From 67b8970cde0bd69c8696380a2538d3ef1644db1d Mon Sep 17 00:00:00 2001
From: jsiegle <joshs@alleninstitute.org>
Date: Mon, 15 Sep 2014 14:14:17 -0700
Subject: [PATCH] Temporarily remove PCA jobs for debugging purposes
---
Source/Processors/SpikeSortBoxes.cpp | 68 ++++++++++++++++------------
1 file changed, 40 insertions(+), 28 deletions(-)
diff --git a/Source/Processors/SpikeSortBoxes.cpp b/Source/Processors/SpikeSortBoxes.cpp
index d399221d3..d917229d9 100644
--- a/Source/Processors/SpikeSortBoxes.cpp
+++ b/Source/Processors/SpikeSortBoxes.cpp
@@ -1758,25 +1758,37 @@ int PCAjob::svdcmp(float **a, int nRows, int nCols, float *w, float **v) {
l = i+1;
rv1[i] = scale*g;
g = s = scale = 0.0;
- if(i < nRows) {
- for(k = i; k < nRows; k++) scale += fabs(a[k][i]);
- if(scale) {
- for(k = i; k < nRows; k++) {
- a[k][i] /= scale;
- s += a[k][i] * a[k][i];
- }
- f = a[i][i];
- g = -SIGN(sqrt(s),f);
- h = f * g - s;
- a[i][i] = f - g;
- for(j = l; j < nCols; j++) {
- for(s = 0.0, k = i; k < nRows; k++) s += a[k][i] * a[k][j];
- f = s / h;
- for(k = i; k < nRows; k++) a[k][j] += f * a[k][i];
- }
- for(k = i; k < nRows; k++) a[k][i] *= scale;
+ if (i < nRows)
+ {
+ for(k = i; k < nRows; k++)
+ {
+ //std::cout << k << " " << i << std::endl;
+ scale += fabs(a[k][i]);
}
- }
+
+ if(scale)
+ {
+ for(k = i; k < nRows; k++)
+ {
+ a[k][i] /= scale;
+ s += a[k][i] * a[k][i];
+ }
+ f = a[i][i];
+ g = -SIGN(sqrt(s),f);
+ h = f * g - s;
+ a[i][i] = f - g;
+
+ for(j = l; j < nCols; j++)
+ {
+ for(s = 0.0, k = i; k < nRows; k++) s += a[k][i] * a[k][j];
+ f = s / h;
+ for(k = i; k < nRows; k++) a[k][j] += f * a[k][i];
+ }
+
+ for(k = i; k < nRows; k++)
+ a[k][i] *= scale;
+ } // end if (scale)
+ } // end if (i < nRows)
w[i] = scale * g;
g = s = scale = 0.0;
if(i < nRows && i != nCols-1) {
@@ -2033,8 +2045,6 @@ void PCAjob::computeSVD()
svdcmp(cov, dim, dim, sigvalues, eigvec);
-
-
std::vector<float> sig;
sig.resize(dim);
for (int k = 0; k < dim; k++)
@@ -2042,19 +2052,18 @@ void PCAjob::computeSVD()
std::vector<int> sortind = sort_indexes(sig);
- //
-
- for (int k=0;k<dim;k++)
+ for (int k = 0; k < dim; k++)
{
pc1[k] = eigvec[k][sortind[0]];
pc2[k] = eigvec[k][sortind[1]];
}
// project samples to find the display range
- float min1=1e10,min2=1e10,max1=-1e10,max2=-1e10;
- for (int j=0;j<spikes.size();j++)
+ float min1 = 1e10, min2 = 1e10, max1 = -1e10, max2 = -1e10;
+
+ for (int j = 0; j < spikes.size(); j++)
{
float sum1 = 0, sum2=0;
- for (int k=0;k<dim;k++)
+ for (int k = 0; k < dim; k++)
{
SpikeObject spike = spikes[j];
sum1 += spikeDataIndexToMicrovolts(&spike,k) * pc1[k];
@@ -2109,8 +2118,11 @@ void PCAcomputingThread::run()
// 1. Compute Covariance matrix
// 2. Apply SVD on covariance matrix
// 3. Extract the two principal components corresponding to the largest singular values
- J.computeCov();
- J.computeSVD();
+
+ // Take these out for now:
+ //J.computeCov();
+ //J.computeSVD();
+
// 4. Report to the spike sorting electrode that PCA is finished
*(J.reportDone) = true;
}
--
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