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- | ===== 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(): 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) === |
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) == | + | === timestamps (ts) === |
+ | |||
+ | [[https://github.com/vandermeerlab/vandermeerlab/tree/master/code-matlab/shared/datatypes/ts|ts folder on GitHub]] | ||
Basics: | Basics: | ||
- | * ts(): 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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* MultiRaster(): see below | * MultiRaster(): see below | ||
- | == 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) == | + | ==== Low-level utility functions ==== |
- | === Low-level utility functions === | + | * [[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) | ||
- | * nearest_idx3(): | + | ===== Visualization functions ===== |
- | ==== Visualization functions ==== | + | * the amazing MultiRaster ([[https://github.com/vandermeerlab/vandermeerlab/blob/master/code-matlab/example_workflows/MultiRaster_usage.m|examples]]) |
- | ==== Loading functions ==== | + | ===== Loading/converting functions ===== |
- | ==== Analysis functions ==== | + | ===== Analysis functions ===== |