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analysis:matlab-overview [2017/06/30 21:13]
mvdm
analysis:matlab-overview [2017/07/02 16:49]
mvdm [interval (iv)]
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 ==== Utility functions common to multiple data types ==== ==== Utility functions common to multiple data types ====
  
-  * restrict(): restricts times in data object (iv, ts, tsd) to specific intervals+  * [[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
  
 ==== Utility 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 integrity of iv struct +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​iv/​CheckIV.m | CheckIV()]]: check integrity of iv struct 
-  * SelectIV(): specify intervals to keep+  * [[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
  
 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   * 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]]) ===+=== timestamps (ts) === 
 + 
 +[[https://​github.com/​vandermeerlab/​vandermeerlab/​tree/​master/​code-matlab/​shared/​datatypes/​ts|ts folder on GitHub]]
  
 Basics: Basics:
  
-  * [[ts() | https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​ts.m]]constructor +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​ts.m|ts()]] constructor 
-  * CheckTS(): check integrity of ts struct +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​CheckTS.m | CheckTS()]]: check integrity of ts struct 
-  * SelectTS(): specify ts data to keep. (Also performs reordering) +  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​SelectTS.m | SelectTS()]]: specify ts data to keep. (Also performs reordering) 
-  * concatenateTS():​ concatenate two ts objects+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​concatenateTS.m | concatenateTS()]]: concatenate two ts objects
  
 Analysis operations: Analysis operations:
  
-  * 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/​getSpikeCount.m | getSpikeCount()]]: returns spike counts (number of spikes) in a nCells x 1 vector of ts input 
-  * ShuffleTS():​ shuffle spikes in ts struct+  * [[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​shared/​datatypes/​ts/​ShuffleTS.m | ShuffleTS()]]: shuffle spikes in ts struct
  
 Visualization:​ Visualization:​
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 === timestamped data (tsd) === === 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) ===  === tuning curve (tc) === 
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 ==== Low-level utility functions ==== ==== Low-level utility functions ====
  
-  * nearest_idx3():​+  * [[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) ​
  
 ===== Visualization functions ===== ===== Visualization functions =====
 +
 +  * the amazing MultiRaster ([[https://​github.com/​vandermeerlab/​vandermeerlab/​blob/​master/​code-matlab/​example_workflows/​MultiRaster_usage.m|examples]])
  
 ===== Loading/​converting functions ===== ===== Loading/​converting functions =====
  
 ===== Analysis functions ===== ===== Analysis functions =====
analysis/matlab-overview.txt · Last modified: 2018/07/07 10:19 (external edit)