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Sample source code for the agents in C#
1. Sample code of Experiment Design Agent
Design Method Interface
public interface IdesignMethods
{
experiment sample{get;set;}
List<experiment> workingexps{get;set;}
bool finish {get;set;}
int iteration_count{get;set;}
string name{ get; set; }
void method();
}
Simplex Search Method
using
using
using
using
System;
System.Collections.Generic;
System.Text;
utilities;
namespace design_agent
{
class simplex_alg : IdesignMethods
{
//******************************
private double accurate_index = 0.0005;
private double reflection_rate=1;
private double expansion_rate=2;
private double contraction_rate=-0.5;
private double reduction_rate=0.5;
//******************************
//******INTERFACE**********
public List<experiment> workingexps { get; set; }
public int iteration_count { get; set; }
public experiment sample { get; set; }
public bool finish { get; set; }
public string name { get; set; }
public double currentobj { get; set; }
//*************************
private
private
private
private
experiment[] simplex;
bool firstrun = true;
int inputnum;
experiment gravity_exp;
public simplex_alg()
{
finish=false;
workingexps = new List<experiment>();
name="simplex";
}
private void init_exps()
{
Random rand = new Random();
inputnum = 0;
foreach (parameter p in sample.exp_settting.paras)
{
if (p.isInput)
inputnum++;
}
simplex = new experiment[inputnum+1];
experiment e = new experiment();
for (int i = 0; i < inputnum+1; i++)
{
e = new experiment();
e =sample.clone();
e.ID = Guid.NewGuid();
e.name="simplex_"+iteration_count;
foreach (parameter x in e.exp_settting.paras)
{
if (x.isInput)
{
int value=rand.Next(0,100);
x.setvalue((double)value / 100 * (x.max - x.min) + x.min);
}
else
x.value = -1;
}
e.done = false;
workingexps.Add(e);
simplex[i] = e;
}
}
private void stepalg()
{
for (int i = 0; i < inputnum + 1;i++ )
{
experiment temp = new experiment();
temp = ifready_exp(simplex[i]);
if (temp == null)
{
return;
}
simplex[i] = temp;
}
if (this.ss() <= accurate_index)
{
finish = true;
List<experiment> finallist=new List<experiment>();
for(int i=0;i<=inputnum;i++)
{
finallist.Add(simplex[i]);
}
util.exportExperiments(finallist, "final simplex", "simplex result");
return;
}
Console.WriteLine(iteration_count+"
this.ss());
simplex=util.sort_exparray(simplex);
gravity_exp = this.gravity();
experiment r = this.reflection();
experiment c = this.contraction();
experiment e = this.expansion();
experiment x1=simplex[0];
Current best: {0};
ss={1}", simplex[0].obj_value,
experiment xn=simplex[inputnum-1];
experiment tempr = this.ifready_exp(r);
if (tempr!=null)
{
r = tempr;
if (r.obj_value >= x1.obj_value && r.obj_value <= xn.obj_value)
{
Console.WriteLine("
reflection");
simplex[inputnum] = r;
iteration_count++;
stepalg();
}
else if (r.obj_value < x1.obj_value)
{
experiment tempe = this.ifready_exp(e);
if (tempe!=null)
{
e = tempe;
if (e.obj_value > r.obj_value)
{
Console.WriteLine("
espansion");
simplex[inputnum]=e;
iteration_count++;
stepalg();
}
else
{
Console.WriteLine("
reflection");
simplex[inputnum]=r;
iteration_count++;
stepalg();
}
}
else
{
//Console.WriteLine("
espansion not finish.");
return;
}
}
else
{
experiment tempc = this.ifready_exp(c);
if (tempc!=null)
{
c = tempc;
if (c.obj_value < simplex[inputnum].obj_value)
{
Console.WriteLine("
constraction");
simplex[inputnum] = c;
iteration_count++;
stepalg();
}
else
{
Console.WriteLine("
reduction");
this.reduction();
iteration_count++;
stepalg();
}
}
else
{
//Console.WriteLine("constraction not finish.");
return;
}
}
}
else
{
//Console.WriteLine("reflection not finish.");
return;
}
}
private bool ifready(experiment e)
{
bool add = false;
foreach (experiment s in workingexps)
{
if (s.compare_ignore_result(e))
{
if (s.done)
{
e = s;
return true;
}
}
else add = true;
}
if (add) workingexps.Add(e);
return false;
}
private experiment ifready_exp(experiment e)
{
bool add = false;
foreach (experiment s in workingexps)
{
if (s.compare_ignore_result(e))
{
if (s.done)
{
return s;
}
}
else add = true;
}
if (add) workingexps.Add(e);
return null;
}
private experiment reflection()
{
experiment e = sample.clone();
e.ID = Guid.NewGuid();
e.name = "simplex_" + iteration_count;
List<parameter> x0 = gravity_exp.exp_settting.paras;
List<parameter> xnplus = simplex [inputnum].exp_settting.paras;
for (int i = 0; i < e.exp_settting.paras.Count; i++)
{
e.exp_settting.paras[i].setvalue(x0[i].value+reflection_rate*(x0[i].valuexnplus[i].value));
}
return e;
}
private experiment contraction()
{
experiment e = sample.clone();
e.ID = Guid.NewGuid();
e.name = "simplex_" + iteration_count;
List<parameter> x0 = gravity_exp.exp_settting.paras;
List<parameter> xnplus = simplex[inputnum+1-1].exp_settting.paras;
for (int i = 0; i < e.exp_settting.paras.Count; i++)
{
e.exp_settting.paras[i].setvalue(x0[i].value + contraction_rate * (x0[i].value xnplus[i].value));
}
return e;
}
private experiment expansion()
{
experiment e = sample.clone();
e.ID = Guid.NewGuid();
e.name = "simplex_" + iteration_count;
List<parameter> x0 = gravity_exp.exp_settting.paras;
List<parameter> xnplus = simplex[inputnum+1-1].exp_settting.paras;
for (int i = 0; i < e.exp_settting.paras.Count; i++)
{
e.exp_settting.paras[i].setvalue(x0[i].value + expansion_rate * (x0[i].value xnplus[i].value));
}
return e;
}
private void reduction()
{
for (int j = 1; j < inputnum+1; j++ )
{
for (int i = 0; i < simplex[j].exp_settting.paras.Count; i++)
{
if(simplex[j].exp_settting.paras[i].isInput)
simplex[j].exp_settting.paras[i].setvalue(simplex[j].exp_settting.paras[i].value + reduction_rate *
(simplex[j].exp_settting.paras[i].value - simplex[0].exp_settting.paras[i].value));
}
simplex[j].ID = Guid.NewGuid();
}
}
private experiment gravity()
{
experiment g = sample.clone();
g.name = "simplex_" + iteration_count;
foreach(parameter p in g.exp_settting.paras)
{
if (p.isInput) p.value = 0;
}
for(int j=0; j<inputnum; j++)
{
experiment e = simplex[j];
for (int i = 0; i < inputnum; i++)
{
if(g.exp_settting.paras[i].isInput)
g.exp_settting.paras[i].value = g.exp_settting.paras[i].value +
e.exp_settting.paras[i].value;
}
}
foreach (parameter p in g.exp_settting.paras)
{
if (p.isInput) p.setvalue(p.value / (inputnum));
}
return g;
}
public void method()
{
if (firstrun)
{
init_exps();
firstrun = false;
return;
}
stepalg ();
}
private double ss()
{
double s = 0;
double avg = 0;
double sum = 0;
foreach (experiment x in simplex)
{
double r = x.obj_value;
sum = sum + r;
}
avg = sum / (inputnum+1);
foreach (experiment x in simplex)
{
double r = x.obj_value;
s = s + (r - avg) * (r - avg);
}
return Math.Pow(s,0.5);
}
}
}
Artificial Neural Network Method
using
using
using
using
using
using
using
using
System;
System.Collections.Generic;
System.Text;
NeuronDotNet.Core;
NeuronDotNet.Core.Backpropagation;
NeuronDotNet.Core.Initializers;
Util;
utilities;
namespace design_agent
{
class ann_alg : IdesignMethods
{
//******INTERFACE**********
public List<experiment> workingexps { get; set; }
public int iteration_count { get; set; }
public experiment sample { get; set; }
public bool finish { get; set; }
public string name { get; set; }
public double currentobj { get; set; }
//*************************
List<experiment> ReadyToExcuteExps;
private bool firstrun = true;
private double accurate_index = 0.005;
private int numOfParameter = 0;
private int batchsize = 5;
//ann
private
private
private
private
private
private
private
private
private
List<experiment> testexps;
LinearLayer inputlayer;
SigmoidLayer hiddenlayer;
SigmoidLayer outputlayer;
BackpropagationNetwork network;
int neuronCount = 10;
double learningRate = 0.25;
int cycles = 1000;
TrainingSet trainingset;
public ann_alg()
{
foreach (parameter p in sample.exp_settting.paras)
{
if(p.isInput)
numOfParameter ++;
}
}
private void method()
{
if (firstrun)
{
init();
firstrun = false;
return;
}
annalg();
}
private void init()
{
Random rand = new Random();
experiment e = new experiment();
for (int i = 0; i < batchsize; i++)
{
e = new experiment();
e = sample.clone();
e.ID = Guid.NewGuid();
e.name = "ann_" + iteration_count;
foreach (parameter x in e.exp_settting.paras)
{
if (x.isInput)
{
int value = rand.Next(0, 100);
x.setvalue((double)value / 100 * (x.max - x.min) + x.min);
}
else
x.value = -1;
}
e.done = false;
workingexps.Add(e);
}
inputlayer = new LinearLayer(numOfParameter);
hiddenlayer = new SigmoidLayer(neuronCount);
new BackpropagationConnector(inputlayer, hiddenlayer).Initializer = new RandomFunction(0d,
0.3d);
new BackpropagationConnector(hiddenlayer, outputlayer).Initializer = new RandomFunction(0d,
0.3d);
network = new BackpropagationNetwork(inputlayer, outputlayer);
network.SetLearningRate(learningRate);
trainingset = new TrainingSet(numOfParameter, 1);
}
private void annalg()
{
for (int i = 0; i < batchsize; i++)
{
experiment temp = new experiment();
temp = ifready_exp(testexps[i]);
if (temp == null)
{
return;
}
testexps[i] = temp;
}
testfinish();
if (finish) return;
testexps = new List<experiment>();
for (int i = 0; i < workingexps.Count; i++)
{
experiment temp = new experiment();
temp = ifready_exp(testexps[i]);
if (temp == null)
{
return;
}
workingexps[i] = temp;
double[] input = new double[numOfParameter];
int j = 0;
foreach (parameter p in workingexps[i].exp_settting.paras)
{
if (p.isInput)
{
input[j] = p.value / p.max;
j++;
}
}
double[] output={workingexps[i].calobj()};
trainingset.Add(new TrainingSample(input, output));
}
network.Learn(trainingset, cycles);
Random rand = new Random();
experiment e = new experiment();
for (int i = 0; i < batchsize; i++)
{
e = new experiment();
e = sample.clone();
e.ID = Guid.NewGuid();
e.name = "ann_" + iteration_count;
foreach (parameter x in e.exp_settting.paras)
{
if (x.isInput)
{
int value = rand.Next(0, 100);
x.setvalue((double)value / 100 * (x.max - x.min) + x.min);
}
else
x.value = -1;
}
e.done = false;
workingexps.Add(e);
testexps.Add(e);
}
}
private void testfinish()
{
double ss = 0;
for (int i = 0; i < batchsize;i++ )
{
double[] input=new double[numOfParameter];
int j = 0;
foreach (parameter p in testexps[i].exp_settting.paras)
{
if (p.isInput)
{
input[j] = p.value / p.max;
j++;
}
}
double[] output;
output = network.Run(input);
testexps[i].calobj();
ss = ss + (output[0] - testexps[i].obj_value) * (output[0] - testexps[i].obj_value);
}
ss = ss / batchsize;
if (ss <= accurate_index)
finish = true;
}
private experiment ifready_exp(experiment e)
{
bool add = false;
foreach (experiment s in workingexps)
{
if (s.compare_ignore_result(e))
{
if (s.done)
{
return s;
}
}
else add = true;
}
if (add) workingexps.Add(e);
return null;
}
}
}
2. Sample code for Execution Agent
Experimentation Interface
public interface IExperimentation
{
List<experiment> exps { set; get; }
experimentSetting standardset { set; get; }
plate[] exp_plates { get; set; }
void start();
}
Script Composing code
public Script precip_script(Script scr, layout ly, operations op)
{
//gettips
string trans = "";
bool[] tips = new bool[8];
for (int i = 0; i < 8; i++)
{
tips[i] = false;
}
for (int i = 0; i < experiments.Length; i++)
{
tips[i] = true;
}
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
//explocation[] currentlocs = this.allocate();
//add salt
double[] saltcon = new double[experiments.Length];
double[] volumn = new double[12];
string[] wells = new string[experiments.Length];
for (int i = 0; i < experiments.Length; i++)
{
foreach (parameter x in experiments[i].exp_settting.paras)
{
if (x.name.Contains("salt"))
saltcon[i] = x.value;
}
volumn[i] = saltcon[i] * totalvolumn / salt_init_con;
wells[i] = currentlocs[i].wells;
}
trans = op.aspirate(tips, "ZZ Water", volumn, salt_grid, salt_site, salt_location);
scr.AddScriptLine(trans);
trans = op.dispense(tips, "ZZ Water", volumn, currentlocs[0].grid, currentlocs[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
//change tips
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
//add buffer
buffer bf = new buffer();
double min = 0;
double max = 0;
foreach (parameter x in standardset.paras)
{
if (x.name == "ph")
{
min = x.min;
max = x.max;
}
}
bf.conn(buffertype, max, min);
double[] ph = new double[experiments.Length];
double[] ratio = new double[experiments.Length];
double[] chemicalA = new double[12];
double[] chemicalB = new double[12];
for (int i = 0; i < experiments.Length; i++)
{
foreach (parameter x in experiments[i].exp_settting.paras)
{
if (x.name.Contains( "ph"))
{
ph[i] = x.value;
}
}
ratio[i] = bf.getRatio(initAcon, ph[i]);
chemicalA[i] = totalvolumn * bufferstrength / initAcon * (1 - (1 / (ratio[i] + 1)));
chemicalB[i] = totalvolumn * bufferstrength / initBcon * (1 / (ratio[i] + 1));
}
//add chemicalA
trans = op.aspirate(tips, "ZZ Water", chemicalA, bufferA_grid, bufferA_site,
bufferA_location);
scr.AddScriptLine(trans);
trans = op.dispense(tips, "ZZ Water", chemicalA, currentlocs[0].grid, currentlocs[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
//change tips
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
//add chemicalB
trans = op.aspirate(tips, "ZZ Water", chemicalB, bufferB_grid, bufferB_site,
bufferB_location);
scr.AddScriptLine(trans);
trans = op.dispense(tips, "ZZ Water", chemicalB, currentlocs[0].grid, currentlocs[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
//change tips
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
//add sample
double[] tempsamplevolume = new double[12];
for (int i = 0; i < experiments.Length; i++)
{
tempsamplevolume[i] = samplevolume;
}
trans = op.aspirate(tips, "ZZ Water", tempsamplevolume, samplegrid, samplesite,
samplelocation);
scr.AddScriptLine(trans);
trans = op.dispense(tips, "ZZ Water", tempsamplevolume, currentlocs[0].grid,
currentlocs[0].site, op.wellselection_96(wells));
scr.AddScriptLine(trans);
//change tips
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
//add Water
double[] Watervolume = new double[12];
for (int i = 0; i < experiments.Length; i++)
{
Watervolume[i] = totalvolumn - samplevolume - chemicalA[i] - chemicalB[i] - volumn[i];
}
trans = op.aspirate(tips, "ZZ Water", Watervolume, Watergrid, Watersite, Waterlocation);
scr.AddScriptLine(trans);
trans = op.dispense(tips, "ZZ Water", Watervolume, currentlocs[0].grid,
currentlocs[0].site, op.wellselection_96(wells));
scr.AddScriptLine(trans);
//change tips
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
//mix
double[] mixvolume = new double[12];
for (int i = 0; i < experiments.Length; i++)
{
mixvolume[i] = totalvolumn / 4;
}
trans = op.mix(tips, "ZZ Water", mixvolume, currentlocs[0].grid, currentlocs[0].site,
op.wellselection_96(wells), 3);
scr.AddScriptLine(trans);
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
//transfer explabware to reader for shaking
scr.AddScriptLine("FACTS(\"ReaderNETwork\",\"ReaderNETwork_Open\",\"\",\"0\",\"\");");
trans = op.transfer(currentlocs[0].grid, 45, currentlocs[0].site + 1, 1, "MP 3Pos",
"Infinite 200", "ZZ 96 Well Microplate tianyi");
scr.AddScriptLine(trans);
scr.AddScriptLine("FACTS(\"ReaderNETwork\",\"ReaderNETwork_Close\",\"\",\"0\",\"\");");
//shake
shaker s = new shaker();
scr.AddScriptLine(s.scr);
//transfer plateback
scr.AddScriptLine("FACTS(\"ReaderNETwork\",\"ReaderNETwork_Open\",\"\",\"0\",\"\");");
trans = op.transfer(45, currentlocs[0].grid, 1, currentlocs[0].site + 1, "Infinite 200",
"MP 3Pos", "ZZ 96 Well Microplate tianyi");
scr.AddScriptLine(trans);
scr.AddScriptLine("FACTS(\"ReaderNETwork\",\"ReaderNETwork_Close\",\"\",\"0\",\"\");");
//dilute solution 30 fold
if (first)
{
filterlocs = currentlocs;
first = false;
}
this.allocate();
//change tips
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
//first
for (int i = 0; i < experiments.Length; i++)
{
volumn[i] = totalvolumn / 6;
wells[i] = filterlocs[i].wells;
}
trans = op.aspirate(tips, "ZZ Water", volumn, filterlocs[0].grid, filterlocs[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
for (int i = 0; i < experiments.Length; i++)
{
wells[i] = currentlocs[i].wells;
}
trans = op.dispense(tips, "ZZ Water", volumn, currentlocs[0].grid, currentlocs[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
for (int i = 0; i < experiments.Length; i++)
{
Watervolume[i] = totalvolumn * 5 / 6;
}
trans = op.aspirate(tips, "ZZ Water", Watervolume, Watergrid, Watersite, Waterlocation);
scr.AddScriptLine(trans);
trans = op.dispense(tips, "ZZ Water", Watervolume, currentlocs[0].grid,
currentlocs[0].site, op.wellselection_96(wells));
scr.AddScriptLine(trans);
explocation[] filterlocs_2 = currentlocs;
this.allocate();
//second
for (int i = 0; i < experiments.Length; i++)
{
volumn[i] = totalvolumn / 6;
wells[i] = filterlocs_2[i].wells;
}
trans = op.aspirate(tips, "ZZ Water", volumn, filterlocs_2[0].grid, filterlocs_2[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
for (int i = 0; i < experiments.Length; i++)
{
wells[i] = currentlocs[i].wells;
}
trans = op.dispense(tips, "ZZ Water", volumn, currentlocs[0].grid, currentlocs[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
for (int i = 0; i < experiments.Length; i++)
{
Watervolume[i] = totalvolumn * 5 / 6;
}
trans = op.aspirate(tips, "ZZ Water", Watervolume, Watergrid, Watersite, Waterlocation);
scr.AddScriptLine(trans);
trans = op.dispense(tips, "ZZ Water", Watervolume, currentlocs[0].grid,
currentlocs[0].site, op.wellselection_96(wells));
scr.AddScriptLine(trans);
//transfer liquid to filter plate
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
trans = op.getditi2(tips, "DiTi 1000ul");
scr.AddScriptLine(trans);
for (int i = 0; i < experiments.Length; i++)
{
volumn[i] = totalvolumn * 0.9;
wells[i] = currentlocs[i].wells;
}
trans = op.aspirate(tips, "ZZ Water", volumn, currentlocs[0].grid, currentlocs[0].site,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
for (int i = 0; i < experiments.Length; i++)
{
wells[i] = filterlocs[i].wells;
}
trans = op.dispense(tips, "ZZ Water", volumn, filtergrid, filtersite,
op.wellselection_96(wells));
scr.AddScriptLine(trans);
trans = op.drop_tips(tips, ly.getditiwastegrid(), ly.getditiwastesite(), 70, 10, 0);
scr.AddScriptLine(trans);
//transfer to vaccum pump
trans = op.transfer(filtergrid, 36, filtersite + 1, 4, "MP 3Pos", "Te-VacS SC", "ZZ 96
Well Microplate tianyi");
scr.AddScriptLine(trans);
//do filtration
VacS v = new VacS();
scr.AddScriptLine(v.setpressdiff(700));
scr.AddScriptLine(v.applyvaccumfront(700));
scr = v.setduration(60, scr);
scr.AddScriptLine(v.ventfront());
scr.AddScriptLine(v.deactive());
//move explabware back
trans = op.transfer(36, filtergrid, 4, filtersite + 1, "Te-VacS SC", "MP 3Pos", "ZZ 96
Well Microplate tianyi");
scr.AddScriptLine(trans);
//remove VacS cap
scr = op.moveVaScap(scr, 36);
explabwaresite = currentlocs[0].site;
explabwaregrid = currentlocs[0].grid;
filterlocs = currentlocs;
return scr;
}
3. Sample code for assay agent
Sample code for controlling platereader
public void fixed_uvab(string label, int numofreads, int settletime, int wavelength)
{
if (m_oHelper.HasAbsorbanceFixed())
{
// ---------------------------------------// ATTENTION: For script creators
// The ID´s must be unique and ascending!!!
// ---------------------------------------int nInnerID = 1000;
bool bDeviceIsM1000 =
(m_oServer.ConnectedReader.Information.GetInstrumentName().Equals("S3"));
assay_agent.platereaderUtil.Absorbance oAbs = new
assay_agent.platereaderUtil.Absorbance(m_oHelper, nInnerID, bDeviceIsM1000);
oAbs.composescript(label, numofreads, settletime, wavelength);
// Get the measurement reading object
MeasurementReading oMeasurementReading = oAbs.MeasurementReading;
int nID = 0;
// Build measurement script file
TecanFile oFile = Helper.CreateTecanFile();
TecanMeasurement oMeasurement = Helper.CreateTecanMeasurement(++nID);
MeasurementManualCycle oCycle = Helper.CreateManualCycle(++nID);
String sPlateName = m_oPlate.FilenameWithoutExtension;
CyclePlate oPlate = Helper.CreatePlate(sPlateName, ++nID);
string sRange = m_sAvailablePlateRange;
PlateRange oRange = Helper.CreateRange(sRange, ++nID);
MeasurementAbsorbance oAbsMeas = new MeasurementAbsorbance();
oAbsMeas.Name = "ABS";
oAbsMeas.ID = ++nID;
Well oWell = Helper.CreateWell(++nID);
oWell.Actions.Add(oMeasurementReading);
oAbsMeas.Actions.Add(oWell);
oPlate.Actions.Add(oRange);
oRange.Actions.Add(oAbsMeas);
oCycle.Actions.Add(oPlate);
oMeasurement.Actions.Add(oCycle);
oFile.DocumentContent = oMeasurement;
m_oCurrentMeasurementFile = oFile;
string filepath = utilities.util.getfilepath("abs.xml");
FileHandling.Save(oFile, filepath);
// Convert the Tecan file object to a string
XmlSupport objXML = new XmlSupport();
XmlNode objNode = oFile.GetXmlNode(objXML);
objXML.AddXmlNode(objNode);
m_sScript = objXML.XmlDocumentAsString();
}
}
Sample code for HPLC peaks clustering
class hplc
{
class CSVparser
{
const double maxRET = 10;
const double minRET = 5;
const int init_cluster_num = 10;
const bool reduce_cluster = true;
//for calibration curve
List<string[]> parseCSV(string path)
{
List<string[]> parsedData = new List<string[]>();
try
{
using (StreamReader readFile = new StreamReader(path))
{
string line;
string[] row;
while ((line = readFile.ReadLine()) != null)
{
row = line.Split(',');
parsedData.Add(row);
}
}
}
catch (Exception e)
{
Console.Write(e.ToString());
Console.Read();
}
return parsedData;
}
//int[0]: RetTime
//int[1]: Area
//int[2]: Area(%)
List<double[]> retrievedata()
{
string aPath = Environment.CurrentDirectory;
aPath = aPath + "\\hplc";
DirectoryInfo dir = new DirectoryInfo(aPath);
DirectoryInfo[] subdir = dir.GetDirectories();
List<double[]> hplcdata = new List<double[]>();
int index = 0;
foreach (DirectoryInfo d in subdir)
{
String temp = aPath + "\\" + d.Name + "\\REPORT02.CSV";
List<string[]> csvdata = this.parseCSV(temp);
String[] getid = d.Name.Split(new char[] { '.' });
index = int.Parse(getid[0].Substring(6));
//Console.WriteLine(d.Name+"
"+index);
foreach (string[] s in csvdata)
{
double[] data = new double[4];
data[0] = Double.Parse(s[1]);
data[1] = Double.Parse(s[4]);
data[2] = index;
data[3] = 0;
if (data[0] > minRET && data[0] < maxRET)
hplcdata.Add(data);
}
//index++;
}
return hplcdata;
}
//double[0] cluster center
//double[1] x
//double[2] c
public List<double[]> concentrations(double[] s)
{
List<double[]> hplcdata = this.retrievedata();
cluster_alg cluster = new cluster_alg(hplcdata, s);
return hplcdata;
}
public static int idforsearch;
private static bool getdatabyid(double[] hplcdata)
{
bool b = false;
if (hplcdata[2] == idforsearch)
{
}
return b;
}
}
class cluster_alg
{
int k;
List<double[]> data;
double[] centers;
double[] number;
public cluster_alg(int k1, List<double[]> data1, bool reduce)
{
this.k = k1;
this.data = data1;
data.TrimExcess();
centers = new double[k];
data.Sort
(
delegate(double[] a1, double[] a2)
{
return a1[0].CompareTo(a2[0]);
}
);
this.cluster_init();
double before = 99999;
double after = 0;
while (before != after)
{
before = sd(data);
this.cluster_main();
after = sd(data);
}
if (reduce)
{
for (int i = 0; i < 1000; i++)
{
optcluster();
before = 99999;
after = 0;
while (before != after)
{
before = sd(data);
this.cluster_main();
after = sd(data);
}
}
}
}
public cluster_alg(List<double[]> data1, double[] c)
{
this.k = c.Length;
this.data = data1;
data.TrimExcess();
centers = new double[k];
data.Sort
(
delegate(double[] a1, double[] a2)
{
return a1[0].CompareTo(a2[0]);
}
);
centers = c;
double before = 99999;
double after = 0;
while (before != after)
{
before = sd(data);
this.cluster_main();
after = sd(data);
}
}
void cluster_init()
{
Random r = new Random();
for (int i = 0; i < k; i++)
{
int index = (int)r.Next(data.Count / k * (i), data.Count / k * (i + 1));
double[] temp = data[index];
temp[3] = i;
centers[i] = temp[0];
}
}
void cluster_main()
{
for (int i = 0; i < data.Count; i++)
{
double[] aRecord = data[i];
double distance = 9999999999;
for (int j = 0; j < k; j++)
{
if (distance > (Math.Abs(centers[j] - aRecord[0])))
{
distance = Math.Abs(centers[j] - aRecord[0]);
aRecord[3] = j;
}
}
}
number = new double[k];
for (int j = 0; j < k; j++)
{
double[] sum = new double[k];
sum[j] = 0;
int n = 0;
for (int i = 0; i < data.Count; i++)
{
double[] aRecord = data[i];
if (aRecord[3] == j)
{
sum[j] = sum[j] + aRecord[0];
n++;
}
}
centers[j] = sum[j] / n;
number[j] = n;
}
}
double sd(List<double[]> sample)
{
double sdd = 0;
for (int i = 0; i < k; i++)
{
double temp = 0;
for (int j = 0; j < sample.Count; j++)
{
double[] aRecord = sample[j];
if ((int)aRecord[3] == i)
{
temp = temp + (centers[i] - aRecord[0]) * (centers[i] - aRecord[0]);
}
}
sdd = temp + sdd;
}
return sdd;
}
void optcluster()
{
List<double[]> centerinfo = new List<double[]>();
for (int i = 0; i < k; i++)
{
double[] temp = new double[2];
temp[0] = centers[i];
temp[1] = number[i];
centerinfo.Add(temp);
}
centerinfo.TrimExcess();
centerinfo.Sort(
delegate(double[] a1, double[] a2)
{
return (a2[1].CompareTo(a1[1]));
}
);
int count = 0;
int n = 0;
for (int i = 0; i < k; i++)
{
if (n < 0.8 * data.Count)
{
double[] aInfo = centerinfo[i];
n = n + (int)aInfo[1];
count = i + 1;
}
}
centers = new double[count];
for (int i = 0; i < count; i++)
{
double[] aInfo = centerinfo[i];
centers[i] = aInfo[0];
}
k = count;
number = new double[k];
}
}
4. Sample code for Coordinate Agent
Defining experiment
public class experiment
{
public Guid ID;
public double obj_value;
public string name;
public experimentSetting exp_settting;
public bool done;
public experiment clone()
{
experiment e = new experiment();
e.ID = this.ID;
e.name = this.name;
e.obj_value = this.obj_value; ;
e.exp_settting.obj_function = this.exp_settting.obj_function;
e.exp_settting.paras = new List<parameter>();
e.exp_settting.proteins = new List<protein>();
foreach (parameter p in this.exp_settting.paras)
{
parameter ap = new parameter();
ap.alias = p.alias;
ap.interval = p.interval;
ap.isInput = p.isInput;
ap.max = p.max;
ap.min = p.min;
ap.name = p.name;
ap.value = p.value;
e.exp_settting.paras.Add(ap);
}
foreach (protein p in this.exp_settting.proteins)
{
protein ap = new protein();
ap.name = p.name;
ap.retentiontime = p.retentiontime;
e.exp_settting.proteins.Add(ap);
}
return e;
}
public experiment clone(experiment e)
{
e = new experiment();
e.ID = this.ID;
e.name = this.name;
e.obj_value = this.obj_value; ;
e.exp_settting.obj_function = this.exp_settting.obj_function;
e.exp_settting.paras = new List<parameter>();
e.exp_settting.proteins = new List<protein>();
foreach (parameter p in this.exp_settting.paras)
{
parameter ap = new parameter();
ap.alias = p.alias;
ap.interval = p.interval;
ap.isInput = p.isInput;
ap.max = p.max;
ap.min = p.min;
ap.name = p.name;
ap.value = p.value;
e.exp_settting.paras.Add(ap);
}
foreach (protein p in this.exp_settting.proteins)
{
protein ap = new protein();
ap.name = p.name;
ap.retentiontime = p.retentiontime;
e.exp_settting.proteins.Add(ap);
}
return e;
}
public experiment ()
{
//ID=999999999;
obj_value=-9999999999;
exp_settting=new experimentSetting();
done=false;
ID = new Guid();
}
public XmlElement getXmlElement (XmlDocument temp)
{
if (this.done) this.obj_value=this.calobj();
XmlElement exp=temp.CreateElement("experiment");
exp.SetAttribute("ID", this.ID.ToString());
exp.SetAttribute("obj_value", this.obj_value.ToString());
exp.SetAttribute("name", this.name);
exp.SetAttribute("done", this.done.ToString());
exp.AppendChild(this.exp_settting.getXmlElement(temp));
return exp;
}
public bool compare(experiment e)
{
if (e.exp_settting.compare(this.exp_settting))
return true;
else
return false;
}
public bool compare_ignore_result(experiment e)
{
if(e.exp_settting.compare_ignore_result(this.exp_settting))
return true;
else
return false;
}
public double calobj ()
{
Assembly code=this.objclass();
Type tp=code.GetType("objcalculation.calobj");
MethodInfo mi=tp.GetMethod("cal");
double objvalue=(double)mi.Invoke(null,null);
this.obj_value = Math.Round(objvalue, 2);
return this.obj_value;
}
private string trans_objfunc()
{
string code = "using System;\n"+
"namespace objcalculation\n"+
"{\n"+
"public static class calobj \n"+
"{ \n";
code = code + "\n" +
"public static double cal() \n" +
"{\n" ;
foreach (parameter p in this.exp_settting.paras)
{
if (p.isInput)
{
code = code + "double " + p.alias +"="+ p.value +";\n";
}
}
code = code +
"return " + this.exp_settting.obj_function + ";\n" +
"}\n"+
"}\n"+
"}\n";
return code;
}
private Assembly objclass ()
{
CSharpCodeProvider provider = new CSharpCodeProvider ();
CompilerParameters ps = new CompilerParameters ();
ps.GenerateExecutable = false;
ps.GenerateInMemory = true;
StringBuilder classSource = new StringBuilder ();
classSource.Append (this.trans_objfunc ());
//Console.WriteLine (classSource.ToString ());
CompilerResults result = provider.CompileAssemblyFromSource (ps,
classSource.ToString ());
//Console.WriteLine(result.Errors.Count);
Assembly assembly = result.CompiledAssembly;
return assembly;
}
public void writetodatabase()
{
if (!this.done)
{
Console.WriteLine("Write experiment data failed! The experiment has not been
finished!");
return;
}
List<experiment> exps = new List<experiment>();
String conn_string = "Provider=Microsoft.Jet.OLEDB.4.0;Data
Source=|DataDirectory|\\tecan_database.mdb";
System.Data.OleDb.OleDbConnection dataCon = new System.Data.OleDb.OleDbConnection();
dataCon.ConnectionString = conn_string;
dataCon.Open();
String query_string;
OleDbCommand query=null;
OleDbDataReader reader;
//parameters
List<int> paraids = new List<int>();
List<double> values = new List<double>();
foreach (parameter p in this.exp_settting.paras)
{
query_string = "select * from [paras] where name='" + p.name + "'";
query = new OleDbCommand(query_string, dataCon);
reader = query.ExecuteReader();
if (reader.Read())
{
paraids.Add((int)reader.GetValue(0));
values.Add(p.value);
}
else
{
query_string = "insert into" +
"[paras] ([name], [max], [min], [interval],[isinput],[alias]) values (" +
"'" +
p.name + "', " +
p.max + ", " +
p.min + ", " +
p.interval + ", " +
p.isInput + ", '" +
p.alias + "')";
query = new OleDbCommand(query_string, dataCon);
query.ExecuteNonQuery();
query = new OleDbCommand("SELECT @@IDENTITY", dataCon);
reader = query.ExecuteReader();
reader.Read();
int id = (int)reader.GetValue(0);
paraids.Add(id);
values.Add(p.value);
}
}
//proteins
List<int> proids=new List<int>();
foreach (protein p in this.exp_settting.proteins)
{
//reader = new OleDbDataReader();
query_string = "select * from [protein] where name='" + p.name + "'";
query = new OleDbCommand(query_string, dataCon);
reader = query.ExecuteReader();
if (reader.Read())
{
proids.Add((int)reader.GetValue(0));
}
else
{
query_string = "insert into" +
"[protein] ([name], [retention]) values (" +
"'" +
p.name + "', " +
p.retentiontime + ")";
query = new OleDbCommand(query_string, dataCon);
query.ExecuteNonQuery();
query = new OleDbCommand("SELECT @@IDENTITY", dataCon);
reader = query.ExecuteReader();
reader.Read();
int id = (int)reader.GetValue(0);
proids.Add(id);
}
}
//exp-setting
int setid;
query_string = "select * from [exp_setting] where obj='" + this.exp_settting.obj_function
+ "'";
query = new OleDbCommand(query_string, dataCon);
reader = query.ExecuteReader();
if (reader.Read())
{
setid = (int)reader.GetValue(0);
}
else
{
query_string = "insert into" +
"[exp_setting] ([obj]) values (" +
"'" +
this.exp_settting.obj_function + "' " +
")";
query = new OleDbCommand(query_string, dataCon);
query.ExecuteNonQuery();
query = new OleDbCommand("SELECT @@IDENTITY", dataCon);
//reader = new OleDbDataReader();
reader = query.ExecuteReader();
reader.Read();
setid = (int)reader.GetValue(0);
//setting-protein
for (int i = 0; i < proids.Count; i++)
{
query_string = "insert into" +
"[setting-proteins] ([proid],[setid]) values (" +
proids[i] + "," +
setid +
")";
query = new OleDbCommand(query_string, dataCon);
query.ExecuteNonQuery();
}
}
//exp
query_string = "insert into" +
"[exp] ([name],[exp_setting_id],[obj_value]) values (" +
"'" + this.name + "', " +
setid + ", " +
this.calobj() +
")";
query = new OleDbCommand(query_string, dataCon);
query.ExecuteNonQuery();
query = new OleDbCommand("SELECT @@IDENTITY", dataCon);
reader = query.ExecuteReader();
reader.Read();
int expid = (int)reader.GetValue(0);
//para-exp
for (int i=0;i<paraids.Count;i++)
{
query_string = "insert into" +
"[para-exp] ([exp_id],[para_id],[value]) values (" +
expid + "," +
paraids[i] +","+
values[i] +
")";
query = new OleDbCommand(query_string, dataCon);
query.ExecuteNonQuery();
}
query.Dispose();
reader.Dispose();
dataCon.Dispose();
}
}
public class experimentSetting
{
public string obj_function;
public List<parameter> paras;
public List<protein> proteins;
public experimentSetting ()
{
paras=new List<parameter>();
proteins=new List<protein>();
}
public XmlElement getXmlElement (XmlDocument temp)
{
XmlElement setting=temp.CreateElement("setting");
foreach (parameter p in paras) {
setting.AppendChild (p.getXmlElement (temp));
}
foreach (protein p in proteins) {
setting.AppendChild (p.getXmlElement(temp));
}
setting.SetAttribute("obj_function", obj_function);
return setting;
}
public bool compare(experimentSetting es)
{
if (es.obj_function == this.obj_function && this.compare_paras(es.paras) &&
this.compare_proteins(es.proteins))
{
return true;
}
return false;
}
public bool compare_ignore_result(experimentSetting es)
{
if (es.obj_function == this.obj_function && this.compare_paras_ignore_result(es.paras) &&
this.compare_proteins(es.proteins))
{
return true;
}
return false;
}
public bool compare_paras(List<parameter> ps)
{
if (this.paras.Count == ps.Count)
{
foreach (parameter pa in ps)
{
bool a = false;
foreach (parameter pb in this.paras)
{
if (pa.compare(pb))
{
a = true;
break;
}
}
if (!a)
return false;
}
}
return true;
}
public bool compare_paras_ignore_result(List<parameter> ps)
{
if (this.paras.Count == ps.Count)
{
foreach (parameter pa in ps)
{
bool a = false;
foreach (parameter pb in this.paras)
{
if (pa.compare_ignore_result(pb))
{
a = true;
break;
}
}
if (!a)
return false;
}
}
return true;
}
public bool compare_proteins(List<protein> ps)
{
if (this.paras.Count == ps.Count)
{
foreach (protein pa in ps)
{
bool a = false;
foreach (protein pb in this.proteins)
{
if (pa.compare(pb))
{
a = true;
break;
}
}
if (!a)
return false;
}
}
return true;
}
}
public class parameter
{
public string name;
public double value;
public double max;
public double min;
public double interval;
public bool isInput;
public string alias;
public XmlElement getXmlElement(XmlDocument temp)
{
XmlElement para=temp.CreateElement("parameter");
para.SetAttribute("name",this.name);
para.SetAttribute("value", this.value.ToString());
para.SetAttribute("max", this.max.ToString());
para.SetAttribute("min", this.min.ToString());
para.SetAttribute("interval", this.interval.ToString());
para.SetAttribute("isInput", this.isInput.ToString());
para.SetAttribute("alias", this.alias);
return para;
}
public void setvalue(double v)
{
if (v >= this.max)
{
this.value = max;
return;
}
if (v <= this.min)
{
this.value = min;
return;
}
if (this.isInput)
{
double test = max;
while (test > v)
{
test = test - interval;
}
double left = v - test;
double right = test + interval - v;
if (left >= right)
{
this.value = test + interval;
}
else
{
this.value = test;
}
}
string delimStr = ".";
char[] delimiter = delimStr.ToCharArray();
string words = this.interval.ToString();
string[] split = null;
split = words.Split(delimiter);
this.value=Math.Round(this.value,split[1].Length);
}
public bool compare(parameter p)
{
bool b = false;
if (p.alias == this.alias
&& p.interval == this.interval
&& p.isInput == this.isInput
&& p.max == this.max
&& p.min == this.min
&& p.name == this.name
&& p.value == this.value)
b = true;
return b;
}
public bool compare_ignore_result(parameter p)
{
bool b = false;
if (p.alias == this.alias
&& p.interval == this.interval
&& p.isInput == this.isInput
&& p.max == this.max
&& p.min == this.min
&& p.name == this.name
&& !this.isInput)
b = true;
else if (p.alias == this.alias
&& p.interval == this.interval
&& p.isInput == this.isInput
&& p.max == this.max
&& p.min == this.min
&& p.name == this.name
&& Math.Abs(p.value-this.value)<this.interval)
return true;
return b;
}
}
public class protein
{
public string name;
public double retentiontime;
public XmlElement getXmlElement(XmlDocument temp)
{
XmlElement pro=temp.CreateElement("protein");
pro.SetAttribute("name",this.name);
pro.SetAttribute("retention_time", this.retentiontime.ToString());
return pro;
}
public bool compare(protein p)
{
bool b = false;
if (p.name == this.name && p.retentiontime == this.retentiontime)
b = true;
return b;
}
}
Defining platform layout
public class explocation
{
//public string labwarename;
public int grid;
public int site;
public string wells;
public bool used;
}
public class layout
{
public explocation[,] locs;
public class carrier_info
{
public int name;
public int grid;
public List<labware_info> labwares;
}
public class labware_info
{
public int name;
public int site;
public string nickname;
public bool ifexplocation;
}
public class exp_location
{
//public string name;
public int site;
public int grid;
}
public List<carrier_info> layoutlist;
private bool first = true;
public List<exp_location> explocs;
public void load_layout(int id)
{
String conn_string = "Provider=Microsoft.Jet.OLEDB.4.0;Data
Source=|DataDirectory|\\tecan_database.mdb";
System.Data.OleDb.OleDbConnection dataCon = new System.Data.OleDb.OleDbConnection();
dataCon.ConnectionString = conn_string;
dataCon.Open();
String query_string;
query_string = "select * from layout_tree where layout_id=" + id + " order by carrier,
carrier_grid";
OleDbCommand query = new OleDbCommand(query_string, dataCon);
OleDbDataAdapter adapter = new OleDbDataAdapter(query_string, dataCon);
OleDbDataReader reader = query.ExecuteReader();
carrier_info temp_carrier = new carrier_info();
int carrier_name = 0;
int carrier_grid = 0;
carrier_info aCarrier = new carrier_info();
layoutlist = new List<carrier_info>();
bool a = true;
while (reader.Read())
{
//print(reader.GetValue(0) + "
" + reader.GetValue(2));
if ((int)reader.GetValue(0) == carrier_name && (int)reader.GetValue(2) == carrier_grid)
{
labware_info aLabware = new labware_info();
aLabware.name = (int)reader.GetValue(1);
aLabware.site = (int)reader.GetValue(3);
aLabware.nickname = (string)reader.GetValue(5);
aLabware.ifexplocation = (bool)reader.GetBoolean(6);
aCarrier.labwares.Add(aLabware);
}
else
{
if (!a)
{
layoutlist.Add(aCarrier);
}
a = false;
aCarrier = new carrier_info();
aCarrier.labwares = new List<labware_info>();
aCarrier.name = (int)reader.GetValue(0);
carrier_name = (int)reader.GetValue(0);
aCarrier.grid = (int)reader.GetValue(2);
carrier_grid = (int)reader.GetValue(2);
labware_info aLabware = new labware_info();
aLabware.name = (int)reader.GetValue(1);
aLabware.site = (int)reader.GetValue(3);
aLabware.nickname = (string)reader.GetValue(5);
aLabware.ifexplocation = (bool)reader.GetBoolean(6);
aCarrier.labwares.Add(aLabware);
}
}
layoutlist.Add(aCarrier);
reader.Dispose();
query.Dispose();
adapter.Dispose();
dataCon.Close();
dataCon.Dispose();
}
public Script layout_script(Script scr)
{
explocs = new List<exp_location>();
String conn_string = "Provider=Microsoft.Jet.OLEDB.4.0;Data
Source=|DataDirectory|\\tecan_database.mdb";
System.Data.OleDb.OleDbConnection dataCon = new System.Data.OleDb.OleDbConnection();
dataCon.ConnectionString = conn_string;
dataCon.Open();
String query_string;
foreach (carrier_info x in layoutlist)
{
query_string = "select * from carrier where ID=" + x.name;
OleDbCommand query = new OleDbCommand(query_string, dataCon);
OleDbDataAdapter adapter = new OleDbDataAdapter(query_string, dataCon);
OleDbDataReader reader = query.ExecuteReader();
string name;
while (reader.Read())
{
name = (string)reader.GetValue(1);
scr.AddCarrier(name, x.grid);
}
//int i=0;
foreach (labware_info y in x.labwares)
{
query_string = "select * from labware where ID=" + y.name;
OleDbCommand query2 = new OleDbCommand(query_string, dataCon);
OleDbDataAdapter adapter2 = new OleDbDataAdapter(query_string, dataCon);
OleDbDataReader reader2 = query2.ExecuteReader();
string carriername = "";
while (reader2.Read())
{
carriername = (string)reader2.GetValue(1);
}
if (y.site != 0)
scr.AddLabware(carriername, x.grid, y.site, y.nickname);
//i++;
if (y.ifexplocation)
{
exp_location el = new exp_location();
el.site = y.site;
el.grid = x.grid;
explocs.Add(el);
}
query2.Dispose();
adapter2.Dispose();
reader2.Dispose();
}
query.Dispose();
adapter.Dispose();
reader.Dispose();
}
dataCon.Close();
dataCon.Dispose();
if (first)
{
locs = new explocation[explocs.Count, 96];
for (int i = 0; i < explocs.Count; i++)
{
for (int j = 0; j < 96; j++)
{
locs[i, j] = new explocation();
}
}
layout.exp_location[] templocs = explocs.ToArray();
for (int i = 0; i < explocs.Count; i++)
{
for (int j = 0; j < 96; j++)
{
locs[i, j].grid = templocs[i].grid;
locs[i, j].site = templocs[i].site;
locs[i, j].used = false;
locs[i, j].wells = transwellstring(j);
}
}
first = false;
}
return scr;
}
private string transwellstring(int well)
{
string wellstring = "";
int x = (int)well / 8;
int y = well - x * 8;
x = x + 1;
wellstring = Convert.ToChar(65 + y) + "" + x;
return wellstring;
}
public int getditiwastegrid()
{
int grid = 0;
foreach (layout.carrier_info x in layoutlist)
{
foreach (layout.labware_info y in x.labwares)
{
if (y.nickname == "diti_waste")
{
grid = x.grid;
}
}
}
return grid;
}
public int getditiwastesite()
{
int site = 0;
foreach (layout.carrier_info x in layoutlist)
{
foreach (layout.labware_info y in x.labwares)
{
if (y.nickname == "diti_waste")
{
site = y.site - 1;
}
}
}
return site;
}
public int getwastegrid()
{
int wastegrid = 0;
foreach (layout.carrier_info x in layoutlist)
{
foreach (layout.labware_info y in x.labwares)
{
if (y.nickname == "waste")
{
wastegrid = x.grid;
}
}
}
return wastegrid;
}
public int getwastesite()
{
int wastesite = 0;
foreach (layout.carrier_info x in layoutlist)
{
foreach (layout.labware_info y in x.labwares)
{
if (y.nickname == "waste")
{
wastesite = y.site - 1;
}
}
}
return wastesite;
}
public int getcleanergrid()
{
int cleanergrid = 0;
foreach (layout.carrier_info x in layoutlist)
{
foreach (layout.labware_info y in x.labwares)
{
if (y.nickname == "shallow")
{
cleanergrid = x.grid;
}
}
}
return cleanergrid;
}
public int getcleanersite()
{
int cleanersite = 0;
foreach (layout.carrier_info x in layoutlist)
{
foreach (layout.labware_info y in x.labwares)
{
if (y.nickname == "shallow")
{
cleanersite = y.site - 1;
}
}
}
return cleanersite;
}
}
Define buffer and related calculation
public class buffer
{
public class buffertype
{
public int id;
public int[] charge = new int[2];
public double[] K = new double[3];
public String[] type = new String[2];
}
List<buffertype> bufferResults = new List<buffertype>();
private double ratio;
public void conn(String perference, double phmax, double phmin)
{
String conn_string = "Provider=Microsoft.Jet.OLEDB.4.0;Data
Source=|DataDirectory|\\tecan_database.mdb";
//print(conn_string);
System.Data.OleDb.OleDbConnection dataCon = new System.Data.OleDb.OleDbConnection();
dataCon.ConnectionString = conn_string;
dataCon.Open();
String query_string;
if (perference != "N/A")
query_string = "select * from buffer_system where buffer_name='" + perference + "' and
maxpH>" + phmax + " and minpH<" + phmin;
else
query_string = "select * from buffer_system where maxpH>" + phmax + " and minpH<" +
phmin;
OleDbCommand query = new OleDbCommand(query_string, dataCon);
OleDbDataAdapter adapter = new OleDbDataAdapter(query_string, dataCon);
OleDbDataReader reader = query.ExecuteReader();
// decision module to deal wth the situation when more than one result show up
while (reader.Read())
{
buffertype aBuffer = new buffertype();
//read chemicals
int caid = (int)reader.GetValue(1);
int cbid = (int)reader.GetValue(2);
String chemicalquery = "select chemical.charge, chemical.base, type.type from chemical
inner join type on chemical.type=type.ID where chemical.ID=" + caid + " or chemical.ID=" + cbid;
query = new OleDbCommand(chemicalquery, dataCon);
adapter = new OleDbDataAdapter(chemicalquery, dataCon);
OleDbDataReader aReader = query.ExecuteReader();
int baseid = 0;
int i = 0;
while (aReader.Read())
{
aBuffer.charge[i] = (int)aReader.GetValue(0);
aBuffer.type[i] = (String)aReader.GetValue(2);
aBuffer.id = (int)reader.GetValue(0);
if (aBuffer.type[i].Equals("salt")) baseid = (int)reader.GetValue(1);
i++;
}
// read K values of the base
String Kquery = "select * from base where ID=" + baseid;
query = new OleDbCommand(Kquery, dataCon);
adapter = new OleDbDataAdapter(Kquery, dataCon);
OleDbDataReader bReader = query.ExecuteReader();
while (bReader.Read())
{
aBuffer.K[0] = (double)bReader.GetValue(2);
aBuffer.K[1] = (double)bReader.GetValue(3);
aBuffer.K[2] = (double)bReader.GetValue(4);
}
bufferResults.Add(aBuffer);
aReader.Dispose();
bReader.Dispose();
}
dataCon.Close();
this.selectbuffer(bufferResults);
}
//assume concentrations of two solutions are same
private void calvolume(double c, double ph)
{
buffertype aBuffer = new buffertype();
int charge = 0;
aBuffer = bufferResults[0];
int typenum = 0;
if (aBuffer.type[0].Equals(aBuffer.type[1])) typenum = 0;
else if (aBuffer.type[0].Equals("acid") || aBuffer.type[1].Equals("acid")) typenum = 1;
else typenum = 2;
for (int i = 0; i < 2; i++)
{
if (aBuffer.type[i].Equals("salt"))
{
charge = aBuffer.charge[i];
}
}
switch (typenum)
{
case 0:
this.calSalt(c, ph, aBuffer.K[0], aBuffer.K[1], aBuffer.K[2]);
break;
case 1:
this.calAcid(c, ph, aBuffer.K[0], aBuffer.K[1], aBuffer.K[2], charge);
break;
case 2:
this.calAlkali(c, ph, aBuffer.K[0], aBuffer.K[1], aBuffer.K[2], charge);
break;
}
}
private void selectbuffer(List<buffertype> bufferResults)
{
//if (bufferResults.Count == 1) print("selected!");
}
private double calSalt(double c, double ph, double k1, double k2, double k3)
{
double hyd = Math.Pow(10, -ph);
k1 = Math.Pow(10, -k1);
k2 = Math.Pow(10, -k2);
k3 = Math.Pow(10, -k3);
double
double
double
double
r0
r1
r2
r3
=
=
=
=
1;
hyd / k1;
hyd / k2;
hyd / k3;
r1 = r0 / r1;
r2 = r1 / r2;
r3 = r2 / r3;
double sum = r0 + r1 + r2 + r3;
r0
r1
r2
r3
=
=
=
=
r0
r1
r2
r3
/
/
/
/
sum
sum
sum
sum
*
*
*
*
c
c
c
c
/
/
/
/
1000;
1000;
1000;
1000;
ratio = (r0 + r1) / (r2 + r3);
return ratio;
}
private double calAcid(double c, double ph, double k1, double k2, double k3, int charge)
{
double hyd = Math.Pow(10, -ph);
k1 = Math.Pow(10, -k1);
k2 = Math.Pow(10, -k2);
k3 = Math.Pow(10, -k3);
double
double
double
double
r0
r1
r2
r3
=
=
=
=
1;
hyd / k1;
hyd / k2;
hyd / k3;
r1 = r0 / r1;
r2 = r1 / r2;
r3 = r2 / r3;
double sum = r0 + r1 + r2 + r3;
r0
r1
r2
r3
=
=
=
=
r0
r1
r2
r3
/
/
/
/
sum
sum
sum
sum
*
*
*
*
c
c
c
c
/
/
/
/
1000;
1000;
1000;
1000;
sum = r0 + r1 + r2 + r3;
double Cl = hyd + c * charge / 1000 - Math.Pow(10, ph - 14) - sum;
ratio = Cl / sum;
return ratio;
}
private double calAlkali(double c, double ph, double k1, double k2, double k3, int charge)
{
double hyd = Math.Pow(10, -ph);
k1 = Math.Pow(10, -k1);
k2 = Math.Pow(10, -k2);
k3 = Math.Pow(10, -k3);
double
double
double
double
r0
r1
r2
r3
=
=
=
=
1;
hyd / k1;
hyd / k2;
hyd / k3;
r1 = r0 / r1;
r2 = r1 / r2;
r3 = r2 / r3;
double sum = r0 + r1 + r2 + r3;
r0
r1
r2
r3
=
=
=
=
r0
r1
r2
r3
/
/
/
/
sum
sum
sum
sum
*
*
*
*
c
c
c
c
/
/
/
/
1000;
1000;
1000;
1000;
sum = r0 + r1 + r2 + r3;
double OH = sum + Math.Pow(10, ph - 14) - hyd - charge * c / 1000;
ratio = OH / sum;
return ratio;
}
public double getRatio(double c, double ph)
{
this.calvolume(c, ph);
return ratio;
}
}