/**
* score = 1 - penalty of histogram overlap score all ON:OFF pairs and report the worst score
*
* <p>overlap penalty: for each bin, compute geometric mean of two ON:OFF histogram values, add
* add bin penalty to total penalty alternative is to penalize the min of the two ON:OFF histogram
* values
*/
public static void evaluateGateHistogramOverlap(Gate g) {
ArrayList<Double> scores_conv_overlap = new ArrayList<Double>();
ArrayList<Integer> ons = new ArrayList<Integer>();
ArrayList<Integer> offs = new ArrayList<Integer>();
// get ons and offs
for (int i = 0; i < g.get_logics().size(); ++i) {
if (g.get_logics().get(i) == 1) {
ons.add(i);
} else if (g.get_logics().get(i) == 0) {
offs.add(i);
}
}
// compute scores of all on-off pairs
for (int on = 0; on < ons.size(); ++on) {
for (int off = 0; off < offs.size(); ++off) {
// if(!Args.dontcare_rows.contains(on) && !Args.dontcare_rows.contains(off)) {
double median_on =
Math.pow(
Math.E,
HistogramUtil.median(
g.get_histogram_reus().get(ons.get(on)), g.get_histogram_bins()));
double median_off =
Math.pow(
Math.E,
HistogramUtil.median(
g.get_histogram_reus().get(offs.get(off)), g.get_histogram_bins()));
double score = 1 - median_off / median_on;
double overlap_penalty = 0.0;
// if ON histogram is lower than OFF histogram, broken circuit
if (score < 0) {
scores_conv_overlap.add(0.0);
continue;
} else {
double[] on_norm = HistogramUtil.normalize(g.get_histogram_reus().get(ons.get(on)));
double[] off_norm = HistogramUtil.normalize(g.get_histogram_reus().get(offs.get(off)));
// penalty is sum of geometric means for each bin
// total counts have been normalized to 1
for (int bin = 0; bin < g.get_histogram_bins().get_NBINS(); ++bin) {
overlap_penalty += Math.sqrt(on_norm[bin] * off_norm[bin]); // geometric mean
// overlap_penalty += Math.min( on_norm[bin] , off_norm[bin]); //min of the two bin
// counts
}
}
score = 1 - overlap_penalty;
scores_conv_overlap.add(score);
// }
}
}
Collections.sort(scores_conv_overlap);
g.get_scores().set_conv_overlap(scores_conv_overlap.get(0)); // worst
}
@Override
public ArrayList<Map> getObjects() {
ArrayList<Map> objects = new ArrayList<>();
ArrayList<Double> REU_TITR = new ArrayList<Double>();
REU_TITR.add(0.018806664);
REU_TITR.add(0.028666538);
REU_TITR.add(0.051722065);
REU_TITR.add(0.14837545);
REU_TITR.add(0.261559417);
REU_TITR.add(0.447725869);
REU_TITR.add(0.687508549);
REU_TITR.add(1.131011516);
REU_TITR.add(1.891798237);
REU_TITR.add(3.27479675);
REU_TITR.add(4.549973162);
REU_TITR.add(8.687342616);
HistogramBins hbins = new HistogramBins();
hbins.init();
GateLibrary gate_library = new GateLibrary(0, 0);
ArrayList<String> gate_names = new ArrayList<String>();
gate_names.add("an0_AmeR");
gate_names.add("js2_AmtR");
gate_names.add("js2_BM3R1");
gate_names.add("js2_BetI");
gate_names.add("js2_HlyIIR");
gate_names.add("js2_IcaRA");
gate_names.add("js2_LitR");
gate_names.add("js2_PhlF");
gate_names.add("js2_SrpR");
gate_names.add("js_QacR");
gate_names.add("js2_LitR");
for (String gate_name : gate_names) {
Gate g = new Gate();
g.Name = gate_name;
gate_library.get_GATES_BY_NAME().put(g.Name, g);
}
for (Gate g : gate_library.get_GATES_BY_NAME().values()) {
String gate_name = g.Name;
String rootpath = collection_writer.getRootPath();
String filepath = rootpath + "/resources/data/nor_gates/cytometry_cb1/";
HistogramUtil.getTransferFunctionHistogramTitrations(
gate_name, gate_library, hbins, filepath);
LinkedHashMap obj = new LinkedHashMap();
obj.put("collection", "gate_cytometry"); // tag
obj.put("gate_name", gate_name);
ArrayList<LinkedHashMap> titrations = new ArrayList<LinkedHashMap>();
for (int i = 0; i < REU_TITR.size(); ++i) {
Double inREU = REU_TITR.get(i);
ArrayList<Double> out_reu_bins = new ArrayList<Double>();
ArrayList<Double> out_reu_counts = new ArrayList<Double>();
for (int j = 0; j < hbins.get_NBINS(); ++j) {
double[] normalized = HistogramUtil.normalize(g.get_xfer_hist().get_xfer_binned().get(i));
out_reu_bins.add(Math.pow(10, hbins.get_LOG_BIN_CENTERS()[j]));
out_reu_counts.add(normalized[j]);
}
LinkedHashMap titration = new LinkedHashMap();
titration.put("maps_to_variable", "x");
titration.put("input", inREU);
titration.put("output_bins", out_reu_bins);
titration.put("output_counts", out_reu_counts);
titrations.add(titration);
}
obj.put("cytometry_data", titrations);
objects.add(obj);
// org.cellocad.ucf_writers_tetr.ConstraintFileWriter.JSONPrettyPrint(obj,
// "resources/UCF/Eco1C1G1T1.gate_cytometry.json", true);
}
return objects;
}
