func (lhc *LHComponent) Sample(v wunit.Volume) Liquid {
// need to jig around with units a bit here
// Should probably just make Vunit, Cunit etc. wunits anyway
meas := wunit.ConcreteMeasurement{lhc.Vol, wunit.ParsePrefixedUnit(lhc.Vunit)}
// we need some logic potentially
if v.SIValue() > meas.SIValue() {
wutil.Error(errors.New(fmt.Sprintf("LHComponent ID: %s Not enough volume for sample", lhc.ID)))
} else if v.SIValue() == meas.SIValue() {
return lhc
}
smp := CopyLHComponent(lhc)
// need a convention here
smp.Vol = v.RawValue()
smp.Vunit = v.Unit().PrefixedSymbol()
meas.Subtract(&v.ConcreteMeasurement)
lhc.Vol = meas.RawValue()
return smp
}
func choose_plate_assignments(component_volumes map[string]wunit.Volume, plate_types []*wtype.LHPlate, weight_constraint map[string]float64) map[string]map[*wtype.LHPlate]int {
//
// optimization is set up as follows:
//
// let:
// Xk = Number of wells of type Y containing component Z (k = 1...YZ)
// Vy = Working volume of well Y
// RVy = Residual volume of well Y
// TVz = Total volume of component Z required
// WRy = Rate of wells of type y in their plate
// PMax = Maximum number of plates
// WMax = Maximum number of wells
//
// Minimise:
// sum of Xk Wrv RVy
//
// Subject to:
// sum of Xk Vy >= TVz for each component Z
// sum of WRy Xk <= PMax
// sum of Xk <= WMax
//
// setup
lp := glpk.New()
defer lp.Delete()
lp.SetProbName("Assignments")
lp.SetObjName("Z")
// CHECK THIS
lp.SetObjDir(glpk.MAX)
// constraints:
// total component volume
// number of plates
// number of wells
n_rows := len(component_volumes) + 2
lp.AddRows(n_rows)
cur := 1
component_order := make([]string, len(component_volumes))
// volume constraints
for cmp, vol := range component_volumes {
component_order[cur-1] = cmp
lp.SetRowBnds(cur, glpk.LO, vol.ConvertTo(wunit.ParsePrefixedUnit("ul")), 99999.0)
cur += 1
}
// from now on we always have to use component_order
// plate number constraints
max_n_plates := weight_constraint["MAX_N_PLATES"] - 1.0
lp.SetRowBnds(cur, glpk.UP, -99999.0, max_n_plates)
cur += 1
// well number constraints
max_n_wells := weight_constraint["MAX_N_WELLS"]
lp.SetRowBnds(cur, glpk.UP, -99999.0, max_n_wells)
cur += 1
// set up the matrix columns
num_cols := len(component_order) * len(plate_types)
lp.AddCols(num_cols)
cur = 1
for _, component := range component_order {
for _, plate := range plate_types {
// set up objective coefficient, column name and lower bound
rv := plate.Welltype.ResidualVolume()
coef := rv.ConvertTo(wunit.ParsePrefixedUnit("ul")) * weight_constraint["RESIDUAL_VOLUME_WEIGHT"]
lp.SetObjCoef(cur, coef)
lp.SetColName(cur, component+"_"+plate.PlateName)
lp.SetColBnds(cur, glpk.LO, 0.0, 0.0)
lp.SetColKind(cur, glpk.IV)
cur += 1
}
}
// now set up the constraint coefficients
cur = 1
ind := wutil.Series(0, num_cols)
for c, _ := range component_order {
row := make([]float64, num_cols+1)
col := 0
for i := 0; i < len(component_order); i++ {
for j := 0; j < len(plate_types); j++ {
vc := 0.0
// pick out a set of columns according to which row we're on
// volume constraints are the working volumes of the wells
if c == i {
vol := wunit.NewVolume(plate_types[j].Welltype.Vol, plate_types[j].Welltype.Vunit)
rvol := wunit.NewVolume(plate_types[j].Welltype.Rvol, plate_types[j].Welltype.Vunit)
vol.Subtract(&rvol)
vc = vol.ConvertTo(wunit.ParsePrefixedUnit("ul"))
}
row[col+1] = vc
col += 1
}
}
lp.SetMatRow(cur, ind, row)
cur += 1
}
// now the plate constraint
row := make([]float64, num_cols+1)
col := 1
for i := 0; i < len(component_order); i++ {
for j := 0; j < len(plate_types); j++ {
// the coefficient here is 1/the number of this well type per plate
r := 1.0 / float64(plate_types[j].Nwells)
row[col] = r
col += 1
}
}
lp.SetMatRow(cur, ind, row)
cur += 1
// finally the well constraint
row = make([]float64, num_cols+1)
col = 1
for i := 0; i < len(component_order); i++ {
for j := 0; j < len(plate_types); j++ {
// the number of wells is constrained so we just count
row[col] = 1.0
col += 1
}
}
lp.SetMatRow(cur, ind, row)
iocp := glpk.NewIocp()
iocp.SetPresolve(true)
iocp.SetMsgLev(0)
lp.Intopt(iocp)
// check constraints
/*
for i := 1; i <= n_rows; i++ {
fmt.Println("ROW : ", i, " VAL : ", lp.MipRowVal(i))
}
*/
// fill assignments - this is the number of wells in the plate of each type needed
assignments := make(map[string]map[*wtype.LHPlate]int, len(component_volumes))
cur = 1
for i := 0; i < len(component_order); i++ {
cmap := make(map[*wtype.LHPlate]int)
for j := 0; j < len(plate_types); j++ {
nwells := lp.MipColVal(cur)
if nwells > 0 {
//fmt.Println(component_order[i], " : ", plate_types[j].Type, " N WELLS: ", nwells)
cmap[plate_types[j]] = int(nwells)
}
cur += 1
}
assignments[component_order[i]] = cmap
}
return assignments
}
func (lhc *LHComponent) Add(v wunit.Volume) {
meas := wunit.ConcreteMeasurement{lhc.Vol, wunit.ParsePrefixedUnit(lhc.Vunit)}
meas.Add(&v)
lhc.Vol = meas.RawValue()
}
