[chronojump] extrema was missing on RDotNet

[Xavier de Blas <xaviblas src gnome org>]

commit 2656249341c13042991f8300f40f1e81b7298e19
Author: Xavier de Blas <xaviblas gmail com>
Date:   Mon Mar 10 17:21:02 2014 +0100

    extrema was missing on RDotNet

 .../howto-bootloader-and-firmware.txt              |    2 +-
 encoder/Makefile.am                                |    3 +-
 encoder/util.R                                     |   74 ++++++++++++++++++++
 src/constants.cs                                   |    1 +
 src/gui/encoder.cs                                 |    3 +
 src/utilEncoder.cs                                 |    5 ++
 6 files changed, 86 insertions(+), 2 deletions(-)
---
diff --git a/chronopic-firmware/howto-bootloader-and-firmware.txt 
b/chronopic-firmware/howto-bootloader-and-firmware.txt
index d6e7cee..8202167 100644
--- a/chronopic-firmware/howto-bootloader-and-firmware.txt
+++ b/chronopic-firmware/howto-bootloader-and-firmware.txt
@@ -51,7 +51,7 @@ sembla que es grava amb 3F32
 2.A encoder 20MHz grabar firmware:
 ----------------------------------
 
-Cal que el click estigui posat a 20
+Cal que el clock estigui posat a 20
 
 per 20MHz cal el pydownloader-wx,pero no va pq necessita python 2.6
 anem a agafar el pydownloader de la web (sense wx) i compilar-lo
diff --git a/encoder/Makefile.am b/encoder/Makefile.am
index d05d6f7..927f37b 100644
--- a/encoder/Makefile.am
+++ b/encoder/Makefile.am
@@ -2,4 +2,5 @@ encoderdatadir = @datadir@/@PACKAGE@/encoder
 
 dist_encoderdata_DATA = pyserial_pyper.py \
             graph.R \
-            inertia-momentum.R
+            inertia-momentum.R \
+            util.R
diff --git a/encoder/util.R b/encoder/util.R
new file mode 100644
index 0000000..2fa0c1e
--- /dev/null
+++ b/encoder/util.R
@@ -0,0 +1,74 @@
+#extrema function is part of R EMD package
+#It's included here to save time, because 'library("EMD")' is quite time consuming
+
+extrema <- function(y, ndata = length(y), ndatam1 = ndata - 1) {
+
+       minindex <- maxindex <- NULL; nextreme <- 0; cross <- NULL; ncross <- 0 
+
+       z1 <- sign(diff(y))
+       index1 <- seq(1, ndatam1)[z1 != 0]; z1 <- z1[z1 != 0]  
+
+       if (!(is.null(index1) || all(z1==1) || all(z1==-1))) {
+
+               index1 <- index1[c(z1[-length(z1)] != z1[-1], FALSE)] + 1 
+               z1 <- z1[c(z1[-length(z1)] != z1[-1], FALSE)]  
+
+               nextreme <- length(index1)
+
+               if(nextreme >= 2)
+                       for(i in 1:(nextreme-1)) {
+                               tmpindex <- index1[i]:(index1[i+1]-1)
+                               if(z1[i] > 0) {
+                                       tmpindex <- tmpindex[y[index1[i]] == y[tmpindex]]
+                                       maxindex <- rbind(maxindex, c(min(tmpindex), max(tmpindex)))
+                               } else {
+                                       tmpindex <- tmpindex[y[index1[i]] == y[tmpindex]]
+                                       minindex <- rbind(minindex, c(min(tmpindex), max(tmpindex)))
+                               }     
+                       } 
+
+               tmpindex <- index1[nextreme]:ndatam1  
+               if(z1[nextreme] > 0) {
+                       tmpindex <- tmpindex[y[index1[nextreme]] == y[tmpindex]]
+                       maxindex <- rbind(maxindex, c(min(tmpindex), max(tmpindex)))
+               } else {
+                       tmpindex <- tmpindex[y[index1[nextreme]] == y[tmpindex]]
+                       minindex <- rbind(minindex, c(min(tmpindex), max(tmpindex)))
+               }  
+
+               ### Finding the index of zero crossing  
+
+               if (!(all(sign(y) >= 0) || all(sign(y) <= 0) || all(sign(y) == 0))) {
+                       index1 <- c(1, index1)
+                       for (i in 1:nextreme) {
+                               if (y[index1[i]] == 0) {
+                                       tmp <- c(index1[i]:index1[i+1])[y[index1[i]:index1[i+1]] == 0]
+                                       cross <- rbind(cross, c(min(tmp), max(tmp)))                 
+                               } else
+                                       if (y[index1[i]] * y[index1[i+1]] < 0) {
+                                               tmp <- min(c(index1[i]:index1[i+1])[y[index1[i]] * 
y[index1[i]:index1[i+1]] <= 0])
+                                               if (y[tmp] == 0) {
+                                                       tmp <- c(tmp:index1[i+1])[y[tmp:index1[i+1]] == 0]
+                                                       cross <- rbind(cross, c(min(tmp), max(tmp))) 
+                                               } else 
+                                                       cross <- rbind(cross, c(tmp-1, tmp)) 
+                                       }
+                       }
+                       #if (y[ndata] == 0) {
+                       #    tmp <- c(index1[nextreme+1]:ndata)[y[index1[nextreme+1]:ndata] == 0]
+                       #    cross <- rbind(cross, c(min(tmp), max(tmp)))         
+                       #} else
+                       if (any(y[index1[nextreme+1]] * y[index1[nextreme+1]:ndata] <= 0)) {
+                               tmp <- min(c(index1[nextreme+1]:ndata)[y[index1[nextreme+1]] * 
y[index1[nextreme+1]:ndata] <= 0])
+                               if (y[tmp] == 0) {
+                                       tmp <- c(tmp:ndata)[y[tmp:ndata] == 0]
+                                       cross <- rbind(cross, c(min(tmp), max(tmp))) 
+                               } else
+                                       cross <- rbind(cross, c(tmp-1, tmp))
+                       }
+                       ncross <- nrow(cross)        
+               }
+       } 
+
+       list(minindex=minindex, maxindex=maxindex, nextreme=nextreme, cross=cross, ncross=ncross)
+}    
diff --git a/src/constants.cs b/src/constants.cs
index 71c907f..a1918d6 100644
--- a/src/constants.cs
+++ b/src/constants.cs
@@ -615,6 +615,7 @@ public class Constants
        public static string EncoderScriptCaptureWindows = "pyserial_pyper_windows.exe";
        public static string EncoderScriptGraph = "graph.R";
        public static string EncoderScriptInertiaMomentum = "inertia-momentum.R";
+       public static string EncoderScriptUtilR = "util.R";
        //no longer used:
        //public static string EncoderScriptGraphCall = 
                //"/home/xavier/informatica/progs_meus/chronojump/chronojump/encoder/call_graph.py";
diff --git a/src/gui/encoder.cs b/src/gui/encoder.cs
index 469cde9..14130fc 100644
--- a/src/gui/encoder.cs
+++ b/src/gui/encoder.cs
@@ -1804,6 +1804,9 @@ public partial class ChronoJumpWindow
                }
                */
 
+               //load extrema method copied from EMD package
+               rengine.Evaluate("source('" + UtilEncoder.GetEncoderScriptUtilR() + "')");
+
                try {
                        // .NET Framework array to R vector.
                        NumericVector group1 = rengine.CreateNumericVector(new double[] { 30.02, 29.99, 
30.11, 29.97, 30.01, 29.99 });
diff --git a/src/utilEncoder.cs b/src/utilEncoder.cs
index 0c26d89..2fbfa55 100644
--- a/src/utilEncoder.cs
+++ b/src/utilEncoder.cs
@@ -166,6 +166,11 @@ public class UtilEncoder
                                Util.GetDataDir(), "encoder", Constants.EncoderScriptInertiaMomentum);
        }
        
+       public static string GetEncoderScriptUtilR() {
+               return System.IO.Path.Combine(
+                               Util.GetDataDir(), "encoder", Constants.EncoderScriptUtilR);
+       }
+       
        
        /********** end of encoder paths ************/