Merge pull request #18 from CIDARLAB/casestudy/n10matrix

Added a matrix for N=10

Author: PrashantVaidyanathan

fpSelection/caseStudies/fpbase/seed0rank0matrix.csv

@@ -0,0 +1,11 @@
+,T-Sapphire,mKelly2,Sirius,miRFP670,mEmerald,mKeima,iFP1.4,mKalama1,miRFP720,TagRFP-T
+Violet (B),1.0,0.0,0.007986949899912821,0.0,0.2115173622032521,0.011320250946328055,0.0,0.4612716063942493,0.0,1.6676958783427712E-4
+Yel/Grn (A),0.0,0.28179631708403724,0.0,0.00397105824329659,1.6425520158325137E-4,0.0,0.0,0.0,0.0,1.0
+UV (A),2.899210231862116E-4,0.0,1.0,0.0,0.0,0.0,0.0,0.03670770245967755,0.0,0.0
+Red (B),0.0,0.04517925054167844,0.0,1.0,2.9081738741205827E-5,0.0,0.0,0.0,0.0,0.0
+Blue (A),0.04347776852771244,0.0,0.0,0.0,1.0,0.00343073882440439,0.0,0.0,0.0,6.911925243532591E-4
+Violet (C),0.03203228505500069,0.0,0.0,0.0,0.007380918915115408,1.0,0.0,0.0022710094477892562,0.0,0.028282340251470327
+Violet (E),0.0,0.0,0.0,0.0,0.0,0.08368808121466456,1.0,0.0,0.0,8.473114863450691E-4
+Violet (A),0.0153367566964738,0.0,0.05805469436684404,0.0,4.4308893155085334E-4,0.0,0.0,1.0,0.0,0.0
+Red (C),0.0,0.01809664328957377,0.0,0.8788937597835339,1.5521921148430897E-6,0.0,1.0,0.0,0.7989515699583776,0.0
+Yel/Grn (C),0.0,0.014742151183734653,0.0,0.0,4.0192899288262585E-4,0.0,0.0,0.0,0.0,1.0

fpSelection/caseStudies/fpbase/seed0rank0matrixAnalysis.csv

@@ -0,0 +1,11 @@
+,T-Sapphire,mKelly2,Sirius,miRFP670,mEmerald,mKeima,iFP1.4,mKalama1,miRFP720,TagRFP-T,Total Bleed-through as % of signal
+Violet (B),1,0,0.00798695,0,0.211517362,0.011320251,0,0.461271606,0,1.67E-04,0.692262939
+Yel/Grn (A),0,0.281796317,0,0.003971058,1.64E-04,0,0,0,0,1,3.56333725
+UV (A),2.90E-04,0,1,0,0,0,0,0.036707702,0,0,3.70E-02
+Red (B),0,0.045179251,0,1,2.91E-05,0,0,0,0,0,4.52E-02
+Blue (A),0.043477769,0,0,0,1,0.003430739,0,0,0,6.91E-04,0.0475997
+Violet (C),0.032032285,0,0,0,0.007380919,1,0,0.002271009,0,0.02828234,0.069966554
+Violet (E),0,0,0,0,0,0.083688081,1,0,0,8.47E-04,0.084535393
+Violet (A),0.015336757,0,0.058054694,0,4.43E-04,0,0,1,0,0,0.07383454
+Red (C),0,0.018096643,0,0.87889376,1.55E-06,0,1,0,0.79895157,0,2.374351621
+Yel/Grn (C),0,0.014742151,0,0,4.02E-04,0,0,0,0,1,0.01514408

fpSelection/src/test/java/org/cidarlab/fpSelection/FPbaseTest.java

@@ -65,18 +65,32 @@ public void testFPbase()  throws IOException, InterruptedException{
     }
 
     @Test
-    public void testIterationCount(){
-        double temp = 1000000;
-        double rate = 0.001;
+    public void testSelectionMatrix() throws IOException, InterruptedException{
+        String resfp = basefp + "fpbase" + Utilities.getSeparater() + "results_seed0.csv";
+        List<String[]> lines = Utilities.getCSVFileContentAsList(resfp);
+
+        Cytometer harvardCytoflex = fpFortessaParse.parse(harvardCytoFlexfp, false);
+        Map<String, Fluorophore> fpmap = fpSpectraParse.parse(spectrafp);
+        List<SelectionInfo> selection = TestUtilities.getConfiguration(lines.get(0),3,fpmap,harvardCytoflex);
+
+        TestUtilities.printConfigSignals(selection,basefp + "fpbase" + Utilities.getSeparater() + "seed0rank0matrix.csv");
+    }
 
-        int count = 0;
 
+    private static int getIterationCount(double temp, double rate){
+        int count = 0;
         while(temp > 1){
             count++;
             temp *= (1 - rate);
         }
-        Assert.assertEquals(count,13809);
+        return count;
 
+    }
+    @Test
+    public void testIterationCount(){        
+        Assert.assertEquals(getIterationCount(1000000,0.001),13809);
+        Assert.assertEquals(getIterationCount(10000,0.001),9206);
+        
     }
 
     @Test

fpSelection/src/test/java/org/cidarlab/fpSelection/TestUtilities.java

@@ -54,7 +54,92 @@ public static String toString(List<SelectionInfo> selection) {
         //line += snr.getSignalNoiseList().get(maps.get(key)).getKey() + "," + snr.getSignalNoiseList().get(maps.get(key)).getValue();
         return line;
     }
-    
+   
+
+    public static Laser getLaser(Cytometer c, String lname) {
+        for (Laser l : c.lasers) {
+            if (l.getName().equals(lname)) {
+                return l;
+            }
+        }
+        System.out.println("This shouldn't happen");
+        return null;
+    }
+
+    public static Detector getDetector(Laser l, String dname) {
+        for (Detector d : l.detectors) {
+            if (d.identifier.equals(dname)) {
+                return d;
+            }
+        }
+        System.out.println("This shouldn't happen");
+        return null;
+    }
+
+    public static List<SelectionInfo> getConfiguration(String[] row, int features, Map<String, Fluorophore> fpmap, Cytometer c) {
+        int n = row.length / features;
+        List<SelectionInfo> config = new ArrayList<SelectionInfo>();
+        for (int i = 0; i < row.length-1; i += features) {
+            Fluorophore fp = fpmap.get(row[i]);
+            Laser l = getLaser(c, row[i + 1]);
+            Detector d = getDetector(l, row[i + 2]);
+            SelectionInfo si = new SelectionInfo();
+            si.setSelectedFluorophore(fp);
+            si.setSelectedLaser(l);
+            si.setSelectedDetector(d);
+            config.add(si);
+        }
+        
+        return config;
+    }
+
+    private static List<Double> normalize(List<Double> vals) {
+        double max = vals.get(0);
+        for (Double d : vals) {
+            if (d > max) {
+                max = d;
+            }
+        }
+        List<Double> norm = new ArrayList<Double>();
+        for (Double d : vals) {
+            if (max != 0)
+                norm.add(d / max);
+            else
+                norm.add(d);
+        }
+        return norm;
+    }
+
+    public static void printConfigSignals(List<SelectionInfo> config, String filefp) {
+
+        List<String> lines = new ArrayList<String>();
+
+        List<Fluorophore> fps = new ArrayList<Fluorophore>();
+        String header = "";
+        for (SelectionInfo si : config) {
+            fps.add(si.getSelectedFluorophore());
+            //header += ("," + si.getSelectedLaser().getName() + " (" + si.getSelectedDetector().identifier + ")");
+            header += ("," + si.getSelectedFluorophore().name);
+        }
+        lines.add(header);
+
+        for (int i = 0; i < config.size(); i++) {
+            SelectionInfo si = config.get(i);
+            String configline = si.getSelectedLaser().getName() + " (" + si.getSelectedDetector().identifier + ")";
+
+            List<Double> sigs = new ArrayList<Double>();
+            for (Fluorophore fp : fps) {
+                sigs.add(fp.express(si.getSelectedLaser(), si.getSelectedDetector()));
+            }
+            for (Double d : normalize(sigs)) {
+                configline += ("," + d);
+            }
+            lines.add(configline);
+        }
+
+        Utilities.writeToFile(filefp, lines);
+
+    }
 
     //Get Random set of fluorophores - Seeded
     private static List<Fluorophore> getRandomFluorophores(int n, List<Fluorophore> fluorophores,ThreadLocal<Random> threadrandom){