endrov.typeLineage.expression
Class ExpUtil

java.lang.Object
  endrov.typeLineage.expression.ExpUtil

public class ExpUtil
extends java.lang.Object

Util functions to mess around with expression levels

Constructor Summary

ExpUtil()

Method Summary

static java.util.TreeMap<EvDecimal,Tuple<java.lang.Double,java.lang.Double>>	calculateCorrectExposureChange20100709(EvContainer imset, EvChannel ch, Lineage lin, java.lang.String expName, java.util.SortedSet<EvDecimal> frames, java.util.Map<EvDecimal,java.lang.Double> bg) Correct for background etc.
static void	clearExp(Lineage lin, java.lang.String expName)
static void	correctBG2(Lineage lin, java.lang.String expName, java.util.SortedSet<EvDecimal> frames, java.util.SortedMap<EvDecimal,java.lang.Double> bgsignal) Correct for background etc.
static void	correctExposureChange(java.util.TreeMap<EvDecimal,Tuple<java.lang.Double,java.lang.Double>> corrections, EvDecimal frame, double[] sig) Correct for background etc.
static void	correctExposureChange(java.util.TreeMap<EvDecimal,Tuple<java.lang.Double,java.lang.Double>> corrections, Lineage lin, java.lang.String expName) Correct for background etc.
static java.lang.Double	getSignalMax(java.util.Collection<double[][][]> sig) Get maximum value for expression
static java.lang.Double	getSignalMax(Lineage lin, java.lang.String expName) Get maximum value for expression
static java.lang.Double	getSignalMin(java.util.Collection<double[][][]> sig) Get minimum value for expression
static java.lang.Double	getSignalMin(Lineage lin, java.lang.String expName) Get minimum value for expression
static boolean	isNumber(java.lang.String s)
static Tuple<java.lang.String,java.lang.String>	nameDateFromOSTName(java.lang.String n)
static void	normalizeSignal(double[] sig, double max, double min, double normalizedVal)
static void	normalizeSignal(Lineage lin, java.lang.String expName, double max, double min, double normalizedVal) Normalize expression such that maximum is 1.0

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExpUtil

public ExpUtil()

Method Detail

correctBG2

public static void correctBG2(Lineage lin,
                              java.lang.String expName,
                              java.util.SortedSet<EvDecimal> frames,
                              java.util.SortedMap<EvDecimal,java.lang.Double> bgsignal)

Correct for background etc. Signal has already been divided by exposure time. Try to keep bg signal constant? **this does not work well**. in fact, background is almost constant

calculateCorrectExposureChange20100709

public static java.util.TreeMap<EvDecimal,Tuple<java.lang.Double,java.lang.Double>> calculateCorrectExposureChange20100709(EvContainer imset,
                                                                                                                           EvChannel ch,
                                                                                                                           Lineage lin,
                                                                                                                           java.lang.String expName,
                                                                                                                           java.util.SortedSet<EvDecimal> frames,
                                                                                                                           java.util.Map<EvDecimal,java.lang.Double> bg)

Correct for background etc. Return table of correction values so it can be applied again. Will be used for non-AP

correctExposureChange

public static void correctExposureChange(java.util.TreeMap<EvDecimal,Tuple<java.lang.Double,java.lang.Double>> corrections,
                                         Lineage lin,
                                         java.lang.String expName)

Correct for background etc. Use given table of corrections

correctExposureChange

public static void correctExposureChange(java.util.TreeMap<EvDecimal,Tuple<java.lang.Double,java.lang.Double>> corrections,
                                         EvDecimal frame,
                                         double[] sig)

Correct for background etc. Use given table of corrections

clearExp

public static void clearExp(Lineage lin,
                            java.lang.String expName)

normalizeSignal

public static void normalizeSignal(Lineage lin,
                                   java.lang.String expName,
                                   double max,
                                   double min,
                                   double normalizedVal)

Normalize expression such that maximum is 1.0

normalizeSignal

public static void normalizeSignal(double[] sig,
                                   double max,
                                   double min,
                                   double normalizedVal)

getSignalMax

public static java.lang.Double getSignalMax(Lineage lin,
                                            java.lang.String expName)

Get maximum value for expression

getSignalMax

public static java.lang.Double getSignalMax(java.util.Collection<double[][][]> sig)

Get maximum value for expression

getSignalMin

public static java.lang.Double getSignalMin(Lineage lin,
                                            java.lang.String expName)

Get minimum value for expression

getSignalMin

public static java.lang.Double getSignalMin(java.util.Collection<double[][][]> sig)

Get minimum value for expression

nameDateFromOSTName

public static Tuple<java.lang.String,java.lang.String> nameDateFromOSTName(java.lang.String n)

isNumber

public static boolean isNumber(java.lang.String s)