichies is then formatted. Using high quality determination of Fibonacci or Lucas number phyllotaxy, a Linear Discrimnation Analysis (LDA) is used to predict Fibonacci or Lucas phyllotaxy.The SIMULATIONS code creates noisy, simulated images of mammillaria for monojugate and bijugate Fibonacci and Lucas phyllotactic modes. Polar images and frequency vectors are calculated as above. LDA for four phyllotactic modes with monojugate and bijugate forms of Fibonacci and Lucas phyllotaxy, and two modes of only monojugate Fibonacci and Lucas, are performed and compared. Comparison of the two LDA models suggests that the bijugate phyllotaxy classes are not supported and models should only consider monojugate Fibonacci and Lucas phyllotaxy.