[ifcsoft] 8 new revisions pushed by kyle.tha...@gmail.com on 2011-05-31 19:01 GMT
ifc...@googlecode.com
Revision: 498e656cda03
Author: kthayer
Date: Thu May 26 13:45:16 2011
Log: Remove extension from data set name.
http://code.google.com/p/ifcsoft/source/detail?r=498e656cda03
Revision: 1438077f1a22
Author: kthayer
Date: Fri May 27 13:54:45 2011
Log: Data Set viewer wasn't handling synchronized data sets properly.
http://code.google.com/p/ifcsoft/source/detail?r=1438077f1a22
Revision: 49d51e27911b
Author: kthayer
Date: Tue May 31 11:54:02 2011
Log: Merge
http://code.google.com/p/ifcsoft/source/detail?r=49d51e27911b
Revision: f12feb8a4898
Author: sjabba2@10D_BIOS036
Date: Thu May 26 08:20:43 2011
Log: UnionData overrides the "findstats()" command in DataSet.
http://code.google.com/p/ifcsoft/source/detail?r=f12feb8a4898
Revision: 0d8684402c79
Author: kthayer
Date: Tue May 31 11:55:02 2011
Log: Merge
http://code.google.com/p/ifcsoft/source/detail?r=0d8684402c79
Revision: 00d65e205dbe
Author: AABoyles
Date: Mon May 30 19:16:24 2011
Log: Changed Displayed text in Calculate SOM -> Advanced Options
from "Clas...
http://code.google.com/p/ifcsoft/source/detail?r=00d65e205dbe
Revision: 0144e99219e6
Author: AABoyles
Date: Mon May 30 20:41:15 2011
Log: Changed tile text from "Density Map" to "Hit Histogram". Also
Updated...
http://code.google.com/p/ifcsoft/source/detail?r=0144e99219e6
Revision: f19985eec44a
Author: kthayer
Date: Tue May 31 11:58:57 2011
Log: Merge
http://code.google.com/p/ifcsoft/source/detail?r=f19985eec44a
==============================================================================
Revision: 498e656cda03
Author: kthayer
Date: Thu May 26 13:45:16 2011
Log: Remove extension from data set name.
http://code.google.com/p/ifcsoft/source/detail?r=498e656cda03
Modified:
/src/ifcSoft/model/dataSet/RawData.java
=======================================
--- /src/ifcSoft/model/dataSet/RawData.java Mon May 23 15:32:41 2011
+++ /src/ifcSoft/model/dataSet/RawData.java Thu May 26 13:45:16 2011
@@ -80,6 +80,9 @@
name = filename;
}
}
+ if(name.endsWith(".csv") || name.endsWith(".fcs")){
+ name = name.substring(0, name.length()-4);
+ }
}
/**
==============================================================================
Revision: 1438077f1a22
Author: kthayer
Date: Fri May 27 13:54:45 2011
Log: Data Set viewer wasn't handling synchronized data sets properly.
http://code.google.com/p/ifcsoft/source/detail?r=1438077f1a22
Modified:
/src/ifcSoft/view/DataSetViewer.fx
/src/ifcSoft/view/synchDataSets/SynchDataTable.fx
=======================================
--- /src/ifcSoft/view/DataSetViewer.fx Wed Apr 20 08:26:49 2011
+++ /src/ifcSoft/view/DataSetViewer.fx Fri May 27 13:54:45 2011
@@ -102,7 +102,7 @@
return null;
}
- var finaldsp:DataSetProxy =
mainMediator.getDataSet(dataSetSelect.getDataSets());
+ var finaldsp:DataSetProxy =
mainMediator.getDataSet(dataSetSelect.getDataSets(),
dataSetSelect.getSynchColumns());
if(finaldsp == null){
println("Error in data set combination");
return null;
=======================================
--- /src/ifcSoft/view/synchDataSets/SynchDataTable.fx Mon May 16 15:24:37
2011
+++ /src/ifcSoft/view/synchDataSets/SynchDataTable.fx Fri May 27 13:54:45
2011
@@ -292,9 +292,6 @@
return true;
}
- /*override function getName():String{
- return name;
- }*/
function attemptAlign(){
for(colName in initialColNames){
==============================================================================
Revision: 49d51e27911b
Author: kthayer
Date: Tue May 31 11:54:02 2011
Log: Merge
http://code.google.com/p/ifcsoft/source/detail?r=49d51e27911b
Modified:
/src/ifcSoft/model/dataSet/RawData.java
=======================================
--- /src/ifcSoft/model/dataSet/RawData.java Thu May 26 13:45:16 2011
+++ /src/ifcSoft/model/dataSet/RawData.java Tue May 31 11:54:02 2011
@@ -26,12 +26,9 @@
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
-import java.io.Reader;
-import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.util.LinkedList;
-import java.util.StringTokenizer;
/**
*
@@ -361,23 +358,12 @@
length = 0;
int dataRows = 0;
+ String st[];
while(line != null){
- StringTokenizer st = new StringTokenizer(line, ",");
-
+ st = line.split(",");
//if the column labels aren't set, then this is the first read
if(columnLabels == null){
- columnLabels = new String[st.countTokens()];
- for(int i = 0; i < columnLabels.length; i++){
- columnLabels[i] = st.nextToken();
- if(columnLabels[i].contentEquals("F0") ||
- columnLabels[i].contentEquals("\"F0\"")){
- columnLabels[i] = "SSC-A";
- }
- if(columnLabels[i].contentEquals("F1") ||
- columnLabels[i].contentEquals("\"F1\"") ){
- columnLabels[i] = "FSC-A";
- }
- }
+ columnLabels = st;
if(columnLabels[0].equalsIgnoreCase("name") ||
columnLabels[0].equalsIgnoreCase("file")){
hasNames = true;
String temp[] = new String[columnLabels.length-1];
@@ -390,11 +376,11 @@
}else{//the column labels have been read
float[] thisrow = new float[columnLabels.length];
boolean didLoadRow = true;
- String name = null;
+ String pointName = null;
if(hasNames){
- name = st.nextToken();
- }
- if(st.countTokens() != columnLabels.length){
+ pointName = st[0];
+ }
+ if(st.length != columnLabels.length){
System.out.println("Error reading FCS, columns in row"
+dataRows+" didn't match");
didLoadRow = false;
@@ -402,7 +388,7 @@
try{
for(int i = 0; i < columnLabels.length; i++){
- thisrow[i] = Float.parseFloat(st.nextToken());
+ thisrow[i] = Float.parseFloat(st[i]);
}
}catch(Exception e){
didLoadRow = false;
@@ -413,7 +399,7 @@
if(didLoadRow){
tempData.add(thisrow);
if(hasNames){
- tempNames.add(name);
+ tempNames.add(pointName);
}
dataRows++;
loadProgress++;
@@ -541,19 +527,4 @@
return (String[]) newLabels.toArray(new String[0]);
}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-}
+}
==============================================================================
Revision: f12feb8a4898
Author: sjabba2@10D_BIOS036
Date: Thu May 26 08:20:43 2011
Log: UnionData overrides the "findstats()" command in DataSet.
http://code.google.com/p/ifcsoft/source/detail?r=f12feb8a4898
Modified:
/src/ifcSoft/model/dataSet/DataSet.java
/src/ifcSoft/model/dataSet/UnionData.java
=======================================
--- /src/ifcSoft/model/dataSet/DataSet.java Wed Apr 20 08:26:49 2011
+++ /src/ifcSoft/model/dataSet/DataSet.java Thu May 26 08:20:43 2011
@@ -233,7 +233,6 @@
* Find the mins, maxes and means.
*/
protected void findstats() {
- //TODO: This should be overridden in UnionData since that is easier to
compute there.
for(int k = 0; k < getDimensions(); k++){
mins[k] = Float.MAX_VALUE;
maxes[k] = Float.MIN_VALUE;
=======================================
--- /src/ifcSoft/model/dataSet/UnionData.java Mon May 16 15:24:37 2011
+++ /src/ifcSoft/model/dataSet/UnionData.java Thu May 26 08:20:43 2011
@@ -89,33 +89,9 @@
means = new double[dimensions];
//just find min min, max max and do a weighted sum for mean
- for(int k = 0; k < getDimensions(); k++){
- mins[k] = Float.MAX_VALUE;
- maxes[k] = Float.MIN_VALUE;
- means[k] = 0;
- }
-
- for(int i = 0; i < parentSets.size(); i++){
- DataSet ds = parentSets.get(i).getData();
- for(int k = 0; k < getDimensions(); k++){
- if(ds.getMin(k) < mins[k]){
- mins[k] = ds.getMin(k);
- }
- if(ds.getMax(k) > maxes[k]){
- maxes[k] =ds.getMax(k);
- }
- means[k] +=ds.getMean(k) * (ds.length() *1.0 / length); //add the
mean that that set contributes
- }
- //if(parentSets.get(i))
- }
-
-
- /*for(int k = 0; k < getDimensions(); k++){
- System.out.println("dim");
- System.out.println("\tmin of dim " + k+ " is "+mins[k]);
- System.out.println("\tmean of dim " + k+ " is "+means[k]);
- System.out.println("\tmax of dim " + k+ " is "+maxes[k]);
- }*/
+ findstats();
+
+
}
@@ -266,6 +242,29 @@
}
return ret;
}
+
+ @Override
+ protected void findstats() {
+ for(int k = 0; k < getDimensions(); k++){
+ mins[k] = Float.MAX_VALUE;
+ maxes[k] = Float.MIN_VALUE;
+ means[k] = 0; //for now we'll use it to keep sums
+ }
+
+ for(int i = 0; i < parentSets.size(); i++){
+ DataSet currentset = parentSets.get(i).getData();
+ for(int k = 0; k < getDimensions(); k++){
+ means[k]+= (currentset.length()/(double) this.length)*
currentset.means[k];
+
+ if(currentset.mins[k] < mins[k]){
+ mins[k] = currentset.mins[k];
+ }
+ if(currentset.maxes[k] > maxes[k]){
+ maxes[k] = currentset.maxes[k];
+ }
+ }
+ }
+ }
/**
*
==============================================================================
Revision: 0d8684402c79
Author: kthayer
Date: Tue May 31 11:55:02 2011
Log: Merge
http://code.google.com/p/ifcsoft/source/detail?r=0d8684402c79
==============================================================================
Revision: 00d65e205dbe
Author: AABoyles
Date: Mon May 30 19:16:24 2011
Log: Changed Displayed text in Calculate SOM -> Advanced Options
from "Classic SOM" to "Incremental SOM"
http://code.google.com/p/ifcsoft/source/detail?r=00d65e205dbe
Modified:
/src/ifcSoft/model/som/SOMSettings.java
=======================================
--- /src/ifcSoft/model/som/SOMSettings.java Thu Apr 28 09:12:49 2011
+++ /src/ifcSoft/model/som/SOMSettings.java Mon May 30 19:16:24 2011
@@ -36,12 +36,11 @@
public static final String PCACOMP = "Principal Components";
public static final String PCACOMPDECAY = "Principal Components
(decaying comp. weight)";
-
public static final String LINEARINIT = "Linear Initialization";
public static final String RANDOMINIT = "Random Initialization";
public static final String FILEINIT = "Load SOM file";
- public static final String CLASSICSOM = "Classic SOM";
+ public static final String CLASSICSOM = "Incremental SOM";
public static final String BATCHSOM = "Batch SOM";
public DataSetProxy datasetproxy;
==============================================================================
Revision: 0144e99219e6
Author: AABoyles
Date: Mon May 30 20:41:15 2011
Log: Changed tile text from "Density Map" to "Hit Histogram". Also
Updated Comments to reflect. Did not refactor code (i.e. change variable
names).
http://code.google.com/p/ifcsoft/source/detail?r=0144e99219e6
Modified:
/src/ifcSoft/model/som/SOMRetrieveFns.java
/src/ifcSoft/view/som/SOMMediator.java
/src/ifcSoft/view/som/SOMmaps.fx
=======================================
--- /src/ifcSoft/model/som/SOMRetrieveFns.java Fri Feb 11 10:49:36 2011
+++ /src/ifcSoft/model/som/SOMRetrieveFns.java Mon May 30 20:41:15 2011
@@ -315,7 +315,7 @@
/**
- * Return the total Density Map.
+ * Return the total Hit Histogram (Density Map).
* @return
*/
static public synchronized int[][] getDensityMap(SOM som){
=======================================
--- /src/ifcSoft/view/som/SOMMediator.java Tue May 24 12:18:54 2011
+++ /src/ifcSoft/view/som/SOMMediator.java Mon May 30 20:41:15 2011
@@ -536,7 +536,7 @@
}
/**
- * Get the overall Density Map image.
+ * Get the overall Hit Histogram (Density Map) image.
* @return
*/
public BufferedImage getDenstiyMapImg(){
@@ -583,7 +583,7 @@
}
/**
- * Get the Density Map of a combination of subsets and other sets.
+ * Get the Hit Histogram (Density Map) of a combination of subsets and
other sets.
* @param selectedSubSets
* @param selectedDataSets
* @return
=======================================
--- /src/ifcSoft/view/som/SOMmaps.fx Tue May 24 12:18:54 2011
+++ /src/ifcSoft/view/som/SOMmaps.fx Mon May 30 20:41:15 2011
@@ -498,7 +498,7 @@
somMaps:this
densityMap: 0
img: somHolder.blankmap
- name: "Density Map"
+ name: "Hit Histogram"
min: 0
max: 1
};
==============================================================================
Revision: f19985eec44a
Author: kthayer
Date: Tue May 31 11:58:57 2011
Log: Merge
http://code.google.com/p/ifcsoft/source/detail?r=f19985eec44a