Advection code for calculating fraction of dendrite-bearing region of chemosensory hair array during flicking

Code to accompany an upcoming publication: "Ontogenetic changes in the olfactory antennules of the shore crab, Hemigrapsus oregonensis, maintain sniffing function during growth" by Lindsay D. Waldrop, Miranda Hann, Amy Henry, Agnes Kim, Ayesha Punjabi, and M. A. R. Koehl. This code models fluid movement via a forward-Euler method with lagragian fluid parcel-tracking. All files (including the associate data files, found at dx.doi.org/10.6084/m9.figshare.928567 ) should be in the same directory.

The file makenewdataCh3.m transforms data files Event###_flickdata.mat into the code-useable form Event###_newdata.mat by reinterpolating velocities onto a 1000 by 1000 grid and streamlining the information in flickdata structured to only what is needed to run the advection code. The file ch3sniff.m starts the simulation and calls in_ch3sniff.m to initialize parameters, creates the lagrangian array, and loads required data.