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--- post:matlab_to_df.r [2019/08/21 14:53] – pseudomoaner
+++ post:matlab_to_df.r [2020/12/17 01:15] (current) – pseudomoaner
@@ Line 1: / Line 1: @@
 ====== matlab_to_df.R ======
-Description:
+**Class:** Script
-Author: Elisa Granato
+**Description:** Converts the Matlab-based procTracks structure into an R-based dataframe.
-<code rsplus>
+Note that variable names may need to be edited in this script to match your version of procTracks.
+If you are using the Matlab-based version of FAST, you will also need to re-save your track data in v6 .mat format for this script to work. Input the following commands to the Matlab command line to do this:
+<code matlab>
+clear all
+load('C:/Path/To/Target/Mat/Tracks.mat')
+save('C:/Path/To/Resaved/Mat/Tracks.mat','procTracks','rawFromMappings','rawToMappings','rawTracks',...
+    'trackTimes','toMappings','fromMappings','trackSettings','trackableData','linkStats','-v6')
+</code>
+Track .mat files for the stand-alone version of FAST are natively output in -v6 format.
+**Dependencies:**
+  * [[https://cran.r-project.org/web/packages/R.matlab/index.html|R.matlab]]
+  * [[https://cran.r-project.org/web/packages/data.table/vignettes/datatable-intro.html|data.table]]
+**Author:** Elisa Granato
+<code rsplus matlab_to_df.R>
 # matlab_to_df.R, (c) Elisa Granato, 2019
@@ Line 66: / Line 86: @@
 #reshaping the data to have column names with variables
-# vector containing all variables/measurement labels of interest:
+# EDIT VARIABLE NAMES HERE
+# Most variable names correspond to the fields of procTracks. Channel names should be written in the order of their indices (e.g. in the below case, channel 1 = brightfield, channel 2 = GFP, channel 3 = Pi)
 variables <- c("x","y","smoothx","smoothy","theta","vmag","smoothTheta","smoothVmag","majorLen","minorLen","area","phi","bf.mean","gfp.mean","pi.mean","bf.std","gfp.std","pi.std")