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[lightning.git] / pca.go

diff --git a/pca.go b/pca.go
index b23838d771060d9f0eb4168ba8380b2f1ff16f2a..bebd6765b7f06517a7e4d4131b94553c1703b4b3 100644 (file)
--- a/pca.go
+++ b/pca.go
@@ -109,7 +109,7 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
                        Name:        "lightning pca-go",
                        Client:      arvados.NewClientFromEnv(),
                        ProjectUUID: *projectUUID,
-                       RAM:         432000000000,
+                       RAM:         100000000000, // maybe 10x input size?
                        VCPUs:       2,
                        Priority:    *priority,
                }
@@ -155,20 +155,27 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
                log.Printf("recode one-hot: %d rows, %d cols", rows, cols)
                data, cols = recodeOnehot(data, cols)
        }
-       log.Printf("running fit+transform: %d rows, %d cols", rows, cols)
-       pca, err := nlp.NewPCA(*components).FitTransform(array2matrix(rows, cols, data).T())
+       cgs = nil
+
+       log.Printf("creating matrix backed by array: %d rows, %d cols", rows, cols)
+       mtx := array2matrix(rows, cols, data).T()
+
+       log.Print("fitting")
+       transformer := nlp.NewPCA(*components)
+       transformer.Fit(mtx)
+       log.Printf("transforming")
+       mtx, err = transformer.Transform(mtx)
        if err != nil {
                return 1
        }
+       mtx = mtx.T()
 
-       log.Print("transposing result")
-       pca = pca.T()
-       rows, cols = pca.Dims()
+       rows, cols = mtx.Dims()
        log.Printf("copying result to numpy output array: %d rows, %d cols", rows, cols)
        out := make([]float64, rows*cols)
        for i := 0; i < rows; i++ {
                for j := 0; j < cols; j++ {
-                       out[i*cols+j] = pca.At(i, j)
+                       out[i*cols+j] = mtx.At(i, j)
                }
        }