User Tools

Site Tools


analysis:matlab-overview

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
analysis:matlab-overview [2017/06/30 20:33]
mvdm created
analysis:matlab-overview [2017/07/02 16:51]
mvdm [Visualization functions]
Line 1: Line 1:
-===== Overview of common functions =====+====== Overview of common functions ​======
  
-==== Utility functions ====+===== Utility functions ​=====
  
-=== Utility functions common to multiple data types ===+==== Utility functions common to multiple data types ====
  
-  * restrict()+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​util/​restrict.m | restrict()]]:​ restricts times in data object (iv, ts, tsd) to specific intervals 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​util/​getd.m | getd()]]: helper function to return data corresponding to label target_field
  
-=== Functions ​associated with specific data types ===+==== Utility functions ​associated with specific data types ====
  
-== interval (iv) ==+=== interval (iv) ==
 + 
 +[[https://​github.com/​vandermeerlab/​vandermeerlab/​tree/​master/​code-matlab/​shared/​datatypes/​iv | iv folder on GitHub]]
  
 Basics: Basics:
  
-  * iv(): constructor +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​iv.m | iv()]]: constructor 
-  * CheckIV(): check if IV is correctly formatted+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​CheckIV.m | CheckIV()]]: check integrity of iv struct 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​SelectIV.m | SelectIV()]]:​ specify intervals to keep
  
 Simple operations: Simple operations:
  
-  * ResizeIV(): expand or contract intervals by specified amount +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​ResizeIV.m | ResizeIV()]]: expand or contract intervals by specified amount 
-  * InvertIV(): "​flips"​ included intervals to non-included,​ and vice versa +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​InvertIV.m | InvertIV()]]: "​flips"​ included intervals to non-included,​ and vice versa 
-  * MergeIV(): merge touching, overlapping,​ or nearby intervals within an iv struct +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​MergeIV.m | MergeIV()]]: merge touching, overlapping,​ or nearby intervals within an iv struct
-  * SelectIV(): specify intervals to keep+
  
 Set operations: Set operations:
  
-  * UnionIV(): set union of iv objects +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​UnionIV.m | UnionIV()]]: set union of iv objects 
-  * IntersectIV():​ set intersect, keep only those iv1's that include a piece of iv2 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​IntersectIV.m |  ​IntersectIV()]]: set intersect, keep only those iv1's that include a piece of iv2 
-  * DifferenceIV():​ set difference, keep only those iv1's that DO NOT include a piece of iv2+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​DifferenceIV.m | DifferenceIV()]]: set difference, keep only those iv1's that DO NOT include a piece of iv2
  
 Analysis operations: Analysis operations:
  
-  * TSDtoIV(): create interval data from tsd by tresholding+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​TSDfromIV.m | TSDtoIV()]]: create interval data from tsd by tresholding 
 +  * MultiRaster():​ see below
  
 Visualization:​ Visualization:​
  
-  * PlotTSDfromIV():​ display intervals defined relative to tsd+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​PlotTSDfromIV.m | PlotTSDfromIV()]]: display intervals defined relative to tsd 
 + 
 +=== timestamps (ts) === 
 + 
 +[[https://​github.com/​vandermeerlab/​vandermeerlab/​tree/​master/​code-matlab/​shared/​datatypes/​ts|ts folder on GitHub]] 
 + 
 +Basics: 
 + 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​ts.m|ts()]] constructor 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​CheckTS.m | CheckTS()]]:​ check integrity of ts struct 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​SelectTS.m | SelectTS()]]:​ specify ts data to keep. (Also performs reordering) 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​concatenateTS.m | concatenateTS()]]:​ concatenate two ts objects 
 + 
 +Analysis operations:​ 
 + 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​getSpikeCount.m | getSpikeCount()]]:​ returns spike counts (number of spikes) in a nCells x 1 vector of ts input 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​ShuffleTS.m | ShuffleTS()]]:​ shuffle spikes in ts struct 
 + 
 +Visualization:​ 
 + 
 +  * MultiRaster():​ see below 
 + 
 +=== timestamped data (tsd) === 
 + 
 +[[https://​github.com/​vandermeerlab/​vandermeerlab/​tree/​master/​code-matlab/​shared/​datatypes/​tsd|tsd folder on GitHub]] 
 + 
 +Basics and selection:​ 
 + 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​tsd.m | tsd()]]: constructor 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​CheckTSD.m|CheckTSD()]]:​ check integrity of tsd struct 
 +  * getd(): get (raw) data with specified label 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​TSD_SelectChannel.m|TSD_SelectChannel()]]:​ returns tsd containing only channels with labels in channel_label 
 + 
 +Merging: 
 + 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​MergeTSD.m|MergeTSD()]]:​ Merge data from multiple TSDs into a single, new TSD 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​UnionTSD.m|UnionTSD()]]:​ returns the union (merge) of two TSD inputs 
 + 
 +Analysis: 
 + 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​TSD_getidx2.m|TSD_getidx2()]]:​ returns idxs into ts or tsd, delimited by input interval(s) 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​TSDbyZ.m | TSDbyZ()]]: compute averages of the values in tsd_in binned by z's cfg.edge 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​tsd/​TSDbySpace.m |TSDbySpace()]]:​ construct 2D matrix with spatial averages of the values in tsd_in 
 + 
 +=== tuning curve (tc) === 
  
-== timestamps (ts) ==+==== Low-level utility functions ====
  
-== timestamped ​data (tsd==+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​util/​nearest_idx3.m | nearest_idx3()]]:​ return the indices of ''​lookupvalues''​ that are closest to the numbers in ''​data''​ 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​util/​ndhist.m | ndhist()]]: fast N-dimensional histogram ​(useful for plotting place fields
  
-== tuning curve (tc) == +===== Visualization functions =====
  
-==== Visualization functions ====+  * the amazing [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​viz/​MultiRaster.m | MultiRaster]] ([[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​example_workflows/​MultiRaster_usage.m|examples]]) 
 +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​viz/​scatterplotC.m | scatterplotC()]]:​ scatterplot with additional variable plotted as color, useful for plotting phase precession in space
  
-==== Loading functions ====+===== Loading/​converting ​functions ​=====
  
-==== Analysis functions ====+===== Analysis functions ​=====
analysis/matlab-overview.txt · Last modified: 2018/07/07 10:19 (external edit)