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 <br>http://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. It calls the file sniffadonly.m to advance the forward-Euler by one time step. It tests the final array of fluid parcels for inclusion within the array and returns a total fraction that represents the fluid parcels remaining in the array after a full stroke.

本代码配套于即将发表的学术论文："《俄勒冈滨蟹（Hemigrapsus oregonensis）嗅觉触角（olfactory antennules）的个体发育变化在生长过程中维持嗅探功能》"，作者为Lindsay D. Waldrop、Miranda Hann、Amy Henry、Agnes Kim、Ayesha Punjabi及M. A. R. Koehl。本代码采用拉格朗日（Lagrangian）流体质点追踪结合前向欧拉法（forward-Euler method）对流体运动进行建模。所有文件（包括位于http://dx.doi.org/10.6084/m9.figshare.928567的关联数据文件）均需置于同一目录下。文件makenewdataCh3.m可将Event###_flickdata.mat格式的数据文件转换为代码可用的Event###_newdata.mat格式：通过将速度场重插值至1000×1000网格，并将flickdata结构体中的信息精简为仅运行平流（advection）代码所需的内容。文件ch3sniff.m用于启动模拟，其调用in_ch3sniff.m初始化参数、创建拉格朗日数组并加载所需数据；同时调用sniffadonly.m文件，以单时间步长推进前向欧拉法计算。该代码会对最终的流体质点数组进行是否处于目标阵列内的检测，并返回总占比，该占比代表完整划动后仍保留在该阵列内的流体质点比例。