/**
* *********************************************************************
*
* <p>Synopsis [ ]
*
* <p>*********************************************************************
*/
public static void simulateHistogramREU(Gate g, GateLibrary gate_library, Args options) {
if (g.is_unvisited()) {
g.set_unvisited(false);
ArrayList<Gate> children = g.getChildren();
for (Gate child : children) {
if (child.is_unvisited()) {
simulateHistogramREU(child, gate_library, options);
}
}
// initialize
g.get_histogram_reus().clear();
for (int i = 0; i < g.get_logics().size(); ++i) { // rows in truth table
g.get_histogram_reus().add(new double[g.get_histogram_bins().get_NBINS()]);
for (int j = 0; j < g.get_histogram_bins().get_NBINS(); ++j) {
g.get_histogram_reus().get(i)[j] = 0.0;
}
}
if (g.Type == GateType.OUTPUT_OR || g.Type == GateType.OUTPUT) {
g.set_histogram_reus(GateUtil.getSumOfGateInputHistograms(g, gate_library, options));
} else if (g.Type == GateType.AND) {
g.set_histogram_reus(GateUtil.getANDOfGateInputHistograms(g));
} else if (g.Type == GateType.NOT || g.Type == GateType.NOR) {
// 2. For each row: for each bin: for each output bin: add normalizeToValue
ArrayList<double[]> input_convreus =
GateUtil.getSumOfGateInputHistograms(g, gate_library, options);
g.set_in_histogram_reus(input_convreus);
for (int i = 0; i < input_convreus.size(); ++i) {
/*if(Args.dontcare_rows.contains(i)) {
for(int bin=0; bin< g.get_histogram_reus().get(i).length; ++bin) {
g.get_histogram_reus().get(i)[bin] = 0.0;
}
continue;
}*/
double[] convhist = input_convreus.get(i);
for (int bin = 0; bin < g.get_histogram_bins().get_NBINS(); ++bin) {
double fractional_counts = convhist[bin];
double[] xslice = g.get_xfer_hist().get_xfer_interp().get(bin);
for (int xslice_bin = 0;
xslice_bin < g.get_histogram_bins().get_NBINS();
++xslice_bin) {
g.get_histogram_reus().get(i)[xslice_bin] += xslice[xslice_bin] * fractional_counts;
}
}
}
}
// evaluateGateHistogramOverlap(g); //to compute gate scores
}
}
@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;
}