TITLE:: FluidMDS
summary:: Dimensionality Reduction with Multidimensional Scaling
categories:: Dimensionality Reduction, Data Processing
related:: Classes/FluidMDS, Classes/FluidDataSet

DESCRIPTION::

Multidimensional scaling of a link::Classes/FluidDataSet::

https://scikit-learn.org/stable/modules/manifold.html#multi-dimensional-scaling-mds


CLASSMETHODS::


METHOD:: new
Make a new instance
ARGUMENT:: server
The server on which to run this model

METHOD:: euclidean
Euclidean distance (default)

METHOD:: sqeuclidean
Squared Euclidean distance

METHOD:: manhattan
Manhattan distance

METHOD:: max
Minowski max

METHOD:: min
Minowski max

METHOD:: kl
Symmetric Kulback Leiber divergance (only makes sense with non-negative data)

METHOD:: cosine
Cosine distance

INSTANCEMETHODS::

PRIVATE:: init

METHOD:: fitTransform
Fit the model to a link::Classes/FluidDataSet:: and write the new projected data to a destination FluidDataSet.
ARGUMENT:: sourceDataSet
Source data, or the DataSet name
ARGUMENT:: destDataSet
Destination data, or the DataSet name
ARGUMENT:: numDimensions
The number of dimensions to reduce to
ARGUMENT:: distanceMetric
The distance metric to use (integer, 0-6, see flags above)
ARGUMENT:: action
Run when done

EXAMPLES::

code::

//Preliminaries: we want some audio, a couple of FluidDataSets, some Buffers, a FluidStandardize and a FluidMDS
(
~audiofile = File.realpath(FluidBufPitch.class.filenameSymbol).dirname +/+ "../AudioFiles/Tremblay-ASWINE-ScratchySynth-M.wav";
~raw = FluidDataSet(s,\mds_help_12D);
~standardized = FluidDataSet(s,\mds_help_12Ds);
~reduced = FluidDataSet(s,\mds_help_2D);
~audio = Buffer.read(s,~audiofile);
~mfcc_feature = Buffer.new(s);
~stats = Buffer.alloc(s, 7, 12);
~standardizer  = FluidStandardize(s);
~mds = FluidMDS(s);
)


// Load audio and run an mfcc analysis, which gives us 13 points (we'll throw the 0th away)
(
~audio = Buffer.read(s,~audiofile);
FluidBufMFCC.process(s,~audio, features: ~mfcc_feature);
)

// Divide the time series in 100, and take the mean of each segment and add this as a point to
// the 'raw' FluidDataSet
(
{
	var trig = LocalIn.kr(1, 1);
	var buf =  LocalBuf(12, 1);
    var count = PulseCount.kr(trig) - 1;
	var chunkLen = (~mfcc_feature.numFrames / 100).asInteger;
	var stats = FluidBufStats.kr(
			source: ~mfcc_feature, startFrame: count * chunkLen,
		    startChan:1, numFrames: chunkLen, stats: ~stats, trig: trig
	);
	var rd = BufRd.kr(12, ~stats, DC.kr(0), 0, 1);
	var bufWr, dsWr;
	12.do{|i|
		bufWr = BufWr.kr(rd[i], buf, DC.kr(i));
	};
	dsWr = FluidDataSetWr.kr(\mds_help_12D, buf: buf, trig: Done.kr(stats));
	LocalOut.kr( Done.kr(dsWr));
	FreeSelf.kr(count - 99);
}.play;
)



//First standardize our DataSet, so that the MFCC dimensions are on comensurate scales
//Then apply the MDS in-place on the standardized data to get 2 dimensions, using a Euclidean distance metric
//Download the DataSet contents into an array for plotting
(
~reducedarray = Array.new(100);
~standardizer.fitTransform(~raw, ~standardized);
~mds.fitTransform(~standardized, ~reduced, 2, FluidMDS.euclidean, action:{
	~reduced.dump{|x| 100.do{|i|
		~reducedarray.add(x["data"][i.asString])
     }}});
)

//Visualise the 2D projection of our original 12D data
(
d = ~reducedarray.flatten(1).unlace.deepCollect(1, { |x| x.normalize});
// d = [20.collect{1.0.rand}, 20.collect{1.0.rand}];
w = Window("scatter", Rect(128, 64, 200, 200));
w.drawFunc = {
    Pen.use {
        d[0].size.do{|i|
            var x = (d[0][i]*200);
            var y = (d[1][i]*200);
            var r = Rect(x,y,5,5);
            Pen.fillColor = Color.blue;
            Pen.fillOval(r);
        }
    }
};
w.refresh;
w.front;
)

::